1
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Kovalevsky A, Aniana A, Coates L, Bonnesen PV, Nashed NT, Louis JM. Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors. J Biol Chem 2023:104886. [PMID: 37271339 PMCID: PMC10238122 DOI: 10.1016/j.jbc.2023.104886] [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: 03/21/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/06/2023] Open
Abstract
The effect of mutations of the catalytic dyad residues of SARS-CoV-2 main protease (MProWT) on the thermodynamics of binding of covalent inhibitors comprising nitrile [nirmatrelvir (NMV), NBH2], aldehyde (GC373) and ketone (BBH1) warheads to MPro is examined together with room temperature X-ray crystallography. When lacking the nucleophilic C145, NMV binding is ∼400-fold weaker corresponding to 3.5 kcal/mol and 13.3 °C decreases in free energy (ΔG) and thermal stability (Tm), respectively, relative to MProWT. The H41A mutation results in a 20-fold increase in the dissociation constant (Kd), and 1.7 kcal/mol and 1.4 °C decreases in ΔG and Tm, respectively. Increasing the pH from 7.2 to 8.2 enhances NMV binding to MProH41A, whereas no significant change is observed in binding to MProWT. Structures of the four inhibitor complexes with MPro1-304/C145A show that the active site geometries of the complexes are nearly identical to that of MProWT with the nucleophilic sulfur of C145 positioned to react with the nitrile or the carbonyl carbon. These results support a two-step mechanism for the formation of the covalent complex involving an initial non-covalent binding followed by a nucleophilic attack by the thiolate anion of C145 on the warhead carbon. Noncovalent inhibitor ensitrelvir (ESV) exhibits a binding affinity to MProWT that is similar to NMV but differs in its thermodynamic signature from NMV. The binding of ESV to MProC145A also results in a significant, but smaller, increase in Kd and decrease in ΔG and Tm, relative to NMV.
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Affiliation(s)
- Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA.
| | - Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN, 37831, USA
| | - Peter V Bonnesen
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Nashaat T Nashed
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892-0520, USA.
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2
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Unmasking the Conformational Stability and Inhibitor Binding to SARS-CoV-2 Main Protease Active Site Mutants and Miniprecursor. J Mol Biol 2022; 434:167876. [PMID: 36334779 PMCID: PMC9628131 DOI: 10.1016/j.jmb.2022.167876] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/05/2022]
Abstract
We recently demonstrated that inhibitor binding reorganizes the oxyanion loop of a monomeric catalytic domain of SARS CoV-2 main protease (MPro) from an unwound (E) to a wound (active, E*) conformation, independent of dimerization. Here we assess the effect of the flanking N-terminal residues, to imitate the MPro precursor prior to its autoprocessing, on conformational equilibria rendering stability and inhibitor binding. Thermal denaturation (Tm) of C145A mutant, unlike H41A, increases by 6.8 °C, relative to wild-type mature dimer. An inactivating H41A mutation to maintain a miniprecursor containing TSAVL[Q or E] of the flanking nsp4 sequence in an intact form [(-6)MProH41A and (-6*)MProH41A, respectively], and its corresponding mature MProH41A were systematically examined. While the H41A mutation exerts negligible effect on Tm and dimer dissociation constant (Kdimer) of MProH41A, relative to the wild type MPro, both miniprecursors show a 4-5 °C decrease in Tm and > 85-fold increase in Kdimer as compared to MProH41A. The Kd for the binding of the covalent inhibitor GC373 to (-6*)MProH41A increases ∼12-fold, relative to MProH41A, concomitant with its dimerization. While the inhibitor-free dimer exhibits a state in transit from E to E* with a conformational asymmetry of the protomers' oxyanion loops and helical domains, inhibitor binding restores the asymmetry to mature-like oxyanion loop conformations (E*) but not of the helical domains. Disorder of the terminal residues 1-2 and 302-306 observed in both structures suggest that N-terminal autoprocessing is tightly coupled to the E-E* equilibrium and stable dimer formation.
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3
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Viral proteases as therapeutic targets. Mol Aspects Med 2022; 88:101159. [PMID: 36459838 PMCID: PMC9706241 DOI: 10.1016/j.mam.2022.101159] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Some medically important viruses-including retroviruses, flaviviruses, coronaviruses, and herpesviruses-code for a protease, which is indispensable for viral maturation and pathogenesis. Viral protease inhibitors have become an important class of antiviral drugs. Development of the first-in-class viral protease inhibitor saquinavir, which targets HIV protease, started a new era in the treatment of chronic viral diseases. Combining several drugs that target different steps of the viral life cycle enables use of lower doses of individual drugs (and thereby reduction of potential side effects, which frequently occur during long term therapy) and reduces drug-resistance development. Currently, several HIV and HCV protease inhibitors are routinely used in clinical practice. In addition, a drug including an inhibitor of SARS-CoV-2 main protease, nirmatrelvir (co-administered with a pharmacokinetic booster ritonavir as Paxlovid®), was recently authorized for emergency use. This review summarizes the basic features of the proteases of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and SARS-CoV-2 and discusses the properties of their inhibitors in clinical use, as well as development of compounds in the pipeline.
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4
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Harrison JJEK, Passos DO, Bruhn JF, Bauman JD, Tuberty L, DeStefano JJ, Ruiz FX, Lyumkis D, Arnold E. Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation. SCIENCE ADVANCES 2022; 8:eabn9874. [PMID: 35857464 PMCID: PMC9258950 DOI: 10.1126/sciadv.abn9874] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Key proteins of retroviruses and other RNA viruses are translated and subsequently processed from polyprotein precursors by the viral protease (PR). Processing of the HIV Gag-Pol polyprotein yields the HIV structural proteins and enzymes. Structures of the mature enzymes PR, reverse transcriptase (RT), and integrase (IN) aided understanding of catalysis and design of antiretrovirals, but knowledge of the Pol precursor architecture and function before PR cleavage is limited. We developed a system to produce stable HIV-1 Pol and determined its cryo-electron microscopy structure. RT in Pol has a similar arrangement to the mature RT heterodimer, and its dimerization may draw together two PR monomers to activate proteolytic processing. HIV-1 thus may leverage the dimerization interfaces in Pol to regulate assembly and maturation of polyprotein precursors.
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Affiliation(s)
- Jerry Joe E. K. Harrison
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
- Department of Chemistry, University of Ghana, Legon, Ghana
| | | | - Jessica F. Bruhn
- The Salk Institute for Biological Studies, La Jolla, CA, USA
- NanoImaging Services, San Diego, CA, USA
| | - Joseph D. Bauman
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Lynda Tuberty
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Jeffrey J. DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA
| | - Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
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5
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Hu S, Ma L, Dong B, Shan Q, Zhou J, Zhang G, Wang M, Cen S, Zhu M, Wang J, Wang Y. A kind of HIV-1 protease inhibitors containing phenols with antiviral activity against DRV-resistant variants. Bioorg Med Chem 2022; 64:116760. [PMID: 35483138 DOI: 10.1016/j.bmc.2022.116760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 11/30/2022]
Abstract
Based upon the preliminary design of enhancing genetic barrier to drug-resistant viral mutants by maximizing hydrogen-bonding or other van der Waals contacts, we have designed, synthesized and biologically evaluated a new class of HIV-1 protease inhibitors with phenol derived P2 ligands and nitro or halogens in P2' ligands. Results indicate that a majority of inhibitors exhibit robust enzyme inhibitory with IC50 values in picomolar or single digit nanomolar ranges. Among which, compound 17d displays potency with IC50 value of 21 pM and high protease selectivity. Of note, 17d exhibits greater antiviral activity against the DRV-resistant variant than the efficacy against the wild type virus. Furthermore, the molecular modeling studies demonstrate important interactions between 17d and the active sites of both the wild-type and DRV-resistant HIV-1 protease, as well as furnish insights for further optimization of new inhibitors.
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Affiliation(s)
- Shangjiu Hu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Ling Ma
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Biao Dong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Qi Shan
- Tianjin Institute of Pharmaceutical Research, Tianjin 300462, China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua 321004, China
| | - Guoning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Minghua Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Mei Zhu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
| | - Juxian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
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6
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Precursors of Viral Proteases as Distinct Drug Targets. Viruses 2021; 13:v13101981. [PMID: 34696411 PMCID: PMC8537868 DOI: 10.3390/v13101981] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022] Open
Abstract
Viral proteases are indispensable for successful virion maturation, thus making them a prominent drug target. Their enzyme activity is tightly spatiotemporally regulated by expression in the precursor form with little or no activity, followed by activation via autoprocessing. These cleavage events are frequently triggered upon transportation to a specific compartment inside the host cell. Typically, precursor oligomerization or the presence of a co-factor is needed for activation. A detailed understanding of these mechanisms will allow ligands with non-canonical mechanisms of action to be designed, which would specifically modulate the initial irreversible steps of viral protease autoactivation. Binding sites exclusive to the precursor, including binding sites beyond the protease domain, can be exploited. Both inhibition and up-regulation of the proteolytic activity of viral proteases can be detrimental for the virus. All these possibilities are discussed using examples of medically relevant viruses including herpesviruses, adenoviruses, retroviruses, picornaviruses, caliciviruses, togaviruses, flaviviruses, and coronaviruses.
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7
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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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8
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Weber IT, Wang YF, Harrison RW. HIV Protease: Historical Perspective and Current Research. Viruses 2021; 13:v13050839. [PMID: 34066370 PMCID: PMC8148205 DOI: 10.3390/v13050839] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/01/2021] [Accepted: 05/03/2021] [Indexed: 12/15/2022] Open
Abstract
The retroviral protease of human immunodeficiency virus (HIV) is an excellent target for antiviral inhibitors for treating HIV/AIDS. Despite the efficacy of therapy, current efforts to control the disease are undermined by the growing threat posed by drug resistance. This review covers the historical background of studies on the structure and function of HIV protease, the subsequent development of antiviral inhibitors, and recent studies on drug-resistant protease variants. We highlight the important contributions of Dr. Stephen Oroszlan to fundamental knowledge about the function of the HIV protease and other retroviral proteases. These studies, along with those of his colleagues, laid the foundations for the design of clinical inhibitors of HIV protease. The drug-resistant protease variants also provide an excellent model for investigating the molecular mechanisms and evolution of resistance.
