1
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Akaberi D, Chinthakindi PK, Båhlström A, Palanisamy N, Sandström A, Lundkvist Å, Lennerstrand J. Identification of a C2-symmetric diol based human immunodeficiency virus protease inhibitor targeting Zika virus NS2B-NS3 protease. J Biomol Struct Dyn 2019; 38:5526-5536. [PMID: 31880199 DOI: 10.1080/07391102.2019.1704882] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Zika virus (ZIKV) is an emerging mosquito-borne flavivirus and infection by ZIKV Asian lineage is known to cause fetal brain anomalies and Guillain-Barrés syndrome. The WHO declared ZIKV a global public health emergency in 2016. However, currently neither vaccines nor antiviral prophylaxis/treatments are available. In this study, we report the identification of a C2-symmetric diol-based Human immunodeficiency virus type-1 (HIV) protease inhibitor active against ZIKV NS2B-NS3 protease. The compound, referred to as 9b, was identified by in silico screening of a library of 6265 protease inhibitors. Molecular dynamics (MD) simulation studies revealed that compound 9b formed a stable complex with ZIKV protease. Interaction analysis of compound 9b's binding pose from the cluster analysis of MD simulations trajectories predicted that 9b mostly interacted with ZIKV NS3. Although designed as an aspartyl protease inhibitor, compound 9b was found to inhibit ZIKV serine protease in vitro with IC50 = 143.25 ± 5.45 µM, in line with the in silico results. Additionally, linear interaction energy method (LIE) was used to estimate binding affinities of compounds 9b and 86 (a known panflavivirus peptide hybrid with IC50 = 1.64 ± 0.015 µM against ZIKV protease). The LIE method correctly predicted the binding affinity of compound 86 to be lower than that of 9b, proving to be superior to the molecular docking methods in scoring and ranking compounds. Since most of the reported ZIKV protease inhibitors are positively charged peptide-hybrids, with our without electrophilic warheads, compound 9b represents a less polar and more drug-like non-peptide hit compound useful for further optimization.Communicated by Ramaswamy Sarma.
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Affiliation(s)
- Dario Akaberi
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala University Hospital, Uppsala, Sweden.,Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Praveen K Chinthakindi
- The Beijer Laboratory, Department of Medicinal Chemistry, Drug Design and Discovery, Uppsala University, Uppsala, Sweden
| | - Amanda Båhlström
- The Beijer Laboratory, Department of Medicinal Chemistry, Drug Design and Discovery, Uppsala University, Uppsala, Sweden
| | - Navaneethan Palanisamy
- HBIGS, University of Heidelberg, Heidelberg, Germany.,Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Anja Sandström
- The Beijer Laboratory, Department of Medicinal Chemistry, Drug Design and Discovery, Uppsala University, Uppsala, Sweden
| | - Åke Lundkvist
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Johan Lennerstrand
- Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala University Hospital, Uppsala, Sweden
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2
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Vadhadiya PM, Jean MA, Bouzriba C, Tremblay T, Lagüe P, Fortin S, Boukouvalas J, Giguère D. Diversity-Oriented Synthesis of Diol-Based Peptidomimetics as Potential HIV Protease Inhibitors and Antitumor Agents. Chembiochem 2018; 19:1779-1791. [PMID: 29858881 DOI: 10.1002/cbic.201800247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Indexed: 12/15/2022]
Abstract
Peptidomimetic HIV protease inhibitors are an important class of drugs used in the treatment of AIDS. The synthesis of a new type of diol-based peptidomimetics is described. Our route is flexible, uses d-glucal as an inexpensive starting material, and makes minimal use of protection/deprotection cycles. Binding affinities from molecular docking simulations suggest that these compounds are potential inhibitors of HIV protease. Moreover, the antiproliferative activities of compounds 33 a, 35 a, and 35 b on HT-29, M21, and MCF7 cancer cell lines are in the low micromolar range. The results provide a platform that could facilitate the development of medically relevant asymmetrical diol-based peptidomimetics.
