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Glass DC, Krishnan M, Smith JC, Baudry J. Three entropic classes of side chain in a globular protein. J Phys Chem B 2013; 117:3127-34. [PMID: 23421556 DOI: 10.1021/jp400564q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The relationship between the NMR methyl group axial order parameter and the side chain conformational entropy is investigated in inhibitor-bound and apo human HIV protease using molecular dynamics simulation. Three distinct entropic classes of methyl-bearing side chains, determined by the topological distance of the methyl group from the protein backbone (i.e., the number of χ-bonds between the Cα and the carbon of the CH3 group), are revealed by atomistic trajectory analyses performed in the local frame of reference of individual methyl probes. The results demonstrate that topologically equivalent methyl groups experience similar nonbonded microenvironments regardless of the type of residues to which they are attached. Similarly, methyl groups that belong to the same side chain but that are not topologically equivalent exhibit different thermodynamic and dynamic properties. The two-parameter classification (based upon entropy and methyl axial order parameter) of side chains described here permits improved estimates of the conformational entropies of proteins from NMR motional parameters.
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Affiliation(s)
- Dennis C Glass
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008 Oak Ridge, Tennessee 37831-6309, United States
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Ishikita H, Warshel A. Predicting Drug-Resistant Mutations of HIV Protease. Angew Chem Int Ed Engl 2008; 47:697-700. [DOI: 10.1002/anie.200704178] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Figueiredo A, Moore KL, Mak J, Sluis-Cremer N, de Bethune MP, Tachedjian G. Potent nonnucleoside reverse transcriptase inhibitors target HIV-1 Gag-Pol. PLoS Pathog 2006; 2:e119. [PMID: 17096588 PMCID: PMC1635531 DOI: 10.1371/journal.ppat.0020119] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Accepted: 09/25/2006] [Indexed: 11/19/2022] Open
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) target HIV-1 reverse transcriptase (RT) by binding to a pocket in RT that is close to, but distinct, from the DNA polymerase active site and prevent the synthesis of viral cDNA. NNRTIs, in particular, those that are potent inhibitors of RT polymerase activity, can also act as chemical enhancers of the enzyme's inter-subunit interactions. However, the consequences of this chemical enhancement effect on HIV-1 replication are not understood. Here, we show that the potent NNRTIs efavirenz, TMC120, and TMC125, but not nevirapine or delavirdine, inhibit the late stages of HIV-1 replication. These potent NNRTIs enhanced the intracellular processing of Gag and Gag-Pol polyproteins, and this was associated with a decrease in viral particle production from HIV-1-transfected cells. The increased polyprotein processing is consistent with premature activation of the HIV-1 protease by NNRTI-enhanced Gag-Pol multimerization through the embedded RT sequence. These findings support the view that Gag-Pol multimerization is an important step in viral assembly and demonstrate that regulation of Gag-Pol/Gag-Pol interactions is a novel target for small molecule inhibitors of HIV-1 production. Furthermore, these drugs can serve as useful probes to further understand processes involved in HIV-1 particle assembly and maturation. HIV-1 encodes reverse transcriptase (RT), an enzyme that is essential for virus replication. Nonnucleoside reverse transcriptase inhibitors (NNRTIs) are allosteric inhibitors of the HIV-1 RT. In HIV-1-infected cells NNRTIs block the RT-catalyzed synthesis of a double-stranded DNA copy of the viral genomic RNA, which is an early step in the virus life cycle. Potent NNRTIs have the novel feature of promoting the interaction between the two RT subunits. However, the importance of this effect on the inhibition of HIV-1 replication has not been defined. In this study, the authors show that potent NNRTIs block an additional step in the virus life cycle. NNRTIs increase the intracellular processing of viral polyproteins called Gag and Gag-Pol that express the HIV-1 structural proteins and viral enzymes. Enhanced polyprotein processing is associated with a decrease in viral particles released from NNRTI-treated cells. NNRTI enhanced polyprotein processing is likely due to the drug binding to RT, expressed as part of the Gag-Pol polyprotein and promoting the interaction between separate Gag-Pol polyproteins. This leads to premature activation of the Gag-Pol embedded HIV-1 protease, resulting in a decrease in full-length viral polyproteins available for assembly and budding from the host cell membrane. This study provides proof-of-concept that small molecules can modulate the interactions between Gag-Pol polyproteins and suggests a new target for the development of HIV-1 antiviral drugs.
