1
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Liu H, Laporte AG, Gónzalez Pinardo D, Fernández I, Hazelard D, Compain P. An Unexpected Lewis Acid-Catalyzed Cascade during the Synthesis of the DEF-Benzoxocin Ring System of Nogalamycin and Menogaril: Mechanistic Elucidation by Intermediate Trapping Experiments and Density Functional Theory Studies. J Org Chem 2024; 89:5634-5649. [PMID: 38554093 DOI: 10.1021/acs.joc.4c00134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2024]
Abstract
An unexpected Lewis acid-catalyzed carbohydrate rearrangement of a 1,5-bis-glycopyranoside to the product of a formal intramolecular C-aryl glycosylation reaction is reported. Mechanistic studies based mainly on intermediate trapping experiments and density functional theory (DFT) calculations reveal a cascade process involving three transient (a)cyclic oxocarbenium cations, the breaking of three single C(sp3)-O bonds, and the formation of three single bonds (i.e., exo-, endo-, and C-glycosidic bonds), leading to the 2,6-epoxybenzoxocine skeleton of bioactive natural glycoconjugates related to serjanione A and mimocaesalpin E. DFT calculations established that the generation of the pyran moiety embedded in the bridged benzoxocin ring system is likely to proceed through an unusual ring-closure of an ortho-quinone methide intermediate in which the attacking nucleophile is a carbonyl oxygen.
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Affiliation(s)
- Haijuan Liu
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Université de Strasbourg, Université de Haute-Alsace, CNRS (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), 25 Rue Becquerel, 67000 Strasbourg, France
| | - Adrien G Laporte
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Université de Strasbourg, Université de Haute-Alsace, CNRS (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), 25 Rue Becquerel, 67000 Strasbourg, France
| | - Daniel Gónzalez Pinardo
- Departamento de Química Orgánica and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Israel Fernández
- Departamento de Química Orgánica and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Damien Hazelard
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Université de Strasbourg, Université de Haute-Alsace, CNRS (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), 25 Rue Becquerel, 67000 Strasbourg, France
| | - Philippe Compain
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Université de Strasbourg, Université de Haute-Alsace, CNRS (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), Ecole Européenne de Chimie, Polymères et Matériaux (ECPM), 25 Rue Becquerel, 67000 Strasbourg, France
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2
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Zhang J, Sun WN, Jiang Z, Jia SK, Mei GJ. Diastereodivergent and Regioselective Synthesis of Tetrahydrofuro[2,3- b]furans with Four Consecutive Stereocenters. J Org Chem 2024; 89:4134-4144. [PMID: 38394632 DOI: 10.1021/acs.joc.4c00069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Base-catalyzed diastereodivergent and regioselective domino processes of triketone enones with arylacetaldehydes for the synthesis of tetrahydrofuro[2,3-b]furans with four consecutive stereocenters are reported. Good yields and diastereoselectivities are obtained when DBU is employed as a catalyst; in contrast, Et3N delivers a different diastereomer in excellent diastereoselectivity. This work offers many advantages, including switchable diastereoselectivity, cheap base catalysts, and a simple operation.
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Affiliation(s)
- Jing Zhang
- Advanced Research Institute and School of Pharmaceutical Science, Taizhou University, Jiaojiang, Zhejiang 318000, P. R. China
| | - Wen-Na Sun
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, Henan,P. R. China
| | - Zhiwei Jiang
- Advanced Research Institute and School of Pharmaceutical Science, Taizhou University, Jiaojiang, Zhejiang 318000, P. R. China
| | - Shi-Kun Jia
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, Henan,P. R. China
- Pingyuan Laboratory (Zhengzhou University), Zhengzhou 450001, P. R. China
| | - Guang-Jian Mei
- Green Catalysis Center, and College of Chemistry, Zhengzhou University, Zhengzhou 450001, Henan,P. R. China
- Pingyuan Laboratory (Zhengzhou University), Zhengzhou 450001, P. R. China
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3
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Wong-Sam A, Wang YF, Kneller DW, Kovalevsky AY, Ghosh AK, Harrison RW, Weber IT. HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics. J Mol Graph Model 2022; 117:108315. [PMID: 36108568 PMCID: PMC10091457 DOI: 10.1016/j.jmgm.2022.108315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 01/14/2023]
Abstract
Antiretroviral drug resistance is a therapeutic obstacle for people with HIV. HIV protease inhibitors darunavir and lopinavir are recommended for resistant infections. We characterized a protease mutant (PR10x) derived from a highly resistant clinical isolate including 10 mutations associated with resistance to lopinavir and darunavir. Compared to the wild-type protease, PR10x exhibits ∼3-fold decrease in catalytic efficiency and Ki values of 2-3 orders of magnitude worse for darunavir, lopinavir, and potent investigational inhibitor GRL-519. Crystal structures of the mutant were solved in a ligand-free form and in complex with GRL-519. The structures show altered interactions in the active site, flap-core interface, hydrophobic core, hinge region, and 80s loop compared to the corresponding wild-type protease structures. The ligand-free crystal structure exhibits a highly curled flap conformation which may amplify drug resistance. Molecular dynamics simulations performed for 1 μs on ligand-free dimers showed extremely large fluctuations in the flaps for PR10x compared to equivalent simulations on PR with a single L76V mutation or wild-type protease. This analysis offers insight about the synergistic effects of mutations in highly resistant variants.
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Affiliation(s)
- Andres Wong-Sam
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Yuan-Fang Wang
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Daniel W Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Andrey Y Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Robert W Harrison
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA; Department of Computer Science, Georgia State University, Atlanta, GA, 30303, USA
| | - Irene T Weber
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA; Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
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4
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Ghosh AK, Weber IT, Mitsuya H. Beyond darunavir: recent development of next generation HIV-1 protease inhibitors to combat drug resistance. Chem Commun (Camb) 2022; 58:11762-11782. [PMID: 36200462 PMCID: PMC10942761 DOI: 10.1039/d2cc04541a] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
We report our recent development of a conceptually new generation of exceptionally potent non-peptidic HIV-1 protease inhibitors that displayed excellent pharmacological and drug-resistance profiles. Our X-ray structural studies of darunavir and other designed inhibitors from our laboratories led us to create a variety of inhibitors incorporating fused ring polycyclic ethers and aromatic heterocycles to promote hydrogen bonding interactions with the backbone atoms of HIV-1 protease as well as van der Waals interactions with residues in the S2 and S2' subsites. We have also incorporated specific functionalities to enhance van der Waals interactions in the S1 and S1' subsites. The combined effects of these structural templates are critical to the inhibitors' exceptional potency and drug-like properties. We highlight here our molecular design strategies to promote backbone hydrogen bonding interactions to combat drug-resistance and specific design of polycyclic ether templates to mimic peptide-like bonds in the HIV-1 protease active site. Our medicinal chemistry and drug development efforts led to the development of new generation inhibitors significantly improved over darunavir and displaying unprecedented antiviral activity against multidrug-resistant HIV-1 variants.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA.