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Affiliation(s)
- Irene T. Weber
- Department of Biology, Georgia State University, Atlanta, GA 30302, USA;
- Correspondence:
| | - Yuan-Fang Wang
- Department of Biology, Georgia State University, Atlanta, GA 30302, USA;
| | - Robert W. Harrison
- Department of Computer Science, Georgia State University, Atlanta, GA 30302, USA;
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9
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Bonar MM, Tabler CO, Haqqani AA, Lapointe LE, Galiatsos JA, Joussef-Piña S, Quiñones-Mateu ME, Tilton JC. Nanoscale flow cytometry reveals interpatient variability in HIV protease activity that correlates with viral infectivity and identifies drug-resistant viruses. Sci Rep 2020; 10:18101. [PMID: 33093566 PMCID: PMC7583244 DOI: 10.1038/s41598-020-75118-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 10/06/2020] [Indexed: 11/26/2022] Open
Abstract
HIV encodes an aspartyl protease that is activated during, or shortly after, budding of viral particles from the surface of infected cells. Protease-mediated cleavage of viral polyproteins is essential to generating infectious viruses, a process known as ‘maturation’ that is the target of FDA-approved antiretroviral drugs. Most assays to monitor protease activity rely on bulk analysis of millions of viruses and obscure potential heterogeneity of protease activation within individual particles. In this study we used nanoscale flow cytometry in conjunction with an engineered FRET reporter called VIral ProteasE Reporter (VIPER) to investigate heterogeneity of protease activation in individual, patient-derived viruses. We demonstrate previously unappreciated interpatient variation in HIV protease processing efficiency that impacts viral infectivity. Additionally, monitoring of protease activity in individual virions distinguishes between drug sensitivity or resistance to protease inhibitors in patient-derived samples. These findings demonstrate the feasibility of monitoring enzymatic processes using nanoscale flow cytometry and highlight the potential of this technology for translational clinical discovery, not only for viruses but also other submicron particles including exosomes, microvesicles, and bacteria.
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Affiliation(s)
- Michał M Bonar
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Caroline O Tabler
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Aiman A Haqqani
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Lauren E Lapointe
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jake A Galiatsos
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Samira Joussef-Piña
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Miguel E Quiñones-Mateu
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.,Department of Microbiology and Immunology, University of Otago, Dunedin, 9016, New Zealand
| | - John C Tilton
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
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10
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Kneller DW, Agniswamy J, Harrison RW, Weber IT. Highly drug-resistant HIV-1 protease reveals decreased intra-subunit interactions due to clusters of mutations. FEBS J 2020; 287:3235-3254. [PMID: 31920003 PMCID: PMC7343616 DOI: 10.1111/febs.15207] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/16/2019] [Accepted: 01/08/2020] [Indexed: 01/07/2023]
Abstract
Drug-resistance is a serious problem for treatment of the HIV/AIDS pandemic. Potent clinical inhibitors of HIV-1 protease show several orders of magnitude worse inhibition of highly drug-resistant variants. Hence, the structure and enzyme activities were analyzed for HIV protease mutant HIV-1 protease (EC 3.4.23.16) (PR) with 22 mutations (PRS5B) from a clinical isolate that was selected by machine learning to represent high-level drug-resistance. PRS5B has 22 mutations including only one (I84V) in the inhibitor binding site; however, clinical inhibitors had poor inhibition of PRS5B activity with kinetic inhibition value (Ki ) values of 4-1000 nm or 18- to 8000-fold worse than for wild-type PR. High-resolution crystal structures of PRS5B complexes with the best inhibitors, amprenavir (APV) and darunavir (DRV) (Ki ~ 4 nm), revealed only minor changes in protease-inhibitor interactions. Instead, two distinct clusters of mutations in distal regions induce coordinated conformational changes that decrease favorable internal interactions across the entire protein subunit. The largest structural rearrangements are described and compared to other characterized resistant mutants. In the protease hinge region, the N83D mutation eliminates a hydrogen bond connecting the hinge and core of the protease and increases disorder compared to highly resistant mutants PR with 17 mutations and PR with 20 mutations with similar hinge mutations. In a distal β-sheet, mutations G73T and A71V coordinate with accessory mutations to bring about shifts that propagate throughout the subunit. Molecular dynamics simulations of ligand-free dimers show differences consistent with loss of interactions in mutant compared to wild-type PR. Clusters of mutations exhibit both coordinated and antagonistic effects, suggesting PRS5B may represent an intermediate stage in the evolution of more highly resistant variants. DATABASES: Structural data are available in Protein Data Bank under the accession codes 6P9A and 6P9B for PRS5B/DRV and PRS5B/APV, respectively.
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Affiliation(s)
- Daniel W. Kneller
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States of America
| | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States of America
| | - Robert W. Harrison
- Department of Computer Science, Georgia State University, Atlanta, Georgia 30303, United States of America
| | - Irene T. Weber
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States of America,Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States of America,Author of correspondence:
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11
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Kumar M, Mandal K, Blakeley MP, Wymore T, Kent SBH, Louis JM, Das A, Kovalevsky A. Visualizing Tetrahedral Oxyanion Bound in HIV-1 Protease Using Neutrons: Implications for the Catalytic Mechanism and Drug Design. ACS OMEGA 2020; 5:11605-11617. [PMID: 32478251 PMCID: PMC7254801 DOI: 10.1021/acsomega.0c00835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
HIV-1 protease is indispensable for virus propagation and an important therapeutic target for antiviral inhibitors to treat AIDS. As such inhibitors are transition-state mimics, a detailed understanding of the enzyme mechanism is crucial for the development of better anti-HIV drugs. Here, we used room-temperature joint X-ray/neutron crystallography to directly visualize hydrogen atoms and map hydrogen bonding interactions in a protease complex with peptidomimetic inhibitor KVS-1 containing a reactive nonhydrolyzable ketomethylene isostere, which, upon reacting with the catalytic water molecule, is converted into a tetrahedral intermediate state, KVS-1TI. We unambiguously determined that the resulting tetrahedral intermediate is an oxyanion, rather than the gem-diol, and both catalytic aspartic acid residues are protonated. The oxyanion tetrahedral intermediate appears to be unstable, even though the negative charge on the oxyanion is delocalized through a strong n → π* hyperconjugative interaction into the nearby peptidic carbonyl group of the inhibitor. To better understand the influence of the ketomethylene isostere as a protease inhibitor, we have also examined the protease structure and binding affinity with keto-darunavir (keto-DRV), which similar to KVS-1 includes the ketomethylene isostere. We show that keto-DRV is a significantly less potent protease inhibitor than DRV. These findings shed light on the reaction mechanism of peptide hydrolysis catalyzed by HIV-1 protease and provide valuable insights into further improvements in the design of protease inhibitors.
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Affiliation(s)
- Mukesh Kumar
- Protein Crystallography
Section, Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Kalyaneswar Mandal
- Departments of Chemistry, and Biochemistry and Molecular Biology,
Institute for Biophysical Dynamics, University
of Chicago, Chicago, Illinois 60637, United States
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue−Langevin, 38000 Grenoble, France
| | - Troy Wymore
- Department of Chemistry, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Stephen B. H. Kent
- Departments of Chemistry, and Biochemistry and Molecular Biology,
Institute for Biophysical Dynamics, University
of Chicago, Chicago, Illinois 60637, United States
| | - John M. Louis
- Laboratory of Chemical Physics, National
Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, United States
| | - Amit Das
- Protein Crystallography
Section, Radiation Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Andrey Kovalevsky
- Neutron Scattering
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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12
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Voshavar C. Protease Inhibitors for the Treatment of HIV/AIDS: Recent Advances and Future Challenges. Curr Top Med Chem 2019; 19:1571-1598. [PMID: 31237209 DOI: 10.2174/1568026619666190619115243] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 02/07/2023]
Abstract
Acquired Immunodeficiency Syndrome (AIDS) is a chronic disease characterized by multiple life-threatening illnesses caused by a retro-virus, Human Immunodeficiency Virus (HIV). HIV infection slowly destroys the immune system and increases the risk of various other infections and diseases. Although, there is no immediate cure for HIV infection/AIDS, several drugs targeting various cruxes of HIV infection are used to slow down the progress of the disease and to boost the immune system. One of the key therapeutic strategies is Highly Active Antiretroviral Therapy (HAART) or ' AIDS cocktail' in a general sense, which is a customized combination of anti-retroviral drugs designed to combat the HIV infection. Since HAART's inception in 1995, this treatment was found to be effective in improving the life expectancy of HIV patients over two decades. Among various classes of HAART treatment regimen, Protease Inhibitors (PIs) are known to be widely used as a major component and found to be effective in treating HIV infection/AIDS. For the past several years, a variety of protease inhibitors have been reported. This review outlines the drug design strategies of PIs, chemical and pharmacological characteristics of some mechanism-based inhibitors, summarizes the recent developments in small molecule based drug discovery with HIV protease as a drug target. Further discussed are the pharmacology, PI drug resistance on HIV PR, adverse effects of HIV PIs and challenges/impediments in the successful application of HIV PIs as an important class of drugs in HAART regimen for the effective treatment of AIDS.
