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  • 151.
    Hovstadius, Peter
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Sciences, Clinical Pharmacology.
    Preclinical and Clinical Development of the Novel Cyanoguanidine CHS 828 for Cancer Treatment2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    CHS 828 is a cyanoguanidine with anti-tumour properties which has shown promising effects in several preclinical models. This thesis describes both preclinical and clinical studies aiming to investigate disease specific activity, clinical tolerability and efficacy of CHS 828.

    In paper I we investigated CHS 828 activity in a cell line panel with human myeloma cells, three of these cell-lines were also tested in vivo using a hollow fibre rat-model. In paper II we investigated CHS 828 activity in primary human tumour samples from patients. CHS 828 showed an effect on all tumour cell types tested both the primary human tumour samples and the myeloma cell lines. Notably, CHS 828 showed a high relative in vitro activity against tumour cells from chronic lymphocytic leukaemia and high-grade lymphoma.

    In a phase I trial we determined the maximum tolerated dose (MTD) of CHS 828. Haematological toxicity was generally mild and dominated by transient thrombocytopenia and lymphocytopenia. Non-haematological toxicity was mostly of gastrointestinal origin. The recommended phase two dose (RPTD) of CHS 828 was estimated to be 20 mg once daily for five days in cycles of 28 days duration.

    In a phase II trial we investigated the effect of CHS 828 on patients diagnosed with B-CLL. In total 12 patients were enrolled. CHS 828 was found to be well tolerated and the most common haematological toxicity was thrombocytopenia. Non-haematological toxicities were generally mild. Transient decreases in lymphocyte counts could be discerned coinciding with drug dosing, but no sustained clinical responses could be achieved.

    In conclusion, CHS 828 demonstrated marked effects in the preclinical investigations suggesting haematological malignancies as the main target. The clinical phase I study established a safe dose and the subsequent phase II trial in B-CLL patients showed biological effect but with no clinical disease response.

    List of papers
    1. Cytotoxic effect in vivo and in vitro of CHS 828 on human myeloma cell lines
    Open this publication in new window or tab >>Cytotoxic effect in vivo and in vitro of CHS 828 on human myeloma cell lines
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    2004 In: Anti-Cancer Drugs, Vol. 15, no 1, p. 63-70Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-93817 (URN)
    Available from: 2005-11-24 Created: 2005-11-24Bibliographically approved
    2. Activity of CHS 828 in primary cultures of human hematological and solid tumors in vitro
    Open this publication in new window or tab >>Activity of CHS 828 in primary cultures of human hematological and solid tumors in vitro
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    2001 In: Anti-Cancer Drugs, Vol. 12, no 10, p. 821-827Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-93818 (URN)
    Available from: 2005-11-24 Created: 2005-11-24Bibliographically approved
    3. A Phase I Study of CHS 828 in Patients with Solid Tumor Malignancy
    Open this publication in new window or tab >>A Phase I Study of CHS 828 in Patients with Solid Tumor Malignancy
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    2002 (English)In: Clinical Cancer Research, ISSN 1078-0432, E-ISSN 1557-3265, Vol. 8, no 9, p. 2843-2850Article in journal (Refereed) Published
    Abstract [en]

    CHS 828 is a cyanoguanidine, which has demonstrated potent antitumor activity in preclinical tumor models. The activity of CHS 828 in vitro showed only low to moderate correlation to other antineoplastic agents suggesting a unique mechanism of action. Ten females and 6 males (median age 58 years) with solid tumors refractory to standard therapy were included in this Phase I study. The study drug was administered to fasting patients as a single oral dose on days 1–5 of each treatment cycle. Patients received one to six cycles of treatment. The doses ranged from 30 mg to 200 mg (total dose within a cycle). Hematological toxicity was generally mild and dominated by transient thrombocytopenia and lymphocytopenia. Nonhematological toxicity most frequently consisted of nausea, vomiting, diarrhea, fatigue, and localized genital mucositis. The dose-limiting toxicities were thrombocytopenia, thrombosis, esophagitis, diarrhea, and constipation. The recommended Phase II dose of CHS 828 was 20 mg once daily for 5 days in cycles of 28 days duration. The extent of systemic exposure of CHS 828 across patients was approximately dose proportional. The time at which the highest drug concentration occurs was 2.2 ± 1.3 h and half-life was 2.1 ± 0.52 h (mean ± SD). Large intra- and interindividual variation in dose level-adjusted maximum plasma concentration and the area under the curve from time 0 h to infinity were observed. There was an apparent inverse relationship between systemic exposure of CHS 828, and thrombocyte and lymphocyte nadir levels. No objective tumor responses were observed, and 7 patients showed stable disease after two courses of therapy.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-93819 (URN)12231525 (PubMedID)
    Available from: 2005-11-24 Created: 2005-11-24 Last updated: 2017-12-14Bibliographically approved
    4. A phase II study of the IkB kinase inhibitor CHS 828 in patients with chronic lymphocytic leukemia
    Open this publication in new window or tab >>A phase II study of the IkB kinase inhibitor CHS 828 in patients with chronic lymphocytic leukemia
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    Article in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-93820 (URN)
    Available from: 2005-11-24 Created: 2005-11-24Bibliographically approved
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  • 152.
    Hsu, Yu-Ming
    et al.
    Kaohsiung Med Univ, Coll Pharm, Grad Inst Nat Prod, Kaohsiung 80708, Taiwan..
    Chang, Fang-Rong
    Kaohsiung Med Univ, Coll Pharm, Grad Inst Nat Prod, Kaohsiung 80708, Taiwan.;Kaohsiung Med Univ, Ctr Infect Dis & Canc Res, Kaohsiung 80708, Taiwan.;Kaohsiung Med Univ, Res Ctr Environm Med, Kaohsiung 80708, Taiwan.;Natl Sun Yat Sen Univ, Dept Marine Biotechnol & Resources, Kaohsiung 80424, Taiwan.;Kaohsiung Med Univ Hosp, Ctr Canc, Kaohsiung 80708, Taiwan..
    Lo, I-Wen
    Kaohsiung Med Univ, Coll Pharm, Grad Inst Nat Prod, Kaohsiung 80708, Taiwan..
    Lai, Kuei-Hung
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy. Kaohsiung Med Univ, Coll Pharm, Grad Inst Nat Prod, Kaohsiung 80708, Taiwan..
    El-Shazly, Mohamed
    Ain Shams Univ, Fac Pharm, Dept Pharmacognosy & Nat Prod Chem, Cairo 11566, Egypt..
    Wu, Tung-Ying
    China Med Univ Hosp, Chinese Med Res & Dev Ctr, Taichung 40402, Taiwan. China Med Univ Hosp, Ctr Mol Med, Taichung 40402, Taiwan..
    Du, Ying-Chi
    Kaohsiung Med Univ, Coll Pharm, Grad Inst Nat Prod, Kaohsiung 80708, Taiwan..
    Hwang, Tsong-Long
    Chang Gung Univ Sci & Technol, Res Ctr Chinese Herbal Med, Res Ctr Ind Human Ecol, Taoyuan 33302, Taiwan.;Chang Gung Mem Hosp, Dept Anesthesiol, Taoyuan 33302, Taiwan. China Med Univ, Sch Pharm, Coll Pharm, Taichung 40402, Taiwan. China Med Univ, Res Ctr Chinese Herbal Med, Taichung 40402, Taiwan..
    Cheng, Yuan-Bin
    Kaohsiung Med Univ, Coll Pharm, Grad Inst Nat Prod, Kaohsiung 80708, Taiwan.;Kaohsiung Med Univ, Ctr Infect Dis & Canc Res, Kaohsiung 80708, Taiwan.;Kaohsiung Med Univ, Res Ctr Nat Prod & Drug Dev, Kaohsiung 80708, Taiwan..
    Wu, Yang-Chang
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy. Kaohsiung Med Univ, Coll Pharm, Grad Inst Nat Prod, Kaohsiung 80708, Taiwan.;Ain Shams Univ, Fac Pharm, Dept Pharmacognosy & Nat Prod Chem, Cairo 11566, Egypt.;China Med Univ Hosp, Chinese Med Res & Dev Ctr, Taichung 40402, Taiwan. China Med Univ Hosp, Ctr Mol Med, Taichung 40402, Taiwan.;Chang Gung Univ, Grad Inst Nat Prod, Coll Med, Taoyuan 33302, Taiwan..
    Zoanthamine-Type Alkaloids from the Zoanthid Zoanthus kuroshio Collected in Taiwan and Their Effects on Inflammation2016In: Journal of natural products (Print), ISSN 0163-3864, E-ISSN 1520-6025, Vol. 79, no 10, p. 2674-2680Article in journal (Refereed)
    Abstract [en]

    Zoanthus kuroshio is a colorful zoanthid with a fluorescent pink oral disc and brown tentacles, which dominates certain parts of the Taiwanese and Japanese coasts. This sea anemone is a rich source of biologically active alkaloids. In the current investigation, two novel halogenated zoanthamines [5 alpha-iodozoanthenamine (1) and 11 beta-chloro-11-deoxykuroshine A (2)], along with four new zoanthamines [18-epi-kuroshine A (3), 7 alpha-hydroxykuroshine E (4), 5 alpha-methoxykuroshine E (5), and 18-epi-kuroshine E (6)], and six known compounds were isolated from Z. kuroshio. Compounds 1 and 2 are the first examples of halogenated zoanthamine-type alkaloids isolated from nature. Compounds 3 and 6 are the first zoanthamine stereoisomers with a cis-junction of the A/B rings. All isolated compounds were evaluated for their anti-inflammatory activities by measuring their effects on superoxide anion generation and elastase release by human neutrophils in response to fMLP.

  • 153.
    Hugerth, Andreas M.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Pharmacy, Department of Pharmaceutical Chemistry.
    Effects of polyelectrolyte conformation, charge density and ion specificity in polyelectrolyte and polyelectrolyte-drug interaction2000Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The central theme is how the structural characteristics of sulphated polyelectrolytes and theirinteraction with counter- and coions determine the degree of polyelectrolyte self-association (gelformation), interaction with oppositely charged polyelectrolyte and polyelectrolyte-amphiphilic druginteraction in protolytic solvent medium. Such knowledge is essential for understanding and regulatingthe interaction between polyelectrolytes as well as between polyelectrolytes and a drug substance in apharmaceutical formulation and for its fate in the human organism.

    The gel formation of the sulphated polyelectrolyte ê-carrageenan was found to be dependent on theextent of inter-chain helical association and thus the nature of the polyelectrolyte counterions. This wasshown from the relationship between the gel-sol melting temperature of the hydrophobic microdomains(T0), the fraction of polymer in helical conformation at T0, and the storage modulus of the samples inthe gel-state. Interaction between the oppositely charged polyelectrolytes carrageenan and chitosanresulted in the formation of polyelectrolyte complexes with a charge ratio of unity. However, in casesof inter helical association of carrageenan chitosan acted as a bridging element producing complexeswith a charge ratio below unity. This mechanism may be used to control the charge ratio ofpolyelectrolyte complexes.

    The solvation characteristics of the polyelectrolyte counterions also affected the polyelectrolyte-amphiphilic drug interaction (amitriptyline). The binding isotherm was shifted to a higher concentrationof free amphiphile according to the counterion sequence Li+ < Na+ < K+ < Rb+ ≈Cs+. The change inGibbs free energy per monomer amphiphile originating from exchanging the counterions (Li+ for Cs+),was of the order of kT. This is of the same order of magnitude as that obtained by significantlychanging the hydrophobicity of the amphiphilic drug molecule. Increasing the polyelectrolyte chargedensity decreased the critical aggregation concentration, increased the degree of cooperativity andincreased the magnitude of ion specific effects. Furthermore, the dependence of the. critical aggregationconcentration on ionic strength was linear and the polymer flexibility affected the efficiency of thepolycounterion properties of the polyelectrolyte. The binding isotherms, micropolarity, microviscosityand surface tension indicated the amitriptyline-polyelectrolyte interaction to be qualitatively andquantitatively similar to that observed for "typical" cationic surfactants.

  • 154.
    Hughes, Diarmaid
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    Karlén, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Discovery and preclinical development of new antibiotics2014In: Upsala Journal of Medical Sciences, ISSN 0300-9734, E-ISSN 2000-1967, Vol. 119, no 2, p. 162-169Article, review/survey (Refereed)
    Abstract [en]

    Antibiotics are the medical wonder of our age, but an increasing frequency of resistance among key pathogens is rendering them less effective. If this trend continues the consequences for cancer patients, organ transplant patients, and indeed the general community could be disastrous. The problem is complex, involving abuse and overuse of antibiotics (selecting for an increasing frequency of resistant bacteria), together with a lack of investment in discovery and development (resulting in an almost dry drug development pipeline). Remedial approaches to the problem should include taking measures to reduce the selective pressures for resistance development, and taking measures to incentivize renewed investment in antibiotic discovery and development. Bringing new antibiotics to the clinic is critical because this is currently the only realistic therapy that can ensure the level of infection control required for many medical procedures. Here we outline the complex process involved in taking a potential novel antibiotic from the initial discovery of a hit molecule, through lead and candidate drug development, up to its entry into phase I clinical trials. The stringent criteria that a successful drug must meet, balancing high efficacy in vivo against a broad spectrum of pathogens, with minimal liabilities against human targets, explain why even with sufficient investment this process is prone to a high failure rate. This emphasizes the need to create a well-funded antibiotic discovery and development pipeline that can sustain the continuous delivery of novel candidate drugs into clinical trials, to ensure the maintenance of the advanced medical procedures we currently take for granted.

  • 155.
    Hultén, Johan
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Pharmacy, Department of Pharmaceutical Chemistry.
    Cyclic sulfamides as HIV-1 protease inhibitors: Synthesis, X-ray structure analysis and structure-activity relationship1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Human Immunodeficiency Virus (HIV) is the causative agent of Acquired Immune Deficiency Syndrome (AIDS). Inhibition of HIV-1 protease leads to immature and non-infectious viral particles. The synthesis of a number of cyclic HIV-1 protease inhibitors and the subsequent evaluation in an enzyme assay is presented in this thesis. A centrally positioned water molecule (W301), unique to retroviral proteases, guided the design ofthe inhibitors.

    A synthetic procedure utilising carbohydrates as chiral starting materials has been used to gain control of the stereochemistry of the target compounds. Synthesis of four C2-symmetric cyclic urea inhibitors revealed the importance of correct stereochemistry in rigid cyclic structures for activity. According to the X-ray crystal structures of the cyclic inhibitors, in complex with the protease, a displacement of the water molecule W301 by aurea carbonyl, or alternatively by a sulfamide group was accomplished.

    Changing the water-mimicking group from urea to sulfamide resulted in an unexpected non-symmetric binding mode as deduced from comparison of the X-ray crystal structure of a urea and a sulfamide inhibitor in complex with the protease. A small X-ray structure of a sulfamide inhibitor in absence of the protease established that thenon-symmetric conformation of the inhibitor was an inherent feature of the sulfamide scaffold and not induced by the protease.

    In an attempt to establish the structure activity relationship (SAR) of the sulfamide class of inhibitors, symmetric and non-symmetrically substituted sulfamide inhibitors were prepared. A comparative molecular field analysis (CoMFA) was performed to rationalise the SAR and give a model of predictive value. The cyclic inhibitors wereevaluated against a series of mutant forms of the protease and found to have a considerably lower affinity towards I84V and V82A than towards the wild type enzyme.

  • 156.
    Huynh, Ngoc Hang
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Pharmacy, Department of Pharmaceutical Chemistry.
    Enantioseparation of drugs and related compounds using chiral mobile phase additives1998Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Neutral and anionic chiral mobile phase additives have been employed to separate enantiomers of drugs and related compounds using aqueous buffer solution and hydro-organic solvent mixtures as mobile phases.

    Ester derivatives of tartaric acid, e. g. (2R,3R)-dicyclohexyl tartrate, was adsorbed on an achiral solid phase of porous graphitic carbon (PGC) and acted as a chiral stationary phase for the enantiomer separation of neutral, acidic and basic compounds (e.g. atropine, mandelic acid, ephedrine) The antipode, (2S,3S)-dicyclohexyl tartrate was applied for the determination of the enantiomeric impurity of a pharmaceutical preparation of (S)-atropine.

    (2R,3R)-(-)-Dibenzoyl-tartaric acid mono (dimethylamide), a tartaric acid amide derivative having a free carboxylic group was also adsorbed on PGC and simultaneously acted as a chiral counter ion to several racemic drugs. Complete chiral resolution was obtained for several β-blocking agents (e.g. alprenolol, metoprolol and propranolol) and antiulcer agents (e.g. omeprazole and lansoprazole)

    In contrast to the tartaric acid derivatives, N-protected di-and tripeptides, e.g. N-benzyloxycarbonyl-glycyl-L-proline (L-ZGP), had low affinity to PGC when dissolved in mobile phase of methanol. Nevertheless they gave high enantiomeric resolution for several racemic drugs of pharmacological interest (e.g. terbutalin, alprenolol, trimipramine and promethazine) by acting as a counter ion to the solute enantiomers. This chiral counter ion enabled the determination of the enantiomeric composition of mefloquine at micro-molar levels in biological fluids.

    When charged selectors were used, solute retention conformed with ion-pair retention mechanism. Counter ion concentration and pH were the main parameters utilized to control both retention and enantioselectivity. Other achiral additives e.g. organic modifiers, co-ions etc might also influence the enantioselective retetion. Thus many factors could be used to regulate the chiral separation by ion-pair chromatography. The chemometric approach, using experimental design and multivariate data analysis, was shown to be an effective tool for optimization of the separation of mefloquine. (1S,3S,4S)-(+)-3-bromocamphor-10-sulfonic acid was used as a counter ion.

