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Viral proteases as therapeutic targets. Mol Aspects Med 2022; 88:101159. [PMID: 36459838 PMCID: PMC9706241 DOI: 10.1016/j.mam.2022.101159] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Some medically important viruses-including retroviruses, flaviviruses, coronaviruses, and herpesviruses-code for a protease, which is indispensable for viral maturation and pathogenesis. Viral protease inhibitors have become an important class of antiviral drugs. Development of the first-in-class viral protease inhibitor saquinavir, which targets HIV protease, started a new era in the treatment of chronic viral diseases. Combining several drugs that target different steps of the viral life cycle enables use of lower doses of individual drugs (and thereby reduction of potential side effects, which frequently occur during long term therapy) and reduces drug-resistance development. Currently, several HIV and HCV protease inhibitors are routinely used in clinical practice. In addition, a drug including an inhibitor of SARS-CoV-2 main protease, nirmatrelvir (co-administered with a pharmacokinetic booster ritonavir as Paxlovid®), was recently authorized for emergency use. This review summarizes the basic features of the proteases of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and SARS-CoV-2 and discusses the properties of their inhibitors in clinical use, as well as development of compounds in the pipeline.
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Owoicho O, Tapela K, Djomkam Zune AL, Nghochuzie NN, Isawumi A, Mosi L. Suboptimal antimicrobial stewardship in the COVID-19 era: is humanity staring at a postantibiotic future? Future Microbiol 2021; 16:919-925. [PMID: 34319168 PMCID: PMC8317972 DOI: 10.2217/fmb-2021-0008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In the absence of potent antimicrobial agents, it is estimated that bacterial infections could cause millions of deaths. The emergence of COVID-19, its complex pathophysiology and the high propensity of patients to coinfections has resulted in therapeutic regimes that use a cocktail of antibiotics for disease management. Suboptimal antimicrobial stewardship in this era and the slow pace of drug discovery could result in large-scale drug resistance, narrowing future antimicrobial therapeutics. Thus, judicious use of current antimicrobials is imperative to keep up with existing and emerging infectious pathogens. Here, we provide insights into the potential implications of suboptimal antimicrobial stewardship, resulting from the emergence of COVID-19, on the spread of antimicrobial resistance.
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Affiliation(s)
- Oloche Owoicho
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.,Department of Biochemistry, Cell & Molecular Biology, College of Basic & Applied Sciences, University of Ghana, Accra, Ghana.,Department of Biological Sciences, Benue State University, Makurdi, Nigeria
| | - Kesego Tapela
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.,Department of Biochemistry, Cell & Molecular Biology, College of Basic & Applied Sciences, University of Ghana, Accra, Ghana.,West African Network of Infectious Diseases ACEs (WANIDA), French National Research Institute for Sustainable Development, France
| | - Alexandra Lindsey Djomkam Zune
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.,Department of Biochemistry, Cell & Molecular Biology, College of Basic & Applied Sciences, University of Ghana, Accra, Ghana
| | - Nora Nganyewo Nghochuzie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.,Department of Biochemistry, Cell & Molecular Biology, College of Basic & Applied Sciences, University of Ghana, Accra, Ghana.,Medical Research Council Unit, The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Abiola Isawumi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.,Department of Biochemistry, Cell & Molecular Biology, College of Basic & Applied Sciences, University of Ghana, Accra, Ghana
| | - Lydia Mosi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana.,Department of Biochemistry, Cell & Molecular Biology, College of Basic & Applied Sciences, University of Ghana, Accra, Ghana
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Bastys T, Gapsys V, Walter H, Heger E, Doncheva NT, Kaiser R, de Groot BL, Kalinina OV. Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors. Retrovirology 2020; 17:13. [PMID: 32430025 PMCID: PMC7236880 DOI: 10.1186/s12977-020-00520-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/04/2020] [Indexed: 02/07/2023] Open
Abstract
Background HIV-1 can develop resistance to antiretroviral drugs, mainly through mutations within the target regions of the drugs. In HIV-1 protease, a majority of resistance-associated mutations that develop in response to therapy with protease inhibitors are found in the protease’s active site that serves also as a binding pocket for the protease inhibitors, thus directly impacting the protease-inhibitor interactions. Some resistance-associated mutations, however, are found in more distant regions, and the exact mechanisms how these mutations affect protease-inhibitor interactions are unclear. Furthermore, some of these mutations, e.g. N88S and L76V, do not only induce resistance to the currently administered drugs, but contrarily induce sensitivity towards other drugs. In this study, mutations N88S and L76V, along with three other resistance-associated mutations, M46I, I50L, and I84V, are analysed by means of molecular dynamics simulations to investigate their role in complexes of the protease with different inhibitors and in different background sequence contexts. Results Using these simulations for alchemical calculations to estimate the effects of mutations M46I, I50L, I84V, N88S, and L76V on binding free energies shows they are in general in line with the mutations’ effect on \documentclass[12pt]{minimal}
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\begin{document}$$IC_{50}$$\end{document}IC50 values. For the primary mutation L76V, however, the presence of a background mutation M46I in our analysis influences whether the unfavourable effect of L76V on inhibitor binding is sufficient to outweigh the accompanying reduction in catalytic activity of the protease. Finally, we show that L76V and N88S changes the hydrogen bond stability of these residues with residues D30/K45 and D30/T31/T74, respectively. Conclusions We demonstrate that estimating the effect of both binding pocket and distant mutations on inhibitor binding free energy using alchemical calculations can reproduce their effect on the experimentally measured \documentclass[12pt]{minimal}
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\begin{document}$$IC_{50}$$\end{document}IC50 values. We show that distant site mutations L76V and N88S affect the hydrogen bond network in the protease’s active site, which offers an explanation for the indirect effect of these mutations on inhibitor binding. This work thus provides valuable insights on interplay between primary and background mutations and mechanisms how they affect inhibitor binding.
