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Schmidt T, Louis JM, Marius Clore G. Probing the Interaction between HIV-1 Protease and the Homodimeric p66/p66' Reverse Transcriptase Precursor by Double Electron-Electron Resonance EPR Spectroscopy. Chembiochem 2020; 21:3051-3055. [PMID: 32558168 PMCID: PMC7678880 DOI: 10.1002/cbic.202000263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/16/2020] [Indexed: 11/08/2022]
Abstract
Following excision from the Gag-Pol polyprotein, HIV-1 reverse transcriptase is released as an asymmetric homodimer comprising two p66 subunits that are structurally dissimilar but identical in amino acid sequence. Subsequent cleavage of the RNase H domain from only one of the subunits, denoted p66', results in the formation of the mature p66/p51 enzyme in which catalytic activity resides in the p66 subunit, and the p51 subunit (derived from p66') provides a supporting structural scaffold. Here, we probe the interaction of the p66/p66' asymmetric reverse transcriptase precursor with HIV-1 protease by pulsed Q-band double electron-electron resonance EPR spectroscopy to measure distances between nitroxide labels introduced at surface-engineered cysteine residues. The data suggest that the flexible, exposed linker between the RNaseH and connection domains in the open state of the p66' subunit binds to the active site of protease in a configuration that is similar to that of extended peptide substrates.
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Affiliation(s)
- Thomas Schmidt
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520 (USA)
| | - John M. Louis
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520 (USA)
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520 (USA)
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2
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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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3
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Srb P, Svoboda M, Benda L, Lepšík M, Tarábek J, Šícha V, Grüner B, Grantz-Šašková K, Brynda J, Řezáčová P, Konvalinka J, Veverka V. Capturing a dynamically interacting inhibitor by paramagnetic NMR spectroscopy. Phys Chem Chem Phys 2019; 21:5661-5673. [PMID: 30794275 DOI: 10.1039/c9cp00416e] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Transient and fuzzy intermolecular interactions are fundamental to many biological processes. Despite their importance, they are notoriously challenging to characterize. Effects induced by paramagnetic ligands in the NMR spectra of interacting biomolecules provide an opportunity to amplify subtle manifestations of weak intermolecular interactions observed for diamagnetic ligands. Here, we present an approach to characterizing dynamic interactions between a partially flexible dimeric protein, HIV-1 protease, and a metallacarborane-based ligand, a system for which data obtained by standard NMR approaches do not enable detailed structural interpretation. We show that for the case where the experimental data are significantly averaged to values close to zero the standard fitting of pseudocontact shifts cannot provide reliable structural information. We based our approach on generating a large ensemble of full atomic models, for which the experimental data can be predicted, ensemble averaged and finally compared to the experiment. We demonstrate that a combination of paramagnetic NMR experiments, quantum chemical calculations, and molecular dynamics simulations offers a route towards structural characterization of dynamic protein-ligand complexes.
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Affiliation(s)
- Pavel Srb
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
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4
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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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5
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Potempa M, Lee SK, Kurt Yilmaz N, Nalivaika EA, Rogers A, Spielvogel E, Carter CW, Schiffer CA, Swanstrom R. HIV-1 Protease Uses Bi-Specific S2/S2' Subsites to Optimize Cleavage of Two Classes of Target Sites. J Mol Biol 2018; 430:5182-5195. [PMID: 30414407 DOI: 10.1016/j.jmb.2018.10.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 10/31/2018] [Accepted: 10/31/2018] [Indexed: 11/16/2022]
Abstract
Retroviral proteases (PRs) have a unique specificity that allows cleavage of sites with or without a P1' proline. A P1' proline is required at the MA/CA cleavage site due to its role in a post-cleavage conformational change in the capsid protein. However, the HIV-1 PR prefers to have large hydrophobic amino acids flanking the scissile bond, suggesting that PR recognizes two different classes of substrate sequences. We analyzed the cleavage rate of over 150 combinations of six different HIV-1 cleavage sites to explore rate determinants of cleavage. We found that cleavage rates are strongly influenced by the two amino acids flanking the amino acids at the scissile bond (P2-P1/P1'-P2'), with two complementary sets of rules. When P1' is proline, the P2 side chain interacts with a polar region in the S2 subsite of the PR, while the P2' amino acid interacts with a hydrophobic region of the S2' subsite. When P1' is not proline, the orientations of the P2 and P2' side chains with respect to the scissile bond are reversed; P2 residues interact with a hydrophobic face of the S2 subsite, while the P2' amino acid usually engages hydrophilic amino acids in the S2' subsite. These results reveal that the HIV-1 PR has evolved bi-functional S2 and S2' subsites to accommodate the steric effects imposed by a P1' proline on the orientation of P2 and P2' substrate side chains. These results also suggest a new strategy for inhibitor design to engage the multiple specificities in these subsites.
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Affiliation(s)
- Marc Potempa
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sook-Kyung Lee
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ellen A Nalivaika
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Amy Rogers
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ean Spielvogel
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Charles W Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ronald Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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6
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Nguyen VD, Nguyen HLT, Do LC, Van Tuan V, Thuong PT, Phan TN. A New Saponin with Anti-HIV-1 Protease Activity from Acacia pennata. Nat Prod Commun 2018. [DOI: 10.1177/1934578x1801300408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We investigated the phytochemicals from an ethanol extract of Acacia pennata (L.) Willd stems, a Vietnam medicinal plant, which led to the isolation of a new saponin termed 21β- O-[(2 E)-6-hydroxyl-2,6-dimethyl-2,7-octadienoyl] pitheduloside G (1), as well as pitheduloside G (2), a known saponin. The structures of compounds 1 and 2 were elucidated via spectroscopy and compared with those reported in the literature. The isolates (1 and 2) were tested for their inhibitory effects on human immunodeficiency virus type 1 (HIV-1) protease (PR). We found that the new compound, 21β- O-[(2 E)-6-hydroxyl-2,6-dimethyl-2,7-octadienoyl] pitheduloside G (1), possessed potent anti-HIV-1 PR activity, with a half-maximum inhibitory concentration (IC50) value of 2.0 ± 0.2 μM. In contrast, pitheduloside G (2) exhibited much less inhibition, with an IC50value of 18 ± 0.5 μM. Both compounds were nontoxic in human embryonic kidney 293T cells at concentrations effective against HIV-1 PR. This is the first report regarding the isolation of an anti-HIV-1 PR compound (1) from an Acacia plant species.
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Affiliation(s)
- Van-Dung Nguyen
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, 334 Nguyen Trai Street, ThanhXuan District, Hanoi, Vietnam
| | - Hong-Loan Thi Nguyen
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, 334 Nguyen Trai Street, ThanhXuan District, Hanoi, Vietnam
| | - Linh-Chi Do
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, 334 Nguyen Trai Street, ThanhXuan District, Hanoi, Vietnam
| | - Vu Van Tuan
- Department of Herbal Analysis and Standardization, National Institute of Medicinal Materials, 3B Quang Trung, Hanoi, Vietnam
| | - Phuong Thien Thuong
- Department of Herbal Analysis and Standardization, National Institute of Medicinal Materials, 3B Quang Trung, Hanoi, Vietnam
| | - Tuan-Nghia Phan
- Key Laboratory of Enzyme and Protein Technology, VNU University of Science, 334 Nguyen Trai Street, ThanhXuan District, Hanoi, Vietnam
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7
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Handa B, Keech E, Conway E, Broadhurst A, Ritchie A. Design and Synthesis of a Quenched Fluorogenic Peptide Substrate for Human Cytomegalovirus Proteinase. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029500600408] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A fluorogenic peptide substrate for HCMV proteinase was synthesized by solid-phase peptide synthesis. The amino acid sequence of this substrate is derived from the maturation cleavage site (M site) of the natural substrate, the assembly protein precursor. The minimum sequence for efficient cleavage requires at least seven residues (P4-P3′). A systematic modification of the peptide substrate was carried out to identify positions suitable for the introduction of the fluorescent donor and the quencher acceptor groups.
