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Goldfarb NE, Ohanessian M, Biswas S, McGee TD, Mahon BP, Ostrov DA, Garcia J, Tang Y, McKenna R, Roitberg A, Dunn BM. Defective hydrophobic sliding mechanism and active site expansion in HIV-1 protease drug resistant variant Gly48Thr/Leu89Met: mechanisms for the loss of saquinavir binding potency. Biochemistry 2015; 54:422-33. [PMID: 25513833 PMCID: PMC4303317 DOI: 10.1021/bi501088e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
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HIV drug resistance continues to
emerge; consequently, there is
an urgent need to develop next generation antiretroviral therapeutics.1 Here we report on the structural and kinetic
effects of an HIV protease drug resistant variant with the double
mutations Gly48Thr and Leu89Met (PRG48T/L89M), without
the stabilizing mutations Gln7Lys, Leu33Ile, and Leu63Ile. Kinetic
analyses reveal that PRG48T/L89M and PRWT share
nearly identical Michaelis–Menten parameters; however, PRG48T/L89M exhibits weaker binding for IDV (41-fold), SQV (18-fold),
APV (15-fold), and NFV (9-fold) relative to PRWT. A 1.9
Å resolution crystal structure was solved for PRG48T/L89M bound with saquinavir (PRG48T/L89M-SQV) and compared
to the crystal structure of PRWT bound with saquinavir
(PRWT-SQV). PRG48T/L89M-SQV has
an enlarged active site resulting in the loss of a hydrogen bond in
the S3 subsite from Gly48 to P3 of SQV, as well as less favorable
hydrophobic packing interactions between P1 Phe of SQV and the S1
subsite. PRG48T/L89M-SQV assumes a more open conformation
relative to PRWT-SQV, as illustrated by the downward
displacement of the fulcrum and elbows and weaker interatomic flap
interactions. We also show that the Leu89Met mutation disrupts the
hydrophobic sliding mechanism by causing a redistribution of van der
Waals interactions in the hydrophobic core in PRG48T/L89M-SQV. Our mechanism for PRG48T/L89M-SQV drug resistance
proposes that a defective hydrophobic sliding mechanism results in
modified conformational dynamics of the protease. As a consequence,
the protease is unable to achieve a fully closed conformation that
results in an expanded active site and weaker inhibitor binding.
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Affiliation(s)
- Nathan E Goldfarb
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §Departments of Pathology, Immunology, and Laboratory Medicine, University of Florida , Gainesville, Florida 32601-0245, United States
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2
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Demir A, Oguariri RM, Magis A, Ostrov DA, Imamichi T, Dunn BM. Kinetic characterization of newly discovered inhibitors of various constructs of human T-cell leukemia virus-1 (HTLV-1) protease and their effect on HTLV-1-infected cells. Antivir Ther 2012; 17:883-92. [PMID: 22436331 DOI: 10.3851/imp2090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2011] [Indexed: 10/28/2022]
Abstract
BACKGROUND Human T-cell leukemia virus-1 (HTLV-1) was the first identified human retrovirus and was shown to be associated with diseases such as adult T-cell leukemia lymphoma and tropical spastic paraparesis/HTLV-1 associated myelopathy. Retroviral proteases (PRs) are essential for viral replication by processing viral Gag and Gag-(Pro)-Pol polyproteins during maturation. Full-length HTLV-1 PR is 125 residues long; whether the C-terminal region is required for catalytic activity is still controversial. In this study, we characterized the effect of C-terminal amino acids of HTLV-1 PR for PR activity and examined the binding of compounds identified by in silico screening. One compound showed inhibition against the virus in infected cells. METHODS Truncated (116-, 121- and 122-residue) forms of HTLV-1 PR were prepared and proteins from expression of the genes were purified. In silico screening was performed by docking small molecules into the active site of HTLV-1 PR. The kinetic constants k(cat), K(m), k(cat)/K(m) and inhibition constants K(i) for inhibitors identified by the computational screening were determined. Western blot and ELISA analyses were used to determine the effect of the most potent PR inhibitors on HTLV-1 protein processing in infected cells. RESULTS The constructs showed similar catalytic efficiency constants (k(cat)/K(m)); thus HTLV-1 PR C-terminal amino acids are not essential for full activity. Computational screening revealed new PR inhibitors and some were shown to be inhibitory in enzyme assays. In HTLV-1-infected cells, one of the small molecules inhibited HTLV-1 gag cleavage and decreased the amount of HTLV-1 p19 produced in the cells. CONCLUSIONS We have identified an HTLV-1 PR inhibitor that is biologically functional. Inhibitor screening will continue to develop possible drugs for therapy of HTLV-1 infection.
