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Lennerstrand, Johan
Publications (10 of 37) Show all publications
Palanisamy, N. & Lennerstrand, J. (2018). Biophysical Studies on HCV 1a NS3/4A Protease and Its Catalytic Triad in Wild Type and Mutants by the In Silico Approach.. Interdisciplinary sciences: computational life sciences, 10(1), 143-156
Open this publication in new window or tab >>Biophysical Studies on HCV 1a NS3/4A Protease and Its Catalytic Triad in Wild Type and Mutants by the In Silico Approach.
2018 (English)In: Interdisciplinary sciences: computational life sciences, ISSN 1913-2751, Vol. 10, no 1, p. 143-156Article in journal (Refereed) Published
Abstract [en]

The hepatitis C virus (HCV), of the family flaviviridae, is one of the major causes of chronic liver diseases. Until the year 2012, HCV infections were treated using PEG-interferon and ribavirin combinations, which have a low cure rate and severe side effects. Currently, many direct-acting antivirals (DAAs) are available, e.g. protease inhibitors, NS5A and polymerase inhibitors. These drugs have proven to be efficient in interferon-free treatment combinations and capable of enhancing the cure rate to above 90 %. Unlike PEG-interferon and ribavirin combinations, DAAs select for resistance in HCV. The R155K mutation in the HCV was found to resist all the currently available protease inhibitors. Here, we studied biophysical parameters like pocket (cavity) geometries and stabilizing residues of HCV 1a NS3/4A protease in wild type and mutants. We also studied HCV 1a NS3/4A protease's catalytic residues: their accessibility, energy, flexibility and binding to Phase II oral protease inhibitor vedroprevir (GS-9451), and compared these parameters between wild type and mutant(s). All these studies were performed using various bioinformatics tools (e.g. Swiss-PdbViewer and Schrödinger's Maestro) and web servers (e.g. DoGSiteScorer, SRide, ASA-View, WHAT IF, elNémo, CABS-flex, PatchDock and PLIP). From our study, we found that introduction of R155K, A156T or D168A mutation to wild-type NS3/4A protease increases the pocket's volume, surface (in the R155K mutant, surface decreases), lipo surface and depth and decreases the number of stabilizing residues. Additionally, differences in catalytic residues' solvent accessibility, energy, root-mean-square deviation (RMSD) and flexibility between wild type and mutants might explain changes in the protease activity and the resistance to protease inhibitors.

Keywords
Biophysical studies, Hepatitis C virus (HCV), Mutants, NS3/4A protease, Vedroprevir (GS-9451)
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:uu:diva-318093 (URN)10.1007/s12539-016-0177-4 (DOI)000426823400014 ()27311576 (PubMedID)
Available from: 2017-03-23 Created: 2017-03-23 Last updated: 2018-05-15Bibliographically approved
Palanisamy, N., Akaberi, D. & Lennerstrand, J. (2018). Protein backbone flexibility pattern is evolutionarily conserved in the Flaviviridae family: A case of NS3 protease in Flavivirus and Hepacivirus. Molecular Phylogenetics and Evolution, 118, 58-63
Open this publication in new window or tab >>Protein backbone flexibility pattern is evolutionarily conserved in the Flaviviridae family: A case of NS3 protease in Flavivirus and Hepacivirus
2018 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 118, p. 58-63Article in journal (Refereed) Published
Abstract [en]

Viruses belonging to the Flaviviridae family have been an important health concern for humans, animals and birds alike. No specific treatment is available yet for many of the viral infections caused by the members of this family. Lack of specific drugs against these viruses is mainly due to lack of protein structure information. It has been known that protein backbone fluctuation pattern is highly conserved in protein pairs with similar folds, in spite of the lack of sequence similarity. We hypothesized that this concept should also hold true for proteins (especially enzymes) of viruses included in different genera of the Flaviviridae family, as we know that the sequence similarity between them is low. Using available NS3 protease crystal structures of the Flaviviridae family, our preliminary results have shown that the C alpha (i.e. backbone) fluctuation patterns are highly similar between Flaviviruses and a Hepacivirus (i.e. hepatitis C virus, HCV). This has to be validated further experimentally.