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Affiliation(s)
- B.K. Handa
- Department of Physical Methods, Roche Products Limited, PO Box 8, Welwyn Garden City, Hertfordshire AL7 3AY, UK
| | - E. Keech
- Department of Physical Methods, Roche Products Limited, PO Box 8, Welwyn Garden City, Hertfordshire AL7 3AY, UK
| | - E.A. Conway
- Department of Physical Methods, Roche Products Limited, PO Box 8, Welwyn Garden City, Hertfordshire AL7 3AY, UK
| | - A. Broadhurst
- Department of Biology, Roche Products Limited, PO Box 8, Welwyn Garden City, Hertfordshire AL7 3AY, UK
| | - A. Ritchie
- Department of Biology, Roche Products Limited, PO Box 8, Welwyn Garden City, Hertfordshire AL7 3AY, UK
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8
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Billich A, Billich S, Rosenwirth B. Assay Systems for HIV-1 Proteinase and Their Use for Evaluation of Inhibitors. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029100200201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- A. Billich
- Sandoz Forschungsinstitut GmbH, Department of AntiRetroviral Therapy, Brunnerstr. 59, A-1235 Vienna, Austria
| | - S. Billich
- Sandoz Forschungsinstitut GmbH, Department of AntiRetroviral Therapy, Brunnerstr. 59, A-1235 Vienna, Austria
| | - B. Rosenwirth
- Sandoz Forschungsinstitut GmbH, Department of AntiRetroviral Therapy, Brunnerstr. 59, A-1235 Vienna, Austria
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9
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Billich A, Scholz D, Charpiot B, Gstach H, Lehr P, Peichl P, Rosenwirth B. Potent and Orally Bioavailable HIV-1 Proteinase Inhibitors Containing the 2-aminobenzylstatine Moiety. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029500600507] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In order to design HIV proteinase inhibitors which combine antiviral potency in HIV-infected cells with good oral bioavailability, new derivatives of 2-aminobenzylstatine containing HIV-1 proteinase inhibitors were synthesized. Compounds showing the desired profile emerged from a series of modifications at the P3′ moiety of the parent inhibitor [1], and are characterized by the presence of hydroxy or methoxy substituents at the C-terminal benzylamide. The most potent congeners, compounds [15] and [19], were evaluated in more detail and proved inhibitory to HIV-1 replication in primary T4 lymphocytes with EC90 = 2.2 and 2.7 nM, respectively. They also exhibited adequate oral bioavailability in the range of [13] to 42% in mice and rats. Thus, further investigation of this type of HIV proteinase inhibitor seems warranted.
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Affiliation(s)
- A. Billich
- Sandoz Research Institute, Brunner Strasse 59, A-1235, Vienna, Austria
| | - D. Scholz
- Sandoz Research Institute, Brunner Strasse 59, A-1235, Vienna, Austria
| | - B. Charpiot
- Sandoz Research Institute, Brunner Strasse 59, A-1235, Vienna, Austria
| | - H. Gstach
- Sandoz Research Institute, Brunner Strasse 59, A-1235, Vienna, Austria
| | - P. Lehr
- Sandoz Research Institute, Brunner Strasse 59, A-1235, Vienna, Austria
| | - P. Peichl
- Sandoz Research Institute, Brunner Strasse 59, A-1235, Vienna, Austria
| | - B. Rosenwirth
- Sandoz Research Institute, Brunner Strasse 59, A-1235, Vienna, Austria
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10
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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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11
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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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12
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Konvalinka J, Kräusslich HG, Müller B. Retroviral proteases and their roles in virion maturation. Virology 2015; 479-480:403-17. [PMID: 25816761 DOI: 10.1016/j.virol.2015.03.021] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 02/12/2015] [Accepted: 03/05/2015] [Indexed: 10/23/2022]
Abstract
Proteolytic processing of viral polyproteins is essential for retrovirus infectivity. Retroviral proteases (PR) become activated during or after assembly of the immature, non-infectious virion. They cleave viral polyproteins at specific sites, inducing major structural rearrangements termed maturation. Maturation converts retroviral enzymes into their functional form, transforms the immature shell into a metastable state primed for early replication events, and enhances viral entry competence. Not only cleavage at all PR recognition sites, but also an ordered sequence of cleavages is crucial. Proteolysis is tightly regulated, but the triggering mechanisms and kinetics and pathway of morphological transitions remain enigmatic. Here, we outline PR structures and substrate specificities focusing on HIV PR as a therapeutic target. We discuss design and clinical success of HIV PR inhibitors, as well as resistance development towards these drugs. Finally, we summarize data elucidating the role of proteolysis in maturation and highlight unsolved questions regarding retroviral maturation.
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Affiliation(s)
- Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n. 2, 166 10 Prague 6, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43 Prague 2, Czech Republic
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit, Heidelberg, Germany.
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany; Molecular Medicine Partnership Unit, Heidelberg, Germany
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13
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Schimer J, Pávová M, Anders M, Pachl P, Šácha P, Cígler P, Weber J, Majer P, Řezáčová P, Kräusslich HG, Müller B, Konvalinka J. Triggering HIV polyprotein processing by light using rapid photodegradation of a tight-binding protease inhibitor. Nat Commun 2015; 6:6461. [PMID: 25751579 PMCID: PMC4366505 DOI: 10.1038/ncomms7461] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/29/2015] [Indexed: 12/23/2022] Open
Abstract
HIV protease (PR) is required for proteolytic maturation in the late phase of HIV replication and represents a prime therapeutic target. The regulation and kinetics of viral polyprotein processing and maturation are currently not understood in detail. Here we design, synthesize, validate and apply a potent, photodegradable HIV PR inhibitor to achieve synchronized induction of proteolysis. The compound exhibits subnanomolar inhibition in vitro. Its photolabile moiety is released on light irradiation, reducing the inhibitory potential by 4 orders of magnitude. We determine the structure of the PR-inhibitor complex, analyze its photolytic products, and show that the enzymatic activity of inhibited PR can be fully restored on inhibitor photolysis. We also demonstrate that proteolysis of immature HIV particles produced in the presence of the inhibitor can be rapidly triggered by light enabling thus to analyze the timing, regulation and spatial requirements of viral processing in real time. The study of HIV proteolysis during maturation and replication can be difficult since different steps in these processes occur simultaneously. Here, the authors present a photolabile HIV protease inhibitor which can be deactivated by light irradiation, allowing synchronized induction of viral maturation.
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Affiliation(s)
- Jiří Schimer
- 1] Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic [2] Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Marcela Pávová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic
| | - Maria Anders
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic
| | - Pavel Šácha
- 1] Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic [2] Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Petr Cígler
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic
| | - Jan Weber
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic
| | - Pavel Majer
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic
| | - Hans-Georg Kräusslich
- 1] Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany [2] Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Barbara Müller
- 1] Department of Infectious Diseases, Virology, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany [2] Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Jan Konvalinka
- 1] Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo n.2, 166 10, Prague 6, Czech Republic [2] Department of Biochemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague 2, Czech Republic
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14
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Yedidi RS, Muhuhi JM, Liu Z, Bencze KZ, Koupparis K, O'Connor CE, Kovari IA, Spaller MR, Kovari LC. Design, synthesis and evaluation of a potent substrate analog inhibitor identified by scanning Ala/Phe mutagenesis, mimicking substrate co-evolution, against multidrug-resistant HIV-1 protease. Biochem Biophys Res Commun 2013; 438:703-8. [PMID: 23921229 DOI: 10.1016/j.bbrc.2013.07.117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 07/28/2013] [Indexed: 10/26/2022]
Abstract
Multidrug-resistant (MDR) clinical isolate-769, human immunodeficiency virus type-1 (HIV-1) protease (PDB ID: 1TW7), was shown to exhibit wide-open flaps and an expanded active site cavity, causing loss of contacts with protease inhibitors. In the current study, the expanded active site cavity of MDR769 HIV-1 protease was screened with a series of peptide-inhibitors that were designed to mimic the natural substrate cleavage site, capsid/p2. Scanning Ala/Phe chemical mutagenesis approach was incorporated into the design of the peptide series to mimic the substrate co-evolution. Among the peptides synthesized and evaluated, a lead peptide (6a) with potent activity (IC50: 4.4nM) was identified against the MDR769 HIV-1 protease. Isothermal titration calorimetry data showed favorable binding profile for 6a against both wild type and MDR769 HIV-1 protease variants. Nuclear magnetic resonance spectrum of (15)N-labeled MDR769 HIV-1 protease in complex with 6a showed some major perturbations in chemical shift, supporting the peptide induced conformational changes in protease. Modeling analysis revealed multiple contacts between 6a and MDR769 HIV-1 protease. The lead peptide-inhibitor, 6a, with high potency and good binding profile can be used as the basis for developing potent small molecule inhibitors against MDR variants of HIV.
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Affiliation(s)
- Ravikiran S Yedidi
- Department of Biochemistry and Molecular Biology, School of Medicine, Wayne State University, Detroit, MI 48201, USA
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15
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Pokorná J, Heyda J, Konvalinka J. Ion specific effects of alkali cations on the catalytic activity of HIV-1 protease. Faraday Discuss 2013; 160:359-70; discussion 389-403. [PMID: 23795510 DOI: 10.1039/c2fd20094e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Human immunodeficiency virus 1 protease (HIV-1 PR), an important therapeutic target for the treatment of AIDS, is one of the most well-studied enzymes. However, there is still much to learn about the regulation of the activity and inhibition of this key viral enzyme. Specifically, the mechanism of activation of HIV-1 PR from the viral polyprotein upon HIV maturation is still not understood. It has been suggested that external factors like pH or salt concentration might contribute to regulation of this crucial step in the viral life cycle. Recently, we analyzed the activity of HIV-1 PR in aqueous solutions of sodium and potassium chloride by experimental determination of enzyme kinetics and molecular dynamics simulations. We showed that the effect of salt concentration is cation-specific [Heyda et al., Phys. Chem. Chem. Phys., 2009 (11), 7599]. In this study, we extended this analysis for other alkali cations and found that the dependence of the initial velocity of peptide substrate hydrolysis on the nature of the cation follows the Hofmeister series, with the exception of caesium. Significantly higher catalytic efficiencies both in terms of substrate binding (K(M)) and turnover number (kcat) are observed in the presence of K+ compared to Na+ or Li+ at corresponding salt concentrations. Molecular dynamics simulations suggest that both lithium and sodium are attracted more strongly than potassium and caesium to the protein surface, mostly due to stronger interactions with carboxylate side chain groups of aspartates and glutamates. Furthermore, we observed a surprising decrease in the K(M) value for a specific substrate at very low salt concentration. The molecular mechanism of this phenomenon will be further analyzed.
