1
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Sharma S, Ali ME. How do the mutations in PfK13 protein promote anti-malarial drug resistance? J Biomol Struct Dyn 2023; 41:7329-7338. [PMID: 36153000 DOI: 10.1080/07391102.2022.2120539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/27/2022] [Indexed: 10/14/2022]
Abstract
Plasmodium falciparum develops resistance to artemisinin upon exposure to the anti-malarial drug. Various mutations in the Plasmodium falciparum Kelch13 (PfK13) protein such as Y493H, R539T, I543T and C580Y have been associated with anti-malarial drug resistance. These mutations impede the regular ubiquitination process that eventually invokes drug resistance. However, the relationship between the mutation and the mechanism of drug resistance has not yet been fully elucidated. The comparative protein dynamics are studied by performing the classical molecular dynamics (MD) simulations and subsequent analysis of the trajectories adopting root-mean-square fluctuations, the secondary-structure predictions and the dynamical cross-correlation matrix analysis tools. Here, we observed that the mutations in the Kelch-domain do not have any structural impact on the mutated site; however, it significantly alters the overall dynamics of the protein. The loop-region of the BTB-domain especially for Y493H and C580Y mutants is found to have the enhanced dynamical fluctuations. The enhanced fluctuations in the BTB-domain could affect the protein-protein (PfK13-Cullin) binding interactions in the ubiquitination process and eventually lead to anti-malarial drug resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shikha Sharma
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab, India
| | - Md Ehesan Ali
- Institute of Nano Science and Technology, Sector-81, Mohali, Punjab, India
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2
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Maschietto F, Morzan UN, Tofoleanu F, Gheeraert A, Chaudhuri A, Kyro GW, Nekrasov P, Brooks B, Loria JP, Rivalta I, Batista VS. Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase. Nat Commun 2023; 14:2239. [PMID: 37076500 PMCID: PMC10115891 DOI: 10.1038/s41467-023-37956-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 04/06/2023] [Indexed: 04/21/2023] Open
Abstract
Allosteric drugs have the potential to revolutionize biomedicine due to their enhanced selectivity and protection against overdosage. However, we need to better understand allosteric mechanisms in order to fully harness their potential in drug discovery. In this study, molecular dynamics simulations and nuclear magnetic resonance spectroscopy are used to investigate how increases in temperature affect allostery in imidazole glycerol phosphate synthase. Results demonstrate that temperature increase triggers a cascade of local amino acid-to-amino acid dynamics that remarkably resembles the allosteric activation that takes place upon effector binding. The differences in the allosteric response elicited by temperature increase as opposed to effector binding are conditional to the alterations of collective motions induced by either mode of activation. This work provides an atomistic picture of temperature-dependent allostery, which could be harnessed to more precisely control enzyme function.
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Affiliation(s)
- Federica Maschietto
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA.
| | - Uriel N Morzan
- International Center for Theoretical Physics, Strada Costiera 11, 34151, Trieste, Italy.
| | - Florentina Tofoleanu
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA
- Treeline Biosciences, 500 Arsenal Street, Watertown, MA, 02472, USA
| | - Aria Gheeraert
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, 69364, Lyon, France
- Dipartimento di Chimica Industriale "Toso Montanari", Alma Mater Studiorum, Università di Bologna, Bologna, Italy
| | - Apala Chaudhuri
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Gregory W Kyro
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA
| | - Peter Nekrasov
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA
| | - Bernard Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA
| | - J Patrick Loria
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
| | - Ivan Rivalta
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, 69364, Lyon, France.
- Dipartimento di Chimica Industriale "Toso Montanari", Alma Mater Studiorum, Università di Bologna, Bologna, Italy.
| | - Victor S Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT, 06520-8107, USA.
