1
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Tran TT, Fanucci GE. Natural Polymorphisms D60E and I62V Stabilize a Closed Conformation in HIV-1 Protease in the Absence of an Inhibitor or Substrate. Viruses 2024; 16:236. [PMID: 38400012 PMCID: PMC10892587 DOI: 10.3390/v16020236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
HIV infection remains a global health issue plagued by drug resistance and virological failure. Natural polymorphisms (NPs) contained within several African and Brazilian protease (PR) variants have been shown to induce a conformational landscape of more closed conformations compared to the sequence of subtype B prevalent in North America and Western Europe. Here we demonstrate through experimental pulsed EPR distance measurements and molecular dynamic (MD) simulations that the two common NPs D60E and I62V found within subtypes F and H can induce a closed conformation when introduced into HIV-1PR subtype B. Specifically, D60E alters the conformation in subtype B through the formation of a salt bridge with residue K43 contained within the nexus between the flap and hinge region of the HIV-1 PR fold. On the other hand, I62V modulates the packing of the hydrophobic cluster of the cantilever and fulcrum, also resulting in a more closed conformation.
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Affiliation(s)
| | - Gail E. Fanucci
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
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2
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Wieske LHE, Atilaw Y, Poongavanam V, Erdélyi M, Kihlberg J. Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds. Chemistry 2023; 29:e202202798. [PMID: 36286339 PMCID: PMC10107787 DOI: 10.1002/chem.202202798] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 12/15/2022]
Abstract
The ability to adjust conformations in response to the polarity of the environment, i.e. molecular chameleonicity, is considered to be important for conferring both high aqueous solubility and high cell permeability to drugs in chemical space beyond Lipinski's rule of 5. We determined the conformational ensembles populated by the antiviral drugs asunaprevir, simeprevir, atazanavir and daclatasvir in polar (DMSO-d6 ) and non-polar (chloroform) environments with NMR spectroscopy. Daclatasvir was fairly rigid, whereas the first three showed large flexibility in both environments, that translated into major differences in solvent accessible 3D polar surface area within each conformational ensemble. No significant differences in size and polar surface area were observed between the DMSO-d6 and chloroform ensembles of these three drugs. We propose that such flexible compounds are characterized as "partial molecular chameleons" and hypothesize that their ability to adopt conformations with low polar surface area contributes to their membrane permeability and oral absorption.
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Affiliation(s)
- Lianne H E Wieske
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | | | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
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3
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C S V, Munusami P. Revealing the drug resistance mechanism of saquinavir due to G48V and V82F mutations in subtype CRF01_AE HIV-1 protease: molecular dynamics simulation and binding free energy calculations. J Biomol Struct Dyn 2023; 41:1000-1017. [PMID: 34919029 DOI: 10.1080/07391102.2021.2016486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Human immunodeficiency virus-1 (HIV-1) protease is one of the important targets in AIDS therapy. The majority of HIV infections are caused due to non-B subtypes in developing countries. The co-occurrence of mutations along with naturally occurring polymorphisms in HIV-1 protease cause resistance to the FDA approved drugs, thereby posing a major challenge in the treatment of antiretroviral therapy. In this work, the resistance mechanism against SQV due to active site mutations G48V and V82F in CRF01_AE (AE) protease was explored. The binding free energy calculations showed that the direct substitution of valine at position 48 introduces a bulkier side chain, directly impairing the interaction with SQV in the binding pocket. Also, the intramolecular hydrogen bonding network of the neighboring residues is altered, indirectly affecting the binding of SQV. Interestingly, the substitution of phenylalanine at position 82 induces conformational changes in the 80's loop and the flap region, thereby favoring the binding of SQV. The V82F mutant structure also maintains similar intramolecular hydrogen bond interactions as observed in AE-WT.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vasavi C S
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Punnagai Munusami
- Department of Chemistry, Arignar Anna Government Arts & Science College, Karaikal, Puducherry (U.T), India
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4
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Wang C, Chen L, Wang R, Tang W, Zhao B. Effects of the G48M mutant on the dynamics properties and binding mechanism of PR with SQV and ATV. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2055013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Chao Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, People’s Republic of China
| | - Lin Chen
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, People’s Republic of China
| | - Ruige Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, People’s Republic of China
| | - Wanxia Tang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, People’s Republic of China
| | - Bing Zhao
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, People’s Republic of China
- Heilongjiang Provincial Key Laboratory of Surface Active Agent and Auxiliary, Qiqihar, People’s Republic of China
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5
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Prediction and molecular field view of drug resistance in HIV-1 protease mutants. Sci Rep 2022; 12:2913. [PMID: 35190671 PMCID: PMC8861105 DOI: 10.1038/s41598-022-07012-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/07/2022] [Indexed: 12/04/2022] Open
Abstract
Conquering the mutational drug resistance is a great challenge in anti-HIV drug development and therapy. Quantitatively predicting the mutational drug resistance in molecular level and elucidating the three dimensional structure-resistance relationships for anti-HIV drug targets will help to improve the understanding of the drug resistance mechanism and aid the design of resistance evading inhibitors. Here the MB-QSAR (Mutation-dependent Biomacromolecular Quantitative Structure Activity Relationship) method was employed to predict the molecular drug resistance of HIV-1 protease mutants towards six drugs, and to depict the structure resistance relationships in HIV-1 protease mutants. MB-QSAR models were constructed based on a published data set of Ki values for HIV-1 protease mutants against drugs. Reliable MB-QSAR models were achieved and these models display both well internal and external prediction abilities. Interpreting the MB-QSAR models supplied structural information related to the drug resistance as well as the guidance for the design of resistance evading drugs. This work showed that MB-QSAR method can be employed to predict the resistance of HIV-1 protease caused by polymorphic mutations, which offer a fast and accurate method for the prediction of other drug target within the context of 3D structures.
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6
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Novel HIV PR inhibitors with C4-substituted bis-THF and bis-fluoro-benzyl target the two active site mutations of highly drug resistant mutant PR S17. Biochem Biophys Res Commun 2021; 566:30-35. [PMID: 34111669 DOI: 10.1016/j.bbrc.2021.05.094] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 11/22/2022]
Abstract
The emergence of multidrug resistant (MDR) HIV strains severely reduces the effectiveness of antiretroviral therapy. Clinical inhibitor darunavir (1) has picomolar binding affinity for HIV-1 protease (PR), however, drug resistant variants like PRS17 show poor inhibition by 1, despite the presence of only two mutated residues in the inhibitor-binding site. Antiviral inhibitors that target MDR proteases like PRS17 would be valuable as therapeutic agents. Inhibitors 2 and 3 derived from 1 through substitutions at P1, P2 and P2' positions exhibit 3.4- to 500-fold better inhibition than clinical inhibitors for PRS17 with the exception of amprenavir. Crystal structures of PRS17/2 and PRS17/3 reveal how these inhibitors target the two active site mutations of PRS17. The substituted methoxy P2 group of 2 forms new interactions with G48V mutation, while the modified bis-fluoro-benzyl P1 group of 3 forms a halogen interaction with V82S mutation, contributing to improved inhibition of PRS17.
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7
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Mavian C, Coman RM, Zhang X, Pomeroy S, Ostrov DA, Dunn BM, Sleasman JW, Goodenow MM. Molecular Docking-Based Screening for Novel Inhibitors of the Human Immunodeficiency Virus Type 1 Protease that Effectively Reduce the Viral Replication in Human Cells. JOURNAL OF AIDS & CLINICAL RESEARCH 2021; 12:841. [PMID: 34950525 PMCID: PMC8694022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Therapeutic pressure by protease inhibitors (PIs) contributes to accumulation of mutations in the HIV type 1 (HIV-1) protease (PR) leading to development of drug resistance with subsequent therapy failure. Current PIs target the active site of PR in a competitive manner. Identification of molecules that exploit non-active site mechanisms of inhibition is essential to overcome resistance to current PIs. Potential non-active site HIV-1 protease (PR) inhibitors (PI) were identified by in silico screening of almost 140,000 molecules targeting the hinge region of PR. Inhibitory activity of best docking compounds was tested in an in vitro PR inhibition biochemical assay. Five compounds inhibited PR from multiple HIV-1 sub-types in vitro and reduced replicative capacity by PI-sensitive or multi-PI resistant HIV-1 variants in human cells ex vivo. Antiviral activity was boosted when combined with Ritonavir, potentially diminishing development of drug resistance, while providing effective treatment for drug resistant HIV-1 variants.
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Affiliation(s)
- Carla Mavian
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Roxana M Coman
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA,Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Xinrui Zhang
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Steve Pomeroy
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - David A. Ostrov
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Ben M Dunn
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - John W. Sleasman
- Pediatric Allergy, Immunology, and Pulmonary Medicine, Duke University, Durham, NC 27710, USA
| | - Maureen M Goodenow
- Office of AIDS Research, National Institutes of Health, USA,Address for Correspondence: Maureen M Goodenow, Office of AIDS Research, National Institutes of Health, USA, Tel: + 3522132304;
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8
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Vanangamudi M, Nair PC, Engels SEM, Palaniappan S, Namasivayam V. Structural Insights to Human Immunodeficiency Virus (HIV-1) Targets and Their Inhibition. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:63-95. [PMID: 34258737 DOI: 10.1007/978-981-16-0267-2_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human immunodeficiency virus (HIV) is a deadly virus that attacks the body's immune system, subsequently leading to AIDS (acquired immunodeficiency syndrome) and ultimately death. Currently, there is no vaccine or effective cure for this infection; however, antiretrovirals that act at various phases of the virus life cycle have been useful to control the viral load in patients. One of the major problems with antiretroviral therapies involves drug resistance. The three-dimensional structure from crystallography studies are instrumental in understanding the structural basis of drug binding to various targets. This chapter provides key insights into different targets and drugs used in the treatment from a structural perspective. Specifically, an insight into the binding characteristics of drugs at the active and allosteric sites of different targets and the importance of targeting allosteric sites for design of new-generation antiretrovirals to overcome complex and resistant forms of the virus has been reviewed.