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Affiliation(s)
- Paresh M Vadhadiya
- Département de Chimie, Université Laval-RQRM, 1045 Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
| | - Marc-Alexandre Jean
- Département de Chimie, Université Laval-RQRM, 1045 Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
| | - Chahrazed Bouzriba
- CHU de Québec-Université Laval Research Center, Oncology Division, Hôpital Saint-François d'Assise, 10 rue de l'Espinay, Quebec City, QC, G1L 3L5, Canada
- Faculté de Pharmacie, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Thomas Tremblay
- Département de Chimie, Université Laval-RQRM, 1045 Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
| | - Patrick Lagüe
- Départment de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, 1045, Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
| | - Sébastien Fortin
- CHU de Québec-Université Laval Research Center, Oncology Division, Hôpital Saint-François d'Assise, 10 rue de l'Espinay, Quebec City, QC, G1L 3L5, Canada
- Faculté de Pharmacie, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - John Boukouvalas
- Département de Chimie, Université Laval-RQRM, 1045 Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
| | - Denis Giguère
- Département de Chimie, Université Laval-RQRM, 1045 Avenue de la Médecine, Quebec City, QC, G1V 0A6, Canada
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3
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Duan LL, Zhu T, Li YC, Zhang QG, Zhang JZH. Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations. Sci Rep 2017; 7:42223. [PMID: 28155907 PMCID: PMC5290483 DOI: 10.1038/srep42223] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/06/2017] [Indexed: 01/01/2023] Open
Abstract
Molecular dynamics simulations in explicit water are carried out to study the binding of six inhibitors to HIV-1 protease (PR) for up to 700 ns using the standard AMBER force field and polarized protein-specific charge (PPC). PPC is derived from quantum mechanical calculation for protein in solution and therefore it includes electronic polarization effect. Our results show that in all six systems, the bridging water W301 drifts away from the binding pocket in AMBER simulation. However, it is very stable in all six complexes systems using PPC. Especially, intra-protease, protease-inhibitor hydrogen bonds are dynamic stabilized in MD simulation. The computed binding free energies of six complexes have a significantly linear correlation with those experiment values and the correlation coefficient is found to be 0.91 in PPC simulation. However, the result from AMBER simulation shows a weaker correlation with the correlation coefficient of −0.51 due to the lack of polarization effect. Detailed binding interactions of W301, inhibitors with PR are further analyzed and discussed. The present study provides important information to quantitative understanding the interaction mechanism of PR-inhibitor and PR-W301 and these data also emphasizes the importance of both the electronic polarization and the bridging water molecule in predicting precisely binding affinities.
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Affiliation(s)
- Li L Duan
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - T Zhu
- Department of Chemistry, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Yu C Li
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Qing G Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - John Z H Zhang
- Department of Chemistry, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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4
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Motwani HV, De Rosa M, Odell LR, Hallberg A, Larhed M. Aspartic protease inhibitors containing tertiary alcohol transition-state mimics. Eur J Med Chem 2014; 90:462-90. [PMID: 25481814 DOI: 10.1016/j.ejmech.2014.11.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 11/12/2014] [Accepted: 11/19/2014] [Indexed: 11/30/2022]
Abstract
Aspartic proteases (APs) are a class of enzymes engaged in the proteolytic digestion of peptide substrates. APs play important roles in physiological and infectious pathways, making them plausible drug targets. For instance in the treatment of HIV infections, access to an efficient combination of protease and reverse transcriptase inhibitors have changed a terminal illness to a chronic but manageable disease. However, the benefits have been limited due to the emergence of drug resistant viral strains, poor pharmacokinetic properties of peptidomimetic inhibitors and adverse effects associated with the treatment. In the 1980s, D. Rich and co-workers proposed a novel strategy for the development of AP inhibitors by replacing the secondary hydroxyl group with a tertiary alcohol as part of the transition state (TS) mimicking moiety. This strategy has been extensively explored over the last decade with a common belief that masking of the polar group, e.g. by intramolecular hydrogen bonding, has the potential to enhance transcellular transport. This is the first review presenting the advances of AP inhibitors comprising a tertiary hydroxyl group. The inhibitors have been classified into different tert-hydroxy TS mimics and their design strategies, synthesis, biological activities, structure-activity-relationships and X-ray structures are discussed.
