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Sethuvasan S, Sugumar P, Ponnuswamy M, Ponnuswamy S. N-Benzyl-2,7-diphenyl-1,4-diazepan-5-one analogues: Synthesis, spectral characterization, stereochemistry, crystal structure and molecular docking studies. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.05.065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Oehme DP, Brownlee RTC, Wilson DJD. Can cyclic HIV protease inhibitors bind in a non-preferred form? An ab initio, DFT and MM-PB(GB)SA study. J Mol Model 2013; 19:1125-42. [DOI: 10.1007/s00894-012-1660-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 10/21/2012] [Indexed: 10/27/2022]
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3
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Bhattacharya AK, Rana KC, Pannecouque C, De Clercq E. An Efficient Synthesis of a Hydroxyethylamine (HEA) Isostere and Its α-Aminophosphonate and Phosphoramidate Derivatives as Potential Anti-HIV Agents. ChemMedChem 2012; 7:1601-11. [DOI: 10.1002/cmdc.201200271] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 06/12/2012] [Indexed: 11/09/2022]
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4
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Nimmanpipug P, Khampa C, Lee VS, Nangola S, Tayapiwatana C. Identification of amino acid residues of a designed ankyrin repeat protein potentially involved in intermolecular interactions with CD4: Analysis by molecular dynamics simulations. J Mol Graph Model 2011; 31:65-75. [DOI: 10.1016/j.jmgm.2011.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 08/30/2011] [Accepted: 09/01/2011] [Indexed: 11/16/2022]
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Loughlin WA, Tyndall JDA, Glenn MP, Hill TA, Fairlie DP. Update 1 of: Beta-Strand Mimetics. Chem Rev 2011; 110:PR32-69. [DOI: 10.1021/cr900395y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wendy A. Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Matthew P. Glenn
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Timothy A. Hill
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - David P. Fairlie
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
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Raza A, Sham YY, Vince R. Design and synthesis of sulfoximine based inhibitors for HIV-1 protease. Bioorg Med Chem Lett 2008; 18:5406-10. [DOI: 10.1016/j.bmcl.2008.09.044] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2008] [Revised: 09/09/2008] [Accepted: 09/10/2008] [Indexed: 10/21/2022]
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8
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Damm KL, Carlson HA. Exploring Experimental Sources of Multiple Protein Conformations in Structure-Based Drug Design. J Am Chem Soc 2007; 129:8225-35. [PMID: 17555316 DOI: 10.1021/ja0709728] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Receptor flexibility must be incorporated into structure-based drug design in order to portray a more accurate representation of a protein in solution. Our approach is to generate pharmacophore models based on multiple conformations of a protein and is very similar to solvent mapping of hot spots. Previously, we had success using computer-generated conformations of apo human immunodeficiency virus-1 protease (HIV-1p). Here, we examine the use of an NMR ensemble versus a collection of crystal structures, and we compare back to our previous study based on computer-generated conformations. To our knowledge, this is the first direct comparison of an NMR ensemble and a collection of crystal structures to incorporate protein flexibility in structure-based drug design. To provide an accurate comparison between the experimental sources, we used bound structures for our multiple protein structure (MPS) pharmacophore models. The models from an NMR ensemble and a collection of crystal structures were both able to discriminate known HIV-1p inhibitors from decoy molecules and displayed superior performance over models created from single conformations of the protein. Although the active-site conformations were already predefined by bound ligands, the use of MPS allows us to overcome the cross-docking problem and generate a model that does not simply reproduce the chemical characteristics of a specific ligand class. We show that there is more structural variation between 28 structures in an NMR ensemble than 90 crystal structures bound to a variety of ligands. MPS models from both sources performed well, but the model determined using the NMR ensemble appeared to be the most general yet accurate representation of the active site. This work encourages the use of NMR models in structure-based design.
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Affiliation(s)
- Kelly L Damm
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, USA
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Affiliation(s)
- Wendy A Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia.