Keywords
Flaviviridae, Protein C alpha fluctuation, Viral evolution, Zika virus (ZIKV), Hepatitis C virus (HCV)
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:uu:diva-343889 (URN)10.1016/j.ympev.2017.09.015 (DOI)000417227900007 ()28951254 (PubMedID)
Available from: 2018-03-05 Created: 2018-03-05 Last updated: 2018-03-08Bibliographically approved
Kjellin, M., Wesslén, T., Löfblad, E., Lennerstrand, J. & Lannergård, A. (2018). The effect of the first-generation HCV-protease inhibitors boceprevir and telaprevir and the relation to baseline NS3 resistance mutations in genotype 1: experience from a small Swedish cohort. Upsala Journal of Medical Sciences, 123(1), 50-56
Open this publication in new window or tab >>The effect of the first-generation HCV-protease inhibitors boceprevir and telaprevir and the relation to baseline NS3 resistance mutations in genotype 1: experience from a small Swedish cohort
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2018 (English)In: Upsala Journal of Medical Sciences, ISSN 0300-9734, E-ISSN 2000-1967, Vol. 123, no 1, p. 50-56Article in journal (Refereed) Published
Abstract [en]

Background: The clinical experience with protease-inhibitor (PI) triple regimen appears disappointing regarding effect, side effects, high work load, and costs. This real-world study evaluates baseline and emerging resistance-associated substitutions (RASs) and their significance for treatment outcome.

Method: Thirty-six genotype 1a/b patients treated according to Swedish recommendations during 2011-2013 with triple therapy including pegylated interferon and ribavirin in combination with a protease-inhibitor, either boceprevir (BOC) or telaprevir (TVR), were retrospectively evaluated. Frozen serum samples from the patients were tested for resistance with pan-genotypic population sequencing.

Results: Overall, 56% (20/36) of the patients achieved sustained viral response (SVR). The SVR was comparable between BOC (64%; 9/14) and TVR (50%; 11/22) (p = 0.07), and the IL28B type non-CC (48%; 12/25) and CC (46%; 6/13) (p = 0.77). The SVR was higher in patients without cirrhosis (89.5%; 17/19) (p < 0.0005), in treatment-naive patients (70%; 14/20) (p = 0.02), and those with low viral load (<800,000 IU/mL) (66.7%; 8/12) (p < 0.0002), compared to those with cirrhosis (17.6%; 3/17), treatment-experienced (37.5%; 6/16), and high viral load (>800,000 IU/mL) (50%; 12/24).

Conclusion: PI triple regimes were highly effective in treatment-naive patients without cirrhosis, but in this real-world cohort an inferior effect was evident in cirrhotic and treatment-experienced patients. Although tested on a limited sample, the baseline resistance testing seems to have no impact on prediction of therapy outcome. The reason could be that the baseline RASs T54S and V55A have relatively low resistance towards BOC and TVR. Emerging RASs, mainly R155K, with known high resistance to BOC and TVR were frequently found in non-responders.

Place, publisher, year, edition, pages
TAYLOR & FRANCIS LTD, 2018
Keywords
Boceprevir, hepatitis C, protease inhibitor, RAS, resistance association substitution, telaprevir
National Category
Gastroenterology and Hepatology
Identifiers
urn:nbn:se:uu:diva-354543 (URN)10.1080/03009734.2018.1441928 (DOI)000428060300006 ()29536805 (PubMedID)
Funder
Erik, Karin och Gösta Selanders Foundation
Available from: 2018-07-20 Created: 2018-07-20 Last updated: 2018-07-20Bibliographically approved
Palanisamy, N. & Lennerstrand, J. (2017). Computational prediction of Usutu virus E protein B cell and T cell epitopes for potential vaccine development.. Scandinavian Journal of Immunology, 85(5), 350-364
Open this publication in new window or tab >>Computational prediction of Usutu virus E protein B cell and T cell epitopes for potential vaccine development.
2017 (English)In: Scandinavian Journal of Immunology, ISSN 0300-9475, E-ISSN 1365-3083, Vol. 85, no 5, p. 350-364Article in journal (Refereed) Published
Abstract [en]

Usutu virus (family Flaviviridae), once confined to Africa, has emerged in Europe a decade ago. The virus has been spreading throughout Europe at a greater pace mostly affecting avian species. While most bird species remain asymptomatic carriers of this virus, few bird species are highly susceptible. Lately, Usutu virus (USUV) infections in humans were reported sporadically with severe neuroinvasive symptoms like meningoencephalitis. Since so much is unknown about this virus, which potentially may cause severe diseases in humans, there is a need for more studies of this virus. In the present study, we have used computational tools to predict potential B-cell and T-cell epitopes of USUV envelope (E) protein. We found that amino acids between positions 68 and 84 could be a potential B-cell epitope while amino acids between positions 53 and 69 could be a potential MHC class-I and class-II restricted T-cell epitope. By homology 3D modeling of USUV E protein, we found that the predicted B-cell epitope was predominantly located in the coil region while T-cell epitope was located in the beta strand region of the E protein. Additionally, the potential MHC class-I T-cell epitope (LAEVRSYCYL) was predicted to bind to nearly 24 HLAs (IC50 ≤5000 nM) covering nearly 86.44% of the Black population and 96.90% of the Caucasoid population. Further, in vivo studies are needed to validate the predicted epitopes.

