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Abstract
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Accurate determination
of the binding affinity of the ligand to
the receptor remains a difficult problem in computer-aided drug design.
Here, we study and compare the efficiency of Jarzynski’s equality
(JE) combined with steered molecular dynamics and the linear interaction
energy (LIE) method by assessing the binding affinity of 23 small
compounds to six receptors, including β-lactamase, thrombin,
factor Xa, HIV-1 protease (HIV), myeloid cell leukemia-1, and cyclin-dependent
kinase 2 proteins. It was shown that Jarzynski’s nonequilibrium
binding free energy ΔGneqJar correlates with the available
experimental data with the correlation levels R =
0.89, 0.86, 0.83, 0.80, 0.83, and 0.81 for six data sets, while for
the binding free energy ΔGLIE obtained
by the LIE method, we have R = 0.73, 0.80, 0.42,
0.23, 0.85, and 0.01. Therefore, JE is recommended to be used for
ranking binding affinities as it provides accurate and robust results.
In contrast, LIE is not as reliable as JE, and it should be used with
caution, especially when it comes to new systems.
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Affiliation(s)
- Kiet Ho
- Institute for Computational Sciences and Technology, Quang Trung Software City, SBI Building, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Duc Toan Truong
- Institute for Computational Sciences and Technology, Quang Trung Software City, SBI Building, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam.,Department of Theoretical Physics, Faculty of Physics and Engineering Physics, Ho Chi Minh University of Science, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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2
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Himmel DM, Arnold E. Non-Nucleoside Reverse Transcriptase Inhibitors Join Forces with Integrase Inhibitors to Combat HIV. Pharmaceuticals (Basel) 2020; 13:ph13060122. [PMID: 32545407 PMCID: PMC7345359 DOI: 10.3390/ph13060122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/17/2022] Open
Abstract
In the treatment of acquired immune deficiency syndrome (AIDS), the diarylpyrimidine (DAPY) analogs etravirine (ETR) and rilpivirine (RPV) have been widely effective against human immunodeficiency virus (HIV) variants that are resistant to other non-nucleoside reverse transcriptase inhibitors (NNRTIs). With non-inferior or improved efficacy, better safety profiles, and lower doses or pill burdens than other NNRTIs in the clinic, combination therapies including either of these two drugs have led to higher adherence than other NNRTI-containing treatments. In a separate development, HIV integrase strand transfer inhibitors (INSTIs) have shown efficacy in treating AIDS, including raltegravir (RAL), elvitegravir (EVG), cabotegravir (CAB), bictegravir (BIC), and dolutegravir (DTG). Of these, DTG and BIC perform better against a wide range of resistance mutations than other INSTIs. Nevertheless, drug-resistant combinations of mutations have begun to emerge against all DAPYs and INSTIs, attributable in part to non-adherence. New dual therapies that may promote better adherence combine ETR or RPV with an INSTI and have been safer and non-inferior to more traditional triple-drug treatments. Long-acting dual- and triple-therapies combining ETR or RPV with INSTIs are under study and may further improve adherence. Here, highly resistant emergent mutations and efficacy data on these novel treatments are reviewed. Overall, ETR or RPV, in combination with INSTIs, may be treatments of choice as long-term maintenance therapies that optimize efficacy, adherence, and safety.
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Affiliation(s)
- Daniel M. Himmel
- Himmel Sci Med Com, L.L.C., Bala Cynwyd, PA 19004, USA
- Correspondence: ; Tel.: +1-848-391-5973
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA;
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Lawal MM, Sanusi ZK, Govender T, Maguire GE, Honarparvar B, Kruger HG. From Recognition to Reaction Mechanism: An Overview on the Interactions between HIV-1 Protease and its Natural Targets. Curr Med Chem 2020; 27:2514-2549. [DOI: 10.2174/0929867325666181113122900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 11/04/2018] [Accepted: 11/07/2018] [Indexed: 12/28/2022]
Abstract
Current investigations on the Human Immunodeficiency Virus Protease (HIV-1
PR) as a druggable target towards the treatment of AIDS require an update to facilitate further
development of promising inhibitors with improved inhibitory activities. For the past two
decades, up to 100 scholarly reports appeared annually on the inhibition and catalytic mechanism
of HIV-1 PR. A fundamental literature review on the prerequisite of HIV-1 PR action
leading to the release of the infectious virion is absent. Herein, recent advances (both computationally
and experimentally) on the recognition mode and reaction mechanism of HIV-1 PR
involving its natural targets are provided. This review features more than 80 articles from
reputable journals. Recognition of the natural Gag and Gag-Pol cleavage junctions by this
enzyme and its mutant analogs was first addressed. Thereafter, a comprehensive dissect of
the enzymatic mechanism of HIV-1 PR on its natural polypeptide sequences from literature
was put together. In addition, we highlighted ongoing research topics in which in silico
methods could be harnessed to provide deeper insights into the catalytic mechanism of the
HIV-1 protease in the presence of its natural substrates at the molecular level. Understanding
the recognition and catalytic mechanism of HIV-1 PR leading to the release of an infective
virion, which advertently affects the immune system, will assist in designing mechanismbased
inhibitors with improved bioactivity.
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Affiliation(s)
- Monsurat M. Lawal
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Zainab K. Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Glenn E.M. Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
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4
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Gonelli CA, Khoury G, Center RJ, Purcell DFJ. HIV-1-based Virus-like Particles that Morphologically Resemble Mature, Infectious HIV-1 Virions. Viruses 2019; 11:v11060507. [PMID: 31159488 PMCID: PMC6630479 DOI: 10.3390/v11060507] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/23/2019] [Accepted: 05/29/2019] [Indexed: 01/04/2023] Open
Abstract
A prophylactic vaccine eliciting both broad neutralizing antibodies (bNAbs) to the HIV-1 envelope glycoprotein (Env) and strong T cell responses would be optimal for preventing HIV-1 transmissions. Replication incompetent HIV-1 virus-like particles (VLPs) offer the opportunity to present authentic-structured, virion-associated Env to elicit bNAbs, and also stimulate T cell responses. Here, we optimize our DNA vaccine plasmids as VLP expression vectors for efficient Env incorporation and budding. The original vector that was used in human trials inefficiently produced VLPs, but maximized safety by inactivating RNA genome packaging, enzyme functions that are required for integration into the host genome, and deleting accessory proteins Vif, Vpr, and Nef. These original DNA vaccine vectors generated VLPs with incomplete protease-mediated cleavage of Gag and were irregularly sized. Mutations to restore function within the defective genes revealed that several of the reverse transcriptase (RT) deletions mediated this immature phenotype. Here, we made efficient budding, protease-processed, and mature-form VLPs that resembled infectious virions by introducing alternative mutations that completely removed the RT domain, but preserved most other safety mutations. These VLPs, either expressed from DNA vectors in vivo or purified after expression in vitro, are potentially useful immunogens that can be used to elicit antibody responses that target Env on fully infectious HIV-1 virions.
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Affiliation(s)
- Christopher A Gonelli
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.
| | - Georges Khoury
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.
| | - Rob J Center
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.
- Viral Entry and Vaccines Laboratory, Disease Elimination, Burnet Institute, Melbourne, Victoria 3004, Australia.
| | - Damian F J Purcell
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia.
