1
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Gupta R, Singh M, Pathania R. Chemical genetic approaches for the discovery of bacterial cell wall inhibitors. RSC Med Chem 2023; 14:2125-2154. [PMID: 37974958 PMCID: PMC10650376 DOI: 10.1039/d3md00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/10/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.
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Affiliation(s)
- Rinki Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
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2
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Verma A, Kumar V, Naik B, Masood Khan J, Singh P, Erik Joakim Saris P, Gupta S. Screening and molecular dynamics simulation of compounds inhibiting MurB enzyme of drug-resistant Mycobacterium tuberculosis: An in-silico approach. Saudi J Biol Sci 2023; 30:103730. [PMID: 37483837 PMCID: PMC10362793 DOI: 10.1016/j.sjbs.2023.103730] [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: 05/27/2023] [Revised: 06/20/2023] [Accepted: 06/30/2023] [Indexed: 07/25/2023] Open
Abstract
Mycobacterium tuberculosis (MTB) is becoming more and more resistant to drugs and it is a common problem, making current antimicrobials ineffective and highlighting the need for new TB drugs. One of the promising targets for treating MTB is MurB enzymes. This study aimed to identify potential inhibitors of MurB enzymes in M. tuberculosis, as drug resistance among MTB is a significant problem. Attempts are being made to conduct a virtual screening of 30,417 compounds, and thirty-two compounds were chosen for further analysis based on their binding conformations. The selected compounds were assessed for their drug-likeness, pharmacokinetics, and physiochemical characteristics, and seven compounds with binding energy lower than flavin (FAD) were identified. Further, molecular dynamics simulation analysis of these seven compounds found that four of them, namely DB12983, DB15688, ZINC084726167, and ZINC254071113 formed stable complexes with the MurB binding site, exhibiting promising inhibitory activity. These compounds have not been mentioned in any other study, indicating their novelty. The study suggests that these four compounds could be promising candidates for treating MTB, but their effectiveness needs to be validated through in vitro and in vivo experiments. Overall, the findings of this study provide new insight into potential drug targets and candidates for combating drug-resistant MTB.
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Affiliation(s)
- Ankit Verma
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, India 248140
| | - Vijay Kumar
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, India 248140
| | - Bindu Naik
- Department of Food Science and Technology, Graphic Era (Deemed to be University), Bell Road, Clement Town, Dehradun 248002, Uttarakhand, India
| | - Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia
| | - Pallavi Singh
- Department of Biotechnology, Graphic Era (Deemed to be University), Bell Road, Clement town, 248002 Dehradun, Uttarakhand, India
| | - Per Erik Joakim Saris
- Department of Microbiology, Faculty of Agriculture and Forestry, University of Helsinki, Finland
| | - Sanjay Gupta
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, India 248140
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3
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Anti-Tuberculosis Mur Inhibitors: Structural Insights and the Way Ahead for Development of Novel Agents. Pharmaceuticals (Basel) 2023; 16:ph16030377. [PMID: 36986477 PMCID: PMC10058398 DOI: 10.3390/ph16030377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Mur enzymes serve as critical molecular devices for the synthesis of UDP-MurNAc-pentapeptide, the main building block of bacterial peptidoglycan polymer. These enzymes have been extensively studied for bacterial pathogens such as Escherichia coli and Staphylococcus aureus. Various selective and mixed Mur inhibitors have been designed and synthesized in the past few years. However, this class of enzymes remains relatively unexplored for Mycobacterium tuberculosis (Mtb), and thus offers a promising approach for drug design to overcome the challenges of battling this global pandemic. This review aims to explore the potential of Mur enzymes of Mtb by systematically scrutinizing the structural aspects of various reported bacterial inhibitors and implications concerning their activity. Diverse chemical scaffolds such as thiazolidinones, pyrazole, thiazole, etc., as well as natural compounds and repurposed compounds, have been reviewed to understand their in silico interactions with the receptor or their enzyme inhibition potential. The structural diversity and wide array of substituents indicate the scope of the research into developing varied analogs and providing valuable information for the purpose of modifying reported inhibitors of other multidrug-resistant microorganisms. Therefore, this provides an opportunity to expand the arsenal against Mtb and overcome multidrug-resistant tuberculosis.