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Affiliation(s)
- Jana Pokorná
- Gilead and IOCB Research Center Prague, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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16
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Schimer J, Cígler P, Veselý J, Grantz Šašková K, Lepšík M, Brynda J, Řezáčová P, Kožíšek M, Císařová I, Oberwinkler H, Kraeusslich HG, Konvalinka J. Structure-Aided Design of Novel Inhibitors of HIV Protease Based on a Benzodiazepine Scaffold. J Med Chem 2012; 55:10130-5. [DOI: 10.1021/jm301249q] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jiří Schimer
- Institute of Organic Chemistry
and Biochemistry, Gilead Sciences and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo
n. 2, 166 10, Prague 6, Czech Republic
| | - Petr Cígler
- Institute of Organic Chemistry
and Biochemistry, Gilead Sciences and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo
n. 2, 166 10, Prague 6, Czech Republic
| | | | - Klára Grantz Šašková
- Institute of Organic Chemistry
and Biochemistry, Gilead Sciences and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo
n. 2, 166 10, Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry
and Biochemistry, Gilead Sciences and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo
n. 2, 166 10, Prague 6, Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry
and Biochemistry, Gilead Sciences and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo
n. 2, 166 10, Prague 6, Czech Republic
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic,
Vídeňská 1083, Prague 4, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry
and Biochemistry, Gilead Sciences and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo
n. 2, 166 10, Prague 6, Czech Republic
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic,
Vídeňská 1083, Prague 4, Czech Republic
| | - Milan Kožíšek
- Institute of Organic Chemistry
and Biochemistry, Gilead Sciences and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo
n. 2, 166 10, Prague 6, Czech Republic
| | | | - Heike Oberwinkler
- Department of Infectious Diseases,
Virology, Heidelberg University, Im Neuenheimer
Feld 324, 69120 Heidelberg,
Germany
| | - Hans-Georg Kraeusslich
- Department of Infectious Diseases,
Virology, Heidelberg University, Im Neuenheimer
Feld 324, 69120 Heidelberg,
Germany
| | - Jan Konvalinka
- Institute of Organic Chemistry
and Biochemistry, Gilead Sciences and IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo
n. 2, 166 10, Prague 6, Czech Republic
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17
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Sayer JM, Aniana A, Louis JM. Mechanism of dissociative inhibition of HIV protease and its autoprocessing from a precursor. J Mol Biol 2012; 422:230-44. [PMID: 22659320 DOI: 10.1016/j.jmb.2012.05.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 05/15/2012] [Accepted: 05/15/2012] [Indexed: 11/17/2022]
Abstract
Dimerization is indispensible for release of the human immunodeficiency virus protease (PR) from its precursor (Gag-Pol) and ensuing mature-like catalytic activity that is crucial for virus maturation. We show that a single-chain Fv fragment (scFv) of a previously reported monoclonal antibody (mAb1696), which recognizes the N-terminus of PR, dissociates a dimeric mature D25N PR mutant with an enhanced dimer dissociation constant (K(d)) in the sub-micromolar range to form predominantly a monomer-scFv complex at a 1:1 ratio, along with small (5-10%) amounts of a dimer-scFv complex. Enzyme kinetics indicate a mixed mechanism of inhibition of the wild-type PR, which exhibits a K(d)<10nM, with effects both on K(m) and k(cat) at an scFv-to-PR ratio of 10:1. ScFv binds to the N-terminal peptide P(1)QITLW(6) of PR and to PR monomers with dissociation constants of ≤30 nM and ~100 nM, respectively. Consistent with an ~400-fold increase in the dissociation of the antibody (K(Ab)) on even addition of an acetyl group to P(1) of the peptide, the antibody fails to inhibit N-terminal autoprocessing of the PR from a model precursor (at ~5 μM). However, subsequent to this cleavage, it sequesters the PR, thus blocking autoprocessing at its C-terminus. A second monoclonal antibody [PRM1 (human monoclonal antibody to PR)], which recognizes part of the flap region (residues 41-47) of the mature PR and its precursor, does not inhibit autoprocessing and ensuing catalytic activity. However, its failure to recognize drug-resistant clinical mutants of PR may be beneficial to monitor the selection of mutations in this region under drug pressure.
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Affiliation(s)
- Jane M Sayer
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD 20892, USA
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18
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Mutations in HIV-1 gag and pol compensate for the loss of viral fitness caused by a highly mutated protease. Antimicrob Agents Chemother 2012; 56:4320-30. [PMID: 22644035 DOI: 10.1128/aac.00465-12] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During the last few decades, the treatment of HIV-infected patients by highly active antiretroviral therapy, including protease inhibitors (PIs), has become standard. Here, we present results of analysis of a patient-derived, multiresistant HIV-1 CRF02_AG recombinant strain with a highly mutated protease (PR) coding sequence, where up to 19 coding mutations have accumulated in the PR. The results of biochemical analysis in vitro showed that the patient-derived PR is highly resistant to most of the currently used PIs and that it also exhibits very poor catalytic activity. Determination of the crystal structure revealed prominent changes in the flap elbow region and S1/S1' active site subsites. While viral loads in the patient were found to be high, the insertion of the patient-derived PR into a HIV-1 subtype B backbone resulted in reduction of infectivity by 3 orders of magnitude. Fitness compensation was not achieved by elevated polymerase (Pol) expression, but the introduction of patient-derived gag and pol sequences in a CRF02_AG backbone rescued viral infectivity to near wild-type (wt) levels. The mutations that accumulated in the vicinity of the processing sites spanning the p2/NC, NC/p1, and p6pol/PR proteins lead to much more efficient hydrolysis of corresponding peptides by patient-derived PR in comparison to the wt enzyme. This indicates a very efficient coevolution of enzyme and substrate maintaining high viral loads in vivo under constant drug pressure.
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19
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Ivanov AS, Gnedenko OV, Molnar AA, Mezentsev YV, Lisitsa AV, Archakov AI. PROTEIN–PROTEIN INTERACTIONS AS NEW TARGETS FOR DRUG DESIGN: VIRTUAL AND EXPERIMENTAL APPROACHES. J Bioinform Comput Biol 2011; 5:579-92. [PMID: 17636863 DOI: 10.1142/s0219720007002825] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 02/08/2007] [Accepted: 02/08/2007] [Indexed: 11/18/2022]
Abstract
Protein–protein and protein–ligand interactions play a central role in biochemical reactions, and understanding these processes is an important task in different fields of biomedical science and drug discovery. Proteins often work in complex assemblies of several macromolecules and small ligands. The structural and functional description of protein–protein interactions (PPI) is very important for basic-, as well as applied research. The interface areas of protein complexes have unique structure and properties, so PPI represent prospective targets for a new generation of drugs. One of the key targets of PPI inhibitors are oligomeric enzymes. This report shows interactive links between virtual and experimental approaches in a total pipeline "from gene to drug" and using Surface Plasmon Resonance technology for experimentally assessing PPI. Our research is conducted on two oligomeric enzymes — HIV-1 protease (HIVp) (homo-dimer) and bacterial L-asparaginase (homo-tetramer). Using methods of molecular modeling and computational alanine scanning we obtained structural and functional description of PPI in these two enzymes. We also presented a real example of application of integral approach in searching inhibitors of HIVp dimerization — from virtual database mining up to experimental testing of lead compounds.
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Affiliation(s)
- Alexis S Ivanov
- V.N.Orechovich Institute of Biomedical Chemistry RAMS, Pogodinskaya str. 10, Moscow, 119121, Russia.
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20
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Li M, Gustchina A, Matúz K, Tözsér J, Namwong S, Goldfarb NE, Dunn BM, Wlodawer A. Structural and biochemical characterization of the inhibitor complexes of xenotropic murine leukemia virus-related virus protease. FEBS J 2011; 278:4413-24. [PMID: 21951660 DOI: 10.1111/j.1742-4658.2011.08364.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interactions between the protease (PR) encoded by the xenotropic murine leukemia virus-related virus and a number of potential inhibitors have been investigated by biochemical and structural techniques. It was observed that several inhibitors used clinically against HIV PR exhibit nanomolar or even subnanomolar values of K(i) , depending on the exact experimental conditions. Both TL-3, a universal inhibitor of retroviral PRs, and some inhibitors originally shown to inhibit plasmepsins were also quite potent, whereas inhibition by pepstatin A was considerably weaker. Crystal structures of the complexes of xenotropic murine leukemia virus-related virus PR with TL-3, amprenavir and pepstatin A were solved at high resolution and compared with the structures of complexes of these inhibitors with other retropepsins. Whereas TL-3 and amprenavir bound in a predictable manner, spanning the substrate-binding site of the enzyme, two molecules of pepstatin A bound simultaneously in an unprecedented manner, leaving the catalytic water molecule in place.