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Affiliation(s)
- Anna Figueiredo
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Australia
- Department of Microbiology, Monash University, Clayton, Australia
| | - Katie L Moore
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Australia
| | - Johnson Mak
- HIV Assembly Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Nicolas Sluis-Cremer
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | | | - Gilda Tachedjian
- Molecular Interactions Group, Macfarlane Burnet Institute for Medical Research and Public Health, Melbourne, Australia
- Department of Microbiology, Monash University, Clayton, Australia
- Department of Medicine, Monash University, Prahran, Australia
- * To whom correspondence should be addressed. E-mail:
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Davis DA, Read-Connole E, Pearson K, Fales HM, Newcomb FM, Moskovitz J, Yarchoan R. Oxidative modifications of kynostatin-272, a potent human immunodeficiency virus type 1 protease inhibitor: potential mechanism for altered activity in monocytes/macrophages. Antimicrob Agents Chemother 2002; 46:402-8. [PMID: 11796349 PMCID: PMC127045 DOI: 10.1128/aac.46.2.402-408.2002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies have indicated that human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs) are less active at blocking viral replication in HIV-1 infected peripheral blood monocytes/macrophages (M/M) than in HIV-1-infected T cells. We explored the hypothesis that oxidative modification and/or metabolism of the PIs in M/M might account for this reduced potency. We first tested the susceptibility of several PIs (kynostatin-272 [KNI-272], saquinavir, indinavir, ritonavir, or JE-2147) to oxidation after exposure to hydrogen peroxide (H(2)O(2)): only KNI-272 was highly susceptible to oxidation. Treatment of KNI-272 with low millimolar concentrations of H(2)O(2) resulted in mono-oxidation of the sulfur in the S-methyl cysteine (methioalanine) moiety, as determined by reversed-phase high-performance liquid chromatography and mass spectrometry (RP-HPLC/MS). Higher concentrations of H(2)O(2) led to an additional oxidation of the sulfur in the thioproline moiety of KNI-272. None of the PIs were metabolized or oxidized when added to T cells and cultured for up to 12 days. However, when KNI-272 was added to M/M, the concentration of the original KNI-272 steadily decreased with a corresponding increase in the production of three KNI-272 metabolites as identified by RP-HPLC/MS. The structures of these metabolites were different from those produced by H(2)O(2) treatment. The two major products of M/M metabolism of KNI-272 were identified as isomeric forms of KNI-272 oxidized solely on the thioproline ring. Both metabolites had reduced capacities to inhibit HIV-1 protease activity when tested in a standard HIV-1 protease assay. These studies demonstrate that antiviral compounds can be susceptible to oxidative modification in M/M and that this can affect their antiviral potency.
