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S S, N H, Fasim A, More SS, Das Mitra S. Identification of a potential inhibitor for New Delhi metallo-β-lactamase 1 (NDM-1) from FDA approved chemical library- a drug repurposing approach to combat carbapenem resistance. J Biomol Struct Dyn 2023; 41:7700-7711. [PMID: 36165602 DOI: 10.1080/07391102.2022.2123402] [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: 03/21/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
Superbugs producing New Delhi metallo-β-lactamase 1 (NDM-1) enzyme is a growing crisis, that is adversely affecting the global health care system. NDM-1 empowers the bacteria to inactivate entire arsenal of β-lactam antibiotics including carbapenem (the last resort antibiotic) and remains ineffective to all the available β lactamase inhibitors used in the clinics. Limited therapeutic option available for rapidly disseminating NDM-1 producing bacteria makes it imperative to identify a potential inhibitor for NDM-1 enzyme. With drug repurposing approach, in this study, we used virtual screening of available Food and Drug Administration (FDA) approved chemical library (ZINC12 database) and captured 'adapalene' (FDA drug) as a potent inhibitor candidate for NDM-1 enzyme. Active site docking with NDM-1, showed adapalene with binding energy -9.21 kcal/mol and interacting with key amino acid residues (Asp124, His122, His189, His250, Cys208) in the active site of NDM-1. Further, molecular dynamic simulation of NDM-1 docked with the adapalene at 100 ns displayed a stable conformation dynamic, with relative RMSD and RMSF in the acceptable range. Subsequently, in vitro enzyme assays using recombinant NDM-1 protein demonstrated inhibition of NDM-1 by adapalene. Further, the combination of adapalene plus meropenem (carbapenem antibiotic) showed synergistic effect against the NDM-1 producing carbapenem (meropenem) resistant clinical isolates (Escherichia coli and Klebsiella pneumoniae). Overall, our data indicated that adapalene can be a potential inhibitor candidate for NDM-1 enzyme that can contribute to the development of a suitable adjuvant to save the activity of carbapenem antibiotic against infections caused by NDM-1 positive gram-negative bacteria. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shailaja S
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
| | - Harshitha N
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
| | - Aneesa Fasim
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
| | - Sunil S More
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
| | - Susweta Das Mitra
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
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Enzyme Inhibitors: The Best Strategy to Tackle Superbug NDM-1 and Its Variants. Int J Mol Sci 2021; 23:ijms23010197. [PMID: 35008622 PMCID: PMC8745225 DOI: 10.3390/ijms23010197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 01/06/2023] Open
Abstract
Multidrug bacterial resistance endangers clinically effective antimicrobial therapy and continues to cause major public health problems, which have been upgraded to unprecedented levels in recent years, worldwide. β-Lactam antibiotics have become an important weapon to fight against pathogen infections due to their broad spectrum. Unfortunately, the emergence of antibiotic resistance genes (ARGs) has severely astricted the application of β-lactam antibiotics. Of these, New Delhi metallo-β-lactamase-1 (NDM-1) represents the most disturbing development due to its substrate promiscuity, the appearance of variants, and transferability. Given the clinical correlation of β-lactam antibiotics and NDM-1-mediated resistance, the discovery, and development of combination drugs, including NDM-1 inhibitors, for NDM-1 bacterial infections, seems particularly attractive and urgent. This review summarizes the research related to the development and optimization of effective NDM-1 inhibitors. The detailed generalization of crystal structure, enzyme activity center and catalytic mechanism, variants and global distribution, mechanism of action of existing inhibitors, and the development of scaffolds provides a reference for finding potential clinically effective NDM-1 inhibitors against drug-resistant bacteria.