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Affiliation(s)
- Murugesan Vanangamudi
- Department of Pharmaceutical Chemistry, Amity Institute of Pharmacy, Amity University Gwalior, Gwalior, Madhya Pradesh, India
| | - Pramod C Nair
- Department of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
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9
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Tran TT, Liu Z, Fanucci GE. Conformational landscape of non-B variants of HIV-1 protease: A pulsed EPR study. Biochem Biophys Res Commun 2020; 532:219-224. [PMID: 32863004 DOI: 10.1016/j.bbrc.2020.08.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 08/12/2020] [Indexed: 02/02/2023]
Abstract
HIV infection is a global health epidemic with current FDA-approved HIV-1 Protease inhibitors (PIs) designed against subtype B protease, yet they are used in HIV treatment world-wide regardless of patient HIV classification. In this study, double electron-electron resonance (DEER) electron paramagnetic resonance (EPR) spectroscopy was utilized to gain insights in how natural polymorphisms in several African and Brazilian protease (PR) variants affect the conformational landscape both in the absence and presence of inhibitors. Findings show that Subtypes F and H HIV-1 PR adopt a primarily closed conformation in the unbound state with two secondary mutations, D60E and I62V, postulated to be responsible for the increased probability for closed conformation. In contrast, subtype D, CRF_AG, and CRF_BF HIV-1 PR adopt a primarily semi-open conformation, as observed for PI-naïve-subtype B when unbound by substrate or inhibitor. The impact that inhibitor binding has on shifting the conformational land scape of these variants is also characterized, where analysis provides classification of inhibitor induced shifts away from the semi-open state into weak, moderate and strong effects. The findings are compared to those for prior studies of inhibitor induced conformational shifts in PI-naïve Subtype B, C and CRF_AE.
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Affiliation(s)
- Trang T Tran
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, USA
| | - Zhanglong Liu
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, USA
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611, USA.
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10
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Melo R, Lemos A, Preto AJ, Bueschbell B, Matos-Filipe P, Barreto C, Almeida JG, Silva RDM, Correia JDG, Moreira IS. An Overview of Antiretroviral Agents for Treating HIV Infection in Paediatric Population. Curr Med Chem 2020; 27:760-794. [PMID: 30182840 DOI: 10.2174/0929867325666180904123549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/11/2018] [Accepted: 07/11/2018] [Indexed: 12/19/2022]
Abstract
Paediatric Acquired ImmunoDeficiency Syndrome (AIDS) is a life-threatening and infectious disease in which the Human Immunodeficiency Virus (HIV) is mainly transmitted through Mother-To- Child Transmission (MTCT) during pregnancy, labour and delivery, or breastfeeding. This review provides an overview of the distinct therapeutic alternatives to abolish the systemic viral replication in paediatric HIV-1 infection. Numerous classes of antiretroviral agents have emerged as therapeutic tools for downregulation of different steps in the HIV replication process. These classes encompass Non- Nucleoside Analogue Reverse Transcriptase Inhibitors (NNRTIs), Nucleoside/Nucleotide Analogue Reverse Transcriptase Inhibitors (NRTIs/NtRTIs), INtegrase Inhibitors (INIs), Protease Inhibitors (PIs), and Entry Inhibitors (EIs). Co-administration of certain antiretroviral drugs with Pharmacokinetic Enhancers (PEs) may boost the effectiveness of the primary therapeutic agent. The combination of multiple antiretroviral drug regimens (Highly Active AntiRetroviral Therapy - HAART) is currently the standard therapeutic approach for HIV infection. So far, the use of HAART offers the best opportunity for prolonged and maximal viral suppression, and preservation of the immune system upon HIV infection. Still, the frequent administration of high doses of multiple drugs, their inefficient ability to reach the viral reservoirs in adequate doses, the development of drug resistance, and the lack of patient compliance compromise the complete HIV elimination. The development of nanotechnology-based drug delivery systems may enable targeted delivery of antiretroviral agents to inaccessible viral reservoir sites at therapeutic concentrations. In addition, the application of Computer-Aided Drug Design (CADD) approaches has provided valuable tools for the development of anti-HIV drug candidates with favourable pharmacodynamics and pharmacokinetic properties.
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Affiliation(s)
- Rita Melo
- Centro de Ciencias e Tecnologias Nucleares, Instituto Superior Tecnico, Universidade de Lisboa, CTN, Estrada Nacional 10 (km 139,7), Bobadela LRS 2695-066, Portugal.,CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Agostinho Lemos
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal.,GIGA Cyclotron Research Centre In Vivo Imaging, University of Liège, Liège 4000, Belgium
| | - António J Preto
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Beatriz Bueschbell
- Pharmaceutical Chemistry I, PharmaCenter, Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | - Pedro Matos-Filipe
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Carlos Barreto
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - José G Almeida
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Rúben D M Silva
- Centro de Ciencias e Tecnologias Nucleares, Instituto Superior Tecnico, Universidade de Lisboa, CTN, Estrada Nacional 10 (km 139,7), Bobadela LRS 2695-066, Portugal
| | - João D G Correia
- Centro de Ciencias e Tecnologias Nucleares, Instituto Superior Tecnico, Universidade de Lisboa, CTN, Estrada Nacional 10 (km 139,7), Bobadela LRS 2695-066, Portugal
| | - Irina S Moreira
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal.,Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht 3584CH, Netherland
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11
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Ngo ST, Hong ND, Quynh Anh LH, Hiep DM, Tung NT. Effective estimation of the inhibitor affinity of HIV-1 protease via a modified LIE approach. RSC Adv 2020; 10:7732-7739. [PMID: 35492181 PMCID: PMC9049864 DOI: 10.1039/c9ra09583g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 02/06/2020] [Indexed: 01/07/2023] Open
Abstract
The inhibition of the Human Immunodeficiency Virus Type 1 Protease (HIV-1 PR) can prevent the synthesis of new viruses. Computer-aided drug design (CADD) would enhance the discovery of new therapies, through which the estimation of ligand-binding affinity is critical to predict the most efficient inhibitor. A time-consuming binding free energy method would reduce the usefulness of CADD. The modified linear interaction energy (LIE) approach emerges as an appropriate protocol that performs this task. In particular, the polar interaction free energy, which is obtained via numerically resolving the linear Poisson–Boltzmann equation, plays as an important role in driving the binding mechanism of the HIV-1 PR + inhibitor complex. The electrostatic interaction energy contributes to the attraction between two molecules, but the vdW interaction acts as a repulsive factor between the ligand and the HIV-1 PR. Moreover, the ligands were found to adopt a very strong hydrophobic interaction with the HIV-1 PR. Furthermore, the results obtained corroborate the high accuracy and precision of computational studies with a large correlation coefficient value R = 0.83 and a small RMSE δRMSE = 1.25 kcal mol−1. This method is less time-consuming than the other end-point methods, such as the molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and free energy perturbation (FEP) approaches. Overall, the modified LIE approach would provide ligand-binding affinity with HIV-1 PR accurately, precisely, and rapidly, resulting in a more efficient design of new inhibitors. The inhibition of the Human Immunodeficiency Virus Type 1 Protease (HIV-1 PR) can prevent the synthesis of new viruses.![]()
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | - Nam Dao Hong
- University of Medicine and Pharmacy at Ho Chi Minh City
- Ho Chi Minh City
- Vietnam
| | - Le Huu Quynh Anh
- Department of Climate Change and Renewable Energy
- Ho Chi Minh City University of Natural Resources and Environment
- Ho Chi Minh City
- Vietnam
| | | | - Nguyen Thanh Tung
- Institute of Materials Science & Graduate University of Science and Technology
- Vietnam Academy of Science and Technology
- Hanoi
- Vietnam
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12
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Agniswamy J, Kneller DW, Brothers R, Wang YF, Harrison RW, Weber IT. Highly Drug-Resistant HIV-1 Protease Mutant PRS17 Shows Enhanced Binding to Substrate Analogues. ACS OMEGA 2019; 4:8707-8719. [PMID: 31172041 PMCID: PMC6545544 DOI: 10.1021/acsomega.9b00683] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/07/2019] [Indexed: 05/24/2023]
Abstract
We report the structural analysis of highly drug-resistant human immunodeficiency virus protease (PR) variant PRS17, rationally selected by machine learning, in complex with substrate analogues. Crystal structures were solved of inhibitor-free inactive PRS17-D25N, wild-type PR/CA-p2 complex, and PRS17 in complex with substrate analogues, CA-p2 and p2-NC. Peptide analogues p2-NC and CA-p2 exhibit inhibition constants of 514 and 22 nM, respectively, for PRS17 or approximately 3-fold better than for PR. CA-p2 is a better inhibitor of PRS17 than are clinical inhibitors (K i = 50-8390 nM) except for amprenavir (K i = 11 nM). G48V resistance mutation induces curled flap tips in PRS17-D25N structure. The inner P2-P2' residues of substrate analogues in PRS17 complexes maintain similar conformations to those of wild-type complex, while significant conformational changes are observed in the peripheral residues P3, P4' of CA-p2 and P3, P4, and P3' of p2-NC. The loss of β-branched side chain by V82S mutation initiates a shift in 80's loop and reshapes the S3/S3' subsite, which enhances substrate binding with new hydrogen bonds and van der Waals interactions that are absent in the wild-type structures. The steric hindrance caused by G48V mutation in the flap of PRS17 contributes to altered binding interactions of P3 Arg, P4' norleucine of CA-p2, and P4 and P3' of p2-NC with the addition of new hydrogen bonds and van der Waals contacts. The enhanced interaction of PRS17 with substrate analogues agrees with their relative inhibition, suggesting that this mutant improves substrate binding while decreasing affinity for clinical inhibitors.
