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Chuntakaruk H, Hengphasatporn K, Shigeta Y, Aonbangkhen C, Lee VS, Khotavivattana T, Rungrotmongkol T, Hannongbua S. FMO-guided design of darunavir analogs as HIV-1 protease inhibitors. Sci Rep 2024; 14:3639. [PMID: 38351065 PMCID: PMC10864397 DOI: 10.1038/s41598-024-53940-1] [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: 06/03/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
The prevalence of HIV-1 infection continues to pose a significant global public health issue, highlighting the need for antiretroviral drugs that target viral proteins to reduce viral replication. One such target is HIV-1 protease (PR), responsible for cleaving viral polyproteins, leading to the maturation of viral proteins. While darunavir (DRV) is a potent HIV-1 PR inhibitor, drug resistance can arise due to mutations in HIV-1 PR. To address this issue, we developed a novel approach using the fragment molecular orbital (FMO) method and structure-based drug design to create DRV analogs. Using combinatorial programming, we generated novel analogs freely accessible via an on-the-cloud mode implemented in Google Colab, Combined Analog generator Tool (CAT). The designed analogs underwent cascade screening through molecular docking with HIV-1 PR wild-type and major mutations at the active site. Molecular dynamics (MD) simulations confirmed the assess ligand binding and susceptibility of screened designed analogs. Our findings indicate that the three designed analogs guided by FMO, 19-0-14-3, 19-8-10-0, and 19-8-14-3, are superior to DRV and have the potential to serve as efficient PR inhibitors. These findings demonstrate the effectiveness of our approach and its potential to be used in further studies for developing new antiretroviral drugs.
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Affiliation(s)
- Hathaichanok Chuntakaruk
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, 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
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Vannajan Sanghiran Lee
- Chemistry Department, Faculty of Science, University Malaya, Kuala Lumpur, 50603, Malaysia
| | - Tanatorn Khotavivattana
- Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand.
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Supot Hannongbua
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Sang D, Dong B, Liu Y, Tian J. Chemoselective Cleavage of Acylsulfonamides and Sulfonamides by Aluminum Halides. J Org Chem 2022; 87:3586-3595. [PMID: 35157468 DOI: 10.1021/acs.joc.1c03133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The chemoselective cleavage of C-N bonds of amides, sulfonamides, and acylsulfonamides by aluminum halides is described. AlCl3 and AlI3 display complementary reactivities toward N-alkyl and N-acyl moieties. N-Alkylacylsulfonamides, secondary N-(tert-butyl)sulfonamides, and tertiary N-(tert-butyl)amides undergo N-dealkylation upon treatments with AlI3 generated in situ from aluminum and iodine in acetonitrile. In contrast, AlCl3 preferentially cleaves N-acyl groups of tertiary and secondary sulfonamides.
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Affiliation(s)
- Dayong Sang
- College of Chemical Engineering and Pharmacy, Jingchu University of Technology, Jingmen, Hubei 448000, P. R. China
| | - Bingqian Dong
- College of Chemical Engineering and Pharmacy, Jingchu University of Technology, Jingmen, Hubei 448000, P. R. China.,School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan, Hubei 430205, P. R. China
| | - Yunfeng Liu
- College of Chemical Engineering and Pharmacy, Jingchu University of Technology, Jingmen, Hubei 448000, P. R. China
| | - Juan Tian
- College of Chemical Engineering and Pharmacy, Jingchu University of Technology, Jingmen, Hubei 448000, P. R. China
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Gallou I, Senanayake CH. cis-1-Amino-2-indanol in Drug Design and Applications to Asymmetric Processes. Chem Rev 2006; 106:2843-74. [PMID: 16836302 DOI: 10.1021/cr050970a] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Isabelle Gallou
- Department of Chemical Development, Boehringer Ingelheim Pharmaceuticals Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, USA
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