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3
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Dakshinamoorthy A, Asmita A, Senapati S. Comprehending the Structure, Dynamics, and Mechanism of Action of Drug-Resistant HIV Protease. ACS OMEGA 2023; 8:9748-9763. [PMID: 36969469 PMCID: PMC10034783 DOI: 10.1021/acsomega.2c08279] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/23/2023] [Indexed: 06/18/2023]
Abstract
Since the emergence of the Human Immunodeficiency Virus (HIV) in the 1980s, strategies to combat HIV-AIDS are continuously evolving. Among the many tested targets to tackle this virus, its protease enzyme (PR) was proven to be an attractive option that brought about numerous research publications and ten FDA-approved drugs to inhibit the PR activity. However, the drug-induced mutations in the enzyme made these small molecule inhibitors ineffective with prolonged usage. The research on HIV PR, therefore, remains a thrust area even today. Through this review, we reiterate the importance of understanding the various structural and functional components of HIV PR in redesigning the structure-based small molecule inhibitors. We also discuss at length the currently available FDA-approved drugs and how these drug molecules induced mutations in the enzyme structure. We then recapitulate the reported mechanisms on how these drug-resistant variants remain sufficiently active to cleave the natural substrates. We end with the future scope covering the recently proposed strategies that show promise to deal with the mutations.
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4
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Ahsan M, Pindi C, Senapati S. Mechanism of darunavir binding to monomeric HIV-1 protease: a step forward in the rational design of dimerization inhibitors. Phys Chem Chem Phys 2022; 24:7107-7120. [PMID: 35262154 DOI: 10.1039/d2cp00024e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HIV protease (HIVPR) is a key target in AIDS therapeutics. All ten FDA-approved drugs that compete with substrates in binding to this dimeric enzyme's active site have become ineffective due to the emergence of drug resistant mutants. Blocking the dimerization interface of HIVPR is thus being explored as an alternate strategy. The latest drug, darunavir (DRV), which exhibited a high genetic barrier to viral resistance, is said to have a dual mode of action - (i) binding to the dimeric active site, and (ii) preventing the dimerization by binding to the HIVPR monomer. Despite several reports on DRV complexation with dimeric HIVPR, the mode and mechanism of the binding of DRV to the HIVPR monomer are poorly understood. In this study, we utilized all-atomic MD simulations and umbrella sampling techniques to identify the best possible binding mode of DRV to the monomeric HIVPR and its mechanism of association. The results suggest that DRV binds between the active site and the flap of the monomer, and the flap plays a crucial role in directing the drug to bind and driving the other protein domains to undergo induced fit changes for stronger complexation. The obtained binding mode of DRV was validated by comparing with various mutational data from clinical isolates to reported in vitro mutations. The identified binding pose was also able to successfully reproduce the experimental Ki value in the picomolar range. The residue-level information extracted from this study could accelerate the structure-based drug designing approaches targeting HIVPR dimerization.
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Affiliation(s)
- Mohd Ahsan
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
| | - Chinmai Pindi
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
| | - Sanjib Senapati
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India.
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5
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Combining Molecular Dynamic Information and an Aspherical-Atom Data Bank in the Evaluation of the Electrostatic Interaction Energy in Multimeric Protein-Ligand Complex: A Case Study for HIV-1 Protease. Molecules 2021; 26:molecules26133872. [PMID: 34202892 PMCID: PMC8270314 DOI: 10.3390/molecules26133872] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/19/2021] [Accepted: 06/22/2021] [Indexed: 11/23/2022] Open
Abstract
Computational analysis of protein–ligand interactions is of crucial importance for drug discovery. Assessment of ligand binding energy allows us to have a glimpse of the potential of a small organic molecule to be a ligand to the binding site of a protein target. Available scoring functions, such as in docking programs, all rely on equations that sum each type of protein–ligand interactions in order to predict the binding affinity. Most of the scoring functions consider electrostatic interactions involving the protein and the ligand. Electrostatic interactions constitute one of the most important part of total interactions between macromolecules. Unlike dispersion forces, they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In this study, complexes of HIV-1 protease with inhibitor molecules (JE-2147 and darunavir) were analyzed by using charge densities from the transferable aspherical-atom University at Buffalo Databank (UBDB). Moreover, we analyzed the electrostatic interaction energy for an ensemble of structures, using molecular dynamic simulations to highlight the main features of electrostatic interactions important for binding affinity.
