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Ghosh AK, Yadav M, Sharma A, Johnson M, Ghosh AK, Prasad R, Amano M, Gerlits O, Kovalevsky A, Mitsuya H. Potent HIV‑1 protease inhibitors containing oxabicyclo octanol-derived P2-ligands: Design, synthesis, and X‑ray structural studies of inhibitor-HIV-1 protease complexes. Bioorg Med Chem Lett 2025; 120:130109. [PMID: 39848476 PMCID: PMC11956850 DOI: 10.1016/j.bmcl.2025.130109] [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: 11/22/2024] [Revised: 01/02/2025] [Accepted: 01/19/2025] [Indexed: 01/25/2025]
Abstract
We describe here the design, synthesis, and X-ray structural studies of a new class of HIV-1 protease inhibitors containing 8-oxabicyclo[3.2.1]octanol-derived P2 ligands. We investigated the functional effect of these stereochemically defined fused-poly cyclic ligands on enzyme inhibition and antiviral activity in MT-2 cells. The tricyclic core of 8-oxabicyclo[3.2.1]octan-6-ol is designed to interact with the residues in the S2 subsite of HIV-1 protease. The syntheses of the ligands were carried out using the [5+2]-cycloaddition as the key step. Several inhibitors exhibited potent enzyme inhibitory activity. High resolution room-temperature X-ray structures of inhibitor-bound HIV-1 protease were determined. These structures provided important molecular insights for further design and optimization of inhibitor potency.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA.
| | - Monika Yadav
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ashish Sharma
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Megan Johnson
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ajay K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Rangu Prasad
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Masayuki Amano
- Department of Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN 37303, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Hiroaki Mitsuya
- Department of Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan; Department of Refractory Infectious Diseases, 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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2
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Ur Rehman M, Chuntakaruk H, Amphan S, Suroengrit A, Hengphasatporn K, Shigeta Y, Rungrotmongkol T, Krusong K, Boonyasuppayakorn S, Aonbangkhen C, Khotavivattana T. Design, Synthesis, and Biological Evaluation of Darunavir Analogs as HIV-1 Protease Inhibitors. ACS BIO & MED CHEM AU 2024; 4:242-256. [PMID: 39431267 PMCID: PMC11487539 DOI: 10.1021/acsbiomedchemau.4c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 09/06/2024] [Accepted: 09/06/2024] [Indexed: 10/22/2024]
Abstract
Darunavir, a frontline treatment for HIV infection, faces limitations due to emerging multidrug resistant (MDR) HIV strains, necessitating the development of analogs with improved activity. In this study, a combinatorial in silico approach was used to initially design a series of HIV-1 PI analogs with modifications at key sites, P1' and P2', to enhance interactions with HIV-1 PR. Fifteen analogs with promising binding scores were selected for synthesis and evaluated for the HIV-1 PR inhibition activity. The variation of P2' substitution was found to be effective, as seen in 5aa (1.54 nM), 5ad (0.71 nM), 5ac (0.31 nM), 5ae (0.28 nM), and 5af (1.12 nM), featuring halogen, aliphatic, and alkoxy functionalities on the phenyl sulfoxide motif exhibited superior inhibition against HIV-1 PR compared to DRV, with minimal cytotoxicity observed in Vero and 293T cell lines. Moreover, computational studies demonstrated the potential of selected analogs to inhibit various HIV-1 PR mutations, including I54M and I84V. Further structural dynamics and energetic analyses confirmed the stability and binding affinity of promising analogs, particularly 5ae, which showed strong interactions with key residues in HIV-1 PR. Overall, this study underscores the importance of flexible moieties and interaction enhancement at the S2' subsite of HIV-1 PR in developing effective DRV analogs to combat HIV and other global health issues.
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Affiliation(s)
- Muhammad
Asad Ur Rehman
- Center
of Excellence in Natural Products Chemistry, Department of Chemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Hathaichanok Chuntakaruk
- Center
of Excellence in Structural and Computation Biology, Department of
Biochemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
- Program
in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Soraat Amphan
- Center
of Excellence in Structural and Computation Biology, Department of
Biochemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Aphinya Suroengrit
- Center
of Excellence in Applied Medical Virology, Department of Microbiology,
Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Research
Affairs, Faculty of Medicine, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Kowit Hengphasatporn
- Center
for
Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru Shigeta
- Center
for
Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Thanyada Rungrotmongkol
- Center
of Excellence in Structural and Computation Biology, Department of
Biochemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
- Program
in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kuakarun Krusong
- Center
of Excellence in Structural and Computation Biology, Department of
Biochemistry, Faculty of Science, Chulalongkorn
University, Bangkok 10330, Thailand
| | - Siwaporn Boonyasuppayakorn
- Center
of Excellence in Applied Medical Virology, Department of Microbiology,
Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Chanat Aonbangkhen
- Center
of Excellence in Natural Products Chemistry, Department of Chemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tanatorn Khotavivattana
- Center
of Excellence in Natural Products Chemistry, Department of Chemistry,
Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
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3
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Wehrhan L, Keller BG. Fluorinated Protein-Ligand Complexes: A Computational Perspective. J Phys Chem B 2024; 128:5925-5934. [PMID: 38886167 PMCID: PMC11215785 DOI: 10.1021/acs.jpcb.4c01493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/20/2024]
Abstract
Fluorine is an element renowned for its unique properties. Its powerful capability to modulate molecular properties makes it an attractive substituent for protein binding ligands; however, the rational design of fluorination can be challenging with effects on interactions and binding energies being difficult to predict. In this Perspective, we highlight how computational methods help us to understand the role of fluorine in protein-ligand binding with a focus on molecular simulation. We underline the importance of an accurate force field, present fluoride channels as a showcase for biomolecular interactions with fluorine, and discuss fluorine specific interactions like the ability to form hydrogen bonds and interactions with aryl groups. We put special emphasis on the disruption of water networks and entropic effects.