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Affiliation(s)
- Hitesh V Motwani
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Maria De Rosa
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Luke R Odell
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Anders Hallberg
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Mats Larhed
- Department of Medicinal Chemistry, Organic Pharmaceutical Chemistry, BMC, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden.
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5
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Synthesis and molecular modelling studies of novel carbapeptide analogs for inhibition of HIV-1 protease. Eur J Med Chem 2012; 53:13-21. [DOI: 10.1016/j.ejmech.2012.03.027] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 11/23/2022]
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6
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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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7
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Gehret TC, Frobese AS, Zerbe JS, Chenault HK. Convenient Large-Scale Synthesis of d-Glucaro-1,4:6,3-dilactone. J Org Chem 2009; 74:8373-6. [DOI: 10.1021/jo9015985] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Troy C. Gehret
- Central Research & Development, E. I. DuPont de Nemours & Co., Experimental Station, Wilmington, Delaware 19880
| | - A. Stephen Frobese
- Central Research & Development, E. I. DuPont de Nemours & Co., Experimental Station, Wilmington, Delaware 19880
| | - James S. Zerbe
- Central Research & Development, E. I. DuPont de Nemours & Co., Experimental Station, Wilmington, Delaware 19880
| | - H. Keith Chenault
- Central Research & Development, E. I. DuPont de Nemours & Co., Experimental Station, Wilmington, Delaware 19880
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8
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Affiliation(s)
- Benson J. Edagwa
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Carol M. Taylor
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
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9
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Bäck M, Nyhlén J, Kvarnström I, Appelgren S, Borkakoti N, Jansson K, Lindberg J, Nyström S, Hallberg A, Rosenquist Å, Samuelsson B. Design, synthesis and SAR of potent statine-based BACE-1 inhibitors: Exploration of P1 phenoxy and benzyloxy residues. Bioorg Med Chem 2008; 16:9471-86. [DOI: 10.1016/j.bmc.2008.09.041] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Revised: 09/10/2008] [Accepted: 09/16/2008] [Indexed: 10/21/2022]
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10
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Park H, Min K, Kwak HS, Koo KD, Lim D, Seo SW, Choi JU, Platt B, Choi DY. Synthesis, SAR, and X-ray structure of human BACE-1 inhibitors with cyclic urea derivatives. Bioorg Med Chem Lett 2008; 18:2900-4. [DOI: 10.1016/j.bmcl.2008.03.081] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Revised: 03/28/2008] [Accepted: 03/29/2008] [Indexed: 10/22/2022]
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11
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Wannberg J, Sabnis YA, Vrang L, Samuelsson B, Karlén A, Hallberg A, Larhed M. A new structural theme in C2-symmetric HIV-1 protease inhibitors: ortho-substituted P1/P1' side chains. Bioorg Med Chem 2006; 14:5303-15. [PMID: 16621572 DOI: 10.1016/j.bmc.2006.03.045] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2005] [Revised: 03/21/2006] [Accepted: 03/24/2006] [Indexed: 11/28/2022]
Abstract
In this report, the rapid syntheses of 24 novel C2-symmetric HIV-1 protease inhibitors are described. Two ortho-iodobenzyloxy containing C-terminal duplicated inhibitors served as starting materials for microwave-enhanced palladium(0)-catalyzed carbon-carbon bond forming reactions (Suzuki, Sonogashira, Heck, and Negishi). Highly potent inhibitors equipped with ortho-functionalized P1/P1' side chains as the structural theme were identified. Computational efforts were applied to study the binding mode of this class of inhibitors and to establish structure-activity relationships. The overall orientation of the inhibitors in the active site was reproduced by docking which suggested three possible conformations of the P1/P1' groups of which two seem more plausible.
