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Safavi A, Ghodousi ES, Ghavamizadeh M, Sabaghan M, Azadbakht O, veisi A, Babaei H, Nazeri Z, Darabi MK, Zarezade V. Computational investigation of novel farnesyltransferase inhibitors using 3D-QSAR pharmacophore modeling, virtual screening, molecular docking and molecular dynamics simulation studies: A new insight into cancer treatment. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130667] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Ghasemi S, Sharifi S, Shahbazi Mojarrad J. Design, Synthesis and Biological Evaluation of Novel Piperazinone Derivatives as Cytotoxic Agents. Adv Pharm Bull 2020; 10:423-429. [PMID: 32665901 PMCID: PMC7335995 DOI: 10.34172/apb.2020.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 11/23/2019] [Accepted: 12/08/2019] [Indexed: 11/09/2022] Open
Abstract
Purpose: In this study, a series of piperazin-2-one derivatives were prepared through bioisosteric substitution of the imidazole ring of L-778,123 (imidazole-containing FTase inhibitor) and rearrangement of groups based on the tipifarnib structure. Final compounds were evaluated for their cytotoxic activities on cancer and normal cell lines by MTT assay. Methods: Methyl α-bromophenylacetic acid and 1-(3-chlorophenyl) piperazin-2-one were synthesized using previously described methods. Methyl 2-(4-chlorophenyl)-2-(4-(3- chlorophenyl)-3-oxopiperazin-1-yl) acetate was prepared by reaction between these two compounds in presence of potassium carbonate. Finally, methoxy group of ester was substituted by various amines such as guanidine, thiourea, urea and hydrazide. The synthesized compounds were tested for their cytotoxicity against colon cancer (HT-29) and lung cancer (A549) cell lines as well as MRC-5 (normal fetal lung fibroblasts) cells as a healthy cell line using MTT colorimetric assay method. Results: Replacement of imidazole moiety with guanidine, thiourea, and hydrazide could increase cytotoxicity toward all three cell lines. Some substituents, such as amine, urea, and hydroxylamine exhibited significant cytotoxicity (<500 µM) but lower than L-778,123 as standard compound. Hydroxyl and methoxy substituents did not show significant cytotoxicity. Imidazole substituent group revealed cytotoxicity similar to L-778,123 All compounds showed lower cytotoxic activity against normal cell lines compared with cancer cell lines. Conclusion: It seems the electron density of substituted groups and rearrangement of groups may significantly increase cytotoxic activity.
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Affiliation(s)
- Saeed Ghasemi
- Department of Medicinal Chemistry, School of Pharmacy, Guilan University of Medical Sciences, Rasht, Iran
| | - Simin Sharifi
- Dental and Periodontal Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javid Shahbazi Mojarrad
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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Kashyap A, Singh PK, Satpati S, Verma H, Silakari O. Pharmacophore modeling and molecular dynamics approach to identify putative DNA Gyrase B inhibitors for resistant tuberculosis. J Cell Biochem 2018; 120:3149-3159. [DOI: 10.1002/jcb.27579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/08/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Aanchal Kashyap
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab India
| | - Pankaj Kumar Singh
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab India
| | - Suresh Satpati
- Institute of Life Sciences, Department of Pharmaceutical Sciences and Drug Research Bhubaneswar Orissa India
| | - Himanshu Verma
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab India
| | - Om Silakari
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab India
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Du Y, Yu A, Zhang Y, Jia J, Meng X. Cs2CO3-Promoted Michael Addition-[2,3]-Sigmatropic Rearrangement Domino Reaction: Facile Synthesis of a 3-Substituted Indoles Bearing a Homoallyl Sulfide Moiety. ASIAN J ORG CHEM 2016. [DOI: 10.1002/ajoc.201600343] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yanlong Du
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion; School of Chemistry & Chemical Engineering; Tianjin University of Technology; Tianjin 300384 P. R. China
| | - Aimin Yu
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion; School of Chemistry & Chemical Engineering; Tianjin University of Technology; Tianjin 300384 P. R. China
| | - Youquan Zhang