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Affiliation(s)
- Mi Li
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702-1201, USA
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21
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Zhao H, Holmes SS, Baker GA, Challa S, Bose HS, Song Z. Ionic derivatives of betulinic acid as novel HIV-1 protease inhibitors. J Enzyme Inhib Med Chem 2011; 27:715-21. [PMID: 21985312 DOI: 10.3109/14756366.2011.611134] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Betulinic acid is a natural product possessing abundant and favourable biological activity, including anti-cancer, anti-malarial, anti-inflammatory and anti-HIV properties, while causing minimal toxicity to unaffected cells. The full biological potency of betulinic acid cannot be fully unlocked, however, for a number of reasons, a primary one being its limited solubility in aqueous and biologically pertinent organic media. Aiming to improve the water solubility of betulinic acid without disrupting its structurally related bioactivity, we have prepared different ionic derivatives of betulinic acid. Inhibition bioassays on HIV-1 protease-catalysed peptide hydrolysis indicate significantly improved performance resulting from converting the betulinic acid to organic salt form. Indeed, for one particular cholinium-based derivative, its water solubility is improved more than 100 times and the half maximal inhibitory concentration (IC(50)) value (22 μg mL(-1)) was one-third that of wide-type betulinic acid (60 μg mL(-1)). These encouraging results advise that additional studies of ionic betulinic acid derivatives as a therapeutic solution against HIV-1 infection are warranted.
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Affiliation(s)
- Hua Zhao
- Department of Natural Sciences, Savannah State University, Savannah, GA 31404, USA.
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22
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Pecina A, Přenosil O, Fanfrlík J, Řezáč J, Granatier J, Hobza P, Lepšík M. On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes. ACTA ACUST UNITED AC 2011. [DOI: 10.1135/cccc2011035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A novel computational protocol for determining the most probable protonation states in protein/ligand complexes is presented. The method consists in treating large parts of the enzyme using the corrected semiempirical quantum chemical (QM) method – PM6-D2 for optimization and PM6-DH2 for single-point energies – while the rest is calculated using molecular mechanics (MM) within a hybrid QM/MM fashion. The surrounding solvent is approximated by an implicit model. This approach is applied to two model systems, two different carboxylate pairs in one general and one unique HIV-1 protease/inhibitor complex. The effect of the size of the movable QM part is investigated in a series of several sizes, 3-, 6-, 8- and 10-Å regions surrounding the inhibitor. For the smallest region (< 450 atoms) the computationally more costly DFT QM/MM optimizations are performed as a check of the correctness. Proton transfer (PT) phenomena occur at both the PM6-D2 and DFT levels, which underlines the requirement for a QM approach. The barriers of PT are checked in model carboxylic acid pairs using the highly accurate MP2 and CCSD(T) values. An important result of this study is the fine-tuning of the protocol which can be used in further applications; its limitations are also shown, pointing to future developments. The calculations reveal which protonation variants of the active site are the most stable. In conclusion, the presented protocol can also be utilized for defining probable isomers in biomolecular systems. It can also serve as a preparatory step for further interaction-energy and binding-score calculations.
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23
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Kay J, Dunn BM. Substrate specificity and inhibitors of aspartic proteinases. Scandinavian Journal of Clinical and Laboratory Investigation 2011. [DOI: 10.1080/00365519209104651] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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24
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Fanfrlík J, Bronowska AK, Rezác J, Prenosil O, Konvalinka J, Hobza P. A reliable docking/scoring scheme based on the semiempirical quantum mechanical PM6-DH2 method accurately covering dispersion and H-bonding: HIV-1 protease with 22 ligands. J Phys Chem B 2011; 114:12666-78. [PMID: 20839830 DOI: 10.1021/jp1032965] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this study, we introduce a fast and reliable rescoring scheme for docked complexes based on a semiempirical quantum mechanical PM6-DH2 method. The method utilizes a PM6-based Hamiltonian with corrections for dispersion energy and hydrogen bonds. The total score is constructed as the sum of the PM6-DH2 interaction enthalpy, the empirical force field (AMBER) interaction entropy, and the sum of the deformation (PM6-DH2, SMD) and the desolvation (SMD) energies of the ligand. The main advantage of the procedure is the fact that we do not add any empirical parameter for either an individual component of the total score or an individual protein-ligand complex. This rescoring method is applied to a very challenging system, namely, the HIV-1 protease with a set of ligands. As opposed to the conventional DOCK procedure, the PM6-DH2 rescoring based on all of the terms distinguishes between binders and nonbinders and provides a reliable correlation of the theoretical and experimental binding free energies. Such a dramatic improvement, resulting from the PM6-DH2 rescoring of all the complexes, provides a valuable yet inexpensive tool for rational drug discovery and de novo ligand design.
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Affiliation(s)
- Jindrich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague 6, Czech Republic
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25
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Louis JM, Ishima R, Aniana A, Sayer JM. Revealing the dimer dissociation and existence of a folded monomer of the mature HIV-2 protease. Protein Sci 2010; 18:2442-53. [PMID: 19798742 DOI: 10.1002/pro.261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Purification and in vitro protein-folding schemes were developed to produce monodisperse samples of the mature wild-type HIV-2 protease (PR2), enabling a comprehensive set of biochemical and biophysical studies to assess the dissociation of the dimeric protease. An E37K substitution in PR2 significantly retards autoproteolytic cleavage during expression. Furthermore, it permits convenient measurement of the dimer dissociation of PR2(E37K) (elevated K(d) approximately 20 nM) by enzyme kinetics. Differential scanning calorimetry reveals a T(m) of 60.5 for PR2 as compared with 65.7 degrees C for HIV-1 protease (PR1). Consistent with weaker binding of the clinical inhibitor darunavir (DRV) to PR2, the T(m) of PR2 increases by 14.8 degrees C in the presence of DRV as compared with 22.4 degrees C for PR1. Dimer interface mutations, such as a T26A substitution in the active site (PR2(T26A)) or a deletion of the C-terminal residues 96-99 (PR2(1-95)), drastically increase the K(d) (>10(5)-fold). PR2(T26A) and PR2(1-95) consist predominantly of folded monomers, as determined by nuclear magnetic resonance (NMR) and size-exclusion chromatography coupled with multiangle light scattering and refractive index measurements (SMR), whereas wild-type PR2 and its active-site mutant PR2(D25N) are folded dimers. Addition of twofold excess active-site inhibitor promotes dimerization of PR2(T26A) but not of PR2(1-95), indicating that subunit interactions involving the C-terminal residues are crucial for dimer formation. Use of SMR and NMR with PR2 facilitates probing for potential inhibitors that restrict protein folding and/or dimerization and, thus, may provide insights for the future design of inhibitors to circumvent drug resistance.
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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, USA.
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26
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Vathipadiekal V, Umasankar PK, Patole MS, Rao M. Molecular cloning, over expression, and activity studies of a peptidic HIV-1 protease inhibitor: designed synthetic gene to functional recombinant peptide. Peptides 2010; 31:16-21. [PMID: 19818820 DOI: 10.1016/j.peptides.2009.09.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 09/29/2009] [Accepted: 09/29/2009] [Indexed: 11/18/2022]
Abstract
The aspartic protease inhibitor (ATBI) purified from a Bacillus sp. is a potent inhibitor of several proteases including recombinant HIV-1 protease, pepsin, and fungal aspartic protease. In this study, we report the cloning, and over expression of a synthetic gene coding for ATBI in Escherichia coli and establish a purification protocol. The ATBI molecule consists of eleven amino acids and is peptidic in nature. We used the peptide sequence data of ATBI to synthesize complementary oligonucleotides, which were annealed and subsequently cloned in-frame with the gene for glutathione-S-transferase (GST). The expression of the resulting fusion protein was induced in E. coli BL21-A1 cells using arabinose. The recombinant peptide was purified using a reduced glutathione column, and cleaved with Factor Xa to remove the GST tag. The resultant product was further purified to homogeneity using RP-HPLC. Mass spectroscopy analysis revealed that the purified peptide had a molecular weight of 1186Da which matches the theoretical molecular weight of the amino acids present in the synthetic gene. The recombinant peptide was found to be active in vitro against HIV-1 protease, pepsin, and fungal aspartic protease. The protocol described in this study may be used to clone pharmaceutically important peptide molecules.