| | - Irene T Weber
- Departments of Biology and Chemistry, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303, USA
| | - Hiroaki Mitsuya
- Departments of Hematology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD 20892, USA
- Center for Clinical Sciences, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655, Japan
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5
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Wu M, Han Z, Ni H, Wang N, Ding K, Lu Y. Phosphine-catalyzed Divergent Domino Processes between γ-Substituted Allenoates and Carbonyl-Activated Alkenes. Chem Sci 2022; 13:3161-3168. [PMID: 35414887 PMCID: PMC8926293 DOI: 10.1039/d1sc06364b] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/10/2022] [Indexed: 11/25/2022] Open
Abstract
Highly enantioselective and chemodivergent domino reactions between γ-substituted allenoates and activated alkenes have been developed. In the presence of NUSIOC-Phos, triketone enone substrates smoothly reacted with γ-substituted allenoates to form bicyclic furofurans in good yields with high stereoselectivities. Alternatively, the reaction between diester-activated enone substrates and γ-substituted allenoates formed chiral conjugated 1,3-dienes in good yields with excellent enantioselectivities. Notably, by employing substrates with subtle structural difference, under virtually identical reaction conditions, we were able to access two types of chiral products, which are of biological relevance and synthetic importance. Highly enantioselective and chemodivergent domino reactions between γ-substituted allenoates and activated alkenes have been developed.![]()
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Affiliation(s)
- Mingyue Wu
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543 Singapore
| | - Zhaobin Han
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Huanzhen Ni
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543 Singapore
| | - Nengzhong Wang
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543 Singapore
| | - Kuiling Ding
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
| | - Yixin Lu
- Department of Chemistry, National University of Singapore 3 Science Drive 3 Singapore 117543 Singapore
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6
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D’Orsi R, Funicello M, Laurita T, Lupattelli P, Berti F, Chiummiento L. The Pseudo-Symmetric N-benzyl Hydroxyethylamine Core in a New Series of Heteroarylcarboxyamide HIV-1 Pr Inhibitors: Synthesis, Molecular Modeling and Biological Evaluation. Biomolecules 2021; 11:1584. [PMID: 34827582 PMCID: PMC8615997 DOI: 10.3390/biom11111584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 11/16/2022] Open
Abstract
Here, we report the synthesis, enzyme inhibition and structure-activity relationship studies of a new potent class of HIV-1 protease inhibitors, which contain a pseudo-symmetric hydroxyethylamine core and heteroarylcarboxyamide moieties. The simple synthetic pathway furnished nine compounds in a few steps with high yields. The compounds were designed taking into account our previous results on other series of inhibitors with different substituents at P' and P'' and different ways of linking them to the inhibitor core. Potent inhibitory activity was obtained with nanomolar IC50 values measured with a standard fluorimetric test in 100 mM MES buffer, pH 5.5, containing 400 mM NaCl, 1 mM EDTA, 1 mM DTT and 1 mg/ml BSA. Compounds 9a-c, containing the indole ring in P1, exhibited an HIV-1 protease inhibitory activity more powerful than darunavir in the same assay. To obtain molecular insight into the binding properties of these compounds, docking analysis was performed, and their binding properties were also compared.
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Affiliation(s)
- Rosarita D’Orsi
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Maria Funicello
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Teresa Laurita
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Paolo Lupattelli
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
| | - Federico Berti
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via Licio Giorgieri 1, 34127 Trieste, Italy
| | - Lucia Chiummiento
- Dipartimento di Scienze, Università della Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy; (R.D.); (M.F.); (T.L.); (P.L.)
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7
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Wu YJ, Meanwell NA. Geminal Diheteroatomic Motifs: Some Applications of Acetals, Ketals, and Their Sulfur and Nitrogen Homologues in Medicinal Chemistry and Drug Design. J Med Chem 2021; 64:9786-9874. [PMID: 34213340 DOI: 10.1021/acs.jmedchem.1c00790] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Acetals and ketals and their nitrogen and sulfur homologues are often considered to be unconventional and potentially problematic scaffolding elements or pharmacophores for the design of orally bioavailable drugs. This opinion is largely a function of the perception that such motifs might be chemically unstable under the acidic conditions of the stomach and upper gastrointestinal tract. However, even simple acetals and ketals, including acyclic molecules, can be sufficiently robust under acidic conditions to be fashioned into orally bioavailable drugs, and these structural elements are embedded in many effective therapeutic agents. The chemical stability of molecules incorporating geminal diheteroatomic motifs can be modulated by physicochemical design principles that include the judicious deployment of proximal electron-withdrawing substituents and conformational restriction. In this Perspective, we exemplify geminal diheteroatomic motifs that have been utilized in the discovery of orally bioavailable drugs or drug candidates against the backdrop of understanding their potential for chemical lability.
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Affiliation(s)
- Yong-Jin Wu
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, 100 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Nicholas A Meanwell
- Department of Discovery and Chemistry and Molecular Technologies, Bristol-Myers Squibb PRI, PO Box 4000, Princeton, New Jersey 08543-4000, United States
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8
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Peng K, Gao MY, Yi YY, Guo J, Dong ZB. Copper/Nickel-Catalyzed Selective C-S/S-S Bond Formation Starting from O
-Alkyl Phenylcarbamothioates. European J Org Chem 2020. [DOI: 10.1002/ejoc.201901884] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kang Peng
- School of Chemistry and Environmental Engineering; Wuhan Institute of Technology; 430205 Wuhan China
| | - Ming-Yuan Gao
- School of Chemistry and Environmental Engineering; Wuhan Institute of Technology; 430205 Wuhan China
| | - Yu-Yan Yi
- School of Chemistry and Environmental Engineering; Wuhan Institute of Technology; 430205 Wuhan China
| | - Jia Guo
- Key Laboratory of Green Chemical Process; Ministry of Education; Wuhan Institute of Technology; 430205 Wuhan China
- Hubei Key Laboratory of Novel Reactor and Green Chemistry Technology; Ministry of Education; Wuhan Institute of Technology; 430205 Wuhan China
| | - Zhi-Bing Dong
- School of Chemistry and Environmental Engineering; Wuhan Institute of Technology; 430205 Wuhan China
- Key Laboratory of Green Chemical Process; Ministry of Education; Wuhan Institute of Technology; 430205 Wuhan China
- Hubei Key Laboratory of Novel Reactor and Green Chemistry Technology; Ministry of Education; Wuhan Institute of Technology; 430205 Wuhan China
- Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules; Ministry of Education; Hubei University; 430062 Wuhan China
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9
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Structural studies of antiviral inhibitor with HIV-1 protease bearing drug resistant substitutions of V32I, I47V and V82I. Biochem Biophys Res Commun 2019; 514:974-978. [PMID: 31092330 DOI: 10.1016/j.bbrc.2019.05.064] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 12/23/2022]
Abstract
HIV-1 protease inhibitors are effective in HIV/AIDS therapy, although drug resistance is a severe problem. This study examines the effects of four investigational inhibitors against HIV-1 protease with drug resistant mutations of V32I, I47V and V82I (PRTri) that model the inhibitor-binding site of HIV-2 protease. These inhibitors contain diverse chemical modifications on the darunavir scaffold and form new interactions with wild type protease, however, the measured inhibition constants for PRTri mutant range from 17 to 40 nM or significantly worse than picomolar values reported for wild type enzyme. The X-ray crystal structure of PRTri mutant in complex with inhibitor 1 at 1.5 Å resolution shows minor changes in interactions with inhibitor compared with the corresponding wild type PR complex. Instead, the basic amine at P2 of inhibitor together with mutation V82I induces two alternate conformations for the side chain of Arg8 with new interactions with inhibitor and Leu10. Hence, inhibition is influenced by small coordinated changes in hydrophobic interactions.
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10
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Design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors incorporating aminothiochromane and aminotetrahydronaphthalene carboxamide derivatives as the P2 ligands. Eur J Med Chem 2018; 160:171-182. [PMID: 30340140 PMCID: PMC6237192 DOI: 10.1016/j.ejmech.2018.09.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 01/07/2023]
Abstract
We describe the design, synthesis, and biological evaluation of a series of novel HIV-1 protease inhibitors with carboxamide derivatives as the P2 ligands. We have specifically designed aminothiochromane and aminotetrahydronaphthalene-based carboxamide ligands to promote hydrogen bonding and van der Waals interactions in the active site of HIV-1 protease. Inhibitors 4e and 4j have shown potent enzyme inhibitory and antiviral activity. High resolution X-ray crystal structures of 4d- and 4k-bound HIV-1 protease revealed molecular insights into the ligand-binding site interactions.
