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Chuntakaruk H, Boonpalit K, Kinchagawat J, Nakarin F, Khotavivattana T, Aonbangkhen C, Shigeta Y, Hengphasatporn K, Nutanong S, Rungrotmongkol T, Hannongbua S. Machine learning-guided design of potent darunavir analogs targeting HIV-1 proteases: A computational approach for antiretroviral drug discovery. J Comput Chem 2024; 45:953-968. [PMID: 38174739 DOI: 10.1002/jcc.27298] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/30/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024]
Abstract
In the pursuit of novel antiretroviral therapies for human immunodeficiency virus type-1 (HIV-1) proteases (PRs), recent improvements in drug discovery have embraced machine learning (ML) techniques to guide the design process. This study employs ensemble learning models to identify crucial substructures as significant features for drug development. Using molecular docking techniques, a collection of 160 darunavir (DRV) analogs was designed based on these key substructures and subsequently screened using molecular docking techniques. Chemical structures with high fitness scores were selected, combined, and one-dimensional (1D) screening based on beyond Lipinski's rule of five (bRo5) and ADME (absorption, distribution, metabolism, and excretion) prediction implemented in the Combined Analog generator Tool (CAT) program. A total of 473 screened analogs were subjected to docking analysis through convolutional neural networks scoring function against both the wild-type (WT) and 12 major mutated PRs. DRV analogs with negative changes in binding free energy (ΔΔ G bind ) compared to DRV could be categorized into four attractive groups based on their interactions with the majority of vital PRs. The analysis of interaction profiles revealed that potent designed analogs, targeting both WT and mutant PRs, exhibited interactions with common key amino acid residues. This observation further confirms that the ML model-guided approach effectively identified the substructures that play a crucial role in potent analogs. It is expected to function as a powerful computational tool, offering valuable guidance in the identification of chemical substructures for synthesis and subsequent experimental testing.
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Affiliation(s)
- Hathaichanok Chuntakaruk
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Center of Excellence in Structural and Computational Biology, Chulalongkorn University, Bangkok, Thailand
| | - Kajjana Boonpalit
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Jiramet Kinchagawat
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Fahsai Nakarin
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Tanatorn Khotavivattana
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chanat Aonbangkhen
- Center of Excellence in Natural Products Chemistry (CENP), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Ibaraki, Japan
| | | | - Sarana Nutanong
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Center of Excellence in Structural and Computational Biology, Chulalongkorn University, Bangkok, Thailand
| | - Supot Hannongbua
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Department of Chemistry, Faculty of Science, Center of Excellence in Computational Chemistry (CECC), Chulalongkorn University, Bangkok, Thailand
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2
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Sever B, Otsuka M, Fujita M, Ciftci H. A Review of FDA-Approved Anti-HIV-1 Drugs, Anti-Gag Compounds, and Potential Strategies for HIV-1 Eradication. Int J Mol Sci 2024; 25:3659. [PMID: 38612471 PMCID: PMC11012182 DOI: 10.3390/ijms25073659] [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: 01/11/2024] [Revised: 03/22/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) is an enormous global health threat stemming from human immunodeficiency virus (HIV-1) infection. Up to now, the tremendous advances in combination antiretroviral therapy (cART) have shifted HIV-1 infection from a fatal illness into a manageable chronic disorder. However, the presence of latent reservoirs, the multifaceted nature of HIV-1, drug resistance, severe off-target effects, poor adherence, and high cost restrict the efficacy of current cART targeting the distinct stages of the virus life cycle. Therefore, there is an unmet need for the discovery of new therapeutics that not only bypass the limitations of the current therapy but also protect the body's health at the same time. The main goal for complete HIV-1 eradication is purging latently infected cells from patients' bodies. A potential strategy called "lock-in and apoptosis" targets the budding phase of the life cycle of the virus and leads to susceptibility to apoptosis of HIV-1 infected cells for the elimination of HIV-1 reservoirs and, ultimately, for complete eradication. The current work intends to present the main advantages and disadvantages of United States Food and Drug Administration (FDA)-approved anti-HIV-1 drugs as well as plausible strategies for the design and development of more anti-HIV-1 compounds with better potency, favorable pharmacokinetic profiles, and improved safety issues.