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Affiliation(s)
- Johnson Agniswamy
- Department
of Biology, Georgia State University, P.O. Box 4010, Atlanta, Georgia 30302, United
States
| | - Daniel W. Kneller
- Department
of Biology, Georgia State University, P.O. Box 4010, Atlanta, Georgia 30302, United
States
| | - Rowan Brothers
- Department
of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, Georgia 30302, United
States
| | - Yuan-Fang Wang
- Department
of Biology, Georgia State University, P.O. Box 4010, Atlanta, Georgia 30302, United
States
| | - Robert W. Harrison
- Department
of Computer Science, Georgia State University, P.O. Box 5060, Atlanta, Georgia 30302, United
States
| | - Irene T. Weber
- Department
of Biology, Georgia State University, P.O. Box 4010, Atlanta, Georgia 30302, United
States
- Department
of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, Georgia 30302, United
States
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13
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C.S. V, Tamizhselvi R, Munusami P. Exploring the drug resistance mechanism of active site, non-active site mutations and their cooperative effects in CRF01_AE HIV-1 protease: molecular dynamics simulations and free energy calculations. J Biomol Struct Dyn 2019; 37:2608-2626. [DOI: 10.1080/07391102.2018.1492459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Vasavi C.S.
- School of Biosciences and Technology, VIT University, Vellore, India
| | | | - Punnagai Munusami
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
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14
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Maphumulo SI, Halder AK, Govender T, Maseko S, Maguire GEM, Honarparvar B, Kruger HG. Exploring the flap dynamics of the South African HIV subtype C protease in presence of FDA-approved inhibitors: MD study. Chem Biol Drug Des 2018; 92:1899-1913. [PMID: 30003668 DOI: 10.1111/cbdd.13364] [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] [Received: 12/05/2017] [Accepted: 07/09/2018] [Indexed: 01/01/2023]
Abstract
HIV-1 protease (HIV PR) is considered as one of the most attractive targets for the treatment of HIV and the impact of flap dynamics of HIV PR on the binding affinities of protease inhibitors (PIs) is a crucial ongoing research field. Recently, our research group evaluated the binding affinities of different FDA approved PIs against the South African HIV-1 subtype C (C-SA) protease (PR). The CSA-HIV PR displayed weaker binding affinity for most of the clinical PIs compared to HIV-1 B subtype for West and Central Europe, the Americas. In the current work, the flap dynamics of four different systems of HIV-1 C-SA PR complexed to FDA approved second generation PIs and its impact on binding was explored over the molecular dynamic trajectories. It was observed that the interactions of the selected drugs with the binding site residues of the protease may not be the major contributor for affinity towards PIs. Various post-MD analyses were performed, also entropic contributions, solvation free energies and hydrophobic core formation interactions were studied to assess how the flap dynamics of C-SA PR which is affected by such factors. From these contributions, large van der Waals interactions and low solvation free energies were found to be major factors for the higher activity of ATV against C-SA HIV PR. Furthermore, a comparatively stable hydrophobic core may be responsible for higher stability of the PR flaps of the ATV complex. The outcome of this study provides significant guidance to how the flap dynamics of C-SA PR is affected by various factors as a result of the binding affinity of various protease inhibitors. It will also assist with the design of potent inhibitors against C-SA HIV PR that apart from binding in the active site of PR can interacts with the flaps to prevent opening of the flaps resulting in inactivation of the protease.
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Affiliation(s)
- Siyabonga I Maphumulo
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Amit K Halder
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sibusiso Maseko
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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15
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Hidaka K, Kimura T, Sankaranarayanan R, Wang J, McDaniel KF, Kempf DJ, Kameoka M, Adachi M, Kuroki R, Nguyen JT, Hayashi Y, Kiso Y. Identification of Highly Potent Human Immunodeficiency Virus Type-1 Protease Inhibitors against Lopinavir and Darunavir Resistant Viruses from Allophenylnorstatine-Based Peptidomimetics with P2 Tetrahydrofuranylglycine. J Med Chem 2018; 61:5138-5153. [PMID: 29852069 DOI: 10.1021/acs.jmedchem.7b01709] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The emergence of drug-resistant HIV from a widespread antiviral chemotherapy targeting HIV protease in the past decades is unavoidable and provides a challenge to develop alternative inhibitors. We synthesized a series of allophenylnorstatine-based peptidomimetics with various P3, P2, and P2́ moieties. The derivatives with P2 tetrahydrofuranylglycine (Thfg) were found to be potent against wild type HIV-1 protease and the virus, leading to a highly potent compound 21f (KNI-1657) against lopinavir/ritonavir- or darunavir-resistant strains. Co-crystal structures of 21f and the wild-type protease revealed numerous key hydrogen bonding interactions with Thfg. These results suggest that the strategy to design allophenylnorstatine-based peptidomimetics combined with Thfg residue would be promising for generating candidates to overcome multidrug resistance.
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Affiliation(s)
- Koushi Hidaka
- Laboratory of Medicinal Chemistry, Faculty of Pharmaceutical Sciences , Kobe Gakuin University , Kobe 650-8586 , Japan
| | - Tooru Kimura
- Department of Medicinal Chemistry , Kyoto Pharmaceutical University , Kyoto 607-8412 , Japan
| | - Rajesh Sankaranarayanan
- Department of Medicinal Chemistry , Kyoto Pharmaceutical University , Kyoto 607-8412 , Japan
| | - Jun Wang
- Department of Medicinal Chemistry , Kyoto Pharmaceutical University , Kyoto 607-8412 , Japan
| | - Keith F McDaniel
- Global Pharmaceutical Research and Development , AbbVie , North Chicago , Illinois 60064 , United States
| | - Dale J Kempf
- Global Pharmaceutical Research and Development , AbbVie , North Chicago , Illinois 60064 , United States
| | - Masanori Kameoka
- Department of International Health , Kobe University Graduate School of Health Sciences , Kobe 654-0142 , Japan
| | - Motoyasu Adachi
- Quantum Beam Science Drectorate , National Institutes for Quantum and Radiological Science and Technology , Tokai , Ibaraki 319-1106 , Japan
| | - Ryota Kuroki
- Quantum Beam Science Center , Japan Atomic Energy Agency , Tokai , Ibaraki 319-1195 , Japan
| | - Jeffrey-Tri Nguyen
- Department of Medicinal Chemistry , Kyoto Pharmaceutical University , Kyoto 607-8412 , Japan
| | - Yoshio Hayashi
- Department of Medicinal Chemistry , Tokyo University of Pharmacy and Life Sciences , Tokyo 192-0392 , Japan
| | - Yoshiaki Kiso
- Laboratory of Peptide Sciences , Nagahama Institute of Bio-Science and Technology , Nagahama 526-0829 , Japan
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16
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Irwin BWJ, Huggins DJ. Estimating Atomic Contributions to Hydration and Binding Using Free Energy Perturbation. J Chem Theory Comput 2018; 14:3218-3227. [PMID: 29712434 DOI: 10.1021/acs.jctc.8b00027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We present a general method called atom-wise free energy perturbation (AFEP), which extends a conventional molecular dynamics free energy perturbation (FEP) simulation to give the contribution to a free energy change from each atom. AFEP is derived from an expansion of the Zwanzig equation used in the exponential averaging method by defining that the system total energy can be partitioned into contributions from each atom. A partitioning method is assumed and used to group terms in the expansion to correspond to individual atoms. AFEP is applied to six example free energy changes to demonstrate the method. Firstly, the hydration free energies of methane, methanol, methylamine, methanethiol, and caffeine in water. AFEP highlights the atoms in the molecules that interact favorably or unfavorably with water. Finally AFEP is applied to the binding free energy of human immunodeficiency virus type 1 protease to lopinavir, and AFEP reveals the contribution of each atom to the binding free energy, indicating candidate areas of the molecule to improve to produce a more strongly binding inhibitor. FEP gives a single value for the free energy change and is already a very useful method. AFEP gives a free energy change for each "part" of the system being simulated, where part can mean individual atoms, chemical groups, amino acids, or larger partitions depending on what the user is trying to measure. This method should have various applications in molecular dynamics studies of physical, chemical, or biochemical phenomena, specifically in the field of computational drug discovery.
