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Lee J, Drinkwater N, McGowan S, Scammells P. A Structure-Activity Relationship Study of Novel Hydroxamic Acid Inhibitors around the S1 Subsite of Human Aminopeptidase N. ChemMedChem 2020; 16:234-249. [PMID: 32945135 DOI: 10.1002/cmdc.202000527] [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: 07/17/2020] [Indexed: 12/24/2022]
Abstract
Aminopeptidase N (APN/CD13) is a zinc-dependent ubiquitous transmembrane ectoenzyme that is widely present in different types of cells. APN is one of the most extensively studied metalloaminopeptidases as an anti-cancer target due to its significant role in the regulation of metastasis and angiogenesis. Previously, we identified a potent and selective APN inhibitor, N-(2-(Hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro-[1,1'-biphenyl]-4-yl)ethyl)-4-(methylsulfonamido)benzamide (3). Herein, we report the further modifications performed to explore SAR around the S1 subsite of APN and to improve the physicochemical properties. A series of hydroxamic acid analogues were synthesised, and the pharmacological activities were evaluated in vitro. N-(1-(3'-Fluoro-[1,1'-biphenyl]-4-yl)-2-(hydroxyamino)-2-oxoethyl)-4-(methylsulfonamido)benzamide (6 f) was found to display an extremely potent inhibitory activity in the sub-nanomolar range.
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Affiliation(s)
- Jisook Lee
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Campus, Parkville, VIC, 3052, Australia
| | - Nyssa Drinkwater
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia
| | - Sheena McGowan
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia
| | - Peter Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville Campus, Parkville, VIC, 3052, Australia
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Amin SA, Jha T. Fight against novel coronavirus: A perspective of medicinal chemists. Eur J Med Chem 2020; 201:112559. [PMID: 32563814 PMCID: PMC7289749 DOI: 10.1016/j.ejmech.2020.112559] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 12/30/2022]
Abstract
The ongoing novel coronavirus disease (COVID-19) pandemic makes us painfully perceive that our bullet shells are blank so far for fighting against severe human coronavirus (HCoV). In spite of vast research work, it is crystal clear that the evident does not warrant the commercial blossoming of anti-HCoV drugs. In this circumstance, drug repurposing and/or screening of databases are the only fastest option. This study is an initiative to recapitulate the medicinal chemistry of severe acute respiratory syndrome (SARS)-CoV-2 (SARS-CoV-2). The aim is to present an exquisite delineation of the current research from the perspective of a medicinal chemist to allow the rapid development of anti-SARS-CoV-2 agents.
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Affiliation(s)
- Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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Amin SA, Ghosh K, Gayen S, Jha T. Chemical-informatics approach to COVID-19 drug discovery: Monte Carlo based QSAR, virtual screening and molecular docking study of some in-house molecules as papain-like protease (PLpro) inhibitors. J Biomol Struct Dyn 2020; 39:4764-4773. [PMID: 32568618 PMCID: PMC7332872 DOI: 10.1080/07391102.2020.1780946] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
World Health Organization characterized novel coronavirus disease (COVID-19), caused by severe acute respiratory syndrome (SARS) coronavirus-2 (SARS-CoV-2) as world pandemic. This infection has been spreading alarmingly by causing huge social and economic disruption. In order to response quickly, the inhibitors already designed against different targets of previous human coronavirus infections will be a great starting point for anti-SARS-CoV-2 inhibitors. In this study, our approach integrates different ligand based drug design strategies of some in-house chemicals. The study design was composed of some major aspects: (a) classification QSAR based data mining of diverse SARS-CoV papain-like protease (PLpro) inhibitors, (b) QSAR based virtual screening (VS) to identify in-house molecules that could be effective against putative target SARS-CoV PLpro and (c) finally validation of hits through receptor-ligand interaction analysis. This approach could be used to aid in the process of COVID-19 drug discovery. It will introduce key concepts, set the stage for QSAR based screening of active molecules against putative SARS-CoV-2 PLpro enzyme. Moreover, the QSAR models reported here would be of further use to screen large database. This study will assume that the reader is approaching the field of QSAR and molecular docking based drug discovery against SARS-CoV-2 PLpro with little prior knowledge. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
- Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Kalyan Ghosh
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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Banerjee S, Amin SA, Baidya SK, Adhikari N, Jha T. Exploring the structural aspects of ureido-amino acid-based APN inhibitors: a validated comparative multi-QSAR modelling study. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:325-345. [PMID: 32174187 DOI: 10.1080/1062936x.2020.1734080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
The zinc-dependent enzyme aminopeptidase N (APN) is a member of the M1 metalloenzyme family. The multi-functionality of APN as a peptidase, a receptor and a signalling molecule has provided it the access to influence a number of disease conditions namely viral diseases, angiogenesis, cellular metastasis and invasion including different cancer conditions. Hence, the development of potent APN inhibitors is a possible route for the treatment of diseases related to the activity of APN. In this study, different QSAR approaches have been adopted to identify the structural features of a group of hydroxamate-based ureido-amino acid derivative APN inhibitors. This study was able to identify different constitutional aspects of these APN inhibitors which are important for their inhibitory potency. Additionally, some of these observations were also aligned with the observations of previously performed QSAR studies conducted on different APN inhibitors. Therefore, the results of this study may help to design potent and effective APN inhibitors in the future.
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Affiliation(s)
- S Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University , Kolkata, India
| | - S A Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University , Kolkata, India
| | - S K Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University , Kolkata, India
| | - N Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University , Kolkata, India
| | - T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University , Kolkata, India
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Abstract
The mercapturic acid pathway is a major route for the biotransformation of xenobiotic and endobiotic electrophilic compounds and their metabolites. Mercapturic acids (N-acetyl-l-cysteine S-conjugates) are formed by the sequential action of the glutathione transferases, γ-glutamyltransferases, dipeptidases, and cysteine S-conjugate N-acetyltransferase to yield glutathione S-conjugates, l-cysteinylglycine S-conjugates, l-cysteine S-conjugates, and mercapturic acids; these metabolites constitute a "mercapturomic" profile. Aminoacylases catalyze the hydrolysis of mercapturic acids to form cysteine S-conjugates. Several renal transport systems facilitate the urinary elimination of mercapturic acids; urinary mercapturic acids may serve as biomarkers for exposure to chemicals. Although mercapturic acid formation and elimination is a detoxication reaction, l-cysteine S-conjugates may undergo bioactivation by cysteine S-conjugate β-lyase. Moreover, some l-cysteine S-conjugates, particularly l-cysteinyl-leukotrienes, exert significant pathophysiological effects. Finally, some enzymes of the mercapturic acid pathway are described as the so-called "moonlighting proteins," catalytic proteins that exert multiple biochemical or biophysical functions apart from catalysis.
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Affiliation(s)
- Patrick E Hanna
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, USA
| | - M W Anders
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, USA
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Synthesis, anticancer activity, structure–activity relationship and binding mode of interaction studies of substituted pentanoic acids. Future Med Chem 2019; 11:1679-1702. [PMID: 31370697 DOI: 10.4155/fmc-2018-0361] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: Simultaneous inhibition of MMP-2 and HDAC8 may be an effective strategy to target cancer. Methodology: In continuation of our earlier efforts, a series of substituted pentanoic acids (1–18) were synthesized and checked for their biological activity along with some earlier reported compounds (19 –35). Results: Compounds 18 and 31 were found to induce apoptosis effectively in a dose-dependent fashion in Jurkat-E6.1 cell line. They reduced the expression of both MMP-2 and HDAC8 effectively. 31 also produced prominent intensity of fluorescence to bring nick in Jurkat-E6.1 cells. 31 also showed cellular arrest in sub-G0 phase. Conclusion: Such compounds may be useful to battle against cancer.
