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Chowdhury S, Nandi N. Computational study of the mechanism of binding of antifungal icofungipen in the active site of eukaryotic isoleucyl tRNA synthetase from Candida albicans. J Biomol Struct Dyn 2024:1-11. [PMID: 38444320 DOI: 10.1080/07391102.2024.2323143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024]
Abstract
The eukaryotic fungal species Candida albicans is a critical infective pathogenic agent. The β-amino acid, Icofungipen, is an effective inhibitor of Candida albicans. Icofungipen binds at the active site of the isoleucyl tRNA synthetase (IleRS) from Candida albicans (CaIleRS) and halts protein translation in fungus. In the present work, we have investigated the mechanism of binding of Icogungipen (abbreviated as IFP). Molecular dynamics (MD) simulations show that the carboxylic acid group of IFP in the CaIleRS: IFP complex is more oriented towards the Connective Polypeptide (CP) core loop compared to the carboxylic acid group of Ile in the CaIleRS: Ile complex. The Arg 410 of the CP core loop near the substrate is extended towards the IFP. Due to the difference in the conformation of residues of the CP core loop, the KMSKR loop is more proximal to the CP core loop in CaIleRS: IFP. The editing domain which is covalently linked with the CP core loop in the CaIleRS: IFP complex is also oriented in such a way that the active site cavity is narrow and longer. The metadynamics calculation shows that the IFP is trapped in a deeper potential well compared to Ile which is due to the effective closure of the gateway of the active site by KMSKR and CP core loop. The thin, long shape of the active site and the closed gate of the active site in CaIleRS: IFP complex is responsible for the effective capture of IFP relative to Ile in the active site.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shilpi Chowdhury
- Department of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal, India
| | - Nilashis Nandi
- Department of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal, India
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Takeuchi M, Teshima M, Okubo S, Aoki S. In silico
and
in vitro
Identification of Compounds with Dual Pharmacological Activity against Metionyl‐tRNA Synthetase and Isoleucyl‐tRNA Synthetase of
Staphylococcus aureus. ChemistrySelect 2023. [DOI: 10.1002/slct.202300460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Masamune Takeuchi
- Department of Bioscience & Bioinformatics Kyushu Institute of Technology 680-4 Kawadu Iizuka Fukuoka Japan. (Shunsuke Aoki
| | - Mio Teshima
- Department of Bioscience & Bioinformatics Kyushu Institute of Technology 680-4 Kawadu Iizuka Fukuoka Japan. (Shunsuke Aoki
| | - Saya Okubo
- Department of Bioscience & Bioinformatics Kyushu Institute of Technology 680-4 Kawadu Iizuka Fukuoka Japan. (Shunsuke Aoki
| | - Shunsuke Aoki
- Department of Bioscience & Bioinformatics Kyushu Institute of Technology 680-4 Kawadu Iizuka Fukuoka Japan. (Shunsuke Aoki
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3
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Chowdhury S, Ghosh P, Nandi N. Computational Methods for Molecular Understanding of the Antibiotic-Aminoacyl tRNA Synthetase Interaction. Curr Protoc 2023; 3:e699. [PMID: 36892286 DOI: 10.1002/cpz1.699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Developing an understanding of the interactions between an antibiotic and its binding site in a pathogen cell is the key to antibiotic design-an important cost-saving methodology compared to the costly and time-consuming random trial-and-error approach. The rapid development of antibiotic resistance provides an impetus for such studies. Recent years have witnessed the beginning of the use of combined computational techniques, including computer simulations and quantum mechanical computations, to understand how antibiotics bind at the active site of aminoacyl tRNA synthetases (aaRSs) from pathogens. Such computational protocols assist the knowledge-based design of antibiotics targeting aaRSs, which are their validated targets. After the ideas behind the protocols and their strategic planning are discussed, the protocols are described along with their major outcomes. This is followed by an integration of results from the different basic protocols. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Analysis of active-site residues from primary sequence of synthetase and transfer RNAs Basic Protocol 2: Molecular dynamics simulation-based protocol to study the structure and dynamics of the aaRS active site:antibiotic complex Basic Protocol 3: Quantum mechanical method-based protocol to study the structure and dynamics of the aaRS active site:antibiotic complex.