  • 157.
    Högberg, Marita
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Pharmacy, Department of Pharmaceutical Chemistry.
    Synthesis and structure activity relationship studies of non-nucleoside HIV-1 reverse transcriptase inhibitors1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    HIV-1 reverse transcriptase (RT) is a target for anti-HIV chemotherapy. A series of PETT PhenylEthylThiazoleThiourea) non-nucleoside HIV-1 RT inhibitors were synthesised. All compounds were tested in an HIV-1 RT enzyme assay, and in cell culture using MT-4 cells and wild-type virus. Many compounds were also tested in HIV-1 RT enzyme assays with three constructed mutants, Ile100, Cys181 and Asn103, and in cell culture using virus containing a mutation in residue 100, 181 or 103.

    The lead PETT compound, N-(2-phenethyl)-N'-(2-thiazolyl)thiourea, has an IC50 of 0.9 µM in an HIV-1 RT enzyme assay and an ED50 of 1.3 µM in an HIV-1 cell culture assay. The optimisation of this compound resulted in a clinical candidate, trovirdine, N-[2-(2-pyridylethyl)]-N'-[2-(5-bromopyridyl)]thiourea, which inhibits HIV-1 RT with an IC50 of 15 nM and has an ED50 of 20 nM in cell culture. Further optimisation produced more potent thiourea compounds comprising 2, 3, 6-trisubstituted phenethyl 5-chloro, 5-bromo or 5-cyano-2-pyridyl thiourea analogs. The IC50 and ED50 values of the most active of these analogs were 1 to 5 nM. Bioisosteric substitution of the thiourea moiety of PETT compounds with cyanoguanidine, guanidine and sulfonyldiamide is studied. Finally, the synthesis and structure activity relationship studies of highly potent, conformationally restricted, racemic and enantiomeric cyclopropyl urea analogs are described with enhanced antiviral activities even on mutant form of HIV-1 virus in the nanomolar range.

    The three-dimensional structures of complexes between HIV-1 RT and an enantiomeric pair of cyclopropyl compounds have been determined. The structures show similar binding in the NNI binding pocket. The cyclopropyl moiety of both enantiomers has close-packing interactions with leucine residue 100, valine residue 179 and tyrosine residue 181, but in addition to these interactions the cyclopropyl moiety of the (+)-enantiomer has extensive hydrophobic close-packing interactions with glutamine residue 1138.

  • 158.
    Ida, Björs
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Analytical Pharmaceutical Chemistry.
    Development of separation method for analysis of oligonucleotides using LC-UV/MS2018Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Introduction

    Oligonucleotides are short nucleic acid chains, usually 19-27mer long. They bind to their corresponding chain, making a specific inhibition possible. In pharmaceuticals, this can be used to inhibit the expression of a gene or protein of interest. Oligonucleotides are usually analyzed based on separation using both hydrophobic and ion-exchange properties. In this project, the possibility to use a mixed-mode column to separate these oligonucleotides and their impurities were explored.

    Method

    Liquid chromatography is used as the separation method and the method of detection is both mass spectrometry and UV. Three different columns are evaluated; C18, DNAPac RP, and mixed-mode RP/WAX.

    Results and discussion

    Different compositions of mobile phases and gradients are evaluated based on a literature study. Triethylamine, triethylammonium acetate, ammonium formate, hexafluoroisopropanol is used along with both methanol and acetonitrile. Phosphate buffer is evaluated on LC-UV. The results from the C18 column displays a good separation of the oligonucleotides, whilst the DNAPac RP is not as sufficient using the same mobile phases. The mixed-mode column provides good separation and selectivity using phosphate buffer and UV detection.

    Conclusion

    Mixed-mode column has the potential to be used for separation of oligonucleotides and one future focus would be to make the mobile phase compatible with mass spectrometry. Phosphate buffer and UV detection seems to be the go-to mobile phase using mixed-mode column even though MS is a more powerful tool for the characterization and identification of oligonucleotides. This provides a hint about the challenge in making the mobile phase MS compatible.

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  • 159.
    Ilari, Andrea
    et al.
    Univ Roma La Sapienza, CNR, Inst Mol Biol & Pathol, I-00185 Rome, Italy.;Univ Roma La Sapienza, Dept Biochem Sci, I-00185 Rome, Italy..
    Fiorillo, Annarita
    Univ Roma La Sapienza, CNR, Inst Mol Biol & Pathol, I-00185 Rome, Italy.;Univ Roma La Sapienza, Dept Biochem Sci, I-00185 Rome, Italy..
    Poser, Elena
    Univ Roma La Sapienza, CNR, Inst Mol Biol & Pathol, I-00185 Rome, Italy.;Univ Roma La Sapienza, Dept Biochem Sci, I-00185 Rome, Italy..
    Lalioti, Vasiliki S.
    Univ Autonoma Madrid, CSIC, Ctr Biol Mol Severo Ochoa, Dept Biol Celular & Inmunol, Canto Blanco, Spain.;Ctr Invest Biomed Red Enfermedades Hepat & Digest, Madrid, Spain..
    Sundell, Gustav N.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Ivarsson, Ylva
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry. Uppsala Univ, Dept Chem BMC, S-75123 Uppsala, Sweden..
    Genovese, Ilaria
    Univ Roma La Sapienza, CNR, Inst Mol Biol & Pathol, I-00185 Rome, Italy.;Univ Roma La Sapienza, Dept Biochem Sci, I-00185 Rome, Italy..
    Colotti, Gianni
    Univ Roma La Sapienza, CNR, Inst Mol Biol & Pathol, I-00185 Rome, Italy.;Univ Roma La Sapienza, Dept Biochem Sci, I-00185 Rome, Italy..
    Structural basis of Sorcin-mediated calcium-dependent signal transduction2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 16828Article in journal (Refereed)
    Abstract [en]

    Sorcin is an essential penta-EF hand calcium binding protein, able to confer the multi-drug resistance phenotype to drug-sensitive cancer cells and to reduce Endoplasmic Reticulum stress and cell death. Sorcin silencing blocks cell cycle progression in mitosis and induces cell death by triggering apoptosis. Sorcin participates in the modulation of calcium homeostasis and in calcium-dependent cell signalling in normal and cancer cells. The molecular basis of Sorcin action is yet unknown. The X-ray structures of Sorcin in the apo (apoSor) and in calcium bound form (CaSor) reveal the structural basis of Sorcin action: calcium binding to the EF1-3 hands promotes a large conformational change, involving a movement of the long D-helix joining the EF1-EF2 sub-domain to EF3 and the opening of EF1. This movement promotes the exposure of a hydrophobic pocket, which can accommodate in CaSor the portion of its N-terminal domain displaying the consensus binding motif identified by phage display experiments. This domain inhibits the interaction of sorcin with PDCD6, a protein that carries the Sorcin consensus motif, co-localizes with Sorcin in the perinuclear region of the cell and in the midbody and is involved in the onset of apoptosis.

  • 160.
    Ilari, Andrea
    et al.
    Univ Roma La Sapienza, CNR, Inst Mol Biol & Pathol, I-00185 Rome, Italy.;Univ Roma La Sapienza, Dept Biochem Sci, I-00185 Rome, Italy..
    Fiorillo, Annarita
    Univ Roma La Sapienza, CNR, Inst Mol Biol & Pathol, I-00185 Rome, Italy.;Univ Roma La Sapienza, Dept Biochem Sci, I-00185 Rome, Italy..
    Poser, Elena
    Univ Roma La Sapienza, CNR, Inst Mol Biol & Pathol, I-00185 Rome, Italy.;Univ Roma La Sapienza, Dept Biochem Sci, I-00185 Rome, Italy..
    Lalioti, Vasiliki S.
    Univ Autonoma Madrid, CSIC, Ctr Biol Mol Severo Ochoa, Dept Biol Celular & Inmunol, Canto Blanco, Spain.;Ctr Invest Biomed Red Enfermedades Hepat & Digest, Madrid, Spain..
    Sundell, Gustav N.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Biochemistry.
    Ivarsson, Ylva
    Uppsala Univ, Dept Chem BMC, S-75123 Uppsala, Sweden..
    Genovese, Ilaria
    Univ Roma La Sapienza, CNR, Inst Mol Biol & Pathol, I-00185 Rome, Italy.;Univ Roma La Sapienza, Dept Biochem Sci, I-00185 Rome, Italy..
    Colotti, Gianni
    Univ Roma La Sapienza, CNR, Inst Mol Biol & Pathol, I-00185 Rome, Italy.;Univ Roma La Sapienza, Dept Biochem Sci, I-00185 Rome, Italy..
    Structural basis of Sorcin-mediated calcium-dependent signal transduction2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 16828Article in journal (Refereed)
    Abstract [en]

    Sorcin is an essential penta-EF hand calcium binding protein, able to confer the multi-drug resistance phenotype to drug-sensitive cancer cells and to reduce Endoplasmic Reticulum stress and cell death. Sorcin silencing blocks cell cycle progression in mitosis and induces cell death by triggering apoptosis. Sorcin participates in the modulation of calcium homeostasis and in calcium-dependent cell signalling in normal and cancer cells. The molecular basis of Sorcin action is yet unknown. The X-ray structures of Sorcin in the apo (apoSor) and in calcium bound form (CaSor) reveal the structural basis of Sorcin action: calcium binding to the EF1-3 hands promotes a large conformational change, involving a movement of the long D-helix joining the EF1-EF2 sub-domain to EF3 and the opening of EF1. This movement promotes the exposure of a hydrophobic pocket, which can accommodate in CaSor the portion of its N-terminal domain displaying the consensus binding motif identified by phage display experiments. This domain inhibits the interaction of sorcin with PDCD6, a protein that carries the Sorcin consensus motif, co-localizes with Sorcin in the perinuclear region of the cell and in the midbody and is involved in the onset of apoptosis.

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  • 161.
    Isaksson, Rebecka
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Preparative Medicinal Chemistry.
    Ligands of the Angiotensin II Type 2 Receptor: Exploring structure and function of the AT2R ligand C382019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The renin-angiotensin-aldosterone-system (RAAS) control blood-pressure regulation, exerted by the main effector peptide angiotensin II (AngII) binding the angiotensin II type 1 receptor (AT1R). While hypertension is the most known disease caused by over-activity in RAAS, several proteins in the system exhibit protective functions.

    One of these protective proteins is the GPCR angiotensin II type 2 receptor (AT2R). After decades of research its biological role remain to be fully elucidated, exemplified by the two AT2R ligands currently in clinical trials; agonist C21 for treatment of idiopathic pulmonary fibrosis, and antagonist EMA401 for treatment of peripheral neuropathic pain. Making a minor structural change in C21 shifted the pharmacological profile, generating the regioisomer antagonist C38. The renewed interest in AT2R antagonists as potential drugs to treat neuropathic pain make continued studies of antagonist C38 highly interesting. 

    The aim of this thesis was to continue exploring the structure-activity relationship of antagonist C38 by investigating three chemical motifs to identify compounds with better drug-like properties. Developing a new chemical method, transesterification of sulfonyl carbamates, allowed quick modification of one of the motifs. Reducing the length of the sulfonyl carbamate chain significantly increased metabolic stability in liver microsomes without losing affinity for AT2R. Using a model substrate, the transesterification reaction was applied in a microwave heated continuous-flow system.

    Adding small substituents to the central phenyl ring generated a second library of ligands with retained affinity, but with no observed increase in metabolic stability. Docking studies with this library and a recently presented crystal structure of AT2R, resulted in a proposed binding mode of C38. Replacing the imidazole head group with bicyclic amides slightly improved affinity. While metabolic stability improved compared to previously published amide analogs, the bicyclic ligands were inferior to C38. Developing an assay based on RAW264.7 macrophages allowed a new evaluation of the functional activity exhibited by C38. In contrast to previous research, C21 and C38 both display agonistic functional activity in the macrophage assay.

    In summary, the work presented in this thesis expand the structure-activity relationship of C38 and its pharmacological profile. Two new ligands were identified that could serve as tools in murine models of neuropathic pain.

    List of papers
    1. Rapid and straightforward transesterification of sulfonyl carbamates
    Open this publication in new window or tab >>Rapid and straightforward transesterification of sulfonyl carbamates
    2016 (English)In: Tetrahedron Letters, ISSN 0040-4039, E-ISSN 1359-8562, Vol. 57, no 13, p. 1476-1478Article in journal (Refereed) Published
    Abstract [en]

    A fast and convenient method for the alkoxy exchange of sulfonyl carbamates by simply heating in a chosen alkyl alcohol is described. No catalysts or additives are required. Microwave heating at 100-120 degrees C for 20-60 min resulted in good to excellent yields (53-93%) of alkyl (arylsulfonyl)carbamates where the alkyl part originates from the alcohol solvent. The developed protocol was applied to the synthesis of an angiotensin II type 2 receptor (AT2R) ligand.

    Keywords
    Sulfonyl carbamates, O-alkyl exchange, Transesterification, Carboxylic acid bioisosteres, AT2R ligand
    National Category
    Organic Chemistry
    Identifiers
    urn:nbn:se:uu:diva-294300 (URN)10.1016/j.tetlet.2016.02.071 (DOI)000372690800018 ()
    Funder
    EU, FP7, Seventh Framework Programme, REGPOT-CT-2013-316149-InnovaBalt
    Available from: 2016-05-19 Created: 2016-05-18 Last updated: 2019-04-04Bibliographically approved
    2. Microwave Promoted Transcarbamylation Reaction of Sulfonylcarbamates under Continuous-Flow Conditions
    Open this publication in new window or tab >>Microwave Promoted Transcarbamylation Reaction of Sulfonylcarbamates under Continuous-Flow Conditions
    Show others...
    2016 (English)In: Organic Process Research & Development, ISSN 1083-6160, E-ISSN 1520-586X, Vol. 20, no 2, p. 440-445Article in journal (Refereed) Published
    Abstract [en]

    Successful conditions for the transcarbamylation/transesterification reaction of sulfonylcarbamates with alcohols by microwave heating under continuous flow conditions were developed. After optimization of the processes, two series of O-alkylsulfonylcarbamates were obtained in high yields and purities using microwave transparent borosilicate tube reactors. In order to also illustrate the usefulness of the protocol in a medicinal chemistry context, the methodology was used for the synthesis of three angiotensin II type 2 receptor ligands.

    National Category
    Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy) Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-282387 (URN)10.1021/acs.oprd.5b00323 (DOI)000370767600033 ()
    Funder
    EU, FP7, Seventh Framework Programme, REGPOT-CT-2013-316149-InnovaBalt
    Available from: 2016-04-05 Created: 2016-04-05 Last updated: 2019-04-04Bibliographically approved
    3. A convenient transesterification method for synthesis of AT2 receptor ligands with improved stability in human liver microsomes
    Open this publication in new window or tab >>A convenient transesterification method for synthesis of AT2 receptor ligands with improved stability in human liver microsomes
    Show others...
    2018 (English)In: Bioorganic & Medicinal Chemistry Letters, ISSN 0960-894X, E-ISSN 1464-3405, Vol. 28, no 3, p. 519-522Article in journal (Refereed) Published
    Abstract [en]

    A series of AT2R ligands have been synthesized applying a quick, simple, and safetransesterification-type reaction whereby the sulfonyl carbamate alkyl tail ofthe selective AT2R antagonist C38 was varied. Furthermore, a limited number ofcompounds where acyl sulfonamides and sulfonyl ureas served as carboxylic acidbioisosteres were synthesized and evaluated. By reducing the size of the alkylchain of the sulfonyl carbamates, ligands 7a and 7b were identified withsignificantly improved in vitro metabolic stability in both human and mouse livermicrosomes as compared to C38 while retaining the AT2R binding affinity andAT2R/AT1R selectivity. Eight of the compounds synthesized exhibit an improvedstability in human microsomes as compared to C38.

    Place, publisher, year, edition, pages
    Elsevier, 2018
    Keywords
    AT(2)R antagonists, Angiotensin II type 2 receptor antagonists, Liver microsomes, Sulfonyl carbamates, Transesterification
    National Category
    Organic Chemistry Medicinal Chemistry
    Identifiers
    urn:nbn:se:uu:diva-343592 (URN)10.1016/j.bmcl.2017.11.042 (DOI)000424285600053 ()29279275 (PubMedID)
    Funder
    Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
    Available from: 2018-02-28 Created: 2018-02-28 Last updated: 2020-06-05Bibliographically approved
    4. A Series of Analogues to the AT2R Prototype Antagonist C38 Allow Fine Tuning of the Previously Reported Antagonist Binding Mode
    Open this publication in new window or tab >>A Series of Analogues to the AT2R Prototype Antagonist C38 Allow Fine Tuning of the Previously Reported Antagonist Binding Mode
    Show others...
    2019 (English)In: ChemistryOpen, ISSN 2191-1363, Vol. 8, no 1, p. 114-125Article in journal (Refereed) Published
    Abstract [en]

    We here report on our continued studies of ligands binding tothe promising drug target angiotensin II type 2 receptor (AT2R). Two series of compounds were synthesized and investigated. The first series explored the effects of adding small substituents to the phenyl ring of the known selective nonpeptide AT2R antagonist C38, generating small but significant shifts in AT2R affinity. One compound in the first series was equipotent to C38 and showed similar kinetic solubility, and stability in both human and mouse liver microsomes. The second series was comprised of new bicyclic derivatives, amongst which one ligand exhibited a five-fold improved affinity to AT2R ascompared to C38. The majority of the compounds in the second series, including the most potent ligand, were inferior to C38 with regard to stability in both human and mouse microsomes. In contrast to our previously reported findings, ligands with shorter carbamate alkyl chains only demonstrated slightly improved stability in microsomes. Based on data presented herein, a more adequate, tentative model of the binding modes of ligand analogues to the prototype AT2R antagonist C38 is proposed, as deduced from docking redefined by molecular dynamic simulations.