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Affiliation(s)
- Tomas Bastys
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany.,Saarbrücken Graduate School of Computer Science, University of Saarland, 66123, Saarbrücken, Germany
| | - Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Hauke Walter
- Medizinisches Labor Stendal, 39576, Stendal, Germany
| | - Eva Heger
- Institute of Virology, University of Cologne, 50935, Cologne, Germany
| | - Nadezhda T Doncheva
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany.,Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, 50935, Cologne, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Olga V Kalinina
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany. .,Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany. .,Faculty of Medicine, Saarland University, 66421, Homburg, Germany.
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Semi-quantification of HIV-1 protease inhibitor concentrations in clinical samples of HIV-infected patients using a gold nanoparticle-based immunochromatographic assay. Anal Chim Acta 2019; 1071:86-97. [DOI: 10.1016/j.aca.2019.04.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/16/2022]
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Wong-Sam A, Wang YF, Zhang Y, Ghosh AK, Harrison RW, Weber IT. Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap-Core Interface of HIV-1 Protease. ACS OMEGA 2018; 3:12132-12140. [PMID: 30288468 PMCID: PMC6167001 DOI: 10.1021/acsomega.8b01683] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/13/2018] [Indexed: 06/08/2023]
Abstract
Four HIV-1 protease (PR) inhibitors, clinical inhibitors lopinavir and tipranavir, and two investigational compounds 4 and 5, were studied for their effect on the structure and activity of PR with drug-resistant mutation L76V (PRL76V). Compound 5 exhibited the best K i value of 1.9 nM for PRL76V, whereas the other three inhibitors had K i values of 4.5-7.6 nM, 2-3 orders of magnitude worse than for wild-type enzymes. Crystal structures showed only minor differences in interactions of inhibitors with PRL76V compared to wild-type complexes. The shorter side chain of Val76 in the mutant lost hydrophobic interactions with Lys45 and Ile47 in the flap, and with Asp30 and Thr74 in the protein core, consistent with decreased stability. Inhibitors forming additional polar interactions with the flaps or dimer interface of PRL76V were unable to compensate for the decrease in internal hydrophobic contacts. These structures provide insights for inhibitor design.
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Affiliation(s)
- Andres Wong-Sam
- Department
of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of
Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Yuan-Fang Wang
- Department
of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of
Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Ying Zhang
- Department
of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of
Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
- RNA Therapeutics Institute and Department of Biochemistry and Molecular
Pharmacology, University of Massachusetts
Medical School, Worcester, Massachusetts 01605, United States
| | - Arun K. Ghosh
- Department of Chemistry and Department
of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Robert W. Harrison
- Department
of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of
Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Irene T. Weber
- Department
of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of
Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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Charpentier C, Lambert-Niclot S, Alteri C, Storto A, Flandre P, Svicher V, Perno CF, Brun-Vézinet F, Calvez V, Marcelin AG, Ceccherini-Silberstein F, Descamps D. Description of the L76V resistance protease mutation in HIV-1 B and "non-B" subtypes. PLoS One 2013; 8:e54381. [PMID: 23349869 PMCID: PMC3548776 DOI: 10.1371/journal.pone.0054381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 12/11/2012] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE To describe the prevalence of the L76V protease inhibitors resistance-associated mutation (PI-RAM) in relation with patients' characteristics and protease genotypic background in HIV-1 B- and "non-B"-infected patients. METHODS Frequency of the L76V mutation between 1998 and 2010 was surveyed in the laboratory database of 3 clinical centers. Major PI-RAMs were identified according to the IAS-USA list. Fisher's and Wilcoxon tests were used to compare variables. RESULTS Among the overall 29,643 sequences analyzed, the prevalence of L76V was 1.50%, while was 5.42% in PI-resistant viruses. Since 2008 the prevalence of L76V was higher in "non-B"-infected than in B-infected patients each year. Median time since diagnosis of HIV-1 infection and median time under antiretroviral-based regimen were both shorter in "non-B"- than in B-infected patients (8 vs 11 years, P<0.0001; and 7 vs 8 years, P = 0.004). In addition, "non-B"-infected patients had been pre-exposed to a lower number of PI (2 vs 3, P = 0.016). The L76V was also associated with a lower number of major PI-RAMs in "non-B" vs B samples (3 vs 4, P = 0.0001), and thus it was more frequent found as single major PI-RAM in "non-B" vs B subtype (10% vs 2%, P = 0.014). CONCLUSIONS We showed an impact of viral subtype on the selection of the L76V major PI-RAM with a higher prevalence in "non-B" subtypes observed since 2008. In addition, in "non-B"-infected patients this mutation appeared more rapidly and was associated with less PI-RAM.
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Affiliation(s)
- Charlotte Charpentier
- Laboratoire de Virologie, Assistance Publique-Hôpitaux de Paris (AP-HP), Groupe Hospitalier Bichat-Claude Bernard, HUPNVS, Université Paris Diderot, Paris 7, PRES Sorbonne Paris Cité, EA4409, Paris, France.
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