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Mitra SD, Irshad P, Anusree M, Rekha I, Shailaja S, Suresh J, Aishwarya G, Shrestha S, Shome BR. Whole genome global insight of antibiotic resistance gene repertoire and virulome of high - risk multidrug-resistant Uropathogenic Escherichiacoli. Microb Pathog 2021; 161:105256. [PMID: 34695556 DOI: 10.1016/j.micpath.2021.105256] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/06/2021] [Accepted: 10/14/2021] [Indexed: 12/17/2022]
Abstract
Elucidation of genetic determinants via whole genome sequence (WGS) analyses can help understand the high risk multidrug-resistant (MDR) Uropathogenic Escherichia coli (UPEC) associated with urinary tract infections (UTI) and its evasion strategies from treatment. We investigated the WGS of 30 UPEC strains from UTI samples across the world (2016-2019) and found 25 UPEC strains carrying 2-23 antibiotic resistance genes (ARGs) scattered across 1-3 plasmids per strain. Different ARGs (blaTEM, blaCTXM, blaNDM, blaOXA, blaCMY) encoding extended-spectrum beta-lactamases (TEM, CTXM, CMY) and carbapenemases (NDM, OXA) were found in 24/30, ARGs encoding aminoglycoside modifying enzymes (AAC, APH, AAD) variants in 23/30, trimethoprim ARGs (dfrA17, dfrA12, dfrA5, dfrB4 variants) encoding dihydrofolate reductase in 19/30 and sulfonamide ARGs (sul1, sul2, sul3) encoding dihydropteroate synthase and macrolide ARGs (mph1) encoding macrolide 2' phosphotransferase in 15/30 UPEC strains. Collectively the ARGs were distributed in different combinations in 40 plasmids across UPEC strains with 20 plasmids displaying co-occurrence of multiple ARGs conferring resistance to beta lactam, aminoglycoside, sulfonamide, trimethoprim and macrolide antibiotics. These resistance plasmids belonged to seven incompatibility groups (IncF, IncI, IncC, IncH, IncN, IncB and Col), with IncFI and IncFII being the predominant resistance plasmids. Additionally, we observed co-occurrence of specific mutation pattern in quinolone resistance determining region (QRDR) viz., DNA gyrase (gyrA: S83L, D87N), and topoisomerase IV (parC: S80I, E84V; parE: I529L) in 18/30 strains. The strains also harbored diverse virulence genes, such as fimH, gad, iss, iha, ireA, iroN, cnf1 and san. Multilocus sequence typing (MLST) reconfirmed ST131(n = 10) as the predominant global high-risk clonal strain causing UTI. In summary, our findings contribute to better understand the plasmid mediated ARGs and its encoded enzymes that may contribute in antibiotic inactivation/modification or alteration in the antibiotic target site in high risk MDR hypervirulent UPEC strains causing UTI. The study reinforces the need to characterize and design appropriate inhibitors to counterattack different enzymes and devise strategies to curtail resistance plasmid.
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Affiliation(s)
- Susweta Das Mitra
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India.
| | - Pir Irshad
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - M Anusree
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - Injeti Rekha
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - S Shailaja
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - Janshi Suresh
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - G Aishwarya
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - Smeeta Shrestha
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, 560078, India
| | - Bibek Ranjan Shome
- ICAR- National Institute of Veterinary Epidemiology & Disease Informatics, Bangalore, India
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Bilal H, Zhang G, Rehman T, Han J, Khan S, Shafiq M, Yang X, Yan Z, Yang X. First Report of blaNDM-1 Bearing IncX3 Plasmid in Clinically Isolated ST11 Klebsiella pneumoniae from Pakistan. Microorganisms 2021; 9:microorganisms9050951. [PMID: 33924918 PMCID: PMC8146611 DOI: 10.3390/microorganisms9050951] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 02/05/2023] Open
Abstract
The New Delhi Metallo-β-lactamase (NDM) is among the most threatening forms of carbapenemases produced by K. pneumoniae, well-known to cause severe worldwide infections. The molecular epidemiology of blaNDM-1-harboring K. pneumoniae is not well elucidated in Pakistan. Herein, we aim to determine the antibiotics-resistance profile, genes type, molecular type, and plasmid analysis of 125 clinically isolated K. pneumoniae strains from urine samples during July 2018 to January 2019 in Pakistan. A total of 34 (27.2%) K. pneumoniae isolates were carbapenemases producers, and 23 (18.4%) harbored the blaNDM-1 gene. The other carbapenemases encoding genes, i.e., blaIMP-1 (7.2%), blaVIM-1 (3.2%), and blaOXA-48 (2.4%) were also detected. The Multi Locus Sequence Typing (MLST) results revealed that all blaNDM-1-harboring isolates were ST11. The other sequence types detected were ST1, ST37, and ST105. The cluster analysis of Xbal Pulsed Field Gel Electrophoresis (PFGE) revealed variation amongst the clusters of the identical sequence type isolates. The blaNDM-1 gene in all of the isolates was located on a 45-kb IncX3 plasmid, successfully transconjugated. For the first time, blaNDM-1-bearing IncX3 plasmids were identified from Pakistan, and this might be a new primary vehicle for disseminating blaNDM-1 in Enterobacteriaceae as it has a high rate of transferability.
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Affiliation(s)
- Hazrat Bilal
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, China; (H.B.); (G.Z.); (J.H.); (S.K.); (X.Y.); (Z.Y.)
| | - Gaojian Zhang
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, China; (H.B.); (G.Z.); (J.H.); (S.K.); (X.Y.); (Z.Y.)
| | - Tayyab Rehman
- Institute of Basic Medical Sciences, Khyber Medical University, Phase V, Hayatabad, Peshawar 25120, Khyber Pakhtunkhwa, Pakistan;
| | - Jianxion Han
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, China; (H.B.); (G.Z.); (J.H.); (S.K.); (X.Y.); (Z.Y.)
| | - Sabir Khan
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, China; (H.B.); (G.Z.); (J.H.); (S.K.); (X.Y.); (Z.Y.)
| | - Muhammad Shafiq
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China;
| | - Xuegang Yang
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, China; (H.B.); (G.Z.); (J.H.); (S.K.); (X.Y.); (Z.Y.)
| | - Zhongkang Yan
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, China; (H.B.); (G.Z.); (J.H.); (S.K.); (X.Y.); (Z.Y.)
| | - Xingyuan Yang
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, China; (H.B.); (G.Z.); (J.H.); (S.K.); (X.Y.); (Z.Y.)
- Correspondence:
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