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Sethiya A, Joshi D, Manhas A, Sahiba N, Agarwal DK, Jha PC, Agarwal S. Glycerol based carbon sulfonic acid catalyzed synthesis, in silico studies and in vitro biological evaluation of isonicotinohydrazide derivatives as potent antimicrobial and anti-tubercular agents. Heliyon 2023; 9:e13226. [PMID: 36785822 PMCID: PMC9918772 DOI: 10.1016/j.heliyon.2023.e13226] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
The present pathway involves synthesis of isonicotinohydrazide derivatives using isoniazid and diversely substituted aldehydes in the presence of EtOH and catalytic amount of glycerol based carbon sulfonic acid catalyst. The developed pathway has so many merits like excellent yields (91-98%), short reaction time (4-10 min), easy reaction set up, no need of column chromatography, large substrate scope, easily recyclable and reusable catalyst. The synthesized compounds were screened for antimicrobial and anti-tubercular activity and it was observed that compounds possessed high biological potency against the Gram positive and Gram negative bacterial and fungal strains. Regarding anti-tubercular activity, compound 3m exhibited high % inhibition against Mycobacterium tuberculosis H37RV strain. Based on the outcome of in vitro studies, all the synthesized compounds were docked against E. coli (1KZN), C. albicans (1IYL), and M. tuberculosis H 37 Rv strain (2NSD). The synthesized derivatives were docked within the binding site of 1KZN, and 1IYL. However, with 2NSD, apart from 3h, all the derivatives displayed interaction within the binding cavity of the protein. All the crucial interactions with Asn46, Asp73, and Arg136 in 1KZN, His227, Leu451 in 1IYL, and Tyr158 in 2NSD were witnessed in the top-scored docked candidates. Molecular docking studies revealed the importance of the substitution at R position on isonicotinohydrazide scaffold. The nitrogen atoms of hydrazide moiety were involved in forming hydrogen bonding with the active site amino acids, and the substitution at the R position occupy the hydrophobic position in the binding pocket. Also, the functional groups present on the substituted R position were involved in forming hydrogen bonding with the crucial active site residues.
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Affiliation(s)
- Ayushi Sethiya
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, MLSU, Udaipur, Raj., India
| | - Deepkumar Joshi
- Department of Chemistry, M.N. Sheth Science College, HNGU, Patan, Gujarat, India
| | - Anu Manhas
- Department of Chemistry, Pandit Deendayal Energy University, Gandhinagar-382007, Gujarat, India
| | - Nusrat Sahiba
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, MLSU, Udaipur, Raj., India
| | - Dinesh K. Agarwal
- VenkateshwarInsitute of Pharmacy, Sai Tirupati University, Udaipur, Rajasthan, India
| | - Prakash C. Jha
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar-382030, Gujarat, India
| | - Shikha Agarwal
- Synthetic Organic Chemistry Laboratory, Department of Chemistry, MLSU, Udaipur, Raj., India,Corresponding author.
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Paul RK, Ahmad I, Patel H, Kumar V, Raza K. Phytochemicals from Amberboa ramosa as potential DPP-IV inhibitors for the management of Type-II Diabetes Mellitus: Inferences from In-silico Investigations. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Paul RK, Nath V, Kumar V. Structure based virtual screening of natural compounds and molecular dynamics simulation: Butirosin as Dipeptidyl peptidase (DPP-IV) inhibitor. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Shawon J, Khan AM, Shahriar I, Halim MA. Improving the binding affinity and interaction of 5-Pentyl-2-Phenoxyphenol against Mycobacterium Enoyl ACP reductase by computational approach. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Manhas A, Kumar S, Jha PC. Identification of the natural compound inhibitors against Plasmodium falciparum plasmepsin-II via common feature based screening and molecular dynamics simulations. J Biomol Struct Dyn 2020; 40:31-43. [PMID: 32794426 DOI: 10.1080/07391102.2020.1806110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Malaria is counted amongst the deadly disease caused by Plasmodium falciparum. Recently, plasmepsin-II enzyme has gained much importance as an attractive drug target for the exploration of antimalarials. Therefore, the common feature pharmacophore models were generated from the crystallized complexes of the plasmepsin-II proteome. These models were subjected to a series of validation procedures, i.e. test set and Güner Henry studies to enlist the representative models. The selected representative hypotheses incorporating the most essential chemical features (common ZHHA) were screened against the natural product database to retrieve the potential candidates. To ensure the selection of the drug-like candidates, prior to screening, filtering steps (Drug-likeness and ADMET filters) were employed on the selected database. To study the interaction pattern of the candidates within the protein, these molecules were advanced to the molecular docking studies. Subsequently, based on the selected cut-off criteria obtained via redocking of the reference (4Z22), 15 compounds showed higher docking score (> -16.05 kcal/mol), and displayed the presence of hydrogen bonding with the crucial amino acids, i.e. Asp34 and Asp214. Further, the stability of the docked molecules was scrutinized via molecular dynamics simulations, and the results were compared with the reference compound 4Z22. All the docked compounds showed stable dynamics behaviour. Thus, in the present contribution, the combination of screening and stability procedures resulted in the identification of 15 hits that can serve as a new chemical space in the designing of the novel antimalarials.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anu Manhas
- Department of Chemistry, Pandit Deendayal Petroleum University, Gujarat, India.,School of Applied Material Sciences, Central University of Gujarat, Gujarat, India
| | - Sujeet Kumar
- School of Applied Material Sciences, Central University of Gujarat, Gujarat, India
| | - Prakash C Jha
- School of Applied Material Sciences, Central University of Gujarat, Gujarat, India
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Manhas A, Dubey S, Jha PC. A profound computational study to prioritize the natural compound inhibitors against the P. falciparum orotidine-5-monophosphate decarboxylase enzyme. J Biomol Struct Dyn 2019; 38:2704-2716. [DOI: 10.1080/07391102.2019.1644197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Anu Manhas
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Saikat Dubey
- Centre for Applied Chemistry, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Prakash C. Jha
- Centre for Applied Chemistry, Central University of Gujarat, Gandhinagar, Gujarat, India
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Manhas A, Patel D, Lone MY, Jha PC. Identification of natural compound inhibitors against PfDXR: A hybrid structure-based molecular modeling approach and molecular dynamics simulation studies. J Cell Biochem 2019; 120:14531-14543. [PMID: 30994966 DOI: 10.1002/jcb.28714] [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] [Received: 11/20/2018] [Revised: 01/18/2019] [Accepted: 01/24/2019] [Indexed: 12/30/2022]
Abstract
In the present contribution, multicomplex-based pharmacophore studies were carried out on the structural proteome of Plasmodium falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase. Among the constructed models, a representative model with complementary features, accountable for the inhibition was used as a primary filter for the screening of database molecules. Auxiliary evaluations of the screened molecules were performed via drug-likeness and molecular docking studies. Subsequently, the stability of the docked inhibitors was envisioned by molecular dynamics simulations, principle component analysis, and molecular mechanics-Poisson-Boltzmann surface area-based free binding energy calculations. The stability assessment of the hits was done by comparing with the reference (beta-substituted fosmidomycin analog, LC5) to prioritize more potent candidates. All the complexes showed stable dynamic behavior while three of them displayed higher binding free energy compared with the reference. The work resulted in the identification of the compounds with diverse scaffolds, which could be used as initial leads for the design of novel PfDXR inhibitors.