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion; School of Chemistry & Chemical Engineering; Tianjin University of Technology; Tianjin 300384 P. R. China
| | - Jiru Jia
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion; School of Chemistry & Chemical Engineering; Tianjin University of Technology; Tianjin 300384 P. R. China
| | - Xiangtai Meng
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion; School of Chemistry & Chemical Engineering; Tianjin University of Technology; Tianjin 300384 P. R. China
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Pharmacophore modelling, validation, 3D virtual screening, docking, design and in silico ADMET simulation study of histone deacetylase class-1 inhibitors. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1057-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Virtual lead identification of farnesyltransferase inhibitors based on ligand and structure-based pharmacophore techniques. Pharmaceuticals (Basel) 2013; 6:700-15. [PMID: 24276257 PMCID: PMC3816728 DOI: 10.3390/ph6060700] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 05/05/2013] [Accepted: 05/06/2013] [Indexed: 11/27/2022] Open
Abstract
Farnesyltransferase enzyme (FTase) is considered an essential enzyme in the Ras signaling pathway associated with cancer. Thus, designing inhibitors for this enzyme might lead to the discovery of compounds with effective anticancer activity. In an attempt to obtain effective FTase inhibitors, pharmacophore hypotheses were generated using structure-based and ligand-based approaches built in Discovery Studio v3.1. Knowing the presence of the zinc feature is essential for inhibitor’s binding to the active site of FTase enzyme; further customization was applied to include this feature in the generated pharmacophore hypotheses. These pharmacophore hypotheses were thoroughly validated using various procedures such as ROC analysis and ligand pharmacophore mapping. The validated pharmacophore hypotheses were used to screen 3D databases to identify possible hits. Those which were both high ranked and showed sufficient ability to bind the zinc feature in active site, were further refined by applying drug-like criteria such as Lipiniski’s “rule of five” and ADMET filters. Finally, the two candidate compounds (ZINC39323901 and ZINC01034774) were allowed to dock using CDOCKER and GOLD in the active site of FTase enzyme to optimize hit selection.
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Ghasemi S, Davaran S, Sharifi S, Asgari D, Abdollahi A, Shahbazi Mojarrad J. Comparison of Cytotoxic Activity of L778123 as a Farnesyltranferase Inhibitor and Doxorubicin against A549 and HT-29 Cell Lines. Adv Pharm Bull 2013; 3:73-7. [PMID: 24312815 DOI: 10.5681/apb.2013.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Revised: 10/07/2012] [Accepted: 10/08/2012] [Indexed: 11/17/2022] Open
Abstract
PURPOSE Farnesyltransferase (FTase) is a zinc-dependent enzyme that adds a farnesyl group to the Ras proteins. L778, 123 is a potent peptidomimetic imidazole-containing FTase inhibitor. METHODS L778123 was synthesized according to known methods and evaluated alone and in combination with doxorubicin against A549 (adenocarcinomic human alveolar basal epithelial cells) and HT29 (human colonic adenocarcinoma) cell lines by MTT assay. RESULTS L778123 showed weak cytotoxic activity with IC50 of 100 and 125 for A549 and HT-29 cell lines, respectively. The combination of doxorubicin and L778123 can decrease IC50 of doxorubicin in both cell lines significantly. CONCLUSION It can be concluded that L778, 123 can be a good agent for combination therapy.
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Affiliation(s)
- Saeed Ghasemi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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Ghasemi S, Sharifi S, Davaran S, Danafar H, Asgari D, Mojarrad JS. Synthesis and Cytotoxicity Evaluation of Some Novel 1-(3-Chlorophenyl)piperazin-2-one Derivatives Bearing Imidazole Bioisosteres. Aust J Chem 2013. [DOI: 10.1071/ch13031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A series of substituted 3-chlorophenylpiperazinone derivatives were synthesised using L-778123 (an imidazole-containing FTase inhibitor) as a model by bioisosteric replacement of the imidazole ring. The final compounds were evaluated against two human cancer cell lines including A549 (lung cancer) and HT-29 (colon cancer) by MTT assay. The results showed that substitution of imidazole ring with 1-amidinourea, semicarbazide, and thiobiuret led to improvement of cytotoxic activity against both cell lines.