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Amin SA, Adhikari N, Jha T. Design of Aminopeptidase N Inhibitors as Anti-cancer Agents. J Med Chem 2018; 61:6468-6490. [DOI: 10.1021/acs.jmedchem.7b00782] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Sk. Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata 700032, West Bengal, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata 700032, West Bengal, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P.O. Box 17020, Kolkata 700032, West Bengal, India
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Exploration of structural and physicochemical properties of small molecules to inhibit NMDA functionality. Struct Chem 2018. [DOI: 10.1007/s11224-018-1103-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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9
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Possible anticancer agents: synthesis, pharmacological activity, and molecular modeling studies on some 5-N
-Substituted-2-N-(substituted benzenesulphonyl)-L(+)Glutamines. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1858-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Structural exploration of PPARγ modulators through pharmacophore mapping, fragment-based design, docking, and molecular dynamics simulation analyses. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1727-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Robust design of some selective matrix metalloproteinase-2 inhibitors over matrix metalloproteinase-9 through in silico/fragment-based lead identification and de novo lead modification: Syntheses and biological assays. Bioorg Med Chem 2016; 24:4291-4309. [DOI: 10.1016/j.bmc.2016.07.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/11/2016] [Accepted: 07/12/2016] [Indexed: 12/28/2022]
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Yang Z, Lu ZQ, Zhang YJ, Li YB, Wang ZY, Zhang YL, Zhuang PW, Bai G. Looking for agonists of β2 adrenergic receptor from Fuzi and Chuanwu by virtual screening and dual-luciferase reporter assay. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2016; 18:550-561. [PMID: 26700061 DOI: 10.1080/10286020.2015.1123692] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 11/17/2015] [Indexed: 06/05/2023]
Abstract
More and more studies demonstrated that β2 adrenergic receptor (β2-AR) plays a crucial role for the treatment of heart failure. Chuanwu and Fuzi have been used over thousands of years in China for the treatment of heart failure. Considering the effects of these herbs are very similar to β2-AR agonists, we presume whether β2-AR agonists can be found from Fuzi and Chuanwu. Fuzi and Chuanwu decoction were used to receive the luciferase reporter activity assay to verify the hypothesis, and the result is positive and encouraging. For it is very difficult to get all of the monomer compounds of Fuzi and Chuanwu, virtual screening was used to find potential β2-AR agonists and a cell-based β2-AR agonist functional evaluation model, combined with a luciferase reporter assay system, was used to confirm the final result. In this research, 45 compounds were identified as β2-AR agonists, and four compounds were verified and the rest need further experiment.
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Affiliation(s)
- Zhen Yang
- a Tianjin State Key Laboratory of Modern Chinese Medicine , Tianjin University of Traditional Chinese Medicine , Tianjin , China
| | - Zhi-Qiang Lu
- a Tianjin State Key Laboratory of Modern Chinese Medicine , Tianjin University of Traditional Chinese Medicine , Tianjin , China
| | - Yan-Jun Zhang
- a Tianjin State Key Laboratory of Modern Chinese Medicine , Tianjin University of Traditional Chinese Medicine , Tianjin , China
| | - Yu-Bo Li
- a Tianjin State Key Laboratory of Modern Chinese Medicine , Tianjin University of Traditional Chinese Medicine , Tianjin , China
| | - Zeng-Yong Wang
- b State Key Laboratory of Medicinal Chemical Biology , Nankai University , Tianjin 300071 , China
| | - Yan-Ling Zhang
- c School of Chinese Pharmacy , Beijing University of Traditional Chinese Medicine , Beijing 100102 , China
| | - Peng-Wei Zhuang
- a Tianjin State Key Laboratory of Modern Chinese Medicine , Tianjin University of Traditional Chinese Medicine , Tianjin , China
- d Tianjin JF-Pharmaland Technology Development Co., Ltd. , Tianjin 300457 , China
| | - Gang Bai
- b State Key Laboratory of Medicinal Chemical Biology , Nankai University , Tianjin 300071 , China
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Nandy A, Roy K, Saha A. Exploring molecular fingerprints of selective PPARδ agonists through comparative and validated chemometric techniques. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:363-382. [PMID: 25986170 DOI: 10.1080/1062936x.2015.1039576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Peroxysome proliferator-activated receptors (PPARs) have grown greatly in importance due to their role in the metabolic profile. Among three subtypes (α, γ and δ), we here consider the least investigated δ subtype to explore the molecular fingerprints of selective PPARδ agonists. Validated QSAR models (regression based 2D-QSAR, HQSAR and KPLS) and molecular docking with dynamics analyses support the inference of classification-based Bayesian and recursive models. Chemometric studies indicate that the presence of ether linkages and heterocyclic rings has optimum influence in imparting selective bioactivity. Pharmacophore models and docking with molecular dynamics analyses postulate the occurrence of aromatic rings, HB acceptor and a hydrophobic region as crucial molecular fragments for development of PPARδ modulators. Multi-chemometric studies suggest the essential structural requirements of a molecule for imparting potent and selective PPARδ modulation.