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5
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Lawal MM, Sanusi ZK, Govender T, Tolufashe GF, Maguire GEM, Honarparvar B, Kruger HG. Unraveling the concerted catalytic mechanism of the human immunodeficiency virus type 1 (HIV-1) protease: a hybrid QM/MM study. Struct Chem 2018. [DOI: 10.1007/s11224-018-1251-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Zondagh J, Williams A, Achilonu I, Dirr HW, Sayed Y. Overexpression, Purification and Functional Characterisation of Wild-Type HIV-1 Subtype C Protease and Two Variants Using a Thioredoxin and His-Tag Protein Fusion System. Protein J 2018; 37:369-379. [PMID: 29869126 DOI: 10.1007/s10930-018-9779-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In recent years, various strategies have been used to overexpress and purify HIV-1 protease because it is an essential drug target in anti-retroviral therapy. Obtaining sufficient quantities of the enzyme, however, remains challenging. Overexpression of large quantities is prevented due to the enzyme's autolytic nature and its inherent cytotoxicity in Escherichia coli cells. Here, we describe a novel HIV-1 protease purification method using a thioredoxin-hexahistidine fusion system for the wild-type and two variant proteases. The fusion proteases were overexpressed in E. coli and recovered by immobilised metal ion affinity chromatography. The proteases were cleaved from the fusion constructs using thrombin. When compared to the standard overexpression and purification protocol in use in our laboratory, the expression of the fusion-derived wild-type protease was increased from 0.83 to 2.5 mg/l of culture medium. The expression levels of the two variant proteases ranged from 1.5 to 2 mg/l of culture medium. The fusion wild-type and variant proteases were inactive before the cleavage of the thioredoxin-hexahistidine fusion tag as no enzymatic activity was observed. The proteases were, however, active after cleavage of the tag. The novel thioredoxin-hexahistidine fusion system, therefore, enables the successful overexpression and purification of catalytically active HIV-1 proteases.
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Affiliation(s)
- Jake Zondagh
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, 2050, South Africa
| | - Alison Williams
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, 2050, South Africa
| | - Ikechukwu Achilonu
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, 2050, South Africa
| | - Heini W Dirr
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, 2050, South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of Witwatersrand, Johannesburg, 2050, South Africa.
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7
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Vo JN, Campbell PR, Mahfuz NN, Ramli R, Pagendam D, Barnard R, Geering ADW. Characterization of the banana streak virus capsid protein and mapping of the immunodominant continuous B-cell epitopes to the surface-exposed N terminus. J Gen Virol 2016; 97:3446-3457. [DOI: 10.1099/jgv.0.000643] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Jenny N. Vo
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, GPO Box 267, Brisbane, Queensland 4001, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
- Plant Biosecurity Cooperative Research Centre, LPO Box 5012, Bruce, Australian Capital Territory 2617, Australia
| | - Paul R. Campbell
- Plant Biosecurity Cooperative Research Centre, LPO Box 5012, Bruce, Australian Capital Territory 2617, Australia
- Queensland Department of Agriculture, Fisheries and Forestry, GPO Box 267, Brisbane, Queensland 4001, Australia
| | - Nur N. Mahfuz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Ras Ramli
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Daniel Pagendam
- CSIRO Mathematics, Informatics and Statistics, Ecosciences Precinct, 41 Boggo Road, Dutton Park, Queensland 4102, Australia
| | - Ross Barnard
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Andrew D. W. Geering
- Plant Biosecurity Cooperative Research Centre, LPO Box 5012, Bruce, Australian Capital Territory 2617, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, GPO Box 267, Brisbane, Queensland 4001, Australia
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Billich A, Billich S, Rosenwirth B. Assay Systems for HIV-1 Proteinase and Their Use for Evaluation of Inhibitors. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029100200201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- A. Billich
- Sandoz Forschungsinstitut GmbH, Department of AntiRetroviral Therapy, Brunnerstr. 59, A-1235 Vienna, Austria
| | - S. Billich
- Sandoz Forschungsinstitut GmbH, Department of AntiRetroviral Therapy, Brunnerstr. 59, A-1235 Vienna, Austria
| | - B. Rosenwirth
- Sandoz Forschungsinstitut GmbH, Department of AntiRetroviral Therapy, Brunnerstr. 59, A-1235 Vienna, Austria
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The Race against Protease Activation Defines the Role of ESCRTs in HIV Budding. PLoS Pathog 2016; 12:e1005657. [PMID: 27280284 PMCID: PMC4900648 DOI: 10.1371/journal.ppat.1005657] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 05/03/2016] [Indexed: 11/26/2022] Open
Abstract
HIV virions assemble on the plasma membrane and bud out of infected cells using interactions with endosomal sorting complexes required for transport (ESCRTs). HIV protease activation is essential for maturation and infectivity of progeny virions, however, the precise timing of protease activation and its relationship to budding has not been well defined. We show that compromised interactions with ESCRTs result in delayed budding of virions from host cells. Specifically, we show that Gag mutants with compromised interactions with ALIX and Tsg101, two early ESCRT factors, have an average budding delay of ~75 minutes and ~10 hours, respectively. Virions with inactive proteases incorporated the full Gag-Pol and had ~60 minutes delay in budding. We demonstrate that during budding delay, activated proteases release critical HIV enzymes back to host cytosol leading to production of non-infectious progeny virions. To explain the molecular mechanism of the observed budding delay, we modulated the Pol size artificially and show that virion release delays are size-dependent and also show size-dependency in requirements for Tsg101 and ALIX. We highlight the sensitivity of HIV to budding “on-time” and suggest that budding delay is a potent mechanism for inhibition of infectious retroviral release. ESCRTs are implicated in cellular processes which require fission of budding membranes. Likely the most studied of these processes is the HIV-ESCRT interactions. The canonical view is that interference with ESCRT recruitment results in a late budding arrest of virions at the plasma membrane and this mechanistic view of ESCRTs has shaped our understanding of their function in almost all cell biology. In this manuscript, we present a full kinetic analysis of HIV virion release under all known mutations in Gag that affect HIV-ESCRT interactions. Our data show that contrary to the canonical view, a defect in ESCRT recruitment does not inhibit virion budding, however it creates a delay. We further show that during budding delay, activated proteases release critical HIV enzymes back to host cytosol, leading to budding of non-infectious progeny virions. We suggest that budding delay is a potent mechanism for inhibition of infectious retroviral release and can be the basis for developing antiviral treatments which slow the budding process and therefore disproportionally affect infectious retroviral release. We also suggest that such budding delay may be one of the mechanisms underlying cellular innate immune responses which inhibit the spread of retroviral infection.
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10
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Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools. Catalysts 2016; 6. [PMID: 27885336 PMCID: PMC5119520 DOI: 10.3390/catal6060082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations.
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Purification and characterization of naturally occurring HIV-1 (South African subtype C) protease mutants from inclusion bodies. Protein Expr Purif 2016; 122:90-6. [PMID: 26917227 DOI: 10.1016/j.pep.2016.02.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/02/2016] [Accepted: 02/20/2016] [Indexed: 11/20/2022]
Abstract
Human immunodeficiency virus (HIV) infections in sub-Saharan Africa represent about 56% of global infections. Many studies have targeted HIV-1 protease for the development of drugs against AIDS. Recombinant HIV-1 protease is used to screen new drugs from synthetic compounds or natural substances. Along with the wild type (C-SA) we also over-expressed and characterized two mutant forms from patients that had shown resistance to protease inhibitors. Using recombinant DNA technology, we constructed three recombinant plasmids in pGEX-6P-1 and expressed them containing a sequence encoding wild type HIV protease and two mutants (I36T↑T contains 100 amino acids and L38L↑N↑L contains 101 amino acids). These recombinant proteins were isolated from inclusion bodies by using QFF anion exchange and GST trap columns. In SDS-PAGE, we obtained these HIV proteases as single bands of approximately 11.5, 11.6 and 11.7 kDa for the wild type, I36T↑Tand L38L↑N↑L mutants, respectively. The enzyme was recovered efficiently (0.25 mg protein/L of Escherichia coli culture) and had high specific activity of 2.02, 2.20 and 1.33 μmol min(-1) mg(-1) at an optimal pH of 5 and temperature of 37 °C for the wild type, I36T↑T and L38L↑N↑L, respectively. The method employed here provides an easy and rapid purification of the HIV-1(C-SA) protease from the inclusion bodies, with high yield and high specific activities.