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4
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Kumari M, Singh R, Subbarao N. Exploring the interaction mechanism between potential inhibitor and multi-target Mur enzymes of mycobacterium tuberculosis using molecular docking, molecular dynamics simulation, principal component analysis, free energy landscape, dynamic cross-correlation matrices, vector movements, and binding free energy calculation. J Biomol Struct Dyn 2022; 40:13497-13526. [PMID: 34662260 DOI: 10.1080/07391102.2021.1989040] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Multi-targeting enzyme approaches are considered to be the most significant in suppressing pathogen growth and disease control for MDR and XDR-resistant Mycobacterium tuberculosis. The multiple Mur enzymes involved in peptidoglycan biosynthesis play a key role in a cell's growth. Firstly, homology modeling was employed to construct the 3 D structure of the Mur enzymes. The computational approaches, including molecular docking and molecular dynamics simulations and MM-PBSA methods, were performed to explore the detailed interaction mechanism to evaluate the inhibitory activity against targeted proteins. The computational calculations revealed that the best-docked phytochemical compound (gallomyricitrin) inhibits the selected targets: Mur enzymes by forming stable hydrogen bonds. The analysis of RMSD, RMSF, Rg, PCA, DCCM, cross-correlation network, FEL, H-bond, and vector movement reveal that the docked complex of MurA, MurI, MurG, MurC, and MurE is more stable compared to MurB, MurF, MurD, and MurX docked complexes during MD simulations. Moreover, FEL exposed that gallomyricitrin stabilized to the minimum global energy of Mur Enzymes. The PCA, DCCM, and vector movements and binding free energy results provided further evidence for the stability of gallomyricitrin's interactions inside the binding sites by forming hydrogen bonds. The cross-correlation analysis reveals that Mur enzymes exhibit a positive and negative correlated motion between residues in different protein domains. The computational results contribute in several ways to our understanding of inhibition activity and provide a basic insight into the binding activity of gallomyricitrin as a multi-target drug for tuberculosis. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Madhulata Kumari
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ruhar Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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5
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Kumari M, Waseem M, Subbarao N. Discovery of multi-target mur enzymes inhibitors with anti-mycobacterial activity through a Scaffold approach. J Biomol Struct Dyn 2022; 41:2878-2899. [PMID: 35174764 DOI: 10.1080/07391102.2022.2040593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In the present study, we generated a ligand-based scaffold model from a known bioactive datasets of mur enzymes of other species to identify multi-targeting inhibitors as antitubercular agents. Compounds in the ChEMBL database were first filtered to screen for substructure molecules ofMtb's multi-target enzymes. 5'-O-(5-Amino-5-deoxy-β-D-ribofuranosyl)uridine has been identified as scaffold to develop compounds targeting Mtb's mur enzymes. A library of Murcko scaffolds was extracted and evaluated for their in-silico antitubercular activity against Mtb's mur enzymes. The screened compounds were subjected to molecular docking, molecular dynamics simulations, MM/PBSA calculation with Mtb's mur enzymes to evaluate the mechanism of interaction to assess inhibitory activity against the target protein. The results revealed that 15 compounds have higher docking scores and good interactions with multiple mur enzymes of Mtb. From the docking analysis, compound HPT had the best score and binding affinity with the all mur enzymes. Further, protein-ligand interactions were evaluated by molecular dynamics simulations to assess their stability throughout 100 ns period. From the MD trajectory, we calculated RMSD, RMSF, Rg, PCA, DCCM, FEL, hydrogen bonding, and vector motion. Furthermore, the binding free energies of the all nine mur enzymes with compound HPT exhibited good binding affinity might show the anti-mycobacterial activity. The compound HPT revealed from this computational study could act as potent anti-mycobacterial inhibitors and further serve as lead scaffolds to develop more potent pharmaceutical molecules targeting multiple mur enzymes of Mtb based on 5'-O-(5-Amino-5-deoxy-β-D-ribofuranosyl)uridine in the future. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Madhulata Kumari