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Affiliation(s)
- David A Davis
- HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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Kuhelj R, Rizzo CJ, Chang CH, Jadhav PK, Towler EM, Korant BD. Inhibition of human endogenous retrovirus-K10 protease in cell-free and cell-based assays. J Biol Chem 2001; 276:16674-82. [PMID: 11278433 DOI: 10.1074/jbc.m008763200] [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: 11/06/2022] Open
Abstract
A full-length and C-terminally truncated version of human endogenous retrovirus (HERV)-K10 protease were expressed in Escherichia coli and purified to homogeneity. Both versions of the protease efficiently processed HERV-K10 Gag polyprotein substrate. HERV-K10 Gag was also cleaved by human immunodeficiency virus, type 1 (HIV-1) protease, although at different sites. To identify compounds that could inhibit protein processing dependent on the HERV-K10 protease, a series of cyclic ureas that had previously been shown to inhibit HIV-1 protease was tested. Several symmetric bisamides acted as very potent inhibitors of both the truncated and full-length form of HERV-K10 protease, in subnanomolar or nanomolar range, respectively. One of the cyclic ureas, SD146, can inhibit the processing of in vitro translated HERV-K10 Gag polyprotein substrate by HERV-K10 protease. In addition, in virus-like particles isolated from the teratocarcinoma cell line NCCIT, there is significant accumulation of Gag and Gag-Pol precursors upon treatment with SD146, suggesting the compound efficiently blocks HERV-K Gag processing in cells. This is the first report of an inhibitor able to block cell-associated processing of Gag polypeptides of an endogenous retrovirus.
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Affiliation(s)
- R Kuhelj
- Department of Virology, Experimental Station, DuPont Pharmaceuticals, Wilmington, Delaware 19880, USA
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Davis DA, Yusa K, Gillim LA, Newcomb FM, Mitsuya H, Yarchoan R. Conserved cysteines of the human immunodeficiency virus type 1 protease are involved in regulation of polyprotein processing and viral maturation of immature virions. J Virol 1999; 73:1156-64. [PMID: 9882317 PMCID: PMC103936 DOI: 10.1128/jvi.73.2.1156-1164.1999] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated the role of the two highly conserved cysteine residues, cysteines 67 and 95, of the human immunodeficiency virus type 1 (HIV-1) protease in regulating the activity of that protease during viral maturation. To this end, we generated four HIV-1 molecular clones: the wild type, containing both cysteine residues; a protease mutant in which the cysteine at position 67 was replaced by an alanine (C67A); a C95A protease mutant; and a double mutant (C67A C95A). When immature virions were produced in the presence of an HIV-1 protease inhibitor, KNI-272, and the inhibitor was later removed, limited polyprotein processing was observed for wild-type virion preparations over a 20-h period. Treatment of immature wild-type virions with the reducing agent dithiothreitol considerably improved the rate and extent of Gag processing, suggesting that the protease is, in part, reversibly inactivated by oxidation of the cysteine residues. In support of this, C67A C95A virions processed Gag up to fivefold faster than wild-type virions in the absence of a reducing agent. Furthermore, oxidizing agents, such as H2O2 and diamide, inhibited Gag processing of wild-type virions, and this effect was dependent on the presence of cysteine 95. Electron microscopy revealed that a greater percentage of double-mutant virions than wild-type virions developed a mature-like morphology on removal of the inhibitor. These studies provide evidence that under normal culture conditions the cysteines of the HIV-1 protease are susceptible to oxidation during viral maturation, thus preventing immature virions from undergoing complete processing following their release. This is consistent with the cysteines being involved in the regulation of viral maturation in cells under oxidative stress.
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Affiliation(s)
- D A Davis
- HIV and AIDS Malignancy Branch, Medicine Branch, National Cancer Institute, Bethesda, Maryland 20892, USA.
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Hodge CN, Lam PYS, Eyermann CJ, Jadhav PK, Ru Y, Fernandez CH, De Lucca GV, Chang CH, Kaltenbach RF, Holler ER, Woerner F, Daneker WF, Emmett G, Calabrese JC, Aldrich PE. Calculated and Experimental Low-Energy Conformations of Cyclic Urea HIV Protease Inhibitors. J Am Chem Soc 1998. [DOI: 10.1021/ja972357h] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- C. Nicholas Hodge
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Patrick Y. S. Lam
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Charles J. Eyermann
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Prabhakar K. Jadhav
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Y. Ru
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Christina H. Fernandez
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - George V. De Lucca
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Chong-Hwan Chang
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Robert F. Kaltenbach
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Edward R. Holler
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Francis Woerner
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Wayne F. Daneker
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - George Emmett
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Joseph C. Calabrese
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
| | - Paul E. Aldrich
- Contribution from the Chemical and Physical Sciences Department, Research Division, DuPont Merck Pharmaceutical Company, P.O. Box 80500, Wilmington, Delaware 19880-0500, and Central Research Department, DuPont Company, Wilmington, Delaware 19880-0328
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Wilkerson WW, Dax S, Cheatham WW. Nonsymmetrically substituted cyclic urea HIV protease inhibitors. J Med Chem 1997; 40:4079-88. [PMID: 9406598 DOI: 10.1021/jm970288b] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A series of nonsymmetrically substituted cyclic ureacarboxamides was synthesized and evaluated for antiviral activity as a function of the inhibition of HIV-protease. Selected protease inhibitors were also evaluated for oral bioavailability. The synthesis, pharmacology, quantitative structure-activity relationship (QSAR), and pharmacokinetics for the series will be discussed.
