In silico studies on potential MCF-7 inhibitors: a combination of pharmacophore and 3D-QSAR modeling, virtual screening, molecular docking, and pharmacokinetic analysis

2016 ◽  
Vol 35 (9) ◽  
pp. 1950-1967 ◽  
Author(s):  
Bharti Badhani ◽  
Rita Kakkar
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
In Silico ◽  
3D Qsar ◽  
Pharmacokinetic Analysis ◽  
Qsar Modeling ◽  
In Silico Studies ◽  
Mcf 7

Molecular Modeling Studies on 2,4-Disubstituted Imidazopyridines as Anti-Malarials: Atom-Based 3D-QSAR, Molecular Docking, Virtual Screening, In-Silico ADMET and Theoretical Analysis

2021 ◽  
pp. 2150012
Author(s):  
Suraj N. Mali ◽  
Anima Pandey
Keyword(s):  
Molecular Docking ◽  
Molecular Modeling ◽  
Virtual Screening ◽  
In Silico ◽  
Energy Gap ◽  
3D Qsar ◽  
Modeling Studies ◽  
In Vitro Investigation ◽  
In Silico Admet ◽  
Molecular Modeling Studies

Malarial parasites have been reported for moderate-high resistance towards classical antimalarial agents and henceforth development of newer novel chemical entities targeting multiple targets rather than targeting single target will be a highly promising strategy in antimalarial drug discovery. Herein, we carried out molecular modeling studies on 2,4-disubstituted imidazopyridines as anti-hemozoin formation inhibitors by using Schrödinger’s molecular modeling package (2020_4). We have developed statistically robust atom-based 3D-QSAR model (training set, [Formula: see text]; test set, [Formula: see text]; [Formula: see text] [Formula: see text]; root-mean-square error, [Formula: see text]; standard deviation, [Formula: see text]). Our molecular docking, in-silico ADMET analysis showed that dataset molecule 37, has highly promising results. Our ligand-based virtual screening resulted in top five ZINC hits, among them ZINC73737443 hit was observed with lesser energy gap, i.e. 7.85[Formula: see text]eV, higher softness value (0.127[Formula: see text]eV), and comparatively good docking score of [Formula: see text]10.2[Formula: see text]kcal/mol. Our in-silico analysis for a proposed hit, ZINC73737443 showed that this molecule has good ADMET, in-silico nonames toxic as well as noncarcinogenic profile. We believe that further experimental as well as the in-vitro investigation will throw more lights on the identification of ZINC73737443 as a potential antimalarial agent.

In silico rational design and virtual screening of antixoidant tripeptides based on 3D-QSAR modeling

2019 ◽  
Vol 1193 ◽  
pp. 223-230 ◽  
Author(s):  
Haiqiong Guo ◽  
Yuxuan Wang ◽  
Qingxiu He ◽  
Yuping Zhang ◽  
Yong Hu ◽  
...  
Keyword(s):  
Virtual Screening ◽  
In Silico ◽  
Rational Design ◽  
3D Qsar ◽  
Qsar Modeling

scholarly journals Evaluation of Phytochemicals of Cassia occidentalis L. for their Binding Affinities to SARS-CoV-2 3C-Like Protease: An in Silico Approach

2020 ◽  
pp. 8-14
Author(s):  
Tohmina Afroze Bondhon ◽  
Md. Aynal Haque Rana ◽  
Anamul Hasan ◽  
Rownak Jahan ◽  
Khoshnur Jannat ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
In Silico ◽  
Binding Affinities ◽  
Autodock Vina ◽  
Cassia Occidentalis ◽  
Main Protease ◽  
In Silico Studies ◽  
The World ◽  
Docking Approach

Aims: Corona virus SARS-CoV-2, otherwise known as COVID-19 has created a pandemic resulting in social and financial crisis throughout the world. The virus has no known drugs or vaccines for preventive or therapeutic purposes. The objective of the present study was to screen phytochemicals from Cassia occidentalis L. in virtual screening (in silico) studies to evaluate their potential of binding to the main 3C-like protease of the virus and so stop its replication. Study Design: Molecular docking approach was used for virtual screening studies. Place and Duration of Study: University of Development Alternative between April and July 2020. Methodology: Molecular docking (blind) were done with the help of Autodock Vina. We have used the pdb file (6LU7) of the main protease of SARS-CoV-2 3C-like protease or SARS-CoV-2 3CLpro (monomeric form) to study binding of the phytochemicals. Results: Of the nine phytochemicals studied, the C-glycosidic flavonoids, cassiaoccidentalins A-C demonstrated excellent binding affinities to the protease. The compounds bound to the active site of the protease with binding energy values of -8.2 to-8.4 kcal/mol. Conclusion: The in silico studies suggest that the compounds merit actual COVID-19 inhibitory tests and have potential for anti-COVID-19 use.