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mohd Waseem
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Naidu Subbarao
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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6
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Privalsky TM, Soohoo AM, Wang J, Walsh CT, Wright GD, Gordon EM, Gray NS, Khosla C. Prospects for Antibacterial Discovery and Development. J Am Chem Soc 2021; 143:21127-21142. [PMID: 34860516 PMCID: PMC8855840 DOI: 10.1021/jacs.1c10200] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The rising prevalence of multidrug-resistant bacteria is an urgent health crisis that can only be countered through renewed investment in the discovery and development of antibiotics. There is no panacea for the antibacterial resistance crisis; instead, a multifaceted approach is called for. In this Perspective we make the case that, in the face of evolving clinical needs and enabling technologies, numerous validated antibacterial targets and associated lead molecules deserve a second look. At the same time, many worthy targets lack good leads despite harboring druggable active sites. Creative and inspired techniques buoy discovery efforts; while soil screening efforts frequently lead to antibiotic rediscovery, researchers have found success searching for new antibiotic leads by studying underexplored ecological niches or by leveraging the abundance of available data from genome mining efforts. The judicious use of "polypharmacology" (i.e., the ability of a drug to alter the activities of multiple targets) can also provide new opportunities, as can the continued search for inhibitors of resistance enzymes with the capacity to breathe new life into old antibiotics. We conclude by highlighting available pharmacoeconomic models for antibacterial discovery and development while making the case for new ones.
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Affiliation(s)
- Thomas M. Privalsky
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States
| | - Alexander M. Soohoo
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, United States
| | - Jinhua Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, United States,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 United States
| | - Christopher T. Walsh
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States,Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States
| | - Gerard D. Wright
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8N 3Z5, Canada
| | - Eric M. Gordon
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States,Department of Medicine, Stanford University, Stanford, CA 94305, United States
| | - Nathanael S. Gray
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States,Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, United States
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA 94305, United States,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, United States,Stanford ChEM-H, Stanford University, Stanford, CA 94305, United States,Corresponding Author: Correspondence to
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7
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Shinde Y, Ahmad I, Surana S, Patel H. The Mur Enzymes Chink in the Armour of Mycobacterium tuberculosis cell wall. Eur J Med Chem 2021; 222:113568. [PMID: 34118719 DOI: 10.1016/j.ejmech.2021.113568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 02/02/2023]
Abstract
TUBERCULOSIS: (TB) transmitted by Mycobacterium tuberculosis (Mtb) is one of the top 10 causes of death globally. Currently, the widespread occurrence of resistance toward Mtb strains is becoming a significant concern to public health. This scenario exaggerated the need for the discovery of novel targets and their inhibitors. Targeting the "Mtb cell wall peptidoglycan synthesis" is an attractive strategy to overcome drug resistance. Mur enzymes (MurA-MurF) play essential roles in the peptidoglycan synthesis by catalyzing the ligation of key amino acid residues to the stem peptide. These enzymes are unique and confined to the eubacteria and are absent in humans, representing potential targets for anti-tubercular drug discovery. Mtb Mur ligases with the same catalytic mechanism share conserved amino acid regions and structural features that can conceivably exploit for the designing of the inhibitors, which can simultaneously target more than one isoforms (MurC-MurF) of the enzyme. In light of these findings in the current review, we have discussed the recent advances in medicinal chemistry of Mtb Mur enzymes (MurA-MurF) and their inhibitors, offering attractive multi-targeted strategies to combat the problem of drug-resistant in M. tuberculosis.