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27
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Heyda J, Pokorná J, Vrbka L, Vácha R, Jagoda-Cwiklik B, Konvalinka J, Jungwirth P, Vondrášek J. Ion specific effects of sodium and potassium on the catalytic activity of HIV-1 protease. Phys Chem Chem Phys 2009; 11:7599-604. [DOI: 10.1039/b905462f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Billich A, Aziz A, Lehr P, Charpiot B, Gstach H, Scholz D. Kinetic and Binding Studies on [125I]SDZ-283471, A Radiolabeled Inhibitor of Hiv-1 Proteinase. ACTA ACUST UNITED AC 2008. [DOI: 10.3109/14756369309040764] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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29
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Sasková KG, Kozísek M, Lepsík M, Brynda J, Rezácová P, Václavíková J, Kagan RM, Machala L, Konvalinka J. Enzymatic and structural analysis of the I47A mutation contributing to the reduced susceptibility to HIV protease inhibitor lopinavir. Protein Sci 2008; 17:1555-64. [PMID: 18560011 DOI: 10.1110/ps.036079.108] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Lopinavir (LPV) is a second-generation HIV protease inhibitor (PI) designed to overcome resistance development in patients undergoing long-term antiviral therapy. The mutation of isoleucine at position 47 of the HIV protease (PR) to alanine is associated with a high level of resistance to LPV. In this study, we show that recombinant PR containing a single I47A substitution has the inhibition constant (K(i) ) value for lopinavir by two orders of magnitude higher than for the wild-type PR. The addition of the I47A substitution to the background of a multiply mutated PR species from an AIDS patient showed a three-order-of-magnitude increase in K(i) in vitro relative to the patient PR without the I47A mutation. The crystal structure of I47A PR in complex with LPV showed the loss of van der Waals interactions in the S2/S2' subsites. This is caused by the loss of three side-chain methyl groups due to the I47A substitution and by structural changes in the A47 main chain that lead to structural changes in the flap antiparallel beta-strand. Furthermore, we analyzed possible interaction of the I47A mutation with secondary mutations V32I and I54V. We show that both mutations in combination with I47A synergistically increase the relative resistance to LPV in vitro. The crystal structure of the I47A/I54V PR double mutant in complex with LPV shows that the I54V mutation leads to a compaction of the flap, and molecular modeling suggests that the introduction of the I54V mutation indirectly affects the strain of the bound inhibitor in the PR binding cleft.
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Affiliation(s)
- Klára Grantz Sasková
- Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic
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30
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Kozísek M, Bray J, Rezácová P, Sasková K, Brynda J, Pokorná J, Mammano F, Rulísek L, Konvalinka J. Molecular analysis of the HIV-1 resistance development: enzymatic activities, crystal structures, and thermodynamics of nelfinavir-resistant HIV protease mutants. J Mol Biol 2007; 374:1005-16. [PMID: 17977555 DOI: 10.1016/j.jmb.2007.09.083] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 09/24/2007] [Accepted: 09/26/2007] [Indexed: 11/17/2022]
Abstract
Human immunodeficiency virus (HIV) encodes an aspartic protease (PR) that cleaves viral polyproteins into mature proteins, thus leading to the formation of infectious particles. Protease inhibitors (PIs) are successful virostatics. However, their efficiency is compromised by antiviral resistance. In the PR sequence of viral variants resistant to the PI nelfinavir, the mutations D30N and L90M appear frequently. However, these two mutations are seldom found together in vivo, suggesting that there are two alternative evolutionary pathways leading to nelfinavir resistance. Here we analyze the proteolytic activities, X-ray structures, and thermodynamics of inhibitor binding to HIV-1 PRs harboring the D30N and L90M mutations alone and in combination with other compensatory mutations. Vitality values obtained for recombinant mutant proteases and selected PR inhibitors confirm the crucial role of mutations in positions 30 and 90 for nelfinavir resistance. The combination of the D30N and L90M mutations significantly increases the enzyme vitality in the presence of nelfinavir, without a dramatic decrease in the catalytic efficiency of the recombinant enzyme. Crystal structures, molecular dynamics simulations, and calorimetric data for four mutants (D30N, D30N/A71V, D30N/N88D, and D30N/L90M) were used to augment our kinetic data. Calorimetric analysis revealed that the entropic contribution to the mutant PR/nelfinavir interaction is less favorable than the entropic contribution to the binding of nelfinavir by wild-type PR. This finding is supported by the structural data and simulations; nelfinavir binds most strongly to the wild-type protease, which has the lowest number of protein-ligand hydrogen bonds and whose structure exhibits the greatest degree of fluctuation upon inhibitor binding.
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Affiliation(s)
- Milan Kozísek
- Gilead Sciences and IOCB Research Center, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
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31
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Ishima R, Torchia DA, Louis JM. Mutational and Structural Studies Aimed at Characterizing the Monomer of HIV-1 Protease and Its Precursor. J Biol Chem 2007; 282:17190-9. [PMID: 17412697 DOI: 10.1074/jbc.m701304200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An experimental protocol for folding the mature human immunodeficiency virus-1 (HIV-1) protease is presented that facilitates NMR studies at a low protein concentration of approximately 20 micoM. Under these conditions, NMR spectra show that the mature protease lacking its terminal beta-sheet residues 1-4 and 96-99 (PR(5-95)) exhibits a stable monomer fold spanning the region 10-90 that is similar to that of the single subunit of the wild-type dimer and the dimer bearing a D25N mutation (PR(D25N)). Urea-induced unfolding monitored both by changes in (1)H-(15)N heteronuclear single quantum correlation spectra and by protein fluorescence indicates that although PR(5-95) monomer displays a transition profile similar to that of the PR(D25N) dimer (50% unfolded (U(50)) = approximately 1.9 M), extending the protease with 4 residues (SFNF) of its N-terminally flanking sequence in the Gag-Pol precursor ((SFNF)PR(D25N)) decreases the stability of the fold (U(50) = approximately 1.5 M). Assigned backbone chemical shifts were used to elucidate differences in the stability of the PR(T26A) (U(50) = 2.5 M) and (SFNF)PR(D25N) monomers and compared with PR(D25N/T26A) monomer. Discernible differences in the backbone chemical shifts were observed for N-terminal protease residues 3-6 of (SFNF)PR(D25N) that may relate to the increase in the equilibrium dissociation constant (K(d)) and the very low catalytic activity of the protease prior to its autoprocessing at its N terminus from the Gag-Pol precursor.
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Affiliation(s)
- Rieko Ishima
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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32
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Kiss AL, Hornung B, Rádi K, Gengeliczki Z, Sztáray B, Juhász T, Szeltner Z, Harmat V, Polgár L. The acylaminoacyl peptidase from Aeropyrum pernix K1 thought to be an exopeptidase displays endopeptidase activity. J Mol Biol 2007; 368:509-20. [PMID: 17350041 DOI: 10.1016/j.jmb.2007.02.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Revised: 01/30/2007] [Accepted: 02/07/2007] [Indexed: 10/23/2022]
Abstract
Mammalian acylaminoacyl peptidase, a member of the prolyl oligopeptidase family of serine peptidases, is an exopeptidase, which removes acylated amino acid residues from the N terminus of oligopeptides. We have investigated the kinetics and inhibitor binding of the orthologous acylaminoacyl peptidase from the thermophile Aeropyrum pernix K1 (ApAAP). Complex pH-rate profiles were found with charged substrates, indicating a strong electrostatic effect in the surroundings of the active site. Unexpectedly, we have found that oligopeptides can be hydrolysed beyond the N-terminal peptide bond, demonstrating that ApAAP exhibits endopeptidase activity. It was thought that the enzyme is specific for hydrophobic amino acids, in particular phenylalanine, in accord with the non-polar S1 subsite of ApAAP. However, cleavage after an Ala residue contradicted this notion and demonstrated that P1 residues of different nature may bind to the S1 subsite depending on the remaining peptide residues. The crystal structures of the complexes formed between the enzyme and product-like inhibitors identified the oxyanion-binding site unambiguously and demonstrated that the phenylalanine ring of the P1 peptide residue assumes a position different from that established in a previous study, using 4-nitrophenylphosphate. We have found that the substrate-binding site extends beyond the S2 subsite, being capable of binding peptides with a longer N terminus. The S2 subsite displays a non-polar character, which is unique among the enzymes of this family. The S3 site was identified as a hydrophobic region that does not form hydrogen bonds with the inhibitor P3 residue. The enzyme-inhibitor complexes revealed that, upon ligand-binding, the S1 subsite undergoes significant conformational changes, demonstrating the plasticity of the specificity site.
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Affiliation(s)
- András L Kiss
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest 112, P.O. Box 7, Hungary
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33
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Kawe M, Forrer P, Amstutz P, Plückthun A. Isolation of Intracellular Proteinase Inhibitors Derived from Designed Ankyrin Repeat Proteins by Genetic Screening. J Biol Chem 2006; 281:40252-63. [PMID: 17050543 DOI: 10.1074/jbc.m602506200] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The specific intracellular inhibition of protein activity at the protein level is a highly valuable tool for the validation or modulation of cellular processes. We demonstrate here the use of designed ankyrin repeat proteins (DARPins) as tailor-made intracellular proteinase inhibitors. Site-specific proteolytic processing plays a critical role in the regulation of many biological processes, ranging from basic cellular functions to the propagation of viruses. The NIa(pro) proteinase of tobacco etch virus, a major plant pathogen, can be functionally expressed in Escherichia coli without harming the bacterium. To identify inhibitors of this proteinase, we first selected binders to it from combinatorial libraries of DARPins and tested this pool with a novel in vivo screen for proteinase inhibition. For this purpose, a hybrid protein consisting of the omega subunit of E. coli RNA polymerase was covalently fused to a DNA-binding protein, the lambdacI repressor, containing an NIa(pro) cleavage site in the linker between the two proteins. Thus, this transcriptional activator is inactivated by site-specific proteolytic cleavage, and inhibitors of this cleavage can be identified by the reconstitution of transcription of a reporter gene. Following this two-step approach of selection and screening, we could rapidly isolate NIa(pro) proteinase inhibitors active inside the cell from highly diverse combinatorial DARPin libraries. These findings underline the great potential of DARPins for modulation of protein functionality in the intracellular space. In addition, our novel genetic screen can help to select and identify tailor-made proteinase inhibitors based on other protein scaffolds or even on low molecular weight compounds.