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6
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Gupta S, Balasubramanian S, Senapati S. Understanding the mechanism of HIV-1 protease inhibition by monoclonal antibodies. J Mol Graph Model 2021; 103:107826. [PMID: 33418466 DOI: 10.1016/j.jmgm.2020.107826] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/10/2020] [Accepted: 12/14/2020] [Indexed: 01/06/2023]
Abstract
HIV-1 protease is an essential enzyme in the life cycle of human immunodeficiency virus (HIV) and hence is one of the most important targets for antiviral drug design. Although there are ten FDA approved drugs against HIV protease (PR), their long term usage elicits mutations leading to drug resistance. As a result, novel therapeutic approaches are being explored including synthetic antibodies. Recently, a murine monoclonal antibody, mAB1696 (mAB) was reported to inhibit PR by preventing dimerization. Crystallographic data could reveal only six protease residues that interact with mAB. The present study employs a range of computational techniques, starting from protein-protein docking to all-atomic molecular dynamics simulations to generate plausible 3D structures of PR-mAB complex. Results show that mAB interacts very strongly with several PR dimer interface residues, such as Gln7, Arg8 (N-terminal), Cys95, Leu97 (C-terminal), Thr26, Gly27 (active site), Gly49, Ile50 (flap), apart from its interactions with the PR epitope region, Pro1-Trp6 (N-terminal). These observations support the hypothesis that binding of mAB prevents the dimerization of PR. The interactions and binding conformations identified in this study could form the basis for designing allosteric inhibitors preventing the dimerization of HIV-1 Protease.
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Affiliation(s)
- Suchetana Gupta
- BJM School of Biosciences and Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Sangeetha Balasubramanian
- BJM School of Biosciences and Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Sanjib Senapati
- BJM School of Biosciences and Department of Biotechnology, Indian Institute of Technology Madras, Chennai, 600036, India.
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7
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Roy P, Roy S, Sengupta N. Disulfide Reduction Allosterically Destabilizes the β-Ladder Subdomain Assembly within the NS1 Dimer of ZIKV. Biophys J 2020; 119:1525-1537. [PMID: 32946768 DOI: 10.1016/j.bpj.2020.08.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/13/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
The Zika virus (ZIKV) was responsible for a recent debilitating epidemic that till date has no cure. A potential way to reduce ZIKV virulence is to limit the action of the nonstructural proteins involved in its viral replication. One such protein, NS1, encoded as a monomer by the viral genome, plays a major role via symmetric oligomerization. We examine the homodimeric structure of the dominant β-ladder segment of NS1 with extensive all atom molecular dynamics. We find it stably bounded by two spatially separated interaction clusters (C1 and C2) with significant differences in the nature of their interactions. Four pairs of distal, intramonomeric disulfide bonds are found to be coupled to the stability, local structure, and wettability of the interfacial region. Symmetric reduction of the intramonomeric disulfides triggers marked dynamical heterogeneity, interfacial wettability, and asymmetric salt-bridging propensity. Harnessing the model-free Lipari-Szabo based formalism for estimation of conformational entropy (Sconf), we find clear signatures of heterogeneity in the monomeric conformational entropies. The observed asymmetry, very small in the unperturbed state, expands significantly in the reduced states. This allosteric effect is most noticeable in the electrostatically bound C2 cluster that underlies the greatest stability in the unperturbed state. Allosteric induction of conformational and thermodynamic asymmetry is expected to affect the pathways leading to symmetric higher-ordered oligomerization, and thereby affect crucial replication pathways.
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Affiliation(s)
- Priti Roy
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Subhajit Roy
- Centre for Excellence in Basic Sciences (CBS), University of Mumbai, Vidyanagari, Mumbai, India
| | - Neelanjana Sengupta
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India.
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8
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Ahsan M, Pindi C, Senapati S. Electrostatics Plays a Crucial Role in HIV-1 Protease Substrate Binding, Drugs Fail to Take Advantage. Biochemistry 2020; 59:3316-3331. [PMID: 32822154 DOI: 10.1021/acs.biochem.0c00341] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV-1 protease (HIVPR) is an important drug target for combating AIDS. This enzyme is an aspartyl protease that is functionally active in its dimeric form. Nuclear magnetic resonance reports have convincingly shown that a pseudosymmetry exists at the HIVPR active site, where only one of the two aspartates remains protonated over the pH range of 2.5-7.0. To date, all HIVPR-targeted drug design strategies focused on maximizing the size-shape complementarity and van der Waals interactions of the small molecule drugs with the deprotonated, symmetric active site envelope of crystallized HIVPR. However, these strategies were ineffective with the emergence of drug resistant protease variants, primarily due to the steric clashes at the active site. In this study, we traced a specificity in the substrate binding motif that emerges primarily from the asymmetrical electrostatic potential present in the protease active site due to the uneven protonation. Our detailed results from atomistic molecular dynamics simulations show that while such a specific mode of substrate binding involves significant electrostatic interactions, none of the existing drugs or inhibitors could utilize this electrostatic hot spot. As the electrostatic is long-range interaction, it can provide sufficient binding strength without the necessity of increasing the bulkiness of the inhibitors. We propose that introducing the electrostatic component along with optimal fitting at the binding pocket could pave the way for promising designs that might be more effective against both wild type and HIVPR resistant variants.