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12
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Four Amino Acid Changes in HIV-2 Protease Confer Class-Wide Sensitivity to Protease Inhibitors. J Virol 2015; 90:1062-9. [PMID: 26559830 DOI: 10.1128/jvi.01772-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 11/02/2015] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED Protease is essential for retroviral replication, and protease inhibitors (PI) are important for treating HIV infection. HIV-2 exhibits intrinsic resistance to most FDA-approved HIV-1 PI, retaining clinically useful susceptibility only to lopinavir, darunavir, and saquinavir. The mechanisms for this resistance are unclear; although HIV-1 and HIV-2 proteases share just 38 to 49% sequence identity, all critical structural features of proteases are conserved. Structural studies have implicated four amino acids in the ligand-binding pocket (positions 32, 47, 76, and 82). We constructed HIV-2ROD9 molecular clones encoding the corresponding wild-type HIV-1 amino acids (I32V, V47I, M76L, and I82V) either individually or together (clone PRΔ4) and compared the phenotypic sensitivities (50% effective concentration [EC50]) of mutant and wild-type viruses to nine FDA-approved PI. Single amino acid replacements I32V, V47I, and M76L increased the susceptibility of HIV-2 to multiple PI, but no single change conferred class-wide sensitivity. In contrast, clone PRΔ4 showed PI susceptibility equivalent to or greater than that of HIV-1 for all PI. We also compared crystallographic structures of wild-type HIV-1 and HIV-2 proteases complexed with amprenavir and darunavir to models of the PRΔ4 enzyme. These models suggest that the amprenavir sensitivity of PRΔ4 is attributable to stabilizing enzyme-inhibitor interactions in the P2 and P2' pockets of the protease dimer. Together, our results show that the combination of four amino acid changes in HIV-2 protease confer a pattern of PI susceptibility comparable to that of HIV-1, providing a structural rationale for intrinsic HIV-2 PI resistance and resolving long-standing questions regarding the determinants of differential PI susceptibility in HIV-1 and HIV-2. IMPORTANCE Proteases are essential for retroviral replication, and HIV-1 and HIV-2 proteases share a great deal of structural similarity. However, only three of nine FDA-approved HIV-1 protease inhibitors (PI) are active against HIV-2. The underlying reasons for intrinsic PI resistance in HIV-2 are not known. We examined the contributions of four amino acids in the ligand-binding pocket of the enzyme that differ between HIV-1 and HIV-2 by constructing HIV-2 clones encoding the corresponding HIV-1 amino acids and testing the PI susceptibilities of the resulting viruses. We found that the HIV-2 clone containing all four changes (PRΔ4) was as susceptible as HIV-1 to all nine PI. We also modeled the PRΔ4 enzyme structure and compared it to existing crystallographic structures of HIV-1 and HIV-2 proteases complexed with amprenavir and darunavir. Our findings demonstrate that four positions in the ligand-binding cleft of protease are the primary cause of HIV-2 PI resistance.
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Wei Y, Li J, Chen Z, Wang F, Huang W, Hong Z, Lin J. Multistage virtual screening and identification of novel HIV-1 protease inhibitors by integrating SVM, shape, pharmacophore and docking methods. Eur J Med Chem 2015; 101:409-18. [PMID: 26185005 DOI: 10.1016/j.ejmech.2015.06.054] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 06/28/2015] [Accepted: 06/29/2015] [Indexed: 11/30/2022]
Abstract
The HIV-1 protease has proven to be a crucial component of the HIV replication machinery and a reliable target for anti-HIV drug discovery. In this study, we applied an optimized hierarchical multistage virtual screening method targeting HIV-1 protease. The method sequentially applied SVM (Support Vector Machine), shape similarity, pharmacophore modeling and molecular docking. Using a validation set (270 positives, 155,996 negatives), the multistage virtual screening method showed a high hit rate and high enrichment factor of 80.47% and 465.75, respectively. Furthermore, this approach was applied to screen the National Cancer Institute database (NCI), which contains 260,000 molecules. From the final hit list, 6 molecules were selected for further testing in an in vitro HIV-1 protease inhibitory assay, and 2 molecules (NSC111887 and NSC121217) showed inhibitory potency against HIV-1 protease, with IC50 values of 62 μM and 162 μM, respectively. With further chemical development, these 2 molecules could potentially serve as HIV-1 protease inhibitors.
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Affiliation(s)
- Yu Wei
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China; College of Pharmacy, Nankai University, Tianjin 300071, PR China
| | - Jinlong Li
- College of Pharmacy, Nankai University, Tianjin 300071, PR China
| | - Zeming Chen
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China; College of Life Sciences, Nankai University, Tianjin 300071, PR China
| | - Fengwei Wang
- Department of Oncology, Tianjin Union Medical Center, Tianjin 300180, PR China
| | | | - Zhangyong Hong
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China; College of Life Sciences, Nankai University, Tianjin 300071, PR China.
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China; College of Pharmacy, Nankai University, Tianjin 300071, PR China.
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Schimer J, Pávová M, Anders M, Pachl P, Šácha P, Cígler P, Weber J, Majer P, Řezáčová P, Kräusslich HG, Müller B, Konvalinka J. Triggering HIV polyprotein processing by light using rapid photodegradation of a tight-binding protease inhibitor. Nat Commun 2015; 6:6461. [PMID: 25751579 PMCID: PMC4366505 DOI: 10.1038/ncomms7461] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/29/2015] [Indexed: 12/23/2022] Open
Abstract
HIV protease (PR) is required for proteolytic maturation in the late phase of HIV replication and represents a prime therapeutic target. The regulation and kinetics of viral polyprotein processing and maturation are currently not understood in detail. Here we design, synthesize, validate and apply a potent, photodegradable HIV PR inhibitor to achieve synchronized induction of proteolysis. The compound exhibits subnanomolar inhibition in vitro. Its photolabile moiety is released on light irradiation, reducing the inhibitory potential by 4 orders of magnitude. We determine the structure of the PR-inhibitor complex, analyze its photolytic products, and show that the enzymatic activity of inhibited PR can be fully restored on inhibitor photolysis. We also demonstrate that proteolysis of immature HIV particles produced in the presence of the inhibitor can be rapidly triggered by light enabling thus to analyze the timing, regulation and spatial requirements of viral processing in real time. The study of HIV proteolysis during maturation and replication can be difficult since different steps in these processes occur simultaneously. Here, the authors present a photolabile HIV protease inhibitor which can be deactivated by light irradiation, allowing synchronized induction of viral maturation.
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Affiliation(s)
- Jiří Schimer
- 1] Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic [2] Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Marcela Pávová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic
| | - Maria Anders
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic
| | - Pavel Šácha
- 1] Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic [2] Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Petr Cígler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic
| | - Hans-Georg Kräusslich
- 1] Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany [2] Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Barbara Müller
- 1] Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany [2] Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Jan Konvalinka
- 1] Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic [2] Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague 2, Czech Republic
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15
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McKinstry WJ, Hijnen M, Tanwar HS, Sparrow LG, Nagarajan S, Pham ST, Mak J. Expression and purification of soluble recombinant full length HIV-1 Pr55(Gag) protein in Escherichia coli. Protein Expr Purif 2014; 100:10-8. [PMID: 24810910 DOI: 10.1016/j.pep.2014.04.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/23/2014] [Accepted: 04/25/2014] [Indexed: 11/17/2022]
Abstract
The HIV-1 Gag precursor protein, Pr55(Gag), is a multi-domain polyprotein that drives HIV-1 assembly. The morphological features of HIV-1 suggested Pr55(Gag) assumes a variety of different conformations during virion assembly and maturation, yet structural determination of HIV-1 Pr55(Gag) has not been possible due to an inability to express and to isolate large amounts of full-length recombinant Pr55(Gag) for biophysical and biochemical analyses. This challenge is further complicated by HIV-1 Gag's natural propensity to multimerize for the formation of viral particle (with ∼2500 Gag molecules per virion), and this has led Pr55(Gag) to aggregate and be expressed as inclusion bodies in a number of in vitro protein expression systems. This study reported the production of a recombinant form of HIV-1 Pr55(Gag) using a bacterial heterologous expression system. Recombinant HIV-1 Pr55(Gag) was expressed with a C-terminal His×6 tag, and purified using a combination of immobilized metal affinity chromatography and size exclusion chromatography. This procedure resulted in the production of milligram quantities of high purity HIV-1 Pr55(Gag) that has a mobility that resembles a trimer in solution using size exclusion chromatography analysis. The high quantity and purity of the full length HIV Gag will be suitable for structural and functional studies to further understand the process of viral assembly, maturation and the development of inhibitors to interfere with the process.