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Affiliation(s)
- Benedict W J Irwin
- Theory of Condensed Matter Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , United Kingdom
| | - David J Huggins
- Theory of Condensed Matter Group, Cavendish Laboratory , University of Cambridge , 19 J J Thomson Avenue , Cambridge CB3 0HE , United Kingdom.,Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom
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17
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Sun H, Li Y, Shen M, Li D, Kang Y, Hou T. Characterizing Drug-Target Residence Time with Metadynamics: How To Achieve Dissociation Rate Efficiently without Losing Accuracy against Time-Consuming Approaches. J Chem Inf Model 2017; 57:1895-1906. [PMID: 28749138 DOI: 10.1021/acs.jcim.7b00075] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Drug-target residence time plays a vital role in drug efficacy. However, there is still no effective strategy to predict drug residence time. Here, we propose to use the optimized (or minimized) structures derived from holo-state proteins to calculate drug residence time, which could give a comparable or even better prediction accuracy compared with those calculated utilizing a large number of molecular dynamics (MD) structures based on the Poisson process. Besides, in addition to the Poisson process, one may use fewer samples for predicting residence time due to the reason that, in a large extent, the calculated drug residence time is stable and independent of the number of samples used for the prediction. With remarkably reduced computational load, the proposed strategy may be promising for large-scale drug residence time prediction, such as post-processing in virtual screening (VS) and lead compound optimization.
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Affiliation(s)
- Huiyong Sun
- College of Pharmaceutical Sciences, Zhejiang University , Hangzhou, Zhejiang 310058, P. R. China.,State Key Lab of CAD&CG, Zhejiang University , Hangzhou, Zhejiang 310058, P. R. China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University , Suzhou, Jiangsu 215123, P. R. China
| | - Mingyun Shen
- Yangtze River Pharmaceutical Group , Taizhou, Jiangsu 225300, P. R. China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University , Hangzhou, Zhejiang 310058, P. R. China
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University , Hangzhou, Zhejiang 310058, P. R. China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University , Hangzhou, Zhejiang 310058, P. R. China.,State Key Lab of CAD&CG, Zhejiang University , Hangzhou, Zhejiang 310058, P. R. China
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18
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Ngo ST, Nguyen MT, Nguyen MT. Determination of the absolute binding free energies of HIV-1 protease inhibitors using non-equilibrium molecular dynamics simulations. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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19
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Shionyu-Mitsuyama C, Hijikata A, Tsuji T, Shirai T. Classification of ligand molecules in PDB with graph match-based structural superposition. ACTA ACUST UNITED AC 2016; 17:135-146. [PMID: 28012138 DOI: 10.1007/s10969-016-9209-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 12/05/2016] [Indexed: 10/20/2022]
Abstract
The fast heuristic graph match algorithm for small molecules, COMPLIG, was improved by adding a structural superposition process to verify the atom-atom matching. The modified method was used to classify the small molecule ligands in the Protein Data Bank (PDB) by their three-dimensional structures, and 16,660 types of ligands in the PDB were classified into 7561 clusters. In contrast, a classification by a previous method (without structure superposition) generated 3371 clusters from the same ligand set. The characteristic feature in the current classification system is the increased number of singleton clusters, which contained only one ligand molecule in a cluster. Inspections of the singletons in the current classification system but not in the previous one implied that the major factors for the isolation were differences in chirality, cyclic conformations, separation of substructures, and bond length. Comparisons between current and previous classification systems revealed that the superposition-based classification was effective in clustering functionally related ligands, such as drugs targeted to specific biological processes, owing to the strictness of the atom-atom matching.
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Affiliation(s)
- Clara Shionyu-Mitsuyama
- Department of Bioscience, Nagahama Institute of Bio-science and Technology, 1266 Tamura, Nagahama, 526-0829, Japan
| | - Atsushi Hijikata
- Department of Bioscience, Nagahama Institute of Bio-science and Technology, 1266 Tamura, Nagahama, 526-0829, Japan
| | - Toshiyuki Tsuji
- Department of Bioscience, Nagahama Institute of Bio-science and Technology, 1266 Tamura, Nagahama, 526-0829, Japan
| | - Tsuyoshi Shirai
- Department of Bioscience, Nagahama Institute of Bio-science and Technology, 1266 Tamura, Nagahama, 526-0829, Japan.
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20
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Liu Z, Huang X, Hu L, Pham L, Poole KM, Tang Y, Mahon BP, Tang W, Li K, Goldfarb NE, Dunn BM, McKenna R, Fanucci GE. Effects of Hinge-region Natural Polymorphisms on Human Immunodeficiency Virus-Type 1 Protease Structure, Dynamics, and Drug Pressure Evolution. J Biol Chem 2016; 291:22741-22756. [PMID: 27576689 DOI: 10.1074/jbc.m116.747568] [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: 07/11/2016] [Revised: 08/30/2016] [Indexed: 11/06/2022] Open
Abstract
Multidrug resistance to current Food and Drug Administration-approved HIV-1 protease (PR) inhibitors drives the need to understand the fundamental mechanisms of how drug pressure-selected mutations, which are oftentimes natural polymorphisms, elicit their effect on enzyme function and resistance. Here, the impacts of the hinge-region natural polymorphism at residue 35, glutamate to aspartate (E35D), alone and in conjunction with residue 57, arginine to lysine (R57K), are characterized with the goal of understanding how altered salt bridge interactions between the hinge and flap regions are associated with changes in structure, motional dynamics, conformational sampling, kinetic parameters, and inhibitor affinity. The combined results reveal that the single E35D substitution leads to diminished salt bridge interactions between residues 35 and 57 and gives rise to the stabilization of open-like conformational states with overall increased backbone dynamics. In HIV-1 PR constructs where sites 35 and 57 are both mutated (e.g. E35D and R57K), x-ray structures reveal an altered network of interactions that replace the salt bridge thus stabilizing the structural integrity between the flap and hinge regions. Despite the altered conformational sampling and dynamics when the salt bridge is disrupted, enzyme kinetic parameters and inhibition constants are similar to those obtained for subtype B PR. Results demonstrate that these hinge-region natural polymorphisms, which may arise as drug pressure secondary mutations, alter protein dynamics and the conformational landscape, which are important thermodynamic parameters to consider for development of inhibitors that target for non-subtype B PR.
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Affiliation(s)
- Zhanglong Liu
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Xi Huang
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Lingna Hu
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Linh Pham
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Katye M Poole
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Yan Tang
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Brian P Mahon
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Wenxing Tang
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Kunhua Li
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
| | - Nathan E Goldfarb
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Ben M Dunn
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Robert McKenna
- the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610
| | - Gail E Fanucci
- From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and
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21
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Liu Z, Casey TM, Blackburn ME, Huang X, Pham L, de Vera IMS, Carter JD, Kear-Scott JL, Veloro AM, Galiano L, Fanucci GE. Pulsed EPR characterization of HIV-1 protease conformational sampling and inhibitor-induced population shifts. Phys Chem Chem Phys 2016; 18:5819-31. [PMID: 26489725 PMCID: PMC4758878 DOI: 10.1039/c5cp04556h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The conformational landscape of HIV-1 protease (PR) can be experimentally characterized by pulsed-EPR double electron-electron resonance (DEER). For this characterization, nitroxide spin labels are attached to an engineered cysteine residue in the flap region of HIV-1 PR. DEER distance measurements from spin-labels contained within each flap of the homodimer provide a detailed description of the conformational sampling of apo-enzyme as well as induced conformational shifts as a function of inhibitor binding. The distance distribution profiles are further interpreted in terms of a conformational ensemble scheme that consists of four unique states termed "curled/tucked", "closed", "semi-open" and "wide-open" conformations. Reported here are the DEER results for a drug-resistant variant clinical isolate sequence, V6, in the presence of FDA approved protease inhibitors (PIs) as well as a non-hydrolyzable substrate mimic, CaP2. Results are interpreted in the context of the current understanding of the relationship between conformational sampling, drug resistance, and kinetic efficiency of HIV-1PR as derived from previous DEER and kinetic data for a series of HIV-1PR constructs that contain drug-pressure selected mutations or natural polymorphisms. Specifically, these collective results support the notion that inhibitor-induced closure of the flaps correlates with inhibitor efficiency and drug resistance. This body of work also suggests DEER as a tool for studying conformational sampling in flexible enzymes as it relates to function.
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Affiliation(s)
- Zhanglong Liu
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Thomas M Casey
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Mandy E Blackburn
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Xi Huang
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Linh Pham
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Ian Mitchelle S de Vera
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Jeffrey D Carter
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Jamie L Kear-Scott
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Angelo M Veloro
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Luis Galiano
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
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22
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Nakashima M, Ode H, Suzuki K, Fujino M, Maejima M, Kimura Y, Masaoka T, Hattori J, Matsuda M, Hachiya A, Yokomaku Y, Suzuki A, Watanabe N, Sugiura W, Iwatani Y. Unique Flap Conformation in an HIV-1 Protease with High-Level Darunavir Resistance. Front Microbiol 2016; 7:61. [PMID: 26870021 PMCID: PMC4737996 DOI: 10.3389/fmicb.2016.00061] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/14/2016] [Indexed: 11/13/2022] Open
Abstract
Darunavir (DRV) is one of the most powerful protease inhibitors (PIs) for treating human immunodeficiency virus type-1 (HIV-1) infection and presents a high genetic barrier to the generation of resistant viruses. However, DRV-resistant HIV-1 infrequently emerges from viruses exhibiting resistance to other protease inhibitors. To address this resistance, researchers have gathered genetic information on DRV resistance. In contrast, few structural insights into the mechanism underlying DRV resistance are available. To elucidate this mechanism, we determined the crystal structure of the ligand-free state of a protease with high-level DRV resistance and six DRV resistance-associated mutations (including I47V and I50V), which we generated by in vitro selection. This crystal structure showed a unique curling conformation at the flap regions that was not found in the previously reported ligand-free protease structures. Molecular dynamics simulations indicated that the curled flap conformation altered the flap dynamics. These results suggest that the preference for a unique flap conformation influences DRV binding. These results provide new structural insights into elucidating the molecular mechanism of DRV resistance and aid to develop PIs effective against DRV-resistant viruses.