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Affiliation(s)
- Belgin Sever
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, Eskisehir 26470, Türkiye;
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
| | - Masami Otsuka
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
- Department of Drug Discovery, Science Farm Ltd., Kumamoto 862-0976, Japan
| | - Mikako Fujita
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
| | - Halilibrahim Ciftci
- Medicinal and Biological Chemistry Science Farm Joint Research Laboratory, Faculty of Life Sciences, Kumamoto University, Kumamoto 862-0973, Japan;
- Department of Drug Discovery, Science Farm Ltd., Kumamoto 862-0976, Japan
- Department of Bioengineering Sciences, Izmir Katip Celebi University, Izmir 35620, Türkiye
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He LL, Wang X, O'Neill Rothenberg D, Xu X, Wang HH, Deng X, Cui ZN. A novel strategy to control Pseudomonas syringae through inhibition of type III secretion system. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 194:105471. [PMID: 37532345 DOI: 10.1016/j.pestbp.2023.105471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 08/04/2023]
Abstract
Pseudomonas syringae (P. syringae) is a highly prevalent Gram-negative pathogen with over 60 pathogenic variants that cause yield losses of up to 80% in various crops. Traditional control methods mainly involve the application of antibiotics to inactivate pathogenic bacteria, but large-scale application of antibiotics has led to the development of bacterial resistance. Gram-negative pathogens including P. syringae commonly use the type III secretion system (T3SS) as a transport channel to deliver effector proteins into host cells, disrupting host defences and facilitating virulence, providing a novel target for antibacterial drug development. In this study, we constructed a high-throughput screening reporter system based on our previous work to screen for imidazole, oxazole and thiazole compounds. The screening indicated that the three compounds (II-14, II-15 and II-24) significantly inhibited hrpW and hrpL gene promoter activity without influencing the growth of P. syringae, and the inhibitory activity was better than that of the positive control sulforaphane (4-methylsulfinylbutyl isothiocyanate, SFN) at 50 μM. Three compounds suppressed the transcript levels of representative T3SS genes to different degrees, suggesting that the compounds may suppress the expression of T3SS by modulating the HrpR/S-HrpL regulatory pathway. Inoculation experiments indicated that all three compounds suppressed the pathogenicity of Pseudomonas syringae pv. tomato DC3000 in tomato and Pseudomonas syringae pv. phaseolicola 1448A in bean to varying degrees. One representative compound, II-15, significantly inhibited the secretion of the Pst DC3000 AvrPto effector protein. These findings provide a theoretical basis for the development of novel P. syringae T3SS inhibitors for application in disease prevention and control.
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Affiliation(s)
- Lu-Lu He
- National Key Laboratory of Green Pesticide, Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Xin Wang
- National Key Laboratory of Green Pesticide, Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | | | - Xiaoli Xu
- Instrumental Analysis & Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Hai-Hong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Xin Deng
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR 999077, China; Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
| | - Zi-Ning Cui
- National Key Laboratory of Green Pesticide, Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China.
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Hu S, Chen J, Cao JX, Zhang SS, Gu SX, Chen FE. Quinolines and isoquinolines as HIV-1 inhibitors: Chemical structures, action targets, and biological activities. Bioorg Chem 2023; 136:106549. [PMID: 37119785 DOI: 10.1016/j.bioorg.2023.106549] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/09/2023] [Accepted: 04/13/2023] [Indexed: 05/01/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1), a lentivirus that causes acquired immunodeficiency syndrome (AIDS), poses a serious threat to global public health. Since the advent of the first drug zidovudine, a number of anti-HIV agents acting on different targets have been approved to combat HIV/AIDS. Among the abundant heterocyclic families, quinoline and isoquinoline moieties are recognized as promising scaffolds for HIV inhibition. This review intends to highlight the advances in diverse chemical structures and abundant biological activity of quinolines and isoquinolines as anti-HIV agents acting on different targets, which aims to provide useful references and inspirations to design and develop novel HIV inhibitors for medicinal chemists.