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Affiliation(s)
- Johan Wannberg
- Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
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12
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Fernández M, Caballero J. Modeling of activity of cyclic urea HIV-1 protease inhibitors using regularized-artificial neural networks. Bioorg Med Chem 2006; 14:280-94. [PMID: 16202604 DOI: 10.1016/j.bmc.2005.08.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2005] [Revised: 08/04/2005] [Accepted: 08/05/2005] [Indexed: 11/26/2022]
Abstract
Artificial neural networks (ANNs) were used to model both inhibition of HIV-1 protease (K(i)) and inhibition of HIV replication (IC90) for 55 cyclic urea derivatives using constitutional and 2D descriptors. As a preliminary step, linear dependences were established by multiple linear regression (MLR) approaches, selecting the relevant descriptors by genetic algorithm (GA) feature selection. For ANN models non-linear GA feature selection was also applied. Non-linear modeling of K(i) overcame the results of the linear one using four properties, keeping in mind standard Pearson R correlation coefficients (0.931 vs. 0.862) and leave one out (LOO) cross-validation analysis (Q(LOO)2 = 0.703 vs. 0.510). On the other hand, IC90 modeling was insoluble by a linear approach: no predictive model was achieved; however, a non-linear relation was encountered according to statistic results (R = 0.891; Q(LOO)2 = 0.568). The best non-linear models suggested the influence of the presence of nitrogen atoms and the molecular volume distribution in the inhibitor structures on the HIV-1 protease inhibition as well as that the inhibition of HIV replication was dependent on the occurrence of five-member rings. Finally, inhibitors were well distributed regarding its activity levels in a Kohonen self-organizing map built using the input variables of the best non-linear models.
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Affiliation(s)
- Michael Fernández
- Molecular Modeling Group, Center for Biotechnological Studies, University of Matanzas, Matanzas, Cuba
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13
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Affiliation(s)
- Wendy A Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia.
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14
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Lindberg J, Pyring D, Löwgren S, Rosenquist A, Zuccarello G, Kvarnström I, Zhang H, Vrang L, Classon B, Hallberg A, Samuelsson B, Unge T. Symmetric fluoro-substituted diol-based HIV protease inhibitors. Ortho-fluorinated and meta-fluorinated P1/P1'-benzyloxy side groups significantly improve the antiviral activity and preserve binding efficacy. ACTA ACUST UNITED AC 2004; 271:4594-602. [PMID: 15560801 DOI: 10.1111/j.1432-1033.2004.04431.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV-1 protease is a pivotal enzyme in the later stages of the viral life cycle which is responsible for the processing and maturation of the virus particle into an infectious virion. As such, HIV-1 protease has become an important target for the treatment of AIDS, and efficient drugs have been developed. However, negative side effects and fast emerging resistance to the current drugs have necessitated the development of novel chemical entities in order to exploit different pharmacokinetic properties as well as new interaction patterns. We have used X-ray crystallography to decipher the structure-activity relationship of fluoro-substitution as a strategy to improve the antiviral activity and the protease inhibition of C2-symmetric diol-based inhibitors. In total we present six protease-inhibitor complexes at 1.8-2.3 A resolution, which have been structurally characterized with respect to their antiviral and inhibitory activities, in order to evaluate the effects of different fluoro-substitutions. These C2-symmetric inhibitors comprise mono- and difluoro-substituted benzyloxy side groups in P1/P1' and indanoleamine side groups in P2/P2'. The ortho- and meta-fluorinated P1/P1'-benzyloxy side groups proved to have the most cytopathogenic effects compared with the nonsubstituted analog and related C2-symmetric diol-based inhibitors. The different fluoro-substitutions are well accommodated in the protease S1/S1' subsites, as observed by an increase in favorable Van der Waals contacts and surface area buried by the inhibitors. These data will be used in the development of potent inhibitors with different pharmacokinetic profiles towards resistant protease mutants.