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Li K, Hu J, Liu H, Tong X. Amine-catalyzed formal (3 + 3) annulations of 2-(acetoxymethyl)buta-2,3-dienoate with sulfur ylides: synthesis of 4H-pyrans bearing a vinyl sulfide group. Chem Commun (Camb) 2012; 48:2900-2. [PMID: 22311117 DOI: 10.1039/c2cc30242j] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A DABCO-catalyzed (3 + 3) annulation between 2-(acetoxymethyl)buta-2,3-dienoate and sulfur ylides has been developed, which provides a facile method for the synthesis of 4H-pyrans bearing a vinyl sulfide group.
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Affiliation(s)
- Kun Li
- Shanghai Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology, Shanghai 200237, PR China
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Zhu X, Huang D, Lan X, Tang C, Zhu Y, Han J, Huang W, Qian H. The first pharmacophore model for potent G protein-coupled receptor 119 agonist. Eur J Med Chem 2011; 46:2901-7. [DOI: 10.1016/j.ejmech.2011.04.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/23/2011] [Accepted: 04/04/2011] [Indexed: 10/18/2022]
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Deshpande S, Jaiswal S, Katti SB, Prabhakar YS. CoMFA and CoMSIA analysis of tetrahydroquinolines as potential antimalarial agents. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2011; 22:473-488. [PMID: 21598193 DOI: 10.1080/1062936x.2011.569945] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used on a dataset of compounds, some of them having been reported to inhibit Plasmodium falciparum protein, farnesyltransferase. The co-crystal structure of the lead molecule, BMS-214662 bound to Rat-PFT was used as a template. CoMFA yielded a good model, with r²(ncv) = 0.909, r²(cv) = 0.617 and was validated using an external set r²(pred) = 0.748). It compared favourably with CoMSIA. In the CoMFA model the steric and electrostatic fields exerted an almost equal influence on activity. The contour maps indicated the necessity for sterically large electropositive groups with electronegative tail to be present in these molecules for activity, and sterically large electronegative moieties on the sulfonamide linker. By incorporating these features some new compounds have been identified for further investigation.
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Affiliation(s)
- S Deshpande
- Medicinal and Process Chemistry Division, Central Drug Research Institute, CSIR, Lucknow, India
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Developing consensus 3D-QSAR and pharmacophore models for several beta-secretase, farnesyl transferase and histone deacetylase inhibitors. J Mol Model 2011; 18:675-92. [DOI: 10.1007/s00894-011-1094-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Accepted: 04/14/2011] [Indexed: 12/20/2022]
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Hari Narayana Moorthy NS, Sousa SF, Ramos MJ, Fernandes PA. Structural feature study of benzofuran derivatives as farnesyltransferase inhibitors. J Enzyme Inhib Med Chem 2011; 26:777-91. [DOI: 10.3109/14756366.2011.552885] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- N. S. Hari Narayana Moorthy
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
| | - Sergio F. Sousa
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
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Saxena S, Chaudhaery SS, Varshney K, Saxena AK. Pharmacophore-based virtual screening and docking studies on Hsp90 inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2010; 21:445-462. [PMID: 20818581 DOI: 10.1080/1062936x.2010.501817] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Hsp90 (Heat shock protein 90) is an important therapeutic target for the treatment of cancer. To identify important chemical features for Hsp90 inhibitory activity, a 3D-QSAR pharmacophore model was developed using a set of 61 inhibitors (a training set of 31 and a test set of 30 compounds) belonging to a series of 2-amino-6-halopurine and 7'-substituted benzothiazolothio- and pyridinothiazolothio-purines. The best HypoGen model consisted of five pharmacophoric features: one hydrogen bond acceptor (HBA), one hydrogen bond donor (HBD) and three hydrophobic (HY) groups. It showed a high correlation coefficient (r = 0.943) and low root mean square deviation (RMSD = 0.751). This model was validated against 30 known Hsp90 inhibitors, where it showed a high predictive value for R(2)pred = 0.805], thus confirming that HY, HBA and HBD features are essential for Hsp90 inhibition. The validated pharmacophore model (Hypo-1) was used as a 3D query for virtual screening to retrieve potential inhibitors from the Maybridge and National Cancer Institute (NCI) databases. The hit compounds were subsequently subjected to molecular docking studies and, finally, five hits were prioritized as potential leads based on GoldScore function.