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Abstract
The discovery and development of more than a dozen drugs in the past 15 years for the treatment of AIDS offer an excellent example of progress in the field of rational drug design. At this time, the principal targets are reverse transcriptase and protease, enzymes encoded by the human immunodeficiency virus. The introduction of protease inhibitors, in particular, has drastically decreased the mortality and morbidity associated with AIDS. This review presents the methods used to develop such drugs and discusses the remaining problems, such as the rapid emergence of drug resistance.
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Affiliation(s)
- Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA.
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Yamauchi T, Higashiyama K, Kubo H, Ohmiya S. Synthesis of C2-symmetrical chiral diamines: diastereoselective addition to bis(1,3-oxazolidinyl)alkanes with Grignard reagents. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s0957-4166(00)00268-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Wlodawer A, Vondrasek J. Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 1998; 27:249-84. [PMID: 9646869 DOI: 10.1146/annurev.biophys.27.1.249] [Citation(s) in RCA: 487] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Retroviral protease (PR) from the human immunodeficiency virus type 1 (HIV-1) was identified over a decade ago as a potential target for structure-based drug design. This effort was very successful. Four drugs are already approved, and others are undergoing clinical trials. The techniques utilized in this remarkable example of structure-assisted drug design included crystallography, NMR, computational studies, and advanced chemical synthesis. The development of these drugs is discussed in detail. Other approaches to designing HIV-1 PR inhibitors, based on the concepts of symmetry and on the replacement of a water molecule that had been found tetrahedrally coordinated between the enzyme and the inhibitors, are also discussed. The emergence of drug-induced mutations of HIV-1 PR leads to rapid loss of potency of the existing drugs and to the need to continue the development process. The structural basis of drug resistance and the ways of overcoming this phenomenon are mentioned.
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Affiliation(s)
- A Wlodawer
- Macromolecular Structure Laboratory, ABL-Basic Research Program, National Cancer Institute-Frederick Cancer Research and Development Center, Maryland 21702, USA.
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13
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Qian X, Morís-Varas F, Fitzgerald MC, Wong CH. C2-symmetrical tetrahydroxyazepanes as inhibitors of glycosidases and HIV/FIV proteases. Bioorg Med Chem 1996; 4:2055-69. [PMID: 9022971 DOI: 10.1016/s0968-0896(96)00218-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
C2-Symmetrical tetrahydroxyazepanes were synthesized as inhibitors for glycosidases. Tetrahydroxyazepane 1 is a non-specific inhibitor of various glycosidases, while compounds 2, 3 and 4 specifically inhibit beta-N-acetylglucosaminidase, beta-glucosidase, and alpha-fucosidase, respectively, with Ki in the micromolar range. Compound 1 is not an inhibitor of HIV/FIV proteases, but its 3,6-difluorobenzyl derivatives are moderate inhibitors of both enzymes.