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Affiliation(s)
- Sha Hu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Jiong Chen
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Jin-Xu Cao
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China; Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Wuhan Institute of Technology, Wuhan 430205, China
| | - Shuang-Shuang Zhang
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China; Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Wuhan Institute of Technology, Wuhan 430205, China
| | - Shuang-Xi Gu
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China; Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Wuhan Institute of Technology, Wuhan 430205, China.
| | - Fen-Er Chen
- Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering & Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; Pharmaceutical Research Institute, Wuhan Institute of Technology, Wuhan 430205, China; Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Wuhan Institute of Technology, Wuhan 430205, China; Department of Chemistry, Fudan University, Shanghai 200433, China.
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Al-Warhi T, Elimam DM, Elsayed ZM, Abdel-Aziz MM, Maklad RM, Al-Karmalawy AA, Afarinkia K, Abourehab MAS, Abdel-Aziz HA, Eldehna WM. Development of novel isatin thiazolyl-pyrazoline hybrids as promising antimicrobials in MDR pathogens. RSC Adv 2022; 12:31466-31477. [PMID: 36382148 PMCID: PMC9629177 DOI: 10.1039/d2ra04385h] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/27/2022] [Indexed: 11/07/2022] Open
Abstract
Microbial Multidrug Resistance (MDR) is an emerging global crisis. Derivatization of natural or synthetic scaffolds is among the most reliable strategies to search for and obtain novel antimicrobial agents for the treatment of MDR infections. Here, we successfully manipulated the synthetically flexible isatin moieties to synthesize 22 thiazolyl-pyrazolines hybrids, and assessed their potential antimicrobial activities in vitro against various MDR pathogens, using the broth microdilution calorimetric XTT reduction method. We chose 5 strains to represent the major MDR microorganisms, viz: Methicillin-resistant S. aureus (MRSA), and Vancomycin-resistant E. faecalis (VRE) as Gram-positive bacteria; Carbapenem-resistant K. pneumonia (CRKP), and Extended-spectrum beta-lactamase E. coli (ESBL-E), as Gram-negative bacteria; and Fluconazole-resistant C. albicans (FRCA), as a yeast-like unicellular fungus. The cytotoxicity of compounds 9f and 10h towards mammalian lung fibroblast (MRC-5) cells demonstrated their potential satisfactory safety margin as represented by their relatively high IC50 values. The target compounds showed promising anti-MDR activities, suggesting they are potential leads for further development and in vivo studies. As promising antimicrobials against MDR pathogens, two novel series of isatin thiazolyl-pyrazoline conjugates were developed. Compounds 9f and 10h were the most effective against the tested MDR strains.![]()
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Affiliation(s)
- Tarfah Al-Warhi
- Department of Chemistry, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia
| | - Diaaeldin M. Elimam
- Department of Pharmacognosy, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Zainab M. Elsayed
- Scientific Research and Innovation Support Unit, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Marwa M. Abdel-Aziz
- The Regional Center for Mycology & Biotechnology, Al-Azhar University, Cairo, Egypt
| | - Raed M. Maklad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
| | - Ahmed A. Al-Karmalawy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, 6th of October City, Giza, 12566, Egypt
| | - Kamyar Afarinkia
- Institute of Cancer Therapeutics, University of Bradford, Bradford, BD7 1DP, UK
| | - Mohammed A. S. Abourehab
- Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Hatem A. Abdel-Aziz
- Department of Applied Organic Chemistry, National Research Center, P.O. Box 12622, Dokki, Giza, Egypt
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, 33516, Egypt
- School of Biotechnology, Badr University in Cairo, Badr City, 11829, Egypt
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