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Su HL, Lai SJ, Tsai KC, Fung KM, Lung TL, Hsu HM, Wu YC, Liu CH, Lai HX, Lin JH, Tseng TS. Structure-guided identification and characterization of potent inhibitors targeting PhoP and MtrA to combat mycobacteria. Comput Struct Biotechnol J 2024; 23:1477-1488. [PMID: 38623562 PMCID: PMC11016868 DOI: 10.1016/j.csbj.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
Mycobacteria are causative agents of tuberculosis (TB), which is a global health concern. Drug-resistant TB strains are rapidly emerging, thereby necessitating the urgent development of new drugs. Two-component signal transduction systems (TCSs) are signaling pathways involved in the regulation of various bacterial behaviors and responses to environmental stimuli. Applying specific inhibitors of TCSs can disrupt bacterial signaling, growth, and virulence, and can help combat drug-resistant TB. We conducted a comprehensive pharmacophore-based inhibitor screening and biochemical and biophysical examinations to identify, characterize, and validate potential inhibitors targeting the response regulators PhoP and MtrA of mycobacteria. The constructed pharmacophore model Phar-PR-n4 identified effective inhibitors of formation of the PhoP-DNA complex: ST132 (IC50 = 29 ± 1.6 µM) and ST166 (IC50 = 18 ± 1.3 µM). ST166 (KD = 18.4 ± 4.3 μM) and ST132 (KD = 14.5 ± 0.1 μM) strongly targeted PhoP in a slow-on, slow-off manner. The inhibitory potency and binding affinity of ST166 and ST132 for MtrAC were comparable to those of PhoP. Structural analyses and molecular dynamics simulations revealed that ST166 and ST132 mainly interact with the α8-helix and C-terminal β-hairpin of PhoP, with functionally essential residue hotspots for structure-based inhibitor optimization. Moreover, ST166 has in vitro antibacterial activity against Macrobacterium marinum. Thus, ST166, with its characteristic 1,2,5,6-tetrathiocane and terminal sulphonic groups, has excellent potential as a candidate for the development of novel antimicrobial agents to combat pathogenic mycobacteria.
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Affiliation(s)
- Han-Li Su
- Department of Emergency Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City 600, Taiwan
| | - Shu-Jung Lai
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung, Taiwan
| | - Keng-Chang Tsai
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Kit-Man Fung
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei 11529, Taiwan
| | - Tse-Lin Lung
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
| | - Hsing-Mien Hsu
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
| | - Yi-Chen Wu
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
| | - Ching-Hui Liu
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
| | - Hui-Xiang Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
| | - Jiun-Han Lin
- Department of Industrial Technology, Ministry of Economic Affairs, Taipei, Taiwan
- Food Industry Research and Development Institute, Hsinchu City, Taiwan
| | - Tien-Sheng Tseng
- Institute of Molecular Biology, National Chung Hsing University, Taichung,Taiwan
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Wu YC, Lai HX, Li JM, Fung KM, Tseng TS. Discovery of a potent inhibitor, D-132, targeting AsfvPolX, via protein-DNA complex-guided pharmacophore screening and in vitro molecular characterizations. Virus Res 2024; 344:199359. [PMID: 38521505 PMCID: PMC10995865 DOI: 10.1016/j.virusres.2024.199359] [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: 01/15/2024] [Revised: 03/15/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
The heightened transmissibility and capacity of African swine fever virus (ASFV) induce fatal diseases in domestic pigs and wild boars, posing significant economic repercussions and global threats. Despite extensive research efforts, the development of potent vaccines or treatments for ASFV remains a persistent challenge. Recently, inhibiting the AsfvPolX, a key DNA repair enzyme, emerges as a feasible strategy to disrupt viral replication and control ASFV infections. In this study, a comprehensive approach involving pharmacophore-based inhibitor screening, coupled with biochemical and biophysical analyses, were implemented to identify, characterize, and validate potential inhibitors targeting AsfvPolX. The constructed pharmacophore model, Phar-PolX-S, demonstrated efficacy in identifying a potent inhibitor, D-132 (IC50 = 2.8 ± 0.2 µM), disrupting the formation of the AsfvPolX-DNA complex. Notably, D-132 exhibited strong binding to AsfvPolX (KD = 6.9 ± 2.2 µM) through a slow-on-fast-off binding mechanism. Employing molecular modeling, it was elucidated that D-132 predominantly binds in-between the palm and finger domains of AsfvPolX, with crucial residues (R42, N48, Q98, E100, F102, and F116) identified as hotspots for structure-based inhibitor optimization. Distinctively characterized by a 1,2,5,6-tetrathiocane with modifications at the 3 and 8 positions involving ethanesulfonates, D-132 holds considerable promise as a lead compound for the development of innovative agents to combat ASFV infections.
