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N MP, C GPD, R M. Exploring natural products library to identify potential inhibitors targeting isoniazid-resistant tuberculosis. J Biomol Struct Dyn 2023:1-15. [PMID: 37993985 DOI: 10.1080/07391102.2023.2283159] [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: 07/13/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023]
Abstract
Mycobacterium tuberculosis (MTB) causing tuberculosis (TB) infection is a leading source of illness and death in developing nations, and the emergence of drug-resistant TB remains a significant global threat and a challenge in treating the disease. Mutations in the inhA and katG genes are connected to the principal molecular mechanism of isoniazid (INH) resistance, and continuous treatment of INH for more than a decade led to the evolution of INH resistant-TB (inhR-TB). Structure-based drug discovery approaches on traditional natural compounds are the contemporary source to identify significant lead molecules. This work focuses on discovering effective small compounds from natural compound libraries and applying pharmacophore-based virtual screening to filter out the molecules. The best-identified hit complexes were used for molecular dynamics simulations (MDS) to observe their stability and compactness. A three-dimensional e-pharmacophore hypothesis and screening generated 62 hits based on phase fitness scores from the pharmacophore-based virtual screening. Molecular docking experiments in Maestro's GLIDE module indicated that ZINC000002383126 and ASN22022 may be potential inhibitors of inhA and katG (native, inhA mutants S94A, Y158A, Y158F and Y158S and D137S, Y229F, S315T, W321F, and R418L mutants of katG). In addition, MDS analysis indicated that the native and mutant docked complexes of inhA and katG had good stability and remained compact in the binding pocket of the targets. In vitro studies can further validate the compounds that can act as INH competitive inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Madhana Priya N
- Department of Biotechnology, Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
| | - George Priya Doss C
- Laboratory of Integrative Genomics, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Magesh R
- Department of Biotechnology, Faculty of Biomedical Sciences & Technology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
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2
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Yadav A, Kesharwani A, Chaurasia DK, Katara P. Mining of molecular insights of CYP2A6 and its variants complex with coumarin (CYP2A6*-coumarin) using molecular dynamics simulation. J Biomol Struct Dyn 2023; 41:4081-4092. [PMID: 35427216 DOI: 10.1080/07391102.2022.2062785] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/02/2022] [Indexed: 10/18/2022]
Abstract
CYP2A6 is a very important enzyme that plays a crucial role in nicotine compounds and is responsible for the metabolism of more than 3% drugs of total metabolized drugs by the CYP family and reported as one of very important pharmacogenes. CYP2A6 is highly polymorphic in nature and reported with more than 40 variants, most of these variants are SNPs originated and population specific. It has been well observed and reported that the presence of these population-specific non-synonymous SNPs in CYP2A6 alters the rate of drug metabolism and as a functional consequence, drugs produce an abnormal response. Though genomics and pharmacogenomics studies are there, very less is known about the structural effects of these SNPs on molecular-interaction and folding of CYP2A6. To fill the knowledge gap, SNPs based four variants, i.e., CYP2A6*2, CYP2A6*18, CYP2A6*21, and CYP2A6*35, which are frequently reported in the South Asian population, were considered for the study. Coumarin (DB04665), a well reported drug, is considered as a model substance, and the effect of all four variants on 'CYP2A6*-coumarin' complex was studied. MD simulation-based analysis (at 200 ns) was performed and comparative analysis with respect to wild type 'CYP2A6-coumarin' complex was done. Though observation didn't find any global effect on complete complex but found some crucial minor-local alteration in interaction and folding process. It is assumed that the change due to SNPs in the single amino acid did not bring global change in physiochemical properties of CYP2A6* but caused local-trivial changes which are very crucial for its metabolic activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anamika Yadav
- Computational omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj, India
| | - Akanksha Kesharwani
- Computational omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj, India
- Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Dheeraj Kumar Chaurasia
- Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Pramod Katara
- Computational omics Lab, Centre of Bioinformatics, University of Allahabad, Prayagraj, India