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Affiliation(s)
- Anu Manhas
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Dhaval Patel
- Department of Bioinformatics and Stśructural Biology, Indian Institute of Advanced Research, Gujarat, India
| | - Mohsin Y Lone
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India.,Department of Chemistry, Indian Institute of Technology, Gandhinagar, Gujarat, India
| | - Prakash C Jha
- Centre for Applied Chemistry, Central University of Gujarat, Gandhinagar, Gujarat, India
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Manhas A, Lone MY, Jha PC. Multicomplex-based pharmacophore modeling in conjunction with multi-target docking and molecular dynamics simulations for the identification of PfDHFR inhibitors. J Biomol Struct Dyn 2019; 37:4181-4199. [DOI: 10.1080/07391102.2018.1540362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Anu Manhas
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
| | - Mohsin Y. Lone
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar, Gujarat, India
| | - Prakash C. Jha
- Centre for Applied Chemistry, Central University of Gujarat, Gandhinagar, Gujarat, India
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Manhas A, Lone MY, Jha PC. In search of the representative pharmacophore hypotheses of the enzymatic proteome of Plasmodium falciparum: a multicomplex-based approach. Mol Divers 2018; 23:453-470. [DOI: 10.1007/s11030-018-9885-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 10/06/2018] [Indexed: 01/17/2023]
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Manhas A, Patel A, Lone MY, Jha PK, Jha PC. Identification of
Pf
ENR inhibitors: A hybrid structure‐based approach in conjunction with molecular dynamics simulations. J Cell Biochem 2018; 119:8490-8500. [DOI: 10.1002/jcb.27075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/26/2018] [Indexed: 01/31/2023]
Affiliation(s)
- Anu Manhas
- School of Chemical Sciences Central University of Gujarat Gandhinagar Gujarat India
| | - Anjali Patel
- Department of Physics M. S. University of Baroda Vadodara Gujarat India
| | - Mohsin Y. Lone
- School of Chemical Sciences Central University of Gujarat Gandhinagar Gujarat India
- Department of Chemistry Indian Institute of Technology Gandhinagar Gujarat India
| | - Prafulla K. Jha
- Department of Physics M. S. University of Baroda Vadodara Gujarat India
| | - Prakash C. Jha
- Centre for Applied Chemistry Central University of Gujarat Gandhinagar Gujarat India
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Modi P, Patel S, Chhabria MT. Identification of some novel pyrazolo[1,5-a]pyrimidine derivatives as InhA inhibitors through pharmacophore-based virtual screening and molecular docking. J Biomol Struct Dyn 2018; 37:1736-1749. [PMID: 29663870 DOI: 10.1080/07391102.2018.1465852] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The InhA inhibitors play key role in mycolic acid synthesis by preventing the fatty acid biosynthesis pathway. In this present article, Pharmacophore modelling and molecular docking study followed by in silico virtual screening could be considered as effective strategy to identify newer enoyl-ACP reductase inhibitors. Pyrrolidine carboxamide derivatives were opted to generate pharmacophore models using HypoGen algorithm in Discovery studio 2.1. Further it was employed to screen Zinc and Minimaybridge databases to identify and design newer potent hit molecules. The retrieved newer hits were further evaluated for their drug likeliness and docked against enoyl acyl carrier protein reductase. Here, novel pyrazolo[1,5-a]pyrimidine analogues were designed and synthesized with good yields. Structural elucidation of synthesized final molecules was perform through IR, MASS, 1H-NMR, 13C-NMR spectroscopy and further tested for its in vitro anti-tubercular activity against H37Rv strain using Microplate Alamar blue assay (MABA) method. Most of the synthesized compounds displayed strong anti-tubercular activities. Further, these potent compounds were gauged for MDR-TB, XDR-TB and cytotoxic study.
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Affiliation(s)
- Palmi Modi
- a Department of Pharmaceutical Chemistry , L. M. College of Pharmacy , Ahmedabad 380009 , Gujarat , India.,b Department of Pharmacy , Dharmsinh Desai University , Nadiad 387001 , Gujarat , India
| | - Shivani Patel
- a Department of Pharmaceutical Chemistry , L. M. College of Pharmacy , Ahmedabad 380009 , Gujarat , India.,c Division of Biological and Life Sciences , Ahmedabad University , Ahmedabad 380009 , Gujarat , India
| | - Mahesh T Chhabria
- a Department of Pharmaceutical Chemistry , L. M. College of Pharmacy , Ahmedabad 380009 , Gujarat , India
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Wang N, Ren JX, Xie Y. Identification of novel DHFR inhibitors for treatment of tuberculosis by combining virtual screening with in vitro activity assay. J Biomol Struct Dyn 2018; 37:1054-1061. [DOI: 10.1080/07391102.2018.1448721] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Nan Wang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Science, Peking Union Medical College, 151 Malianwa North Road, Haidian District, Beijing 100193, PR China
| | - Ji-Xia Ren
- College of Life Science, Liaocheng University, Liaocheng 252059, PR China
| | - Yong Xie
- College of Life Science, Liaocheng University, Liaocheng 252059, PR China
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Exploration of Mycobacterium tuberculosis structural proteome: An in-silico approach. J Theor Biol 2018; 439:14-23. [DOI: 10.1016/j.jtbi.2017.11.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 07/19/2017] [Accepted: 11/28/2017] [Indexed: 12/20/2022]
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