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Affiliation(s)
- Yi-Chen Wu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40202, Taiwan
| | - Hui-Xiang Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40202, Taiwan
| | - Ji-Min Li
- Institute of Precision Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan; Center of Excellence for Metabolic Associated Fatty Liver Disease, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Kit-Man Fung
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Tien-Sheng Tseng
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40202, Taiwan.
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Paul P, Karar M, Alam MN, Dutta D, Majumdar T, Mallick A. Circumstantial Overdose Management of an Efficient Cancer Cell Photosensitizer with Preclinical Evidence: A Biophysical Study. ACS APPLIED BIO MATERIALS 2020; 3:8049-8060. [PMID: 35019544 DOI: 10.1021/acsabm.0c01121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this article, pharmacological management of circumstantial overdose of an anticancer drug, Harmine (HM), under in vitro and in vivo conditions is described and further validated by employing in silico methods. HM, an efficient cancer cell photosensitizer, interacts extensively with nontoxic β-cyclodextrin (β-CD). Steady-state fluorescence studies and molecular docking analysis established differential nature of molecular inclusion depending on the relative concentrations of β-CD. Presently, β-CD is commonly used as a standard drug-delivery vehicle but its application for controlled drug withdrawal is rarely explored. Flow cytometric results and in vivo investigations on a zebrafish model showed that conditional overdose of preadministered drug molecules can be efficiently removed by encapsulating successfully within nontoxic β-CDs, albeit by controlled application of the same. This is an approach to manage the cytotoxicity of a drug in a safe way that is already administered. We believe that this β-CD-mediated withdrawal of drugs may find possible applications in controlled capturing of excess or unused drug inside living systems and reducing the unwanted toxicity associated with chemotherapeutics.
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Affiliation(s)
- Provakar Paul
- Department of Chemistry, University of Kalyani, Nadia, Kalyani, West Bengal 741235, India
| | - Monaj Karar
- Department of Chemistry, University of Kalyani, Nadia, Kalyani, West Bengal 741235, India
| | - Md Nur Alam
- Department of Life Sciences, Presidency University, Kolkata 700073 West Bengal, India
| | - Debanjan Dutta
- Department of MRDG, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Tapas Majumdar
- Department of Chemistry, University of Kalyani, Nadia, Kalyani, West Bengal 741235, India
| | - Arabinda Mallick
- Department of Chemistry, Kazi Nazrul University, Asansol, West Bengal 713340, India
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Kaur M, Kaur B, Kaur J, Kaur A, Bhatti R, Singh P. Role of water in cyclooxygenase catalysis and design of anti-inflammatory agents targeting two sites of the enzyme. Sci Rep 2020; 10:10764. [PMID: 32612190 PMCID: PMC7329864 DOI: 10.1038/s41598-020-67655-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/12/2020] [Indexed: 11/15/2022] Open
Abstract
While designing the anti-inflammatory agents targeting cyclooxygenase-2 (COX-2), we first identified a water loop around the heme playing critical role in the enzyme catalysis. The results of molecular dynamic studies supported by the strong hydrogen-bonding equilibria of the participating atoms, radical stabilization energies, the pKa of the H-donor/acceptor sites and the cyclooxygenase activity of pertinent muCOX-2 ravelled the working of the water–peptide channel for coordinating the flow of H·/electron between the heme and Y385. Based on the working of H·/electron transfer channel between the 12.5 Å distant radical generation and the radical disposal sites, a series of molecules was designed and synthesized. Among this category of compounds, an appreciably potent anti-inflammatory agent exhibiting IC50 0.06 μM against COX-2 and reversing the formalin induced analgesia and carageenan induced inflammation in mice by 90% was identified. Further it was revealed that, justifying its bidentate design, the compound targets water loop (heme bound site) and the arachidonic acid binding pockets of COX-2.
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Affiliation(s)
- Manpreet Kaur
- UGC Sponsored Centre for Advanced Studies, Department of Chemistry, Guru Nanak Dev University, Amritsar, 143005, India
| | - Baljit Kaur
- UGC Sponsored Centre for Advanced Studies, Department of Chemistry, Guru Nanak Dev University, Amritsar, 143005, India
| | - Jagroop Kaur
- UGC Sponsored Centre for Advanced Studies, Department of Chemistry, Guru Nanak Dev University, Amritsar, 143005, India
| | - Anudeep Kaur
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, 143005, India
| | - Rajbir Bhatti
- Department of Pharmaceutical Sciences, Guru Nanak Dev University, Amritsar, 143005, India
| | - Palwinder Singh
- UGC Sponsored Centre for Advanced Studies, Department of Chemistry, Guru Nanak Dev University, Amritsar, 143005, India.
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Discovery of Potent Neuraminidase Inhibitors Using a Combination of Pharmacophore-Based Virtual Screening and Molecular Simulation Approach. Appl Biochem Biotechnol 2017; 184:1421-1440. [DOI: 10.1007/s12010-017-2625-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/02/2017] [Indexed: 01/20/2023]
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