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Affiliation(s)
- Ahu Demir
- University of Florida College of Medicine Biochemistry and Molecular Biology, Gainesville, FL, USA
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3
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Clemente JC, Robbins A, Graña P, Paleo MR, Correa JF, Villaverde MC, Sardina FJ, Govindasamy L, Agbandje-McKenna M, McKenna R, Dunn BM, Sussman F. Design, synthesis, evaluation, and crystallographic-based structural studies of HIV-1 protease inhibitors with reduced response to the V82A mutation. J Med Chem 2008; 51:852-60. [PMID: 18215016 DOI: 10.1021/jm701170f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In our quest for HIV-1 protease inhibitors that are not affected by the V82A resistance mutation, we have synthesized and tested a second generation set of C2-symmetric HIV-1 protease inhibitors that contain a cyclohexane group at P1 and/or P1'. The binding affinity results indicate that these compounds have an improved response to the appearance of the V82A mutation than the parent compound. The X-ray structure of one of these compounds with the V82A HIV-1 PR variant provides the structural rationale for the better resistance profile of these compounds. Moreover, scrutiny of the X-ray structure suggests that the ring of the Cha side chain might be in a boat rather than in the chair conformation, a result supported by molecular dynamics simulations.
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Affiliation(s)
- José C Clemente
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610, USA
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4
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Clemente JC, Coman RM, Thiaville MM, Janka LK, Jeung JA, Nukoolkarn S, Govindasamy L, Agbandje-McKenna M, McKenna R, Leelamanit W, Goodenow MM, Dunn BM. Analysis of HIV-1 CRF_01 A/E protease inhibitor resistance: structural determinants for maintaining sensitivity and developing resistance to atazanavir. Biochemistry 2006; 45:5468-77. [PMID: 16634628 PMCID: PMC2518317 DOI: 10.1021/bi051886s] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of HIV-1 protease mutants has been designed in an effort to analyze the contribution to drug resistance provided by natural polymorphisms as well as therapy-selective (active and non-active site) mutations in the HIV-1 CRF_01 A/E (AE) protease when compared to that of the subtype B (B) protease. Kinetic analysis of these variants using chromogenic substrates showed differences in substrate specificity between pretherapy B and AE proteases. Inhibition analysis with ritonavir, indinavir, nelfinavir, amprenavir, saquinavir, lopinavir, and atazanavir revealed that the natural polymorphisms found in A/E can influence inhibitor resistance. It was also apparent that a high level of resistance in the A/E protease, as with B protease, is due to it aquiring a combination of active site and non-active site mutations. Structural analysis of atazanavir bound to a pretherapy B protease showed that the ability of atazanavir to maintain its binding affinity for variants containing some resistance mutations is due to its unique interactions with flap residues. This structure also explains why the I50L and I84V mutations are important in decreasing the binding affinity of atazanavir.