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Gavadia R, Rasgania J, Basil MV, Chauhan V, Kumar S, Jakhar K. Synthesis of Isoniazid analogs with Promising Antituberculosis Activity and Bioavailability: Biological Evaluation and Computational Studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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Barozi V, Musyoka TM, Sheik Amamuddy O, Tastan Bishop Ö. Deciphering Isoniazid Drug Resistance Mechanisms on Dimeric Mycobacterium tuberculosis KatG via Post-molecular Dynamics Analyses Including Combined Dynamic Residue Network Metrics. ACS OMEGA 2022; 7:13313-13332. [PMID: 35474779 PMCID: PMC9025985 DOI: 10.1021/acsomega.2c01036] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/22/2022] [Indexed: 05/12/2023]
Abstract
Resistance mutations in Mycobacterium tuberculosis (Mtb) catalase peroxidase protein (KatG), an essential enzyme in isoniazid (INH) activation, reduce the sensitivity of Mtb to first-line drugs, hence presenting challenges in tuberculosis (TB) management. Thus, understanding the mutational imposed resistance mechanisms remains of utmost importance in the quest to reduce the TB burden. Herein, effects of 11 high confidence mutations in the KatG structure and residue network communication patterns were determined using extensive computational approaches. Combined traditional post-molecular dynamics analysis and comparative essential dynamics revealed that the mutant proteins have significant loop flexibility around the heme binding pocket and enhanced asymmetric protomer behavior with respect to wild-type (WT) protein. Heme contact analysis between WT and mutant proteins identified a reduction to no contact between heme and residue His270, a covalent bond vital for the heme-enabled KatG catalytic activity. Betweenness centrality calculations showed large hub ensembles with new hubs especially around the binding cavity and expanded to the dimerization domain via interface in the mutant systems, providing possible compensatory allosteric communication paths for the active site as a result of the mutations which may destabilize the heme binding pocket and the loops in its vicinity. Additionally, an interesting observation came from Eigencentrality hubs, most of which are located in the C-terminal domain, indicating relevance of the domain in the protease functionality. Overall, our results provide insight toward the mechanisms involved in KatG-INH resistance in addition to identifying key regions in the enzyme functionality, which can be used for future drug design.
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Affiliation(s)
- Victor Barozi
- Research Unit in Bioinformatics
(RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140 South Africa
| | - Thommas Mutemi Musyoka
- Research Unit in Bioinformatics
(RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140 South Africa
| | - Olivier Sheik Amamuddy
- Research Unit in Bioinformatics
(RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140 South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics
(RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda 6140 South Africa
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Raphoko LA, Lekgau K, Lebepe CM, Leboho TC, Matsebatlela TM, Nxumalo W. Synthesis of novel quinoxaline-alkynyl derivatives and their anti-Mycobacterium tuberculosis activity. Bioorg Med Chem Lett 2021; 35:127784. [PMID: 33422606 DOI: 10.1016/j.bmcl.2021.127784] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/29/2020] [Accepted: 01/03/2021] [Indexed: 11/26/2022]
Abstract
The study report on the synthesis of a series of novel quinoxaline-alkynyl derivatives that were evaluated for their activity against Mycobacterium tuberculosis (Mtb) H37RV strain. A total of 19 compounds bearing an alcohol, aldehyde, mesylate and ester groups on the alkynly group, and also containing a chloro and nitro groups at the 6-position, were prepared. Seven compounds (3c, 4a-b, 5a, 5c, 6c and 6i), were found to have MIC90 < 10 µM, while five compounds (3b, 6a, 6b, 6d and 6h) had MIC90 in the range 10-20 µM. Compounds bearing a nitro substituent in the 6-position were generally more active and demonstrated a better safety profile, when compared to the unsubstituted and 6-chloro derivatives. Of the seven most active compounds, four contained nitro group at the 6-position.
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Affiliation(s)
- Lerato A Raphoko
- Department of Chemistry, Faculty of Science and Agriculture, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa
| | - Karabo Lekgau
- Department of Chemistry, Faculty of Science and Agriculture, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa
| | - Charity M Lebepe
- Department of Chemistry, Faculty of Science and Agriculture, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa
| | - Tlabo C Leboho
- Department of Chemistry, Faculty of Science and Agriculture, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa
| | - Thabe M Matsebatlela
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Science and Agriculture, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa
| | - Winston Nxumalo
- Department of Chemistry, Faculty of Science and Agriculture, University of Limpopo, Private Bag X1106, Sovenga 0727, South Africa.