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Affiliation(s)
- Jimmy Lindberg
- Department of Cell and Molecular Biology, BMC, Uppsala University, Sweden
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15
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Shuman CF, Vrang L, Danielson UH. Improved Structure−Activity Relationship Analysis of HIV-1 Protease Inhibitors Using Interaction Kinetic Data. J Med Chem 2004; 47:5953-61. [PMID: 15537350 DOI: 10.1021/jm0499110] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite the availability of large amounts of data for HIV-protease inhibitors and their effectiveness with wild type and resistant enzyme, there is limited knowledge about how this and other information can be systematically applied to the development of new antiviral compounds. To identify in vitro parameters that correlate with the efficacy of HIV inhibitors in cell culture, the relationships between inhibition, interaction kinetic, and cell culture parameters for HIV-1 protease inhibitors were analyzed. Correlation, cluster, and principal component analysis of data for 37 cyclic and linear compounds revealed that the affinities (K(D)) determined from SPR-biosensor binding studies correlated better to cell culture efficacy (ED(50)) than that of the inhibition constants (K(i)), indicating that the conventional use of K(i) values for structure-activity relationship analysis of HIV-1 inhibitors should be seriously reconsidered. The association and dissociation kinetic rate constants (k(on) and k(off)) alone showed weak correlations with ED(50) values. However, ED(50) values were most related to the free enzyme concentration in the viral particle ([E]), calculated from the rate constants and the total enzyme concentration in a viral particle. A structure-activity relationship analysis of the current data set was found to be valid for all classes of compounds analyzed. In summary, use of affinity, based on interaction kinetic rate constants, rather than inhibition constants, and theoretical consideration of the physiological conditions in the virus particle provide improved structure-activity relationship analysis of HIV-1 protease inhibitors.
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Affiliation(s)
- Cynthia F Shuman
- Department of Biochemistry, Uppsala University, BMC, Box 576, SE-751 23 Uppsala, Sweden
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16
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Bouzide A, Sauvé G, Sévigny G, Yelle J. 1,2,5,6-Tetra- O -benzyl- d -mannitol derivatives as novel HIV protease inhibitors. Bioorg Med Chem Lett 2003; 13:3601-5. [PMID: 14505679 DOI: 10.1016/s0960-894x(03)00677-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The synthesis and structure-activity relationships of HIV protease inhibitors derived from carbohydrate alditols are discussed. We disclose a new series of 1,2,5,6-tetra-O-alkyl-D-mannitol exhibiting sub-micromolar activity against HIV-protease. This series of inhibitors are non-nitrogen containing HIV-protease inhibitors and they are readily prepared in a few chemical steps from inexpensive commercially available starting materials.
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17
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Gossas T, Danielson UH. Analysis of the pH-dependencies of the association and dissociation kinetics of HIV-1 protease inhibitors. J Mol Recognit 2003; 16:203-12. [PMID: 12898670 DOI: 10.1002/jmr.623] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The kinetic constants for the interactions between HIV-1 protease and a selection of inhibitors were determined at different pH-values using a biosensor based interaction assay. Since this technique does not involve a substrate, it was possible to determine the pH-dependencies of the association and dissociation rates of an inhibitor, without the complication of a pH-dependent enzyme-substrate/product equilibrium. The importance of these interactions was evaluated by correlating the free energy changes upon association and dissociation of inhibitors with the predicted change in electrostatic properties of the interacting groups as a result of altered pH. It was found that the kinetic parameters varied with pH in a unique manner for all inhibitors, demonstrating that the kinetic features were associated with the specific structure of each inhibitor. Association and dissociation had different pH-profiles, indicating that the two processes proceeded by different pathways/mechanisms. The energy barrier for dissociation of the enzyme-indinavir complex increased with pH from 4.1 to 7.4, while it was generally reduced for the other inhibitors as the pH was increased from 5.1 to 7.4. The pH-dependent interactions involved in the recognition/binding of inhibitors and in the stabilization of the complex were identified by analysing three-dimensional structures of enzyme-inhibitor complexes. The interaction between the pyridine nitrogen of indinavir with Arg-8 was hypothesized to be responsible for the unique pH-dependency of indinavir. The analysis revealed features of interactions that are significant for understanding enzyme function and for optimization of new drug leads. It also highlighted the importance of environmental conditions on interactions.