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Affiliation(s)
- Chandrashekhar Voshavar
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, United States
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13
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Kneller DW, Agniswamy J, Ghosh AK, Weber IT. Potent antiviral HIV-1 protease inhibitor combats highly drug resistant mutant PR20. Biochem Biophys Res Commun 2019; 519:61-66. [PMID: 31474336 PMCID: PMC7251940 DOI: 10.1016/j.bbrc.2019.08.126] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 08/23/2019] [Indexed: 01/07/2023]
Abstract
Drug-resistance threatens effective treatment of HIV/AIDS. Clinical inhibitors, including darunavir (1), are ineffective for highly resistant protease mutant PR20, however, antiviral compound 2 derived from 1 with fused tricyclic group at P2, extended amino-benzothiazole P2' ligand and two fluorine atoms on P1 shows 16-fold better inhibition of PR20 enzyme activity. Crystal structures of PR20 and wild-type PR complexes reveal how the extra groups of 2 counteract the expanded ligand-binding pocket, dynamic flaps, and faster dimer dissociation of PR20.
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Affiliation(s)
- Daniel W. Kneller
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Irene T. Weber
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA,Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA,Corresponding author: Phone: (+1) 404-413-5411
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14
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Yoo J, Louis JM, Chung HS. Diverse Folding Pathways of HIV-1 Protease Monomer on a Rugged Energy Landscape. Biophys J 2019; 117:1456-1466. [PMID: 31587829 DOI: 10.1016/j.bpj.2019.09.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 08/27/2019] [Accepted: 09/12/2019] [Indexed: 10/26/2022] Open
Abstract
The modern energy landscape theory of protein folding predicts multiple folding pathways connecting a myriad of unfolded conformations and a well-defined folded state. However, direct experimental observation of heterogeneous folding pathways is difficult. Naturally evolved proteins typically exhibit a smooth folding energy landscape for fast and efficient folding by avoiding unfavorable kinetic traps. In this case, rapid fluctuations between unfolded conformations result in apparent two-state behavior and make different pathways indistinguishable. However, the landscape roughness can be different, depending on the selection pressures during evolution. Here, we characterize the unusually rugged folding energy landscape of human immunodeficiency virus-1 protease monomer using single-molecule Förster resonance energy transfer spectroscopy. Our data show that fluctuations between unfolded conformations are slow, which enables the experimental observation of heterogeneous folding pathways as predicted by the landscape theory. Although the landscape ruggedness is sensitive to the mutations and fluorophore locations, the folding rate is similar for various protease constructs. The natural evolution of the protease to have a rugged energy landscape likely results from intrinsic pressures to maintain robust folding when human immunodeficiency virus-1 mutates frequently, which is essential for its survival.
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Affiliation(s)
- Janghyun Yoo
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Hoi Sung Chung
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland.
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15
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Karnati KR, Wang Y. Structural and binding insights into HIV-1 protease and P2-ligand interactions through molecular dynamics simulations, binding free energy and principal component analysis. J Mol Graph Model 2019; 92:112-122. [PMID: 31351319 DOI: 10.1016/j.jmgm.2019.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 12/15/2022]
Abstract
HIV-1 protease (HIV-1-pr) plays an important role in viral replication and maturation, making it one of the most attractive targets for anti-retroviral therapy. To design new effective inhibitors able to combat drug resistance in mutant HIV-1-pr variants, it is essential to gain further understanding about the mechanisms by which the recently proposed inhibitors deactivate the mutant HIV-1-pr variants. In the present work, we explored the interactions between two P2-ligands (DRV, and one new derivative, 4UY) with wild type (WT) and two multiple mutant HIV-1-pr variants (p20 and p51) with all atom molecular dynamics (MD) simulations, binding free energy calculations, and principal component analysis (PCA). The trajectories of MD simulations show that both 4UY and DRV primarily bind with the active sites, flap and 80s loop regions of HIV-1-pr variants through either hydrogen bonds or hydrophobic interactions. More hydrogen bonds and hydrophobic interactions were located for 4UY/HIV-1-pr complexes than for DRV/HIV-1-pr counterparts. More importantly, 4UY was found to have an extra hydrogen bond with the backbone of Gly48' in the flap region of the HIV-1-prs. The flap tip-tip distance (I50-I50') and flap tip-active site distance (I50-D25 and I50'-D25') indicate that the flaps turn more closed in 4UY bound HIV-1-prs than DRV bound ones, and the former also have more compact hydrophobic cavities than the latter. Further, the vector projections from PCA indicate that 4UY/DRV inhibitor binding projects the closing of flap in HIV-1-pr variants. In line with the above trajectory analysis, the thermodynamics calculation with MM-PBSA method suggests much stronger binding affinity for 4UY/HIV-1-pr than DRV/HIV-1-pr by 4.3-6.4 kcal/mol. Although p20 and p51 also induce weaker binding due to multiple mutants for 4UY inhibitor by 1.9-1.8 kcal/mol, their bindings to the new P2 ligand (4UY) are indeed significantly enhanced as compared to DRV. The thermodynamic components responsible for the binding differences and the contribution from key residues to the binding were also discussed in detail.
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Affiliation(s)
- Konda Reddy Karnati
- Department of Chemistry and Forensic Science, Albany State University, Albany, GA, 31705, USA
| | - Yixuan Wang
- Department of Chemistry and Forensic Science, Albany State University, Albany, GA, 31705, USA.
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16
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Miller Jenkins LM, Paine EL, Deshmukh L, Nikolayevskiy H, Lyons GC, Scerba MT, Rosenker KG, Luecke HF, Louis JM, Chertova E, Gorelick RJ, Ott DE, Clore GM, Appella DH. Inhibition of HIV Maturation via Selective Unfolding and Cross-Linking of Gag Polyprotein by a Mercaptobenzamide Acetylator. J Am Chem Soc 2019; 141:8327-8338. [PMID: 31042030 PMCID: PMC8496520 DOI: 10.1021/jacs.9b02743] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
For HIV to become infectious, any new virion produced from an infected cell must undergo a maturation process that involves the assembly of viral polyproteins Gag and Gag-Pol at the membrane surface. The self-assembly of these viral proteins drives formation of a new viral particle as well as the activation of HIV protease, which is needed to cleave the polyproteins so that the final core structure of the virus will properly form. Molecules that interfere with HIV maturation will prevent any new virions from infecting additional cells. In this manuscript, we characterize the unique mechanism by which a mercaptobenzamide thioester small molecule (SAMT-247) interferes with HIV maturation via a series of selective acetylations at highly conserved cysteine and lysine residues in Gag and Gag-Pol polyproteins. The results provide the first insights into how acetylation can be utilized to perturb the process of HIV maturation and reveal a new strategy to limit the infectivity of HIV.
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Affiliation(s)
- Lisa M. Miller Jenkins
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Elliott L. Paine
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Lalit Deshmukh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Herman Nikolayevskiy
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Gaelyn C. Lyons
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Michael T. Scerba
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Kara George Rosenker
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Hans F. Luecke
- Advanced Mass Spectrometry Core, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Elena Chertova
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - David E. Ott
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Daniel H. Appella
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
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17
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Majerová T, Novotný P, Krýsová E, Konvalinka J. Exploiting the unique features of Zika and Dengue proteases for inhibitor design. Biochimie 2019; 166:132-141. [PMID: 31077760 DOI: 10.1016/j.biochi.2019.05.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
Zika and Dengue viruses have attracted substantial attention from researchers in light of recent outbreaks of Dengue fever and increases in cases of congenital microcephaly in areas with Zika incidence. This review summarizes the current state of knowledge about Zika and Dengue proteases. These enzymes have several interesting features: 1) NS3 serine protease requires the activating co-factor NS2B, which is anchored in the membrane of the endoplasmic reticulum; 2) NS2B displays extensive conformational dynamics; 3) NS3 is a multidomain protein with proteolytic, NTPase, RNA 5' triphosphatase and helicase activity and has many protein-protein interaction partners; 4) NS3 is autoproteolytically released from its precursor. Attempts to design tight-binding and specific active-site inhibitors are complicated by the facts that the substrate pocket of the NS2B-NS3 protease is flat and the active-site ligands are charged. The ionic character of potential active-site inhibitors negatively influences their cell permeability. Possibilities to block cis-autoprocessing of the protease precursor have recently been considered. Additionally, potential allosteric sites on NS2B-NS3 proteases have been identified and allosteric compounds have been designed to impair substrate binding and/or block the NS2B-NS3 interaction. Such compounds could be specific to viral proteases, without off-target effects on host serine proteases, and could have favorable pharmacokinetic profiles. This review discusses various groups of inhibitors of these proteases according to their mechanisms of action and chemical structures.
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Affiliation(s)
- Taťána Majerová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic
| | - Pavel Novotný
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic
| | - Eliška Krýsová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic.
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18
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Gadiyaram V, Vishveshwara S, Vishveshwara S. From Quantum Chemistry to Networks in Biology: A Graph Spectral Approach to Protein Structure Analyses. J Chem Inf Model 2019; 59:1715-1727. [DOI: 10.1021/acs.jcim.9b00002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vasundhara Gadiyaram
- IISc Mathematics Initiative (IMI), Indian Institute of Science, C V Raman Road, Bengaluru, Karnataka 560012, India
| | - Smitha Vishveshwara
- Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801-3080, United States
| | - Saraswathi Vishveshwara
- Molecular Biophysics Unit, Indian Institute of Science, C V Raman Road, Bengaluru, Karnataka 560012, India
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19
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Huang L, Li L, Tien C, LaBarbera DV, Chen C. Targeting HIV-1 Protease Autoprocessing for High-throughput Drug Discovery and Drug Resistance Assessment. Sci Rep 2019; 9:301. [PMID: 30670786 PMCID: PMC6343032 DOI: 10.1038/s41598-018-36730-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/23/2018] [Indexed: 01/28/2023] Open
Abstract
HIV-1 protease autoprocessing liberates the free mature protease from its Gag-Pol polyprotein precursor through a series of highly regulated autoproteolysis reactions. Herein, we report the development and validation (Z' ≥ 0.50) of a cell-based functional assay for high-throughput screening (HTS) of autoprocessing inhibitors using fusion precursors in combination with AlphaLISA (amplified luminescent proximity homogeneous assay ELISA). Through pilot screening of a collection of 130 known protease inhibitors, the AlphaLISA assay confirmed all 11 HIV protease inhibitors in the library capable of suppressing precursor autoprocessing at low micromolar concentrations. Meanwhile, other protease inhibitors had no impact on precursor autoprocessing. We next conducted HTS of ~23,000 compounds but found no positive hits. Such high selectivity is advantageous for large-scale HTS campaigns and as anticipated based on assay design because a positive hit needs simultaneously to be nontoxic, cell permeable, and inhibiting precursor autoprocessing. Furthermore, AlphaLISA quantification of fusion precursors carrying mutations known to cause resistance to HIV protease inhibitors faithfully recapitulated the reported resistance, suggesting that precursor autoprocessing is a critical step contributing to drug resistance. Taken together, this reported AlphaLISA platform will provide a useful tool for drug discovery targeting HIV-1 protease autoprocessing and for quantification of PI resistance.