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Affiliation(s)
- Shilpi Chowdhury
- Department of Chemistry, University of Kalyani, Kalyani, West Bengal, India
| | - Poulami Ghosh
- Department of Chemistry, University of Kalyani, Kalyani, West Bengal, India
| | - Nilashis Nandi
- Department of Chemistry, University of Kalyani, Kalyani, West Bengal, India
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4
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Alkatheri AH, Yap PSX, Abushelaibi A, Lai KS, Cheng WH, Erin Lim SH. Microbial Genomics: Innovative Targets and Mechanisms. Antibiotics (Basel) 2023; 12:antibiotics12020190. [PMID: 36830101 PMCID: PMC9951906 DOI: 10.3390/antibiotics12020190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Multidrug resistance (MDR) has become an increasing threat to global health because bacteria can develop resistance to antibiotics over time. Scientists worldwide are searching for new approaches that go beyond traditional antibiotic discovery and development pipelines. Advances in genomics, however, opened up an unexplored therapeutic opportunity for the discovery of new antibacterial agents. Genomic approaches have been used to discover several novel antibiotics that target critical processes for bacterial growth and survival, including histidine kinases (HKs), LpxC, FabI, peptide deformylase (PDF), and aminoacyl-tRNA synthetases (AaRS). In this review, we will discuss the use of microbial genomics in the search for innovative and promising drug targets as well as the mechanisms of action for novel antimicrobial agents. We will also discuss future directions on how the utilization of the microbial genomics approach could improve the odds of antibiotic development having a more successful outcome.
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Affiliation(s)
- Asma Hussain Alkatheri
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Polly Soo-Xi Yap
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor 47500, Malaysia
| | - Aisha Abushelaibi
- Office of Campus Director, Abu Dhabi Colleges, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Kok-Song Lai
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
| | - Wan-Hee Cheng
- Faculty of Health and Life Sciences, INTI International University, Persiaran Perdana BBN, Nilai 71800, Malaysia
| | - Swee-Hua Erin Lim
- Health Sciences Division, Abu Dhabi Women’s College, Higher Colleges of Technology, Abu Dhabi 41012, United Arab Emirates
- Correspondence:
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Volynets GP, Gudzera OI, Usenko MO, Gorbatiuk OB, Yarmoluk SM, Tukalo MA. Probing interactions of aminoacyl-adenylate with Mycobacterium tuberculosis methionyl-tRNA synthetase through in silico site-directed mutagenesis and free energy calculation. J Biomol Struct Dyn 2022:1-9. [PMID: 35930324 DOI: 10.1080/07391102.2022.2107574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Methionyl-tRNA synthetase (MetRS) is an attractive molecular target for antibiotic discovery. Recently, we have developed several classes of small-molecular inhibitors of Mycobacterium tuberculosis MetRS possessing antibacterial activity. In this article, we performed in silico site-directed mutagenesis of aminoacyl-adenylate binding site of M. tuberculosis MetRS in order to identify crucial amino acid residues for substrate interaction. The umbrella sampling algorithm was used to calculate the binding free energy (ΔG) of these mutated forms with methionyl-adenylate analogue. According to the obtained results, the replacement of Glu24 and Leu293 by alanine leads to the most significant decrease in the binding free energy (ΔG) for adenylate analogue with methionyl-tRNA synthetase indicating increasing of the affinity, which in turn causes the loss of compounds inhibitory activity. Therefore, these amino acid residues can be proposed for further experimental site-directed mutagenesis to confirm binding mode of inhibitors and should be taken into account during chemical optimization to overcome resistance due to mutations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Galyna P Volynets
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Olga I Gudzera
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Mariia O Usenko
- Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Oksana B Gorbatiuk
- Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Sergiy M Yarmoluk
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Michael A Tukalo
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
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Scurtu LG, Jinga V, Simionescu O. Fascinating Molecular and Immune Escape Mechanisms in the Treatment of STIs (Syphilis, Gonorrhea, Chlamydia, and Herpes Simplex). Int J Mol Sci 2022; 23:ijms23073550. [PMID: 35408911 PMCID: PMC8998805 DOI: 10.3390/ijms23073550] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 02/04/2023] Open
Abstract
The incidence of syphilis, gonorrhea, chlamydia, and herpes simplex has increased over the last decade, despite the numerous prevention strategies. Worldwide scientists report a surge in drug-resistant infections, particularly in immunocompromised patients. Antigenic variations in syphilis enable long-term infection, but benzathine penicillin G maintains its efficiency, whereas macrolides should be recommended with caution. Mupirocin and zoliflodacin were recently introduced as therapies against ceftriaxone-resistant gonococcus, which poses a larger global threat. The gastrointestinal and prostatic potential reservoirs of Chlamydia trachomatis may represent the key towards complete eradication. Similar to syphilis, macrolides resistance has to be considered in genital chlamydiosis. Acyclovir-resistant HSV may respond to the novel helicase-primase inhibitors and topical imiquimod, particularly in HIV-positive patients. Novel drugs can overcome these challenges while nanocarriers enhance their potency, particularly in mucosal areas. This review summarizes the most recent and valuable discoveries regarding the immunopathogenic mechanisms of these sexually transmitted infections and discusses the challenges and opportunities of the novel molecules and nanomaterials.
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Affiliation(s)
- Lucian G. Scurtu
- Department of Dermatology I, Colentina Clinical Hospital, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020125 Bucharest, Romania;
| | - Viorel Jinga
- Department of Urology, Clinical Hospital Prof. Dr. Th. Burghele, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 030167 Bucharest, Romania;
| | - Olga Simionescu
- Department of Dermatology I, Colentina Clinical Hospital, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020125 Bucharest, Romania;
- Correspondence:
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