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Affiliation(s)
- Masaaki Nakashima
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan
| | - Hirotaka Ode
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Koji Suzuki
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan
| | - Masayuki Fujino
- AIDS Research Center, National Institute of Infectious Diseases Tokyo, Japan
| | - Masami Maejima
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yuki Kimura
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan
| | - Takashi Masaoka
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Junko Hattori
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Masakazu Matsuda
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Atsuko Hachiya
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yoshiyuki Yokomaku
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Atsuo Suzuki
- Department of Biotechnology, Nagoya University Graduate School of Engineering Nagoya, Japan
| | - Nobuhisa Watanabe
- Department of Biotechnology, Nagoya University Graduate School of EngineeringNagoya, Japan; Synchrotron Radiation Research Center, Nagoya UniversityNagoya, Japan
| | - Wataru Sugiura
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | - Yasumasa Iwatani
- Department of Infectious Diseases and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical CenterNagoya, Japan; Department of AIDS Research, Nagoya University Graduate School of MedicineNagoya, Japan
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23
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Chéron N, Jasty N, Shakhnovich EI. OpenGrowth: An Automated and Rational Algorithm for Finding New Protein Ligands. J Med Chem 2015; 59:4171-88. [DOI: 10.1021/acs.jmedchem.5b00886] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nicolas Chéron
- Department of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Naveen Jasty
- Department of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Eugene I. Shakhnovich
- Department of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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24
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Goldfarb NE, Ohanessian M, Biswas S, McGee TD, Mahon BP, Ostrov DA, Garcia J, Tang Y, McKenna R, Roitberg A, Dunn BM. Defective hydrophobic sliding mechanism and active site expansion in HIV-1 protease drug resistant variant Gly48Thr/Leu89Met: mechanisms for the loss of saquinavir binding potency. Biochemistry 2015; 54:422-33. [PMID: 25513833 PMCID: PMC4303317 DOI: 10.1021/bi501088e] [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] [Indexed: 01/03/2023]
Abstract
![]()
HIV drug resistance continues to
emerge; consequently, there is
an urgent need to develop next generation antiretroviral therapeutics.1 Here we report on the structural and kinetic
effects of an HIV protease drug resistant variant with the double
mutations Gly48Thr and Leu89Met (PRG48T/L89M), without
the stabilizing mutations Gln7Lys, Leu33Ile, and Leu63Ile. Kinetic
analyses reveal that PRG48T/L89M and PRWT share
nearly identical Michaelis–Menten parameters; however, PRG48T/L89M exhibits weaker binding for IDV (41-fold), SQV (18-fold),
APV (15-fold), and NFV (9-fold) relative to PRWT. A 1.9
Å resolution crystal structure was solved for PRG48T/L89M bound with saquinavir (PRG48T/L89M-SQV) and compared
to the crystal structure of PRWT bound with saquinavir
(PRWT-SQV). PRG48T/L89M-SQV has
an enlarged active site resulting in the loss of a hydrogen bond in
the S3 subsite from Gly48 to P3 of SQV, as well as less favorable
hydrophobic packing interactions between P1 Phe of SQV and the S1
subsite. PRG48T/L89M-SQV assumes a more open conformation
relative to PRWT-SQV, as illustrated by the downward
displacement of the fulcrum and elbows and weaker interatomic flap
interactions. We also show that the Leu89Met mutation disrupts the
hydrophobic sliding mechanism by causing a redistribution of van der
Waals interactions in the hydrophobic core in PRG48T/L89M-SQV. Our mechanism for PRG48T/L89M-SQV drug resistance
proposes that a defective hydrophobic sliding mechanism results in
modified conformational dynamics of the protease. As a consequence,
the protease is unable to achieve a fully closed conformation that
results in an expanded active site and weaker inhibitor binding.
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Affiliation(s)
- Nathan E Goldfarb
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §Departments of Pathology, Immunology, and Laboratory Medicine, University of Florida , Gainesville, Florida 32601-0245, United States
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25
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Inhibitors of the Human Immunodeficiency Virus Protease. Antiviral Res 2014. [DOI: 10.1128/9781555815493.ch7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Shadrina O, Krotova O, Agapkina J, Knyazhanskaya E, Korolev S, Starodubova E, Viklund A, Lukashov V, Magnani M, Medstrand P, Karpov V, Gottikh M, Isaguliants M. Consensus HIV-1 subtype A integrase and its raltegravir-resistant variants: design and characterization of the enzymatic properties. Biochimie 2014; 102:92-101. [PMID: 24594066 DOI: 10.1016/j.biochi.2014.02.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/21/2014] [Indexed: 11/28/2022]
Abstract
Model studies of the subtype B and non-subtype B integrases are still required to compare their susceptibility to antiretroviral drugs, evaluate the significance of resistance mutations and identify the impact of natural polymorphisms on the level of enzymatic reactivity. We have therefore designed the consensus integrase of the HIV-1 subtype A strain circulating in the former Soviet Union territory (FSU-A) and two of its variants with mutations of resistance to the strand transfer inhibitor raltegravir. Their genes were synthesized, and expressed in E coli; corresponding His-tagged proteins were purified using the affinity chromatography. The enzymatic properties of the consensus integrases and their sensitivity to raltegravir were examined in a series of standard in vitro reactions and compared to the properties of the integrase of HIV-1 subtype B strain HXB2. The consensus enzyme demonstrated similar DNA-binding properties, but was significantly more active than HXB-2 integrase in the reactions of DNA cleavage and integration. All integrases were equally susceptible to inhibition by raltegravir and elvitegravir, indicating that the sporadic polymorphisms inherent to the HXB-2 enzyme have little effect on its susceptibility to drugs. Insensitivity of the mutated enzymes to the inhibitors of strand transfer occurred at a cost of a 30-90% loss of the efficacies of both 3'-processing and strand transfer. This is the first study to describe the enzymatic properties of the consensus integrase of HIV-1 clade A and the effects of the resistance mutations when the complex actions of sporadic sequence polymorphisms are excluded.
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Affiliation(s)
- Olga Shadrina
- Lomonosov Moscow State University, Belozersky Institute of Physical Chemical Biology and Chemistry Department, Leninskie gory 1/40, 119991 Moscow, Russia
| | - Olga Krotova
- Engelhardt Institute of Molecular Biology, Vavilov str 32, 119991 Moscow, Russia; Ivanovsky Institute of Virology, Gamaleja str 16, 123098 Moscow, Russia; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, 17177 Stockholm, Sweden
| | - Julia Agapkina
- Lomonosov Moscow State University, Belozersky Institute of Physical Chemical Biology and Chemistry Department, Leninskie gory 1/40, 119991 Moscow, Russia
| | - Ekaterina Knyazhanskaya
- Lomonosov Moscow State University, Belozersky Institute of Physical Chemical Biology and Chemistry Department, Leninskie gory 1/40, 119991 Moscow, Russia
| | - Sergey Korolev
- Lomonosov Moscow State University, Belozersky Institute of Physical Chemical Biology and Chemistry Department, Leninskie gory 1/40, 119991 Moscow, Russia
| | - Elizaveta Starodubova
- Engelhardt Institute of Molecular Biology, Vavilov str 32, 119991 Moscow, Russia; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, 17177 Stockholm, Sweden
| | - Alecia Viklund
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, 17177 Stockholm, Sweden
| | - Vladimir Lukashov
- Ivanovsky Institute of Virology, Gamaleja str 16, 123098 Moscow, Russia; Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mauro Magnani
- Department of Biomolecular Science, University of Urbino "Carla Bo", Via Saffi, 2, 61029 Urbino, Italy
| | - Patrik Medstrand
- Department of Laboratory Medicine, Lund University, Sölvegatan 19, SE-205 02 Malmö, Sweden
| | - Vadim Karpov
- Engelhardt Institute of Molecular Biology, Vavilov str 32, 119991 Moscow, Russia
| | - Marina Gottikh
- Lomonosov Moscow State University, Belozersky Institute of Physical Chemical Biology and Chemistry Department, Leninskie gory 1/40, 119991 Moscow, Russia.
| | - Maria Isaguliants
- Ivanovsky Institute of Virology, Gamaleja str 16, 123098 Moscow, Russia; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, 17177 Stockholm, Sweden.