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Affiliation(s)
- Liangqun Huang
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Linfeng Li
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - ChihFeng Tien
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Daniel V LaBarbera
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Chaoping Chen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA.
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20
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Humpolíčková J, Weber J, Starková J, Mašínová E, Günterová J, Flaisigová I, Konvalinka J, Majerová T. Inhibition of the precursor and mature forms of HIV-1 protease as a tool for drug evaluation. Sci Rep 2018; 8:10438. [PMID: 29992979 PMCID: PMC6041310 DOI: 10.1038/s41598-018-28638-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/22/2018] [Indexed: 12/31/2022] Open
Abstract
HIV-1 protease (PR) is a homodimeric enzyme that is autocatalytically cleaved from the Gag-Pol precursor. Known PR inhibitors bind the mature enzyme several orders of magnitude more strongly than the PR precursor. Inhibition of PR at the precursor level, however, may stop the process at its rate-limiting step before the proteolytic cascade is initiated. Due to its structural heterogeneity, limited solubility and autoprocessing, the PR precursor is difficult to access by classical methods, and limited knowledge regarding precursor inhibition is available. Here, we describe a cell-based assay addressing precursor inhibition. We used a reporter molecule containing the transframe (TFP) and p6* peptides, PR, and N-terminal fragment of reverse transcriptase flanked by the fluorescent proteins mCherry and EGFP on its N- and C- termini, respectively. The level of FRET between EGFP and mCherry indicates the amount of unprocessed reporter, allowing specific monitoring of precursor inhibition. The inhibition can be quantified by flow cytometry. Additionally, two microscopy techniques confirmed that the reporter remains unprocessed within individual cells upon inhibition. We tested darunavir, atazanavir and nelfinavir and their combinations against wild-type PR. Shedding light on an inhibitor’s ability to act on non-mature forms of PR may aid novel strategies for next-generation drug design.
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Affiliation(s)
- Jana Humpolíčková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Jana Starková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Eva Mašínová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Jana Günterová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Iva Flaisigová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic
| | - Taťána Majerová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic.
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21
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Tien C, Huang L, Watanabe SM, Speidel JT, Carter CA, Chen C. Context-dependent autoprocessing of human immunodeficiency virus type 1 protease precursors. PLoS One 2018; 13:e0191372. [PMID: 29338056 PMCID: PMC5770051 DOI: 10.1371/journal.pone.0191372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/03/2018] [Indexed: 11/29/2022] Open
Abstract
HIV-1 protease autoprocessing is responsible for liberation of free mature protease (PR) from the Gag-Pol polyprotein precursor. A cell-based model system was previously developed to examine the autoprocessing mechanism of fusion precursors carrying the p6*-PR miniprecursor sandwiched between various proteins or epitopes. We here report that precursor autoprocessing is context-dependent as its activity and outcomes can be modulated by sequences upstream of p6*-PR. This was exemplified by the 26aa maltose binding protein (MBP) signal peptide (SigP) when placed at the N-terminus of a fusion precursor. The mature PRs released from SigP-carrying precursors are resistant to self-degradation whereas those released from SigP-lacking fusion precursors are prone to self-degradation. A H69D mutation in PR abolished autoprocessing of SigP-containing fusion precursors whereas it only partially suppressed autoprocessing of fusion precursors lacking SigP. An autoprocessing deficient GFP fusion precursor with SigP exhibited a subcellular distribution pattern distinct from the one without it in transfected HeLa cells. Furthermore, a SigP fusion precursor carrying a substitution at the P1 position released the mature PR and PR-containing fragments that were different from those released from the precursor carrying the same mutation but lacking SigP. We also examined autoprocessing outcomes in viral particles produced by a NL4-3 derived proviral construct and demonstrated the existence of several PR-containing fragments along with the mature PR. Some of these resembled the SigP precursor autoprocessing outcomes. This finding of context-dependent modulation reveals the complexity of precursor autoprocessing regulation that most likely accompanies sequence variation imposed by the evolution of the upstream Gag moiety.
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Affiliation(s)
- ChihFeng Tien
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Liangqun Huang
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Susan M. Watanabe
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | - Jordan T. Speidel
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Carol A. Carter
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York, United States of America
| | - Chaoping Chen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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22
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Binding kinetics and substrate selectivity in HIV-1 protease-Gag interactions probed at atomic resolution by chemical exchange NMR. Proc Natl Acad Sci U S A 2017; 114:E9855-E9862. [PMID: 29087351 DOI: 10.1073/pnas.1716098114] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The conversion of immature noninfectious HIV-1 particles to infectious virions is dependent upon the sequential cleavage of the precursor group-specific antigen (Gag) polyprotein by HIV-1 protease. The precise mechanism whereby protease recognizes distinct Gag cleavage sites, located in the intrinsically disordered linkers connecting the globular domains of Gag, remains unclear. Here, we probe the dynamics of the interaction of large fragments of Gag and various variants of protease (including a drug resistant construct) using Carr-Purcell-Meiboom-Gill relaxation dispersion and chemical exchange saturation transfer NMR experiments. We show that the conformational dynamics within the flaps of HIV-1 protease that form the lid over the catalytic cleft play a significant role in substrate specificity and ordered Gag processing. Rapid interconversion between closed and open protease flap conformations facilitates the formation of a transient, sparsely populated productive complex between protease and Gag substrates. Flap closure traps the Gag cleavage sites within the catalytic cleft of protease. Modulation of flap opening through protease-Gag interactions fine-tunes the lifetime of the productive complex and hence the likelihood of Gag proteolysis. A productive complex can also be formed in the presence of a noncognate substrate but is short-lived owing to lack of optimal complementarity between the active site cleft of protease and the substrate, resulting in rapid flap opening and substrate release, thereby allowing protease to differentiate between cognate and noncognate substrates.
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23
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Weber IT, Harrison RW. Decoding HIV resistance: from genotype to therapy. Future Med Chem 2017; 9:1529-1538. [PMID: 28791894 PMCID: PMC5694023 DOI: 10.4155/fmc-2017-0048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/03/2017] [Indexed: 01/14/2023] Open
Abstract
Genetic variation in HIV poses a major challenge for prevention and treatment of the AIDS pandemic. Resistance occurs by mutations in the target proteins that lower affinity for the drug or alter the protein dynamics, thereby enabling viral replication in the presence of the drug. Due to the prevalence of drug-resistant strains, monitoring the genotype of the infecting virus is recommended. Computational approaches for predicting resistance from genotype data and guiding therapy are discussed. Many prediction methods rely on rules derived from known resistance-associated mutations, however, statistical or machine learning can improve the classification accuracy and assess unknown mutations. Adding classifiers such as information on the atomic structure of the protein can further enhance the predictions.
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Affiliation(s)
- Irene T Weber
- Department of Biology, Georgia State University, PO Box 4010, Atlanta, GA 30302-4010, USA
| | - Robert W Harrison
- Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA
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24
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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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25
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Flynn WF, Haldane A, Torbett BE, Levy RM. Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease. Mol Biol Evol 2017; 34:1291-1306. [PMID: 28369521 PMCID: PMC5435099 DOI: 10.1093/molbev/msx095] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Understanding the complex mutation patterns that give rise to drug resistant viral strains provides a foundation for developing more effective treatment strategies for HIV/AIDS. Multiple sequence alignments of drug-experienced HIV-1 protease sequences contain networks of many pair correlations which can be used to build a (Potts) Hamiltonian model of these mutation patterns. Using this Hamiltonian model, we translate HIV-1 protease sequence covariation data into quantitative predictions for the probability of observing specific mutation patterns which are in agreement with the observed sequence statistics. We find that the statistical energies of the Potts model are correlated with the fitness of individual proteins containing therapy-associated mutations as estimated by in vitro measurements of protein stability and viral infectivity. We show that the penalty for acquiring primary resistance mutations depends on the epistatic interactions with the sequence background. Primary mutations which lead to drug resistance can become highly advantageous (or entrenched) by the complex mutation patterns which arise in response to drug therapy despite being destabilizing in the wildtype background. Anticipating epistatic effects is important for the design of future protease inhibitor therapies.