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11
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Wong-Sam A, Wang YF, Zhang Y, Ghosh AK, Harrison RW, Weber IT. Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap-Core Interface of HIV-1 Protease. ACS OMEGA 2018; 3:12132-12140. [PMID: 30288468 PMCID: PMC6167001 DOI: 10.1021/acsomega.8b01683] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 09/13/2018] [Indexed: 06/08/2023]
Abstract
Four HIV-1 protease (PR) inhibitors, clinical inhibitors lopinavir and tipranavir, and two investigational compounds 4 and 5, were studied for their effect on the structure and activity of PR with drug-resistant mutation L76V (PRL76V). Compound 5 exhibited the best K i value of 1.9 nM for PRL76V, whereas the other three inhibitors had K i values of 4.5-7.6 nM, 2-3 orders of magnitude worse than for wild-type enzymes. Crystal structures showed only minor differences in interactions of inhibitors with PRL76V compared to wild-type complexes. The shorter side chain of Val76 in the mutant lost hydrophobic interactions with Lys45 and Ile47 in the flap, and with Asp30 and Thr74 in the protein core, consistent with decreased stability. Inhibitors forming additional polar interactions with the flaps or dimer interface of PRL76V were unable to compensate for the decrease in internal hydrophobic contacts. These structures provide insights for inhibitor design.
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Affiliation(s)
- Andres Wong-Sam
- Department
of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of
Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Yuan-Fang Wang
- Department
of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of
Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Ying Zhang
- Department
of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of
Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
- RNA Therapeutics Institute and Department of Biochemistry and Molecular
Pharmacology, University of Massachusetts
Medical School, Worcester, Massachusetts 01605, United States
| | - Arun K. Ghosh
- Department of Chemistry and Department
of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Robert W. Harrison
- Department
of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of
Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Irene T. Weber
- Department
of Biology, Molecular Basis of Disease Program, Department of Computer Science, and Department of
Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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12
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Ghosh AK, Brindisi M. Nature Inspired Molecular Design: Stereoselective Synthesis of Bicyclic and Polycyclic Ethers for Potent HIV-1 Protease Inhibitors. ASIAN J ORG CHEM 2018; 7:1448-1466. [PMID: 31595212 PMCID: PMC6781882 DOI: 10.1002/ajoc.201800255] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 12/14/2022]
Abstract
We have developed a conceptually new generation of non-peptidic HIV-1 protease inhibitors incorporating novel structural templates inspired by nature. This has resulted in protease inhibitors with exceptional potency and excellent pharmacological and drug-resistance profiles. The design of a stereochemically defined bis-tetrahydrofuran (bis-THF) scaffold followed by modifications to promote hydrogen bonding interactions with the backbone atoms of HIV-1 protease led to darunavir, the first clinically approved drug for treatment of drug resistant HIV. Subsequent X-ray crystal structure-based design efforts led us to create a range of exceptionally potent inhibitors incorporating other intriguing molecular templates possessing fused ring polycyclic ethers with multiple stereocenters. These structural templates are critical to inhibitors' exceptional potency and drug-like properties. Herein, we will highlight the synthetic strategies that provided access to these complex scaffolds in a stereoselective and optically active form, enabling our medicinal chemistry and drug development efforts.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907 (USA)
| | - Margherita Brindisi
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907 (USA)
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13
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Ghosh AK, Nyalapatla PR, Kovela S, Rao KV, Brindisi M, Osswald HL, Amano M, Aoki M, Agniswamy J, Wang YF, Weber IT, Mitsuya H. Design and Synthesis of Highly Potent HIV-1 Protease Inhibitors Containing Tricyclic Fused Ring Systems as Novel P2 Ligands: Structure-Activity Studies, Biological and X-ray Structural Analysis. J Med Chem 2018; 61:4561-4577. [PMID: 29763303 PMCID: PMC6044451 DOI: 10.1021/acs.jmedchem.8b00298] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The design, synthesis, and biological evaluation of a new class of HIV-1 protease inhibitors containing stereochemically defined fused tricyclic polyethers as the P2 ligands and a variety of sulfonamide derivatives as the P2' ligands are described. A number of ring sizes and various substituent effects were investigated to enhance the ligand-backbone interactions in the protease active site. Inhibitors 5c and 5d containing this unprecedented fused 6-5-5 ring system as the P2 ligand, an aminobenzothiazole as the P2' ligand, and a difluorophenylmethyl as the P1 ligand exhibited exceptional enzyme inhibitory potency and maintained excellent antiviral activity against a panel of highly multidrug-resistant HIV-1 variants. The umbrella-like P2 ligand for these inhibitors has been synthesized efficiently in an optically active form using a Pauson-Khand cyclization reaction as the key step. The racemic alcohols were resolved efficiently using a lipase catalyzed enzymatic resolution. Two high resolution X-ray structures of inhibitor-bound HIV-1 protease revealed extensive interactions with the backbone atoms of HIV-1 protease and provided molecular insight into the binding properties of these new inhibitors.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA,The corresponding author: Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, Phone: (765)-494-5323; Fax: (765)-496-1612,
| | - Prasanth R. Nyalapatla
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Satish Kovela
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Kalapala Venkateswara Rao
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Margherita Brindisi
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Heather L. Osswald
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Masayuki Amano
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto 860-8556, Japan,Department of Medical Technology, Kumamoto Health Science University, Kumamoto 861-5598, Japan
| | - Manabu Aoki
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto 860-8556, Japan,Department of Medical Technology, Kumamoto Health Science University, Kumamoto 861-5598, Japan,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Johnson Agniswamy
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, USA
| | - Yuan-Fang Wang
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, USA
| | - Irene T. Weber
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, USA
| | - Hiroaki Mitsuya
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto 860-8556, Japan,Department of Refractory Viral Infection, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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14
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Ghosh AK, Brindisi M, Nyalapatla PR, Takayama J, Ella-Menye JR, Yashchuk S, Agniswamy J, Wang YF, Aoki M, Amano M, Weber IT, Mitsuya H. Design of novel HIV-1 protease inhibitors incorporating isophthalamide-derived P2-P3 ligands: Synthesis, biological evaluation and X-ray structural studies of inhibitor-HIV-1 protease complex. Bioorg Med Chem 2017; 25:5114-5127. [PMID: 28434781 PMCID: PMC5617771 DOI: 10.1016/j.bmc.2017.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 04/04/2017] [Indexed: 11/29/2022]
Abstract
Based upon molecular insights from the X-ray structures of inhibitor-bound HIV-1 protease complexes, we have designed a series of isophthalamide-derived inhibitors incorporating substituted pyrrolidines, piperidines and thiazolidines as P2-P3 ligands for specific interactions in the S2-S3 extended site. Compound 4b has shown an enzyme Ki of 0.025nM and antiviral IC50 of 69nM. An X-ray crystal structure of inhibitor 4b-HIV-1 protease complex was determined at 1.33Å resolution. We have also determined X-ray structure of 3b-bound HIV-1 protease at 1.27Å resolution. These structures revealed important molecular insight into the inhibitor-HIV-1 protease interactions in the active site.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA.