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Affiliation(s)
- S Saxena
- Medicinal and Process Chemistry Division, Central Drug Research Institute, Lucknow, India
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Kantam ML, Mahendar K, Sreedhar B, Choudary BM, Bhargava SK, Priver SH. Synthesis of α-sulfanyl-β-amino acid derivatives by using nanocrystalline magnesium oxide. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Saxena AK, Saxena S, Chaudhaery SS. Molecular modelling and docking studies on heat shock protein 90 (Hsp90) inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2010; 21:1-20. [PMID: 20373211 DOI: 10.1080/10629360903560504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
An adenosine tri-phosphate (ATP)-dependent molecular chaperone heat shock protein (Hsp90) is of current interest as a potential anticancer drug target. It has several oncogenic client proteins involved in signal transduction, cell cycle regulation and apoptosis. In order to identify essential chemical functional features for Hsp90 inhibition, a pharmacophore model consisting of one hydrogen bond donor, two hydrogen bond acceptor lipid and one hydrophobic feature has been developed using Hypogen (Catalyst 2.0 software) on a total set of 103 inhibitors consisting of 16 and 87 compounds in the training and the test set, respectively. The model shows good correlation for the training (r(2)= 0.887) and the test set ( [image omitted] = 0.692). In view of the X-ray data structure of Hsp90, GOLD 3.2 docking software was used to dock the 16 training set compounds. A good correlation (r(2)= 0.699) was observed between the experimental biological activity and the top-ranked Goldscore. The analysis of conserved patterns across the Hsp90 family, using the human Hsp90 X-ray structure as an alignment template, led to the identification of important amino acids involved in the ligand-binding interactions, which were found to be similar to those observed in docking studies. Hence, the best-generated pharmacophore model can be used for designing new Hsp90 inhibitors.
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Affiliation(s)
- A K Saxena
- Medicinal and Process Chemistry Division, Central Drug Research Institute, Lucknow 226001, India
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Gupta MK, Prabhakar YS. QSAR study on tetrahydroquinoline analogues as plasmodium protein farnesyltransferase inhibitors: a comparison of rationales of malarial and mammalian enzyme inhibitory activities for selectivity. Eur J Med Chem 2008; 43:2751-67. [PMID: 18329140 DOI: 10.1016/j.ejmech.2008.01.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 01/14/2008] [Accepted: 01/14/2008] [Indexed: 11/27/2022]
Abstract
The quantitative structure-activity relationships of Plasmodium falciparum and Rat protein farnesyltransferase (PFT) inhibitory activities of 6-cyano-1-(3-methyl-3H-imidazoly-4-ylmethyl)-3-substituted-1,2,3,4-tetrahydroquinoline (THQ) analogues are investigated in order to explore the similarities/deviations between the two enzymes for these analogues. The structure space of a ligand (BMS-214662) bound to Rat-PFT (PDB code 1SA5) has been used as the conformational space of the compounds under investigation. The study has been carried out using the combinatorial protocol in multiple linear regression with several 2D- and 3D-descriptors from molecular operating environment (MOE) representing the physicochemical and electronic features of the compounds. The molecular potential energy and partially charged van der Waals surface areas have taken part in the PFT models. They suggested in favor of molecular arrangement with minimum energy and low positively/negatively charged surfaces for optimum Pf-PFT inhibitory activity. Furthermore, less hydrophobic compounds are preferred for the activity. The Rat-PFT inhibitory activity models suggested in favor of more negatively as well as more positively charged surface area descriptors for the better activity. The PLS analysis carried out on the descriptors of the Pf-PFT and Rat-PFT models suggested that among the parameters, the partially charged surface areas in the range -0.20 to -0.15 (PEOE_VSA-3) and -0.30 to -0.25 (PEOE_VSA-5), hydrophobicity (a_hyd, logP(o/w) and SlogP_VSA4), and electronic energy (PM3_Eele) of the molecules hold promise for modulating the Pf-PFT/R-PFT inhibitory activities of the compounds. This suggested the possibility of modulating the Pf-PFT/R-PFT inhibitory activities and bringing about selectivity in the THQ analogues for the malarial parasite enzyme.
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Affiliation(s)
- Manish K Gupta
- Medicinal and Process Chemistry Division, Central Drug Research Institute, Lucknow 226001, India
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