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Affiliation(s)
- W W Wilkerson
- DuPont Merck Pharmaceutical Company, Experimental Station, Wilmington, Delaware 19880-0500, USA
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Rayner MM, Cordova B, Jackson DA. Population dynamics studies of wild-type and drug-resistant mutant HIV in mixed infections. Virology 1997; 236:85-94. [PMID: 9299620 DOI: 10.1006/viro.1997.8620] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We have studied the population dynamics in response to selective drug pressure of mixtures of wild-type and mutant HIV viruses exposed to either an inhibitor of the viral protease or a nonnucleoside allosteric inhibitor of the viral reverse transcriptase. In order to quantitate mutant virus present in a mixed population, we developed a selective plaque assay, which appears to be generally applicable to population dynamics studies where the viruses in question differ in the sensitivity to a given drug by at least 10-fold. In this assay system, the titer of virus in a mixture is measured in the absence and presence of a concentration of a specific inhibitor known to suppress virus replication by 99%. Virus detected in the presence of inhibitor corresponds to mutant virus, whereas detection in the absence of drug results in quantitation of the total virion population. Wild-type virus is then estimated by difference. Utilizing this system we studied the fate of mixtures of wild-type and the protease-resistant mutant variant I84V in the presence and absence of the cyclic urea HIV protease inhibitor, DMP 450. We also examined the dynamics of mixtures of wild-type and the resistant mutant variant, L100I, in the presence and absence of the drug DMP 266. In both systems we demonstrated that in the absence of drug, mutant virus is at a selective disadvantage for growth compared to wild-type, whereas in the presence of a specific inhibitor, mutant virus exhibits the selective growth advantage over wild-type virus. Better understanding of HIV population dynamics may allow the development of superior inhibitors and the careful application of combination therapy in the clinical setting.
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Affiliation(s)
- M M Rayner
- Molecular Biology Department, The DuPont Merck Pharmaceutical Company, Wilmington, Delaware 19880, USA
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Sheng N, Pettit SC, Tritch RJ, Ozturk DH, Rayner MM, Swanstrom R, Erickson-Viitanen S. Determinants of the human immunodeficiency virus type 1 p15NC-RNA interaction that affect enhanced cleavage by the viral protease. J Virol 1997; 71:5723-32. [PMID: 9223458 PMCID: PMC191824 DOI: 10.1128/jvi.71.8.5723-5732.1997] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
During human immunodeficiency virus type 1 (HIV-1) virion assembly, cleavage of the Gag precursor by the viral protease results in the transient appearance of a nucleocapsid-p1-p6 intermediate product designated p15NC. Utilizing the p15NC precursor protein produced with an in vitro transcription-translation system or purified after expression in Escherichia coli, we have demonstrated that RNA is required for efficient cleavage of HIV p15NC. Gel mobility shift and nitrocellulose filter binding experiments indicate that purified p15NC protein specifically binds its corresponding mRNA with an estimated Kd of 1.5 nM. Binding was not affected by the presence or absence of zinc or EDTA. Moreover, mutagenesis of the cysteine residues within either of the two Cys-His arrays had no effect on RNA binding or on RNA-dependent cleavage by the viral protease. In contrast, decreased binding of RNA and diminished susceptibility to cleavage in vitro were observed with p15NC-containing mutations in one or more residues within the triplet of basic amino acids present in the region between the two zinc fingers. In addition, we found that 21- to 24-base DNA and RNA oligonucleotides of a particular sequence and secondary structure could substitute for p15 RNA in the enhancement of p15NC cleavage. Virus particles carrying a mutation in the triplet of NC basic residues (P3BE) show delayed cleavage of p15NC and a defect in core formation despite the eventual appearance of fully processed virion protein. These results define determinants of the p15NC-RNA interaction that lead to enhanced protease-mediated cleavage and demonstrate the importance of the triplet of basic residues in formation of the virus core.