| | - Margherita Brindisi
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Prasanth R Nyalapatla
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Jun Takayama
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Jean-Rene Ella-Menye
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Sofiya Yashchuk
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Yuan-Fang Wang
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA
| | - Manabu Aoki
- Department of Hematology, Kumamoto University of Medicine, Kumamoto 860-8556, Japan; Department of Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan
| | - Masayuki Amano
- Department of Hematology, Kumamoto University of Medicine, Kumamoto 860-8556, Japan; Department of Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan
| | - Irene T Weber
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Hiroaki Mitsuya
- Department of Hematology, Kumamoto University of Medicine, Kumamoto 860-8556, Japan; Department of Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch National Cancer Institute, Bethesda, MD 20892, USA; Department of Refractory Viral Infection, National Center for Global Health and Medicine Research Institute, Shinjuku, Tokyo 162-8655, Japan
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15
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Funicello M, Chiummiento L, Tramutola F, Armentano M, Bisaccia F, Miglionico R, Milella L, Benedetti F, Berti F, Lupattelli P. Synthesis and biological evaluation in vitro and in mammalian cells of new heteroaryl carboxyamides as HIV-protease inhibitors. Bioorg Med Chem 2017; 25:4715-4722. [DOI: 10.1016/j.bmc.2017.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 11/16/2022]
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16
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Ghosh AK, Sarkar A, Mitsuya H. HIV-Associated Neurocognitive Disorder (HAND) and the Prospect of Brain-Penetrating Protease Inhibitors for Antiretroviral Treatment. MEDICAL RESEARCH ARCHIVES 2017; 5:1113. [PMID: 29984302 PMCID: PMC6034681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The advent of combined active antiretroviral therapy (cART) dramatically improved HIV management and patient care of HIV-infected individuals. This treatment regimen resulted in a significant reduction of HIV/AIDS-related mortality and greatly improved life expectancies of those patients with access to cART. However, among many HIV-related complications, neurocognitive dysfunction, known as HIV-associated neurocognitive disorder (HAND) has been a major issue. While the cART regimen has been effective in reduction of HAND in many patients, the prevalence of HAND is increasing as HIV/AIDS patients live longer. HIV infection and its subsequent manifestation of HAND is complex. It is evident that the brain can serve as a sanctuary for HIV replication and HAND can remain in patients even with cART treatment due to poor blood-brain barrier permeability of the majority of current antiretroviral agents. Conceivably, cART needs to have improved CNS penetration properties for effective treatment and possible prevention of HAND. Therefore, design and development of new antiretroviral agents that can penetrate into the CNS effectively, could block HIV replication and significantly reduce the viral load in cerebrospinal fluid. This may prevent HAND and related symptoms. HIV protease inhibitors (PIs) are a critical component of cART. Over the years, we have designed and synthesized a range of highly potent and novel PIs including the FDA approved drug, darunavir, which is used as a first-line treatment. In an effort to improve CNS penetration, we have been involved in the design and development of potent PIs with improved in vitro brain penetration properties. Herein we provide a brief review that cover insights and discussion of HAND and our work on PI development to ameliorate HIV-associated neurocognitive disorders.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Anindya Sarkar
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Hiroaki Mitsuya
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto 860-8556, Japan
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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17
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Ghosh AK, Osswald HL, Glauninger K, Agniswamy J, Wang YF, Hayashi H, Aoki M, Weber IT, Mitsuya H. Probing Lipophilic Adamantyl Group as the P1-Ligand for HIV-1 Protease Inhibitors: Design, Synthesis, Protein X-ray Structural Studies, and Biological Evaluation. J Med Chem 2016; 59:6826-37. [PMID: 27389367 PMCID: PMC5360270 DOI: 10.1021/acs.jmedchem.6b00639] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A series of potent HIV-1 protease inhibitors with a lipophilic adamantyl P1 ligand have been designed, synthesized, and evaluated. We have developed an enantioselective synthesis of adamantane-derived hydroxyethylamine isosteres utilizing Sharpless asymmetric epoxidation as the key step. Various inhibitors incorporating P1-adamantylmethyl in combination with P2 ligands such as 3-(R)-THF, 3-(S)-THF, bis-THF, and THF-THP were examined. The S1' pocket was also probed with phenyl and phenylmethyl ligands. Inhibitor 15d, with an isobutyl P1' ligand and a bis-THF P2 ligand, proved to be the most potent of the series. The cLogP value of inhibitor 15d is improved compared to inhibitor 2 with a phenylmethyl P1-ligand. X-ray structural studies of 15d, 15h, and 15i with HIV-1 protease complexes revealed molecular insight into the inhibitor-protein interaction.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA,The corresponding author: Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, Phone: (765)-494-5323; Fax: (765)-496-1612,
| | - Heather L. Osswald
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Kristof Glauninger
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Johnson Agniswamy
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, USA
| | - Yuan-Fang Wang
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, USA
| | - Hironori Hayashi
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto 860-8556, Japan,Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Manabu Aoki
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto 860-8556, Japan,Department of Medical Technology, Kumamoto Health Science University, Kumamoto 861-5598, Japan,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Irene T. Weber
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, USA
| | - Hiroaki Mitsuya
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto 860-8556, Japan,Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo 162-8655, Japan,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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18
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Ghosh AK, Osswald HL, Prato G. Recent Progress in the Development of HIV-1 Protease Inhibitors for the Treatment of HIV/AIDS. J Med Chem 2016; 59:5172-208. [PMID: 26799988 PMCID: PMC5598487 DOI: 10.1021/acs.jmedchem.5b01697] [Citation(s) in RCA: 282] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
HIV-1 protease inhibitors continue to play an important role in the treatment of HIV/AIDS, transforming this deadly ailment into a more manageable chronic infection. Over the years, intensive research has led to a variety of approved protease inhibitors for the treatment of HIV/AIDS. In this review, we outline current drug design and medicinal chemistry efforts toward the development of next-generation protease inhibitors beyond the currently approved drugs.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Heather L. Osswald
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Gary Prato
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
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19
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Hu G, Ma A, Dou X, Zhao L, Wang J. Computational Studies of a Mechanism for Binding and Drug Resistance in the Wild Type and Four Mutations of HIV-1 Protease with a GRL-0519 Inhibitor. Int J Mol Sci 2016; 17:E819. [PMID: 27240358 PMCID: PMC4926353 DOI: 10.3390/ijms17060819] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/16/2016] [Accepted: 05/16/2016] [Indexed: 12/22/2022] Open
Abstract
Drug resistance of mutations in HIV-1 protease (PR) is the most severe challenge to the long-term efficacy of HIV-1 PR inhibitor in highly active antiretroviral therapy. To elucidate the molecular mechanism of drug resistance associated with mutations (D30N, I50V, I54M, and V82A) and inhibitor (GRL-0519) complexes, we have performed five molecular dynamics (MD) simulations and calculated the binding free energies using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. The ranking of calculated binding free energies is in accordance with the experimental data. The free energy spectra of each residue and inhibitor interaction for all complexes show a similar binding model. Analysis based on the MD trajectories and contribution of each residues show that groups R2 and R3 mainly contribute van der Waals energies, while groups R1 and R4 contribute electrostatic interaction by hydrogen bonds. The drug resistance of D30N can be attributed to the decline in binding affinity of residues 28 and 29. The size of Val50 is smaller than Ile50 causes the residue to move, especially in chain A. The stable hydrophobic core, including the side chain of Ile54 in the wild type (WT) complex, became unstable in I54M because the side chain of Met54 is flexible with two alternative conformations. The binding affinity of Ala82 in V82A decreases relative to Val82 in WT. The present study could provide important guidance for the design of a potent new drug resisting the mutation inhibitors.
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Affiliation(s)
- Guodong Hu
- Shandong Provincial Key Laboratory of Biophysics, College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Aijing Ma
- Shandong Provincial Key Laboratory of Biophysics, College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Xianghua Dou
- Shandong Provincial Key Laboratory of Biophysics, College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Liling Zhao
- Shandong Provincial Key Laboratory of Biophysics, College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, College of Physics and Electronic Information, Dezhou University, Dezhou 253023, China.
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20
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Abstract
The virally encoded protease is an important drug target for AIDS therapy. Despite the potency of the current drugs, infections with resistant viral strains limit the long-term effectiveness of therapy. Highly resistant variants of HIV protease from clinical isolates have different combinations of about 20 mutations and several orders of magnitude worse binding affinity for clinical inhibitors. Strategies are being explored to inhibit these highly resistant mutants. The existing inhibitors can be modified by introducing groups with the potential to form new interactions with conserved protease residues, and the flexible flaps. Alternative strategies are discussed, including designing inhibitors to bind to the open conformation of the protease dimer, and inhibition of the protease-catalyzed processing of the Gag-Pol precursor.
