Molecular Docking Approach of Natural Compound from Herbal Medicine in Java against Severe Acute Respiratory Syndrome Coronavirus-2 Receptor

Indonesia's diversity of natural resources presents an intriguing opportunity for the exploration of potential herbal medicines. Numerous compounds, both purified and crude, have been reported to exhibit antiviral activity. The ACE-2 receptor may be a therapeutic target for SARS-CoV-2 infection. We used a search engine to search for herbal medicines with ACE-2 inhibitory activity to predict the potential inhibition of natural compounds (i.e., theaflavin, deoxypodophyllotoxin, gallocatechin, allicin, quercetin, annonamine, Curcumin, 6-gingerol, and cucurbitacin B) to SARS-CoV2 – ACE-2 complex. We performed molecular docking analysis using the ACE-2 protein target from Protein Data Bank. Protein stabilization was carried out to adjust to the body's physiology, carried out using Pymol by removing water atoms and adding hydrogen atoms. Ligands of active compounds from natural resources were selected and downloaded from the PubChem database, then optimized by Pymol software. The complexes of the tested ligand compounds and ACE-2 receptors, which have a bond strength smaller than the control were selected for analysis. Theaflavin, Deoxypodophyllotoxin, Gallocatechin, Curcumin, and Cucurbitacin B had a strong bond affinity than the control ligands. Based on our data, deoxypodophylotoxin and Curcumin had the same interaction amino acid residus compare to the control ligand. This study concludes that deoxypodophyllotoxin and Curcumin have the greatest potential to inhibit the formation of the SARS-Cov2-ACE-2 complex; additionally, these compounds exhibit favorable pharmacological and pharmacodynamic properties. It is suggested that additional research be conducted to determine the biological effects of deoxypodopyllotoxin and Curcumin on ACE-2 receptors.

Download Full-text

Molecular Docking Studies of Bioactive Nicotiflorin against 6W63 Novel Coronavirus 2019 (COVID-19)

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207323999200820162551 ◽

2020 ◽

Vol 23 ◽

Author(s):

Raghvendra Dubey ◽

Kushagra Dubey

Keyword(s):

Molecular Docking ◽

Data Bank ◽

Docking Studies ◽

Molecular Docking Studies ◽

Molegro Virtual Docker ◽

Main Protease ◽

Docking Approach ◽

Inhibitory Potential ◽

Efficacy Parameters ◽

Novel Coronavirus

Background: COVID-19 which is known as the novel coronavirus was reported in December 2019 in Wuhan city, China and many of the patients have been contaminated by environmental contamination and transmission from one human to another. Objective: The objective of work is to establish the inhibitory potential of nicotiflorin, a Kaempferol 3-O-rutinoside flavonoid, against the deadly coronavirus (COVID-19) 6W63 (main protease 3Clpro protein) , using molecular docking approach. Method: The Molegro Virtual Docker software (MVD) with a 30 Å grid resolution was used. The structure was drawn by Chem 3D software and energy minimization was done by the MM2 force field. The protein 6W63 was downloaded from the protein data bank. Molegro modeller was used for score calculations. Result: The molecular docking studies were carried out on nicotiflorin and standard inhibitor X77, where standard inhibitor was observed in a co-crystallized state with main protease 3Clpro protein 6W63. The MolDock score, Rerank Sore and H Bond score of nicotiflorin and standard inhibitor X77 was observed as -173.058, -127.302, -21.9398 and -156.913,- 121.296,-5.7369, respectively. Conclusion: Molecular docking studies have confirmed that the affinity of flavonoid nicotiflorin with the amino acids of the viral protein 6W63 was relatively more than the standard X77. For the effective treatment of novel coronavirus COVID-19, the effectiveness of the identified flavonoid nicotiflorin can further be evaluated for safety and efficacy parameters at both preclinical and clinical stages.

Download Full-text

Molecular Docking Study of Several Antiviral Drugs to Defeat Covid-19

Mapana Journal of Sciences ◽

10.12723/mjs.54.4 ◽

2020 ◽

Vol 19 (3) ◽

pp. 37-46

Author(s):

Jasdev S. Tuteja ◽

Priti Patidar ◽

Shilpa E. Mathew ◽

Anil Prajapati

Keyword(s):

Molecular Docking ◽

Severe Acute Respiratory Syndrome ◽

Active Drug ◽

Data Bank ◽

Docking Study ◽

Antiviral Drugs ◽

Binding Affinities ◽

Molecular Docking Study ◽

Molegro Virtual Docker ◽

Docking Approach

Corona virus is one of the significant pathogens that destructs the human respiratory functioning. Deaths and casualties caused by coronaviruses (CoVs) include the severe acute respiratory syndrome (SARS)-CoV and the Middle East respiratory syndrome (MERS)-CoV. The aim of the work was to compare several antiviral drugs and find out which is the most active drug that might be used in treatment for COVID -19. In this study Molecular Docking approach was used to determine the binding affinities of 62 antiviral molecules. The study was carried out using Molegro Virtual Docker 6.0 with PDB 2GTB procured from RCSB Protein Data Bank. Simeprevir and Telaprevir were discovered to be most potent having high MolDock and Rerank scores of -225.158, -78.4383 and -209.467, -136.155 respectively. Further studies may be conducted to design more potent analogue and defeat COVID-19.