    National Category
    Organic Chemistry Medicinal Chemistry
    Identifiers
    urn:nbn:se:uu:diva-377050 (URN)10.1002/open.201800282 (DOI)000457433000017 ()30697513 (PubMedID)
    Funder
    Swedish National Infrastructure for Computing (SNIC)Swedish Research Council
    Available from: 2019-02-13 Created: 2019-02-13 Last updated: 2019-04-04Bibliographically approved
    5. Direct stimulation of angiotensin II type 2 receptor reduces nitric oxide production in lipopolysaccharide treated mouse macrophages
    Open this publication in new window or tab >>Direct stimulation of angiotensin II type 2 receptor reduces nitric oxide production in lipopolysaccharide treated mouse macrophages
    Show others...
    2020 (English)In: European Journal of Pharmacology, ISSN 0014-2999, E-ISSN 1879-0712, Vol. 868, article id 172855Article in journal (Refereed) Published
    Abstract [en]

    The angiotensin II type 2 receptor (AT2) is upregulated after tissue damage and mediates protective functions in the renin-angiotensin-aldosterone system (RAAS). One of these is to inhibit inducible nitric oxide synthase (iNOS) in activated macrophages. In the present study, we assessed the effect of AT2 receptor ligands on nitric oxide production in murine macrophages as a potential assay to determine the functional activity of an AT2 receptor ligand. Mouse macrophage J744.2 and RAW264.7 were cultivated in lipopolysaccharide (LPS) to induce M1 differentiation and increase iNOS expression. Using Griess reagent and spectrophotometric analysis, the nitric oxide levels were determined, while employing Western blot and immunocytochemistry to determine basal protein expression.

    Using the first reported selective non-peptide AT2 receptor agonist, compound C21, we conclude that activation of AT2 receptor reduces nitric oxide production in M1 macrophages. Furthermore, the AT2 receptor selective ligand compound C38, a regioisomer of C21, reported as a selective AT2 receptor antagonist exhibits a similar effect on nitric oxide production. Thus, we propose C38 acts as a partial agonist in the macrophage system. Monitoring nitric oxide attenuation in M1 J744.1 and RAW264.7 macrophages provides a new method for characterizing functional activity of AT2 receptor ligands, foreseen to be valuable in future drug discovery programs.

    Place, publisher, year, edition, pages
    Elsevier, 2020
    Keywords
    Renin-angiotensin-aldosterone system, Bioassay, Functional activity, Antagonist, Agonist, Inducible nitric oxide synthase
    National Category
    Other Biological Topics Medicinal Chemistry
    Research subject
    Medicinal Chemistry
    Identifiers
    urn:nbn:se:uu:diva-381097 (URN)10.1016/j.ejphar.2019.172855 (DOI)000505215700004 ()31837306 (PubMedID)
    Available from: 2019-04-04 Created: 2019-04-04 Last updated: 2020-01-29Bibliographically approved
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  • 162.
    Isaksson, Rebecka
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Preparative Medicinal Chemistry.
    Casselbrant, Anna
    Department of Gastrosurgical Research and Education, Sahlgrenska Academy.
    Elebring, Erik
    Department of Gastrosurgical Research and Education, Sahlgrenska Academy.
    Hallberg, Mathias
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Larhed, Mats
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Preparative Medicinal Chemistry.
    Fändriks, Lars
    Department of Gastrosurgical Research and Education, Sahlgrenska Academy.
    Direct stimulation of angiotensin II type 2 receptor reduces nitric oxide production in lipopolysaccharide treated mouse macrophages2020In: European Journal of Pharmacology, ISSN 0014-2999, E-ISSN 1879-0712, Vol. 868, article id 172855Article in journal (Refereed)
    Abstract [en]

    The angiotensin II type 2 receptor (AT2) is upregulated after tissue damage and mediates protective functions in the renin-angiotensin-aldosterone system (RAAS). One of these is to inhibit inducible nitric oxide synthase (iNOS) in activated macrophages. In the present study, we assessed the effect of AT2 receptor ligands on nitric oxide production in murine macrophages as a potential assay to determine the functional activity of an AT2 receptor ligand. Mouse macrophage J744.2 and RAW264.7 were cultivated in lipopolysaccharide (LPS) to induce M1 differentiation and increase iNOS expression. Using Griess reagent and spectrophotometric analysis, the nitric oxide levels were determined, while employing Western blot and immunocytochemistry to determine basal protein expression.

    Using the first reported selective non-peptide AT2 receptor agonist, compound C21, we conclude that activation of AT2 receptor reduces nitric oxide production in M1 macrophages. Furthermore, the AT2 receptor selective ligand compound C38, a regioisomer of C21, reported as a selective AT2 receptor antagonist exhibits a similar effect on nitric oxide production. Thus, we propose C38 acts as a partial agonist in the macrophage system. Monitoring nitric oxide attenuation in M1 J744.1 and RAW264.7 macrophages provides a new method for characterizing functional activity of AT2 receptor ligands, foreseen to be valuable in future drug discovery programs.

    Download full text (pdf)
    fulltext
  • 163.
    Isaksson, Rebecka
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Preparative Medicinal Chemistry.
    Lindman, Jens
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Preparative Medicinal Chemistry.
    Wannberg, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sallander, Jessica
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Backlund, Maria
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Baraldi, Dhaniel
    Department of Pharmacology, Monash University.
    Widdop, Robert
    Department of Pharmacology, Monash University.
    Hallberg, Mathias
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Åqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Gutierrez de Teran, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Gising, Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Preparative Medicinal Chemistry.
    Larhed, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Preparative Medicinal Chemistry.
    A Series of Analogues to the AT2R Prototype Antagonist C38 Allow Fine Tuning of the Previously Reported Antagonist Binding Mode2019In: ChemistryOpen, ISSN 2191-1363, Vol. 8, no 1, p. 114-125Article in journal (Refereed)
    Abstract [en]

    We here report on our continued studies of ligands binding tothe promising drug target angiotensin II type 2 receptor (AT2R). Two series of compounds were synthesized and investigated. The first series explored the effects of adding small substituents to the phenyl ring of the known selective nonpeptide AT2R antagonist C38, generating small but significant shifts in AT2R affinity. One compound in the first series was equipotent to C38 and showed similar kinetic solubility, and stability in both human and mouse liver microsomes. The second series was comprised of new bicyclic derivatives, amongst which one ligand exhibited a five-fold improved affinity to AT2R ascompared to C38. The majority of the compounds in the second series, including the most potent ligand, were inferior to C38 with regard to stability in both human and mouse microsomes. In contrast to our previously reported findings, ligands with shorter carbamate alkyl chains only demonstrated slightly improved stability in microsomes. Based on data presented herein, a more adequate, tentative model of the binding modes of ligand analogues to the prototype AT2R antagonist C38 is proposed, as deduced from docking redefined by molecular dynamic simulations.

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    fulltext
  • 164. Ismail, Naadhira O
    et al.
    Odendaal, Clerisa
    Serem, June C
    Strömstedt, Adam A.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Bester, Megan J
    Sayed, Yasien
    Neitz, Albert W H
    Gaspar, Anabella R M
    Antimicrobial function of short amidated peptide fragments from the tick-derived OsDef2 defensin.2019In: Journal of Peptide Science, ISSN 1075-2617, E-ISSN 1099-1387, Vol. 25, no 12, article id e3223Article in journal (Refereed)
    Abstract [en]

    Previously Os, a 22 amino acid sequence of a defensin from the soft tick Ornithodoros savignyi, was found to kill Gram-positive and Gram-negative bacteria at low micromolar concentrations. In this study, we evaluated synthetic peptide analogues of Os for antibacterial activity with an aim to identify minimalized active peptide sequences and in so doing obtain a better understanding of the structural requirements for activity. Out of eight partially overlapping sequences of 10 to 12 residues, only Os(3-12) and Os(11-22) exhibit activity when screened against Gram-positive and Gram-negative bacteria. Carboxyamidation of both peptides increased membrane-mediated activity, although carboxyamidation of Os(11-22) negatively impacted on activity against Staphylococcus aureus. The amidated peptides, Os(3-12)NH2 and Os(11-22)NH2 , have minimum bactericidal concentrations of 3.3 μM against Escherichia coli. Killing was reached within 10 minutes for Os(3-12)NH2 and only during the second hour for Os(11-22)NH2 . In an E. coli membrane liposome system, both Os and Os(3-12)NH2 were identified as membrane disrupting while Os(11-22)NH2 was less active, indicating that in addition to membrane permeabilization, other targets may be involved in bacterial killing. In contrast to Os, the membrane disruptive effect of Os(3-12)NH2 did not diminish in the presence of salt. Neither Os nor its amidated derivatives caused human erythrocyte haemolysis. The contrasting killing kinetics and effects of amidation together with structural and liposome leakage data suggest that the 3-12 fragment relies on a membrane disruptive mechanism while the 11-22 fragment involves additional target mechanisms. The salt-resistant potency of Os(3-12)NH2 identifies it as a promising candidate for further development.

  • 165.
    Jacobsson, Micael
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Structure-Based Virtual Screening: New Methods and Applications in Infectious Diseases2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    A drug discovery project typically starts with a pharmacological hypothesis: that the modulation of a specific molecular biological mechanism would be beneficial in the treatment of the targeted disease. In a small-molecule project, the next step is to identify hits, i.e. molecules that can effect this modulation. These hits are subsequently expanded into hit series, which are optimised with respect to pharmacodynamic and pharmacokinetic properties, through medicinal chemistry. Finally, a drug candidate is clinically developed into a new drug. This thesis concerns the use of structure-based virtual screening in the hit identification phase of drug discovery.

    Structure-based virtual screening involves using the known 3D structure of a target protein to predict binders, through the process of docking and scoring. Docking is the prediction of potential binding poses, and scoring is the prediction of the free energy of binding from those poses. Two new methodologies, based on post-processing of scoring results, were developed and evaluated using model systems. Both methods significantly increased the enrichment of true positives. Furthermore, correlation was observed between scores and simple molecular properties, and identified as a source of false positives in structure-based virtual screening.

    Two target proteins, Mycobacterium tuberculosis ribose-5-phosphate isomerase, a potential drug target in tuberculosis, and Plasmodium falciparum spermidine synthase, a potential drug target in malaria, were subjected to docking and virtual screening. Docking of substrates and products of ribose-5-phosphate isomerase led to hypotheses on the role of individual residues in the active site. Additionally, virtual screening was used to predict 48 potential inhibitors, but none was confirmed as an inhibitor or binder to the target enzyme. For spermidine synthase, structure-based virtual screening was used to predict 32 potential active-site binders. Seven of these were confirmed to bind in the active site.

    List of papers
    1. Improving structure-based virtual screening by multivariate analysis of scoring data
    Open this publication in new window or tab >>Improving structure-based virtual screening by multivariate analysis of scoring data
    Show others...
    2003 In: Journal of Medicinal Chemistry, ISSN 0022-2623, Vol. 46, no 26, p. 5781-5789Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-97599 (URN)
    Available from: 2008-10-10 Created: 2008-10-10Bibliographically approved
    2. Ligand bias of scoring functions in structure-based virtual screening
    Open this publication in new window or tab >>Ligand bias of scoring functions in structure-based virtual screening
    2006 In: Journal of Chemical Information and Modeling, ISSN 1549-9596, Vol. 46, no 3, p. 1334-1343Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-97600 (URN)
    Available from: 2008-10-10 Created: 2008-10-10Bibliographically approved
    3. Mycobacterium tuberculosis ribose-5-phosphate isomerase has a known fold, but a novel active site
    Open this publication in new window or tab >>Mycobacterium tuberculosis ribose-5-phosphate isomerase has a known fold, but a novel active site
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    2004 In: Journal of Molecular Biology, ISSN 0022-2836, Vol. 335, no 3, p. 799-809Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-97601 (URN)
    Available from: 2008-10-10 Created: 2008-10-10 Last updated: 2016-05-09Bibliographically approved
    4. Identification of Plasmodium falciparum spermidine synthase active site binders through structure-based virtual screening
    Open this publication in new window or tab >>Identification of Plasmodium falciparum spermidine synthase active site binders through structure-based virtual screening
    2008 (English)In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 51, no 9, p. 2777-2786Article in journal (Refereed) Published
    Abstract [en]

    Seven novel binders, binding in the active site of Plasmodium falciparum spermidine synthase, were identified by structure-based virtual screening. The binding of these compounds was experimentally verified by NMR techniques. Spermidine synthase, an enzyme involved in the polyamine pathway, has been suggested as a target for treating malaria. The virtual screening protocol combined 3D pharmacophore filtering, docking, and scoring, focusing on finding compounds predicted to form interactions mimicking those of a previously known binder. The virtual screen resulted in the selection of 28 compounds that were acquired and tested from 2.6 million starting structures. Two of the seven binders were predicted to bind in the amino substrate binding pocket. Both of these showed stronger binding upon addition of methylthioadenosine, one of the two products of the enzyme, and a known binder and inhibitor. The five other compounds were predicted to bind in the part of the active site where the other substrate, decarboxylated S-adenosylmethionine, binds. These five compounds all competed for binding with methylthioadenosine.

    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-97602 (URN)10.1021/jm7016144 (DOI)000255500000023 ()18410081 (PubMedID)
    Available from: 2008-10-10 Created: 2008-10-10 Last updated: 2018-01-13Bibliographically approved
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  • 166.
    Jaiteh, Mariama
    et al.
    Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, CNRS and Université Paris Diderot, Paris, France .
    Taly, Antoine
    Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, CNRS and Université Paris Diderot, Paris, France .
    Henin, Jerome
    Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, CNRS and Université Paris Diderot, Paris, France .
    Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 3, article id e0151934Article in journal (Refereed)
    Abstract [en]

    Pentameric ligand-gated ion channels (pLGICs) are ubiquitous neurotransmitter receptors in Bilateria, with a small number of known prokaryotic homologues. Here we describe a new inventory and phylogenetic analysis of pLGIC genes across all kingdoms of life. Our main finding is a set of pLGIC genes in unicellular eukaryotes, some of which are metazoan-like Cys-loop receptors, and others devoid of Cys-loop cysteines, like their prokaryotic relatives. A number of such "Cys-less" receptors also appears in invertebrate metazoans. Together, those findings draw a new distribution of pLGICs in eukaryotes. A broader distribution of prokaryotic channels also emerges, including a major new archaeal taxon, Thaumarchaeota. More generally, pLGICs now appear nearly ubiquitous in major taxonomic groups except multicellular plants and fungi. However, pLGICs are sparsely present in unicellular taxa, suggesting a high rate of gene loss and a non-essential character, contrasting with their essential role as synaptic receptors of the bilaterian nervous system. Multiple alignments of these highly divergent sequences reveal a small number of conserved residues clustered at the interface between the extracellular and transmembrane domains. Only the "Cys-loop" proline is absolutely conserved, suggesting the more fitting name "Pro loop" for that motif, and "Pro-loop receptors" for the superfamily. The infered molecular phylogeny shows a Cys-loop and a Cys-less clade in eukaryotes, both containing metazoans and unicellular members. This suggests new hypotheses on the evolutionary history of the superfamily, such as a possible origin of the Cys-loop cysteines in an ancient unicellular eukaryote. Deeper phylogenetic relationships remain uncertain, particularly around the split between bacteria, archaea, and eukaryotes.

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  • 167.
    Jaiteh, Mariama
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zeifman, Alexey
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Saarinen, Marcus
    Karolinska Inst, Dept Physiol & Pharmacol, Ctr Mol Med, SE-17177 Stockholm, Sweden.
    Svenningsson, Per
    Karolinska Inst, Dept Physiol & Pharmacol, Ctr Mol Med, SE-17177 Stockholm, Sweden.
    Brea, Jose
    Univ Santiago de Compostela, Ctr Res Mol Med & Chron Dis, USEF Screening Platform BioFarma Res Grp, Santiago De Compostela 15706, Spain.
    Loza, Maria Isabel
    Univ Santiago de Compostela, Ctr Res Mol Med & Chron Dis, USEF Screening Platform BioFarma Res Grp, Santiago De Compostela 15706, Spain.
    Carlsson, Jens
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala Univ, Dept Cell & Mol Biol, Sci Life Lab, BMC Box 596, SE-75124 Uppsala, Sweden.
    Docking Screens for Dual Inhibitors of Disparate Drug Targets for Parkinson's Disease2018In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 61, no 12, p. 5269-5278Article in journal (Refereed)
    Abstract [en]

    Modulation of multiple biological targets with a single drug can lead to synergistic therapeutic effects and has been demonstrated to be essential for efficient treatment of CNS disorders. However, rational design of compounds that interact with several targets is very challenging. Here, we demonstrate that structure-based virtual screening can guide the discovery of multi-target ligands of unrelated proteins relevant for Parkinson's disease. A library with 5.4 million molecules was docked to crystal structures of the A(2A) adenosine receptor (A(2A)AR) and monoamine oxidase B (MAO-B). Twenty-four compounds that were among the highest ranked for both binding sites were evaluated experimentally, resulting in the discovery of four dual-target ligands. The most potent compound was an A(2A)AR antagonist with nanomolar affinity (K-i = 19 nM) and inhibited MAO-B with an IC50 of 100 nM. Optimization guided by the predicted binding modes led to the identification of a second potent dual-target scaffold. The two discovered scaffolds were shown to counteract 6-hydroxydopamine-induced neurotoxicity in dopaminergic neuronal-like SH-SY5Y cells. Structure-based screening can hence be used to identify ligands with specific polypharmacological profiles, providing new avenues for drug development against complex diseases.