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21
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Ghosh AK, Martyr CD, Kassekert LA, Nyalapatla PR, Steffey M, Agniswamy J, Wang YF, Weber IT, Amano M, Mitsuya H. Design, synthesis, biological evaluation and X-ray structural studies of HIV-1 protease inhibitors containing substituted fused-tetrahydropyranyl tetrahydrofuran as P2-ligands. Org Biomol Chem 2015; 13:11607-21. [PMID: 26462551 PMCID: PMC4666783 DOI: 10.1039/c5ob01930c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Design, synthesis, biological and X-ray crystallographic studies of a series of potent HIV-1 protease inhibitors are described. Various polar functionalities have been incorporated on the tetrahydropyranyl-tetrahydrofuran-derived P2 ligand to interact with the backbone atoms in the S2-subsite. The majority of the inhibitors showed very potent enzyme inhibitory and antiviral activity. Two high-resolution X-ray structures of 30b- and 30j-bound HIV-1 protease provide insight into ligand-binding site interactions. In particular, the polar functionalities on the P2-ligand appear to form unique hydrogen bonds with Gly48 amide NH and amide carbonyl groups in the flap region.
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Affiliation(s)
- Arun K Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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22
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Umstead WJ, Mukhina OA, Bhuvan Kumar NN, Kutateladze AG. Photoinduced Cycloadditions in the Diversity-Oriented Synthesis Toolbox: Increasing Complexity with Straightforward Postphotochemical Modifications. Aust J Chem 2015; 68:1672-1681. [PMID: 29249834 DOI: 10.1071/ch15266] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Rapid growth of complexity and unprecedented molecular architectures are realized via the excited-state intramolecular proton transfer (ESIPT) in o-acylamidobenzaldehydes and ketones followed by [4+2] or [4+4] cycloadditions with subsequent postphotochemical modifications. The approach is congruent with Diversity-Oriented Synthesis: photoprecursors are synthesized in a modular fashion allowing for up to four diversity inputs. The complexity of the primary photoproducts is further enhanced using straightforward and high-yielding postphotochemical modification steps such as reactions with nitrile oxides, nitrones, Povarov reaction, and oxa-Diels-Alder reaction.
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Affiliation(s)
- Weston J Umstead
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80208
| | - Olga A Mukhina
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80208
| | - N N Bhuvan Kumar
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80208
| | - Andrei G Kutateladze
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80208
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23
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Ghosh AK, Yu X, Osswald HL, Agniswamy J, Wang YF, Amano M, Weber IT, Mitsuya H. Structure-based design of potent HIV-1 protease inhibitors with modified P1-biphenyl ligands: synthesis, biological evaluation, and enzyme-inhibitor X-ray structural studies. J Med Chem 2015; 58:5334-43. [PMID: 26107245 PMCID: PMC4765733 DOI: 10.1021/acs.jmedchem.5b00676] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We report the design, synthesis, X-ray structural studies, and biological evaluation of a novel series of HIV-1 protease inhibitors. We designed a variety of functionalized biphenyl derivatives to make enhanced van der Waals interactions in the S1 subsite of HIV-1 protease. These biphenyl derivatives were conveniently synthesized using a Suzuki-Miyaura cross-coupling reaction as the key step. We examined the potential of these functionalized biphenyl-derived P1 ligands in combination with 3-(S)-tetrahydrofuranyl urethane and bis-tetrahydrofuranyl urethane as the P2 ligands. Inhibitor 21e, with a 2-methoxy-1,1'-biphenyl derivative as P1 ligand and bis-THF as the P2 ligand, displayed the most potent enzyme inhibitory and antiviral activity. This inhibitor also exhibited potent activity against a panel of multidrug-resistant HIV-1 variants. A high resolution X-ray crystal structure of related Boc-derivative 17a-bound HIV-1 protease provided important molecular insight into the ligand-binding site interactions of the biphenyl core in the S1 subsite of HIV-1 protease.
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Affiliation(s)
- Arun K. Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907,The corresponding author: Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, Phone: (765)-494-5323; Fax: (765)-496-1612,
| | - Xufen Yu
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Heather L. Osswald
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Johnson Agniswamy
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303
| | - Yuan-Fang Wang
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303
| | - Masayuki Amano
- Departments of Hematology and Infectious Diseases, Kumamoto University Graduate School of Medical and Pharmaceutical Sciences, Kumamoto 860-8556, Japan
| | - Irene T. Weber
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303
| | - Hiroaki Mitsuya
- Departments of Hematology and Infectious Diseases, Kumamoto University Graduate School of Medical and Pharmaceutical Sciences, Kumamoto 860-8556, Japan,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892,Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
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24
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Rashid S, Bhat BA, Mehta G. Regenerative γ-Lactone Annulations: A Modular, Iterative Approach to Oligo-tetrahydrofuran Molecular Stairs and Related Frameworks. Org Lett 2015; 17:3604-7. [PMID: 26151627 DOI: 10.1021/acs.orglett.5b01707] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A unified, stereocontrolled, regenerative γ-butyrolactone annulation approach has been conceptualized and validated through syntheses of a range of oligo-THFs. The new protocol is short (four steps), simple (table-top reagents), and efficient (50-61% overall yields). Although the scope of this approach is unlimited, it has been demonstrated up to five iterations on commercial γ-butyrolactone to assemble six fused tetrahydrofuran moieties in a staircase-like architecture. A selection of exploratory transformations is presented to exemplify the potential applications of this protocol.
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Affiliation(s)
- Showkat Rashid
- †Medicinal Chemistry Division, Indian Institute of Integrative Medicine (CSIR), Sanatnagar, Srinagar 190005, India
| | - Bilal A Bhat
- †Medicinal Chemistry Division, Indian Institute of Integrative Medicine (CSIR), Sanatnagar, Srinagar 190005, India
| | - Goverdhan Mehta
- ‡School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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25
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Agniswamy J, Louis JM, Shen CH, Yashchuk S, Ghosh AK, Weber IT. Substituted Bis-THF Protease Inhibitors with Improved Potency against Highly Resistant Mature HIV-1 Protease PR20. J Med Chem 2015; 58:5088-95. [PMID: 26010498 DOI: 10.1021/acs.jmedchem.5b00474] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
An extremely drug resistant mutant of HIV-1 protease (PR) bearing 20 mutations (PR20) has been studied with two potent antiviral investigational inhibitors. GRL-5010A and GRL-4410A were designed to introduce hydrogen bond interactions with the flexible flaps of the PR by incorporating gem-difluorines and alkoxy, respectively, at the C4 position of the bis-THF of darunavir. PR20 provides an excellent model for high level resistance, since clinical inhibitors are >1000-fold less active on PR20 than on wild-type enzyme. GRL-5010A and GRL-4410A show inhibition constants of 4.3 ± 7.0 and 1.7 ± 1.8 nM, respectively, for PR20, compared to the binding affinity of 41 ± 1 nM measured for darunavir. Crystal structures of PR20 in complexes with the two inhibitors confirmed the new hydrogen bond interactions with Gly 48 in the flap of the enzyme. The two new compounds are more effective than darunavir in inhibiting mature PR20 and show promise for further development of antiviral agents targeting highly resistant PR mutants.