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Affiliation(s)
- Martin Kawe
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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Abstract
Oxytocin acting via its receptor is involved in the myometrial hyperactivity of preterm labour and possibly also in that of primary dysmenorrhoea. The closely related hormone vasopressin acting on its uterine receptor of type V1a may also contribute to the myometrial hyperactivity of these conditions. Several pharmaceutical compounds inhibiting these receptors are, therefore, under development and one substance, atosiban, has now been registered in many countries for the treatment of preterm labour. This compound blocks both the oxytocin and the vasopressin V1a receptor. The efficacy is at least as pronounced as that of other types of drugs and side effects are much reduced. In this overview, present knowledge about receptor-mediated effects of oxytocin and vasopressin on myometrial activity is summarised. Furthermore, the therapeutic use of oxytocin and vasopressin V1a receptor antagonists in preterm labour and primary dysmenorrhoea is discussed.
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Affiliation(s)
- Mats Akerlund
- Department of Obstetrics and Gynaecology, University Hospital, SE-221 85 Lund, Sweden.
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Majerová-Uhlíková T, Dantuma NP, Lindsten K, Masucci MG, Konvalinka J. Non-infectious fluorimetric assay for phenotyping of drug-resistant HIV proteinase mutants. J Clin Virol 2006; 36:50-9. [PMID: 16527535 DOI: 10.1016/j.jcv.2006.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2005] [Revised: 12/13/2005] [Accepted: 01/31/2006] [Indexed: 11/30/2022]
Abstract
BACKGROUND The introduction of HIV proteinase inhibitors (PIs) as anti-AIDS drugs resulted in decreased mortality and prolonged life expectancy of HIV-positive patients. However, rapid selection of drug-resistant HIV variants is a common complication in patients undergoing highly active anti-retroviral therapy (HAART). Thus, monitoring of clinical resistance development is indispensable for rational pharmacotherapy. OBJECTIVE We present a non-infectious cell-based assay for drug resistance quantification of HIV proteinase (PR) - an important target of HAART. STUDY DESIGN Previously, we showed [Lindsten K, Uhlikova T, Konvalinka J, Masucci MG, Dantuma NP. Cell-based fluorescence assay for human immunodeficiency virus type 1 protease activity. Antimicrob Agents Chemother 2001;45:2616-22] that the expression of a fusion protein (GFP-PR), comprised of HIV-1 proteinase wild-type artificial precursor (PR) and green fluorescent protein (GFP), in transiently transfected tissue culture cells depends on the presence of PR-specific inhibitors (PIs). Here we show that in the GFP-PR reporter the HIV wild-type PR can be replaced by a drug-resistant HIV PR mutant, yielding a simple and biologically relevant tool for the quantitative analysis of drug-resistant HIV PR mutants susceptibility to HIV proteinase inhibitors. RESULTS We cloned a set of GFP-PR reporters, some of which possess a simple, well-defined drug-resistant PR mutant (G48V L90M, V82A, A71V V82T I84V, D30N, K45I); another four complex PR mutants were obtained from patients undergoing HAART. The results were compared with genotyping and enzyme kinetics data. Furthermore, we designed a single inhibitor concentration experiment setup for easy evaluation of drug resistance profiles for mutants of interest. The resistance profiles clearly demonstrate the importance of succession of individual drugs during the treatment for drug resistance development. CONCLUSION We show that the GFP-PR assay might serve as a non-infectious, rapid, cheap, and reliable alternative to the currently used phenotypic assays.
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Affiliation(s)
- Tat'ána Majerová-Uhlíková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo 2, 166 10 Praha 6, Czech Republic
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36
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Broglia RA, Provasi D, Vasile F, Ottolina G, Longhi R, Tiana G. A folding inhibitor of the HIV-1 protease. Proteins 2005; 62:928-33. [PMID: 16385559 DOI: 10.1002/prot.20849] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Because the human immunodeficiency virus type 1 protease (HIV-1-PR) is an essential enzyme in the viral life cycle, its inhibition can control AIDS. The folding of single-domain proteins, like each of the monomers forming the HIV-1-PR homodimer, is controlled by local elementary structures (LES, folding units stabilized by strongly interacting, highly conserved, as a rule hydrophobic, amino acids). These LES have evolved over myriad generations to recognize and strongly attract each other, so as to make the protein fold fast and be stable in its native conformation. Consequently, peptides displaying a sequence identical to those segments of the monomers associated with LES are expected to act as competitive inhibitors and thus destabilize the native structure of the enzyme. These inhibitors are unlikely to lead to escape mutants as they bind to the protease monomers through highly conserved amino acids, which play an essential role in the folding process. The properties of one of the most promising inhibitors of the folding of the HIV-1-PR monomers found among these peptides are demonstrated with the help of spectrophotometric assays and circular dichroism spectroscopy.
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Affiliation(s)
- R A Broglia
- Dipartimento di Fisica, Università di Milano, Milan, Italy
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37
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Pettit SC, Clemente JC, Jeung JA, Dunn BM, Kaplan AH. Ordered processing of the human immunodeficiency virus type 1 GagPol precursor is influenced by the context of the embedded viral protease. J Virol 2005; 79:10601-7. [PMID: 16051852 PMCID: PMC1182631 DOI: 10.1128/jvi.79.16.10601-10607.2005] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Ordered and accurate processing of the human immunodeficiency virus type 1 (HIV-1) GagPol polyprotein precursor by a virally encoded protease is an indispensable step in the appropriate assembly of infectious viral particles. The HIV-1 protease (PR) is a 99-amino-acid enzyme that is translated as part of the GagPol precursor. Previously, we have demonstrated that the initial events in precursor processing are accomplished by the PR domain within GagPol in cis, before it is released from the polyprotein. Despite the critical role that ordered processing of the precursor plays in viral replication, the forces that define the order of cleavage remain poorly understood. Using an in vitro assay in which the full-length HIV-1 GagPol is processed by the embedded PR, we examined the effect of PR context (embedded within GagPol versus the mature 99-amino-acid enzyme) on precursor processing. Our data demonstrate that the PR domain within GagPol is constrained in its ability to cleave some of the processing sites in the precursor. Further, we find that this constraint is dependent upon the presence of a proline as the initial amino acid in the embedded PR; substitution of an alanine at this position produces enhanced cleavage at additional sites when the precursor is processed by the embedded, but not the mature, PR. Overall, our data support a model in which the selection of processing sites and the order of precursor processing are defined, at least in part, by the structure of GagPol itself.
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Affiliation(s)
- Steven C Pettit
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
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38
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Xu Y, Lu C. Raman spectroscopic study on structure of human immunodeficiency virus (HIV) and hypericin-induced photosensitive damage of HIV. ACTA ACUST UNITED AC 2005; 48:117-32. [PMID: 15986884 DOI: 10.1007/bf02879664] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The first Raman spectra of HIV1-HIV2 in human sera and hypericin-induced photosensitive damage of the virus have been obtained. The prominent Raman lines in the spectra are assigned respectively to the carbohydrates of viral glycoprotein, RNA, protein and lipid. The spectra are dominated by Raman scattering of the carbohydrates. The lines of D-Mannose and N-acetylglucosamine in carbohydrates are obvious and there is a beta-configuration in the anomeric C1 position in D-Mannose. The viral RNA duplexes bound assumes an A-form geometry. The lines of backbone phosphate group, bases (involving interbase hydrogen bonding) and ribose of the RNA are complete and distinct. The secondary structure of the viral protein maintains alpha-helix, beta-sheet, beta-turn and random coil. Its side chains are rich and vary from tryptophan, phenylalanine and "buried" tyrosine; the stable conformation of the S-S bond of gauche-gauche-gauche; the two forms of C-S bonds of gauche and trans; to sulfhydrl group and ionized and unionized carboxyl groups. The viral lipid bilayer molecules are probably in the liquid ordered phase or the gel phase. It was observed that the hypericin-induced photosensitive damage of HIV1-HIV2 in human sera changed various components of HIV1-HIV2 in different degrees: The orderly A-form viral RNA would become a disordered viral RNA. There were a breakage of interbase hydrogen bonds and disruption of vertical base-base stacking interactions. In addition, the groups of ribos and four bases were damaged obviously. A decrease in ordered structure (alpha-helix and beta-sheet) of viral protein is accompanied by an increase in random coil. The Tyr buried in the three-dimensional structure of protein was damaged, but it was still "buried" and the damage of C-S bond of trans form was stronger. The groups of carbohydrates, including D-Mannos and N-acetyl glucosamine, in viral envelope glycoprotein had also been changed. The hydrophilic C-N bond of choline in viral lipid was damaged, which was the possible binding site to hypericin, whereas the viral lipids bilayers were still probably in the liquid ordered phase or the gel phase. So the space structure of HIV1-HIV2 was damaged under the experimental conditions, which might block viral infection and inhibit its growth and breeding. It is apparent that the laser Raman spectra have provided certain direct evidence at the molecular level for photosensitive damage of HIV1-HIV2.