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Al-Khafaji K, Taskin Tok T. Molecular dynamics simulation, free energy landscape and binding free energy computations in exploration the anti-invasive activity of amygdalin against metastasis. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 195:105660. [PMID: 32726718 DOI: 10.1016/j.cmpb.2020.105660] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND OBJECTIVE Historically, amygdalin has been used as alternative medicine or in vitro and in vivo studies, but no single study exists which discusses the structural mechanism of amygdalin at a molecular level. This paper inquiries into the inhibitory actions of amygdalin on the selected targets: AKT1, FAK, and ILK, which are regulators for various mediated signaling pathways, and are associated with cell adhesion, migration, and differentiation. In order to get details at the molecular level of amygdalin's inhibitory activities against chosen proteins, molecular modeling and simulation techniques including double docking, molecular dynamics simulation, free energy landscape analysis, and binding free energy calculation were exerted. METHODS To get molecular level details of amygdalin inhibitory effects against the relevant proteins; here the utilized tools are the following: the double docking, molecular dynamics simulation, free energy landscape analysis, g_mmpbsa, and interaction entropy were used to evaluate the inhibitory activity against targeted proteins. RESULTS The computational calculations revealed that amygdalin inhibits the selected targets via block the ATP-binding pocket of AKT1, FAK, and ILK by forming stable hydrogen bonds. Moreover, free energy landscape, FEL exposed that amygdalin stabilized the global conformations of both FAK and ILK proteins to the minimum global energy besides it reduced the essential dynamics of FAK and ILK proteins. MMPBSA computations provided further evidence for amygdalin's stability inside the ATP-binding pocket of AKT1, FAK, and ILK with a binding free energy of 45.067, -13.033, 13.109 kJ/mol, respectively. The binding free energies are lastly consistent with the hydrogen bonding and pairs within 0.35 nm results. The decomposition of binding energy shows the pivotal amino acid residues responsible for the stability of amygdalin's interactions inside the ATP-binding sites by forming hydrogen bonds. CONCLUSIONS Before this work, it was enigmatic to make predictions about how amygdalin inhibits metastasis of cancer. But the computational results contribute in several ways to our understanding of amygdalin activity and provide a basic insight into the activity of amygdalin as a multi-target drug in the metastasis and invasion of cancer.
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Affiliation(s)
- Khattab Al-Khafaji
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, 27310 Gaziantep, Turkey
| | - Tugba Taskin Tok
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, 27310 Gaziantep, Turkey; Institute of Health Sciences, Department of Bioinformatics and Computational Biology, Gaziantep University, 27310 Gaziantep, Turkey.
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7
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Villamizar-Mogotocoro AF, Vargas-Méndez LY, Kouznetsov VV. Pyridine and quinoline molecules as crucial protagonists in the never-stopping discovery of new agents against tuberculosis. Eur J Pharm Sci 2020; 151:105374. [DOI: 10.1016/j.ejps.2020.105374] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/21/2020] [Accepted: 05/08/2020] [Indexed: 12/13/2022]
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8
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Pharmacoinformatics-based identification of anti-bacterial catalase-peroxidase enzyme inhibitors. Comput Biol Chem 2019; 83:107136. [DOI: 10.1016/j.compbiolchem.2019.107136] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/28/2019] [Accepted: 09/29/2019] [Indexed: 11/17/2022]
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9
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Srivastava G, Darokar MP, Sharma A. Molecular investigation against the resistant mechanism of PncA mutated pyrazinamide resistance and insight into the role of pH environment for pyrazinamide activation. J Biomol Struct Dyn 2019; 38:3411-3431. [PMID: 31448694 DOI: 10.1080/07391102.2019.1659854] [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: 10/26/2022]
Abstract