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Affiliation(s)
- Mohd Ahsan
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Chinmai Pindi
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Sanjib Senapati
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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9
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Molecular Basis of Differential Stability and Temperature Sensitivity of ZIKA versus Dengue Virus Protein Shells. Sci Rep 2020; 10:8411. [PMID: 32439929 PMCID: PMC7242387 DOI: 10.1038/s41598-020-65288-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/22/2020] [Indexed: 11/18/2022] Open
Abstract
Rapid spread of ZIKA virus (ZIKV) and its association with severe birth defects have raised worldwide concern. Recent studies have shown that ZIKV retains its infectivity and remains structurally stable at temperatures up to 40 °C, unlike dengue and other flaviviruses. In spite of recent cryo-EM structures that showed similar architecture of ZIKA and dengue virus (DENV) E protein shells, little is known that makes ZIKV so temperature insensitive. Here, we attempt to unravel the molecular basis of greater thermal stability of ZIKV over DENV2 by executing atomistic molecular dynamics (MD) simulations on the viral E protein shells at 37 °C. Our results suggest that ZIKA E protein shell retains its structural integrity through stronger inter-raft communications facilitated by a series of electrostatic and H-bonding interactions among multiple inter-raft residues. In comparison, the DENV2 E protein shell surface was loosly packed that exhibited holes at all 3-fold vertices, in close agreement with another EM structure solved at 37 °C. The residue-level information obtained from our study could pave way for designing small molecule inhibitors and specific antibodies to inhibit ZIKV E protein assembly and membrane fusion.
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10
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The Determination of HIV-1 RT Mutation Rate, Its Possible Allosteric Effects, and Its Implications on Drug Resistance. Viruses 2020; 12:v12030297. [PMID: 32182845 PMCID: PMC7150816 DOI: 10.3390/v12030297] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 12/31/2022] Open
Abstract
The high mutation rate of the human immunodeficiency virus type 1 (HIV-1) plays a major role in treatment resistance, from the development of vaccines to therapeutic drugs. In addressing the crux of the issue, various attempts to estimate the mutation rate of HIV-1 resulted in a large range of 10−5–10−3 errors/bp/cycle due to the use of different types of investigation methods. In this review, we discuss the different assay methods, their findings on the mutation rates of HIV-1 and how the locations of mutations can be further analyzed for their allosteric effects to allow for new inhibitor designs. Given that HIV is one of the fastest mutating viruses, it serves as a good model for the comprehensive study of viral mutations that can give rise to a more horizontal understanding towards overall viral drug resistance as well as emerging viral diseases.