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Affiliation(s)
- Yashodeep Shinde
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India
| | - Iqrar Ahmad
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India
| | - Sanjay Surana
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India
| | - Harun Patel
- Department of Pharmaceutical Chemistry, R. C. Patel Institute of Pharmaceutical Education and Research, Shirpur, District Dhule, 425405, Maharashtra, India.
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8
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Screening of compound library identifies novel inhibitors against the MurA enzyme of Escherichia coli. Appl Microbiol Biotechnol 2021; 105:3611-3623. [PMID: 33860835 DOI: 10.1007/s00253-021-11272-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 03/27/2021] [Accepted: 04/05/2021] [Indexed: 11/27/2022]
Abstract
Bacterial cell has always been an attractive target for anti-infective drug discovery. MurA (UDP-N-acetylglucosamine enolpyruvyl transferase) enzyme of Escherichia coli (E.coli) is crucial for peptidoglycan biosynthetic pathway, as it is involved in the early stages of bacterial cell wall biosynthesis. In the present study we aim to identify novel chemical structures targeting the MurA enzyme. For screening purpose, we used in silico approach (pharmacophore based strategy) for 52,026 library compounds (Chembridge, Chemdiv and in house synthetics) which resulted in identification of 50 compounds. These compounds were screened in vitro against MurA enzyme and release of inorganic phosphate (Pi) was estimated. Two compounds (IN00152 and IN00156) were found to inhibit MurA enzyme > 70% in primary screening and IC50 of 14.03 to 32.30 μM respectively. These two hits were further evaluated for their mode of inhibition studies and whole-cell activity where we observed 2-4 folds increase in activity in presence of Permeabilizer EDTA (Ethylenediaminetetraacetic acid). Combination studies were also performed with known antibiotics in presence of EDTA. Hits are reported for the first time against this target and our report also support the use of OM permeabilizer in combination with antibacterial compounds to address the permeability and efficacy issue. These lead hits can be further optimized for drug discovery. KEY POINTS: • Emerging Gram negative resistant strains is a matter of concern. • Need for new screening strategies to cope with drying up antibiotics pipeline. • Outer membrane permeabilizers could be useful to improve potency of molecules to reach its target.
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9
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Design and Synthesis of Various 5'-Deoxy-5'-(4-Substituted-1,2,3-Triazol-1-yl)-Uridine Analogues as Inhibitors of Mycobacterium tuberculosis Mur Ligases. Molecules 2020; 25:molecules25214953. [PMID: 33114668 PMCID: PMC7663697 DOI: 10.3390/molecules25214953] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 01/06/2023] Open
Abstract
The synthesis of hitherto unknown 5′-deoxy-5′-(4-substituted-1,2,3-triazol-1-yl)-uridine and its evaluation, through an one-pot screening assay, against MurA-F enzymes involved in Mycobacterium tuberculosis (Mtb), are described. Starting from UDP-N-acetylmuramic acid (UDP-MurNAc), the natural substrate involved in the peptidoglycan biosynthesis, our strategy was to substitute the diphosphate group of UDP-MurNAc by a 1,2,3-triazolo spacer under copper-catalyzed azide-alkyne cycloaddition conditions. The structure-activity relationship was discussed and among the 23 novel compounds developed, N-acetylglucosamine analogues 11c and 11e emerged as the best inhibitors against the Mtb MurA-F enzymes reconstruction pathway with an inhibitory effect of 56% and 50%, respectively, at 100 μM. Both compounds are selective inhibitors of Mtb MurE, the molecular docking and molecular dynamic simulation suggesting that 11c and 11e are occupying the active site of Mtb MurE ligase.
