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Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
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2006 (English)In: FEBS Letters, ISSN 0014-5793, E-ISSN 1873-3468, Vol. 580, no 25, 5910-5916 p.Article in journal (Refereed) Published
Abstract [en]

The plasmepsin proteases from the malaria parasite Plasmodium falciparum are attracting attention as putative drug targets. A recently published crystal structure of Plasmodium malariae plasmepsin IV bound to an allophenylnorstatine inhibitor [Clemente, J.C. et al. (2006) Acta Crystallogr. D 62, 246252] provides the first structural insights regarding interactions of this family of inhibitors with plasmepsins. The compounds in this class are potent inhibitors of HIV-1 protease, but also show nM binding affinities towards plasmepsin IV. Here, we utilize automated docking, molecular dynamics and binding free energy calculations with the linear interaction energy LIE method to investigate the binding of allophenylnorstatine inhibitors to plasmepsin IV from two different species. The calculations yield excellent agreement with experimental binding data and provide new information regarding protonation states of active site residues as well as conformational properties of the inhibitor complexes.

Place, publisher, year, edition, pages
2006. Vol. 580, no 25, 5910-5916 p.
Keyword [en]
malaria, plasmepsin, enzyme inhibitors, linear interaction energy method
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:uu:diva-96523DOI: 10.1016/j.febslet.2006.09.057ISI: 000241707100018PubMedID: 17045991OAI: oai:DiVA.org:uu-96523DiVA: diva2:171125
Available from: 2007-11-23 Created: 2007-11-23 Last updated: 2017-12-14Bibliographically approved
In thesis
1. Binding Free Energy Calculations on Ligand-Receptor Complexes Applied to Malarial Protease Inhibitors
Open this publication in new window or tab >>Binding Free Energy Calculations on Ligand-Receptor Complexes Applied to Malarial Protease Inhibitors
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Malaria is a widespread disease caused by parasites of the genus Plasmodium. Each year 500 million clinical cases are reported resulting in over one million casualties. The most lethal species, P. falciparum, accounts for ~90% of the fatal cases and has developed resistance to chloroquine. The resistant strains are a major problem and calls for novel drugs.

In this thesis, the process of computational inhibitor design is illustrated through the development of P. falciparum aspartic protease inhibitors. These proteases, called plasmepsins, are part of the hemoglobin degradation chain. The hemoglobin is degraded during the intraerythrocytic cycle and serves as the major food source. By inhibiting plasmepsins the parasites can be killed by starvation.

Novel inhibitors with very high affinity were found by using a combination of computational and synthetic chemistry. These inhibitors were selective and did not display any activity on human cathepsin D. The linear interaction energy (LIE) method was utilized in combination with molecular dynamics (MD) simulations to estimate free energies of binding. The MD simulations were also used to characterize the enzyme–inhibitor interactions and explain the binding on a molecular level.

The influence of the partial charge model on binding free energy calculations with the LIE method was assessed. Two semiempirical and six ab initio quantum chemical charge derivation schemes were evaluated. It was found that the fast semiempirical charge models are equally useful in free energy calculations with the LIE method as the rigorous ab initio charge models.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2007. 54 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 372
Keyword
Molecular biology, Plasmodium falciparum, plasmepsins, linear interaction energy, docking, HIV1 reverse trancriptase, Molekylärbiologi
Identifiers
urn:nbn:se:uu:diva-8338 (URN)978-91-554-7043-2 (ISBN)
Public defence
2007-12-14, C2:301, BMC, Husarg. 3, Uppsala, 13:00
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Supervisors
Available from: 2007-11-23 Created: 2007-11-23Bibliographically approved

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Gutiérrez-de-Terán, HugoÅqvist, Johan

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