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Novel PCU cage diol peptides as potential targets against wild-type CSA HIV-1 protease: synthesis, biological screening and molecular modelling studies. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0350-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Huang X, de Vera IMS, Veloro AM, Blackburn ME, Kear JL, Carter JD, Rocca JR, Simmerling C, Dunn BM, Fanucci GE. Inhibitor-induced conformational shifts and ligand-exchange dynamics for HIV-1 protease measured by pulsed EPR and NMR spectroscopy. J Phys Chem B 2012; 116:14235-44. [PMID: 23167829 PMCID: PMC3709468 DOI: 10.1021/jp308207h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Double electron-electron resonance (DEER) spectroscopy was utilized to investigate shifts in conformational sampling induced by nine FDA-approved protease inhibitors (PIs) and a nonhydrolyzable substrate mimic for human immunodeficiency virus type 1 protease (HIV-1 PR) subtype B, subtype C, and CRF_01 A/E. The ligand-bound subtype C protease has broader DEER distance profiles, but trends for inhibitor-induced conformational shifts are comparable to those previously reported for subtype B. Ritonavir, one of the strong-binding inhibitors for subtypes B and C, induces less of the closed conformation in CRF_01 A/E. (1)H-(15)N heteronuclear single-quantum coherence (HSQC) spectra were acquired for each protease construct titrated with the same set of inhibitors. NMR (1)H-(15)N HSQC titration data show that inhibitor residence time in the protein binding pocket, inferred from resonance exchange broadening, shifting or splitting correlates with the degree of ligand-induced flap closure measured by DEER spectroscopy. These parallel results show that the ligand-induced conformational shifts resulting from protein-ligand interactions characterized by DEER spectroscopy of HIV-1 PR obtained at the cryogenic temperature are consistent with more physiological solution protein-ligand interactions observed by solution NMR spectroscopy.
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Affiliation(s)
- Xi Huang
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, USA
| | | | - Angelo M. Veloro
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, USA
| | - Mandy E. Blackburn
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, USA
| | - Jamie L. Kear
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, USA
| | - Jeffery D. Carter
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, USA
| | - James R. Rocca
- Advanced Magnetic Resonance Imaging and Spectroscopy Facility, McKnight Brain Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Carlos Simmerling
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Ben M. Dunn
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610, USA
| | - Gail E. Fanucci
- Department of Chemistry, University of Florida, PO Box 117200, Gainesville, Florida 32611, USA
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30
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Kang H, Sheng Z, Zhu R, Huang Q, Liu Q, Cao Z. Virtual drug screen schema based on multiview similarity integration and ranking aggregation. J Chem Inf Model 2012; 52:834-43. [PMID: 22332590 DOI: 10.1021/ci200481c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The current drug virtual screen (VS) methods mainly include two categories. i.e., ligand/target structure-based virtual screen and that, utilizing protein-ligand interaction fingerprint information based on the large number of complex structures. Since the former one focuses on the one-side information while the later one focuses on the whole complex structure, they are thus complementary and can be boosted by each other. However, a common problem faced here is how to present a comprehensive understanding and evaluation of the various virtual screen results derived from various VS methods. Furthermore, there is still an urgent need for developing an efficient approach to fully integrate various VS methods from a comprehensive multiview perspective. In this study, our virtual screen schema based on multiview similarity integration and ranking aggregation was tested comprehensively with statistical evaluations, providing several novel and useful clues on how to perform drug VS from multiple heterogeneous data sources. (1) 18 complex structures of HIV-1 protease with ligands from the PDB were curated as a test data set and the VS was performed with five different drug representations. Ritonavir ( 1HXW ) was selected as the query in VS and the weighted ranks of the query results were aggregated from multiple views through four similarity integration approaches. (2) Further, one of the ranking aggregation methods was used to integrate the similarity ranks calculated by gene ontology (GO) fingerprint and structural fingerprint on the data set from connectivity map, and two typical HDAC and HSP90 inhibitors were chosen as the queries. The results show that rank aggregation can enhance the result of similarity searching in VS when two or more descriptions are involved and provide a more reasonable similarity rank result. Our study shows that integrated VS based on multiple data fusion can achieve a remarkable better performance compared to that from individual ones and, thus, serves as a promising way for efficient drug screening, taking advantages of the rapidly accumulated molecule representations and heterogeneous data in the pharmacological area.
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Affiliation(s)
- Hong Kang
- School of Life Sciences and Technology, Tongji University, 200092, China
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31
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Makatini MM, Petzold K, Alves CN, Arvidsson PI, Honarparvar B, Govender P, Govender T, Kruger HG, Sayed Y, JerônimoLameira, Maguire GEM, Soliman MES. Synthesis, 2D-NMR and molecular modelling studies of pentacycloundecane lactam-peptides and peptoids as potential HIV-1 wild type C-SA protease inhibitors. J Enzyme Inhib Med Chem 2012; 28:78-88. [PMID: 22339087 DOI: 10.3109/14756366.2011.633907] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this study, eight non-natural peptides and peptoids incorporating the pentacycloundecane (PCU) lactam were designed and synthesized as potential inhibitors of the wild type C-SA HIV-protease. Five of these inhibitors gave IC(50) values ranging from 0.5 up to 0.75 µM against the resistance-prone wild type C-South African HIV-protease. NMR EASY-ROESY studies enabled us to describe the secondary structure of three of these compounds in solution. The 3D structures of the selected cage peptides were also modelled in solution using QM/MM/MD simulations. Satisfactory agreement between the NMR observations and the low energy calculated structures exists. Only one of these inhibitors (11 peptoid), which showed the best IC(50)(0.5 µM), exhibited a definable 3-D structure in solution. Autodock4 and AutodockVina were used to model the potential interaction between these inhibitors and the HIV-PR. It appears that the docking results are too crude to be correlated with the relative narrow range of experimental IC(50) values (0.5-10 µM). The PCU-peptides and peptoides were several orders less toxic (145 μM for 11 and 102 μM for 11 peptoid) to human MT-4 cells than lopinavir (0.025 μM). This is the first example of a polycyclic cage framework to be employed as an HIV-PR transition state analogue inhibitor and can potentially be utilized for other diseases related proteases. [Figure: see text].
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Pentacycloundecane derived hydroxy acid peptides: A new class of irreversible non-scissile ether bridged type isoster as potential HIV-1 wild type C-SA protease inhibitors. Bioorg Chem 2012; 40:19-29. [DOI: 10.1016/j.bioorg.2011.08.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 08/03/2011] [Accepted: 08/04/2011] [Indexed: 11/18/2022]
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Huang L, Li Y, Chen C. Flexible catalytic site conformations implicated in modulation of HIV-1 protease autoprocessing reactions. Retrovirology 2011; 8:79. [PMID: 21985091 PMCID: PMC3210109 DOI: 10.1186/1742-4690-8-79] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Accepted: 10/10/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The HIV-1 protease is initially synthesized as part of the Gag-Pol polyprotein in the infected cell. Protease autoprocessing, by which the protease domain embedded in the precursor catalyzes essential cleavage reactions, leads to liberation of the free mature protease at the late stage of the replication cycle. To examine autoprocessing reactions in transfected mammalian cells, we previously described an assay using a fusion precursor consisting of the mature protease (PR) along with its upstream transframe region (p6*) sandwiched between GST and a small peptide epitope. RESULTS In this report, we studied two autoprocessing cleavage reactions, one between p6* and PR (the proximal site) and the other in the N-terminal region of p6* (the distal site) catalyzed by the embedded protease, using our cell-based assay. A fusion precursor carrying the NL4-3 derived protease cleaved both sites, whereas a precursor with a pseudo wild type protease preferentially autoprocessed the proximal site. Mutagenesis analysis demonstrated that several residues outside the active site (Q7, L33, N37, L63, C67 and H69) contributed to the differential substrate specificity. Furthermore, the cleavage reaction at the proximal site mediated by the embedded protease in precursors carrying different protease sequences or C-terminal fusion peptides displayed varied sensitivity to inhibition by darunavir, a catalytic site inhibitor. On the other hand, polypeptides such as a GCN4 motif, GFP, or hsp70 fused to the N-terminus of p6* had a minimal effect on darunavir inhibition of either cleavage reaction. CONCLUSIONS Taken together, our data suggest that several non-active site residues and the C-terminal flanking peptides regulate embedded protease activity through modulation of the catalytic site conformation. The cell-based assay provides a sensitive tool to study protease autoprocessing reactions in mammalian cells.
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Affiliation(s)
- Liangqun Huang
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523-1870, USA
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34
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[Bioinformatics studies on drug resistance against anti-HIV-1 drugs]. Uirusu 2011; 61:35-47. [PMID: 21972554 DOI: 10.2222/jsv.61.35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
More than 20 drugs have been available for anti-HIV-1 treatment in Japan. Combination therapy with these drugs dramatically decreases in morbidity and mortality of AIDS. However, due to high mutation rate of HIV-1, treatment with ineffective drugs toward patients infected with HIV-1 causes accumulation of mutations in the virus, and emergence of drug resistant viruses. Thus, to achieve appropriate application of the drugs toward the respective patients living with HIV-1, methods for predicting the level of drug-resistance using viral sequence information has been developed on the basis of bioinformatics. Furthermore, ultra-deep sequencing by next-generation sequencer whose data analysis is also based on bioinformatics, or in silico structural modeling have been achieved to understand drug resistant mechanisms. In this review, I overview the bioinformatics studies about drug resistance against anti-HIV-1 drugs.
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35
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Lee J, Goodey NM. Catalytic contributions from remote regions of enzyme structure. Chem Rev 2011; 111:7595-624. [PMID: 21923192 DOI: 10.1021/cr100042n] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Jeeyeon Lee
- Department of Chemistry, 413 Wartik Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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36
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Kolár M, Fanfrlík J, Hobza P. Ligand conformational and solvation/desolvation free energy in protein-ligand complex formation. J Phys Chem B 2011; 115:4718-24. [PMID: 21466174 DOI: 10.1021/jp2010265] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, an extensive sampling of the conformational space of nine HIV-1 protease inhibitors was performed to estimate the uncertainty with which a single-conformation scoring scheme approximates the ligand-protein binding free energy. The SMD implicit solvation/desolvation energy and gas-phase PM6-DH2 energy were calculated for a set of 1600 conformations of each ligand. The probability density functions of the energies were compared with the values obtained from the single-conformation approach and from a short ab initio molecular dynamics simulation. The relative uncertainty in the score within the set of nine inhibitors was calculated to be 3.5 kcal·mol(-1) and 2.7 kcal·mol(-1) for the single-conformation and short dynamics, respectively. These results, though limited to the consideration of flexible ligands, provide a valuable insight into the precision of rigid models in the current computer-aided drug design.