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Affiliation(s)
- Johnson Agniswamy
- †Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
| | - John M Louis
- ‡Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892-0520, United States
| | - Chen-Hsiang Shen
- †Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
| | - Sofiya Yashchuk
- §Department of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Arun K Ghosh
- §Department of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Irene T Weber
- †Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
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26
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Ghosh AK, Xu CX, Osswald HL. Enantioselective Synthesis of Dioxatriquinane Structural Motifs for HIV-1 Protease Inhibitors Using a Cascade Radical Cyclization. Tetrahedron Lett 2015; 56:3314-3317. [PMID: 26185337 DOI: 10.1016/j.tetlet.2015.01.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Synthesis of novel HIV-1 protease inhibitors incorporating dioxatriquinane-derived P2-ligands is described. The tricyclic ligand alcohol contains five contiguous chiral centers. The ligand alcohols were prepared in optically active form by an enzymatic asymmetrization of mesodiacetate, cascade radical cyclization, and Lewis acid catalyzed reduction as the key steps. Inhibitors with dioxatriquinane-derived P2-ligands exhibited low nanomolar HIV-1 protease activity.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Chun-Xiao Xu
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Heather L Osswald
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
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27
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Ghosh AK, Takayama J, Kassekert LA, Ella-Menye JR, Yashchuk S, Agniswamy J, Wang YF, Aoki M, Amano M, Weber IT, Mitsuya H. Structure-based design, synthesis, X-ray studies, and biological evaluation of novel HIV-1 protease inhibitors containing isophthalamide-derived P2-ligands. Bioorg Med Chem Lett 2015; 25:4903-4909. [PMID: 26096678 DOI: 10.1016/j.bmcl.2015.05.052] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 05/19/2015] [Accepted: 05/21/2015] [Indexed: 10/23/2022]
Abstract
We describe the design, synthesis and biological evaluation of a series of novel HIV-1 protease inhibitors bearing isophthalamide derivatives as the P2-P3 ligands. We have investigated a range of acyclic and heterocyclic amides as the extended P2-P3 ligands. These inhibitors displayed good to excellent HIV-1 protease inhibitory activity. Also, a number of inhibitors showed very good antiviral activity in MT cells. Compound 5n has shown an enzyme Ki of 0.17 nM and antiviral IC50 of 14 nM. An X-ray crystal structure of inhibitor 5o-bound to HIV-1 protease was determined at 1.11Å resolution. This structure revealed important molecular insight into the inhibitor-HIV-1 protease interactions in the active site.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA.
| | - Jun Takayama
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Luke A Kassekert
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Jean-Rene Ella-Menye
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Sofiya Yashchuk
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Johnson Agniswamy
- Departments of Biology and Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Yuan-Fang Wang
- Departments of Biology and Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Manabu Aoki
- Departments of Hematology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan
| | - Masayuki Amano
- Departments of Hematology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan
| | - Irene T Weber
- Departments of Biology and Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Hiroaki Mitsuya
- Departments of Hematology and Infectious Diseases, Kumamoto University of Medicine, Kumamoto 860-8556, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD 20892, USA; Center for Clinical Sciences, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655, Japan
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Abstract
The carbamate group is a key structural motif in many approved drugs and prodrugs. There is an increasing use of carbamates in medicinal chemistry and many derivatives are specifically designed to make drug-target interactions through their carbamate moiety. In this Perspective, we present properties and stabilities of carbamates, reagents and chemical methodologies for the synthesis of carbamates, and recent applications of carbamates in drug design and medicinal chemistry.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and
Department of Medicinal Chemistry, Purdue
University, West Lafayette, Indiana 47907, United States
| | - Margherita Brindisi
- Department of Chemistry and
Department of Medicinal Chemistry, Purdue
University, West Lafayette, Indiana 47907, United States
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A novel tricyclic ligand-containing nonpeptidic HIV-1 protease inhibitor, GRL-0739, effectively inhibits the replication of multidrug-resistant HIV-1 variants and has a desirable central nervous system penetration property in vitro. Antimicrob Agents Chemother 2015; 59:2625-35. [PMID: 25691652 DOI: 10.1128/aac.04757-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/11/2015] [Indexed: 01/04/2023] Open
Abstract
We report here that GRL-0739, a novel nonpeptidic HIV-1 protease inhibitor containing a tricycle (cyclohexyl-bis-tetrahydrofuranylurethane [THF]) and a sulfonamide isostere, is highly active against laboratory HIV-1 strains and primary clinical isolates (50% effective concentration [EC50], 0.0019 to 0.0036 μM), with minimal cytotoxicity (50% cytotoxic concentration [CC50], 21.0 μM). GRL-0739 blocked the infectivity and replication of HIV-1NL4-3 variants selected by concentrations of up to 5 μM ritonavir or atazanavir (EC50, 0.035 to 0.058 μM). GRL-0739 was also highly active against multidrug-resistant clinical HIV-1 variants isolated from patients who no longer responded to existing antiviral regimens after long-term antiretroviral therapy, as well as against the HIV-2ROD variant. The development of resistance against GRL-0739 was substantially delayed compared to that of amprenavir (APV). The effects of the nonspecific binding of human serum proteins on the anti-HIV-1 activity of GRL-0739 were insignificant. In addition, GRL-0739 showed a desirable central nervous system (CNS) penetration property, as assessed using a novel in vitro blood-brain barrier model. Molecular modeling demonstrated that the tricyclic ring and methoxybenzene of GRL-0739 have a larger surface and make greater van der Waals contacts with protease than in the case of darunavir. The present data demonstrate that GRL-0739 has desirable features as a compound with good CNS-penetrating capability for treating patients infected with wild-type and/or multidrug-resistant HIV-1 variants and that the newly generated cyclohexyl-bis-THF moiety with methoxybenzene confers highly desirable anti-HIV-1 potency in the design of novel protease inhibitors with greater CNS penetration profiles.
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Bonini C, Chiummiento L, Di Blasio N, Funicello M, Lupattelli P, Tramutola F, Berti F, Ostric A, Miertus S, Frecer V, Kong DX. Synthesis and biological evaluation of new simple indolic non peptidic HIV Protease inhibitors: The effect of different substitution patterns. Bioorg Med Chem 2014; 22:4792-802. [DOI: 10.1016/j.bmc.2014.06.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 06/25/2014] [Accepted: 06/30/2014] [Indexed: 11/30/2022]
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31
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GRL-04810 and GRL-05010, difluoride-containing nonpeptidic HIV-1 protease inhibitors (PIs) that inhibit the replication of multi-PI-resistant HIV-1 in vitro and possess favorable lipophilicity that may allow blood-brain barrier penetration. Antimicrob Agents Chemother 2013; 57:6110-21. [PMID: 24080647 DOI: 10.1128/aac.01420-13] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We designed, synthesized, and identified two novel nonpeptidic human immunodeficiency virus type 1 (HIV-1) protease inhibitors (PIs), GRL-04810 and GRL-05010, containing the structure-based designed privileged cyclic ether-derived nonpeptide P2 ligand, bis-tetrahydrofuranylurethane (bis-THF), and a difluoride moiety, both of which are active against the laboratory strain HIV-1LAI (50% effective concentrations [EC50s], 0.0008 and 0.003 μM, respectively) with minimal cytotoxicity (50% cytotoxic concentrations [CC50s], 17.5 and 37.0 μM, respectively, in CD4(+) MT-2 cells). The two compounds were active against multi-PI-resistant clinical HIV-1 variants isolated from patients who had no response to various antiviral regimens. GRL-04810 and GRL-05010 also blocked the infectivity and replication of each of the HIV-1NL4-3 variants selected by up to 5 μM lopinavir (EC50s, 0.03 and 0.03 μM, respectively) and atazanavir (EC50s, 0.02 and 0.04 μM, respectively). Moreover, they were active against darunavir (DRV)-resistant variants (EC50 in 0.03 to 0.034 μM range for GRL-04810 and 0.026 to 0.043 μM for GRL-05010), while DRV had EC50s between 0.02 and 0.174 μM. GRL-04810 had a favorable lipophilicity profile as determined with the partition (log P) and distribution (log D) coefficients of -0.14 and -0.29, respectively. The in vitro blood-brain barrier (BBB) permeability assay revealed that GRL-04810 and GRL-05010 may have a greater advantage in terms of crossing the BBB than the currently available PIs, with apparent penetration indexes of 47.8 × 10(-6) and 61.8 × 10(-6) cm/s, respectively. The present data demonstrate that GRL-04810 and GRL-05010 exert efficient activity against a wide spectrum of HIV-1 variants in vitro and suggest that two fluorine atoms added to their bis-THF moieties may well enhance their penetration across the BBB.