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10
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Kurnia D, Apriyanti E, Soraya C, Satari MH. Antibacterial Flavonoids Against Oral Bacteria of Enterococcus Faecalis ATCC 29212 from Sarang Semut (Myrmecodia pendans) and Its Inhibitor Activity Against Enzyme MurA. Curr Drug Discov Technol 2020; 16:290-296. [PMID: 30152286 DOI: 10.2174/1570163815666180828113920] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/23/2018] [Accepted: 08/16/2018] [Indexed: 01/28/2023]
Abstract
BACKGROUND A significant number of antibiotics are known to inhibit peptidoglycan synthesis in the cross-linking stage, while the drug fosfomycin is the only one known to inhibit MurA. Escalated antibiotic resistance has had an impact on the efficacy of fosfomycin, thus demanding the discovery of suitable substitutes with improved potential for MurA inhibition. The aim of this work is to isolate antibacterial compounds from Sarang Semut (Myrmecodia pendans) and to evaluate their antibacterial activity against pathogenic oral bacteria of Enterococcus faecalis ATCC 29212 and inhibitory activity against MurA enzyme. METHODS The antibacterial compounds from Sarang Semut were isolated by a bioactivity-guided separation method with various solvents and combination of column chromatography on normal and reverse phases. The compounds with concentrations of 1000 and 5000 ppm were assessed against E. faecalis ATCC 29212 by agar well diffusion method, with chlorhexidine and fosfomycin being used as positive controls. RESULTS Two antibacterial compounds isolated from Sarang Semut were identified as two new flavonoids derivates of 1 (10 mg) and 2 (4 mg). Both compounds were tested for antibacterial activities against E. faecalis. MIC values of compounds 1 and 2 were 8.15 and 8.05 mm at 1000 ppm and 8.62 and 8.55 mm at 5000 ppm, respectively. MBC values were 156 and 625 ppm for 1 and 625 and 2500 ppm for 2, respectively. In an inhibitory murA enzyme activity assay, compounds 1 and 2 were shown to inhibit the enzyme activity by IC50 values of 21.7 and 151.3 ppm. CONCLUSION The study demonstrated that ethyl acetate fraction of Sarang Semut contained antibacterial flavonoids as active constituents that showed activity against E. faecalis. These results showed the plant's potential in herbal medicine and the development of new antibacterial agent for pathogenic dental caries.
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Affiliation(s)
- Dikdik Kurnia
- Department of Chemistry, Faculty of Mathematic and Natural Sciences, Universitas Padjadjaran-Bandung, Sumedang, Indonesia
| | - Eti Apriyanti
- Department of Chemistry, Faculty of Mathematic and Natural Sciences, Universitas Padjadjaran-Bandung, Sumedang, Indonesia
| | - Cut Soraya
- Department of Concervative Dentistry, Faculty of Dentistry, Syiah Kuala Universty, Banda Aceh, Indonesia
| | - Mieke H Satari
- Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran-Bandung, Sumedang, Indonesia
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11
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Maitra A, Munshi T, Healy J, Martin LT, Vollmer W, Keep NH, Bhakta S. Cell wall peptidoglycan in Mycobacterium tuberculosis: An Achilles' heel for the TB-causing pathogen. FEMS Microbiol Rev 2020; 43:548-575. [PMID: 31183501 PMCID: PMC6736417 DOI: 10.1093/femsre/fuz016] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/07/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB), caused by the intracellular pathogen Mycobacterium tuberculosis, remains one of the leading causes of mortality across the world. There is an urgent requirement to build a robust arsenal of effective antimicrobials, targeting novel molecular mechanisms to overcome the challenges posed by the increase of antibiotic resistance in TB. Mycobacterium tuberculosis has a unique cell envelope structure and composition, containing a peptidoglycan layer that is essential for maintaining cellular integrity and for virulence. The enzymes involved in the biosynthesis, degradation, remodelling and recycling of peptidoglycan have resurfaced as attractive targets for anti-infective drug discovery. Here, we review the importance of peptidoglycan, including the structure, function and regulation of key enzymes involved in its metabolism. We also discuss known inhibitors of ATP-dependent Mur ligases, and discuss the potential for the development of pan-enzyme inhibitors targeting multiple Mur ligases.