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Affiliation(s)
- William F. Flynn
- Department of Physics and Astronomy, Rutgers University, New Brunswick, NJ
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA
| | - Allan Haldane
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA
- Department of Chemistry, Temple University, Philadelphia, PA
| | - Bruce E. Torbett
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Ronald M. Levy
- Center for Biophysics and Computational Biology, Temple University, Philadelphia, PA
- Department of Chemistry, Temple University, Philadelphia, PA
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26
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Agniswamy J, Louis JM, Roche J, Harrison RW, Weber IT. Structural Studies of a Rationally Selected Multi-Drug Resistant HIV-1 Protease Reveal Synergistic Effect of Distal Mutations on Flap Dynamics. PLoS One 2016; 11:e0168616. [PMID: 27992544 PMCID: PMC5161481 DOI: 10.1371/journal.pone.0168616] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/02/2016] [Indexed: 12/20/2022] Open
Abstract
We report structural analysis of HIV protease variant PRS17 which was rationally selected by machine learning to represent wide classes of highly drug-resistant variants. Crystal structures were solved of PRS17 in the inhibitor-free form and in complex with antiviral inhibitor, darunavir. Despite its 17 mutations, PRS17 has only one mutation (V82S) in the inhibitor/substrate binding cavity, yet exhibits high resistance to all clinical inhibitors. PRS17 has none of the major mutations (I47V, I50V, I54ML, L76V and I84V) associated with darunavir resistance, but has 10,000-fold weaker binding affinity relative to the wild type PR. Comparable binding affinity of 8000-fold weaker than PR is seen for drug resistant mutant PR20, which bears 3 mutations associated with major resistance to darunavir (I47V, I54L and I84V). Inhibitor-free PRS17 shows an open flap conformation with a curled tip correlating with G48V flap mutation. NMR studies on inactive PRS17D25N unambiguously confirm that the flaps adopt mainly an open conformation in solution very similar to that in the inhibitor-free crystal structure. In PRS17, the hinge loop cluster of mutations, E35D, M36I and S37D, contributes to the altered flap dynamics by a mechanism similar to that of PR20. An additional K20R mutation anchors an altered conformation of the hinge loop. Flap mutations M46L and G48V in PRS17/DRV complex alter the Phe53 conformation by steric hindrance between the side chains. Unlike the L10F mutation in PR20, L10I in PRS17 does not break the inter-subunit ion pair or diminish the dimer stability, consistent with a very low dimer dissociation constant comparable to that of wild type PR. Distal mutations A71V, L90M and I93L propagate alterations to the catalytic site of PRS17. PRS17 exhibits a molecular mechanism whereby mutations act synergistically to alter the flap dynamics resulting in significantly weaker binding yet maintaining active site contacts with darunavir.
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Affiliation(s)
- Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland, United States of America
| | - Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland, United States of America
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, United States of America
| | - Robert W. Harrison
- Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
- Department of Computer Science, Georgia State University, Atlanta, Georgia, United States of America
| | - Irene T. Weber
- Department of Biology, Georgia State University, Atlanta, Georgia, United States of America
- Department of Chemistry, Georgia State University, Atlanta, Georgia, United States of America
- * E-mail:
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27
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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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28
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Gao P, Sun L, Zhou J, Li X, Zhan P, Liu X. Discovery of novel anti-HIV agents via Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry-based approach. Expert Opin Drug Discov 2016; 11:857-71. [PMID: 27400283 DOI: 10.1080/17460441.2016.1210125] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION In recent years, a variety of new synthetic methodologies and concepts have been proposed in the search for new pharmaceutical lead structures and optimization. Notably, the Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry approach has drawn great attention and has become a powerful tool for the generation of privileged medicinal skeletons in the discovery of anti-HIV agents. This is due to the high degree of reliability, complete specificity (chemoselectivity and regioselectivity), mild conditions, and the biocompatibility of the reactants. AREAS COVERED Herein, the authors describe the progress thus far on the discovery of novel anti-HIV agents via the CuAAC click chemistry-based approach. EXPERT OPINION CuAAC click chemistry is a proven protocol for synthesizing triazole products which could serve as basic pharmacophores, act as replacements of traditional scaffold or substituent modification, be a linker of dual-target or dual-site inhibitors and more for the discovery of novel anti-HIV agents. What's more, it also provides convenience and feasibility for dynamic combinatorial chemistry and in situ screening. It is envisioned that click chemistry will draw more attention and make more contributions in anti-HIV drug discovery in the future.
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Affiliation(s)
- Ping Gao
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Lin Sun
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Junsu Zhou
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Xiao Li
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Peng Zhan
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
| | - Xinyong Liu
- a Department of Medicinal Chemistry, Key laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , Jinan , P. R. China
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29
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Louis JM, Roche J. Evolution under Drug Pressure Remodels the Folding Free-Energy Landscape of Mature HIV-1 Protease. J Mol Biol 2016; 428:2780-92. [PMID: 27170547 PMCID: PMC4905781 DOI: 10.1016/j.jmb.2016.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/27/2016] [Accepted: 05/02/2016] [Indexed: 01/08/2023]
Abstract
Using high-pressure NMR spectroscopy and differential scanning calorimetry, we investigate the folding landscape of the mature HIV-1 protease homodimer. The cooperativity of unfolding was measured in the absence or presence of a symmetric active site inhibitor for the optimized wild type protease (PR), its inactive variant PRD25N, and an extremely multidrug-resistant mutant, PR20. The individual fit of the pressure denaturation profiles gives rise to first order, ∆GNMR, and second order, ∆VNMR (the derivative of ∆GNMR with pressure); apparent thermodynamic parameters for each amide proton considered. Heterogeneity in the apparent ∆VNMR values reflects departure from an ideal cooperative unfolding transition. The narrow to broad distribution of ∆VNMR spanning the extremes from inhibitor-free PR20D25N to PR-DMP323 complex, and distinctively for PRD25N-DMP323 complex, indicated large variations in folding cooperativity. Consistent with this data, the shape of thermal unfolding transitions varies from asymmetric for PR to nearly symmetric for PR20, as dimer-inhibitor ternary complexes. Lack of structural cooperativity was observed between regions located close to the active site, including the hinge and tip of the glycine-rich flaps, and the rest of the protein. These results strongly suggest that inhibitor binding drastically decreases the cooperativity of unfolding by trapping the closed flap conformation in a deep energy minimum. To evade this conformational trap, PR20 evolves exhibiting a smoother folding landscape with nearly an ideal two-state (cooperative) unfolding transition. This study highlights the malleability of retroviral protease folding pathways by illustrating how the selection of mutations under drug pressure remodels the free-energy landscape as a primary mechanism.
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Affiliation(s)
- John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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30
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Park JH, Sayer JM, Aniana A, Yu X, Weber IT, Harrison RW, Louis JM. Binding of Clinical Inhibitors to a Model Precursor of a Rationally Selected Multidrug Resistant HIV-1 Protease Is Significantly Weaker Than That to the Released Mature Enzyme. Biochemistry 2016; 55:2390-400. [PMID: 27039930 DOI: 10.1021/acs.biochem.6b00012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have systematically validated the activity and inhibition of a HIV-1 protease (PR) variant bearing 17 mutations (PR(S17)), selected to represent high resistance by machine learning on genotype-phenotype data. Three of five mutations in PR(S17) correlating with major drug resistance, M46L, G48V, and V82S, and five of 11 natural variations differ from the mutations in two clinically derived extreme mutants, PR20 and PR22 bearing 19 and 22 mutations, respectively. PR(S17), which forms a stable dimer (<10 nM), is ∼10- and 2-fold less efficient in processing the Gag polyprotein than the wild type and PR20, respectively, but maintains the same cleavage order. Isolation of a model precursor of PR(S17) flanked by the 56-amino acid transframe region (TFP-p6pol) at its N-terminus, which is impossible upon expression of an analogous PR20 precursor, allowed systematic comparison of inhibition of TFP-p6pol-PR(S17) and mature PR(S17). Resistance of PR(S17) to eight protease inhibitors (PIs) relative to PR (Ki) increases by 1.5-5 orders of magnitude from 0.01 to 8.4 μM. Amprenavir, darunavir, atazanavir, and lopinavir, the most effective of the eight PIs, inhibit precursor autoprocessing at the p6pol/PR site with IC50 values ranging from ∼7.5 to 60 μM. Thus, this process, crucial for stable dimer formation, shows inhibition ∼200-800-fold weaker than that of the mature PR(S17). TFP/p6pol cleavage, which occurs faster, is inhibited even more weakly by all PIs except darunavir (IC50 = 15 μM); amprenavir shows a 2-fold increase in IC50 (∼15 μM), and atazanavir and lopinavir show increased IC50 values of >42 and >70 μM, respectively.
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Affiliation(s)
- Joon H Park
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services , Bethesda, Maryland 20892, United States
| | - Jane M Sayer
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services , Bethesda, Maryland 20892, United States
| | - Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services , Bethesda, Maryland 20892, United States
| | | | | | | | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services , Bethesda, Maryland 20892, United States
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31
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Abstract
The virally encoded protease is an important drug target for AIDS therapy. Despite the potency of the current drugs, infections with resistant viral strains limit the long-term effectiveness of therapy. Highly resistant variants of HIV protease from clinical isolates have different combinations of about 20 mutations and several orders of magnitude worse binding affinity for clinical inhibitors. Strategies are being explored to inhibit these highly resistant mutants. The existing inhibitors can be modified by introducing groups with the potential to form new interactions with conserved protease residues, and the flexible flaps. Alternative strategies are discussed, including designing inhibitors to bind to the open conformation of the protease dimer, and inhibition of the protease-catalyzed processing of the Gag-Pol precursor.
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32
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Mahanti M, Bhakat S, Nilsson UJ, Söderhjelm P. Flap Dynamics in Aspartic Proteases: A Computational Perspective. Chem Biol Drug Des 2016; 88:159-77. [PMID: 26872937 DOI: 10.1111/cbdd.12745] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances in biochemistry and drug design have placed proteases as one of the critical target groups for developing novel small-molecule inhibitors. Among all proteases, aspartic proteases have gained significant attention due to their role in HIV/AIDS, malaria, Alzheimer's disease, etc. The binding cleft is covered by one or two β-hairpins (flaps) which need to be opened before a ligand can bind. After binding, the flaps close to retain the ligand in the active site. Development of computational tools has improved our understanding of flap dynamics and its role in ligand recognition. In the past decade, several computational approaches, for example molecular dynamics (MD) simulations, coarse-grained simulations, replica-exchange molecular dynamics (REMD) and metadynamics, have been used to understand flap dynamics and conformational motions associated with flap movements. This review is intended to summarize the computational progress towards understanding the flap dynamics of proteases and to be a reference for future studies in this field.