Pyrazinamide (PZA), a crucial component of anti-TB therapy, is a prodrug. PZA interacts with PncA protein to be converted into its functional form i.e. pyrazinoic acid (POA). It has unique feature to kill dormant tubercle bacilli of acidic environment. Although significance of pH environment in PZA activation has been investigated in several of previous studies, insight into the significant atomistic variations in the interaction pattern of PZA with PncA, at different pH environments, are still required to be explored. On the other hand, continuously emerging PncA mutants, associated with PZA resistance, have also become a serious threat for global TB control program. Therefore, the current study was designed to understand the role of pH environment in the PZA activation and to explore the PZA resistance mechanism in various PncA mutants. The study included various in silico experiments like molecular docking, MD simulation, binding free energy estimation, PCA and FEL. In our study, we have found pH-3 and pH-5 environment as a highly significant environment for PZA activation. It was found that protonation or deprotonation of PZA activation site (PAS) residues, majorly K48, D56, K96 and E107, resulted in rearrangement of the PAS according to the pH conditions. It has also been observed that positioning of PZA binding near to Fe2+ and residues of catalytic triad (i.e. D8, K96 and C138) also play a very crucial role in the activation of PZA. The overall insight from the current study may help to develop new therapeutics against PncA mutated PZA resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gaurava Srivastava
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - M P Darokar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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10
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Reyes YIA, Franco FC. DFT study on the effect of proximal residues on the Mycobacterium tuberculosis catalase-peroxidase (katG) heme compound I intermediate and its bonding interaction with isoniazid. Phys Chem Chem Phys 2019; 21:16515-16525. [PMID: 31298238 DOI: 10.1039/c9cp01465a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Isoniazid (INH) is converted into isonicotinyl radical through its interaction with the catalase-peroxidase (katG) enzyme present in the cells of Mycobacterium tuberculosis (M. tb.), the bacteria that causes the tuberculosis disease. This process is important because resistance of M. tb. cells to INH treatment has been associated with the failure of completion of this process. However, this process is poorly understood and there are a variety of conflicting theories about the details of the mechanism of this process. One theory suggests that INH binds to katG and transfers a single electron to the heme while the heme is in its two electron oxidized state, compound I [Fe(iv)Por˙+] (CpdI). In this study, DFT calculations at the UB3LYP/6-31g(d)-LANL2DZ level of theory are used to study the M. tb. katG CpdI molecule. Different models of the M. tb. CpdI molecule were prepared and the calculations revealed the impact of Trp321 on the electronic properties of the heme. Without Trp321 the heme assumed a triradical state with single electrons on the πxy and πyz orbitals of Fe and another on the a2u orbital of the porphyrin ring that can either be coupled with the first two, to assume a quartet state, or decoupled to form a doublet state. With Trp321, however, a transfer of an electron from the πTrp orbital to a2u porphyrin orbital leads to loss of radical character of the porphyrin and leaves the Trp321 group with a radical character. INH was observed to have strong interaction with CpdI and the absence of Trp321 significantly decreased the binding energy by 2 kcal mol-1 explaining the importance of Trp321 in the binding of INH. The results in this study show the importance of Trp321 in the binding of INH and its effect on its electronic properties, which is consistent with previous experimental findings that mutation of Trp321 results in an increase in drug resistance.
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Affiliation(s)
- Yves Ira A Reyes
- Chemistry Department, De La Salle University, 2401 Taft Avenue, 0922 Manila, Philippines.
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Reyes YIA, Janairo GC, Franco FC. Theoretical insights on the binding of isoniazid to the active site residues of Mycobacterium tuberculosis catalase-peroxidase. Tuberculosis (Edinb) 2019; 114:61-68. [PMID: 30711159 DOI: 10.1016/j.tube.2018.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/29/2018] [Accepted: 11/14/2018] [Indexed: 10/27/2022]
Abstract
Isoniazid (INH) is known to cause the exclusive lethal action to Mycobacterium tuberculosis (M. tb.) cells because of the pathogen's own catalase-peroxidase (katG) enzyme that converts INH to a very reactive radical. Thus, in order to gain insights on the interaction of INH with the individual active site residues (Res) of katG, this study presents a computational approach via molecular docking and density functional theory (DFT) using augmented models to study the individual INH-Res interactions. Seven amino acid residues directly interacts with INH: Arg104, Asp137, His108, Ile228, Trp107, Tyr229, and Val230. The residues with the highest interaction energies are Arg104 (-39.64 kcal/mol) and Asp137 (-32.85 kcal/mol) mainly due to strong ion-dipole and H-bonding interactions present in the complexes, while the weakest interaction was observed for Ile228 (-13.78 kcal/mol). Molecular electrostatic potential surface revealed complementary regions for dipole interactions and charge distribution analysis further shows that INH generally donates electrons to the residues. The results in this study agrees with the previous experimental findings and provides new insights into the catalase dependent activation of INH and the methods presented may be valuable in the study of biological metabolism of molecules.