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Affiliation(s)
| | - Marcel Hijnen
- Centre for Virology, Burnet Institute, Melbourne, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Hanumant S Tanwar
- CSIRO Materials Science and Engineering, Parkville, Victoria, Australia; School of Medicine, Deakin University, Geelong, Australia
| | - Lindsay G Sparrow
- CSIRO Materials Science and Engineering, Parkville, Victoria, Australia
| | - Sureshbabu Nagarajan
- School of Medicine, Deakin University, Geelong, Australia; CSIRO, Australian Animal Health Laboratory, Geelong, Australia
| | - Son T Pham
- School of Medicine, Deakin University, Geelong, Australia; CSIRO, Australian Animal Health Laboratory, Geelong, Australia
| | - Johnson Mak
- Centre for Virology, Burnet Institute, Melbourne, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia; School of Medicine, Deakin University, Geelong, Australia; CSIRO, Australian Animal Health Laboratory, Geelong, Australia.
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16
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Nunthanavanit P, Ungwitayatorn J. Molecular docking studies of chromone derivatives against wild type and mutant strains of HIV-1 protease. Med Chem Res 2014. [DOI: 10.1007/s00044-014-0992-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Understanding HIV-1 protease autoprocessing for novel therapeutic development. Future Med Chem 2014; 5:1215-29. [PMID: 23859204 DOI: 10.4155/fmc.13.89] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In the infected cell, HIV-1 protease (PR) is initially synthesized as part of the GagPol polyprotein. PR autoprocessing is a virus-specific process by which the PR domain embedded in the precursor catalyzes proteolytic reactions responsible for liberation of free mature PRs, which then recognize and cleave at least ten different peptide sequences in the Gag and GagPol polyproteins. Despite extensive structure and function studies of the mature PRs as well as the successful development of ten US FDA-approved catalytic-site inhibitors, the precursor autoprocessing mechanism remains an intriguing yet-to-be-solved puzzle. This article discusses current understanding of the autoprocessing mechanism, in an effort to prompt the development of novel anti-HIV drugs that selectively target precursor autoprocessing.
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18
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Liu F, Mayer JP. Protein Chemical Synthesis in Drug Discovery. PROTEIN LIGATION AND TOTAL SYNTHESIS I 2014; 362:183-228. [DOI: 10.1007/128_2014_598] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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19
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Abstract
Integrase (IN) is required for lentivirus replication and is a proven drug target for the prevention of AIDS in HIV-1-infected patients. While clinical strand transfer inhibitors disarm the IN active site, allosteric inhibition of enzyme activity through the disruption of IN-IN protein interfaces holds great therapeutic potential. A promising class of allosteric IN inhibitors (ALLINIs), 2-(quinolin-3-yl) acetic acid derivatives, engage the IN catalytic core domain dimerisation interface at the binding site for the host integration co-factor LEDGF/p75. ALLINIs promote IN multimerisation and, independent of LEDGF/p75 protein, block the formation of the active IN-DNA complex, as well as inhibit the IN-LEDGF/p75 interaction in vitro. Yet, rather unexpectedly, the full inhibitory effect of these compounds is exerted during the late phase of HIV-1 replication. ALLINIs impair particle core maturation as well as reverse transcription and integration during the subsequent round of virus infection. Recapitulating the pleiotropic phenotypes observed with numerous IN mutant viruses, ALLINIs provide insight into underlying aspects of IN biology that extend beyond its catalytic activity. Therefore, in addition to the potential to expand our repertoire of HIV-1 antiretrovirals, ALLINIs afford important structural probes to dissect the multifaceted nature of the IN protein throughout the course of HIV-1 replication.
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20
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Könnyű B, Sadiq SK, Turányi T, Hírmondó R, Müller B, Kräusslich HG, Coveney PV, Müller V. Gag-Pol processing during HIV-1 virion maturation: a systems biology approach. PLoS Comput Biol 2013; 9:e1003103. [PMID: 23754941 PMCID: PMC3675044 DOI: 10.1371/journal.pcbi.1003103] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 05/01/2013] [Indexed: 12/19/2022] Open
Abstract
Proteolytic processing of Gag and Gag-Pol polyproteins by the viral protease (PR) is crucial for the production of infectious HIV-1, and inhibitors of the viral PR are an integral part of current antiretroviral therapy. The process has several layers of complexity (multiple cleavage sites and substrates; multiple enzyme forms; PR auto-processing), which calls for a systems level approach to identify key vulnerabilities and optimal treatment strategies. Here we present the first full reaction kinetics model of proteolytic processing by HIV-1 PR, taking into account all canonical cleavage sites within Gag and Gag-Pol, intermediate products and enzyme forms, enzyme dimerization, the initial auto-cleavage of full-length Gag-Pol as well as self-cleavage of PR. The model allows us to identify the rate limiting step of virion maturation and the parameters with the strongest effect on maturation kinetics. Using the modelling framework, we predict interactions and compensatory potential between individual cleavage rates and drugs, characterize the time course of the process, explain the steep dose response curves associated with PR inhibitors and gain new insights into drug action. While the results of the model are subject to limitations arising from the simplifying assumptions used and from the uncertainties in the parameter estimates, the developed framework provides an extendable open-access platform to incorporate new data and hypotheses in the future.
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Affiliation(s)
- Balázs Könnyű
- Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - S. Kashif Sadiq
- Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona, Spain
| | - Tamás Turányi
- Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Rita Hírmondó
- Institute of Biology, Eötvös Loránd University, Budapest, Hungary
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Peter V. Coveney
- Centre for Computational Science, Christopher Ingold Laboratories, University College London, London, United Kingdom
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, Budapest, Hungary
- Research Group of Theoretical Biology and Evolutionary Ecology, Eötvös Loránd University and the Hungarian Academy of Sciences, Budapest, Hungary
- * E-mail:
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21
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Syrén PO. The solution of nitrogen inversion in amidases. FEBS J 2013; 280:3069-83. [DOI: 10.1111/febs.12241] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 03/06/2013] [Accepted: 03/08/2013] [Indexed: 01/06/2023]
Affiliation(s)
- Per-Olof Syrén
- Institute of Technical Biochemistry; University of Stuttgart; Germany
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22
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Michaud V, Bar-Magen T, Turgeon J, Flockhart D, Desta Z, Wainberg MA. The Dual Role of Pharmacogenetics in HIV Treatment: Mutations and Polymorphisms Regulating Antiretroviral Drug Resistance and Disposition. Pharmacol Rev 2012; 64:803-33. [DOI: 10.1124/pr.111.005553] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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23
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Sindhikara DJ, Yoshida N, Hirata F. Placevent: an algorithm for prediction of explicit solvent atom distribution-application to HIV-1 protease and F-ATP synthase. J Comput Chem 2012; 33:1536-43. [PMID: 22522665 DOI: 10.1002/jcc.22984] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 02/10/2012] [Accepted: 03/10/2012] [Indexed: 01/16/2023]
Abstract
We have created a simple algorithm for automatically predicting the explicit solvent atom distribution of biomolecules. The explicit distribution is coerced from the three-dimensional (3D) continuous distribution resulting from a 3D reference interaction site model (3D-RISM) calculation. This procedure predicts optimal location of solvent molecules and ions given a rigid biomolecular structure and the solvent composition. We show examples of predicting water molecules near the KNI-272 bound form of HIV-1 protease and predicting both sodium ions and water molecules near the rotor ring of F-adenosine triphosphate (ATP) synthase. Our results give excellent agreement with experimental structure with an average prediction error of 0.39-0.65 Å. Further, unlike experimental methods, this method does not suffer from the partial occupancy limit. Our method can be performed directly on 3D-RISM output within minutes. It is extremely useful for examining multiple specific solvent-solute interactions, as a convenient method for generating initial solvent structures for molecular dynamics calculations, and may assist in refinement of experimental structures. © 2012 Wiley Periodicals, Inc.
