Molecular modeling of Acetyl-CoA carboxylase (ACC) from Jatropha curcas and virtual screening for identification of inhibitors

Chandrakar, Bina; Jain, Aditya; Roy, Suparna; Gutlapalli, Venkata Ravi; Saraf, Shantanu; Suppahia, Anjana; Verma, Ankit; Tiwari, Archana; Yadav, Mukesh; Nayarisseri, Anuraj

doi:10.1016/j.jopr.2013.07.032

Cited by 17 publications

(8 citation statements)

References 23 publications

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“…The free interface of admetSAR tool was used (http://lmmd.ecust. edu.cn:8000/) (Natchimuthu et al, 2016;Chandrakar et al, 2013;Pandey et al, 2013).The compounds which carried greater affinity score from established compounds and virtual screened compounds after docking were used to analyze the ADMET competency (Sinha et al, 2015;Sinha et al, 2014;Trishang et al, 2019;Vuree et al, 2013;Gudala et al, 2015).…”

Section: Admet Studiesmentioning

confidence: 99%

Identification of High-Affinity Small Molecule Targeting IDH2 for the Clinical Treatment of Acute Myeloid Leukemia

Sweta¹,

Khandelwal²,

Srinitha³

et al. 2019

Asian Pac J Cancer Prev

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According to the American Cancer Society (ACS), Acute Myeloid Leukemia (AML) is a group of hematological diseases, phenotypic and genetically heterogeneous, characterized by clonal expansion of myeloid with diminished capacity for differentiation. It is characterized by the fast growth of white blood cells, red blood cells, platelets, and it's a build-up in the bone marrow restricting the production of traditional blood cells. Once healthy bone marrow cells are replaced with the leukemic cells, it results in a decline in red blood cells, platelets, and healthy white blood cells. Mainly, symptoms that are seen in patients affected by AML are Weight loss, Fatigue, Fever, Night sweat, Loss of appetite, shortness of breath, natural bruising and bleeding, with lots of body

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Section: Admet Studiesmentioning

confidence: 99%

Identification of High-Affinity Small Molecule Targeting IDH2 for the Clinical Treatment of Acute Myeloid Leukemia

Sweta¹,

Khandelwal²,

Srinitha³

et al. 2019

Asian Pac J Cancer Prev

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“…Molecular docking studies revealed the best fit modes of compounds 5a – h by docking with tyrosine kinase. Results obtained after docking analysis provide us with promising compound 5c , based on the best binding affinity value in comparison to standard (all data in supplementary materials ) [ 21 ]. 3D and 2D interface of best fit poses as ligand into receptor site of tyrosine kinase were visualized in Figure 10 A–E [ 22 , 23 , 24 , 25 ].…”

Section: Resultsmentioning

confidence: 99%

Structure-Based Designing, Solvent Less Synthesis of 1,2,3,4-Tetrahydropyrimidine-5-carboxylate Derivatives: A Combined In Vitro and In Silico Screening Approach

et al. 2021

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Objective: In this study, small molecules possessing tetrahydropyrimidine derivatives have been synthesized having halogenated benzyl derivatives and carboxylate linkage. As previously reported, FDA approved halogenated pyrimidine derivatives prompted us to synthesize novel compounds in order to evaluate their biological potential. Methodology: Eight pyrimidine derivatives have been synthesized from ethyl acetoacetate, secondary amine, aromatic benzaldehyde by adding catalytic amount of CuCl2·2H2O via solvent less Grindstone multicomponent reagent method. Molecular structure reactivity and virtual screening were performed to check their biological efficacy as an anti-oxidant, anti-cancer and anti-diabetic agent. These studies were supported by in vitro analysis and QSAR studies. Results: After combined experimental and virtual screening 5c, 5g and 5e could serve as lead compounds, having low IC50 and high binding affinity.

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“…X-ray crystal structure of the ERα in complex with 4-hydroxytamoxifen (OHT)(PDB Id: 3ERT [29] was selected for the present study by considering Resolution (1.9 Å), and R-Value Free (0.262) as speci c selection parameters from the Protein Data Bank [30][31][32][33][34][35][36][37][38]. Before proceeding to dock, the PDB structure was prepared using the Protein Preparation Wizard module(Schrodinger, Inc., LLC, New York, USA) by applying criteria like removal of water molecules, assigning bond orders, lling missing hydrogens, side chains & loops, capping termini, selenomethionine to methionine reconversion, optimization and energy minimization using the OPLS-2005 force eld with default settings [39][40][41][42][43][44][45][46][47][48][49][50].…”

Section: Target Selection and Protein Preparationmentioning

confidence: 99%

Structural insights into conformational stability of ESR1 and structure base screening of new potent inhibitor for the treatment of Breast Cancer

Chopra¹,

Panwar

Madhavi

et al. 2022

Preprint

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Estrogen receptor alpha (ERα), a nuclear receptor proteinencoded by the estrogen receptor1 (ESR1) gene,is an important biomarker in breast cancer diagnosis. Any dysregulation in its expression can actively implicate the development and progression of the disease. ERα is abnormally expressed in around 60% of the active cases, making it animportant therapeutic target. In this study, we report the application of computational approaches to identify suitable drug-like molecules, which share similar ligand binding dynamics with ERα. Structure-based virtual screening(SBVS), docking, and inhibitor dynamics are used to study the ligand binding and interaction profiling of the anticipatedligand molecule, at the active site of the 4-hydroxytamoxifen (OHT) protein (PDB Id: 3ERT). SBVS analysis follows HTVS, SP, and XP protocol in comparison to the ZINC and NCI, to retrieve 20 bestligandhits as effective inhibitors; All the compounds have shown significant interaction with active site residues (Leu346, Thr347, Asp351, Glu353, Trp383, Leu387, and Arg394) of the 4-hydroxytamoxifen. Moreover, the docking study was used to screen the top 5 compounds: ZINC13377936, NCI35753, ZINC35465238, ZINC14726791, and NCI663569. We also, employed molecular dynamics simulations to explore the binding dynamics present at the atomic level. Our MDS results have revealed the compounds (ZINC13377936 and NCI35753) with outstanding binding stability and lesser fluctuations. Both above hits possess a high potential as future therapeutic agents, acting by the mechanism of competitive inhibitionagainst the ERα protein in breast cancer.

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Molecular modeling of Acetyl-CoA carboxylase (ACC) from Jatropha curcas and virtual screening for identification of inhibitors

Cited by 17 publications

References 23 publications

Identification of High-Affinity Small Molecule Targeting IDH2 for the Clinical Treatment of Acute Myeloid Leukemia

Identification of High-Affinity Small Molecule Targeting IDH2 for the Clinical Treatment of Acute Myeloid Leukemia

Structure-Based Designing, Solvent Less Synthesis of 1,2,3,4-Tetrahydropyrimidine-5-carboxylate Derivatives: A Combined In Vitro and In Silico Screening Approach

Structural insights into conformational stability of ESR1 and structure base screening of new potent inhibitor for the treatment of Breast Cancer

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