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11
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Sk MF, Roy R, Kar P. Exploring the potency of currently used drugs against HIV-1 protease of subtype D variant by using multiscale simulations. J Biomol Struct Dyn 2020; 39:988-1003. [PMID: 32000612 DOI: 10.1080/07391102.2020.1724196] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Acquired immune deficiency syndrome (AIDS) is caused by the human immunodeficiency virus (HIV), type 1 and 2. Further, the diversity in HIV-1 has given rise to many serotypes and recombinant strains. The currently used protease inhibitors have been developed for subtype B, although non-B subtype strains account for ∼ 90% of the global HIV infections. Subtype D is spreading rapidly and infecting a large population in North Africa and the Middle East. In the current study, molecular dynamics simulations in conjunction with the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) scheme was used to investigate the potency of four drugs, namely atazanavir (ATV), darunavir (DRV), lopinavir (LPV) and tipranavir (TPV) against the subtype D variant. Our calculations predicted that the potency of the inhibitors decreased in the order TPV > ATV > DRV > LPV. TPV was found to be the most potent against subtype D due to an increase in van der Waals and electrostatic interactions and reduction in the desolvation energy compared to other inhibitors. This result is further supported by the hydrogen bond interactions between inhibitors and protease. Furthermore, our analyses suggested that the binding of TPV induced a more closed conformation of the flap compared to apo or other complexes. It was observed that TPV/PRD has a lower cavity volume relative to the other three complexes leading to a tighter binding. The open conformation of the flap was observed for LPV/PRD. We expect that this study might be useful for designing more potent inhibitors against HIV-1 subtype D. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Md Fulbabu Sk
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol Campus, Indore, Madhya Pradesh, India
| | - Rajarshi Roy
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol Campus, Indore, Madhya Pradesh, India
| | - Parimal Kar
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol Campus, Indore, Madhya Pradesh, India
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12
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Su CTT, Koh DWS, Gan SKE. Reviewing HIV-1 Gag Mutations in Protease Inhibitors Resistance: Insights for Possible Novel Gag Inhibitor Designs. Molecules 2019; 24:molecules24183243. [PMID: 31489889 PMCID: PMC6767625 DOI: 10.3390/molecules24183243] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 12/31/2022] Open
Abstract
HIV protease inhibitors against the viral protease are often hampered by drug resistance mutations in protease and in the viral substrate Gag. To overcome this drug resistance and inhibit viral maturation, targeting Gag alongside protease rather than targeting protease alone may be more efficient. In order to successfully inhibit Gag, understanding of its drug resistance mutations and the elicited structural changes on protease binding needs to be investigated. While mutations on Gag have already been mapped to protease inhibitor resistance, there remain many mutations, particularly the non-cleavage mutations, that are not characterized. Through structural studies to unravel how Gag mutations contributes to protease drug resistance synergistically, it is thus possible to glean insights to design novel Gag inhibitors. In this review, we discuss the structural role of both novel and previously reported Gag mutations in PI resistance, and how new Gag inhibitors can be designed.
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Affiliation(s)
- Chinh Tran-To Su
- Antibody & Product Development Lab, Bioinformatics Institute, A*STAR, Singapore 138671, Singapore
| | - Darius Wen-Shuo Koh
- Antibody & Product Development Lab, Bioinformatics Institute, A*STAR, Singapore 138671, Singapore
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, Bioinformatics Institute, A*STAR, Singapore 138671, Singapore.
- p53 Laboratory, A*STAR, Singapore 138648, Singapore.
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13
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Negre CFA, Morzan UN, Hendrickson HP, Pal R, Lisi GP, Loria JP, Rivalta I, Ho J, Batista VS. Eigenvector centrality for characterization of protein allosteric pathways. Proc Natl Acad Sci U S A 2018; 115:E12201-E12208. [PMID: 30530700 PMCID: PMC6310864 DOI: 10.1073/pnas.1810452115] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Determining the principal energy-transfer pathways responsible for allosteric communication in biomolecules remains challenging, partially due to the intrinsic complexity of the systems and the lack of effective characterization methods. In this work, we introduce the eigenvector centrality metric based on mutual information to elucidate allosteric mechanisms that regulate enzymatic activity. Moreover, we propose a strategy to characterize the range of correlations that underlie the allosteric processes. We use the V-type allosteric enzyme imidazole glycerol phosphate synthase (IGPS) to test the proposed methodology. The eigenvector centrality method identifies key amino acid residues of IGPS with high susceptibility to effector binding. The findings are validated by solution NMR measurements yielding important biological insights, including direct experimental evidence for interdomain motion, the central role played by helix h[Formula: see text], and the short-range nature of correlations responsible for the allosteric mechanism. Beyond insights on IGPS allosteric pathways and the nature of residues that could be targeted by therapeutic drugs or site-directed mutagenesis, the reported findings demonstrate the eigenvector centrality analysis as a general cost-effective methodology to gain fundamental understanding of allosteric mechanisms at the molecular level.