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Affiliation(s)
- Daniel J Sindhikara
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Japan
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24
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Singh N, Frushicheva MP, Warshel A. Validating the vitality strategy for fighting drug resistance. Proteins 2012; 80:1110-22. [PMID: 22275047 DOI: 10.1002/prot.24012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 11/28/2011] [Accepted: 12/06/2011] [Indexed: 11/08/2022]
Abstract
The current challenge in designing effective drugs against HIV-1 is to find novel candidates with high potency, but with a lower susceptibility to mutations associated with drug resistance. Trying to address this challenge, we developed in our previous study (Ishikita and Warshel, Angew Chem Int Ed Engl 2008; 47:697-700) a novel computational strategy for fighting drug resistance by predicting the likely moves of the virus through constraints on binding and catalysis. This has been based on calculating the ratio between the vitality values ((K(i) k(cat)/K(M))(mutant)/(K(i) k(cat)/K(M))(wild-type)) and using it as a guide for predicting the moves of the virus. The corresponding calculations of the binding affinity, K(i), were carried out using the semi-macroscopic version of the protein dipole Langevin dipole (PDLD/S) in its linear response approximation (LRA) in its β version (PDLD/S-LRA/β). We also calculate the proteolytic efficiency, k(cat)/K(M), by evaluating the transition state (TS) binding free energies using the PDLD/S-LRA/β method. Here we provide an extensive validation of our strategy by calculating the vitality of six existing clinical and experimental drug candidates. It is found that the computationally determined vitalities correlate reasonably well with those derived from the corresponding experimental data. This indicates that the calculated vitality may be used to identify mutations that would be most effective for the survival of the virus. Thus, it should be possible to use our approach in screening for mutations that would provide the most effective resistance to any proposed antiviral drug. This ability should be very useful in guiding the design of drug molecules that will lead to the slowest resistance.
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Affiliation(s)
- Nidhi Singh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, USA
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25
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Efficient identification of human immunodeficiency virus type 1 mutants resistant to a protease inhibitor by using a random mutant library. Antimicrob Agents Chemother 2011; 55:5090-8. [PMID: 21876045 DOI: 10.1128/aac.00687-11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Emergence of drug-resistant mutant viruses during the course of antiretroviral therapy is a major hurdle that limits the success of chemotherapeutic treatment to suppress human immunodeficiency virus type 1 (HIV-1) replication and AIDS progression. Development of new drugs and careful patient management based on resistance genotyping data are important for enhancing therapeutic efficacy. However, identifying changes leading to drug resistance can take years of clinical studies, and conventional in vitro assays are limited in generating reliable drug resistance data. Here we present an efficient in vitro screening assay for selecting drug-resistant variants from a library of randomly mutated HIV-1 strains generated by transposon-directed base-exchange mutagenesis. As a test of principle, we screened a library of mutant HIV-1 strains containing random mutations in the protease gene by using a reporter T-cell line in the presence of the protease inhibitor (PI) nelfinavir (NFV). Analysis of replicating viruses from a single round of infection identified 50 amino acid substitutions at 35 HIV-1 protease residue positions. The selected mutant viruses showed specific resistance to NFV and included most of the known NFV resistance mutations. Therefore, the new assay is efficient for identifying changes leading to drug resistance. The data also provide insights into the molecular mechanisms underlying the development of drug resistance.
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26
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Synthesis, in vitro evaluation, and docking studies of novel chromone derivatives as HIV-1 protease inhibitor. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2011.06.035] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Szecsi PB. The aspartic proteases. Scandinavian Journal of Clinical and Laboratory Investigation 2011. [DOI: 10.1080/00365519209104650] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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28
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Abstract
OBJECTIVES The role of proteases in the regulation of apoptosis is becoming increasingly apparent. Whilst many of these proteases are already characterised, some have yet to be identified. Traditionally caspases held the traditional role as the prime mediators of apoptosis; however, attention is now turning towards the contribution made by serine proteases. KEY FINDINGS As unregulated apoptosis is implicated in various disease states, the emergence of this proteolytic family as apoptotic regulators offers novel and alterative opportunities for therapeutic targets. SUMMARY This review presents a brief introduction and overview of proteases in general with particular attention given to those involved in apoptotic processing.
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Affiliation(s)
- Kelly L Moffitt
- Biomolecular Sciences Group, School of Pharmacy, Queen's University of Belfast, Belfast BT97BL, Northern Ireland, UK.
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29
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Pednekar D, Durani S. Protein homomers in point-group assembly: symmetry making and breaking are specific and distinctive in their codes of chemical alphabet in side chains. Proteins 2011; 78:3048-55. [PMID: 20737441 DOI: 10.1002/prot.22828] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Oligomerizing to point-group symmetry, protein oligomers need to have the symmetry broken for biologically crucial functions, such as, allosteric regulation, enzyme catalysis, and so forth. In the making of symmetry, based on self assembly, and the breaking of symmetry, based on intermolecular interactions, proteins may manifest, like their other functions, specific scripts over the coding alphabet in side chains. To address the possibility, we analyzed 82 protein homodimers in their C(2)-symmetry-related side chains across noncrystallographic interfaces, to know if they may be identical or distinct in conformation, and thus conserved or broken in symmetry. We find the propensity to conformational mismatch across interfaces correlated with side-chain chemical structure, low to very low in aromatic Trp, Tyr, His, Phe, and Arg, and high to very high in aliphatic Val, Pro, Met, Glu, Ser, Lys, Gln, Asn, and Asp, related not to polarity but, interestingly, to aromaticity of the structure. The organizational plan having aromatics embedded in a hub of aliphatic-nonpolar groups and a surrounding rim of aliphatic-polar groups, called "hotspot," has been known to direct protein-protein interaction. Finding conformational-mismatch propensities of side chains congruous with their specific chemical roles in protein-protein interaction, we propose that aromatic side chains will drive protein homomers to high symmetry, while polar- and nonpolar aliphatic side chains will drive them to the functionally-necessitated breaks of symmetry. Side chains are in their roles as protein-coding alphabet illuminated in the physics, which is discussed.
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Affiliation(s)
- Deepa Pednekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Mumbai 400076, India
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30
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Chen SL, Zhao DX, Yang ZZ. An estimation method of binding free energy in terms of ABEEMσπ/MM and continuum electrostatics fused into LIE method. J Comput Chem 2010; 32:338-48. [PMID: 20662079 DOI: 10.1002/jcc.21625] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Shu-Ling Chen
- School of Chemistry and chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
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31
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Das A, Mahale S, Prashar V, Bihani S, Ferrer JL, Hosur MV. X-ray Snapshot of HIV-1 Protease in Action: Observation of Tetrahedral Intermediate and Short Ionic Hydrogen Bond SIHB with Catalytic Aspartate. J Am Chem Soc 2010; 132:6366-73. [DOI: 10.1021/ja100002b] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Amit Das
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India, National Institute for Research in Reproductive Health, Parel, Mumbai-400074, India, and LCCP/GSY, Institute de Biologie Structurale, J.-P. Ebel CEA-CNRS-UJF, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - Smita Mahale
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India, National Institute for Research in Reproductive Health, Parel, Mumbai-400074, India, and LCCP/GSY, Institute de Biologie Structurale, J.-P. Ebel CEA-CNRS-UJF, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - Vishal Prashar
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India, National Institute for Research in Reproductive Health, Parel, Mumbai-400074, India, and LCCP/GSY, Institute de Biologie Structurale, J.-P. Ebel CEA-CNRS-UJF, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - Subhash Bihani
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India, National Institute for Research in Reproductive Health, Parel, Mumbai-400074, India, and LCCP/GSY, Institute de Biologie Structurale, J.-P. Ebel CEA-CNRS-UJF, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - J.-L. Ferrer
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India, National Institute for Research in Reproductive Health, Parel, Mumbai-400074, India, and LCCP/GSY, Institute de Biologie Structurale, J.-P. Ebel CEA-CNRS-UJF, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
| | - M. V. Hosur
- Protein Crystallography Section, Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai-400085, India, National Institute for Research in Reproductive Health, Parel, Mumbai-400074, India, and LCCP/GSY, Institute de Biologie Structurale, J.-P. Ebel CEA-CNRS-UJF, 41, rue Jules Horowitz, F-38027 Grenoble Cedex 1, France
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32
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Garrec J, Cascella M, Rothlisberger U, Fleurat-Lessard P. Low Inhibiting Power of N···CO Based Peptidomimetic Compounds against HIV-1 Protease: Insights from a QM/MM Study. J Chem Theory Comput 2010. [DOI: 10.1021/ct9004728] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Julian Garrec
- Université de Lyon, École Normale Supérieure de Lyon, Laboratoire de Chimie − UMR 5182, 46 allée d’Italie, 69364 Lyon Cedex 07, France, Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland, and Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Michele Cascella
- Université de Lyon, École Normale Supérieure de Lyon, Laboratoire de Chimie − UMR 5182, 46 allée d’Italie, 69364 Lyon Cedex 07, France, Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland, and Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Université de Lyon, École Normale Supérieure de Lyon, Laboratoire de Chimie − UMR 5182, 46 allée d’Italie, 69364 Lyon Cedex 07, France, Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland, and Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Paul Fleurat-Lessard
- Université de Lyon, École Normale Supérieure de Lyon, Laboratoire de Chimie − UMR 5182, 46 allée d’Italie, 69364 Lyon Cedex 07, France, Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland, and Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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33
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Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: implications for drug resistance. Structure 2010; 17:1636-1648. [PMID: 20004167 DOI: 10.1016/j.str.2009.10.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 10/01/2009] [Accepted: 10/04/2009] [Indexed: 11/23/2022]
Abstract
Drug-resistant mutations (DRMs) in HIV-1 protease are a major challenge to antiretroviral therapy. Protease-substrate interactions that are determined to be critical for native selectivity could serve as robust targets for drug design that are immune to DRMs. In order to identify the structural mechanisms of selectivity, we developed a peptide-docking algorithm to predict the atomic structure of protease-substrate complexes and applied it to a large and diverse set of cleavable and noncleavable peptides. Cleavable peptides showed significantly lower energies of interaction than noncleavable peptides with six protease active-site residues playing the most significant role in discrimination. Surprisingly, all six residues correspond to sequence positions associated with drug resistance mutations, demonstrating that the very residues that are responsible for native substrate specificity in HIV-1 protease are altered during its evolution to drug resistance, suggesting that drug resistance and substrate selectivity may share common mechanisms.