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Affiliation(s)
- X Qian
- Department of Chemistry, Scripps Research Institute, La Jolla, CA 92037, USA
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Enders D, Meiers M. Diastereo- und enantioselektive Synthese von C2-symmetrischen, geschützten 1,n-Diaminen aus Dialdehyden. Angew Chem Int Ed Engl 1996. [DOI: 10.1002/ange.19961081925] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Randad RS, Lubkowska L, Silva AM, Guerin DM, Gulnik SV, Yu B, Erickson JW. Structure-based design of achiral, nonpeptidic hydroxybenzamide as a novel P2/P2' replacement for the symmetry-based HIV protease inhibitors. Bioorg Med Chem 1996; 4:1471-80. [PMID: 8894104 DOI: 10.1016/0968-0896(96)00140-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A combination of structure-activity studies, kinetic analysis, X-ray crystallographic analysis, and modeling were employed in the design of a novel series of HIV-1 protease (HIV PR) inhibitors. The crystal structure of a complex of HIV PR with SRSS-2,5-bis[N-(tert-butyloxycarbonyl)amino]-3,4-dihydroxy-1, 6-diphenylhexane (1) delineated a crucial water-mediated hydrogen bond between the tert-butyloxy group of the inhibitor and the amide hydrogen of Asp29 of the enzyme. Achiral, nonpeptidic 2-hydroxyphenylacetamide and 3-hydroxybenzamide groups were modeled as novel P2/P2' ligands to replace the crystallographic water molecules and to provide direct interactions with the NH groups of the Asp29/129 residues. Indeed, the symmetry-based inhibitors 7 and 19, possessing 3-hydroxy and 3-aminobenzamide, respectively, as a P2/P2' ligand, were potent inhibitors of HIV PR. The benzamides were superior in potency to the phenylacetamides and have four fewer rotatable bonds. An X-ray crystal structure of the HIV PR/7 complex at 2.1 A resolution revealed an asymmetric mode of binding, in which the 3-hydroxy group of the benzamide ring makes the predicted interaction with the backbone NH of Asp29 on one side of the active site only. An unexpected hydrogen bond with the Gly148 carbonyl group, resulting from rotation of the aromatic ring out of the amide plane, was observed on the other side. The inhibitory potencies of the benzamide compounds were found to be sensitive to the nature and position of substituents on the benzamide ring, and can be rationalized on the basis of the structure of the HIV PR/7 complex. These results partly confirm our initial hypothesis and suggest that optimal inhibitor designs should satisfy a requirement for providing polar interactions with Asp29 NH, and should minimize the conformational entropy loss on binding by reducing the number of freely rotatable bonds in inhibitors.
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Affiliation(s)
- R S Randad
- Structural Biochemistry Program, SAIC-Frederick, National Cancer Institute-Frederick Cancer Research and Development Center, MD 21702, USA
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Silva AM, Cachau RE, Sham HL, Erickson JW. Inhibition and catalytic mechanism of HIV-1 aspartic protease. J Mol Biol 1996; 255:321-46. [PMID: 8551523 DOI: 10.1006/jmbi.1996.0026] [Citation(s) in RCA: 141] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The structure of the HIV-1 protease in complex with a pseudo-C2 symmetric inhibitor, which contains a central difluoroketone motif, has been determined with X-ray diffraction data extending to 1.7 A resolution. The electron density map clearly indicates that the inhibitor is bound in a symmetric fashion as the hydrated, or gemdiol, form of the difluoroketone. Refinement of the complex reveals a unique, and almost symmetric, set of interactions between the geminal hydroxyl groups, the geminal fluorine atoms, and the active-site aspartate residues. Several hydrogen bonding patterns are consistent with that conformation. The lowest energy hydrogen disposition, as determined by semiempirical energy calculations, shows only one active site aspartate protonated. A comparison between the corresponding dihedral angles of the difluorodiol core and those of a hydrated peptide bond analog, calculated ab-initio, shows that the inhibitor core is a mimic of a hydrated peptide bond in a gauche conformation. The feasibility of an anti-gauche transition for a peptide bond after hydration is verified by extensive molecular dynamics simulations. The simulations suggest that rotation about the C-N scissile bond would readily occur after hydration and would be driven by the optimization of the interactions of peptide side-chains with the enzyme. These results, together with the characterization of a transition state leading to bond breakage via a concerted exchange of two protons, suggest a proteolysis mechanism whereby only one active site aspartate is initially protonated. The steps of this mechanism are: asymmetric binding of the substrate; hydration of the peptidic carbonyl by an active site water; proton translocation between the active site aspartate residues simultaneously with carbonyl hydration; optimization of the binding of the entire substrate facilitated by the flexible structure of the hydrated peptide bond, which, in turn, forces the hydrated peptide bond to assume a gauche conformation; simultaneous proton exchange whereby one hydroxyl donates a proton to the charged aspartate, and, at the same time, the nitrogen lone pair accepts a proton from the other aspartate; and, bond breakage and regeneration of the initial protonation state of the aspartate residues.