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32
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Ghosh AK, Parham GL, Martyr CD, Nyalapatla PR, Osswald HL, Agniswamy J, Wang YF, Amano M, Weber IT, Mitsuya H. Highly potent HIV-1 protease inhibitors with novel tricyclic P2 ligands: design, synthesis, and protein-ligand X-ray studies. J Med Chem 2013; 56:6792-802. [PMID: 23947685 PMCID: PMC3800042 DOI: 10.1021/jm400768f] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The design, synthesis, and biological evaluation of a series of HIV-1 protease inhibitors incorporating stereochemically defined fused tricyclic P2 ligands are described. Various substituent effects were investigated to maximize the ligand-binding site interactions in the protease active site. Inhibitors 16a and 16f showed excellent enzyme inhibitory and antiviral activity, although the incorporation of sulfone functionality resulted in a decrease in potency. Both inhibitors 16a and 16f maintained activity against a panel of multidrug resistant HIV-1 variants. A high-resolution X-ray crystal structure of 16a-bound HIV-1 protease revealed important molecular insights into the ligand-binding site interactions, which may account for the inhibitor's potent antiviral activity and excellent resistance profiles.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, United States,The corresponding author: Departments of Chemistry and Medicinal Chemistry Purdue University 560 Oval Drive, West Lafayette, IN 47907 Phone: (765)-494-5323; Fax: (765)-496-1612
| | - Garth L. Parham
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Cuthbert D. Martyr
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Prasanth R. Nyalapatla
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Heather L. Osswald
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Johnson Agniswamy
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, United States
| | - Yuan-Fang Wang
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, United States
| | - Masayuki Amano
- Departments of Hematology and Infectious Diseases, Kumamoto University Graduate School of Medical and Pharmaceutical Sciences, Kumamoto 860-8556, Japan
| | - Irene T. Weber
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, United States
| | - Hiroaki Mitsuya
- Departments of Hematology and Infectious Diseases, Kumamoto University Graduate School of Medical and Pharmaceutical Sciences, Kumamoto 860-8556, Japan,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
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33
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Agniswamy J, Shen CH, Wang YF, Ghosh AK, Rao KV, Xu CX, Sayer JM, Louis JM, Weber IT. Extreme multidrug resistant HIV-1 protease with 20 mutations is resistant to novel protease inhibitors with P1'-pyrrolidinone or P2-tris-tetrahydrofuran. J Med Chem 2013; 56:4017-27. [PMID: 23590295 DOI: 10.1021/jm400231v] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Extreme drug resistant mutant of HIV-1 protease (PR) bearing 20 mutations (PR20) has been studied with the clinical inhibitor amprenavir (1) and two potent antiviral investigational inhibitors GRL-02031 (2) and GRL-0519 (3). Clinical inhibitors are >1000-fold less active on PR20 than on wild-type enzyme, which is consistent with dissociation constants (KL) from isothermal titration calorimetry of 40 nM for 3, 178 nM for amprenavir, and 960 nM for 2. High resolution crystal structures of PR20-inhibitor complexes revealed altered interactions compared with the corresponding wild-type PR complexes in agreement with relative inhibition. Amprenavir lacks interactions due to PR20 mutations in the S2/S2' subsites relative to PR. Inhibitors 2 and 3 lose interactions with Arg8' in PR20 relative to the wild-type enzyme because Arg8' shifts to interact with mutated L10F side chain. Overall, inhibitor 3 compares favorably with darunavir in affinity for PR20 and shows promise for further development.
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Affiliation(s)
- Johnson Agniswamy
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, USA
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34
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GRL-0519, a novel oxatricyclic ligand-containing nonpeptidic HIV-1 protease inhibitor (PI), potently suppresses replication of a wide spectrum of multi-PI-resistant HIV-1 variants in vitro. Antimicrob Agents Chemother 2013; 57:2036-46. [PMID: 23403426 DOI: 10.1128/aac.02189-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
We report that GRL-0519, a novel nonpeptidic human immunodeficiency virus type 1 (HIV-1) protease inhibitor (PI) containing tris-tetrahydrofuranylurethane (tris-THF) and a sulfonamide isostere, is highly potent against laboratory HIV-1 strains and primary clinical isolates (50% effective concentration [EC50], 0.0005 to 0.0007 μM) with minimal cytotoxicity (50% cytotoxic concentration [CC50], 44.6 μM). GRL-0519 blocked the infectivity and replication of HIV-1NL4-3 variants selected by up to a 5 μM concentration of ritonavir, lopinavir, or atazanavir (EC50, 0.0028 to 0.0033 μM). GRL-0519 was also potent against multi-PI-resistant clinical HIV-1 variants isolated from patients who no longer responded to existing antiviral regimens after long-term antiretroviral therapy, highly darunavir (DRV)-resistant variants, and HIV-2ROD. The development of resistance against GRL-0519 was substantially delayed compared to other PIs, including amprenavir (APV) and DRV. The effects of nonspecific binding of human serum proteins on GRL-0519's antiviral activity were insignificant. Our analysis of the crystal structures of GRL-0519 (3OK9) and DRV (2IEN) with protease suggested that the tris-THF moiety, compared to the bis-THF moiety present in DRV, has greater water-mediated polar interactions with key active-site residues of protease and that the tris-THF moiety and paramethoxy group effectively fill the S2 and S2' binding pockets, respectively, of the protease. The present data demonstrate that GRL-0519 has highly favorable features as a potential therapeutic agent for treating patients infected with wild-type and/or multi-PI-resistant variants and that the tris-THF moiety is critical for strong binding of GRL-0519 to the HIV protease substrate binding site and appears to be responsible for its favorable antiretroviral characteristics.
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35
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Zhang H, Wang YF, Shen CH, Agniswamy J, Rao KV, Xu CX, Ghosh AK, Harrison RW, Weber IT. Novel P2 tris-tetrahydrofuran group in antiviral compound 1 (GRL-0519) fills the S2 binding pocket of selected mutants of HIV-1 protease. J Med Chem 2013; 56:1074-83. [PMID: 23298236 DOI: 10.1021/jm301519z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
GRL-0519 (1) is a potent antiviral inhibitor of HIV-1 protease (PR) possessing tris-tetrahydrofuran (tris-THF) at P2. The high resolution X-ray crystal structures of inhibitor 1 in complexes with single substitution mutants PR(R8Q), PR(D30N), PR(I50V), PR(I54M), and PR(V82A) were analyzed in relation to kinetic data. The smaller valine side chain in PR(I50V) eliminated hydrophobic interactions with inhibitor and the other subunit consistent with 60-fold worse inhibition. Asn30 in PR(D30N) showed altered interactions with neighboring residues and 18-fold worse inhibition. Mutations V82A and I54M showed compensating structural changes consistent with 6-7-fold lower inhibition. Gln8 in PR(R8Q) replaced the ionic interactions of wild type Arg8 with hydrogen bond interactions without changing the inhibition significantly. The carbonyl oxygen of Gly48 showed two alternative conformations in all structures likely due to the snug fit of the large tris-THF group in the S2 subsite in agreement with high antiviral efficacy of 1 on resistant virus.