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Affiliation(s)
- Michal Kolár
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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37
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Karthik S, Senapati S. Dynamic flaps in HIV-1 protease adopt unique ordering at different stages in the catalytic cycle. Proteins 2011; 79:1830-40. [PMID: 21465560 DOI: 10.1002/prot.23008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2010] [Revised: 01/13/2011] [Accepted: 01/17/2011] [Indexed: 11/07/2022]
Abstract
The flexibility of HIV-1 protease flaps is known to be essential for the enzymatic activity. Here we attempt to capture a multitude of conformations of the free and substrate-bound HIV-1 protease that differ drastically in their flap arrangements. The substrate binding process suggests the opening of active site gate in conjunction with a reversal of flap tip ordering, from the native semiopen state. The reversed-flap, open-gated enzyme readily transforms to a closed conformation after proper placement of the substrate into the binding cleft. After substrate processing, the closed state protease which possessed opposite flap ordering relative to the semiopen state, encounters another flap reversal via a second open conformation that facilitates the evolution of native semiopen state of correct flap ordering. The complicated transitional pathway, comprising of many high and low energy states, is explored by combining standard and activated molecular dynamics (MD) simulation techniques. The study not only complements the existing findings from X-ray, NMR, EPR, and MD studies but also provides a wealth of detailed information that could help the structure-based drug design process.
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Affiliation(s)
- Suresh Karthik
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
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38
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Resistant mechanism against nelfinavir of subtype C human immunodeficiency virus type 1 proteases. J Mol Struct 2011. [DOI: 10.1016/j.molstruc.2010.11.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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39
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Fanfrlík J, Bronowska AK, Rezác J, Prenosil O, Konvalinka J, Hobza P. A reliable docking/scoring scheme based on the semiempirical quantum mechanical PM6-DH2 method accurately covering dispersion and H-bonding: HIV-1 protease with 22 ligands. J Phys Chem B 2011; 114:12666-78. [PMID: 20839830 DOI: 10.1021/jp1032965] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this study, we introduce a fast and reliable rescoring scheme for docked complexes based on a semiempirical quantum mechanical PM6-DH2 method. The method utilizes a PM6-based Hamiltonian with corrections for dispersion energy and hydrogen bonds. The total score is constructed as the sum of the PM6-DH2 interaction enthalpy, the empirical force field (AMBER) interaction entropy, and the sum of the deformation (PM6-DH2, SMD) and the desolvation (SMD) energies of the ligand. The main advantage of the procedure is the fact that we do not add any empirical parameter for either an individual component of the total score or an individual protein-ligand complex. This rescoring method is applied to a very challenging system, namely, the HIV-1 protease with a set of ligands. As opposed to the conventional DOCK procedure, the PM6-DH2 rescoring based on all of the terms distinguishes between binders and nonbinders and provides a reliable correlation of the theoretical and experimental binding free energies. Such a dramatic improvement, resulting from the PM6-DH2 rescoring of all the complexes, provides a valuable yet inexpensive tool for rational drug discovery and de novo ligand design.
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Affiliation(s)
- Jindrich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague 6, Czech Republic
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40
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Flütsch A, Schroeder T, Grütter MG, Patzke GR. HIV-1 protease inhibition potential of functionalized polyoxometalates. Bioorg Med Chem Lett 2010; 21:1162-6. [PMID: 21256010 PMCID: PMC7126215 DOI: 10.1016/j.bmcl.2010.12.103] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 12/20/2010] [Accepted: 12/21/2010] [Indexed: 11/21/2022]
Abstract
Polyoxometalates (POMs) are interesting biomedical agents due to their versatile anticancer and antiviral properties, such as remarkable anti-HIV activity. Although POMs are tunable and easily accessible inorganic drug prototypes in principle, their full potential can only be tapped by enhancing their biocompatibility, for example, through organic functionalization. We have therefore investigated the HIV-1 protease inhibition potential of functionalized Keggin- and Dawson-type POMs with organic side chains. Their inhibitory performance was furthermore compared to other POM types, and the buffer dependence of the results is discussed. In addition, chemical shift mapping NMR experiments were performed to exclude POM–substrate interactions. Whereas the introduction of organic side chains into POMs is a promising approach in principle, the influence of secondary effects on the reaction system also merits detailed investigation.
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Affiliation(s)
- Andreas Flütsch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Thilo Schroeder
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Markus G. Grütter
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Greta R. Patzke
- Institute of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
- Corresponding author. Tel.: +41 44 635 4691; fax: +41 44 635 6802.
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41
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The effect of clade-specific sequence polymorphisms on HIV-1 protease activity and inhibitor resistance pathways. J Virol 2010; 84:9995-10003. [PMID: 20660190 DOI: 10.1128/jvi.00505-10] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The majority of HIV-1 infections around the world result from non-B clade HIV-1 strains. The CRF01_AE (AE) strain is seen principally in Southeast Asia. AE protease differs by approximately 10% in amino acid sequence from clade B protease and carries several naturally occurring polymorphisms that are associated with drug resistance in clade B. AE protease has been observed to develop resistance through a nonactive-site N88S mutation in response to nelfinavir (NFV) therapy, whereas clade B protease develops both the active-site mutation D30N and the nonactive-site mutation N88D. Structural and biochemical studies were carried out with wild-type and NFV-resistant clade B and AE protease variants. The relationship between clade-specific sequence variations and pathways to inhibitor resistance was also assessed. AE protease has a lower catalytic turnover rate than clade B protease, and it also has weaker affinity for both NFV and darunavir (DRV). This weaker affinity may lead to the nonactive-site N88S variant in AE, which exhibits significantly decreased affinity for both NFV and DRV. The D30N/N88D mutations in clade B resulted in a significant loss of affinity for NFV and, to a lesser extent, for DRV. A comparison of crystal structures of AE protease shows significant structural rearrangement in the flap hinge region compared with those of clade B protease and suggests insights into the alternative pathways to NFV resistance. In combination, our studies show that sequence polymorphisms within clades can alter protease activity and inhibitor binding and are capable of altering the pathway to inhibitor resistance.
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Genoni A, Morra G, Merz KM, Colombo G. Computational study of the resistance shown by the subtype B/HIV-1 protease to currently known inhibitors. Biochemistry 2010; 49:4283-95. [PMID: 20415450 DOI: 10.1021/bi100569u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human immunodeficiency virus type 1 protease (HIV-1 PR) is an essential enzyme in the HIV-1 life cycle. As such, this protein represents a major drug target in AIDS therapy, but emerging resistance to antiretroviral inhibitor cocktails, caused by high viral mutation rates, represents a significant challenge in AIDS treatment. Many mutations are not located within the active site or binding pocket, nor they do significantly modify the three-dimensional structural organization of the enzyme; hence, the mechanism(s) by which they alter inhibitor affinity for the protease remains uncertain. In this article, we present an all-atom computational analysis of the dynamic residue-residue coordination between the active site residues and the rest of the protein and of the energetic properties of different HIV-1 PR complexes. We analyze both the wild-type form and mutated forms that induce drug resistance. In particular, the results show differences between the wild type and the mutants in their mechanism of dynamic coordination, in the signal propagation between the active site residues and the rest of the protein, and in the energy networks responsible for the stabilization of the bound inhibitor conformation. Finally, we propose a dynamic and energetic explanation for HIV-1 protease drug resistance, and, through this model, we identify a possible new site that could be helpful in the design of a new family of HIV-1 PR allosteric inhibitors.
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Affiliation(s)
- Alessandro Genoni
- Istituto di Chimica del Riconoscimento Molecolare, CNR, Via Mario Bianco 9, 20131 Milano, Italy
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43
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Matsuyama S, Aydan A, Ode H, Hata M, Sugiura W, Hoshino T. Structural and energetic analysis on the complexes of clinically isolated subtype C HIV-1 proteases and approved inhibitors by molecular dynamics simulation. J Phys Chem B 2010; 114:521-30. [PMID: 20055526 DOI: 10.1021/jp908314f] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV-1 has a large genetic diversity. Subtype B HIV-1 is commonly found in patients in developed countries. In contrast, an increasing number of patients are infected with the non-B subtype viruses, especially with subtype C HIV-1, in developing countries. It remains to be clarified how mutations or polymorphisms in non-B subtype HIV-1 influence the efficacy of the approved inhibitors. In this study, we have performed molecular dynamics simulations on clinically isolated subtype C HIV-1 proteases in complex with three kinds of approved inhibitors. From the structural and energetic viewpoints, we identified the polymorphisms influencing on the binding of the inhibitors. The effect of the V82I mutation on the association with chemicals and the reason for rare appearance of the D30N mutation in subtype C HIV-1 were discussed in terms of the change of geometry of the residues in HIV-1 protease.