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Affiliation(s)
- A M Silva
- Structural Biochemistry Program, National Cancer Institute, Frederick, MD 21702, USA
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17
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Randad RS, Lubkowska L, Bujacz A, Naik RH, Gulnik SV, Yu B, Silva A, Munshi S, Lynch TM, Clanton DJ, Bhat T, Erickson JW. Structure-based design of achiral anthranilamides as P2/P2′ surrogates for symmetry-based HIV protease inhibitors: design, synthesis, X-ray structure, enzyme inhibition and antiviral activity. Bioorg Med Chem Lett 1995. [DOI: 10.1016/0960-894x(95)00449-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Randad RS, Lubkowska L, Bhat T, Munshi S, Gulnik SV, Yu B, Erickson JW. Symmetry-based HIV Protease inhibitors: rational design of 2-methylbenzamides as novel P2/P2′ ligands. Bioorg Med Chem Lett 1995. [DOI: 10.1016/0960-894x(95)00289-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Kempf DJ. Progress in the discovery of orally bioavailable inhibitors of HIV protease. ACTA ACUST UNITED AC 1995. [DOI: 10.1007/bf02172035] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Baldwin ET, Bhat TN, Gulnik S, Liu B, Topol IA, Kiso Y, Mimoto T, Mitsuya H, Erickson JW. Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analog containing allophenylnorstatine. Structure 1995; 3:581-90. [PMID: 8590019 DOI: 10.1016/s0969-2126(01)00192-7] [Citation(s) in RCA: 120] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND HIV-1 protease (HIV PR), an aspartic protease, cleaves Phe-Pro bonds in the Gag and Gag-Pol viral polyproteins. Substrate-based peptide mimics constitute a major class of inhibitors of HIV PR presently being developed for AIDS treatment. One such compound, KNI-272, which incorporates allophenylnorstatine (Apns)-thioproline (Thp) in place of Phe-Pro, has potent antiviral activity and is undergoing clinical trials. The structure of the enzyme-inhibitor complex should lead to an understanding of the structural basis for its tight binding properties and provide a framework for interpreting the emerging resistance to this drug. RESULTS The three-dimensional crystal structure of KNI-272 bound to HIV PR has been determined to 2.0 A resolution and used to analyze structure-activity data and drug resistance for the Arg8-->Gln and ILe84-->Val mutations in HIV PR. The conformationally constrained Apns-Thp linkage is favorably recognized in its low energy trans conformation, which results in a symmetric mode of binding to the active-site aspartic acids and also explains the unusual preference of HIV PR for the S, or syn, hydroxyl group of the Apns residue. The inhibitor recognizes the enzyme via hydrogen bonds to three bridging water molecules, including one that is coordinated directly to the catalytic Asp125 residue. CONCLUSIONS The structure of the HIV PR/KNI-272 complex illustrates the importance of limiting the conformational degrees of freedom and of using protein-bound water molecules for building potent inhibitors. The binding mode of HIV PR inhibitors can be predicted from the stereochemical relationship between adjacent hydroxyl-bearing and side chain bearing carbon atoms of the P1 substituent. Our structure also provides a framework for designing analogs targeted to drug-resistant mutant enzymes.
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Affiliation(s)
- E T Baldwin
- Frederick Biomedical Supercomputing Center, SAIC-Frederick, NCI-Frederick Cancer Research and Development Center, Maryland 21702, USA
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Baldwin ET, Bhat TN, Liu B, Pattabiraman N, Erickson JW. Structural basis of drug resistance for the V82A mutant of HIV-1 proteinase. NATURE STRUCTURAL BIOLOGY 1995; 2:244-9. [PMID: 7773792 DOI: 10.1038/nsb0395-244] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A major problem in the development of antiviral therapies for AIDS has been the emergence of drug resistance. We report an analysis of the structure of a Val 82 to Ala mutant of HIV-1 proteinase complexed to A-77003, a C2 symmetry-based inhibitor. Modelling studies predicted that the V82A mutation would result in decreased van der Waals' interactions with the phenyl rings of A-77003 in both S1 and S1' subsites. Unexpected rearrangements of the protein backbone, however, resulted in favourable re-packing of inhibitor and enzyme atoms in the S1 but not the S1' subsite. This analysis reveals the importance of enzyme flexibility in accommodating alternate packing arrangements, and can be applied to the re-design of inhibitors targeted to drug resistant variants which emerge in the clinic.