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Affiliation(s)
- A Nandy
- a Department of Chemical Technology , University of Calcutta , Kolkata , India
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Mondal C, Halder AK, Adhikari N, Saha A, Saha KD, Gayen S, Jha T. Comparative validated molecular modeling of p53-HDM2 inhibitors as antiproliferative agents. Eur J Med Chem 2015; 90:860-75. [DOI: 10.1016/j.ejmech.2014.12.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 12/02/2014] [Accepted: 12/06/2014] [Indexed: 01/28/2023]
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Halder AK, Saha A, Saha KD, Jha T. Stepwise development of structure–activity relationship of diverse PARP-1 inhibitors through comparative and validatedin silico modeling techniques and molecular dynamics simulation. J Biomol Struct Dyn 2014; 33:1756-79. [DOI: 10.1080/07391102.2014.969772] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Structural findings of cinnolines as anti-schizophrenic PDE10A inhibitors through comparative chemometric modeling. Mol Divers 2014; 18:655-71. [PMID: 24789056 DOI: 10.1007/s11030-014-9523-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 04/08/2014] [Indexed: 12/13/2022]
Abstract
Schizophrenia is a complex psychiatric disorder associated with the distortion of striatopallidal neurotransmission of central nervous system. Phosphodiesterase10A (PDE10A) enzyme plays crucial role in cellular signaling pathways in schizophrenia. Inhibition of this enzyme may facilitate better treatment of this disease. 2D-QSAR, HQSAR, pharmacophore mapping, molecular docking, and 3D-QSAR analyses were performed on 81 cinnoline derivatives having PDE10A inhibitory activity. 2D-QSAR models were developed by multiple linear regression and partial least square analyses using both atom based and whole molecular descriptors. The best model, having considerable internal (q(2) = 0.812) and external (R(2)(pred) = 0.691) predictabilities, demonstrated importance of atom-based topological and whole molecular E-state as well as 3D topological indices. The best HQSAR model was also found to be statistically significant (q(2) = 0.664, R(2)(pred) = 0.513) and it highlighted some important structural features. PHASE-based pharmacophore hypothesis showed the importance of three hydrogen bond acceptor and one each of ring aromatic and hydrophobic features for higher activity. 3D-QSAR CoMFA and CoMSIA models were generated on two different types of alignment procedures-(1) pharmacophore (PHASE) based and (2) docking (GLIDE) based. GLIDE-based alignment produced better results for both CoMFA (Q(2) = 0.578; R(2)(pred) = 0.841) and CoMSIA (Q(2) = 0.610; R(2)(pred) = 0.824) methods. Molecular dynamics (MDs) simulations were performed for two ligand-receptor complexes and these simulations explored some crucial factors for higher activity. These findings of MD simulations were consistent with the interpretations obtained from other methods of analyses. The current study may help in designing new PDE10A inhibitors of this class.
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Structural findings of quinolone carboxylic acids in cytotoxic, antiviral, and anti-HIV-1 integrase activity through validated comparative molecular modeling studies. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0897-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Adhikari N, Halder AK, Mondal C, Jha T. Exploring structural requirements of aurone derivatives as antimalarials by validated DFT-based QSAR, HQSAR, and COMFA–COMSIA approach. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0590-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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