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Affiliation(s)
- Thomas Gossas
- Department of Biochemistry, Uppsala University, Uppsala, Sweden
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18
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Huang X, Xu L, Luo X, Fan K, Ji R, Pei G, Chen K, Jiang H. Elucidating the inhibiting mode of AHPBA derivatives against HIV-1 protease and building predictive 3D-QSAR models. J Med Chem 2002; 45:333-43. [PMID: 11784138 DOI: 10.1021/jm0102710] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Lamarckian genetic algorithm of AutoDock 3.0 has been used to dock 27 3(S)-amino-2(S)-hydroxyl-4-phenylbutanoic acids (AHPBAs) into the active site of HIV-1 protease (HIVPR). The binding mode was demonstrated in the aspects of the inhibitor's conformation, subsite interaction, and hydrogen bonding. The data of geometrical parameters (tau(1), tau(2), and tau(3) listed in Table 2) and root mean square deviation values as compared with the known inhibitor, kni272,(28) show that both kinds of inhibitors interact with HIVPR in a very similar way. The r(2) value of 0.860 indicates that the calculated binding free energies correlate well with the inhibitory activities. The structural and energetic differences in inhibitory potencies of AHPBAs were reasonably explored. Using the binding conformations of AHPBAs, consistent and highly predictive 3D-QSAR models were developed by performing CoMFA, CoMSIA, and HQSAR analyses. The reasonable r(corss)(2) values were 0.613, 0.530, and 0.717 for CoMFA, CoMSIA, and HQSAR models, respectively. The predictive ability of these models was validated by kni272 and a set of nine compounds that were not included in the training set. Mapping these models back to the topology of the active site of HIVPR leads to a better understanding of vital AHPBA-HIVPR interactions. Structural-based investigations and the final 3D-QSAR results provide clear guidelines and accurate activity predictions for novel HIVPR inhibitors.
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Affiliation(s)
- Xaioqin Huang
- Center for Drug Design and Discovery, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, People's Republic of China
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Ahlsén G, Hultén J, Shuman CF, Poliakov A, Lindgren MT, Alterman M, Samuelsson B, Hallberg A, Danielson UH. Resistance profiles of cyclic and linear inhibitors of HIV-1 protease. Antivir Chem Chemother 2002; 13:27-37. [PMID: 12180647 DOI: 10.1177/095632020201300103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Resistance to anti-HIV protease drugs is a major problem in the design of AIDS drugs with long-term efficacy. To identify structural features associated with a certain resistance profile, the inhibitory properties of a series of symmetric and asymmetric cyclic sulfamide, cyclic urea and linear transition-state analogue inhibitors of HIV-1 protease were investigated using wild-type and mutant enzyme. To allow a detailed structure-inhibition analysis, enzyme with single, double, triple and quadruple combinations of G48V, V82A, 184V and L90M substitutions was used. Kinetic analysis of the mutants revealed that catalytic efficiency was 1-30% of that for the wild-type enzyme, a consequence of reduced kcat in all cases and an increased KM for all mutants except for the G48V enzyme. The overall structure-inhibitory profiles of the cyclic compounds were similar, and the inhibition of the V82A, 184V and G48V/L90M mutants were less efficient than of the wild-type enzyme. The greatest increase in Ki was generally observed for the 184V mutant and least for the G48V/L90M mutant, and additional combinations of mutations did not result in improved inhibition profiles for the cyclic compounds. An extended analysis of additional mutants, and including a set of linear compounds, showed that the profile was unique for each compound, and did not reveal any general structural features associated with a certain inhibition profile. The effects of structural modifications in the inhibitors, or of mutations, were not additive and they differed depending on their context. The results demonstrate the difficulties in predicting resistance, even for closely related compounds, and designing compounds with improved resistance profiles.
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Affiliation(s)
- G Ahlsén
- Department of Biochemistry, Uppsala University, Sweden
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Walker MA, Langston S. Monitor: molecules and profiles. Drug Discov Today 2002. [DOI: 10.1016/s1359-6446(01)02078-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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