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Affiliation(s)
- Yves Ira A Reyes
- Chemistry Department, De La Salle University, 2401 Taft Avenue, 0922, Manila, Philippines
| | - Gerardo C Janairo
- Chemistry Department, De La Salle University, 2401 Taft Avenue, 0922, Manila, Philippines
| | - Francisco C Franco
- Chemistry Department, De La Salle University, 2401 Taft Avenue, 0922, Manila, Philippines.
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Ali A, Gupta D, Srivastava G, Sharma A, Khan AU. Molecular and computational approaches to understand resistance of New Delhi metallo β-lactamase variants (NDM-1, NDM-4, NDM-5, NDM-6, NDM-7)-producing strains against carbapenems. J Biomol Struct Dyn 2018; 37:2061-2071. [PMID: 29749296 DOI: 10.1080/07391102.2018.1475261] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The discovery of NDM-1 and its variants has caused the emergence of antibiotic resistance in the community and hospital setting, causing major concern for health care across the globe. New Delhi Metallo-β-lactamase is known to hydrolyse almost all β-lactam antibiotics. Studies have shown the hydrolytic activates of NDM-1 and some of its variants, however a comparative study of these NDM variants has not been explored in detail. Hence, we proposed to check their catalytic activity by performing a comparative study between NDM-1 and its variants. The study was initiated to clone NDM variants (NDM-1, NDM-4, NDM-5, NDM-6 and NDM-7) followed by overexpression of the recombinant proteins to check their hydrolytic properties against β-lactam antibiotics. The minimum inhibitory concentration of carbapenems antibiotics for blaNDM-5 clone was found four fold increased, whereas no change was observed in the clones having other variants. The hydrolytic activity of carbapenem with NDM-5 variant was found to be augmented as per the kinetics parameter where Km was decreased and kcat, kcat/Km values increased as compared to the NDM-1. Molecular docking studies were employed to identify the variations in the binding ability among all NDM variants with imipenem or meropenem. Simulation studies at 100 ns showed a good stability of NDM-5 with imipenem and meropenem as compared to NDM-1. CD spectroscopy data revealed significant changes in the secondary structure of NDM variants. We conclude that NDM-5 showed higher hydrolytic activity as compared to other variants. This study provides a comparative analysis of the severity of NDM producing strains.
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Affiliation(s)
- Abid Ali
- a Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit , Aligarh Muslim University , Aligarh , Uttar Pradhesh 202002 , India
| | - Divya Gupta
- a Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit , Aligarh Muslim University , Aligarh , Uttar Pradhesh 202002 , India.,b Department of Life sciences , Uttarakhand Technical University , Dehradun , Uttarakhand 248007 , India
| | - Gaurava Srivastava
- c Biotechnology Division, CSIR-CIMAP , Lucknow , Uttar Pradhesh 226015 , India
| | - Ashok Sharma
- c Biotechnology Division, CSIR-CIMAP , Lucknow , Uttar Pradhesh 226015 , India
| | - Asad U Khan
- a Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit , Aligarh Muslim University , Aligarh , Uttar Pradhesh 202002 , India
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Srivastava G, Tripathi S, Kumar A, Sharma A. Molecular insight into multiple RpoB clinical mutants of Mycobacterium tuberculosis: An attempt to probe structural variations in rifampicin binding site underlying drug resistance. Int J Biol Macromol 2018; 120:2200-2214. [DOI: 10.1016/j.ijbiomac.2018.06.184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 06/26/2018] [Accepted: 06/28/2018] [Indexed: 10/28/2022]
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14
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Insight into microtubule destabilization mechanism of 3,4,5-trimethoxyphenyl indanone derivatives using molecular dynamics simulation and conformational modes analysis. J Comput Aided Mol Des 2018. [DOI: 10.1007/s10822-018-0109-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Kumar A, Srivastava G, Negi AS, Sharma A. Docking, molecular dynamics, binding energy-MM-PBSA studies of naphthofuran derivatives to identify potential dual inhibitors against BACE-1 and GSK-3β. J Biomol Struct Dyn 2018; 37:275-290. [DOI: 10.1080/07391102.2018.1426043] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Akhil Kumar
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
| | - Gaurava Srivastava
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
| | - Arvind S. Negi
- Chemical Sciences Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
| | - Ashok Sharma
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, P.O. CIMAP, Lucknow 226015, Uttar Pradesh, India
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