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Affiliation(s)
- Christian F A Negre
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545;
- Department of Chemistry, Yale University, New Haven, CT 06520-8107
- Energy Sciences Institute, Yale University, West Haven, CT 06516-7394
| | - Uriel N Morzan
- Department of Chemistry, Yale University, New Haven, CT 06520-8107;
- Energy Sciences Institute, Yale University, West Haven, CT 06516-7394
| | - Heidi P Hendrickson
- Department of Chemistry, Yale University, New Haven, CT 06520-8107
- Energy Sciences Institute, Yale University, West Haven, CT 06516-7394
- Department of Chemistry, Lafayette College, Easton, PA 18042
| | - Rhitankar Pal
- Department of Chemistry, Yale University, New Haven, CT 06520-8107
- Energy Sciences Institute, Yale University, West Haven, CT 06516-7394
| | - George P Lisi
- Department of Chemistry, Yale University, New Haven, CT 06520-8107
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903
| | - J Patrick Loria
- Department of Chemistry, Yale University, New Haven, CT 06520-8107
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520
| | - Ivan Rivalta
- Université de Lyon, École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, Lyon, France;
- Dipartimento di Chimica Industriale "Toso Montanari," Università degli Studi di Bologna, Viale del Risorgimento, 4I-40136 Bologna, Italy
| | - Junming Ho
- School of Chemistry, University of New South Wales, Sydney NSW 2052, Australia
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT 06520-8107;
- Energy Sciences Institute, Yale University, West Haven, CT 06516-7394
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14
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Ragland DA, Whitfield TW, Lee SK, Swanstrom R, Zeldovich KB, Kurt-Yilmaz N, Schiffer CA. Elucidating the Interdependence of Drug Resistance from Combinations of Mutations. J Chem Theory Comput 2017; 13:5671-5682. [PMID: 28915040 DOI: 10.1021/acs.jctc.7b00601] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV-1 protease is responsible for the cleavage of 12 nonhomologous sites within the Gag and Gag-Pro-Pol polyproteins in the viral genome. Under the selective pressure of protease inhibition, the virus evolves mutations within (primary) and outside of (secondary) the active site, allowing the protease to process substrates while simultaneously countering inhibition. The primary protease mutations impede inhibitor binding directly, while the secondary mutations are considered accessory mutations that compensate for a loss in fitness. However, the role of secondary mutations in conferring drug resistance remains a largely unresolved topic. We have shown previously that mutations distal to the active site are able to perturb binding of darunavir (DRV) via the protein's internal hydrogen-bonding network. In this study, we show that mutations distal to the active site, regardless of context, can play an interdependent role in drug resistance. Applying eigenvalue decomposition to collections of hydrogen bonding and van der Waals interactions from a series of molecular dynamics simulations of 15 diverse HIV-1 protease variants, we identify sites in the protease where amino acid substitutions lead to perturbations in nonbonded interactions with DRV and/or the hydrogen-bonding network of the protease itself. While primary mutations are known to drive resistance in HIV-1 protease, these findings delineate the significant contributions of accessory mutations to resistance. Identifying the variable positions in the protease that have the greatest impact on drug resistance may aid in future structure-based design of inhibitors.
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Affiliation(s)
| | | | - Sook-Kyung Lee
- Department of Biochemistry and Biophysics, and the UNC Center for AIDS Research, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
| | - Ronald Swanstrom
- Department of Biochemistry and Biophysics, and the UNC Center for AIDS Research, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States
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15
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Evolution of inhibitor-resistant natural mutant forms of HIV-1 protease probed by pre-steady state kinetic analysis. Biochimie 2017; 142:125-134. [PMID: 28843613 DOI: 10.1016/j.biochi.2017.08.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/21/2017] [Indexed: 11/23/2022]
Abstract
Pre-steady state kinetic analysis of mechanistic features of substrate binding and processing is crucial for insight into the evolution of inhibitor-resistant forms of HIV-1 protease. These data may provide a correct vector for rational drug design assuming possible intrinsic dynamic effects. These data should also give some clues to the molecular mechanism of protease action and resistance to inhibitors. Here we report pre-steady state kinetics of the interaction of wild type or mutant forms of HIV-1 protease with a FRET-labeled peptide. The three-stage "minimal" kinetic scheme with first and second reversible steps of substrate binding and with following irreversible peptide cleavage step adequately described experimental data. For the first time, a set of "elementary" kinetic parameters of wild type HIV-1 protease and its natural mutant inhibitor-resistant forms MDR-HM, ANAM-11 and prDRV4 were compared. Inhibitors of the first and second generation were used to estimate the inhibitory effects on HIV-1 protease activity. The resulting set of kinetic data supported that the mutant forms are kinetically unaffected by inhibitors of the first generation, proving their functional resistance to these compounds. The second generation inhibitor darunavir inhibited mutant forms MDR-HM and ANAM-11, but was ineffective against prDRV4. Our kinetic data revealed that these inhibitors induced different conformational changes in the enzyme and, thereby they have different mode of binding in the enzyme active site. These data confirmed hypothesis that the driving force of the inhibitor-resistance evolution is disruption of enzyme-inhibitor complex by changing of the contact network in the inhibitor binding site.