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Affiliation(s)
- Shou Matsuyama
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
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44
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Robbins AH, Coman RM, Bracho-Sanchez E, Fernandez MA, Gilliland CT, Li M, Agbandje-McKenna M, Wlodawer A, Dunn BM, McKenna R. Structure of the unbound form of HIV-1 subtype A protease: comparison with unbound forms of proteases from other HIV subtypes. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:233-42. [PMID: 20179334 PMCID: PMC2827345 DOI: 10.1107/s0907444909054298] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 12/16/2009] [Indexed: 04/06/2023]
Abstract
The crystal structure of the unbound form of HIV-1 subtype A protease (PR) has been determined to 1.7 A resolution and refined as a homodimer in the hexagonal space group P6(1) to an R(cryst) of 20.5%. The structure is similar in overall shape and fold to the previously determined subtype B, C and F PRs. The major differences lie in the conformation of the flap region. The flaps in the crystal structures of the unbound subtype B and C PRs, which were crystallized in tetragonal space groups, are either semi-open or wide open. In the present structure of subtype A PR the flaps are found in the closed position, a conformation that would be more anticipated in the structure of HIV protease complexed with an inhibitor. The amino-acid differences between the subtypes and their respective crystal space groups are discussed in terms of the differences in the flap conformations.
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Affiliation(s)
- Arthur H. Robbins
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Roxana M. Coman
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Edith Bracho-Sanchez
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Marty A. Fernandez
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - C. Taylor Gilliland
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Mi Li
- Basic Research Program, SAIC-Frederick, Frederick, Maryland, USA
- Macromolecular Crystallography Laboratory, NCI-Frederick, Frederick, Maryland, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, NCI-Frederick, Frederick, Maryland, USA
| | - Ben M. Dunn
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
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45
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Das D, Koh Y, Tojo Y, Ghosh AK, Mitsuya H. Prediction of potency of protease inhibitors using free energy simulations with polarizable quantum mechanics-based ligand charges and a hybrid water model. J Chem Inf Model 2010; 49:2851-62. [PMID: 19928916 DOI: 10.1021/ci900320p] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reliable and robust prediction of the binding affinity for drug molecules continues to be a daunting challenge. We simulated the binding interactions and free energy of binding of nine protease inhibitors (PIs) with wild-type and various mutant proteases by performing GBSA simulations in which each PI's partial charge was determined by quantum mechanics (QM) and the partial charge accounts for the polarization induced by the protease environment. We employed a hybrid solvation model that retains selected explicit water molecules in the protein with surface-generalized Born (SGB) implicit solvent. We examined the correlation of the free energy with the antiviral potency of PIs with regard to amino acid substitutions in protease. The GBSA free energy thus simulated showed strong correlations (r > 0.75) with antiviral IC(50) values of PIs when amino acid substitutions were present in the protease active site. We also simulated the binding free energy of PIs with P2-bis-tetrahydrofuranylurethane (bis-THF) or related cores, utilizing a bis-THF-containing protease crystal structure as a template. The free energy showed a strong correlation (r = 0.93) with experimentally determined anti-HIV-1 potency. The present data suggest that the presence of selected explicit water in protein and protein polarization-induced quantum charges for the inhibitor, compared to lack of explicit water and a static force-field-based charge model, can serve as an improved lead optimization tool and warrants further exploration.
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Affiliation(s)
- Debananda Das
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-1868, USA
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Kear JL, Blackburn ME, Veloro AM, Dunn BM, Fanucci GE. Subtype polymorphisms among HIV-1 protease variants confer altered flap conformations and flexibility. J Am Chem Soc 2010; 131:14650-1. [PMID: 19788299 DOI: 10.1021/ja907088a] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) protease plays a fundamental role in the maturation and life cycle of the retrovirus HIV-1, as it functions in regulating post-translational processing of the viral polyproteins gag and gag-pol; thus, it is a key target of AIDS antiviral therapy. Accessibility of substrate to the active site is mediated by two flaps, which must undergo a large conformational change from an open to a closed conformation during substrate binding and catalysis. The electron paramagnetic resonance (EPR) method of site-directed spin labeling (SDSL) with double electron-electron resonance (DEER) spectroscopy was utilized to monitor the conformations of the flaps in apo HIV-1 protease (HIV-1PR), subtypes B, C, and F, CRF01_A/E, and patient isolates V6 and MDR 769. The distance distribution profiles obtained from analysis of the dipolar modulated echo curves were reconstructed to yield a set of Gaussian-shaped populations, which provide an analysis of the flap conformations sampled. The relative percentages of each conformer population described as "tucked/curled", "closed", "semi-open", and "wide-open" were determined and compared for various constructs. The results and analyses show that sequence variations among subtypes, CRFs, and patient isolates of apo HIV-1PR alter the average flap conformation in a way that can be understood as inducing shifts in the relative populations, or conformational sampling, of the previously described four conformations for HIV-1PR.
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Affiliation(s)
- Jamie L Kear
- Department of Chemistry, P.O. Box 117200, University of Florida, Gainesville, Florida 32611-7200, USA
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Impact of amino acid variations in Gag and protease of HIV type 1 CRF01_AE strains on drug susceptibility of virus to protease inhibitors. J Acquir Immune Defic Syndr 2009; 52:320-8. [PMID: 19727001 DOI: 10.1097/qai.0b013e3181b4b18c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Protease (PR) inhibitors (PIs) were designed against subtype B virus of human immunodeficiency virus type 1 (HIV-1), but believed to retain its activity against most of the other subtypes. CRF01_AE PR (AE-PR) contains background mutations that are presumed to alter the drug susceptibility of PR. In addition, amino acid variations found in HIV-1 Gag potentially affect the drug susceptibility or catalytic efficiency of PR. METHODS We studied the impact of naturally occurring amino acid substitutions found in AE-PR and CRF01_AE Gag (AE-Gag) on the drug susceptibility of PR to 9 currently available PIs, using the pNL4-3-derived luciferase reporter virus containing AE-Gag and/or AE-PR genes derived from drug treatment-naïve, HIV-1-infected Thai patients. RESULTS Sequencing analysis revealed that several mutations were detected in deduced amino acid sequences of AE-PR and AE-Gag genes, as compared to these genes of pNL4-3. Drug susceptibility tests revealed that AE-PR showed a variety of susceptibilities to 9 PIs compared with pNL4-3 PR. In addition, AE-Gag significantly reduced the drug susceptibility of AE-PR and pNL4-3 PR. CONCLUSION Our results suggest that amino acid variations in AE-PR and AE-Gag play roles in determining the drug susceptibility of CRF01_AE viruses to PIs.
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Loizidou EZ, Zeinalipour-Yazdi CD, Christofides T, Kostrikis LG. Analysis of binding parameters of HIV-1 integrase inhibitors: correlates of drug inhibition and resistance. Bioorg Med Chem 2009; 17:4806-18. [PMID: 19450984 DOI: 10.1016/j.bmc.2009.04.058] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 04/07/2009] [Accepted: 04/09/2009] [Indexed: 12/19/2022]
Abstract
This study undertook an exploratory data analysis of the binding parameters of HIV-1 integrase inhibitors. The study group involved inhibitors in preclinical development from the diketo acid, pyrroloquinoline and naphthyridine carboxamide families and the most advanced inhibitors Raltegravir and Elvitegravir. Distinct differences were observed in the energetics of binding between the studied classes of inhibitors that also correlated with drug resistant patterns. Quantitative-property-activity-relationships correlated experimental IC(50) values to the binding energy and the logarithm of the partition coefficient between n-octanol and water (clogP). The approach followed here serves as an improved basis for the development of 'second generation' integrase inhibitors.
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Affiliation(s)
- Eriketi Z Loizidou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.
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Kandathil AJ, Joseph AP, Kannangai R, Srinivasan N, Abraham OC, Pulimood SA, Sridharan G. Structural basis of drug resistance by genetic variants of HIV type 1 clade c protease from India. AIDS Res Hum Retroviruses 2009; 25:511-9. [PMID: 19400736 DOI: 10.1089/aid.2008.0102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Using computer modeling of three-dimensional structures and structural information available on the crystal structures of HIV-1 protease, we investigated the structural effects of mutations, in treatment-naive and treatment-exposed individuals from India and postulated mechanisms of resistance in clade C variants. A large number of models (14) have been generated by computational mutation of the available crystal structures of drug bound proteases. Localized energy minimization was carried out in and around the sites of mutation in order to optimize the geometry of interactions present. Most of the mutations result in structural differences at the flap that favors the semiopen state of the enzyme. Some of the mutations were also found to confer resistance by affecting the geometry of the active site. The E35D mutation affects the flap structure in clade B strains and E35N and E35K mutation, seen in our modeled strains, have a more profound effect. Common polymorphisms at positions 36 and 63 in clade C also affected flap structure. Apart from a few other residues Gln-58, Asn-83, Asn-88, and Gln-92 and their interactions are important for the transition from the closed to the open state. Development of protease inhibitors by structure-based design requires investigation of mechanisms operative for clade C to improve the efficacy of therapy.
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Affiliation(s)
| | | | - Rajesh Kannangai
- Department of Clinical Virology, Christian Medical College, Vellore, India
| | | | | | | | - Gopalan Sridharan
- Department of Clinical Virology, Christian Medical College, Vellore, India
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Lapins M, Wikberg JES. Proteochemometric Modeling of Drug Resistance over the Mutational Space for Multiple HIV Protease Variants and Multiple Protease Inhibitors. J Chem Inf Model 2009; 49:1202-10. [DOI: 10.1021/ci800453k] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maris Lapins
- Department of Pharmaceutical Pharmacology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Jarl E. S. Wikberg
- Department of Pharmaceutical Pharmacology, Uppsala University, SE-751 24 Uppsala, Sweden
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