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Affiliation(s)
- Arundhati Maitra
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Tulika Munshi
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Jess Healy
- Department of Pharmaceutical and Biological Chemistry, UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Liam T Martin
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Nicholas H Keep
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
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12
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Kumar P, Saumya KU, Giri R. Identification of peptidomimetic compounds as potential inhibitors against MurA enzyme of Mycobacterium tuberculosis. J Biomol Struct Dyn 2019; 38:4997-5013. [PMID: 31755364 DOI: 10.1080/07391102.2019.1696231] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Increasing prevalence of resistance to anti-tubercular drugs has become the foremost challenge now. According to WHO, over half a million of multidrug resistance cases (rifampicin, isoniazid, etc.) were reported in 2017, mostly emerging from countries such as China, India, and Russia. Therefore, developing new drugs or repurposing existing ones is need of the hour. The Mycobacterium cell wall biogenesis pathway offers many attractive targets for drug discovery against Tuberculosis (TB). MurA, a transferase enzyme that catalyzes the initial step of peptidoglycan (PG) biosynthesis, is one among them. A peptidoglycan layer resides over the plasma membrane and is an integral component of the bacterial cell wall. Therefore, disruption of their formation through inhibition of MurA enzyme should lead to deficiency in Mycobacterium cell synthesis. Based on this strategy, we have designed this study where two libraries of peptidomimetic compounds (Asinex & ChemDiv) were first screened against our modeled MurA structure and then validated through molecular dynamic simulations. From our virtual screening, top four compounds (ChemDiv: D675-0102, D675-0217; Asinex: BDE25373574, BDE 26717803) were selected based on their docking scores, binding energies, and interactions with catalytic site residues, for further evaluation. Results revealed stable ligand-MurA interactions throughout 50 ns of MD simulation and also druggability acceptable pharmacokinetic profile for all four compounds. Thus, based on our findings, these compounds could be considered as potential inhibitors of Mycobacterium MurA enzyme and hence be further tested for in vitro experimental validation as TB therapeutic drug candidate.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Kumar Udit Saumya
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India.,BioX Centre, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
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13
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Eniyan K, Rani J, Ramachandran S, Bhat R, Khan IA, Bajpai U. Screening of Antitubercular Compound Library Identifies Inhibitors of Mur Enzymes in Mycobacterium tuberculosis. SLAS DISCOVERY 2019; 25:70-78. [PMID: 31597510 DOI: 10.1177/2472555219881148] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The rapid rise in the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains of Mycobacterium tuberculosis (Mtb) mandates the discovery of novel tuberculosis (TB) drugs. Mur enzymes, which are identified as essential proteins in Mtb and catalyze the cytoplasmic steps in the peptidoglycan biosynthetic pathway, are considered potential drug targets. However, none of the clinical drugs have yet been developed against these enzymes. Hence, the aim of this study was to identify novel inhibitors of Mur enzymes in Mycobacterium tuberculosis. We screened an antitubercular compound library of 684 compounds, using MurB and MurE enzymes of the Mtb Mur pathway as drug targets. For experimental validation, the top hits obtained on in silico screening were screened in vitro, using Mtb Mur enzyme-specific assays. In all, seven compounds were found to show greater than 50% inhibition, with the highest inhibition observed at 77%, and the IC50 for these compounds was found to be in the range of 28-50 μM. Compound 5175112 showed the lowest IC50 (28.69 ± 1.17 μM), and on the basis of (1) the binding affinity, (2) the stability of interaction noted on molecular dynamics simulation, and (3) an in vitro assay, MurE appeared to be its target enzyme. We believe that the overall strategy followed in this study and the results obtained are a good starting point for developing Mur enzyme-specific Mtb inhibitors.