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Affiliation(s)
- Leon Wehrhan
- Department of Chemistry,
Biology and Pharmacy, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Bettina G. Keller
- Department of Chemistry,
Biology and Pharmacy, Freie Universität
Berlin, Arnimallee 22, 14195 Berlin, Germany
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Ghosh AK, Sharma A, Ghazi S. An Enzymatic Route to the Synthesis of Tricyclic Fused Hexahydrofuranofuran P2-Ligand for a Series of Highly Potent HIV-1 Protease Inhibitors. Tetrahedron Lett 2024; 140:155013. [PMID: 38586565 PMCID: PMC10994151 DOI: 10.1016/j.tetlet.2024.155013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
We describe a stereoselective synthesis of an optically active (1R, 3aS, 5R, 6S, 7aR)-octahydro-1,6-epoxy-isobenzo-furan-5-ol derivative. This stereochemically defined heterocycle serves as a high-affinity ligand for a variety of HIV-1 protease inhibitors. The key synthetic steps involve a highly enantioselective enzymatic desymmetrization of meso-1,2(dihydroxymethyl)cyclohex-4-ene and conversion of the resulting optically active alcohol to a methoxy hexahydroisobenzofuran derivative. A substrate controlled stereoselective dihydroxylation afforded syn-1,2-diols. Oxidation of diol provided the substituted 1,2-diketone and L-Selectride reduction provided the corresponding inverted syn-1,2-diols. Acid catalyzed cyclization furnished the ligand alcohol in optically active form.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry, Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Ashish Sharma
- Department of Chemistry, Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Somayeh Ghazi
- Department of Chemistry, Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
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Meng S, Gao Y, Qiang G, Hu Z, Shan Q, Wang J, Wang Y, Mou J. Rational design, synthesis and biological evaluation of novel HIV-1 protease inhibitors containing 2-phenylacetamide derivatives as P2 ligands with potent activity against DRV-Resistant HIV-1 variants. Bioorg Med Chem Lett 2024; 101:129651. [PMID: 38342391 DOI: 10.1016/j.bmcl.2024.129651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/07/2024] [Accepted: 02/06/2024] [Indexed: 02/13/2024]
Abstract
A novel kind of potent HIV-1 protease inhibitors, containing diverse hydroxyphenylacetic acids as the P2-ligands and 4-substituted phenyl sulfonamides as the P2' ligands, were designed, synthesized and evaluated in this work. Majority of the target compounds exhibited good to excellent activity against HIV-1 protease with IC50 values below 200 nM. In particular, compound 18d with a 2-(3,4-dihydroxyphenyl) acetamide as the P2 ligand and a 4- methoxybenzene sulfonamide P2' ligand exhibited inhibitory activity IC50 value of 0.54 nM, which was better than that of the positive control darunavir (DRV). More importantly, no significant decline of the potency against HIV-1DRVRS (DRV-resistant mutation) and HIV-1NL4_3 variant (wild type) for 18d was detected. The molecular docking study of 18d with HIV-1 protease (PDB-ID: 1T3R, www.rcsb.org) revealed possible binding mode with the HIV-1 protease. These results suggested the validity of introducing phenol-derived moieties into the P2 ligand and deserve further optimization which was of great value for future discovery of novel HIV-1 protease.
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Affiliation(s)
- Sihan Meng
- Jiangsu Key Laboratory of New drug and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221006, China; Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yu Gao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Guowei Qiang
- Jiangsu Key Laboratory of New drug and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221006, China
| | - Zhiwei Hu
- School of Basic Medicine, Xuzhou Medical University, Xuzhou 221006, China
| | - Qi Shan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Juxian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
| | - Jie Mou
- Jiangsu Key Laboratory of New drug and Clinical Pharmacy, Xuzhou Medical University, Xuzhou 221006, China.
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