  • 168.
    Jeannot, Frédéric
    et al.
    Sanofi R&D, Therapeut Area Infect Dis, 1541 Ave Marcel Merieux, F-69280 Marcy Letoile, France.
    Taillier, Thomas
    Sanofi R&D, Therapeut Area Infect Dis, 1541 Ave Marcel Merieux, F-69280 Marcy Letoile, France.
    Despeyroux, Pierre
    Sanofi R&D, Therapeut Area Infect Dis, 1541 Ave Marcel Merieux, F-69280 Marcy Letoile, France.
    Renard, Stéphane
    Sanofi R&D, Therapeut Area Infect Dis, 1541 Ave Marcel Merieux, F-69280 Marcy Letoile, France.
    Rey, Astrid
    Sanofi R&D, Therapeut Area Infect Dis, 1541 Ave Marcel Merieux, F-69280 Marcy Letoile, France.
    Mourez, Michaël
    Sanofi R&D, Therapeut Area Infect Dis, 1541 Ave Marcel Merieux, F-69280 Marcy Letoile, France.
    Poeverlein, Christoph
    Sanofi Aventis Deutschland GmbH, Integrated Drug Discovery, R&D, Ind Pk Hoechst, D-65926 Frankfurt, Germany.
    Khichane, Imène
    Sanofi R&D, Analyt Sci, LGCR, 13 Quai Jules Guesde, F-94400 Vitry Sur Seine, France.
    Perrin, Marc-Antoine
    Sanofi R&D, Analyt Sci, LGCR, 13 Quai Jules Guesde, F-94400 Vitry Sur Seine, France.
    Versluys, Stéphanie
    Evotec France, 195 Route Espagne,BP 13669, F-31036 Toulouse 1, France.
    Stavenger, Robert A.
    GlaxoSmithKline, Antibacterial DPU, 1250 Collegeville Rd, Collegeville, PA 19426 USA.
    Huang, Jianzhong
    GlaxoSmithKline, Antibacterial DPU, 1250 Collegeville Rd, Collegeville, PA 19426 USA.
    Germe, Thomas
    John Innes Ctr, Dept Biol Chem, Norwich Res Pk, Norwich NR4 7UH, Norfolk, England.
    Maxwell, Anthony
    John Innes Ctr, Dept Biol Chem, Norwich Res Pk, Norwich NR4 7UH, Norfolk, England.
    Cao, Sha
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Huseby, Douglas L
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Hughes, Diarmaid
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Bacqué, Eric
    Sanofi R&D, Therapeut Area Infect Dis, 1541 Ave Marcel Merieux, F-69280 Marcy Letoile, France.
    Imidazopyrazinones (IPYs): Non-Quinolone Bacterial Topoisomerase Inhibitors Showing Partial Cross-Resistance with Quinolones2018In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 61, no 8, p. 3565-3581Article in journal (Refereed)
    Abstract [en]

    In our quest for new antibiotics able to address the growing threat of multidrug resistant infections caused by Gram-negative bacteria, we have investigated an unprecedented series of non-quinolone bacterial topoisomerase inhibitors from the Sanofi patrimony, named IPYs for imidazopyrazinones, as part of the Innovative Medicines Initiative (IMI) European Gram Negative Antibacterial Engine (ENABLE) organization. Hybridization of these historical compounds with the quinazolinediones, a known series of topoisomerase inhibitors, led us to a novel series of tricyclic IPYs that demonstrated potential for broad spectrum activity, in vivo efficacy, and a good developability profile, although later profiling revealed a genotoxicity risk. Resistance studies revealed partial cross-resistance with fluoroquinolones (FQs) suggesting that IPYs bind to the same region of bacterial topoisomerases as FQs and interact with at least some of the keys residues involved in FQ binding.

  • 169.
    Jiang, Xiangyi
    et al.
    Shandong Univ, Sch Pharmaceut Sci, Dept Med Chem, Key Lab Chem Biol,Minist Educ, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China.
    Yu, Ji
    Shandong Univ, Sch Pharmaceut Sci, Dept Med Chem, Key Lab Chem Biol,Minist Educ, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China.
    Zhou, Zhongxia
    Shandong Univ, Sch Pharmaceut Sci, Dept Med Chem, Key Lab Chem Biol,Minist Educ, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China.
    Kongsted, Jacob
    Univ Southern Denmark, Dept Phys Chem & Pharm, DK-5230 Odense M, Denmark.
    Song, Yuning
    Shandong Univ, Dept Clin Pharm, Qilu Hosp, Jinan, Shandong, Peoples R China.
    Pannecouque, Christophe
    Rega Inst Med Res, Lab Virol & Chemotherapy, Leuven, Belgium.
    De Clercq, Erik
    Rega Inst Med Res, Lab Virol & Chemotherapy, Leuven, Belgium.
    Kang, Dongwei
    Shandong Univ, Sch Pharmaceut Sci, Dept Med Chem, Key Lab Chem Biol,Minist Educ, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China.
    Poongavanam, Vasanthanathan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry. Univ Southern Denmark, Dept Phys Chem & Pharm, DK-5230 Odense M, Denmark.
    Liu, Xinyong
    Shandong Univ, Sch Pharmaceut Sci, Dept Med Chem, Key Lab Chem Biol,Minist Educ, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China.
    Zhan, Peng
    Shandong Univ, Sch Pharmaceut Sci, Dept Med Chem, Key Lab Chem Biol,Minist Educ, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China.
    Molecular design opportunities presented by solvent-exposed regions of target proteins2019In: Medicinal research reviews (Print), ISSN 0198-6325, E-ISSN 1098-1128, Vol. 39, no 6, p. 2194-2238Article, review/survey (Refereed)
    Abstract [en]

    Solvent-exposed regions, or solvent-filled pockets, within or adjacent to the ligand-binding sites of drug-target proteins provide opportunities for substantial modifications of existing small-molecular drug molecules without serious loss of activity. In this review, we present recent selected examples of exploitation of solvent-exposed regions of proteins in drug design and development from the recent medicinal-chemistry literature.

  • 170.
    Jidheden, Claes
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Hansson, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmacy.
    Single Microgels in Core-Shell Equilibrium: A Novel Method for Limited Volume Studies2016In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, no 37, p. 10030-10042Article in journal (Refereed)
    Abstract [en]

    The interactions of cationic surfactant dodecyl-trimethylammonium bromide and cationic protein cytochrome c with anionic polyacrylate microgels have been investigated in microscopic liquid droplets by means of a micropipette technique at ionic strength 0.01 M and pH 8. Experiments on single microgels in solutions of limited amounts of the surfactant provide the first evidence of microgels in a stable biphasic core shell state with the surfactant partitioned to the shell. Under the same conditions, the protein is found to distribute uniformly in the microgels. Quantitative data in the form of swelling and binding isotherms are presented and compared with literature data for macrogels and with predictions of a recent gel theory. Theory is found to be in semiquantitative agreement with the experiments. The importance of polyion-mediated attractions between the protein molecules is analyzed theoretically and proposed to explain the continuous but highly cooperative binding isotherms.

  • 171.
    Johannesson, Petra
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Synthesis of Aldehyde-Functionalized Building Blocks and Their Use for the Cyclization of Peptides: Applications to Angiotensin II2002Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This study addresses the issue of how to convert peptides into drug-like non- peptides with retained biological activities at peptide receptors. Angiotensin II (Asp-Arg-Val-Tyr-Ile-His-Pro-Phe, Ang II) was used as a model peptide.

    Knowledge of the bioactive conformations of endogenous peptides is invaluable for the conversion of peptides into less peptidic analogues. Effectively constrained cyclic analogues, with retained pharmacological activities, may provide valuable information about the bioactive conformations of the peptide in question.

    This thesis describes the development of synthesis for a number of protected, aldehyde-functionalized building blocks for standard solid phase peptide synthesis, and their use for the preparation of cyclic peptide analogues. The effect of variations in the side-chain lengths of the building blocks, on the outcome of the cyclizations was studied. Incorporation of a building block derived from L-aspartic acid afforded bicyclization towards the C-terininal end of the peptide, while for the corresponding L-glutamic acid derived building block, N-terminal directed bicyclization was achieved. A building block derived from L-2-aminoadipic acid was exploited for monocyclization furnishing cis- and trans- vinyl sulfide bridged peptide analogues.

    The described cyclization methods have been applied to the synthesis of a number of conformationally constrained Ang II analogues, for which the pharmacological properties have been evaluated. Two of the Ang II analogues synthesized displayed high affinities and full agonist activities at the AT1 angiotensin receptor, and have proven to be useful tools in the search for the bioactive conformation of Ang II.

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  • 172.
    Johansson, Anja
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Design and Synthesis of Hepatitis C Virus NS3 Protease Inhibitors2003Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Hepatitis C Virus (HCV) is the leading cause of chronic liver disease worldwide as well as the primary indication for liver transplantation. More than 3% of the world’s population is chronically infected with HCV and there is an urgent need for effective therapy. NS3 protease, a viral enzyme required for propagation of HCV in humans, is a promising target for drug development in this area. This thesis addresses the design, synthesis and biochemical evaluation of new HCV NS3 protease inhibitors.

    The main objective of the thesis was the synthesis of peptide-based protease inhibitors of the bifunctional full-length NS3 enzyme (protease-helicase/NTPase). Three types of inhibitors were synthesized: i) classical serine protease inhibitors with electrophilic C-terminals, ii) product-based inhibitors with a C-terminal carboxylate group, and iii) product-based inhibitors with C-terminal carboxylic acid bioisosteres.

    The developmental work included the establishment of an improved procedure for solid-phase peptide synthesis (SPPS) in the N-to-C direction, in contrast to the C-to-N direction of classical SPPS methods. This inverse method facilitated synthesis of the peptides modified at the C-terminal.

    The potency of more than seventy newly synthesized inhibitors was assessed in an in vitro assay using the native form of the protease, i.e. the full-length NS3. The structure-activity relationship (SAR) data achieved was different from SAR data obtained from the more widely used truncated NS3 (protease domain) assay, indicating that the helicase domain of NS3 participates in the binding of the inhibitors.

    The most potent inhibitors identified in this study contained a C-terminal phenyl acyl sulfonamide moiety, i.e. a carboxylic acid bioisostere. It is concluded that the acyl sulfonamide moiety is a promising P1-P1´ spanning entity, which may have potential for use in the development of more drug-like HCV protease inhibitors.

    List of papers
    1. An Improved Procedure for N- to C-Directed (Inverse) Solid-Phase Peptide Synthesis
    Open this publication in new window or tab >>An Improved Procedure for N- to C-Directed (Inverse) Solid-Phase Peptide Synthesis
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    2000 (English)In: Journal of combinatorial chemistry, ISSN 1520-4766, E-ISSN 1520-4774, Vol. 2, no 5, p. 496-507Article in journal (Refereed) Published
    Abstract [en]

    A method for solid-phase peptide synthesis in the N- to C-direction that delivers good coupling yields and a low degree of epimerization is reported. The optimized method involves the coupling, without preactivation, of the resin-bound C-terminal amino acid with excess amounts of amino acid tri-tert-butoxysilyl (Sil) esters, using HATU as coupling reagent and 2,4,6-trimethylpyridine (TMP, collidine) as a base. For the amino acids investigated, the degree of epimerization was typically 5%, except for Ser(t-Bu) which was more easily epimerized (ca. 20%). Five tripeptides (AA(1)-AA(2)-AA(3)) with different properties were used as representative model peptides in the development of the synthetic method: Asp-Leu-Glu, Leu-Ala-Phe, Glu-Asp-Val, Asp-Ser-Ile, and Asp-D-Glu-Leu. The study used different combinations of HATU and TBTU as activating agents, N, N-diisopropylethylamine (DIEA) and TMP as bases, DMF and dichloromethane as solvents, and cupric chloride as an epimerization suppressant. The epimerization of AA(2) in the coupling of AA(3) was further reduced in the presence of cupric chloride. However, the use of this reagent also resulted in a decrease in loading onto the resin and significant cleavage between AA(1) and AA(2). Experiments indicated that the observed suppressing effect of cupric chloride on epimerization in the present system merely seemed to be a result of a base-induced cleavage of the oxazolone system, the key intermediate in the epimerization process. Consequently, the cleavages were most pronounced in slow couplings. An improved synthesis of fully characterized amino acid tri-tert-butoxysilyl (Sil) ester hydrochloride building blocks is presented. The amino acid Sil esters were found to be stable as hydrochlorides but not as free bases. Although only a few peptides have been used in this study, we believe that the facile procedure devised herein should provide an attractive alternative for the solid-phase synthesis of short (six residues or less) C-terminally modified peptides, e.g., in library format.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-90139 (URN)10.1021/cc000022h (DOI)11029175 (PubMedID)
    Available from: 2003-02-26 Created: 2003-02-26 Last updated: 2017-12-14Bibliographically approved
    2. Inhibition of hepatitis C virus NS3 protease activity by product-based peptides is dependent on helicase domain
    Open this publication in new window or tab >>Inhibition of hepatitis C virus NS3 protease activity by product-based peptides is dependent on helicase domain
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    2001 (English)In: Bioorganic & Medicinal Chemistry Letters, ISSN 0960-894X, E-ISSN 1464-3405, Vol. 11, no 2, p. 203-206Article in journal (Refereed) Published
    National Category
    Pharmaceutical Sciences Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-51295 (URN)10.1016/S0960-894X(00)00625-9 (DOI)
    Available from: 2006-03-04 Created: 2006-03-04 Last updated: 2020-06-05Bibliographically approved
    3. Tetrapeptides as potent protease inhibitors of Hepatitis C Virus full-length NS3 (protease-helicase/NTPase)
    Open this publication in new window or tab >>Tetrapeptides as potent protease inhibitors of Hepatitis C Virus full-length NS3 (protease-helicase/NTPase)
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    2002 (English)In: Bioorganic & Medicinal Chemistry, ISSN 0968-0896, E-ISSN 1464-3391, Vol. 10, no 12, p. 3915-22Article in journal (Refereed) Published
    National Category
    Pharmaceutical Sciences Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-91487 (URN)10.1016/S0968-0896(02)00310-3 (DOI)
    Available from: 2004-03-16 Created: 2004-03-16 Last updated: 2018-01-13Bibliographically approved
    4. Acyl sulfonamides as potent protease inhibitors of the hepatitis C virus full-length NS3 (protease-helicase/NTPase): a comparative study of different C-terminals
    Open this publication in new window or tab >>Acyl sulfonamides as potent protease inhibitors of the hepatitis C virus full-length NS3 (protease-helicase/NTPase): a comparative study of different C-terminals
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    2003 (English)In: Bioorganic & Medicinal Chemistry, ISSN 0968-0896, E-ISSN 1464-3391, Vol. 11, no 12, p. 2551-2568Article in journal (Refereed) Published
    National Category
    Pharmaceutical Sciences Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-66026 (URN)10.1016/S0968-0896(03)00179-2 (DOI)
    Available from: 2006-11-13 Created: 2006-11-13 Last updated: 2018-01-10Bibliographically approved
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  • 173.
    Johansson, Senia
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Studies on Cytotoxic and Neutrophil Challenging Polypeptides and Cardiac Glycosides of Plant Origin2001Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis examines the isolation and characterisation (biological and chemical) of polypeptides from plants. A fractionation protocol was developed and applied on 100 plant materials with the aim of isolating highly purified polypeptide fractions from small amounts of plant materials. The polypeptide fractions were analysed and evaluated for peptide content and biological activities. A multitarget functional bioassay was optimised as a method for detecting substances interacting with the inflammatory process of activated neutrophil granulocytes. In this assay, the neutrophil was challenged with an inflammatory mediator, N-formyl methionyl-leucyl-phenylalanine (fMLP), or with platelet activating factor (PAF), to induce exocytotic release of the enzyme elastase, which then was quantified by photometric determination of the product p-nitroanilide (pNA) formed from a chromogenic substrate for elastase. Of the tested extracts, 41% inhibited pNA formation more than 60%, and 3% stimulated formation.

    Phoratoxin B and four new peptides, phoratoxins C-F, were isolated from Phoradendron tomentosum. In addition, the cardiac glycoside digitoxin was isolated from Digitalis purpurea. All these substances expressed cytotoxicity and a neutrophil challenging activity.

    Phoratoxins C-F were similar to earlier described phoratoxins A and B, which belong to the group of thionins. All the peptides were evaluated for cytotoxicity in a human cell line panel. Phoratoxin C was the most potent towards the cell lines (mean IC50: 160 nM), and was therefore investigated further on tumour cells from patients. Correlation analysis of the log IC50 values indicated a mechanism of action different from clinically used archetypal cytotoxic drugs. Phoratoxin C also showed selective toxicity to the solid tumours when compared to the haematological cancer types. The phoratoxin C was 18 times more potent towards the solid tumour samples from breast cancer cells (87 nM) compared to the tested haematological malignancies.

    The structure-activity relationship concerning cytotoxicity was evaluated for digitoxin and related cardiac glycosides. Digitoxin was shown to be potent, with the average IC50 37 nM being within the therapeutic concentration used for cardiac congestion (13-45 nM). Digitoxin expressed selective toxicity towards solid tumours from patients compared to haematological malignancies.

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  • 174.
    Jäverfalk-Hoyes, Emmy
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Development of Methods in CE, CE-MS and MS/MS: Applications in Pharmaceutical, Biomedical and Forensic sciences2001Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Capillary electrophoresis-mass spectrometry has been used successfully for the analysis of a wide range of analytes such as chiral local anaesthetics, sulphonated reactive dyes and endogenous neurotransmitters and neuropeptides.

    The partial filling technique was used in CE-MS for chiral separation of bupivacaine and ropivacaine using the non-volatile selector β-cyclodextrin. By only partially filling the capillary with selector and using capillaries coated with polyacrylamide to suppress the electroosmotic flow, introduction of the selector into the mass spectrometer was avoided. An impurity of 0.25% of the R-enantiomer of ropivacaine in the S-form could be detected.

    The partial filling technique was developed further using CE employing two different selectors in separate plugs in the capillary. This enhanced the separation efficiency and offered greater flexibility in controlling the separation.

    By using transient-isotachophoresis (tITP)-CE-MS it was possible to concentrate and detect classical neurotransmitters and neuropeptides with masses ranging from 104 Da to 1642 Da. γ -Aminopropyltriethoxysilane coated capillaries were used to minimize adsorption of the peptides onto to capillary surface. Endogenous dopamine, glutamate, γ-aminobutyric acid (GABA), acetylcholine, methionine-enkephalin and substance P 1-7 were detected in the striatum of marmoset monkey.

    Sulphonated dyes obtained from single textile fibres were analysed using CE-MS. Capillary electrophoresis was found to be a good way of removing the excess amounts of glucose present in the sample that would otherwise interfere with the electrospray ionisation.