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Affiliation(s)
- N Sheng
- Molecular Biology Department, The DuPont Merck Pharmaceutical Co., Wilmington, Delaware 19880-0336, USA
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Humphrey RW, Ohagen A, Davis DA, Fukazawa T, Hayashi H, Höglund S, Mitsuya H, Yarchoan R. Removal of human immunodeficiency virus type 1 (HIV-1) protease inhibitors from preparations of immature HIV-1 virions does not result in an increase in infectivity or the appearance of mature morphology. Antimicrob Agents Chemother 1997; 41:1017-23. [PMID: 9145862 PMCID: PMC163843 DOI: 10.1128/aac.41.5.1017] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The processing of gag and gag-pol polyproteins by human immunodeficiency virus type 1 (HIV-1) protease is a crucial step in the formation of infectious HIV-1 virions. In this study, we examine whether particles produced in the presence of inhibitors of HIV-1 protease can subsequently undergo gag polyprotein cleavage with restoration of infectivity following removal of the inhibitors. Viral particles produced during 7 days of culture in the presence of the protease inhibitors KNI-272 (10 microM) and saquinavir (5 microM) contained predominantly p55gag polyprotein but little or no p24gag cleavage product. Following resuspension of the particles in medium free of the inhibitor, some gag polyprotein processing was detected in particles produced from the KNI-272-treated cells, but not from the saquinavir-treated cells within the first 3 h. However, the majority of the protein remained as p55gag throughout a 48-h experimental period. The infectivity (50% tissue culture infective dose per milliliter) of the viral particles from KNI-272-treated cells was 10(6)-fold lower than that of control particles and did not significantly increase over the 48 h after the inhibitor was removed, despite the apparent return of protease function in a subset of these virions. This failure to restore infectivity was due neither to a reduction in the number of particles produced by protease inhibitor-treated cells nor to a failure of HIV RNA to be packaged in the virions. These particles also failed to express the mature phenotype by electron microscopy. Thus, while some processing of the gag polyprotein can occur in isolated HIV virions, this does not appear to be sufficient to restore infectivity in the majority of particles. This finding suggests that there may be constraints on postbudding polyprotein processing in the production of viable particles. These results should have positive implications regarding the use of protease inhibitors as anti-HIV drugs.