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Affiliation(s)
- José C. Clemente
- Johnson & Johnson Pharmaceutical Research & Development, LLC, 665 Stockton Dr. Exton, PA 19341, University of Florida College of Medicine
| | | | | | | | | | - Sarawut Nukoolkarn
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayuthaya Rd., Bangkok 10400, Thailand
| | | | | | | | - Wichet Leelamanit
- Department of Biochemistry, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayuthaya Rd., Bangkok 10400, Thailand
| | - Maureen M. Goodenow
- Department of Pathology, Immunology, and Laboratory Medicine, Gainesville, Florida 32610
| | - Ben M. Dunn
- *To whom correspondence should be addressed. Phone: (352) 392-3362, Fax: (352) 846-0412,
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5
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Characteristics of chimeric enzymes constructed between Thermotoga maritima and Agrobacterium tumefaciens β-glucosidases: Role of C-terminal domain in catalytic activity. Enzyme Microb Technol 2006. [DOI: 10.1016/j.enzmictec.2005.08.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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6
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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: 63] [Impact Index Per Article: 3.3] [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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Castanheira P, Samyn B, Sergeant K, Clemente JC, Dunn BM, Pires E, Van Beeumen J, Faro C. Activation, proteolytic processing, and peptide specificity of recombinant cardosin A. J Biol Chem 2005; 280:13047-54. [PMID: 15677463 DOI: 10.1074/jbc.m412076200] [Citation(s) in RCA: 34] [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
Cardosins are model plant aspartic proteases, a group of proteases that are involved in cell death events associated with plant senescence and stress responses. They are synthesized as single-chain zymogens, and subsequent conversion into two-chain mature enzymes is a crucial step in the regulation of their activity. Here we describe the activation and proteolytic processing of recombinant procardosin A. The cleavage sites involved in this multi-step autocatalytic process were determined, some of them using a novel method for C-terminal sequence analysis. Even though the two-chain recombinant enzyme displayed similar properties as natural cardosin A, a single-chain mutant form was engineered based on the processing results and produced in Escherichia coli. Determination of its primary specificity using two combinatorial peptide libraries revealed that this mutant form behaved like the natural enzyme. The primary specificity of the enzyme closely resembles those of cathepsin D and plasmepsins, suggesting that cardosin A shares the same peptide scissile bond preferences of its vacuolar/lysosomal mammalian and protozoan homologues.
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Affiliation(s)
- Pedro Castanheira
- Departamento de Bioquímica, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, Apartado 3126, P-3001-401 Coimbra, Portugal
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Affiliation(s)
- Ben M Dunn
- Department of Biochemistry & Molecular Biology, University of Florida College of Medicine, Gainesville, Florida 32610-0245, USA.
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Goyal K, Jo Kim B, Kim JD, Kim YK, Kitaoka M, Hayashi K. Enhancement of transglycosylation activity by construction of chimeras between mesophilic and thermophilic beta-glucosidase. Arch Biochem Biophys 2002; 407:125-34. [PMID: 12392722 DOI: 10.1016/s0003-9861(02)00470-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The family 3 beta-glucosidase from Thermotoga maritima is a highly thermostable enzyme (85 degrees C) that displays transglycosylation activity. In contrast, the beta-glucosidase from Cellvibrio gilvus is mesophilic (35 degrees C) and displays no such transglycosylation activity. Both enzymes consist of two domains, an N-terminal and a C-terminal domain, and the amino acid identities between the two enzymes in these domains are 32.4 and 36.4%, respectively. In an attempt to identify the molecular basis underpinning the display of transglycosylation activity and the requirements for thermal stability, eight chimeric genes were constructed by shuffling the two parental beta-glucosidase genes at four selected borders, two in the N-terminal domain and two in the C-terminal domain. Of the eight chimeric genes constructed, only two chimeric enzymes (Tm578/606Cg and Tm638/666Cg) gave catalytically active forms and these were the ones shuffled in the C-terminal domain. For these active chimeric enzymes, 80% (Tm578/606Cg) and 88% (Tm638/666Cg) of their amino acid sequences originated from T. maritima. With regard to their thermal profiles, the two active chimeric enzymes, Tm578/606Cg and Tm638/666Cg, displayed profiles intermediate to those of the two parental enzymes as they were optimally active at 65 and 70 degrees C, respectively. These two chimeric enzymes were optimally active at pH 4.1 and 3.9, which is closer to that observed for the T. maritima enzyme (pH 3.2-3.5) than that for the C. gilvus enzyme (pH 6.2-6.5). Kinetic parameters for the chimeric enzymes were investigated with five different substrates including pNP-beta-D-glucopyranoside. The kinetic parameters obtained for the chimeric enzymes were closer to those of the T. maritima enzyme than to those of the C. gilvus enzyme. Transglycosylation activity was observed for both chimeric enzymes and the activity of the Tm578/606Cg chimera was at a level twice that observed with the T. maritima enzyme. This study is an effective demonstration of the usefulness of chimeric enzymes in altering the characteristics of an enzyme.
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Affiliation(s)
- Kshamata Goyal
- Enzyme Laboratory, National Food Research Institute, 2-1-12, Kannondai, Tsukuba, Ibaraki, Japan
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