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34
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Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography. Proc Natl Acad Sci U S A 2009; 106:4641-6. [PMID: 19273847 DOI: 10.1073/pnas.0809400106] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
HIV-1 protease is a dimeric aspartic protease that plays an essential role in viral replication. To further understand the catalytic mechanism and inhibitor recognition of HIV-1 protease, we need to determine the locations of key hydrogen atoms in the catalytic aspartates Asp-25 and Asp-125. The structure of HIV-1 protease in complex with transition-state analog KNI-272 was determined by combined neutron crystallography at 1.9-A resolution and X-ray crystallography at 1.4-A resolution. The resulting structural data show that the catalytic residue Asp-25 is protonated and that Asp-125 (the catalytic residue from the corresponding diad-related molecule) is deprotonated. The proton on Asp-25 makes a hydrogen bond with the carbonyl group of the allophenylnorstatine (Apns) group in KNI-272. The deprotonated Asp-125 bonds to the hydroxyl proton of Apns. The results provide direct experimental evidence for proposed aspects of the catalytic mechanism of HIV-1 protease and can therefore contribute substantially to the development of specific inhibitors for therapeutic application.
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35
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Wittayanarakul K, Hannongbua S, Feig M. Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors. J Comput Chem 2008; 29:673-85. [PMID: 17849388 DOI: 10.1002/jcc.20821] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Binding free energies were calculated for the inhibitors lopinavir, ritonavir, saquinavir, indinavir, amprenavir, and nelfinavir bound to HIV-1 protease. An MMPB/SA-type analysis was applied to conformational samples from 3 ns explicit solvent molecular dynamics simulations of the enzyme-inhibitor complexes. Binding affinities and the sampled conformations of the inhibitor and enzyme were compared between different HIV-1 protease protonation states to find the most likely protonation state of the enzyme in the complex with each of the inhibitors. The resulting set of protonation states leads to good agreement between calculated and experimental binding affinities. Results from the MMPB/SA analysis are compared with an explicit/implicit hybrid scheme and with MMGB/SA methods. It is found that the inclusion of explicit water molecules may offer a slight advantage in reproducing absolute binding free energies while the use of the Generalized Born approximation significantly affects the accuracy of the calculated binding affinities.
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Johnson ECB, Malito E, Shen Y, Rich D, Tang WJ, Kent SBH. Modular total chemical synthesis of a human immunodeficiency virus type 1 protease. J Am Chem Soc 2007; 129:11480-90. [PMID: 17705484 DOI: 10.1021/ja072870n] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
As part of our ongoing studies of the human immunodeficiency virus type 1 (HIV-1) protease enzyme, we set out to develop a modular chemical synthesis of the protein from multiple peptide segments. Our initial attempts were frustrated by the insolubility of intermediate peptide products. To overcome this problem, we designed a synthetic strategy combining the solubility-enhancing properties of C-terminal (Arg)n tags and the biological phenomenon of autoprocessing of the Gag-Pol polyprotein that occurs during maturation of the HIV-1 virus in vivo. Synthesis of a 119-residue peptide chain containing 10 residues of the reverse transcriptase (RT) open reading frame plus an (Arg)(10) tag at the C-terminus was straightforward by native chemical ligation followed by conversion of the Cys residues to Ala by Raney nickel desulfurization. The product polypeptide itself completed the final synthetic step by removing the C-terminal modification under folding conditions, to give the mature 99-residue polypeptide. High-purity homodimeric HIV-1 protease protein was obtained in excellent yield and had full enzymatic activity; the structure of the synthetic enzyme was confirmed by X-ray crystallography to a resolution of 1.07 A. This efficient modular synthesis by a biomimetic autoprocessing strategy will enable the facile synthesis of unique chemical analogues of the HIV-1 protease to further elucidate the molecular basis of enzyme catalysis.
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Affiliation(s)
- Erik C B Johnson
- Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Ben-May Department for Cancer Research, The University of Chicago, Chicago, Illinois 60637, USA
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Nicholson MG, Barber SA, Clements JE. The SIVmac239 Pr55Gag isoform, SIV p43, suppresses proteolytic cleavage of Pr55Gag. Virology 2007; 360:84-91. [PMID: 17092530 PMCID: PMC1855267 DOI: 10.1016/j.virol.2006.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 08/03/2006] [Accepted: 10/03/2006] [Indexed: 10/23/2022]
Abstract
In human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) the gag gene encodes the precursor polyprotein Pr55Gag, which is cleaved by the viral protease to produce the major structural proteins. Recently, it has been shown that HIV and SIV gag RNAs contain internal ribosome entry sites (IRESs) that mediate translation of Pr55Gag [Pr57Gag in HIV type 2 (HIV-2)] isoforms. Previously, we demonstrated that SIVmac239 p43(-), a mutant that does not express the Pr55Gag isoform, SIV p43, replicates more efficiently than wild-type (WT) SIVmac239 in cell culture. In this study, we characterize SIVmac239 p43(-) virion production and demonstrate that, in the absence of SIV p43, cleavage of Pr55Gag is increased in budded virions, resulting in a higher percentage of mature particles. Additionally, intracellular cleavage of Pr55Gag is increased in SIVmac239 p43(-), suggesting that SIV p43 suppresses premature cleavage of Pr55Gag by the viral protease.
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Affiliation(s)
- Michael G. Nicholson
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Sheila A. Barber
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Janice E. Clements
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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Matsui T, Kinoshita-Ida Y, Hayashi-Kisumi F, Hata M, Matsubara K, Chiba M, Katahira-Tayama S, Morita K, Miyachi Y, Tsukita S. Mouse Homologue of Skin-specific Retroviral-like Aspartic Protease Involved in Wrinkle Formation. J Biol Chem 2006; 281:27512-25. [PMID: 16837463 DOI: 10.1074/jbc.m603559200] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Retroviral proteases are encoded in the retroviral genome and are responsible for maturation and assembly of infectious virus particles. A number of retroviral protease sequences with retroviral elements are integrated in every eukaryotic genome as endogenous retroviruses. Recently, retroviral-like aspartic proteases that were not embedded within endogenous retroviral elements were identified throughout the eukaryotic and prokaryotic genomes. However, the physiological role of this novel protease family, especially in mammals, is not known. During the high throughput in situ hybridization screening of mouse epidermis, as a granular layer-expressing clone, we identified a mouse homologue of SASPase (Skin ASpartic Protease), a recently identified retroviral-like aspartic protease. We detected and purified the endogenous 32-kDa (mSASP32) and 15-kDa (mSASP15) forms of mSASP from mouse stratum corneum extracts and determined their amino acid sequences. Next, we bacterially produced recombinant mSASP15 via autoprocessing of GST-mSASP32. Purified recombinant mSASP15 cleaved a quenched fluorogenic peptide substrate, designed from the autoprocessing site for mSASP32 maximally at pH 5.77, which is close to the pH of the epidermal surface. Finally, we generated mSASP-deficient mice that at 5 weeks of age showed fine wrinkles that ran parallel on the lateral trunk without apparent epidermal differentiation defects. These results indicate that the retroviral-like aspartic protease, SASPase, is involved in prevention of fine wrinkle formation via activation in a weakly acidic stratum corneum environment. This study provides the first evidence that retroviral-like aspartic protease is functionally important in mammalian tissue organization.