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Affiliation(s)
- R W Humphrey
- HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Lam PY, Ru Y, Jadhav PK, Aldrich PE, DeLucca GV, Eyermann CJ, Chang CH, Emmett G, Holler ER, Daneker WF, Li L, Confalone PN, McHugh RJ, Han Q, Li R, Markwalder JA, Seitz SP, Sharpe TR, Bacheler LT, Rayner MM, Klabe RM, Shum L, Winslow DL, Kornhauser DM, Hodge CN. Cyclic HIV protease inhibitors: synthesis, conformational analysis, P2/P2' structure-activity relationship, and molecular recognition of cyclic ureas. J Med Chem 1996; 39:3514-25. [PMID: 8784449 DOI: 10.1021/jm9602571] [Citation(s) in RCA: 147] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
High-resolution X-ray structures of the complexes of HIV-1 protease (HIV-1PR) with peptidomimetic inhibitors reveal the presence of a structural water molecule which is hydrogen bonded to both the mobile flaps of the enzyme and the two carbonyls flanking the transition-state mimic of the inhibitors. Using the structure-activity relationships of C2-symmetric diol inhibitors, computed-aided drug design tools, and first principles, we designed and synthesized a novel class of cyclic ureas that incorporates this structural water and preorganizes the side chain residues into optimum binding conformations. Conformational analysis suggested a preference for pseudodiaxial benzylic and pseudodiequatorial hydroxyl substituents and an enantiomeric preference for the RSSR stereochemistry. The X-ray and solution NMR structure of the complex of HIV-1PR and one such cyclic urea, DMP323, confirmed the displacement of the structural water. Additionally, the bound and "unbound" (small-molecule X-ray) ligands have similar conformations. The high degree of preorganization, the complementarity, and the entropic gain of water displacement are proposed to explain the high affinity of these small molecules for the enzyme. The small size probably contributes to the observed good oral bioavailability in animals. Extensive structure-based optimization of the side chains that fill the S2 and S2' pockets of the enzyme resulted in DMP323, which was studied in phase I clinical trials but found to suffer from variable pharmacokinetics in man. This report details the synthesis, conformational analysis, structure-activity relationships, and molecular recognition of this series of C2-symmetry HIV-1PR inhibitors. An initial series of cyclic ureas containing nonsymmetric P2/P2' is also discussed.
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Affiliation(s)
- P Y Lam
- DuPont Merck Pharmaceutical Company, DuPont Merck Experimental Station, Wilmington, Delaware 19880-0500, USA.
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Hodge CN, Aldrich PE, Bacheler LT, Chang CH, Eyermann CJ, Garber S, Grubb M, Jackson DA, Jadhav PK, Korant B, Lam PY, Maurin MB, Meek JL, Otto MJ, Rayner MM, Reid C, Sharpe TR, Shum L, Winslow DL, Erickson-Viitanen S. Improved cyclic urea inhibitors of the HIV-1 protease: synthesis, potency, resistance profile, human pharmacokinetics and X-ray crystal structure of DMP 450. CHEMISTRY & BIOLOGY 1996; 3:301-14. [PMID: 8807858 DOI: 10.1016/s1074-5521(96)90110-6] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Effective HIV protease inhibitors must combine potency towards wild-type and mutant variants of HIV with oral bioavailability such that drug levels in relevant tissues continuously exceed that required for inhibition of virus replication. Computer-aided design led to the discovery of cyclic urea inhibitors of the HIV protease. We set out to improve the physical properties and oral bioavailability of these compounds. RESULTS We have synthesized DMP 450 (bis-methanesulfonic acid salt), a water-soluble cyclic urea compound and a potent inhibitor of HIV replication in cell culture that also inhibits variants of HIV with single amino acid substitutions in the protease. DMP 450 is highly selective for HIV protease, consistent with displacement of the retrovirus-specific structural water molecule. Single doses of 10 mg kg-1 DMP 450 result in plasma levels in man in excess of that required to inhibit wild-type and several mutant HIVs. A plasmid-based, in vivo assay model suggests that maintenance of plasma levels of DMP 450 near the antiviral IC90 suppresses HIV protease activity in the animal. We did identify mutants that are resistant to DMP 450, however; multiple mutations within the protease gene caused a significant reduction in the antiviral response. CONCLUSIONS DMP 450 is a significant advance within the cyclic urea class of HIV protease inhibitors due to its exceptional oral bioavailability. The data presented here suggest that an optimal cyclic urea will provide clinical benefit in treating AIDS if it combines favorable pharmacokinetics with potent activity against not only single mutants of HIV, but also multiply-mutant variants.
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Affiliation(s)
- C N Hodge
- Department of Chemical Sciences, DuPont Merck Pharmaceutical Co., Wilmington, DE 19880, USA.
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