    Automatic function switching, originally developed for use together with liquid chromatography, was found to be a great method for acquiring MS/MS data when doing infusion experiments saving both time and sample without decreasing the quality of the MS/MS data. It was also found to be a more time efficient way than using the precursor ion scanning mode on the Q-TOF to obtain precursor ion data.

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  • 175.
    Kaiser, Nils-Fredrik K.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Fast Chemistry by Microwave Heating: First Descriptions of Highly Enantioselective Microwave Protocols for Metal Catalysis; First Descriptions of in-situ Gas Generation for Fast Combinatorial Microwave Chemistry2001Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Microwave heating was applied to different palladium-catalyzed allylic substitution reactions. The use of various nucleophiles demonstrated C-, N-, O- and S- nucleophilicity. High yields and stereopurities of the corresponding alkyls, amides, ethers and sulfones were afforded after only 30 – 120 s of heating. The sensitive stereocontrol induced by the catalyst and the catalytic activity were sustained (88 to > 99 % enantiomeric excess (ee) ) despite high temperatures (up to 215oC) and forced conditions.

    Rapid molybdenum-catalyzed allylic alkylation was undertaken utilizing microwave heating. This formerly troublesome catalysis was developed into a simple, fast and convenient protocol. The protocol was employed in a structure-activity investigation for optimizing catalytic activity. An electron-rich environment with low steric restriction around the catalyzing molybdenum improved catalytic activity as well as induced stereoselectivity (> 99 % ee).

    A new methodology was developed for performing carbon monoxide reactions without the use of gaseous carbon monoxide from an external source. Solid metal carbonyls of low toxicity were utilized for in situ liberation of carbon monoxide directly into the reaction mixture. The methodology was applied to the combinatorial microwave-assisted synthesis of a small sized substance library of amidated HIV-1 protease inhibitors.

  • 176.
    Kang, Dongwei
    Shandong Univ, Sch Pharmaceut Sci, Dept Med Chem, Key Lab Chem Biol,Minist Educ, 44 West Culture Rd, Jinan 250012, Shandong, Peoples R China.
    Molecular design opportunities presented by solvent-exposed regions of target proteins2019In: Medicinal research reviews (Print), ISSN 0198-6325, E-ISSN 1098-1128, Vol. 39, no 6, p. 2194-2238Article, review/survey (Refereed)
    Abstract [en]

    Solvent-exposed regions, or solvent-filled pockets, within or adjacent to the ligand-binding sites of drug-target proteins provide opportunities for substantial modifications of existing small-molecular drug molecules without serious loss of activity. In this review, we present recent selected examples of exploitation of solvent-exposed regions of proteins in drug design and development from the recent medicinal-chemistry literature.

  • 177.
    Karami, Kiomars
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Pharmacy, Department of Pharmaceutical Chemistry.
    Electrolyte structures and ionization conditions for iontophoretic drug formulation of local anesthetics1999Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Iontophoresis is a modern method of drug delivery by which charged bioactive molecules (drugs) are transferred from an electrolytic reservoir into and through a tissue, normally skin, by means of a weak electric current. The drug is placed in a conductive medium, usually an aqueous solution or a hydrogel, between the "active" electrode and the skin. The circuit is completed by a second "passive" electrode and the skin. Although iontophoresis is a well-known method for transdermal delivery of drugs, basic physicochemical knowledge of this phenomenon is still lacking.

    This thesis aimed to obtain a wide understanding of electrolyte structures and ionization conditions in iontophoresis, and a firm physicochemical basis for improvement of iontophoretic drug formulation of local anesthetics. The precision conductometric technique was used mainly. Lidocaine hydrochloride (LidHCl) was selected as a model local anesthetic substance. The conductance theory of Fuoss, Hsia and Fernandez-Prini was used to interpret the experimental data, with respect to ionization and mobility of LidHCl in different solvent media. LidHCl was studied in the following solvents:, water, propylene glycol (a transdermal enhancer),aqueous propylene glycol (20 weight-% PG) and 1-octanol. To compare the ionization properties of prilocaine hydrochloride (PrilHCl) with those of LidHCl, PrilHCl was studied in the same pharmaceutical aqueous-enhancer medium. Furthermore, the molecular diffusive transport properties of the local anesthetics lidocaine-, prilocaine-,bupivacaine-, etidocaine-, mepivacaine- and ropivacaine hydrochloride in an agarose hydrogel (1 weight-% agarose) were studied.

    The results indicate that, for the solvents studied, LidHCl has the highest ionic mobility in aqueous propylene glycol; u(LidH+) = 1.35 mm2 V-1 min-1. No measurable difference in ionization properties and ionic mobility between LidHCl and PrilHCl in aqueous propylene glycol was observed. Within the concentration range investigated in this solvent, more than 98% of both LidHCl and PrilHCl are in ionized form (LidH+ and PrilH+). Of the six local anesthetics studied by diffusion measurements in agarose hydrogel (1 weight-% agarose) as medium, LidHCl and PrilHCl have the highest diffusion coefficients; D(lido) = 7.79 · 10-6 and D(prilo) = 7.76  · 10-6 cm2/s.

    From a pharmaceutical point of view, it might be interesting to study the possibility of combining lidocaine- and prilocaine hydrochloride in an aqueous-enhancer medium as an iontophoretic drug formulation of local anesthetics.

  • 178.
    Karlsson, Christoffer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Blom, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Johansson, Miranda
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Jansson, Anna M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Scifo, Enzo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Karlén, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Govender, Thavendran
    Catalysis and Peptide Research Unit, University of KwaZulu Natal, South Africa.
    Gogoll, Adolf
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Synthetical Organic Chemistry.
    Phototriggerable peptidomimetics for the inhibition of Mycobacterium turberculosis ribonucleotide reductase by targeting protein-protein binding2015In: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 13, no 9, p. 2612-2621Article in journal (Refereed)
    Abstract [en]

    Incorporation of an artificial amino acid 2 with a stilbene chromophore into peptidomimetics with three to nine amino acids yields phototriggerable candidates for inhibition of the binding between the R1 and R2 subunits of the M. tuberculosis ribonucleotide reductase (RNR). Interstrand hydrogen bond probability was used as a guideline for predicting conformational preferences of the photoisomers. Binding of these inhibitors has been rationalized by docking studies with the R1 unit. Significant differences in binding of the photoisomers were observed. For the shorter peptidomimetics, stronger binding of the Z isomer might indicate hydrophobic interactions between the stilbene chromophore and the binding site.

  • 179.
    Karlsson, Oskar
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Hanrieder, Jörg
    Imaging mass spectrometry in drug development and toxicology2017In: Archives of Toxicology, ISSN 0340-5761, E-ISSN 1432-0738, Vol. 91, no 6, p. 2283-2294Article, review/survey (Refereed)
    Abstract [en]

    During the last decades, imaging mass spectrometry has gained significant relevance in biomedical research. Recent advances in imaging mass spectrometry have paved the way for in situ studies on drug development, metabolism and toxicology. In contrast to whole-body autoradiography that images the localization of radiolabeled compounds, imaging mass spectrometry provides the possibility to simultaneously determine the discrete tissue distribution of the parent compound and its metabolites. In addition, imaging mass spectrometry features high molecular specificity and allows comprehensive, multiplexed detection and localization of hundreds of proteins, peptides and lipids directly in tissues. Toxicologists traditionally screen for adverse findings by histopathological examination. However, studies of the molecular and cellular processes underpinning toxicological and pathologic findings induced by candidate drugs or toxins are important to reach a mechanistic understanding and an effective risk assessment strategy. One of IMS strengths is the ability to directly overlay the molecular information from the mass spectrometric analysis with the tissue section and allow correlative comparisons of molecular and histologic information. Imaging mass spectrometry could therefore be a powerful tool for omics profiling of pharmacological/toxicological effects of drug candidates and toxicants in discrete tissue regions. The aim of the present review is to provide an overview of imaging mass spectrometry, with particular focus on MALDI imaging mass spectrometry, and its use in drug development and toxicology in general.

  • 180.
    Karlsson, Oskar
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Karolinska Inst, Dept Clin Neurosci, Ctr Mol Med, Sweden; Harvard TH Chan Sch Publ Hlth, Dept Environm Hlth, USA.
    Michno, Wojciech
    Ransome, Yusuf
    Hanrieder, Jörg
    MALDI imaging delineates hippocampal glycosphingolipid changes associated with neurotoxin induced proteopathy following neonatal BMAA exposure.2017In: Biochimica et Biophysica Acta, ISSN 0006-3002, E-ISSN 1878-2434, Vol. 1865, no 7, p. 740-746Article in journal (Refereed)
    Abstract [en]

    The environmental toxin β-N-methylamino-L-alanine (BMAA) has been proposed to contribute to neurodegenerative diseases. We have previously shown that neonatal exposure to BMAA results in dose-dependent cognitive impairments, proteomic alterations and progressive neurodegeneration in the hippocampus of adult rats. A high BMAA dose (460mg/kg) also induced intracellular fibril formation, increased protein ubiquitination and enrichment of proteins important for lipid transport and metabolism. The aim of this study was therefore to elucidate the role of neuronal lipids in BMAA-induced neurodegeneration. By using matrix assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS), we characterized the spatial lipid profile in the hippocampus of six month-old rats that were treated neonatally (postnatal days 9-10) with 460mg/kg BMAA. Multivariate statistical analysis revealed long-term changes in distinct ganglioside species (GM, GD, GT) in the dentate gyrus. These changes could be a consequence of direct effects on ganglioside biosynthesis through the b-series (GM3-GD3-GD2-GD1b-GT1b) and may be linked to astrogliosis. Complementary immunohistochemistry experiments towards GFAP and S100β further verified the role of increased astrocyte activity in BMAA-induced brain damage. This highlights the potential of imaging MS for probing chemical changes associated with neuropathological mechanisms in situ. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.

  • 181.
    Kennedy, Amanda
    et al.
    Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden.
    Ballante, Flavio
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Johansson, Johan
    Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden.
    Milligan, Graeme
    Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow.
    Sundström, Linda
    Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden.
    Nordqvist, Anneli
    Cardiovascular Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden.
    Carlsson, Jens
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics.
    Structural Characterization of Agonist Binding to Protease-Activated Receptor 2 through Mutagenesis and Computational Modeling2018In: ACS Pharmacology & Translational Science, ISSN 2575-9108, Vol. 1, no 2, p. 119-133Article in journal (Refereed)
    Abstract [en]

    Protease-activated receptor 2 (PAR2) is a G protein-coupled receptor that is activated by proteolytic cleavage of its N-terminus. The unmasked N-terminal peptide then binds to the transmembrane bundle, leading to activation of intracellular signaling pathways associated with inflammation and cancer. Recently determined crystal structures have revealed binding sites of PAR2 antagonists, but the binding mode of the peptide agonist remains unknown. In order to generate a model of PAR2 in complex with peptide SLIGKV, corresponding to the trypsin-exposed tethered ligand, the orthosteric binding site was probed by iterative combinations of receptor mutagenesis, agonist ligand modifications and data-driven structural modeling. Flexible-receptor docking identified a conserved binding mode for agonists related to the endogenous ligand that was consistent with the experimental data and allowed synthesis of a novel peptide (1-benzyl-1H[1,2,3]triazole-4-yl-LIGKV) with higher functional potency than SLIGKV. The final model may be used to understand the structural basis of PAR2 activation and in virtual screens to identify novel PAR2 agonist and competitive antagonists. The combined experimental and computational approach to characterize agonist binding to PAR2 can be extended to study the many other G protein-coupled receptors that recognize peptides or proteins.

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  • 182.
    Khan, T. M.
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Gunasekera, Sunithi
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Roy, D.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Strömstedt, Adam A.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Göransson, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Structure and Activity Relationship of the Echinochloa Crus-Galli Antimicrobial Peptide 12014In: Journal of Peptide Science, ISSN 1075-2617, E-ISSN 1099-1387, Vol. 20, p. S278-S279Article in journal (Other academic)
  • 183.
    Kirkpatrick, Christine L.
    et al.
    Univ North Carolina Chapel Hill, Dept Chem, Chapel Hill, NC USA..
    Broberg, Christopher A.
    Univ North Carolina Chapel Hill, Dept Chem, Chapel Hill, NC USA..
    McCool, Elijah N.
    Univ North Carolina Chapel Hill, Dept Chem, Chapel Hill, NC USA..
    Lee, Woo Jean
    Univ North Carolina Chapel Hill, Dept Chem, Chapel Hill, NC USA..
    Chao, Alex
    Univ North Carolina Chapel Hill, Dept Chem, Chapel Hill, NC USA..
    McConnell, Evan W.
    Univ North Carolina Chapel Hill, Dept Chem, Chapel Hill, NC USA..
    Pritchard, David A.
    Univ North Carolina Chapel Hill, Dept Biostat, Chapel Hill, NC USA..
    Hebert, Michael
    Univ North Carolina Chapel Hill, Dept Chem, Chapel Hill, NC USA..
    Fleeman, Renee
    Univ S Florida, Dept Cell Biol Microbiol & Mol Biol, Tampa, FL USA..
    Adams, Jessie
    Univ S Florida, Dept Cell Biol Microbiol & Mol Biol, Tampa, FL USA..
    Jamil, Amer
    Univ Agr Faisalabad, Dept Biochem, Faisalabad, Pakistan..
    Madera, Laurence
    Dalhousie Univ, Dept Pathol, Halifax, NS, Canada..
    Strömstedt, Adam A.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Göransson, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Liu, Yufeng
    Univ North Carolina Chapel Hill, Dept Biostat, Dept Genet, Dept Stat & Operat Res, Chapel Hill, NC USA.;Univ North Carolina Chapel Hill, Carolina Ctr Genome Sci, Chapel Hill, NC USA..
    Hoskin, David W.
    Dalhousie Univ, Dept Pathol, Halifax, NS, Canada..
    Shaw, Lindsey N.
    Univ S Florida, Dept Cell Biol Microbiol & Mol Biol, Tampa, FL USA..
    Hicks, Leslie M.
    Univ North Carolina Chapel Hill, Dept Chem, Chapel Hill, NC USA..
    The "PepSAVI-MS" Pipeline for Natural Product Bioactive Peptide Discovery2017In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 89, no 2, p. 1194-1201Article in journal (Refereed)
    Abstract [en]

    The recent increase in extensively drug-resistant bacterial pathogens and the associated increase of morbidity and mortality demonstrate the immediate need for new antibiotic backbones with novel mechanisms of action. Here, we report the development of the PepSAVI-MS pipeline for bioactive peptide discovery. This highly versatile platform employs mass spectrometry and statistics to identify bioactive peptide targets from complex biological samples. We validate the use of this platform through the successful identification of known bioactive peptides from a botanical species, Viola odorata. Using this pipeline, we have widened the known antimicrobial spectrum for V. odorata cyclotides, including antibacterial activity of cycloviolacin O2 against A. baumannii. We further demonstrate the broad applicability of the platform through the identification of novel anticancer activities for cycloviolacins by their cytotoxicity against ovarian, breast, and prostate cancer cell lines.

  • 184.
    Lagerlund, Olof
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Design and Synthesis of Novel Glutamine Synthetase Inhibitors and Development of Palladium(0)-Catalyzed Aminocarbonylation2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Tuberculosis (TB) is a major infectious disease, killing about 2 million people annually throughout the world. Today's TB treatment is a lengthy procedure involving a combination of antibiotics. No new TB drug has been introduced onto the market in the past 40 years, and the emergence of multi- and extensively drug-resistant TB calls for new drugs. Finding new drug targets is important and one such target is the Mycobacterium tuberculosis enzyme glutamine synthetase (GS), which catalyses the formation of glutamine from glutamic acid. In this work, novel GS inhibitors and new Pd(0)-catalyzed methods have been developed.

    A microwave-enhanced Pd(0)-catalyzed α-arylation reaction was developed using water as solvent, and a phenylglycine scaffold was identified using structure-based design. A series of α-arylated phenylglycine derivates was produced at moderate to good yields. Some of these were biologically evaluated against GS.

    A novel scaffold, 3-amino-imidazo[1,2-a]pyridine, was identified by high-throughput screening directed towards GS. This type of compound could be easily produced via a Ugi-type, microwave-promoted multi-component reaction in 20 min. The scaffold was investigated by changing one substituent at a time, and in an experimental design where 8 factors were varied in the same design. Several potent inhibitors were identified; amongst them the most potent inhibitor to date (IC50 = 0.38 µM). Two discrete structure-activity relationships were established, and one of the inhibitors was co-crystallized.

    The first general aminocarbonylation of aryl chlorides and the first aminocarbonylation of alkenyl phosphates were developed. Alkenyl chlorides, bromides and triflates were investigated in the same transformation utilizing Mo(CO)6 as a solid carbon monoxide source. Two different Pd(0)-based catalytic systems were developed. A wide variety of aryl chlorides and amines could be transformed into the corresponding amides with good yields. The alkenyl substrates produced low to good yields.

    List of papers
    1. Microwave-enhanced alpha-arylation of a protected glycine in water: evaluation of 3-phenylglycine derivatives as inhibitors of the tuberculosis enzyme, glutamine synthetase
    Open this publication in new window or tab >>Microwave-enhanced alpha-arylation of a protected glycine in water: evaluation of 3-phenylglycine derivatives as inhibitors of the tuberculosis enzyme, glutamine synthetase
    Show others...
    2007 (English)In: Combinatorial chemistry & high throughput screening, ISSN 1386-2073, E-ISSN 1875-5402, Vol. 10, no 9, p. 783-789Article in journal (Refereed) Published
    Abstract [en]

    A microwave-enhanced, palladium-catalyzed protocol for the alpha-arylation of a protected glycine in neat water is described. This reaction proceeds rapidly, under non-inert conditions, to afford a range of phenylglycine derivatives in moderate to good yields. Based on this arylation, a number of aryl L-methionine-SR-sulfoximine (MSO) analogues were prepared and evaluated for their Mycobacterium tuberculosis glutamine synthetase (TB-GS) inhibitory activity.