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Affiliation(s)
- Takeshi Matsui
- KAN Research Institute Inc., Shimogyo-ku, Kyoto 600-8815, Japan.
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40
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Tozzini V, McCammon JA. A coarse grained model for the dynamics of flap opening in HIV-1 protease. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.07.075] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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41
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Wittayanarakul K, Aruksakunwong O, Saen-oon S, Chantratita W, Parasuk V, Sompornpisut P, Hannongbua S. Insights into saquinavir resistance in the G48V HIV-1 protease: quantum calculations and molecular dynamic simulations. Biophys J 2004; 88:867-79. [PMID: 15542562 PMCID: PMC1305161 DOI: 10.1529/biophysj.104.046110] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The spread of acquired immune deficiency syndrome has increasingly become a great concern owing largely to the failure of chemotherapies. The G48V is considered the key signature residue mutation of HIV-1 protease developing with saquinavir therapy. Molecular dynamics simulations of the wild-type and the G48V HIV-1 protease complexed with saquinavir were carried out to explore structure and interactions of the drug resistance. The molecular dynamics results combined with the quantum-based and molecular mechanics Poisson-Boltzmann surface area calculations indicated a monoprotonation took place on D25, one of the triad active site residues. The inhibitor binding of the triad residues and its interaction energy in the mutant were similar to those in the wild-type. The overall structure of both complexes is almost identical. However, the steric conflict of the substituted valine results in the conformational change of the P2 subsite and the disruption of hydrogen bonding between the -NH of the P2 subsite and the backbone -CO of the mutated residue. The magnitude of interaction energy changes was comparable to the experimental K(i) data. The designing for a new drug should consider a reduction of steric repulsion on P2 to enhance the activity toward this mutant strain.
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42
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Ellenrieder AD, Kremer W, Kattenbeck B, Hantschel O, Horn G, Kalbitzer HR, Modrow S. The central domain of the matrix protein of HIV-1: influence on protein structure and virus infectivity. Biol Chem 2004; 385:303-13. [PMID: 15134345 DOI: 10.1515/bc.2004.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The central region of the matrix protein p17 of HIV-1 is known to be essential during virus assembly. We substituted alanines for amino acid triplets in this region of p17 (amino acid residues 47 to 55: NPG LLE TSE). Introduction of the respective mutations into the gag-coding sequence of HI-proviruses and subsequent transfection into Cos-7 cells led to particle production and release. Exchange of LLE resulted in the production of non-infectious particles. These residues may be important for correct folding and assembly of the processed matrix protein and the production of infectious HIV. In vitro studies of wild-type and mutated matrix proteins using spectroscopic methods (NMR, fluorescence, CD) yielded detailed data about structure and stability. Two-dimensional NMR spectroscopy showed that wild-type and mutant proteins (p17-NPG and p17-TSE) are well folded. Besides structural changes at the mutated site, chemical shift changes indicate small but significant long range structural rearrangements. The stability against chemically and thermally induced unfolding of the mutants p17-NPG and p17-TSE was slightly decreased, while that of p17-LLE was drastically diminished. The alterations have only a local effect on protein folding for the mutants p17-NPG and p17-TSE, and the globular tertiary structure remains nearly unchanged. For p17-LLE, however, the substitutions seem to trigger significant changes in structural elements.
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Affiliation(s)
- Anja-Daniela Ellenrieder
- Institute for Medical Microbiology and Hygiene, University of Regensburg, Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany
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Andersson HO, Fridborg K, Löwgren S, Alterman M, Mühlman A, Björsne M, Garg N, Kvarnström I, Schaal W, Classon B, Karlén A, Danielsson UH, Ahlsén G, Nillroth U, Vrang L, Oberg B, Samuelsson B, Hallberg A, Unge T. Optimization of P1-P3 groups in symmetric and asymmetric HIV-1 protease inhibitors. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:1746-58. [PMID: 12694187 DOI: 10.1046/j.1432-1033.2003.03533.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
HIV-1 protease is an important target for treatment of AIDS, and efficient drugs have been developed. However, the resistance and negative side effects of the current drugs has necessitated the development of new compounds with different binding patterns. In this study, nine C-terminally duplicated HIV-1 protease inhibitors were cocrystallised with the enzyme, the crystal structures analysed at 1.8-2.3 A resolution, and the inhibitory activity of the compounds characterized in order to evaluate the effects of the individual modifications. These compounds comprise two central hydroxy groups that mimic the geminal hydroxy groups of a cleavage-reaction intermediate. One of the hydroxy groups is located between the delta-oxygen atoms of the two catalytic aspartic acid residues, and the other in the gauche position relative to the first. The asymmetric binding of the two central inhibitory hydroxyls induced a small deviation from exact C2 symmetry in the whole enzyme-inhibitor complex. The study shows that the protease molecule could accommodate its structure to different sizes of the P2/P2' groups. The structural alterations were, however, relatively conservative and limited. The binding capacity of the S3/S3' sites was exploited by elongation of the compounds with groups in the P3/P3' positions or by extension of the P1/P1' groups. Furthermore, water molecules were shown to be important binding links between the protease and the inhibitors. This study produced a number of inhibitors with Ki values in the 100 picomolar range.
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Affiliation(s)
- Hans O Andersson
- Institute of Cell and Molecular Biology, Uppsala University, Sweden
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Voisset C, Myers RE, Carne A, Kellam P, Griffiths DJ. Rabbit endogenous retrovirus-H encodes a functional protease. J Gen Virol 2003; 84:215-225. [PMID: 12533718 DOI: 10.1099/vir.0.18670-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent studies have revealed that 'human retrovirus-5' sequences found in human samples belong to a rabbit endogenous retrovirus family named RERV-H. A part of the gag-pro region of the RERV-H genome was amplified by PCR from DNA in human samples and several forms of RERV-H protease were expressed in bacteria. The RERV-H protease was able to cleave itself from a precursor protein and was also able to cleave the RERV-H Gag polyprotein precursor in vitro whereas a form of the protease with a mutation engineered into the active site was inactive. Potential N- and C-terminal autocleavage sites were characterized. The RERV-H protease was sensitive to pepstatin A, showing it to be an aspartic protease. Moreover, it was strongly inhibited by PYVPheStaAMT, a pseudopeptide inhibitor specific for Mason-Pfizer monkey virus and avian myeloblastosis-associated virus. A structural model of the RERV-H protease was constructed that, together with the activity data, confirms that this is a retroviral aspartic protease.
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Affiliation(s)
- Cécile Voisset
- Wohl Virion Centre, Windeyer Institute of Medical Sciences, University College London, 46 Cleveland Street, London W1T 4JF, UK
| | - Richard E Myers
- Wohl Virion Centre, Windeyer Institute of Medical Sciences, University College London, 46 Cleveland Street, London W1T 4JF, UK
| | - Alex Carne
- Institute of Cancer Research, Chester Beatty Laboratories, London, UK
| | - Paul Kellam
- Wohl Virion Centre, Windeyer Institute of Medical Sciences, University College London, 46 Cleveland Street, London W1T 4JF, UK
| | - David J Griffiths
- Wohl Virion Centre, Windeyer Institute of Medical Sciences, University College London, 46 Cleveland Street, London W1T 4JF, UK
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Piana S, Carloni P, Parrinello M. Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease. J Mol Biol 2002; 319:567-83. [PMID: 12051929 DOI: 10.1016/s0022-2836(02)00301-7] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The emergence of compensatory drug-resistant mutations in HIV-1 protease challenges the common view of the reaction mechanism of this enzyme. Here, we address this issue by performing classical and ab initio molecular dynamics simulations (MD) on a complex between the enzyme and a peptide substrate. The classical MD calculation reveals large-scale protein motions involving the flaps and the cantilever. These motions modulate the conformational properties of the substrate at the cleavage site. The ab initio calculations show in turn that substrate motion modulates the activation free energy barrier of the enzymatic reaction dramatically. Thus, the catalytic power of the enzyme does not arise from the presence of a pre-organized active site but from the protein mechanical fluctuations. The implications of this finding for the emergence of drug-resistance are discussed.