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Affiliation(s)
- Kandasamy Eniyan
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Jyoti Rani
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India.,Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Srinivasan Ramachandran
- Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Rahul Bhat
- Clinical Microbiology Division, Council of Scientific and Industrial Research-Indian Institute of Integrative Medicine (CSIR-IIIM), Jammu, India
| | - Inshad Ali Khan
- Clinical Microbiology Division, Council of Scientific and Industrial Research-Indian Institute of Integrative Medicine (CSIR-IIIM), Jammu, India
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India
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14
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Rani J, Silla Y, Borah K, Ramachandran S, Bajpai U. Repurposing of FDA-approved drugs to target MurB and MurE enzymes in Mycobacterium tuberculosis. J Biomol Struct Dyn 2019; 38:2521-2532. [PMID: 31244382 DOI: 10.1080/07391102.2019.1637280] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb) is one amongst the top 10 causes of death worldwide. The growing rise in antibiotic resistance compounded with slow and expensive drug discovery has further aggravated the situation. 'Drug repurposing' is a promising approach where known drugs are examined for a new indication. In the present study, we have attempted to identify drugs that could target MurB and MurE enzymes involved in the muramic acid synthesis pathway (Mur Pathway) in Mtb. FDA-approved drugs from two repositories i.e. Drug Bank (1932 drugs) and e-LEA3D (1852 drugs) were screened against these proteins. Several criteria were applied to study the protein-drug interactions and the consensus drugs were further studied by molecular dynamics (MD) simulation. Our study found Sulfadoxine (-7.3 kcal/mol) and Pyrimethamine (-7.8 kcal/mol) to show stable interaction with MurB while Lifitegrast (-10.5 kcal/mol) and Sildenafil (-9.1 kcal/mol) showed most reliable interaction with MurE. Furthermore, binding free energy (ΔGbind), RMSD and RMSF data and the number of hydrogen bonds corroborated the stability of interactions and hence these drugs for repurposing should be explored further.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jyoti Rani
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India.,G. N. Ramachandran Knowledge of Centre, Council of Scientific and Industrial Research - Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Yumnam Silla
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, India
| | - Kasmika Borah
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, India
| | - Srinivasan Ramachandran
- G. N. Ramachandran Knowledge of Centre, Council of Scientific and Industrial Research - Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India
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15
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Miyachiro MM, Granato D, Trindade DM, Ebel C, Paes Leme AF, Dessen A. Complex Formation between Mur Enzymes from Streptococcus pneumoniae. Biochemistry 2019; 58:3314-3324. [DOI: 10.1021/acs.biochem.9b00277] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Mayara M. Miyachiro
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, São Paulo, Brazil
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), F-38000 Grenoble, France
| | - Daniela Granato
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, São Paulo, Brazil
| | - Daniel Maragno Trindade
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, São Paulo, Brazil
| | - Christine Ebel
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), F-38000 Grenoble, France
| | | | - Andréa Dessen
- Brazilian Biosciences National Laboratory (LNBio), CNPEM, Campinas 13084-971, São Paulo, Brazil
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), F-38000 Grenoble, France
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16
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Jukič M, Gobec S, Sova M. Reaching toward underexplored targets in antibacterial drug design. Drug Dev Res 2018; 80:6-10. [PMID: 30312991 DOI: 10.1002/ddr.21465] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/13/2018] [Accepted: 08/15/2018] [Indexed: 01/03/2023]
Abstract
The increase of antimicrobial resistance necessitates the renewal and strong research involvement in antibacterial drug design. In the following work, we comment on the key approaches used in development of new antibacterials, focusing on intracellular therapeutic targets that have been so far mostly underexplored: the enzymes of the Mur pathway MurA to MurF. We identify common obstacles observed during research on MurA, MurB, and Mur ligases inhibitors and their development into potential antibacterial compounds, and discern several approaches and solutions to tackle the whole-cell activity of designed compounds. Furthermore, we consolidate recent literature reports and encourage the further research on Mur enzymes.
