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Sun N, Du RL, Zheng YY, Guo Q, Cai SY, Liu ZH, Fang ZY, Yuan WC, Liu T, Li XM, Lu YJ, Wong KY. Antibacterial activity of 3-methylbenzo[d]thiazol-methylquinolinium derivatives and study of their action mechanism. J Enzyme Inhib Med Chem 2018; 33:879-889. [PMID: 29722581 PMCID: PMC6010097 DOI: 10.1080/14756366.2018.1465055] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/09/2018] [Accepted: 04/10/2018] [Indexed: 12/19/2022] Open
Abstract
The increasing incidence of multidrug resistant bacterial infection renders an urgent need for the development of new antibiotics. To develop small molecules disturbing FtsZ activity has been recognized as promising approach to search for antibacterial of high potency systematically. Herein, a series of novel quinolinium derivatives were synthesized and their antibacterial activities were investigated. The compounds show strong antibacterial activities against different bacteria strains including MRSA, VRE and NDM-1 Escherichia coli. Among these derivatives, a compound bearing a 4-fluorophenyl group (A2) exhibited a superior antibacterial activity and its MICs to the drug-resistant strains are found lower than those of methicillin and vancomycin. The biological results suggest that these quinolinium derivatives can disrupt the GTPase activity and dynamic assembly of FtsZ, and thus inhibit bacterial cell division and then cause bacterial cell death. These compounds deserve further evaluation for the development of new antibacterial agents targeting FtsZ.
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Affiliation(s)
- Ning Sun
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P.R. China
- Institute of Natural Medicine and Green Chemistry, School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, P.R. China
| | - Ruo-Lan Du
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P.R. China
| | - Yuan-Yuan Zheng
- Institute of Natural Medicine and Green Chemistry, School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, P.R. China
| | - Qi Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, P.R. China
| | - Sen-Yuan Cai
- Institute of Natural Medicine and Green Chemistry, School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, P.R. China
| | - Zhi-Hua Liu
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Zhi-Yuan Fang
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Wen-Chang Yuan
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Ting Liu
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Xiao-Mei Li
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Yu-Jing Lu
- Institute of Natural Medicine and Green Chemistry, School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, P.R. China
- Goldenpomelo Biotechnology Co. Ltd, Meizhou514021, P.R. China
| | - Kwok-Yin Wong
- Department of Applied Biology and Chemical Technology and State Key Laboratory of Chirosciences, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P.R. China
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Danishuddin, Kumar A, Mobeen F, Khan AU. Development of Ligand and Structure-based classification models to design novel inhibitors against antibiotic hydrolyzing enzymes: Integration of web server. J Biomol Struct Dyn 2017; 36:2966-2975. [PMID: 28849700 DOI: 10.1080/07391102.2017.1373034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Danishuddin
- a Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit , Aligarh Muslim University , Aligarh , UP 202002 , India
| | - Amit Kumar
- a Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit , Aligarh Muslim University , Aligarh , UP 202002 , India
| | - Fauzul Mobeen
- a Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit , Aligarh Muslim University , Aligarh , UP 202002 , India
| | - Asad U Khan
- a Medical Microbiology and Molecular Biology Laboratory, Interdisciplinary Biotechnology Unit , Aligarh Muslim University , Aligarh , UP 202002 , India
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3
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Li Y, Zhao Z, Liu Z, Su M, Wang R. AutoT&T v.2: An Efficient and Versatile Tool for Lead Structure Generation and Optimization. J Chem Inf Model 2016; 56:435-53. [DOI: 10.1021/acs.jcim.5b00691] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yan Li
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Zhixiong Zhao
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Zhihai Liu
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Minyi Su
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Renxiao Wang
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
- State
Key Laboratory of Quality Research in Chinese Medicine, Macau Institute
for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, People’s Republic of China
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Ligand deconstruction: Why some fragment binding positions are conserved and others are not. Proc Natl Acad Sci U S A 2015; 112:E2585-94. [PMID: 25918377 DOI: 10.1073/pnas.1501567112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fragment-based drug discovery (FBDD) relies on the premise that the fragment binding mode will be conserved on subsequent expansion to a larger ligand. However, no general condition has been established to explain when fragment binding modes will be conserved. We show that a remarkably simple condition can be developed in terms of how fragments coincide with binding energy hot spots--regions of the protein where interactions with a ligand contribute substantial binding free energy--the locations of which can easily be determined computationally. Because a substantial fraction of the free energy of ligand binding comes from interacting with the residues in the energetically most important hot spot, a ligand moiety that sufficiently overlaps with this region will retain its location even when other parts of the ligand are removed. This hypothesis is supported by eight case studies. The condition helps identify whether a protein is suitable for FBDD, predicts the size of fragments required for screening, and determines whether a fragment hit can be extended into a higher affinity ligand. Our results show that ligand binding sites can usefully be thought of in terms of an anchor site, which is the top-ranked hot spot and dominates the free energy of binding, surrounded by a number of weaker satellite sites that confer improved affinity and selectivity for a particular ligand and that it is the intrinsic binding potential of the protein surface that determines whether it can serve as a robust binding site for a suitably optimized ligand.
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