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Affiliation(s)
- Stefano Piana
- Scuola Internazionale Superiore di Studi Avanzati and Istituto Nazionale di Fisica per la Materia, Via Beirut 2-4, 34014 Trieste, Italy
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The pKa Shift of the Catalytic Aspartyl Dyad in the HIV-1 Protease Complexed with Hydroxyethylene Inhibitors. B KOREAN CHEM SOC 2002. [DOI: 10.5012/bkcs.2002.23.1.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
OBJECTIVE To review the pharmacokinetics, pharmacodynamics, drug interactions, and dosage and administration information of amprenavir. DATA SOURCE An extensive review of the literature (MEDLINE search from 1994 to April 2001) relating to the clinical pharmacology of the HIV protease inhibitors was conducted. Meeting abstracts or full presentations and data submitted to the Food and Drug Administration were also reviewed. STUDY SELECTION AND DATA EXTRACTION The data on pharmacokinetics, pharmacodynamics, drug interactions, and drug resistance were obtained from in vitro studies and open-label and controlled clinical trials. DATA SYNTHESIS Like all HIV protease inhibitors, amprenavir interrupts the maturation phase of the HIV replicative cycle by forming an inhibitor-enzyme complex, which prevents HIV protease from binding with its normal substrates (biologically inactive viral polyproteins). Amprenavir has an enzyme inhibition constant (Ki = 0.6 nM) that falls within the Ki range of the other protease inhibitors. Amprenavir's in vitro 50% inhibitory concentration (IC50) against wild-type clinical HIV isolates is 14.6 +/- 12.5 ng/mL (mean +/- SD). Pharmacodynamic modeling indicates that, as is the case with other protease inhibitors, the concentration-response curve for amprenavir plateaus at amprenavir trough values above the IC50 for these isolates. This exposure-activity relationship, plus such favorable pharmacokinetic parameters as a long terminal elimination half-life (7-10 h), makes amprenavir an attractive drug of choice when considering potent antiretrovirals. The higher trough exposure obtained with amprenavir coadministered with ritonavir may allow effective treatment of patients with decreased susceptibility viral isolates and once-daily dosing. Amprenavir has been approved for adults and children; the recommended capsule doses are 1200 mg twice daily for adults and 20 mg/kg twice daily or 15 mg/kg 3 times daily for children < 13 years of age or adolescents < 50 kg. The recommended dose for amprenavir oral solution is 1.5 mL/kg twice daily or 1.1 mL/kg 3 times daily. CONCLUSIONS The clinical pharmacology, exposure-activity relationship, and drug resistance profile of amprenavir support the use of this potent HIV protease inhibitor in combination antiretroviral regimens, especially for persons who have experienced virologic failure while on protease inhibitor-containing regimens.
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Affiliation(s)
- Brian M Sadler
- GlaxoSmithKline, 5 Moore Dr., Research Triangle Park, NC 27709, USA
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Todd MJ, Gomez J. Enzyme kinetics determined using calorimetry: a general assay for enzyme activity? Anal Biochem 2001; 296:179-87. [PMID: 11554713 DOI: 10.1006/abio.2001.5218] [Citation(s) in RCA: 233] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two techniques for determining enzyme kinetic constants using isothermal titration microcalorimetry are presented. The methods are based on the proportionality between the rate of a reaction and the thermal power (heat/time) generated. (i) An enzyme can be titrated with increasing amounts of substrate, while pseudo-first-order conditions are maintained. (ii) Following a single injection, the change in thermal power as substrate is depleted can be continuously monitored. Both methods allow highly precise kinetic characterization in a single experiment and can be used to measure enzyme inhibition. Applicability is demonstrated using a representative enzyme from each EC classification, including (i) oxidation-reduction activity of DHFR (EC 1.5.1.3); (ii) transferase activity of creatine phosphokinase (EC 2.7.3.2) and hexokinase (EC 2.7.1.1); (iii) hydrolytic activity of Helicobacter pylori urease (EC 3.5.1.5), trypsin (EC 3.4.21.4), and the HIV-1 protease (EC 3.4.21.16); (iv) lyase activity of heparinase (EC 4.1.1.7); and (v) ligase activity of pyruvate carboxylate (EC 6.4.1.1). This nondestructive method is completely general, enabling precise analysis of reactions in spectroscopically opaque solutions, using physiological substrates. Such a universal assay may have wide applicability in functional genomics.
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Affiliation(s)
- M J Todd
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA.
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Piana S, Sebastiani D, Carloni P, Parrinello M. Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site. J Am Chem Soc 2001; 123:8730-7. [PMID: 11535077 DOI: 10.1021/ja003145e] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recent 13C NMR experiment (Smith et al. Nature Struct. Biol. 1996, 3, 946-950) on the Asp 25-Asp25' dyad in pepstatin A/HIV-1 protease measured two separate resonance lines, which were interpreted as being a singly protonated dyad. We address this issue by performing ab initio molecular dynamics calculations on models for this site accompanied by calculations of 13C NMR chemical shifts and isotopic shifts. We find that already on the picosecond time-scale the model proposed by Smith et al. is not stable and evolves toward a different monoprotonated form whose NMR pattern differs from the experimental one. We suggest, instead, a different protonation state in which both aspartic groups are protonated. Despite the symmetric protonation state, the calculated 13C NMR properties are in good agreement with the experiment. We rationalize this result using a simple valence bond model, which explains the chemical inequality of the two C sites. The model calculations, together with our calculations on the complex, allow also the rationalization of 13C NMR properties on other HIV-1 PR/inhibitor complexes. Both putative binding of the substrate to the free enzyme, which has the dyad singly protonated (Piana, S.; Carloni, P. Proteins: Struct., Funct., Genet. 2000, 39, 26-36), and pepstatin A binding to the diprotonated form are consistent with the inverse solvent isotope effect on the onset of inhibition of pepsin by pepstatin and the kinetic iso-mechanism proposed for aspartic proteases (Cho, T.-K.; Rebholz, K.; Northrop, D.B. Biochemistry 1994, 33, 9637-9642).
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Affiliation(s)
- S Piana
- Scuola Internazionale Superiore di Studi Avanzati and Istituto Nazionale di Fisica della Materia, Via Beirut 2-4, 34014 Trieste, Italy
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50
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Feuerbach F, Lucas H. The protease and reverse transcriptase of the tobacco LTR retrotransposon Tnt1 are enzymatically active when expressed in Escherichia coli. PLANT MOLECULAR BIOLOGY 2001; 46:481-9. [PMID: 11485204 DOI: 10.1023/a:1010614918763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The open reading frame (ORF) of the tobacco retrotransposon Tnt1-94 was over-expressed in Escherichia coli to assay its protease and reverse transcriptase (RT) enzymatic activities. In E. coli, Tnt1-94 polyprotein is cleaved off by the element-encoded protease to release a Gag protein with an apparent molecular mass of 37 kDa that forms high-density aggregates. The catalytic site of Tnt1-94 protease (D-T-A) as determined by deletion analysis differs from that of retroviruses and of well-characterized retrotransposons (D-T/S-G). The cleaved or uncleaved ORF of Tnt1-94 displays an exogenous RT activity. Over-expression of plant retrotransposons ORFs in E. coli provides a very useful strategy to assay the enzymatic activities of their proteins and to determine their catalytic sites.
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Affiliation(s)
- F Feuerbach
- Institut National de la Recherche Agronomique, Laboratoire de Biologie Cellulaire, Versailles, France
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