Online ISSN: 2515-8260

Keywords : Molecular docking

An integrated in silico approach to identify bioactive Phytochemicals in Bauhinia Variegata plant as potential lead candidates against SARS-CoV-2 transmission targets

Sunainy Ajrawat, Chhavi Thakur, Hemant Sood

European Journal of Molecular & Clinical Medicine, 2023, Volume 10, Issue 1, Pages 570-583

Bauhinia variegata, a medicinal plant commonly known as Kachnar, belongs to the Leguminosae family. It is primarily found in tropical and warm regions around the world. It is known for its high pharmacological and commercial significance due to the presence of terpenoids, flavanoids, tannins, steroids, reducing sugars and cardiac glycosides, which aid in the cure of number of diseases. This study carried out profiling of Phytochemicals of this medicinal plant by using several in silico computational methodologies against SARS-CoV-2 virus. The 3D structure of Phytochemicals and the three target sites of the SARS-CoV-2 were constructed using Swiss-Model server and pre-processed in BIOVIA Discovery Studio followed by molecular docking carried on with Autodock tools-1.5.6. The pharmacokinetic and toxicological properties of these compounds were assessed using the Swiss ADME and admetSAR web servers, respectively. The potential toxicities generated by these compounds, as well as the energies of molecule-target interactions, hydrogen bonding, and hydrophobic interactions, were determined and analyzed. According to the findings, Phytochemicals such as Beta-sitosterol, Lupeol, Ombuin, and Quercetin exhibited higher binding affinity than the two reference drugs Ivermectin and Lopinavir, taken as comparison in the study. According to the preliminary results, these bioactive compounds exhibit the most promising docking scores with the three target sites of Corona virus. Hence, they could be regarded as prospective  Phytochemicals found in Bauhinia variegata, potentially making this plant an active source of Phytochemicals required for the treatment of corona virus infections. Further experimental validation may necessitate the application of bioethics principles, laws, and regulations.

SARS-CoV2 multiple target inhibitors from Andrographis Paniculata: An in-silico report

Karthikeyan Swaminathan; Kavinkumar Nirmala Karunakaran; Jeevitha priya Manoharan; Subramanian Vidyalakshmi

European Journal of Molecular & Clinical Medicine, 2021, Volume 8, Issue 3, Pages 1653-1685

Coronavirus Disease – 2019 (COVID–19) caused by the novel coronavirus, SARS-CoV2 has plagued the world in pandemic for the past few months. Currently, many groups are investigating on a potent candidate for treating this highly infectious disease. Phytocompounds from many medicinal plants are reported to possess anti-viral and anti-inflammatory properties. The current study emphasizes on evaluating the inhibition efficacy of the phytocompounds from Andrographis paniculata against 10 structural and non-structural SARS-CoV2 proteins by virtual screening. Molecular docking, binding interactions, ADME and toxicity profiling of the selected fifty one phytocompounds were analysed and compared against 10 well studied repurposed drugs. The best docked complexes were subjected to MD simulation for 50 nanoseconds and the compound stigmasterol was observed to be outperforming in the simulation studies. We report that A.paniculata constitutes 65.78% druggable phytocompounds against SARS‐CoV2. We found that the two phytosterols, stigmasterol and stigmasta-5,22-dien-3-ol act as potential lead molecules against multiple target proteins of SARS–CoV2. Based on the literature evidence on Andrographis paniculata and our detailed analysis, this plant and its phytocompounds could be repurposed as a potential anti-COVID agent.


Khairnar N. S.; Patil A. V.; Noolvi M. N.

European Journal of Molecular & Clinical Medicine, 2020, Volume 7, Issue 11, Pages 5201-5214

A novel series of triazolylquinazolin-4-one derivatives have been synthesized and characterized by TLC, melting point, FT-IR, 1H NMR and mass spectroscopy data. The synthesized series of title compounds were subjected for docking studies using Schrodinger Glide software, evaluated for their potential to inhibit enzyme EGFR-tyrosine kinase followed by in-vitro anticancer activity by SRB assay method on HeLa, MCF-7, A-549 cell lines. The series of compounds shows anticancer activity probably by inhibiting the enzyme EGFR-tyrosine kinase.

In-silico directions on Anti-diabetic and pkSCM Predictions of Novel Guanidinopyrimidines

Jayaraman Arikrishnan; Mannathusamy Gopalakrishnan; Srinivasan Pazhamalai; Haridoss Manikandan; Selvarasu Sekar; Panneerselvam Kalaivani

European Journal of Molecular & Clinical Medicine, 2020, Volume 7, Issue 7, Pages 6968-6985

Novel 2-(3-(4-methyl / 4-chlorophenyl)guanidine-1-yl)-4,6-disubstituted phenyl pyrimidine (7) were synthesized by simple condensation between therapeutic chalcone with bioactive biguanide derivatives. It was established by different spectral studies. Furthermore, subject to ADMET prediction using pkSCM server and molecular docking studies against human glucokinase protein (PDB ID: 1V4S) plays an important role in the novel drug development of type 2 diabetes and the synthesized compounds results are compared with currently used FDA approved drug and also the theoretical calculations were performed by DFT method. To learn the compound reactivity; HOMO – LUMO energy-gap, MEP surface and some other properties of the compound 7a were investigated.