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Affiliation(s)
- Yiming Xu
- Laboratory of Visual Information Processing, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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39
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Chatterjee A, Mridula P, Mishra RK, Mittal R, Hosur RV. Folding Regulates Autoprocessing of HIV-1 Protease Precursor. J Biol Chem 2005; 280:11369-78. [PMID: 15632156 DOI: 10.1074/jbc.m412603200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Autoprocessing of HIV-1 protease (PR) precursors is a crucial step in the generation of the mature protease. Very little is known regarding the molecular mechanism and regulation of this important process in the viral life cycle. In this context we report here the first and complete residue level investigations on the structural and folding characteristics of the 17-kDa precursor TFR-PR-C(nn) (161 residues) of HIV-1 protease. The precursor shows autoprocessing activity indicating that the solution has a certain population of the folded active dimer. Removal of the 5-residue extension, C(nn) at the C-terminal of PR enhanced the activity to some extent. However, NMR structural characterization of the precursor containing a mutation, D25N in the PR at pH 5.2 and 32 degrees C under different conditions of partial and complete denaturation by urea, indicate that the precursor has a high tendency to be unfolded. The major population in the ensemble displays some weak folding propensities in both the TFR and the PR regions, and many of these in the PR region are the non-native type. As both D25N mutant and wild-type PR are known to fold efficiently to the same native dimeric form, we infer that TFR cleavage enables removal of the non-native type of preferences in the PR domain to cause constructive folding of the protein. These results indicate that intrinsic structural and folding preferences in the precursor would have important regulatory roles in the autoprocessing reaction and generation of the mature enzyme.
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Affiliation(s)
- Amarnath Chatterjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
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Pettit SC, Everitt LE, Choudhury S, Dunn BM, Kaplan AH. Initial cleavage of the human immunodeficiency virus type 1 GagPol precursor by its activated protease occurs by an intramolecular mechanism. J Virol 2004; 78:8477-85. [PMID: 15280456 PMCID: PMC479095 DOI: 10.1128/jvi.78.16.8477-8485.2004] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Processing of the GagPol polyprotein precursor of human immunodeficiency virus type 1 (HIV-1) is a critical step in viral assembly and replication. The HIV-1 protease (PR) is translated as part of GagPol and is both necessary and sufficient for precursor processing. The PR is active only as a dimer; enzyme activation is initiated when the PR domains in two GagPol precursors dimerize. The precise mechanism by which the PR becomes activated and the subsequent initial steps in precursor processing are not well understood. However, it is clear that processing is initiated by the PR domain that is embedded within the precursor itself. We have examined the earliest events in precursor processing using an in vitro assay in which full-length GagPol is cleaved by its embedded PR. We demonstrate that the embedded, immature PR is as much as 10,000-fold less sensitive to inhibition by an active-site PR inhibitor than is the mature, free enzyme. Further, we find that different concentrations of the active-site inhibitor are required to inhibit the processing of different cleavage sites within GagPol. Finally, our results indicate that the first cleavages carried out by the activated PR within GagPol are intramolecular. Overall, our data support a model of virus assembly in which the first cleavages occur in GagPol upstream of the PR. These intramolecular cleavages produce an extended form of PR that completes the final processing steps accompanying the final stages of particle assembly by an intermolecular mechanism.
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Affiliation(s)
- Steven C Pettit
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, NC 27599-7290, USA
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41
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Kožíšek M, Prejdová J, Souček M, Machala L, Staňková M, Linka M, Brůčková M, Konvalinka J. Characterisation of Mutated Proteinases Derived from HIV-Positive Patients: Enzyme Activity, Vitality and Inhibition. ACTA ACUST UNITED AC 2004. [DOI: 10.1135/cccc20040703] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
HIV protease (PR) specifically cleaves viral polyproteins to yield infectious progeny virus particles. Inactivation of PR leads to loss of virus infectivity and PR thus became an attractive pharmaceutic target. Indeed, seven protease inhibitors (PI) have been approved for clinical use to date. However, emerging resistant viral variants with reduced sensitivity to PIs become a major obstacle to successful control of viral replication. We have previously reported the design, testing and structural analysis of a pseudopeptide inhibitor, QF34, which efficiently inhibits a wide variety of PR variants. In a clinical study, we have monitored more than 100 HIV-positive patients in the Czech Republic undergoing highly active antiretroviral therapy including PI. In this paper we describe kinetic characterisation of two highly resistant PR species isolated from these patients. The mutated proteases accumulated as much as 14 amino acid exchanges and develop resistance to saquinavir, ritonavir, indinavir and nelfinavir with vitality value up to 150. Kinetic analyses revealed that second-generation PI lopinavir and QF34 retained their subnanomolar potency against both multidrug resistant PR variants. These results suggest a route to the design of PIs capable of inhibiting a variety of resistant PR mutants.
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Ishima R, Torchia DA, Lynch SM, Gronenborn AM, Louis JM. Solution structure of the mature HIV-1 protease monomer: insight into the tertiary fold and stability of a precursor. J Biol Chem 2003; 278:43311-9. [PMID: 12933791 DOI: 10.1074/jbc.m307549200] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We present the first solution structure of the HIV-1 protease monomer spanning the region Phe1-Ala95 (PR1-95). Except for the terminal regions (residues 1-10 and 91-95) that are disordered, the tertiary fold of the remainder of the protease is essentially identical to that of the individual subunit of the dimer. In the monomer, the side chains of buried residues stabilizing the active site interface in the dimer, such as Asp25, Asp29, and Arg87, are now exposed to solvent. The flap dynamics in the monomer are similar to that of the free protease dimer. We also show that the protease domain of an optimized precursor flanked by 56 amino acids of the N-terminal transframe region is predominantly monomeric, exhibiting a tertiary fold that is quite similar to that of PR1-95 structure. This explains the very low catalytic activity observed for the protease prior to its maturation at its N terminus as compared with the mature protease, which is an active stable dimer under identical conditions. Adding as few as 2 amino acids to the N terminus of the mature protease significantly increases its dissociation into monomers. Knowledge of the protease monomer structure and critical features of its dimerization may aid in the screening and design of compounds that target the protease prior to its maturation from the Gag-Pol precursor.
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Affiliation(s)
- Rieko Ishima
- Molecular Structural Biology Unit, NIDCR, National Institutes of Health, Bethesda, Maryland 20892-4307, USA
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43
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Hilgeroth A, Lilie H. Structure-activity relationships of first bishydroxymethyl-substituted cage dimeric 4-aryl-1,4-dihydropyridines as HIV-1 protease inhibitors. Eur J Med Chem 2003; 38:495-9. [PMID: 12767599 DOI: 10.1016/s0223-5234(03)00060-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A first series of novel bishydroxymethyl-substituted cage dimeric 4-aryl-1,4-dihydropyridines 5-8 has been synthesised and evaluated as HIV-1 protease and HIV-inhibitors in vitro assays. Moderate activity data of protease inhibition have been found for of the N-Boc substituted compound 8. Reduced activity for compound 6 and almost no residual activity of 5 and 7 emphasise the importance of the tert. butyl substituent for protease inhibitory activity thus supporting a discussed probable binding of the N-acyloxy substituent to the S2/S2' regions of protease.
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Affiliation(s)
- Andreas Hilgeroth
- Department of Pharmacy, Martin-Luther-University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle, Germany.
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Louis JM, Ishima R, Nesheiwat I, Pannell LK, Lynch SM, Torchia DA, Gronenborn AM. Revisiting monomeric HIV-1 protease. Characterization and redesign for improved properties. J Biol Chem 2003; 278:6085-92. [PMID: 12468541 DOI: 10.1074/jbc.m209726200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Interactions between the C-terminal interface residues (96-99) of the mature HIV-1 protease were shown to be essential for dimerization, whereas the N-terminal residues () and Arg(87) contribute to dimer stability (Ishima, R., Ghirlando, R., Tozser, J., Gronenborn, A. M., Torchia, D. A., and Louis, J. M. (2001) J. Biol. Chem. 276, 49110-49116). Here we show that the intramonomer interaction between the side chains of Asp(29) and Arg(87) influences dimerization significantly more than the intermonomer interaction between Asp(29) and Arg(8'). Several mutants, including T26A, destablize the dimer, exhibit a monomer fold, and are prone to aggregation. To alleviate this undesirable property, we designed proteins in which the N- and C-terminal regions can be linked intramolecularly by disulfide bonds. In particular, cysteine residues were introduced at positions 2 and 97 or 98. A procedure for the efficient preparation of intrachain-linked polypeptides is presented, and it is demonstrated that the Q2C/L97C variant exhibits a native-like single subunit fold. It is anticipated that monomeric proteases of this kind will aid in the discovery of novel inhibitors aimed at binding to the monomer at the dimerization interface. This extends the target area of current inhibitors, all of which bind across the active site formed by both subunits in the active dimer.