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Affiliation(s)
- Mukul Mahanti
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Soumendranath Bhakat
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden
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33
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Appadurai R, Senapati S. Dynamical Network of HIV-1 Protease Mutants Reveals the Mechanism of Drug Resistance and Unhindered Activity. Biochemistry 2016; 55:1529-40. [PMID: 26892689 DOI: 10.1021/acs.biochem.5b00946] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HIV-1 protease variants resist drugs by active and non-active-site mutations. The active-site mutations, which are the primary or first set of mutations, hamper the stability of the enzyme and resist the drugs minimally. As a result, secondary mutations that not only increase protein stability for unhindered catalytic activity but also resist drugs very effectively arise. While the mechanism of drug resistance of the active-site mutations is through modulating the active-site pocket volume, the mechanism of drug resistance of the non-active-site mutations is unclear. Moreover, how these allosteric mutations, which are 8-21 Å distant, communicate to the active site for drug efflux is completely unexplored. Results from molecular dynamics simulations suggest that the primary mechanism of drug resistance of the secondary mutations involves opening of the flexible protease flaps. Results from both residue- and community-based network analyses reveal that this precise action of protease is accomplished by the presence of robust communication paths between the mutational sites and the functionally relevant regions: active site and flaps. While the communication is more direct in the wild type, it traverses across multiple intermediate residues in mutants, leading to weak signaling and unregulated motions of flaps. The global integrity of the protease network is, however, maintained through the neighboring residues, which exhibit high degrees of conservation, consistent with clinical data and mutagenesis studies.
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Affiliation(s)
- Rajeswari Appadurai
- BJM School of Biosciences and Department of Biotechnology, Indian Institution of Technology Madras , Chennai 600 036, India
| | - Sanjib Senapati
- BJM School of Biosciences and Department of Biotechnology, Indian Institution of Technology Madras , Chennai 600 036, India
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34
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Abstract
BACKGROUND Drug resistance is one of the most important causes for failure of anti-AIDS treatment. During therapy, multiple mutations accumulate in the HIV genome, eventually rendering the drugs ineffective in blocking replication of the mutant virus. The huge number of possible mutants precludes experimental analysis to explore the molecular mechanisms of resistance and develop improved antiviral drugs. RESULTS In order to solve this problem, we have developed a new algorithm to reveal the most representative mutants from the whole drug resistant mutant database based on our newly proposed unified protein sequence and 3D structure encoding method. Mean shift clustering and multiple regression analysis were applied on genotype-resistance data for mutants of HIV protease and reverse transcriptase. This approach successfully chooses less than 100 mutants with the highest resistance to each drug out of about 10K in the whole database. When considering high level resistance to multiple drugs, the numbers reduce to one or two representative mutants. CONCLUSION This approach for predicting the most representative mutants for each drug has major importance for experimental verification since the results provide a small number of representative sequences, which will be amenable for in vitro testing and characterization of the expressed mutant proteins.
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Affiliation(s)
- Xiaxia Yu
- Department of Computer Science, Georgia State University, 34 Peachtree Street, Atlanta, GA, USA 30303
| | - Irene T Weber
- Department of Biology, Georgia State University, Petit Science Center, Atlanta, GA, USA 30303
| | - Robert W Harrison
- Department of Computer Science, Georgia State University, 34 Peachtree Street, Atlanta, GA, USA 30303
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35
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Roche J, Louis JM, Bax A, Best RB. Pressure-induced structural transition of mature HIV-1 protease from a combined NMR/MD simulation approach. Proteins 2015; 83:2117-23. [PMID: 26385843 DOI: 10.1002/prot.24931] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 09/01/2015] [Accepted: 09/01/2015] [Indexed: 11/10/2022]
Abstract
We investigate the pressure-induced structural changes in the mature human immunodeficiency virus type 1 protease dimer, using residual dipolar coupling (RDC) measurements in a weakly oriented solution. (1)DNH RDCs were measured under high-pressure conditions for an inhibitor-free PR and an inhibitor-bound complex, as well as for an inhibitor-free multidrug resistant protease bearing 20 mutations (PR20). While PR20 and the inhibitor-bound PR were little affected by pressure, inhibitor-free PR showed significant differences in the RDCs measured at 600 bar compared with 1 bar. The structural basis of such changes was investigated by MD simulations using the experimental RDC restraints, revealing substantial conformational perturbations, specifically a partial opening of the flaps and the penetration of water molecules into the hydrophobic core of the subunits at high pressure. This study highlights the exquisite sensitivity of RDCs to pressure-induced conformational changes and illustrates how RDCs combined with MD simulations can be used to determine the structural properties of metastable intermediate states on the folding energy landscape.
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Affiliation(s)
- Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892
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36
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Conformational variation of an extreme drug resistant mutant of HIV protease. J Mol Graph Model 2015; 62:87-96. [PMID: 26397743 DOI: 10.1016/j.jmgm.2015.09.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 09/03/2015] [Accepted: 09/05/2015] [Indexed: 11/24/2022]
Abstract
Molecular mechanisms leading to high level drug resistance have been analyzed for the clinical variant of HIV-1 protease bearing 20 mutations (PR20); which has several orders of magnitude worse affinity for tested drugs. Two crystal structures of ligand-free PR20 with the D25N mutation of the catalytic aspartate (PR20D25N) revealed three dimers with different flap conformations. The diverse conformations of PR20D25N included a dimer with one flap in a unique "tucked" conformation; directed into the active site. Analysis of molecular dynamics (MD) simulations of the ligand-free PR20 and wild-type enzymes showed that the mutations in PR20 alter the correlated interactions between two monomers in the dimer. The two flaps tend to fluctuate more independently in PR20 than in the wild type enzyme. Combining the results of structural analysis by X-ray crystallography and MD simulations; unusual flap conformations and weakly correlated inter-subunit motions may contribute to the high level resistance of PR20.
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37
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Louis JM, Deshmukh L, Sayer JM, Aniana A, Clore GM. Mutations Proximal to Sites of Autoproteolysis and the α-Helix That Co-evolve under Drug Pressure Modulate the Autoprocessing and Vitality of HIV-1 Protease. Biochemistry 2015; 54:5414-24. [PMID: 26266692 DOI: 10.1021/acs.biochem.5b00759] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
N-Terminal self-cleavage (autoprocessing) of the HIV-1 protease precursor is crucial for liberating the active dimer. Under drug pressure, evolving mutations are predicted to modulate autoprocessing, and the reduced catalytic activity of the mature protease (PR) is likely compensated by enhanced conformational/dimer stability and reduced susceptibility to self-degradation (autoproteolysis). One such highly evolved, multidrug resistant protease, PR20, bears 19 mutations contiguous to sites of autoproteolysis in retroviral proteases, namely clusters 1-3 comprising residues 30-37, 60-67, and 88-95, respectively, accounting for 11 of the 19 mutations. By systematically replacing corresponding clusters in PR with those of PR20, and vice versa, we assess their influence on the properties mentioned above and observe no strict correlation. A 10-35-fold decrease in the cleavage efficiency of peptide substrates by PR20, relative to PR, is reflected by an only ∼4-fold decrease in the rate of Gag processing with no change in cleavage order. Importantly, optimal N-terminal autoprocessing requires all 19 PR20 mutations as evaluated in vitro using the model precursor TFR-PR20 in which PR is flanked by the transframe region. Substituting PR20 cluster 3 into TFR-PR (TFR-PR(PR20-3)) requires the presence of PR20 cluster 1 and/or 2 for autoprocessing. In accordance, substituting PR clusters 1 and 2 into TFR-PR20 affects the rate of autoprocessing more drastically (>300-fold) compared to that of TFR-PR(PR20-3) because of the cumulative effect of eight noncluster mutations present in TFR-PR20(PR-12). Overall, these studies imply that drug resistance involves a complex synchronized selection of mutations modulating all of the properties mentioned above governing PR regulation and function.
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Affiliation(s)
- John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services , Bethesda, Maryland 20892, United States
| | - Lalit Deshmukh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services , Bethesda, Maryland 20892, United States
| | - Jane M Sayer
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services , Bethesda, Maryland 20892, United States
| | - Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services , Bethesda, Maryland 20892, United States
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services , Bethesda, Maryland 20892, United States
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38
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Agniswamy J, Louis JM, Shen CH, Yashchuk S, Ghosh AK, Weber IT. Substituted Bis-THF Protease Inhibitors with Improved Potency against Highly Resistant Mature HIV-1 Protease PR20. J Med Chem 2015; 58:5088-95. [PMID: 26010498 DOI: 10.1021/acs.jmedchem.5b00474] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An extremely drug resistant mutant of HIV-1 protease (PR) bearing 20 mutations (PR20) has been studied with two potent antiviral investigational inhibitors. GRL-5010A and GRL-4410A were designed to introduce hydrogen bond interactions with the flexible flaps of the PR by incorporating gem-difluorines and alkoxy, respectively, at the C4 position of the bis-THF of darunavir. PR20 provides an excellent model for high level resistance, since clinical inhibitors are >1000-fold less active on PR20 than on wild-type enzyme. GRL-5010A and GRL-4410A show inhibition constants of 4.3 ± 7.0 and 1.7 ± 1.8 nM, respectively, for PR20, compared to the binding affinity of 41 ± 1 nM measured for darunavir. Crystal structures of PR20 in complexes with the two inhibitors confirmed the new hydrogen bond interactions with Gly 48 in the flap of the enzyme. The two new compounds are more effective than darunavir in inhibiting mature PR20 and show promise for further development of antiviral agents targeting highly resistant PR mutants.