Keywords
E protein, Usutu virus, computational predictions, epitopes, vaccine
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-318094 (URN)10.1111/sji.12544 (DOI)000400011500005 ()28273384 (PubMedID)
Available from: 2017-03-23 Created: 2017-03-23 Last updated: 2017-06-01Bibliographically approved
Bartlett, S. R., Grebely, J., Eltahla, A. A., Reeves, J. D., Howe, A., Miller, V., . . . Applegate, T. L. (2017). Systematic review & expert guidance on methods for sequencing of hepatitis C virus for detection of direct-acting antiviral resistance. Paper presented at International Liver Congress / 52nd Annual Meeting of the European-Association-for-the-Study-of-the-Liver, APR 19-23, 2017, Amsterdam, NETHERLANDS. Journal of Hepatology, 66(1), S323-S323
Open this publication in new window or tab >>Systematic review & expert guidance on methods for sequencing of hepatitis C virus for detection of direct-acting antiviral resistance
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2017 (English)In: Journal of Hepatology, ISSN 0168-8278, E-ISSN 1600-0641, Vol. 66, no 1, p. S323-S323Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
ELSEVIER SCIENCE BV, 2017
National Category
Gastroenterology and Hepatology
Identifiers
urn:nbn:se:uu:diva-333658 (URN)10.1016/S0168-8278(17)30970-4 (DOI)000401056600707 ()
Conference
International Liver Congress / 52nd Annual Meeting of the European-Association-for-the-Study-of-the-Liver, APR 19-23, 2017, Amsterdam, NETHERLANDS
Available from: 2017-12-07 Created: 2017-12-07 Last updated: 2017-12-07Bibliographically approved
Bergfors, A., Leenheer, D., Bergqvist, A., Ameur, A. & Lennerstrand, J. (2016). Analysis of hepatitis C NS5A resistance associated polymorphisms using ultra deep single molecule real time (SMRT) sequencing. Antiviral Research, 126, 81-89
Open this publication in new window or tab >>Analysis of hepatitis C NS5A resistance associated polymorphisms using ultra deep single molecule real time (SMRT) sequencing
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2016 (English)In: Antiviral Research, ISSN 0166-3542, E-ISSN 1872-9096, Vol. 126, p. 81-89Article in journal (Refereed) Published
Abstract [en]

Development of Hepatitis C virus (HCV) resistance against direct-acting antivirals (DAAs), including NS5A inhibitors, is an obstacle to successful treatment of HCV when DAAs are used in sub-optimal combinations. Furthermore, it has been shown that baseline (pre-existing) resistance against DAAs is present in treatment naive-patients and this will potentially complicate future treatment strategies in different HCV genotypes (GTs). Thus the aim was to detect low levels of NS5A resistant associated variants (RAVs) in a limited sample set of treatment-naive patients of HCV GT1a and 3a, since such polymorphisms can display in vitro resistance as high as 60000 fold. Ultra-deep single molecule real time (SMRT) sequencing with the Pacific Biosciences (PacBio) RSII instrument was used to detect these RAVs. The SMRT sequencing was conducted on ten samples; three of them positive with Sanger sequencing (GT1a Q30H and Y93N, and GT3a Y93H), five GT1a samples, and two GT3a non-positive samples. The same methods were applied to the HCV GT1a H77-plasmid in a dilution series, in order to determine the error rates of replication, which in turn was used to determine the limit of detection (LOD), as defined by mean + 3SD, of minority variants down to 0.24%. We found important baseline NS5A RAVs at levels between 0.24 and 0.5%, which could potentially have clinical relevance. This new method with low level detection of baseline RAVs could be useful in predicting the most cost-efficient combination of DAA treatment, and reduce the treatment duration for an HCV infected individual.