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Affiliation(s)
- John M Louis
- Laboratory of Chemical Physics, National Institute Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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Rajesh S, Ami E, Kotake T, Kimura T, Hayashi Y, Kiso Y. An expedient synthesis of N(alpha)-protected-L-tetrahydrofuranylglycine and its application in the synthesis of novel substrate based inhibitors of HIV-1 protease. Bioorg Med Chem Lett 2002; 12:3615-7. [PMID: 12443788 DOI: 10.1016/s0960-894x(02)00781-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Z- and Fmoc-L-tetrahydrofuranylglycines have been obtained from L-vinylglycine through dipolar cycloaddition reaction, and its Fmoc derivative has been applied in the synthesis of modified S9 and S10 substrates of HIV-1 protease. These compounds mostly acted as strong inhibitors, rather than substrates, of the protease, probably due to the favourable interactions of the tetrahydrofuranylglycine moiety at the S(2) site.
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Affiliation(s)
- S Rajesh
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-ku, Japan
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Weber J, Mesters JR, Lepsík M, Prejdová J, Svec M, Sponarová J, Mlcochová P, Skalická K, Strísovský K, Uhlíková T, Soucek M, Machala L, Stanková M, Vondrásek J, Klimkait T, Kraeusslich HG, Hilgenfeld R, Konvalinka J. Unusual binding mode of an HIV-1 protease inhibitor explains its potency against multi-drug-resistant virus strains. J Mol Biol 2002; 324:739-54. [PMID: 12460574 DOI: 10.1016/s0022-2836(02)01139-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Protease inhibitors (PIs) are an important class of drugs for the treatment of HIV infection. However, in the course of treatment, resistant viral variants with reduced sensitivity to PIs often emerge and become a major obstacle to successful control of viral load. On the basis of a compound equipotently inhibiting HIV-1 and 2 proteases (PR), we have designed a pseudopeptide inhibitor, QF34, that efficiently inhibits a wide variety of PR variants. In order to analyze the potency of the inhibitor, we constructed PR species harboring the typical (signature) mutations that confer resistance to commercially available PIs. Kinetic analyses showed that these mutated PRs were inhibited up to 1,000-fold less efficiently by the clinically approved PIs. In contrast, all PR species were effectively inhibited by QF34. In a clinical study, we have monitored 30 HIV-positive patients in the Czech Republic undergoing highly active antiretroviral therapy, and have identified highly PI resistant variants. Kinetic analyses revealed that QF34 retained its subnanomolar potency against multi-drug resistant PR variants. X-ray crystallographic analysis and molecular modeling experiments explained the wide specificity of QF34: this inhibitor binds to the PR in an unusual manner, thus avoiding contact sites that are mutated upon resistance development, and the unusual binding mode and consequently the binding energy is therefore preserved in the complex with a resistant variant. These results suggest a promising route for the design of second-generation PIs that are active against a variety of resistant PR variants.
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Affiliation(s)
- Jan Weber
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Protease of Human Pathogens, Flemingovo n. 2, CZ-16610 Praha 6, Czech Republic
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Hamada Y, Ohtake J, Sohma Y, Kimura T, Hayashi Y, Kiso Y. New water-soluble prodrugs of HIV protease inhibitors based on O-->N intramolecular acyl migration. Bioorg Med Chem 2002; 10:4155-67. [PMID: 12413869 DOI: 10.1016/s0968-0896(02)00322-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To improve the low water-solubility of HIV protease inhibitors, we synthesized water-soluble prodrugs of KNI-272 and KNI-279 which are potent HIV-1 protease inhibitors consisting of an Apns-Thz core structure (Apns; allophenylnorstatine, Thz; thiazolidine-4-carboxylic acid) as an inhibitory machinery. The prodrugs, which contained an O-acyl peptidomimetic structure with an ionized amino group leading to the increase of water-solubility, were designed to regenerate the corresponding parent drugs based on the O-->N intramolecular acyl migration reaction at the alpha-hydroxy-beta-amino acid residue, that is allophenylnorstatine. The synthetic prodrugs 3, 4, 6, and 7 improved the water-solubility (>300mg/mL) more than 4000-fold in comparison with the parent compounds, which is the practically acceptable value as water-soluble drugs. These prodrugs were stable as an HCl salt and in a strongly acidic solution corresponding to gastric juice (pH 2.0), and could be converted to the parent compounds promptly in the aqueous condition from slightly acidic to basic pH at 37 degrees C, with the suitable migration rate, via a five-membered ring intermediate. Using a similar method, we synthesized a prodrug (12) of ritonavir, a clinically useful HIV-1 protease inhibitor as an anti-AIDS drug. In contrast to the prodrugs 3, 4, 6, and 7, the prodrug 12 was very slowly converted to ritonavir probably through a six-membered ring intermediate, with the t(1/2) value of 32h that may not be suitable for practical use.
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Affiliation(s)
- Yoshio Hamada
- Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-Ku, Kyoto, Japan
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48
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Pettit SC, Henderson GJ, Schiffer CA, Swanstrom R. Replacement of the P1 amino acid of human immunodeficiency virus type 1 Gag processing sites can inhibit or enhance the rate of cleavage by the viral protease. J Virol 2002; 76:10226-33. [PMID: 12239298 PMCID: PMC136535 DOI: 10.1128/jvi.76.20.10226-10233.2002] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Processing of the human immunodeficiency virus type 1 (HIV-1) Gag precursor is highly regulated, with differential rates of cleavage at the five major processing sites to give characteristic processing intermediates. We examined the role of the P1 amino acid in determining the rate of cleavage at each of these five sites by using libraries of mutants generated by site-directed mutagenesis. Between 12 and 17 substitution mutants were tested at each P1 position in Gag, using recombinant HIV-1 protease (PR) in an in vitro processing reaction of radiolabeled Gag substrate. There were three sites in Gag (MA/CA, CA/p2, NC/p1) where one or more substitutions mediated enhanced rates of cleavage, with an enhancement greater than 60-fold in the case of NC/p1. For the other two sites (p2/NC, p1/p6), the wild-type amino acid conferred optimal cleavage. The order of the relative rates of cleavage with the P1 amino acids Tyr, Met, and Leu suggests that processing sites can be placed into two groups and that the two groups are defined by the size of the P1' amino acid. These results point to a trans effect between the P1 and P1' amino acids that is likely to be a major determinant of the rate of cleavage at the individual sites and therefore also a determinant of the ordered cleavage of the Gag precursor.
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Affiliation(s)
- Steve C Pettit
- UNC Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7295, USA
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Gutiérrez OA, Salas E, Hernández Y, Lissi EA, Castrillo G, Reyes O, Garay H, Aguilar A, García B, Otero A, Chavez MA, Duarte CA. An immunoenzymatic solid-phase assay for quantitative determination of HIV-1 protease activity. Anal Biochem 2002; 307:18-24. [PMID: 12137774 DOI: 10.1016/s0003-2697(02)00009-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A novel immunoenzymatic procedure for the quantitative determination of HIV protease activity is provided. An N-terminal biotinylated peptide (DU1) that comprises an HIV-1 protease (HIV-PR) cleavage sequence was bound to streptavidin-coated microtiter plates. The bound peptide can be quantified by an immunoenzymatic procedure (enzyme-linked immunosorbent assay, ELISA) that includes a monoclonal antibody (Mab 332) against the peptide (DU1) C-terminal. The incubation of the bound peptide with HIV-PR in solution resulted in a signal decrement, as the peptide was hydrolyzed and the released C-terminal segment washed away. An equation that relates the amount of added enzyme to the kinetics of the reaction was written in order to describe this heterogeneous enzyme-quasi-saturable system. This equation allows quantitative determination of protease activity, a feature widely underrated in previous similar assays. The assay also allows evaluation of the inhibitory activity of HIV-PR inhibitors. Due to the intrinsic advantages of the ELISA format, this method could be used in high-throughput screening of HIV protease inhibitors. The assay can be extended to other proteolytic enzymes.
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Affiliation(s)
- Omar A Gutiérrez
- Facultad de Biología, Centro de Estudios de la Proteínas, Universidad de la Habana, Ciudad Habana, Cuba.
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Abstract
Three fish retroviruses infecting walleyes constitute the recently recognized genus called epsilonretrovirus. The founding member of this group, walleye dermal sarcoma virus (WDSV), induces benign skin tumors in the infected fish and replicates near 4 degrees C. While the viral genomic sequence is known, biochemical characterization of the virus has been limited to the identification of the mature structural and envelope proteins present in virions. We undertook this study to determine the cleavage sites in the WDSV Pro and Pol proteins and to characterize the viral protease (PR) in vitro. A recombinant PR was expressed in and purified from Escherichia coli as a larger fusion with additional nucleocapsid and reverse transcriptase residues flanking the PR domain. Autocleavage produced a functional, mature PR. Autocleavage as well as cleavage of peptides and of Gag protein by the mature PR occurred at a pH optimum of 7.0, higher than that of other retroviral proteases. Analysis of the cleavage sites identified a glutamine residue in the P2 position of all WDSV sites, both in Gag and in Pol. Amino acid sequence alignments of Gag-Pro-Pol from WDSV, walleye epidermal hyperplasia virus type 1, and walleye epidermal hyperplasia virus type 2 showed the P2 glutamine to be conserved in all cleavage sites in these three viruses. Such conservation is unprecedented in other retroviruses.
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Affiliation(s)
- Sharon K Fodor
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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