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Affiliation(s)
- Johnson Agniswamy
- †Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
| | - John M Louis
- ‡Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, United States
| | - Chen-Hsiang Shen
- †Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
| | - Sofiya Yashchuk
- §Department of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Arun K Ghosh
- §Department of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Irene T Weber
- †Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
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39
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Counts CJ, Ho PS, Donlin MJ, Tavis JE, Chen C. A Functional Interplay between Human Immunodeficiency Virus Type 1 Protease Residues 77 and 93 Involved in Differential Regulation of Precursor Autoprocessing and Mature Protease Activity. PLoS One 2015; 10:e0123561. [PMID: 25893662 PMCID: PMC4404164 DOI: 10.1371/journal.pone.0123561] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 03/04/2015] [Indexed: 11/18/2022] Open
Abstract
HIV-1 protease (PR) is a viral enzyme vital to the production of infectious virions. It is initially synthesized as part of the Gag-Pol polyprotein precursor in the infected cell. The free mature PR is liberated as a result of precursor autoprocessing upon virion release. We previously described a model system to examine autoprocessing in transfected mammalian cells. Here, we report that a covariance analysis of miniprecursor (p6*-PR) sequences derived from drug naïve patients identified a series of amino acid pairs that vary together across independent viral isolates. These covariance pairs were used to build the first topology map of the miniprecursor that suggests high levels of interaction between the p6* peptide and the mature PR. Additionally, several PR-PR covariance pairs are located far from each other (>12 Å Cα to Cα) relative to their positions in the mature PR structure. Biochemical characterization of one such covariance pair (77-93) revealed that each residue shows distinct preference for one of three alkyl amino acids (V, I, and L) and that a polar or charged amino acid at either of these two positions abolishes precursor autoprocessing. The most commonly observed 77V is preferred by the most commonly observed 93I, but the 77I variant is preferred by other 93 variances (L, V, or M) in supporting precursor autoprocessing. Furthermore, the 77I93V covariant enhanced precursor autoprocessing and Gag polyprotein processing but decreased the mature PR activity. Therefore, both covariance and biochemical analyses support a functional association between residues 77 and 93, which are spatially distant from each other in the mature PR structure. Our data also suggests that these covariance pairs differentially regulate precursor autoprocessing and the mature protease activity.
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Affiliation(s)
- Christopher J. Counts
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - P. Shing Ho
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Maureen J. Donlin
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
- Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - John E. Tavis
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
- Saint Louis University Liver Center, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Chaoping Chen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
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40
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Potempa M, Lee SK, Wolfenden R, Swanstrom R. The triple threat of HIV-1 protease inhibitors. Curr Top Microbiol Immunol 2015; 389:203-41. [PMID: 25778681 DOI: 10.1007/82_2015_438] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Newly released human immunodeficiency virus type 1 (HIV-1) particles obligatorily undergo a maturation process to become infectious. The HIV-1 protease (PR) initiates this step, catalyzing the cleavage of the Gag and Gag-Pro-Pol structural polyproteins. Proper organization of the mature virus core requires that cleavage of these polyprotein substrates proceeds in a highly regulated, specific series of events. The vital role the HIV-1 PR plays in the viral life cycle has made it an extremely attractive target for inhibition and has accordingly fostered the development of a number of highly potent substrate-analog inhibitors. Though the PR inhibitors (PIs) inhibit only the HIV-1 PR, their effects manifest at multiple different stages in the life cycle due to the critical importance of the PR in preparing the virus for these subsequent events. Effectively, PIs masquerade as entry inhibitors, reverse transcription inhibitors, and potentially even inhibitors of post-reverse transcription steps. In this chapter, we review the triple threat of PIs: the intermolecular cooperativity in the form of a cooperative dose-response for inhibition in which the apparent potency increases with increasing inhibition; the pleiotropic effects of HIV-1 PR inhibition on entry, reverse transcription, and post-reverse transcription steps; and their potency as transition state analogs that have the potential for further improvement that could lead to an inability of the virus to evolve resistance in the context of single drug therapy.
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Affiliation(s)
- Marc Potempa
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, 27599, USA
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41
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Roche J, Louis JM, Bax A. Conformation of inhibitor-free HIV-1 protease derived from NMR spectroscopy in a weakly oriented solution. Chembiochem 2014; 16:214-8. [PMID: 25470009 DOI: 10.1002/cbic.201402585] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Indexed: 11/06/2022]
Abstract
Flexibility of the glycine-rich flaps is known to be essential for catalytic activity of the HIV-1 protease, but their exact conformations at the different stages of the enzymatic pathway remain subject to much debate. Although hundreds of crystal structures of protease-inhibitor complexes have been solved, only about a dozen inhibitor-free protease structures have been reported. These latter structures reveal a large diversity of flap conformations, ranging from closed to semi-open to wide open. To evaluate the average structure in solution, we measured residual dipolar couplings (RDCs) and compared these to values calculated for crystal structures representative of the closed, semi-open, and wide-open states. The RDC data clearly indicate that the inhibitor-free protease, on average, adopts a closed conformation in solution that is very similar to the inhibitor-bound state. By contrast, a highly drug-resistant protease mutant, PR20, adopts the wide-open flap conformation.
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Affiliation(s)
- Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892 (USA).
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42
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Caldarini M, Sonar P, Valpapuram I, Tavella D, Volonté C, Pandini V, Vanoni M, Aliverti A, Broglia R, Tiana G, Cecconi C. The complex folding behavior of HIV-1-protease monomer revealed by optical-tweezer single-molecule experiments and molecular dynamics simulations. Biophys Chem 2014; 195:32-42. [DOI: 10.1016/j.bpc.2014.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/04/2014] [Accepted: 08/04/2014] [Indexed: 12/11/2022]
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43
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Cruz R, Huesgen P, Riley SP, Wlodawer A, Faro C, Overall CM, Martinez JJ, Simões I. RC1339/APRc from Rickettsia conorii is a novel aspartic protease with properties of retropepsin-like enzymes. PLoS Pathog 2014; 10:e1004324. [PMID: 25144529 PMCID: PMC4140852 DOI: 10.1371/journal.ppat.1004324] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 07/09/2014] [Indexed: 11/18/2022] Open
Abstract
Members of the species Rickettsia are obligate intracellular, gram-negative, arthropod-borne pathogens of humans and other mammals. The life-threatening character of diseases caused by many Rickettsia species and the lack of reliable protective vaccine against rickettsioses strengthens the importance of identifying new protein factors for the potential development of innovative therapeutic tools. Herein, we report the identification and characterization of a novel membrane-embedded retropepsin-like homologue, highly conserved in 55 Rickettsia genomes. Using R. conorii gene homologue RC1339 as our working model, we demonstrate that, despite the low overall sequence similarity to retropepsins, the gene product of rc1339 APRc (for Aspartic Protease from Rickettsia conorii) is an active enzyme with features highly reminiscent of this family of aspartic proteases, such as autolytic activity impaired by mutation of the catalytic aspartate, accumulation in the dimeric form, optimal activity at pH 6, and inhibition by specific HIV-1 protease inhibitors. Moreover, specificity preferences determined by a high-throughput profiling approach confirmed common preferences between this novel rickettsial enzyme and other aspartic proteases, both retropepsins and pepsin-like. This is the first report on a retropepsin-like protease in gram-negative intracellular bacteria such as Rickettsia, contributing to the analysis of the evolutionary relationships between the two types of aspartic proteases. Additionally, we have also shown that APRc is transcribed and translated in R. conorii and R. rickettsii and is integrated into the outer membrane of both species. Finally, we demonstrated that APRc is sufficient to catalyze the in vitro processing of two conserved high molecular weight autotransporter adhesin/invasion proteins, Sca5/OmpB and Sca0/OmpA, thereby suggesting the participation of this enzyme in a relevant proteolytic pathway in rickettsial life-cycle. As a novel bona fide member of the retropepsin family of aspartic proteases, APRc emerges as an intriguing target for therapeutic intervention against fatal rickettsioses. Several rickettsiae are pathogenic to humans by causing severe infections, including epidemic typhus (Rickettsia prowazekii), Rocky Mountain spotted fever (Rickettsia rickettsii), and Mediterranean spotted fever (Rickettsia conorii). Progress in correlating rickettsial genes and gene functions has been greatly hampered by the intrinsic difficulty in working with these obligate intracellular bacteria, despite the increasing insights into the mechanisms of pathogenesis of and the immune response to rickettsioses. Therefore, comparison of the multiple available genomes of Rickettsia is proving to be the most practical method to identify new factors that may play a role in pathogenicity. Here, we identified and characterized a novel retropepsin-like enzyme, APRc, that is expressed by at least two pathogenic rickettsial species, R. conorii and R. rickettsii. We have also established that APRc acts to process two major surface antigen/virulence determinants (OmpB/Sca5, OmpA/Sca0) in vitro and we suggest that this processing event is important for protein function. We demonstrate that APRc is specifically inhibited by drugs clinically used to treat HIV infections, providing the exciting possibility of targeting this enzyme for therapeutic intervention. With this work, we demonstrate that retropepsin-type aspartic proteases are indeed present in prokaryotes, suggesting that these enzymes may represent an ancestral form of these proteases.