    Keywords
    arylation, glutamine synthetase, microwave, palladium, tuberculosis, water
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-16614 (URN)10.2174/138620707783018478 (DOI)000253584600005 ()18478959 (PubMedID)
    Available from: 2008-06-05 Created: 2008-06-05 Last updated: 2018-01-12Bibliographically approved
    2. Functionalized 3-amino-imidazo[1,2-a]pyridines: A novel class of drug-like Mycobacterium tuberculosis glutamine synthetase inhibitors
    Open this publication in new window or tab >>Functionalized 3-amino-imidazo[1,2-a]pyridines: A novel class of drug-like Mycobacterium tuberculosis glutamine synthetase inhibitors
    Show others...
    2009 (English)In: Bioorganic & Medicinal Chemistry Letters, ISSN 0960-894X, E-ISSN 1464-3405, Vol. 19, no 16, p. 4790-4793Article in journal (Refereed) Published
    Abstract [en]

    3-Amino-imidazo[1,2-a]pyridines have been identified as a novel class of Mycobacterium tuberculosis glutamine synthetase inhibitors. Moreover, these compounds represent the first drug-like inhibitors of this enzyme. A series of compounds exploring structural diversity in the pyridine and phenyl rings have been synthesized and biologically evaluated. Compound 4n was found to be the most potent inhibitor (IC50 = 0.38 ± 0.02 μM). This compound was significantly more potent than the known inhibitors, L-methionine-SR-sulfoximine and phosphinothricin.

    Keywords
    Mycobacterium tuberculosis, Glutamine synthetase inhibitors, Microwave, 3-Aminoimidazo[1, 2-a]pyridine
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-100360 (URN)10.1016/j.bmcl.2009.06.045 (DOI)000268358800057 ()19560924 (PubMedID)
    Available from: 2009-03-31 Created: 2009-03-31 Last updated: 2020-06-05Bibliographically approved
    3. Synthesis, biological evaluation and X-ray crystallographic studies of imidazo[1,2-a]-pyridine based Mycobacterium tuberculosis glutamine synthetase inhibitors
    Open this publication in new window or tab >>Synthesis, biological evaluation and X-ray crystallographic studies of imidazo[1,2-a]-pyridine based Mycobacterium tuberculosis glutamine synthetase inhibitors
    Show others...
    2012 (English)In: MedChemComm, ISSN 2040-2503, E-ISSN 2040-2511, Vol. 3, no 5, p. 620-626Article in journal (Refereed) Published
    Abstract [en]

    Based on an imidazo[1,2-a]pyridine hit from a high-throughput screen directed at the M. tuberculosis enzyme glutamine synthetase, a hit expansion was performed by synthesizing a series of analogs. A set of 16 molecules was first synthesized according to a statistical molecular design approach. One potent inhibitor was identified (IC50 = 3.0 µM), which led to the synthesis of 17 additional imidazo[1,2-a]pyridines in a follow-up study. Among these, several inhibitors were identified showing single digit micromolar potency. An X-ray structure of one of these revealed the binding mode of this class of inhibitors in the ATP-binding site, and allowed us to rationalize some of the structure-activity relationships observed.

    National Category
    Medicinal Chemistry Medical and Health Sciences
    Research subject
    Chemistry with specialization in Organic Chemistry; Medicinal Chemistry
    Identifiers
    urn:nbn:se:uu:diva-100359 (URN)10.1039/c2md00310d (DOI)000304387300013 ()
    Available from: 2009-03-31 Created: 2009-03-31 Last updated: 2018-01-13Bibliographically approved
    4. Microwave-promoted aminocarbonylations of aryl chlorides using Mo(CO)(6) as a solid carbon monoxide source.
    Open this publication in new window or tab >>Microwave-promoted aminocarbonylations of aryl chlorides using Mo(CO)(6) as a solid carbon monoxide source.
    2005 (English)In: J Comb Chem, ISSN 1520-4766, Vol. 8, no 1, p. 4-6Article in journal (Refereed) Published
    Keywords
    Benzamides/*chemical synthesis/chemistry, Benzene Derivatives/*chemistry, Carbon Monoxide/*chemistry, Catalysis, Combinatorial Chemistry Techniques, Hydrocarbons; Chlorinated/*chemistry, Microwaves, Molecular Structure, Molybdenum/*chemistry, Palladium/chemistry, Research Support; Non-U.S. Gov't
    Identifiers
    urn:nbn:se:uu:diva-75624 (URN)16398545 (PubMedID)
    Available from: 2006-02-13 Created: 2006-02-13 Last updated: 2011-01-11
    5. Aminocarbonylations of Alkenyl Phosphates, Chlorides, Bromides and Triflates with Mo(CO)6 as a Solid CO source
    Open this publication in new window or tab >>Aminocarbonylations of Alkenyl Phosphates, Chlorides, Bromides and Triflates with Mo(CO)6 as a Solid CO source
    2009 (English)In: Tetrahedron, ISSN 0040-4020, E-ISSN 1464-5416, Vol. 65, no 36, p. 7646-7652Article in journal (Refereed) Published
    Abstract [en]

    Palladium-catalyzed aminocarbonylations of alkenyl chlorides, bromides, and triflates were investigated using Mo(CO)6 as a solid carbon monoxide source. The reactions afforded moderate to good yields producing a wide variety of acrylamides after 20 minutes of microwave irradiation. In addition, the aminocarbonylation reaction was, for the first time, expanded to include alkenyl phosphates as starting materials.

    Keywords
    Carbonylation, Microwave, Vinyl halides, Vinyl phosphates, Vinyl triflates, Alkenyl electrophiles, Palladium, Enolizable ketones
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-100358 (URN)10.1016/j.tet.2009.06.101 (DOI)000269340000043 ()
    Available from: 2009-03-31 Created: 2009-03-31 Last updated: 2018-01-13Bibliographically approved
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  • 185.
    Lai, Kuei-Hung
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Studies on anti-leukemic terpenoids from medicinal mushrooms and marine sponges with ChemGPS-NP-based targets investigation of lead compounds2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis investigates the anti-leukemic activity of terpenoids isolated from medicinal mushrooms and marine sponges, as well as their possible targets and mechanisms of action.

    In the first section, we focused on studying the triterpenoidal components of three triterpenoid-enriched medicinal mushrooms Antrodia cinnamomea, Ganoderma lucidum, and Poria cocos, which have been used in folk medicine for centuries and also developed into several contemporary marketed products. We isolated the major and characteristic triterpenoids from these mushrooms, together with six new lanostanoids (II-1II-6). The anti-leukemic activity of the isolates was evaluated in vitro using MTT proliferative assay and seven of them exhibited potential anti-leukemic effect. The active lead compounds were further subjected to computational analyses utilizing the ChemGPS-NP tool. We established a database for the anti-leukemic relevant chemical space of triterpenoids isolated from these three medicinal mushrooms, which could be used as a reference database for further research on anti-leukemic triterpenoids. Our results indicated that the anti-leukemic effect of the active lead compounds was mediated not only through topoisomerases inhibition but also through inhibiting DNA polymerases.

    The second and third sections focused on isolation of anti-leukemic sesterterpenoids from sponges. The investigation of Carteriospongia sp. led to the isolation of two new scalarane-type sesterterpenoids (III-1 and III-2) and one known tetraprenyltoluquinol-related metabolite (III-3). All isolates exhibit an apoptotic mechanism of action against Molt 4 cells, found to be mediated through the disruption of the mitochondrial membrane potential (MMP) and inhibition of topoisomerase IIα expression. Detailed investigation of the apoptotic mechanism of action using molecular docking analysis revealed that compound III-1 might target Hsp90 protein. The apoptotic-inducing effect of III-3 was supported by in vivo experiment by suppressing the volume of xenograft tumor growth (47.58%) compared with the control.

    In the final section of this thesis we studied manoalide and its derivatives, sesterterpenoids isolated from the sponge Luffariella sp.. Manoalide has been studied as a potential anti-inflammatory agent for the last thirty years with more than 200 publications and 40 patents. However, the configurations at positions 24 and 25 were never revealed. In the current study, ten manoalide-type sesterterpenoids (IV-1IV-10) were isolated from Luffariella sp. and their stereoisomers at positions 24 and 25 were identified and separated for the first time. The configuration at positions 24 and 25 showed to have a significant effect on the anti-leukemic activity of manoalide derivatives, with the 24R,25S-isomer exhibiting the most potent anti-leukemic activity. The apoptotic mechanism of action of compound IV-7 against Molt 4 cells was investigated, and the compound was found to trigger MMP disruption and intracellular reactive oxygen species (ROS) generation. Compound IV-7 also inhibited activity against both human topoisomerases, I and II. The in vivo experiment further supported the anti-leukemic effect of IV-7 with a 66.11% tumor volume suppression compared to the control.

    List of papers
    1. Cytotoxic Lanostanoids from Poria cocos
    Open this publication in new window or tab >>Cytotoxic Lanostanoids from Poria cocos
    Show others...
    2016 (English)In: Journal of natural products (Print), ISSN 0163-3864, E-ISSN 1520-6025, Vol. 79, no 11, p. 2805-2813Article in journal (Refereed) Published
    Abstract [en]

    Six new and 16 known lanostanoids were isolated from the sclerotia of Poria cocos. The structures of the new isolates were elucidated to be 16α-hydroxy-3-oxo-24-methyllanosta-5,7,9(11),24(31)-tetraen-21-oic acid (1), 3β,16α,29-trihydroxy-24-methyllanosta-7,9(11),24(31)-trien-21-oic acid (2), 3β,16α,30-trihydroxy-24-methyllanosta-7,9(11),24(31)-trien-21-oic acid (3), 3β-acetoxy-16α,24β-dihydroxylanosta-7,9(11),25-trien-21-oic acid (4), 3β,16α-dihydroxy-7-oxo-24-methyllanosta-8,24(31)-dien-21-oic acid (5), and 3α,16α-dihydroxy-7-oxo-24-methyllanosta-8,24(31)-dien-21-oic acid (6), based on extensive spectroscopic analyses. The absolute configuration of 4 was determined using Mosher's method. The antiproliferative activity of the isolated compounds (except 3 and 4) was evaluated against four leukemic cell lines (Molt 4, CCRF-CEM, HL 60, and K562). Dehydropachymic acid (9), dehydroeburicoic acid (12), pachymic acid (14), and lanosta-7,9(11),24-trien-21-oic acid (20) exhibited an antiproliferative effect on the CCRF-CEM cancer cell line with IC50 values of 2.7, 6.3, 4.9, and 13.1 μM, respectively. Both dehydropachymic acid (9) and dehydroeburicoic acid (12) showed antiproliferative effects against Molt 4 (IC50 13.8 and 14.3 μM) and HL 60 (IC50 7.3 and 6.0 μM) leukemic cell lines. Primary computational analysis using a chemical global positioning system for natural products (ChemGPS-NP) on the active lanostanoids from P. cocos suggested that targets other than topoisomerases may be involved in the antiproliferative activity.

    National Category
    Biochemistry and Molecular Biology Medicinal Chemistry Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-317526 (URN)10.1021/acs.jnatprod.6b00575 (DOI)000394410600006 ()27808511 (PubMedID)
    Note

    De 2 första författarna delar förstaförfattarskapet.

    Available from: 2017-03-15 Created: 2017-03-15 Last updated: 2018-01-13Bibliographically approved
    2. Antileukemic Scalarane Sesterterpenoids and Meroditerpenoid from Carteriospongia (Phyllospongia) sp., Induce Apoptosis via Dual Inhibitory Effects on Topoisomerase II and Hsp90
    Open this publication in new window or tab >>Antileukemic Scalarane Sesterterpenoids and Meroditerpenoid from Carteriospongia (Phyllospongia) sp., Induce Apoptosis via Dual Inhibitory Effects on Topoisomerase II and Hsp90
    Show others...
    2016 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 36170Article in journal (Refereed) Published
    Abstract [en]

    Two new scalarane sesterterpenoids, 12 beta-(3'beta-hydroxybutanoyloxy)-20,24-dimethyl-24-oxo-scalara-16-en-25-al (1) and 12 beta-(3'beta-hydroxypentanoyloxy)-20,24-dimethyl-24-oxo-scalara-16-en-25-al (2), along with one known tetraprenyltoluquinol-related metabolite (3), were isolated from the sponge Carteriospongia sp. In leukemia Molt 4 cells, 1 at 0.0625 mu g/mL (125 nM) triggered mitochondrial membrane potential (MMP) disruption and apoptosis showing more potent effect than 2 and 3. The isolates inhibited topoisomerase II alpha expression. The apoptotic-inducing effect of 3 was supported by the in vivo experiment through suppressing the volume of xenograft tumor growth (47.58%) compared with the control. Compound 1 apoptotic mechanism of action in Molt 4 cells was further elucidated through inducing ROS generation, calcium release and ER stress. Using the molecular docking analysis, 1 exhibited more binding affinity to N-terminal ATP-binding pocket of Hsp90 protein than 17-AAG, a standard Hsp90 inhibitor. The expression of Hsp90 client proteins, Akt, p70(S6k), NF kappa B, Raf-1, p-GSK3 beta, and XIAP, MDM 2 and Rb2, and CDK4 and Cyclin D3, HIF1 and HSF1 were suppressed by the use of 1. However, the expression of Hsp70, acetylated tubulin, and activated caspase 3 were induced after 1 treatment. Our results suggested that the proapoptotic effect of the isolates is mediated through the inhibition of Hsp90 and topoisomerase activities.

    National Category
    Cell and Molecular Biology Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
    Identifiers
    urn:nbn:se:uu:diva-308635 (URN)10.1038/srep36170 (DOI)000386462100001 ()27796344 (PubMedID)
    Available from: 2016-11-30 Created: 2016-11-29 Last updated: 2018-01-13Bibliographically approved
    3. ChemGPS-NP study on antileukemic triterpenoids from widely-used medicinal mushrooms in Asia
    Open this publication in new window or tab >>ChemGPS-NP study on antileukemic triterpenoids from widely-used medicinal mushrooms in Asia
    (English)Manuscript (preprint) (Other academic)
    National Category
    Medicinal Chemistry Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-317552 (URN)
    Available from: 2017-03-16 Created: 2017-03-16 Last updated: 2018-01-13
    4. Separation and identification on stereoisomers of manoalide derivatives and their configuration-depending antileukemic effects in vitro and in vivo
    Open this publication in new window or tab >>Separation and identification on stereoisomers of manoalide derivatives and their configuration-depending antileukemic effects in vitro and in vivo
    (English)Manuscript (preprint) (Other academic)
    National Category
    Pharmacology and Toxicology Cell and Molecular Biology Pharmaceutical Sciences Medicinal Chemistry
    Identifiers
    urn:nbn:se:uu:diva-317553 (URN)
    Available from: 2017-03-16 Created: 2017-03-16 Last updated: 2018-01-13
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  • 186.
    Lai, Kuei-Hung
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Backlund, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    ChemGPS-NP study on antileukemic triterpenoids from widely-used medicinal mushrooms in AsiaManuscript (preprint) (Other academic)
  • 187.
    Lai, Kuei-Hung
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Backlund, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Separation and identification on stereoisomers of manoalide derivatives and their configuration-depending antileukemic effects in vitro and in vivoManuscript (preprint) (Other academic)
  • 188.
    Lai, Kuei-Hung
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Lu, Mei-Chin
    Du, Ying-Chi
    El-Shazly, Mohamed
    Wu, Tung-Ying
    Hsu, Yu-Ming
    Henz, Astrid
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Yang, Juan-Cheng
    Backlund, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Chang, Fang-Rong
    Wu, Yang-Chang
    Cytotoxic Lanostanoids from Poria cocos2016In: Journal of natural products (Print), ISSN 0163-3864, E-ISSN 1520-6025, Vol. 79, no 11, p. 2805-2813Article in journal (Refereed)
    Abstract [en]

    Six new and 16 known lanostanoids were isolated from the sclerotia of Poria cocos. The structures of the new isolates were elucidated to be 16α-hydroxy-3-oxo-24-methyllanosta-5,7,9(11),24(31)-tetraen-21-oic acid (1), 3β,16α,29-trihydroxy-24-methyllanosta-7,9(11),24(31)-trien-21-oic acid (2), 3β,16α,30-trihydroxy-24-methyllanosta-7,9(11),24(31)-trien-21-oic acid (3), 3β-acetoxy-16α,24β-dihydroxylanosta-7,9(11),25-trien-21-oic acid (4), 3β,16α-dihydroxy-7-oxo-24-methyllanosta-8,24(31)-dien-21-oic acid (5), and 3α,16α-dihydroxy-7-oxo-24-methyllanosta-8,24(31)-dien-21-oic acid (6), based on extensive spectroscopic analyses. The absolute configuration of 4 was determined using Mosher's method. The antiproliferative activity of the isolated compounds (except 3 and 4) was evaluated against four leukemic cell lines (Molt 4, CCRF-CEM, HL 60, and K562). Dehydropachymic acid (9), dehydroeburicoic acid (12), pachymic acid (14), and lanosta-7,9(11),24-trien-21-oic acid (20) exhibited an antiproliferative effect on the CCRF-CEM cancer cell line with IC50 values of 2.7, 6.3, 4.9, and 13.1 μM, respectively. Both dehydropachymic acid (9) and dehydroeburicoic acid (12) showed antiproliferative effects against Molt 4 (IC50 13.8 and 14.3 μM) and HL 60 (IC50 7.3 and 6.0 μM) leukemic cell lines. Primary computational analysis using a chemical global positioning system for natural products (ChemGPS-NP) on the active lanostanoids from P. cocos suggested that targets other than topoisomerases may be involved in the antiproliferative activity.