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16
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Appadurai R, Senapati S. How Mutations Can Resist Drug Binding yet Keep HIV-1 Protease Functional. Biochemistry 2017; 56:2907-2920. [DOI: 10.1021/acs.biochem.7b00139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Rajeswari Appadurai
- Department of Biotechnology,
Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, India
| | - Sanjib Senapati
- Department of Biotechnology,
Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600 036, India
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17
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Tang B, Li B, Li B, Li Z, Qin J, Zhou X, Qiu Y, Wu Z, Fang M. The effect of V155M mutation on the complex of hSTING and 2′3′-cGAMP: an in silico study case. RSC Adv 2017. [DOI: 10.1039/c7ra05959k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
All atoms MD simulations for the complexes of WT/V155M hSTING and 2′3′-cGAMP were performed to study the effect of the V155M mutation on SAVI disease at the molecular level.
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Affiliation(s)
- Bowen Tang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- School of Pharmaceutical Sciences
- Xiamen University
- Xiamen 361000
- China
| | - Baicun Li
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- School of Pharmaceutical Sciences
- Xiamen University
- Xiamen 361000
- China
| | - Boqun Li
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- School of Pharmaceutical Sciences
- Xiamen University
- Xiamen 361000
- China
| | - Zan Li
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- School of Pharmaceutical Sciences
- Xiamen University
- Xiamen 361000
- China
| | - Jingbo Qin
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- School of Pharmaceutical Sciences
- Xiamen University
- Xiamen 361000
- China
| | - Xiaoxiao Zhou
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- School of Pharmaceutical Sciences
- Xiamen University
- Xiamen 361000
- China
| | - Yingkun Qiu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- School of Pharmaceutical Sciences
- Xiamen University
- Xiamen 361000
- China
| | - Zhen Wu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- School of Pharmaceutical Sciences
- Xiamen University
- Xiamen 361000
- China
| | - Meijuan Fang
- Fujian Provincial Key Laboratory of Innovative Drug Target Research
- School of Pharmaceutical Sciences
- Xiamen University
- Xiamen 361000
- China
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18
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Su CTT, Ling WL, Lua WH, Haw YX, Gan SKE. Structural analyses of 2015-updated drug-resistant mutations in HIV-1 protease: an implication of protease inhibitor cross-resistance. BMC Bioinformatics 2016; 17:500. [PMID: 28155724 PMCID: PMC5259968 DOI: 10.1186/s12859-016-1372-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Background Strategies to control HIV for improving the quality of patient lives have been aided by the Highly Active Anti-Retroviral Therapy (HAART), which consists of a cocktail of inhibitors targeting key viral enzymes. Numerous new drugs have been developed over the past few decades but viral resistances to these drugs in the targeted viral enzymes are increasingly reported. Nonetheless the acquired mutations often reduce viral fitness and infectivity. Viral compensatory secondary-line mutations mitigate this loss of fitness, equipping the virus with a broad spectrum of resistance against these drugs. While structural understanding of the viral protease and its drug resistance mutations have been well established, the interconnectivity and development of structural cross-resistance remain unclear. This paper reports the structural analyses of recent clinical mutations on the drug cross-resistance effects from various protease and protease inhibitors (PIs) complexes. Methods Using the 2015 updated clinical HIV protease mutations, we constructed a structure-based correlation network and a minimum-spanning tree (MST) based on the following features: (i) topology of the PI-binding pocket, (ii) allosteric effects of the mutations, and (iii) protease structural stability. Results and conclusion Analyis of the network and the MST of dominant mutations conferring resistance to the seven PIs (Atazanavir-ATV, Darunavir-DRV, Indinavir-IDV, Lopinavir-LPV, Nelfinavir-NFV, Saquinavir-SQV, and Tipranavir-TPV) showed that cross-resistance can develop easily across NFV, SQV, LPV, IDV, and DRV, but not for ATV or TPV. Through estimation of the changes in vibrational entropies caused by each reported mutation, some secondary mutations were found to destabilize protease structure. Our findings provide an insight into the mechanism of PI cross-resistance and may also be useful in guiding the selection of PI in clinical treatment to delay the onset of cross drug resistance. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1372-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chinh Tran-To Su
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore.