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Affiliation(s)
- Hongmei Zhang
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA
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36
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Hao GF, Yang GF, Zhan CG. Structure-based methods for predicting target mutation-induced drug resistance and rational drug design to overcome the problem. Drug Discov Today 2012; 17:1121-6. [PMID: 22789991 DOI: 10.1016/j.drudis.2012.06.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2011] [Revised: 06/01/2012] [Accepted: 06/29/2012] [Indexed: 11/15/2022]
Abstract
Drug resistance has become one of the biggest challenges in drug discovery and/or development and has attracted great research interests worldwide. During the past decade, computational strategies have been developed to predict target mutation-induced drug resistance. Meanwhile, various molecular design strategies, including targeting protein backbone, targeting highly conserved residues and dual/multiple targeting, have been used to design novel inhibitors for combating the drug resistance. In this article we review recent advances in development of computational methods for target mutation-induced drug resistance prediction and strategies for rational design of novel inhibitors that could be effective against the possible drug-resistant mutants of the target.
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Affiliation(s)
- Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China
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37
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Agniswamy J, Shen CH, Aniana A, Sayer JM, Louis JM, Weber IT. HIV-1 protease with 20 mutations exhibits extreme resistance to clinical inhibitors through coordinated structural rearrangements. Biochemistry 2012; 51:2819-28. [PMID: 22404139 PMCID: PMC3328860 DOI: 10.1021/bi2018317] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The escape mutant of HIV-1 protease (PR) containing 20 mutations (PR20) undergoes efficient polyprotein processing even in the presence of clinical protease inhibitors (PIs). PR20 shows >3 orders of magnitude decreased affinity for PIs darunavir (DRV) and saquinavir (SQV) relative to PR. Crystal structures of PR20 crystallized with yttrium, substrate analogue p2-NC, DRV, and SQV reveal three distinct conformations of the flexible flaps and diminished interactions with inhibitors through the combination of multiple mutations. PR20 with yttrium at the active site exhibits widely separated flaps lacking the usual intersubunit contacts seen in other inhibitor-free dimers. Mutations of residues 35-37 in the hinge loop eliminate interactions and perturb the flap conformation. Crystals of PR20/p2-NC contain one uninhibited dimer with one very open flap and one closed flap and a second inhibitor-bound dimer in the closed form showing six fewer hydrogen bonds with the substrate analogue relative to wild-type PR. PR20 complexes with PIs exhibit expanded S2/S2' pockets and fewer PI interactions arising from coordinated effects of mutations throughout the structure, in agreement with the strikingly reduced affinity. In particular, insertion of the large aromatic side chains of L10F and L33F alters intersubunit interactions and widens the PI binding site through a network of hydrophobic contacts. The two very open conformations of PR20 as well as the expanded binding site of the inhibitor-bound closed form suggest possible approaches for modifying inhibitors to target extreme drug-resistant HIV.
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Affiliation(s)
- Johnson Agniswamy
- Department of Biology, Molecular Basis of Disease Program, Georgia State University, Atlanta, Georgia 30303, United States
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38
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Ghosh AK, Anderson DD, Weber IT, Mitsuya H. Enhancing protein backbone binding--a fruitful concept for combating drug-resistant HIV. Angew Chem Int Ed Engl 2012; 51:1778-802. [PMID: 22290878 PMCID: PMC7159617 DOI: 10.1002/anie.201102762] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Indexed: 12/02/2022]
Abstract
The evolution of drug resistance is one of the most fundamental problems in medicine. In HIV/AIDS, the rapid emergence of drug-resistant HIV-1 variants is a major obstacle to current treatments. HIV-1 protease inhibitors are essential components of present antiretroviral therapies. However, with these protease inhibitors, resistance occurs through viral mutations that alter inhibitor binding, resulting in a loss of efficacy. This loss of potency has raised serious questions with regard to effective long-term antiretroviral therapy for HIV/AIDS. In this context, our research has focused on designing inhibitors that form extensive hydrogen-bonding interactions with the enzyme's backbone in the active site. In doing so, we limit the protease's ability to acquire drug resistance as the geometry of the catalytic site must be conserved to maintain functionality. In this Review, we examine the underlying principles of enzyme structure that support our backbone-binding concept as an effective means to combat drug resistance and highlight their application in our recent work on antiviral HIV-1 protease inhibitors.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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39
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Ghosh AK, Anderson DD, Weber IT, Mitsuya H. Verstärkung der Bindung an das Proteinrückgrat - ein fruchtbares Konzept gegen die Arzneimittelresistenz von HIV. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201102762] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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40
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Ghosh AK, Anderson DD. Tetrahydrofuran, tetrahydropyran, triazoles and related heterocyclic derivatives as HIV protease inhibitors. Future Med Chem 2011; 3:1181-97. [PMID: 21806380 PMCID: PMC3164575 DOI: 10.4155/fmc.11.68] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
HIV/AIDS remains a formidable disease with millions of individuals inflicted worldwide. Although treatment regimens have improved considerably, drug resistance brought on by viral mutation continues to erode their effectiveness. Intense research efforts are currently underway in search of new and improved therapies. This review is concerned with the design of novel HIV-1 protease inhibitors that incorporate heterocyclic scaffolds and which have been reported within the recent literature (2005-2010). Various examples in this review showcase the essential role heterocycles play as scaffolds and bioisosteres in HIV-1 protease inhibitor drug development. This review will hopefully stimulate the widespread application of these heterocycles in the design of other therapeutic agents.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
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41
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Hohlfeld K, Tomassi C, Wegner JK, Kesteleyn B, Linclau B. Disubstituted Bis-THF Moieties as New P2 Ligands in Nonpeptidal HIV-1 Protease Inhibitors. ACS Med Chem Lett 2011; 2:461-5. [PMID: 24900331 DOI: 10.1021/ml2000356] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 03/27/2011] [Indexed: 11/28/2022] Open
Abstract
A series of darunavir analogues featuring a substituted bis-THF ring as P2 ligand have been synthesized and evaluated. High affinity protease inhibitors (PIs) with an interesting activity on wild-type HIV and a panel of multi-PI resistant HIV-1 mutants containing clinically observed, primary mutations were identified using a cell-based assay. A number of PIs have been synthesized that show equivalent and greater activity for HIV-1 mutant strains as compared to wild-type HIV-1. The activity on the purified enzyme was confirmed for a selection of analogues.
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Affiliation(s)
- Konrad Hohlfeld
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Cyrille Tomassi
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | | | | | - Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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42
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Ghosh AK, Chapsal BD, Baldridge A, Steffey MP, Walters DE, Koh Y, Amano M, Mitsuya H. Design and synthesis of potent HIV-1 protease inhibitors incorporating hexahydrofuropyranol-derived high affinity P(2) ligands: structure-activity studies and biological evaluation. J Med Chem 2011; 54:622-34. [PMID: 21194227 PMCID: PMC3024462 DOI: 10.1021/jm1012787] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The design, synthesis, and evaluation of a new series of hexahydrofuropyranol-derived HIV-1 protease inhibitors are described. We have designed a stereochemically defined hexahydrofuropyranol-derived urethane as the P2-ligand. The current ligand is designed based upon the X-ray structure of 1a-bound HIV-1 protease. The synthesis of (3aS,4S,7aR)-hexahydro-2H-furo[2,3-b]pyran-4-ol, (-)-7, was carried out in optically active form. Incorporation of this ligand provided inhibitor 35a, which has shown excellent enzyme inhibitory activity and antiviral potency. Our structure-activity studies have indicated that the stereochemistry and the position of oxygens in the ligand are important to the observed potency of the inhibitor. Inhibitor 35a has maintained excellent potency against multidrug-resistant HIV-1 variants. An active site model of 35a was created based upon the X-ray structure of 1b-bound HIV-1 protease. The model offers molecular insights regarding ligand-binding site interactions of the hexahydrofuropyranol-derived novel P2-ligand.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States.
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