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Affiliation(s)
- Marko Jukič
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Stanislav Gobec
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
| | - Matej Sova
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
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17
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Hameed HMA, Islam MM, Chhotaray C, Wang C, Liu Y, Tan Y, Li X, Tan S, Delorme V, Yew WW, Liu J, Zhang T. Molecular Targets Related Drug Resistance Mechanisms in MDR-, XDR-, and TDR- Mycobacterium tuberculosis Strains. Front Cell Infect Microbiol 2018; 8:114. [PMID: 29755957 PMCID: PMC5932416 DOI: 10.3389/fcimb.2018.00114] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 03/23/2018] [Indexed: 01/08/2023] Open
Abstract
Tuberculosis (TB) is a formidable infectious disease that remains a major cause of death worldwide today. Escalating application of genomic techniques has expedited the identification of increasing number of mutations associated with drug resistance in Mycobacterium tuberculosis. Unfortunately the prevalence of bacillary resistance becomes alarming in many parts of the world, with the daunting scenarios of multidrug-resistant tuberculosis (MDR-TB), extensively drug-resistant tuberculosis (XDR-TB) and total drug-resistant tuberculosis (TDR-TB), due to number of resistance pathways, alongside some apparently obscure ones. Recent advances in the understanding of the molecular/ genetic basis of drug targets and drug resistance mechanisms have been steadily made. Intriguing findings through whole genome sequencing and other molecular approaches facilitate the further understanding of biology and pathology of M. tuberculosis for the development of new therapeutics to meet the immense challenge of global health.
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Affiliation(s)
- H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yang Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Institute of Health Sciences, Anhui University, Hefei, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Vincent Delorme
- Tuberculosis Research Laboratory, Institut Pasteur Korea, Seongnam-si, South Korea
| | - Wing W Yew
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
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18
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de Oliveira Viana J, Scotti MT, Scotti L. Molecular Docking Studies in Multitarget Antitubercular Drug Discovery. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2018. [DOI: 10.1007/7653_2018_28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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19
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Eniyan K, Dharavath S, Vijayan R, Bajpai U, Gourinath S. Crystal structure of UDP-N-acetylglucosamine-enolpyruvate reductase (MurB) from Mycobacterium tuberculosis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:397-406. [PMID: 29203374 DOI: 10.1016/j.bbapap.2017.11.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 11/23/2017] [Accepted: 11/28/2017] [Indexed: 01/07/2023]
Abstract
The biosynthesis of UDP-N-acetylmuramic acid (UDP-MurNAc) by reduction of UDP-N-acetylglucosamine-enolpyruvate (UDP-GlcNAc-EP) in an NADPH and FAD-dependent reaction in bacteria is one of the key steps in peptidoglycan biosynthesis catalyzed by UDP-N-acetylglucosamine-enolpyruvate reductase (MurB). Here, we present the crystal structure of Mycobacterium tuberculosis MurB (MtbMurB) with FAD as the prosthetic group at 2.0Å resolution. There are six molecules in asymmetric unit in the form of dimers. Each protomer can be subdivided into three domains and the prosthetic group, FAD is bound in the active site between domain I and domain II. Comparison of MtbMurB structure with the structures of the Escherichia coli MurB (in complex with UDP-GlcNAc-EP) and Pseudomonas aeruginosa MurB (in complex with NADPH) showed all three structures share similar domain architecture and residues in the active site. The nicotinamide and the enol pyruvyl moieties are well aligned upon superimposition, both positioned in suitable position for hydride transfer to and from FAD. The comparison studies and MD simulations demonstrate that the two lobes of domain-III become more flexible. The substrates (NADPH and UDP-GlcNAc-EP) binding responsible for open conformation of MurB, suggesting that NADPH and UDP-GlcNAc-EP interactions are conformationally stable. Our findings provide a detail mechanism about the closed to open state by binding of NADPH and UDP-GlcNAc-EP induces the conformational changes of MurB structure that may trigger the MurB catalytic reaction.
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Affiliation(s)
- Kandasamy Eniyan
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | | | | | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India.
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