  • 189.
    Larhed, Mats
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Hallberg, Mathias
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Hallberg, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    NONPEPTIDE AT2 RECEPTOR AGONISTS2016In: Medicinal Chemistry Reviews, ISSN 978-0-9962932-3-5Article, book review (Refereed)
  • 190.
    Larik, Fayaz Ali
    et al.
    Quaid I Azam Univ, Dept Chem, Islamabad 45320, Pakistan..
    Saeed, Aamer
    Quaid I Azam Univ, Dept Chem, Islamabad 45320, Pakistan..
    Shahzad, Danish
    Quaid I Azam Univ, Dept Chem, Islamabad 45320, Pakistan..
    Faisal, Muhammad
    Quaid I Azam Univ, Dept Chem, Islamabad 45320, Pakistan..
    El-Seedi, Hesham
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Mehfooz, Haroon
    Quaid I Azam Univ, Dept Chem, Islamabad 45320, Pakistan..
    Channar, Pervaiz Ali
    Quaid I Azam Univ, Dept Chem, Islamabad 45320, Pakistan..
    Synthetic approaches towards the multi target drug spironolactone and its potent analogues/derivatives2017In: Steroids, ISSN 0039-128X, E-ISSN 1878-5867, Vol. 118, p. 76-92Article, review/survey (Refereed)
    Abstract [en]

    Spironolactone is a well-known multi-target drug and is specifically used for the treatment of high blood pressure and heart failure. It is also used for the treatment of edema, cirrhosis of the liver, malignant, pediatric, nephrosis and primary hyperaldosteronism. Spironolactone in association with thiazide diuretics treats hypertension and in association with furosemide treats bronchopulmonary dyspepsia. The therapeutic mechanism of action of spironolactone involves binding to intracellular mineralocorticoids receptors (MRs) in kidney epithelial cells, thereby inhibiting the binding of aldosterone. Since its first synthesis in 1957 there are several synthetic approaches have been reported throughout the years, Synthetic community has devoted efforts to improve the synthesis of spironolactone and to synthesize its analogues and derivatives. This review aims to provide comprehensive insight for the synthetic endeavors devoted towards the synthesis of a versatile drug spironolactone and its analogues/derivatives.

  • 191. Lauer, Dilyara
    et al.
    Slavic, Svetlana
    Sommerfeld, Manuela
    Thoene-Reineke, Christa
    Sharkovska, Yuliya
    Hallberg, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Dahlof, Bjorn
    Kintscher, Ulrich
    Unger, Thomas
    Steckelings, Ulrike Muscha
    Kaschina, Elena
    Angiotensin Type 2 Receptor Stimulation Ameliorates Left Ventricular Fibrosis and Dysfunction via Regulation of Tissue Inhibitor of Matrix Metalloproteinase 1/Matrix Metalloproteinase 9 Axis and Transforming Growth Factor beta 1 in the Rat Heart2014In: Hypertension, ISSN 0194-911X, E-ISSN 1524-4563, Vol. 63, no 3, p. E60-E67Article in journal (Refereed)
  • 192.
    Lee, Jin-Ching
    et al.
    Kaohsiung Med Univ, Grad Inst Nat Prod, Coll Pharm, Kaohsiung 807, Taiwan.;Kaohsiung Med Univ, Dept Biotechnol, Coll Life Sci, Kaohsiung 807, Taiwan.;Kaohsiung Med Univ, Res Ctr Nat Prod & Drug Dev, Kaohsiung 807, Taiwan..
    Chang, Fang-Rong
    Kaohsiung Med Univ, Grad Inst Nat Prod, Coll Pharm, Kaohsiung 807, Taiwan.;Natl Sun Yat Sen Univ, Dept Marine Biotechnol & Resources, Kaohsiung 804, Taiwan.;Kaohsiung Med Univ Hosp, Ctr Canc, Kaohsiung 807, Taiwan..
    Chen, Shu-Rong
    Kaohsiung Med Univ, Grad Inst Nat Prod, Coll Pharm, Kaohsiung 807, Taiwan..
    Wu, Yu-Hsuan
    Natl Cheng Kung Univ, Inst Basic Med Sci, Coll Med, Tainan 701, Taiwan.;Natl Cheng Kung Univ, Coll Med, Ctr Infect Dis & Signaling Res, Tainan 701, Taiwan..
    Hu, Hao-Chun
    Kaohsiung Med Univ, Grad Inst Nat Prod, Coll Pharm, Kaohsiung 807, Taiwan..
    Wu, Yang-Chang
    China Med Univ, Sch Pharm, Coll Pharm, Taichung 404, Taiwan.;China Med Univ Hosp, Chinese Med Res & Dev Ctr, Taichung 404, Taiwan.;China Med Univ Hosp, Ctr Mol Med, Taichung 404, Taiwan.;China Med Univ, Res Ctr Chinese Herbal Med, Taichung 404, Taiwan..
    Backlund, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Cheng, Yuan-Bin
    Kaohsiung Med Univ, Grad Inst Nat Prod, Coll Pharm, Kaohsiung 807, Taiwan.;Kaohsiung Med Univ, Res Ctr Nat Prod & Drug Dev, Kaohsiung 807, Taiwan.;Kaohsiung Med Univ, Ctr Infect Dis & Canc Res, Kaohsiung 807, Taiwan..
    Anti-Dengue Virus Constituents from Formosan Zoanthid Palythoa mutuki2016In: Marine Drugs, ISSN 1660-3397, E-ISSN 1660-3397, Vol. 14, no 8, article id 151Article in journal (Refereed)
    Abstract [en]

    A new marine ecdysteroid with an alpha-hydroxy group attaching at C-4 instead of attaching at C-2 and C-3, named palythone A (1), together with eight known compounds (2-9) were obtained from the ethanolic extract of the Formosan zoanthid Palythoa mutuki. The structures of those compounds were mainly determined by NMR spectroscopic data analyses. The absolute configuration of 1 was further confirmed by comparing experimental and calculated circular dichroism (CD) spectra. Anti-dengue virus 2 activity and cytotoxicity of five isolated compounds were evaluated using virus infectious system and [3-(4,5-dimethylthiazol-2-yl)5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt (MTS) assays, respectively. As a result, peridinin (9) exhibited strong antiviral activity (IC50 = 4.50 +/- 0.46 mu g/mL), which is better than that of the positive control, 2'CMC. It is the first carotene-like substance possessing anti-dengue virus activity. In addition, the structural diversity and bioactivity of the isolates were compared by using a ChemGPS-NP computational analysis. The ChemGPS-NP data suggested natural products with anti-dengue virus activity locate closely in the chemical space.

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  • 193. Leuzy, Antoine
    et al.
    Rodriguez-Vieitez, Elena
    Saint-Aubert, Laure
    Chiotis, Konstantinos
    Almkvist, Ove
    Savitcheva, Irina
    Jonasson, My
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Radiology. Department of Medical Physics, Uppsala University Hospital, Uppsala, Sweden.
    Lubberink, Mark
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Radiology. Department of Medical Physics, Uppsala University Hospital, Uppsala, Sweden.
    Wall, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Radiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Antoni, Gunnar
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry.
    Nordberg, Agneta
    Longitudinal uncoupling of cerebral perfusion, glucose metabolism, and tau deposition in Alzheimer's disease.2018In: Alzheimer's & Dementia, ISSN 1552-5260, E-ISSN 1552-5279, Vol. 14, no 5, p. 652-663Article in journal (Refereed)
    Abstract [en]

    INTRODUCTION: Cross-sectional findings using the tau tracer [18F]THK5317 (THK5317) have shown that [18F]fluorodeoxyglucose (FDG) positron emission tomography data can be approximated using perfusion measures (early-frame standardized uptake value ratio; ratio of tracer delivery in target to reference regions). In this way, a single positron emission tomography study can provide both functional and molecular information.

    METHODS: We included 16 patients with Alzheimer's disease who completed follow-up THK5317 and FDG studies 17 months after baseline investigations. Linear mixed-effects models and annual percentage change maps were used to examine longitudinal change.

    RESULTS: Limited spatial overlap was observed between areas showing declines in THK5317 perfusion measures and FDG. Minimal overlap was seen between areas showing functional change and those showing increased retention of THK5317.

    DISCUSSION: Our findings suggest a spatiotemporal offset between functional changes and tau pathology and a partial uncoupling between perfusion and metabolism, possibly as a function of Alzheimer's disease severity.

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  • 194.
    Lindgren, Cecilia
    et al.
    Umea Univ, Dept Chem, SE-90187 Umea, Sweden.
    Tyagi, Mohit
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Viljanen, Johan V.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Toms, Johannes
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Ge, Changrong
    Karolinska Inst, Med Inflammat Res, Dept Med Biochem & Biophys, SE-17177 Stockholm, Sweden.
    Zhang, Naru
    Karolinska Inst, Med Inflammat Res, Dept Med Biochem & Biophys, SE-17177 Stockholm, Sweden;Southern Med Univ, Sch Pharmaceut Sci, Guangzhou, Guangdong, Peoples R China.
    Holmdahl, Rikard
    Karolinska Inst, Med Inflammat Res, Dept Med Biochem & Biophys, SE-17177 Stockholm, Sweden;Southern Med Univ, Sch Pharmaceut Sci, Guangzhou, Guangdong, Peoples R China.
    Kihlberg, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Organic Chemistry.
    Linusson, Anna
    Umea Univ, Dept Chem, SE-90187 Umea, Sweden.
    Dynamics Determine Signaling in a Multicomponent System Associated with Rheumatoid Arthritis2018In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 61, no 11, p. 4774-4790Article in journal (Refereed)
    Abstract [en]

    Strategies that target multiple components are usually required for treatment of diseases originating from complex biological systems. The multicomponent system consisting of the DR4 major histocompatibility complex type II molecule, the glycopeptide CI1259-273 from type II collagen, and a T-cell receptor is associated with development of rheumatoid arthritis (RA). We introduced non-native amino acids and amide bond isosteres into CI1259-273 and investigated the effect on binding to DR4 and the subsequent T-cell response. Molecular dynamics simulations revealed that complexes between DR4 and derivatives of CI1259-273 were highly dynamic. Signaling in the overall multicomponent system was found to depend on formation of an appropriate number of dynamic intramolecular hydrogen bonds between DR4 and CI1259-273, together with the positioning of the galactose moiety of CI1259-273 in the DR4 binding groove. Interestingly, the system tolerated modifications at several positions in CI1259-273, indicating opportunities to use analogues to increase our understanding of how rheumatoid arthritis develops and for evaluation as vaccines to treat RA.

  • 195.
    Lindh, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Palladium(II)-Catalyzed Coupling Reactions2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Sustainable chemical processes are becoming increasingly important in all fields of synthetic chemistry. Catalysis can play an important role in developing environmentally benign chemical processes, and transition metals have an important role to play in the area of green chemistry. In particular, palladium(II) catalysis includes many key features for successful green chemistry methods, as demonstrated by a number of eco-friendly oxidation reactions catalyzed by palladium(II).

    The aim of the work presented in this thesis was to develop novel and greener palladium(II)-catalyzed coupling reactions. In striving to achieve this aim, the first open-vessel, room-temperature palladium(II)-catalyzed oxidative Heck reaction, using oxygen from the air as the reoxidant of palladium, was developed.

    In a further investigation of the palladium(II)-catalyzed oxidative Heck reaction, base-free conditions for the transformation were identified and suitable conditions for microwave-assisted oxidative Heck reactions were established.

    A convenient and low-cost palladium(II)-catalyzed method for the synthesis of styrene derivatives, by coupling arylboranes with vinyl acetate, was developed. The reaction mechanism was studied using ESI-MS, which enabled the detection of cationic palladium intermediates in ongoing productive reactions, and a plausible catalytic cycle was proposed.

    In an attempt to make the oxidative Heck and the styrene synthesis reactions more attractive from an industrial point of view, conditions for continuous flow synthesis were identified. The results were generally good and rapid synthesis of the desired products was obtained.

    The first palladium(II)-catalyzed C–P bond-forming Hirao-type reaction, employing arylboranes instead of the commonly used aryl halides, was developed. An ESI-MS study was performed, and a plausible catalytic pathway was suggested.

    Finally, a novel method for synthesizing aryl ketones from benzoic acids and nitriles, via palladium(II)-catalyzed decarboxylation of the benzoic acids, was established. Further, the reaction mechanism was studied by ESI-MS and a plausible catalytic route presented.

    List of papers
    1. Open-air oxidative Heck reactions at room temperature
    Open this publication in new window or tab >>Open-air oxidative Heck reactions at room temperature
    2006 (English)In: Green Chemistry, ISSN 1463-9262, E-ISSN 1463-9270, Vol. 8, no 4, p. 338-343Article in journal (Refereed) Published
    Abstract [en]

    Palladium(II)-catalyzed oxidative Heck arylation reactions proceed at room temperature with atmospheric air as the sole reoxidant. Using arylboronic acids as arylating agents and inexpensive 2,9-dimethyl-1,10-phenanthroline as the supporting ligand, efficient vinylic substitution reactions were obtained both with electron-poor and electron-rich olefins on a 1–50 mmol scale.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-94792 (URN)10.1039/B517152K (DOI)
    Available from: 2006-09-14 Created: 2006-09-14 Last updated: 2017-12-14Bibliographically approved
    2. Efficient palladium(II) catalysis under air. Base-free oxidative heck reactions at room temperature or with microwave heating
    Open this publication in new window or tab >>Efficient palladium(II) catalysis under air. Base-free oxidative heck reactions at room temperature or with microwave heating
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    2007 (English)In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 72, no 21, p. 7957-7962Article in journal (Refereed) Published
    Abstract [en]

    Scope and limitations of the base-free oxidative Heck reaction with arylboronic acids have been explored. Under our conditions, the dmphen−palladium(II)-catalyzed arylation proceeded with air or p-benzoquinone as reoxidants of palladium(0). We found that ambient temperature and mild aerobic conditions allow for the use of substrates sensitive to palladium(II)-catalyzed oxidation. Oxidative Heck couplings, employing different arylboronic acids, were smoothly and regioselectively conducted with both electron-rich and electron-poor olefins, providing high yields even with disubstituted butyl methacrylate, sensitive acrolein, and a vinylboronate ester. Controlled microwave processing was used to reduce reaction times from hours to minutes both in small scale and in 50 mmol scale batch processes.

    Keywords
    Acrylates/*chemistry, Aerobiosis, Benzene Derivatives/*chemistry, Boronic Acids/*chemistry, Catalysis, Chemistry; Organic/*methods, Heat, Microwaves, Oxidation-Reduction, Palladium/*chemistry, Temperature
    National Category
    Pharmaceutical Sciences
    Identifiers
    urn:nbn:se:uu:diva-16615 (URN)10.1021/jo701434s (DOI)000249986500019 ()17887706 (PubMedID)
    Available from: 2008-05-29 Created: 2008-05-29 Last updated: 2018-01-12Bibliographically approved
    3. Synthesis of styrenes by palladium(II)-catalyzed vinylation of arylboronic acids and aryltrifluoroborates by using vinyl acetate
    Open this publication in new window or tab >>Synthesis of styrenes by palladium(II)-catalyzed vinylation of arylboronic acids and aryltrifluoroborates by using vinyl acetate
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    2009 (English)In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 15, no 18, p. 4630-4636Article in journal (Refereed) Published
    Abstract [en]

    Reactions of aromatic and heteroaromatic boronic acids or aryltrifluoroborate salts with vinyl acetate in the presence of a palladium(II) catalyst give the corresponding styrenes in good yields. This Heck reaction proceeds with microwave heating in less than 30 min at 140 degrees C in the absence of base and tolerates a variety of substituents. No palladium reoxidant is needed and the vinylation is performed under non-inert conditions. Mass spectrometry (electrospray ionization mass spectrometry (ESIMS) and tandem mass spectrometry   (MS/MS)) was used to identify cationic palladium-containing complexes in ongoing reactions. The key intermediates that have been detected, together with experiments that used deuterated vinyl acetate, support the existence of catalytically active palladium hydride species, and that it is the arylation of ethylene, not vinyl acetate, which   generates the styrene product. The mechanism of the reaction is discussed in terms of the palladium(II) intermediates mentioned above.

    Keywords
    Heck reaction, mass spectrometry, mechanistic studies, palladium, styrene
    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:uu:diva-102918 (URN)10.1002/chem.200802744 (DOI)000265955200018 ()19274694 (PubMedID)
    Available from: 2009-05-13 Created: 2009-05-12 Last updated: 2017-12-13Bibliographically approved
    4. Continuous Flow Palladium(II): Catalyzed Oxidative Heck Reactions with Arylboronic Acids
    Open this publication in new window or tab >>Continuous Flow Palladium(II): Catalyzed Oxidative Heck Reactions with Arylboronic Acids
    2010 (English)In: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, no 12, p. 2270-2274Article in journal (Refereed) Published
    Abstract [en]

    Palladium(II)-catalyzed oxidative Heck reactions were investigated under continuous flow conditions. Selective, fast and convenient protocols for the coupling of arylboronic acids with electron-rich and electron-poor olefins were developed by using a commercially available flow reactor.

    Keywords
    Continuous flow, cross-coupling, Boron, Palladium, homogeneous catalysis, organic-synthesis, base-free, coupling reactions, room-temperature, bond formation, efficient, catalysis, palladium, air, perspective
    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:uu:diva-130028 (URN)10.1002/ejoc.201000063 (DOI)000277332500004 ()
    Available from: 2010-08-27 Created: 2010-08-27 Last updated: 2017-12-12Bibliographically approved
    5. Microwave-promoted palladium(II)-catalyzed C-P bond formation by using arylboronic acids or aryltrifluoroborates.
    Open this publication in new window or tab >>Microwave-promoted palladium(II)-catalyzed C-P bond formation by using arylboronic acids or aryltrifluoroborates.
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    2009 (English)In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 15, no 47, p. 13069-13074Article in journal (Refereed) Published
    Abstract [en]

    The first Pd-II-catalyzed P arylation has been performed by using palladium acetate, the rigid bidentate ligand dmphen (dmphen=2,9-dimethyl-1,10-phenanthroline), and without the addition of base or acid. Couplings of arylboronic acids or aryl trifluoroborates with H-phosphonate dialkyl esters were conducted in 30 min with controlled microwave (MW) heating under non-inert conditions. Aryl phosphites were also synthesized at room temperature with atmospheric air as the sole reoxidant. The arylated phosphonates were isolated in 44-90% yields. The excellent chemoselectivity of the method was illustrated in the synthesis of a Mycobacterium tuberculosis glutamine synthetase (MTB-GS) inhibitor. Online ESIMS was used to detect cationic palladium species in ongoing reactions directly, and a catalytic cycle has been proposed based on these results.