In-Silico Docking studies of thymoquinone as potential anti-cancer drug target on Lung Cancer Cells


European Journal of Molecular & Clinical Medicine, 2020, Volume 7, Issue 3, Pages 1706-1716

Understanding the inhibitory mechanism of thymoquinone targeting proteins involved in lung cancer. Thymoquinone were reported as possible anti-cancer drug targeting the gene containing protein like GTPase KRas in the cancer inducing pathways and we have used molecular docking in order to understand the underlying mechanism. The target proteins were preferred from various studies in cancer inducing pathways were docked by thymoquinone and also with its analogue poloxime. Protein-ligand complexes were selected based on the binding energy ranked from lowest to highest according to thymoquinone. Our results identified that thymoquinone inhibiting GTPase KRas, Sir-2, ALK5 and β-Catenin,. The docking study also establishes the multifaceted role of thymoquinone as a chemo preventive anti-cancer agent against lung cancer. These in-silico study report would be the substantial platform for the drugs to be focused in future for in-vitro and in-vivo studies for exploring its multitude function for providing a functional strategy for using as a therapeutic agent against cancer.

A Facile Synthesis, Structural Elucidation and Biological Evaluation of dihydropyrimidinone compound

S. Shanmugam; K. Neelakandan; M. Gopalakrishnan; S. Pazhamalai

European Journal of Molecular & Clinical Medicine, 2020, Volume 7, Issue 3, Pages 4038-4056

The chemical structure of the newly synthesized compound Ethyl-6-methyl-2-oxo-4-(3,4,5-trichlorophenyl)-1,2,3,4-tetrahydropyrimidine-5-carboxylate 4 was confirmed by elemental analysis, 1H NMR, 13C NMR, and ESI-HRMS spectral data. In addition, in the form of the complete and partial density of states, the HOMO-LUMO energy gap, and electrostatic potential map, etc., some quantum chemical insights have been obtained. Furthermore, to demonstrate the possible applications of dihydropyrimidinone 4 in nonlinear optics, the polarizability and first hyperpolarizability were measured. Molecular docking is also determined in order to illustrate the over expression of estrogen receptor in 92 % of 2J9M protein. The antitumor activity of these compound was evaluated on breast cancer (MCF-7) cell lines by a cell viability assay utilizing the tetrazolium dye 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). Although with varying degrees, a significant growth inhibitory and cytotoxic effect was observed on MCF-7 cancer cell line. The tested compound 4, was active against MCF-7 cell line (in-vitro analysis) with IC50 values of 45 μM. The compound was subjected for the DPPH & ABTS tests, evaluated its antioxidant activity. With further characterization, mechanism of biological action, this compound 4 shall be a potential / useful candidate as anticancer drug.

Synthesis, antimicrobial activity and Molecular docking study of some novel thiazolidine-2,4-dione derivatives

Pankaj Sharma, Chandra Shekhar Sharma

European Journal of Molecular & Clinical Medicine, 2020, Volume 7, Issue 8, Pages 6075-6087

A series of novel thiazolidine-2,4-diones was synthesized and investigated for antimicrobial activity. The structures of all synthesized compounds were confirmed by means of elemental analysis, IR, 1H NMR, and LCMS. All compounds were evaluated for antimicrobial activity cup plate method against S. aureus, B. anthracis, P. aeruginosa, E. coli, C. albicans and A. niger. Compounds 2d and 2l showed significant activity against gram positive and gram negative bacteria. In case of antifungal activity, the zone of inhibition was ranging from 10 to 23 mm and the compounds 2c and 2e showed significant activity against the fungal strains as compared with fluconazole.

Synthesis, Characterization, ADMET Prediction and Molecular Docking Studies Against COVID-19 Proteins of Novel 2-(3- (4-substituted aryl)guanidine-1-yl)-4- phenyl-6-(thiophene-2-yl)pyrimidines

Jayaraman Arikrishnan; Srinivasan Pazhamalai; Haridoss Manikandan; Selvarasu Sekar; Panneerselvam Kalaivani; Mannathusamy Gopalakrishnan

European Journal of Molecular & Clinical Medicine, 2020, Volume 7, Issue 3, Pages 3930-3948

Novel 2-(3-(4-substitutedaryl)guanidine-1-yl)-4-phenyl-6-(thiophene-2-yl)pyrimidines (7) were synthesized by simple condensation between chalcones with therapeutic biguanide derivatives. The novel guanidinopyrimidine derivatives (7) were characterized by different spectral studies. Furthermore, subjected into ADMET prediction using pkSCM software and molecular docking studies against different kinds novel RNA proteins such as, spike (PDB ID: 6XC3), main protease (3CLpro - PDB ID: 6LU7), RNA-dependent RNA polymerase (RdRp – PDB ID: 6W9Q) and host protein ACE2 (PDB ID:1R42) spike protein and also the activities are compared with FDA approved few human trial drugs such as hydroxychloroquine (HQC), favipiravir and lopinavir.