| | - Wei-Li Ling
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore
| | - Wai-Heng Lua
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore
| | - Yu-Xuan Haw
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore
| | - Samuel Ken-En Gan
- Bioinformatics Institute, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore. .,p53 Laboratory, Agency for Science, Technology, and Research (A*STAR), Singapore, 138648, Singapore.
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19
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Pethe MA, Rubenstein AB, Khare SD. Large-Scale Structure-Based Prediction and Identification of Novel Protease Substrates Using Computational Protein Design. J Mol Biol 2016; 429:220-236. [PMID: 27932294 DOI: 10.1016/j.jmb.2016.11.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/23/2016] [Accepted: 11/30/2016] [Indexed: 12/16/2022]
Abstract
Characterizing the substrate specificity of protease enzymes is critical for illuminating the molecular basis of their diverse and complex roles in a wide array of biological processes. Rapid and accurate prediction of their extended substrate specificity would also aid in the design of custom proteases capable of selectively and controllably cleaving biotechnologically or therapeutically relevant targets. However, current in silico approaches for protease specificity prediction, rely on, and are therefore limited by, machine learning of sequence patterns in known experimental data. Here, we describe a general approach for predicting peptidase substrates de novo using protein structure modeling and biophysical evaluation of enzyme-substrate complexes. We construct atomic resolution models of thousands of candidate substrate-enzyme complexes for each of five model proteases belonging to the four major protease mechanistic classes-serine, cysteine, aspartyl, and metallo-proteases-and develop a discriminatory scoring function using enzyme design modules from Rosetta and AMBER's MMPBSA. We rank putative substrates based on calculated interaction energy with a modeled near-attack conformation of the enzyme active site. We show that the energetic patterns obtained from these simulations can be used to robustly rank and classify known cleaved and uncleaved peptides and that these structural-energetic patterns have greater discriminatory power compared to purely sequence-based statistical inference. Combining sequence and energetic patterns using machine-learning algorithms further improves classification performance, and analysis of structural models provides physical insight into the structural basis for the observed specificities. We further tested the predictive capability of the model by designing and experimentally characterizing the cleavage of four novel substrate motifs for the hepatitis C virus NS3/4 protease using an in vivo assay. The presented structure-based approach is generalizable to other protease enzymes with known or modeled structures, and complements existing experimental methods for specificity determination.
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Affiliation(s)
- Manasi A Pethe
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Aliza B Rubenstein
- Computational Biology & Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Computational Biology & Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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20
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O'Rourke KF, Gorman SD, Boehr DD. Biophysical and computational methods to analyze amino acid interaction networks in proteins. Comput Struct Biotechnol J 2016; 14:245-51. [PMID: 27441044 PMCID: PMC4939391 DOI: 10.1016/j.csbj.2016.06.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/04/2016] [Accepted: 06/13/2016] [Indexed: 12/20/2022] Open
Abstract
Globular proteins are held together by interacting networks of amino acid residues. A number of different structural and computational methods have been developed to interrogate these amino acid networks. In this review, we describe some of these methods, including analyses of X-ray crystallographic data and structures, computer simulations, NMR data, and covariation among protein sequences, and indicate the critical insights that such methods provide into protein function. This information can be leveraged towards the design of new allosteric drugs, and the engineering of new protein function and protein regulation strategies.
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Affiliation(s)
- Kathleen F O'Rourke
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Scott D Gorman
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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