Keywords
Hepatitis C virus, NS5A, Resistance, RAV, Deep sequencing, Pacific biosciences
National Category
Infectious Medicine
Identifiers
urn:nbn:se:uu:diva-279573 (URN)10.1016/j.antiviral.2015.12.005 (DOI)000369680000010 ()26707078 (PubMedID)
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Available from: 2016-03-02 Created: 2016-03-02 Last updated: 2017-11-30Bibliographically approved
Kileng, H., Kjellin, M., Bergfors, A., Duberg, A.-S., Wesslen, L., Danielsson, A., . . . Lennerstrand, J. (2016). Effect of pre-existing Hepatitis C NS3 Q80K variant in Genotype la and NS5A Y93H variant in Genotype 3 for interferon-free treatment combinations with direct antiviral agents (DAAs): Real-life experience from a multicenter study in Sweden and Norway. Paper presented at 67th Annual Meeting of the American-Association-for-the-Study-of-Liver-Diseases (AASLD), NOV 11-15, 2016, Boston, MA. Hepathology, 63(1 SUPP), 1001A-1001A
Open this publication in new window or tab >>Effect of pre-existing Hepatitis C NS3 Q80K variant in Genotype la and NS5A Y93H variant in Genotype 3 for interferon-free treatment combinations with direct antiviral agents (DAAs): Real-life experience from a multicenter study in Sweden and Norway
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2016 (English)In: Hepathology, ISSN 0270-9139, Vol. 63, no 1 SUPP, p. 1001A-1001AArticle in journal, Meeting abstract (Refereed) Published
National Category
Gastroenterology and Hepatology
Identifiers
urn:nbn:se:uu:diva-313678 (URN)000385493804374 ()
Conference
67th Annual Meeting of the American-Association-for-the-Study-of-Liver-Diseases (AASLD), NOV 11-15, 2016, Boston, MA
Available from: 2017-01-24 Created: 2017-01-23 Last updated: 2017-02-13Bibliographically approved
Miller, V., Harrington, P., Howe, A., Kieffer, T., Lennerstrand, J., Lenz, O., . . . Pilot-Matias, T. (2016). Hepatitis C Genotype 4R Resistance-Associated Polymorphisms: The Achilles Heel of the Nonstructural 5A Inhibitors? Reply [Letter to the editor]. Hepatology, 64(2), 698-699
Open this publication in new window or tab >>Hepatitis C Genotype 4R Resistance-Associated Polymorphisms: The Achilles Heel of the Nonstructural 5A Inhibitors? Reply
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2016 (English)In: Hepatology, ISSN 0270-9139, E-ISSN 1527-3350, Vol. 64, no 2, p. 698-699Article in journal, Letter (Refereed) Published
National Category
Gastroenterology and Hepatology
Identifiers
urn:nbn:se:uu:diva-301129 (URN)10.1002/hep.28615 (DOI)000380034500055 ()27113118 (PubMedID)
Available from: 2016-08-23 Created: 2016-08-18 Last updated: 2017-11-28Bibliographically approved
Lontok, E., Harrington, P., Howe, A., Kieffer, T., Lennerstrand, J., Lenz, O., . . . Miller, V. (2015). Hepatitis C virus drug resistance-associated substitutions: State of the art summary. Hepatology, 62(5), 1623-1632
Open this publication in new window or tab >>Hepatitis C virus drug resistance-associated substitutions: State of the art summary
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2015 (English)In: Hepatology, ISSN 0270-9139, E-ISSN 1527-3350, Vol. 62, no 5, p. 1623-1632Article, review/survey (Refereed) Published
Abstract [en]

Hepatitis C virus (HCV) drug development has resulted in treatment regimens composed of interferon-free, all-oral combinations of direct-acting antivirals. While the new regimens are potent and highly efficacious, the full clinical impact of HCV drug resistance, its implications for retreatment, and the potential role of baseline resistance testing remain critical research and clinical questions. In this report, we discuss the viral proteins targeted by HCV direct-acting antivirals and summarize clinically relevant resistance data for compounds that have been approved or are currently in phase 3 clinical trials. Conclusion: This report provides a comprehensive, systematic review of all resistance information available from sponsors' trials as a tool to inform the HCV drug development field.

National Category
Gastroenterology and Hepatology
Identifiers
urn:nbn:se:uu:diva-269130 (URN)10.1002/hep.27934 (DOI)000363264100031 ()26095927 (PubMedID)
Available from: 2015-12-14 Created: 2015-12-14 Last updated: 2017-12-01Bibliographically approved
Leenheer, D., Lindström, I., Ameur, A., Kjellin, M., Wesslen, L., Lannergard, A. & Lennerstrand, J. (2014). Analysis by population-and deep-sequencing of polymorphisms with excessive resistance to NS5A inhibitors in treatment-naive subjects with HCV genotype 1a and 3a. Paper presented at International Workshop on Antiviral Drug Resistance - Meeting the Global Challenge, JUN 03-07, 2014, Berlin, GERMANY. Antiviral Therapy, 19, A109-A109
Open this publication in new window or tab >>Analysis by population-and deep-sequencing of polymorphisms with excessive resistance to NS5A inhibitors in treatment-naive subjects with HCV genotype 1a and 3a
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2014 (English)In: Antiviral Therapy, ISSN 1359-6535, E-ISSN 2040-2058, Vol. 19, p. A109-A109Article in journal (Refereed) Published
National Category
Infectious Medicine
Identifiers
urn:nbn:se:uu:diva-257374 (URN)000354380300095 ()
Conference
International Workshop on Antiviral Drug Resistance - Meeting the Global Challenge, JUN 03-07, 2014, Berlin, GERMANY
Available from: 2015-07-02 Created: 2015-07-01 Last updated: 2017-12-04Bibliographically approved
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