scholarly journals Structural Insight into PRMT5 Inhibitors through Amalgamating Pharmacophore-Based Virtual Screening, ADME-Toxicity and Binding Energy Studies and Identify New Inhibitors by Molecular Docking.

2021 ◽  
Author(s):  
Revanth Bathula ◽  
Sree kanth Sivan ◽  
Gururaj Somadi ◽  
Narasimha Muddagoni ◽  
Goverdhan Lanka ◽  
...  
Keyword(s):  
Free Energy ◽  
Molecular Docking ◽  
Virtual Screening ◽  
Binding Free Energy ◽  
Protein A ◽  
Pharmacophore Model ◽  
Receptor Site ◽  
3D Qsar ◽  
Qsar Modeling ◽  
Energy Prediction

Abstract Protein arginine methyltransferase 5 (PRMT5) is a member of the methyltransferases family, a type II arginine enzyme that is crucial for many cellular processes and is associated with many cancer diseases. In this study, pharmacophore-based 3D QSAR modeling, virtual screening and binding free energy studies were carried out from a set of 61 potent compounds reported being inhibitors of PRMT5 protein. A five-point pharmacophore model (AADHR) was generated and this model is used to generate an atom-based 3-Dimensional quantitative structure-activity relationship (3D-QSAR). The obtained 3D-QSAR model has high correlation coefficient (R2 = 0.91), cross-validation coefficient (Q2 = 0.82), F value (140.3), low RMSE (0.47) and pearson R-value (0.91). A library of 329825 molecules (ChEMBL database) is screened with pharmacophore model to retrieve hit molecules that are further subjected for molecular docking to identify best fit-active conformations binding at the receptor site of PRMT5 protein. Further, we are calculated ADME and toxicity properties using QikProp module and pkCSM server and finally prioritized the lead molecules by binding free energy prediction.

scholarly journals Biological Activity Evaluation and In Silico Studies of Polyprenylated Benzophenones from Garcinia celebica

Biomedicines ◽  
2021 ◽  
Vol 9 (11) ◽  
pp. 1654
Author(s):  
Yenni Pintauli Pasaribu ◽  
Arif Fadlan ◽  
Sri Fatmawati ◽  
Taslim Ersam
Keyword(s):  
Antioxidant Activity ◽  
Molecular Docking ◽  
Cell Lines ◽  
In Silico ◽  
Oral Drug ◽  
Root Bark ◽  
Falciparum Strain ◽  
In Silico Studies ◽  
Mcf 7

This study aimed to isolate polyprenylated benzophenones from the rootbark of Garcinia celebica and assess their activities in vitro and in silico. The antioxidant activity was evaluated by the DPPH, ABTS, and FRAP methods. The cytotoxicity was evaluated against HeLa, MCF-7, A549, and B16 cancer cell lines. The antiplasmodial activity was performed against the chloroquine-sensitive Plasmodium falciparum strain 3D7. Molecular docking was analyzed on alpha-estrogen receptor (3ERT) and P. falciparum lactate dehydrogenase enzyme (1CET). The prediction of ADMET for the compounds was also studied. For the first time, (-)-cycloxanthochymol, isoxanthochymol, and xanthochymol were isolated from the root bark of Garcinia celebica. The antioxidant and cytotoxicity evaluation showed that all benzophenones exhibited antioxidant activity compared to gallic acid and quercetin as positive controls and also exhibited strong activity against HeLa, MCF-7, A549, and B16 cell lines compared to cisplatin as the positive control. The antiplasmodial evaluation showed that isoxanthochymol exhibited activity against the chloroquine-sensitive P. falciparum strain 3D7. In addition, the in silico molecular docking study supported in vitro activities. The ADMET analysis also indicated the isolated benzophenones are potential oral drug candidates.

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