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Affiliation(s)
- E T Baldwin
- Frederick Biomedical Supercomputing Center, PRI/DynCorp, National Cancer Institute-Frederick Cancer Research and Development Center, Maryland 21702-1201, USA
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Bhat TN, Baldwin ET, Liu B, Cheng YS, Erickson JW. X-ray structure of a tethered dimer for HIV-1 protease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1995; 362:439-44. [PMID: 8540354 DOI: 10.1007/978-1-4615-1871-6_56] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- T N Bhat
- Structural Biochemistry Program, Frederick Biomedical Supercomputing Center, PRI/DynCorp, National Cancer Institute, Frederick Cancer Research and Development Center, MD 21702-1201, USA
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Baldwin ET, Bhat TN, Gulnik S, Liu B, Kiso Y, Mitsuya H, Erickson JW. Structure of HIV-1 protease with KNI-272: a transition state mimetic inhibitor containing allophenylnorstatine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1995; 362:445-9. [PMID: 8540355 DOI: 10.1007/978-1-4615-1871-6_57] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- E T Baldwin
- NCI-Frederick Cancer Research and Development Center, PRI/DynCorp, Structural Biochemistry Program, Frederick, Maryland 21702, USA
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Martin JA, Redshaw S, Thomas GJ. Inhibitors of HIV proteinase. PROGRESS IN MEDICINAL CHEMISTRY 1995; 32:239-87. [PMID: 8577919 DOI: 10.1016/s0079-6468(08)70455-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- J A Martin
- Roche Products Ltd., Welwyn Garden City, Herts, UK
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Bhat TN, Baldwin ET, Liu B, Cheng YS, Erickson JW. Crystal structure of a tethered dimer of HIV-1 proteinase complexed with an inhibitor. NATURE STRUCTURAL BIOLOGY 1994; 1:552-6. [PMID: 7664084 DOI: 10.1038/nsb0894-552] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
HIV-1 proteinase (HIV PR) is a dimeric enzyme composed of two identical polypeptide chains that associate with twofold symmetry. We have determined to 1.8 A the crystal structure of a covalently tethered dimer of HIV PR. The tethered dimer:inhibitor complex is identical in nearly every respect to the complex of the same inhibitor with the wild type dimeric molecule, except for the linker region. Our results suggest that the tethered dimer may be a useful surrogate enzyme for studying the effects of single site mutations on substrate and inhibitor binding as well as on enzyme asymmetry, and for simulating independent mutational drift of the two domains which has been proposed to have led to the evolution of modern day, single-chain aspartic proteinases.
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Affiliation(s)
- T N Bhat
- Structural Biochemistry Program, Frederick Biomedical Supercomputing Center, PRI/DynCorp, National Cancer Institute-Frederick Cancer Research and Development Center, Maryland 21702-1201, USA
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29
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Randad RS, Pan W, Gulnik SV, Burt S, Erickson JW. De novo design of nonpeptidic HIV-1 protease inhibitors: Incorporation of structural water. Bioorg Med Chem Lett 1994. [DOI: 10.1016/s0960-894x(01)80339-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Babine RE, Zhang N, Schow SR, Xu Z, Byrn RA, Hastings RC, Semmelhack M, Wick MM, Kerwar SS. Design, structure activity and x-ray crystallographic studies of pseudosymmetrical nonpeptidyl HIV-1 protease inhibitors. Bioorg Med Chem Lett 1994. [DOI: 10.1016/s0960-894x(01)80159-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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