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Affiliation(s)
- Rui Cruz
- The Center for Neuroscience and Cell Biology (CNC), Coimbra, Portugal
- Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - Pitter Huesgen
- Centre for Blood Research and Department of Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean P. Riley
- Vector-Borne Diseases Laboratories, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Carlos Faro
- The Center for Neuroscience and Cell Biology (CNC), Coimbra, Portugal
- Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
| | - Christopher M. Overall
- Centre for Blood Research and Department of Biological and Medical Sciences, Faculty of Dentistry, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Juan J. Martinez
- Vector-Borne Diseases Laboratories, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail: (JJM); (IS)
| | - Isaura Simões
- The Center for Neuroscience and Cell Biology (CNC), Coimbra, Portugal
- Biocant, Biotechnology Innovation Center, Cantanhede, Portugal
- * E-mail: (JJM); (IS)
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44
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Dimerization of HIV-1 protease occurs through two steps relating to the mechanism of protease dimerization inhibition by darunavir. Proc Natl Acad Sci U S A 2014; 111:12234-9. [PMID: 25092296 DOI: 10.1073/pnas.1400027111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dimerization of HIV-1 protease (PR) subunits is an essential process for PR's acquisition of proteolytic activity, which plays a critical role in the maturation of HIV-1. Recombinant wild-type PR (PR(WT)) proved to dimerize, as examined with electrospray ionization mass spectrometry; however, two active site interface PR mutants (PR(T26A) and PR(R87K)) remained monomeric. On the other hand, two termini interface PR mutants (PR(1-C95A) and PR(97/99)) took both monomeric and dimeric forms. Differential scanning fluorimetry indicated that PR(1-C95A) and PR(97/99) dimers were substantially less stable than PR(WT) dimers. These data indicate that intermolecular interactions of two monomers occur first at the active site interface, generating unstable or transient dimers, and interactions at the termini interface subsequently occur, generating stable dimers. Darunavir (DRV), an HIV-1 protease inhibitor, inhibits not only proteolytic activity but also PR dimerization. DRV bound to protease monomers in a one-to-one molar ratio, inhibiting the first step of PR dimerization, whereas conventional protease inhibitors (such as saquinavir) that inhibit enzymatic activity but not dimerization failed to bind to monomers. DRV also bound to mutant PRs containing the transframe region-added PR (TFR-PR(D25N) and TFR-PR(D25N-7AA)), whereas saquinavir did not bind to TFR-PR(D25N) or TFR-PR(D25N-7AA). Notably, DRV failed to bind to mutant PR containing four amino acid substitutions (V32I, L33F, I54M, and I84V) that confer resistance to DRV on HIV-1. To our knowledge, the present report represents the first demonstration of the two-step PR dimerization dynamics and the mechanism of dimerization inhibition by DRV, which should help design further, more potent novel PIs.
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Zhang Y, Chang YCE, Louis JM, Wang YF, Harrison RW, Weber IT. Structures of darunavir-resistant HIV-1 protease mutant reveal atypical binding of darunavir to wide open flaps. ACS Chem Biol 2014; 9:1351-8. [PMID: 24738918 PMCID: PMC4076034 DOI: 10.1021/cb4008875] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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The molecular basis for high resistance
to clinical inhibitors
of HIV-1 protease (PR) was examined for the variant designated PRP51 that was selected for resistance to darunavir (DRV). High
resolution crystal structures of PRP51 with the active
site D25N mutation revealed a ligand-free form and an inhibitor-bound
form showing a unique binding site and orientation for DRV. This inactivating
mutation is known to increase the dimer dissociation constant and
decrease DRV affinity of PR. The PRP51-D25N dimers
were in the open conformation with widely separated flaps, as reported
for other highly resistant variants. PRP51-D25N dimer
bound two DRV molecules and showed larger separation of 8.7 Å
between the closest atoms of the two flaps compared with 4.4 Å
for the ligand-free structure of this mutant. The ligand-free structure,
however, lacked van der Waals contacts between Ile50 and Pro81′
from the other subunit in the dimer, unlike the majority of PR structures.
DRV is bound inside the active site cavity; however, the inhibitor
is oriented almost perpendicular to its typical position and exhibits
only 2 direct hydrogen bond and two water-mediated interactions with
atoms of PRP51-D25N compared with 11 hydrogen bond
interactions seen for DRV bound in the typical position in wild-type
enzyme. The atypical location of DRV may provide opportunities for
design of novel inhibitors targeting the open conformation of PR drug-resistant
mutants.
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Affiliation(s)
| | | | - John M. Louis
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, United States
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46
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Understanding HIV-1 protease autoprocessing for novel therapeutic development. Future Med Chem 2014; 5:1215-29. [PMID: 23859204 DOI: 10.4155/fmc.13.89] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In the infected cell, HIV-1 protease (PR) is initially synthesized as part of the GagPol polyprotein. PR autoprocessing is a virus-specific process by which the PR domain embedded in the precursor catalyzes proteolytic reactions responsible for liberation of free mature PRs, which then recognize and cleave at least ten different peptide sequences in the Gag and GagPol polyproteins. Despite extensive structure and function studies of the mature PRs as well as the successful development of ten US FDA-approved catalytic-site inhibitors, the precursor autoprocessing mechanism remains an intriguing yet-to-be-solved puzzle. This article discusses current understanding of the autoprocessing mechanism, in an effort to prompt the development of novel anti-HIV drugs that selectively target precursor autoprocessing.
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47
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Kimura S, Caldarini M, Broglia RA, Dokholyan NV, Tiana G. The maturation of HIV-1 protease precursor studied by discrete molecular dynamics. Proteins 2013; 82:633-9. [PMID: 24123234 DOI: 10.1002/prot.24440] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 09/06/2013] [Accepted: 09/26/2013] [Indexed: 11/08/2022]
Abstract
The equilibrium properties of a HIV-1-protease precursor are studied by means of an efficient molecular dynamics scheme, which allows for the simulation of the folding of the protein monomers and their dimerization into an active form and compare them with those of the mature protein. The results of the model provide, with atomic detail, an overall account of several experimental findings, including the NMR conformation of the mature dimer, the calorimetric properties of the system, the effects of the precursor tail on the dimerization constant, the secondary chemical shifts of the monomer, and the paramagnetic relaxation enhancement data associated with the conformations of the precursor. It is found that although the mature protein can dimerize in a unique, single way, the precursor populates several dimeric conformations in which monomers are always native-like, but their binding can be non-native.
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Affiliation(s)
- Sachie Kimura
- Department of Physics and INFN, Università degli Studi di Milano, Milano, 20133, Italy
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48
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Louis JM, Tözsér J, Roche J, Matúz K, Aniana A, Sayer JM. Enhanced stability of monomer fold correlates with extreme drug resistance of HIV-1 protease. Biochemistry 2013; 52:7678-88. [PMID: 24079831 PMCID: PMC3888107 DOI: 10.1021/bi400962r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
During treatment, mutations in HIV-1 protease (PR) are selected rapidly that confer resistance by decreasing affinity to clinical protease inhibitors (PIs). As these unique drug resistance mutations can compromise the fitness of the virus to replicate, mutations that restore conformational stability and activity while retaining drug resistance are selected on further evolution. Here we identify several compensating mechanisms by which an extreme drug-resistant mutant bearing 20 mutations (PR20) with >5-fold increased Kd and >4000-fold decreased affinity to the PI darunavir functions. (1) PR20 cleaves, albeit poorly, Gag polyprotein substrates essential for viral maturation. (2) PR20 dimer, which exhibits distinctly enhanced thermal stability, has highly attenuated autoproteolysis, thus likely prolonging its lifetime in vivo. (3) The enhanced stability of PR20 results from stabilization of the monomer fold. Both monomeric PR20(T26A) and dimeric PR20 exhibit Tm values 6-7.5 °C higher than those for their PR counterparts. Two specific mutations in PR20, L33F and L63P at sites of autoproteolysis, increase the Tm of monomeric PR(T26A) by ~8 °C, similar to PR20(T26A). However, without other compensatory mutations as seen in PR20, L33F and L63P substitutions, together, neither restrict autoproteolysis nor significantly reduce binding affinity to darunavir. To determine whether dimer stability contributes to binding affinity for inhibitors, we examined single-chain dimers of PR and PR(D25N) in which the corresponding identical monomer units were covalently linked by GGSSG sequence. Linking of the subunits did not appreciably change the ΔTm on inhibitor binding; thus stabilization by tethering appears to have little direct effect on enhancing inhibitor affinity.
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Affiliation(s)
- John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892
| | - József Tözsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary H-4012
| | - Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892
| | - Krisztina Matúz
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary H-4012
| | - Annie Aniana
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892
| | - Jane M. Sayer
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892
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49
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Agniswamy J, Shen CH, Wang YF, Ghosh AK, Rao KV, Xu CX, Sayer JM, Louis JM, Weber IT. Extreme multidrug resistant HIV-1 protease with 20 mutations is resistant to novel protease inhibitors with P1'-pyrrolidinone or P2-tris-tetrahydrofuran. J Med Chem 2013; 56:4017-27. [PMID: 23590295 DOI: 10.1021/jm400231v] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Extreme drug resistant mutant of HIV-1 protease (PR) bearing 20 mutations (PR20) has been studied with the clinical inhibitor amprenavir (1) and two potent antiviral investigational inhibitors GRL-02031 (2) and GRL-0519 (3). Clinical inhibitors are >1000-fold less active on PR20 than on wild-type enzyme, which is consistent with dissociation constants (KL) from isothermal titration calorimetry of 40 nM for 3, 178 nM for amprenavir, and 960 nM for 2. High resolution crystal structures of PR20-inhibitor complexes revealed altered interactions compared with the corresponding wild-type PR complexes in agreement with relative inhibition. Amprenavir lacks interactions due to PR20 mutations in the S2/S2' subsites relative to PR. Inhibitors 2 and 3 lose interactions with Arg8' in PR20 relative to the wild-type enzyme because Arg8' shifts to interact with mutated L10F side chain. Overall, inhibitor 3 compares favorably with darunavir in affinity for PR20 and shows promise for further development.
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Affiliation(s)
- Johnson Agniswamy
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, USA
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50
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Thirumurugan P, Matosiuk D, Jozwiak K. Click Chemistry for Drug Development and Diverse Chemical–Biology Applications. Chem Rev 2013; 113:4905-79. [DOI: 10.1021/cr200409f] [Citation(s) in RCA: 1309] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Prakasam Thirumurugan
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Dariusz Matosiuk
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Krzysztof Jozwiak
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
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