    Place, publisher, year, edition, pages
    Weinheim: Wiley-VCH Verlag GmbH, 2009
    Keywords
    Boronic acids, microwave chemistry, palladium, P arylation, trifluoroborates
    National Category
    Analytical Chemistry
    Research subject
    Analytical Chemistry
    Identifiers
    urn:nbn:se:uu:diva-113919 (URN)10.1002/chem.200901473 (DOI)000273697100021 ()19856344 (PubMedID)
    Available from: 2010-02-04 Created: 2010-02-04 Last updated: 2017-12-12Bibliographically approved
    6.
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  • 196.
    Lindh, Martin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry.
    Computational Modelling in Drug Discovery: Application of Structure-Based Drug Design, Conformal Prediction and Evaluation of Virtual Screening2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Structure-based drug design and virtual screening are areas of computational medicinal chemistry that use 3D models of target proteins. It is important to develop better methods in this field with the aim of increasing the speed and quality of early stage drug discovery.

    The first part of this thesis focuses on the application of structure-based drug design in the search for inhibitors for the protein 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), one of the enzymes in the DOXP/MEP synthetic pathway. This pathway is found in many bacteria (such as Mycobacterium tuberculosis) and in the parasite Plasmodium falciparum.

    In order to evaluate and improve current virtual screening methods, a benchmarking data set was constructed using publically available high-throughput screening data. The exercise highlighted a number of problems with current data sets as well as with the use of publically available high-throughput screening data. We hope this work will help guide further development of well designed benchmarking data sets for virtual screening methods.

    Conformal prediction is a new method in the computer-aided drug design toolbox that gives the prediction range at a specified level of confidence for each compound. To demonstrate the versatility and applicability of this method we derived models of skin permeability using two different machine learning methods; random forest and support vector machines.

    List of papers
    1. Design, Synthesis, and X-ray Crystallographic Studies of alpha-Aryl Substituted Fosmidomycin Analogues as Inhibitors of Mycobacterium tuberculosis 1-Deoxy-D-xylulose 5-Phosphate Reductoisomerase
    Open this publication in new window or tab >>Design, Synthesis, and X-ray Crystallographic Studies of alpha-Aryl Substituted Fosmidomycin Analogues as Inhibitors of Mycobacterium tuberculosis 1-Deoxy-D-xylulose 5-Phosphate Reductoisomerase
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    2011 (English)In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 54, no 14, p. 4964-4976Article in journal (Refereed) Published
    Abstract [en]

    The natural antibiotic fosmidomycin acts via inhibition of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), an essential enzyme in the non-mevalonate pathway of isoprenoid biosynthesis. Fosmidomycin is active on Mycobacterium tuberculosis DXR (MtDXR), but it lacks antibacterial activity probably because of poor uptake. alpha-Aryl substituted fosmidomycin analogues have more favorable physicochemical properties and are also more active in inhibiting malaria parasite growth. We have solved crystal structures of MtDXR in complex with 3,4-dichlorophenyl substituted fosmidomycin analogues; these show important differences compared to our previously described forsmidomycin-DXR complex. Our best inhibitor has an IC(50) = 0.15 mu M on MtDXR but still lacked activity in a mycobacterial growth assay (MIC > 32 mu g/mL). The combined results, however, provide insights into how DXR accommodates the new inhibitors and serve as an excellent starting point for the design of other novel and more potent inhibitors, particularly against pathogens where uptake is less of a problem, such as the malaria parasite.

    National Category
    Biochemistry and Molecular Biology Other Basic Medicine
    Identifiers
    urn:nbn:se:uu:diva-156614 (URN)10.1021/jm2000085 (DOI)000292892300003 ()21678907 (PubMedID)
    Available from: 2011-08-07 Created: 2011-08-04 Last updated: 2018-01-12Bibliographically approved
    2. Substitution of the phosphonic acid and hydroxamic acid functionalities of the DXR inhibitor FR900098: An attempt to improve the activity against Mycobacterium tuberculosis
    Open this publication in new window or tab >>Substitution of the phosphonic acid and hydroxamic acid functionalities of the DXR inhibitor FR900098: An attempt to improve the activity against Mycobacterium tuberculosis
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    2011 (English)In: Bioorganic & Medicinal Chemistry Letters, ISSN 0960-894X, E-ISSN 1464-3405, Vol. 21, no 18, p. 5403-5407Article in journal (Refereed) Published
    Abstract [en]

    Two series of FR900098/fosmidomycin analogs were synthesized and evaluated for MtDXR inhibition and Mycobacterium tuberculosis whole-cell activity. The design rationale of these compounds involved the exchange of either the phosphonic acid or the hydroxamic acid part for alternative acidic and metal-coordinating functionalities. The best inhibitors provided IC(50) values in the micromolar range, with a best value of 41 mu M.

    Keywords
    Tuberculosis, DXR, Enzyme inhibitor, Fosmidomycin, FR900098
    National Category
    Chemical Sciences
    Identifiers
    urn:nbn:se:uu:diva-158288 (URN)10.1016/j.bmcl.2011.07.005 (DOI)000294051800057 ()
    Available from: 2011-09-07 Created: 2011-09-06 Last updated: 2020-06-05
    3. DXR Inhibition by Potent Mono- and Disubstituted Fosmidomycin Analogues
    Open this publication in new window or tab >>DXR Inhibition by Potent Mono- and Disubstituted Fosmidomycin Analogues
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    2013 (English)In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 56, no 15, p. 6190-6199Article in journal (Refereed) Published
    Abstract [en]

    The antimalarial compound fosmidomycin targets DXR, the enzyme that catalyzes the first committed step in the MEP pathway producing the universally essential isoprenoid precursors, isopentenyl diphosphate and dimethylallyl diphosphate. The MEP pathway is used by a number of pathogens, including Mycobacterium tuberculosis and apicomplexan parasites, and differs from the classical mevalonate pathway that is essential in humans. Using a structure-based approach, we designed a number of analogues of fosmidomycin, including a series that are substituted in both the Cα and the hydroxamate positions. The latter proved to be a stable framework for the design of inhibitors that extend from the cramped substrate-binding site and can, for the first time, bridge the substrate and cofactor binding sites. A number of these compounds are more potent than fosmidomycin in terms of killing Plasmodium falciparum in an in vitro assay; the best has an IC50 of 40 nM.

    Keywords
    Mycobacterium tuberculosis, 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR
    National Category
    Structural Biology
    Research subject
    Biology with specialization in Structural Biology; Medicinal Chemistry
    Identifiers
    urn:nbn:se:uu:diva-196616 (URN)10.1021/jm4006498 (DOI)000323082400015 ()
    Funder
    Swedish Foundation for Strategic Research Swedish Research Council
    Note

    De tre (3) första författarna delar förstaförfattarskapet.

    Available from: 2013-03-11 Created: 2013-03-11 Last updated: 2017-12-06Bibliographically approved
    4. Toward a Benchmarking Data Set Able to Evaluate Ligand- and Structure-based Virtual Screening Using Public HTS Data
    Open this publication in new window or tab >>Toward a Benchmarking Data Set Able to Evaluate Ligand- and Structure-based Virtual Screening Using Public HTS Data
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    2015 (English)In: Journal of Chemical Information and Modeling, ISSN 1549-9596, Vol. 55, no 2, p. 343-353Article in journal (Refereed) Published
    Abstract [en]

    Virtual screening has the potential to accelerate and reduce costs of probe development and drug discovery. To develop and benchmark virtual screening methods, validation data sets are commonly used. Over the years, such data sets have been constructed to overcome the problems of analogue bias and artificial enrichment. With the rapid growth of public domain databases containing high-throughput screening data, such as the PubChem BioAssay database, there is an increased possibility to use such data for validation. In this study, we identify PubChem data sets suitable for validation of both structure- and ligand-based virtual screening methods. To achieve this, high-throughput screening data for which a crystal structure of the bioassay target was available in the PDB were identified. Thereafter, the data sets were inspected to identify structures and data suitable for use in validation studies. In this work, we present seven data sets (MMP13, DUSP3, PTPN22, EPHX2, CTDSP1, MAPK10, and CDK5) compiled using this method. In the seven data sets, the number of active compounds varies between 19 and 369 and the number of inactive compounds between 59 405 and 337 634. This gives a higher ratio of the number of inactive to active compounds than what is found in most benchmark data sets. We have also evaluated the screening performance using docking and 3D shape similarity with default settings. To characterize the data sets, we used physicochemical similarity and 2D fingerprint searches. We envision that these data sets can be a useful complement to current data sets used for method evaluation.

    Place, publisher, year, edition, pages
    American Chemical Society (ACS), 2015
    National Category
    Structural Biology Pharmaceutical Chemistry
    Research subject
    Chemistry with specialization in Bioorganic Chemistry
    Identifiers
    urn:nbn:se:uu:diva-248018 (URN)10.1021/ci5005465 (DOI)000349943100014 ()25564966 (PubMedID)
    Available from: 2015-03-26 Created: 2015-03-26 Last updated: 2018-03-05Bibliographically approved
    5. Predicting the Rate of Skin Penetration Using an Aggregated Conformal Prediction Framework
    Open this publication in new window or tab >>Predicting the Rate of Skin Penetration Using an Aggregated Conformal Prediction Framework
    2017 (English)In: Molecular Pharmaceutics, ISSN 1543-8384, E-ISSN 1543-8392, Vol. 14, no 5, p. 1571-1576Article in journal (Refereed) Published
    Abstract [en]

    Skin serves as a drug administration route, and skin permeability of chemicals is of significant interest in the pharmaceutical and cosmetic industries. An aggregated conformal prediction (ACP) framework was used to build models, for predicting the permeation rate (log K-p) of chemical compounds through human skin. The conformal prediction method gives as an output the prediction range at a given level of confidence for each compound, which enables the user to make a more informed decision when, for example, suggesting the next compound to prepare, Predictive models were built using;both the random forest and the support vector machine methods and were based on experimentally derived permeability data on 211 diverse compounds. The derived models were of similar predictive quality as compared to earlier published models but have the extra advantage of not only presenting a single predicted value for each, compound but also a reliable, individually assigned prediction range. The models use calculated descriptors and can quickly predict the skin permeation rate of new compounds.

    Keywords
    conformal prediction, skin penetration nonconformist, Scikit Learn, random forest, Support vector machines
    National Category
    Basic Medicine
    Identifiers
    urn:nbn:se:uu:diva-323448 (URN)10.1021/acs.molpharmaceut.7b00007 (DOI)000400633300024 ()28335598 (PubMedID)
    Available from: 2017-07-04 Created: 2017-07-04 Last updated: 2018-01-13Bibliographically approved
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  • 197. Lindhe, Örjan
    et al.
    Almqvist, Per
    Kågedal, Matts
    Gustavsson, Sven-Åke
    Bergström, Mats
    Nilsson, Dag
    Antoni, Gunnar
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Preclinical PET Platform.
    Autoradiographic mapping of 5-HT1B/1D binding sites in the Rhesus monkey brain using [carbonyl-11C]zolmitriptan2011In: International Journal of Molecular Imaging, ISSN 2090-1712, E-ISSN 2090-1720Article in journal (Refereed)
    Abstract [en]

    Zolmitriptan is a serotonin 5-HT1B/1D receptor agonist that is an effective and well-tolerated drug for migraine treatment. In a human positron emission tomography study, [11C]zolmitriptan crossed the blood-brain barrier but no clear pattern of regional uptake was discernable. The objective of this study was to map the binding of [11C]zolmitriptan in Rhesus monkey brain using whole hemisphere in vitro autoradiography with [11C]zolmitriptan as a radioligand. In saturation studies, [11C]zolmitriptan showed specific (90%) binding to a population of high-affinity binding sites (Kd 0.95–5.06 nM). There was regional distribution of binding sites with the highest density in the ventral pallidum, followed by the external globus pallidus, substantia nigra, visual cortex, and nucleus accumbens. In competitive binding studies with 5-HT1 receptor antagonists, [11C]zolmitriptan binding was blocked by selective 5-HT1B and 5-HT1D ligands in all target areas. There was no appreciable change in binding with the addition of a 5-HT1A receptor antagonist.

  • 198.
    Lindman, Susanna
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Pharmacy, Department of Pharmaceutical Chemistry.
    Design and synthesis of -turn peptidomimetics: Applications to angiotensin II2001Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This study addresses the issue of how to convert peptides into drug-like non-peptides while retaining the biological activity at peptide receptors. Angiotensin II (Asp-Arg-Val-Tyr-Ile-His-Pro-Phe, Ang II) was used as a model peptide.

    Small bioactive peptides are in most cases conformationally flexible molecules. Rigidified peptide analogues or peptidomimetic scaffolds can be introduced into the peptide, to enforce a particular backbone conformation, and thereby locate the side-chains at defined positions in space. The conformationally constrained analogues are of considerable value in determining biologically active conformation(s) of the studied peptide. The strategy applied in this thesis includes identification of non-pharmacophoric amino acid residues, rigidification, conformational analysis and incorporation of turn mimicking scaffolds in

    Ang II. Several side-chain cyclized (disulfide and methylendithioether) Ang II analogues have been synthesized. The binding studies of the rigidified analogues demonstrated that the compounds designed for the AT1-receptor had affinity for both receptor subtypes, while the compounds designed for the AT2-receptor displayed high selectivity only for this receptor subtype. Conformational evaluation revealed that several of the cyclized Ang II analogues most probably adopt a γ-turn like conformation around Tyr-4 while interacting with the

    Ang II receptor. Based on this hypothesis, three different γ-turn mimetics replacing amino acid residues 3-5 were designed, synthesized and incorporated into Ang II. One of the synthesized pseudopeptides, incorporating an azepine-containing γ-turn mimetic, exerted high binding affinity and agonistic activity. These results strongly support the theory that Ang II adopts a γ-turn like conformation when activating the AT1 receptor. The other Ang II analogues, incorporating bicyclic and aromatic γ-turn mimetics, did not display any binding to the AT1 receptor.

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  • 199.
    Linkuviene, Vaida
    et al.
    Vilnius Univ, Inst Biotechnol, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania.
    Talibov, Vladimir O
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC.
    Danielson, U. Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Matulis, Daumantas
    Vilnius Univ, Inst Biotechnol, Dept Biothermodynam & Drug Design, Sauletekio 7, LT-10257 Vilnius, Lithuania.
    Introduction of Intrinsic Kinetics of Protein-Ligand Interactions and Their Implications for Drug Design2018In: Journal of Medicinal Chemistry, ISSN 0022-2623, E-ISSN 1520-4804, Vol. 61, no 6, p. 2292-2302Article in journal (Refereed)
    Abstract [en]

    Structure kinetic relationship analyses and identification of dominating interactions for optimization of lead compounds should ideally be based on intrinsic rate constants instead of the more easily accessible observed kinetic constants, which also account for binding linked reactions. The intrinsic rate constants for sulfonamide inhibitors and pharmacologically relevant isoforms of carbonic anhydrase were determined by a novel surface plasmon resonance (SPR) biosensor-based approach, using chemodynamic analysis of binding-linked pH-dependent effects. The observed association rates (k(a)(obs)) were pH-dependent and correlated with the fraction of deprotonated inhibitor and protonated zinc-bound water molecule. The intrinsic association rate constants (k(a)(intr)) were pH independent and higher than k(a)(obs). By contrast, the observed and intrinsic dissociation rate constants were identical and pH-independent, demonstrating that the observed association and dissociation mechanisms are inherently different. A model accounting for the differences between intrinsic and observed rate constants was developed, useful also for other interactions with binding-linked protonation reactions.

  • 200.
    Linnanen, Tero
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Pharmacy, Department of Pharmaceutical Chemistry.
    Serotonergic aporphine derivatives: Synthesis and structure-activity relationships2000Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Novel series of well-characterized and stereochemically pure 11-substituted (R)-aporphine derivatives have been prepared and their interaction with serotonin 5-HT7 and 5-HT1A receptors and dopamine D2A and D1 receptors have been studied. Efficient palladium catalyzed reactions were utilized for the diastereoselective synthesis of atropisomers as well as for the synthesis of several of the other (R)-aporphine derivatives. A number of 11-arylated (R)-aporphines displayed high affinity for 5-HT7 and 5-HT1A receptors and derivatives with selectivity for either 5-HT7 or 5-HT1A receptors were obtained by chosing the proper substituents on the 11-phenyl ring. Simultaneous substitution of the 2' and 6' positions of (R)-11-phenylaporphine afforded derivatives, including some atropisomers, with increased 5-HT7 selectivity and several of these analogues were characterized as selective 5-HT7 receptor antagonists. Introduction of substituents in the other positions of the 11-phenyl group resulted in derivatives with selectivity for 5-HT1A receptors.

    In addition, new series of novel pentacyclic (R)-aporphines were synthesized either by the introduction of a methylene group between carbon atoms C1 and C11 in the (R)-aporphine skeleton or by ring expansion reactions of (R)-1,11-carbonylaporphine. These series of derivatives afforded the possibility to introduce substituents/functional groups below, above and in the plane of the ring system thereby allowing for structural extensions into previously unexplored areas of receptor binding sites. Compounds with various affinities for the serotonin and dopamine receptors were obtained and novel 5-HT7 receptor antagonists were identified.

    The identification of selective serotonin 5-HT7 receptor antagonists is of particular interest since only a few putatively selective 5-HT7 receptor antagonistic ligands have been reported.

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