Download Full-text

Molecular Interaction Analysis of COX-2 Against Aryl Amino Alcohol Derivatives from Isoeugenol as Anti Breast Cancer using Molecular Docking

BULLETIN OF CHEMICAL REACTION ENGINEERING AND CATALYSIS ◽

10.9767/bcrec.16.3.10324.581-587 ◽

2021 ◽

Vol 16 (3) ◽

pp. 581-587

Author(s):

Zulfa Zuhrufa ◽

Tatang Shabur Julianto

Keyword(s):

Breast Cancer ◽

Molecular Docking ◽

Amino Alcohol ◽

Interaction Analysis ◽

Data Bank ◽

Docking Studies ◽

Hydroxyl Groups ◽

Cancer Symptoms ◽

Result Show ◽

Docking Approach

Breast cancer occurs due to uncontrolled cells proliferation. The Proliferation causes severe inflammatory which can be the initial stages of cancer symptoms. Aryl amino alcohol compounds from isoeugenol derivatives are proposed for the potential drugs of breast cancer. This study was conducted on iso-eugenol derivatives by adding carbonyl groups, hydroxyl groups, halide compounds and amines to determine the effect on anticancer activity through molecular docking studies. The molecular docking approach is carried out to see the interaction of ligands with protein compounds by using the minimized ligand energy bind with protein active site using protein data bank ID 5GMN. The docking result show that IE-Benzanilide-Cl (11) and IE-Benzanilide-OH (10) have the lowest binding energy (−8.3 kcal/mol and −8.6 kcal/mol) compare to another compounds. AdmetSAR computer simulations show that all compounds have very few toxic effects. The use of aryl amino alcohol derivatives (10 and 11) may be suggested as anti-breast cancer drugs. Copyright © 2021 by Authors, Published by BCREC Group. This is an open access article under the CC BY-SA License (https://creativecommons.org/licenses/by-sa/4.0).

Download Full-text

Molecular Docking Studies of Coronavirus Proteins with Medicinal Plant Based Phytochemicals

Defence Life Science Journal ◽

10.14429/dlsj.6.15704 ◽

2021 ◽

Vol 6 (1) ◽

pp. 57-63

Author(s):

Avinash Marwal ◽

Mukesh Meena ◽

RK Gaur

Keyword(s):

Molecular Docking ◽

Medicinal Plant ◽

Rna Binding ◽

Data Bank ◽

Black Pepper ◽

Docking Studies ◽

Ligand Docking ◽

Main Protease ◽

Pubchem Database ◽

In Silico Molecular Docking

In this study, we presented an in silico molecular docking between the SARS-CoV-2 four proteins [(a) SARS-CoV-2 nucleocapsid protein N-terminal RNA binding domain (6M3M), (b) Nsp9 RNA binding protein of SARS CoV-2 (6W4B), (c) The crystal structure of COVID-19 main protease in apo form (6M03), and (d) Structure of the 2019-nCoV HR2 Domain (6LVN)] available in the PDB (Protein Data Bank), and the medicinal plant-based phytochemicals (retrieved from PubChem database) as ligand molecules i.e. Piperine (Black Pepper), Eugenol (Clove), Alliin (Garlic), Gingerol (Ginger) and Curcumin (Turmeric). All these ligand molecules showed good docking with their respective receptor molecules and their scores range from -8.195 to -5.263. DockThor Portal (a receptor ligand-docking server) which was recently developed and published this year were used in the current study. The obtained results might help in the wet lab conditions to develop better antiviral compounds against SARS-CoV-2.

Download Full-text

Topological and Reactivity Descriptor of Carisoprodol from DFT and Molecular Docking Approach

Journal of Institute of Science and Technology ◽

10.3126/jist.v26i1.37828 ◽

2021 ◽

Vol 26 (1) ◽

pp. 74-82

Author(s):

Tarun Chaudhary ◽

Manoj Kumar Chaudhary ◽

Bhawani Datt Joshi

Keyword(s):

Molecular Docking ◽

Energy Gap ◽

Topological Analysis ◽

Docking Simulation ◽

Vital Role ◽

Hydrogen Atoms ◽

Charge Localization ◽

Donor And Acceptor ◽

Molecular Stability ◽

Docking Approach

This study aims to investigate the optimized structure and optimized parameters of carisoprodol from the DFT/B3LYP/6-31G(d,p) level of theory. The molecular electrostatic potential (MEP) map signifies that the positive potential across hydrogen of the amine group (NH2) and the negative potential around the carbonyl groups (C=O). HOMO-LUMO energy gap was found to be 8.1064 eV. The global and local reactivity parameters describe the possible chemical reactive sites in the molecule. The topological analysis of the electron localization function (ELF) and localized orbital locator (LOL) revealed that the charge localization around hydrogen atoms. The hyper-conjugative interaction between donor and acceptor orbital showed that the interaction LP(2) O4→ σ*(O2-C16) plays a vital role in the molecular stability. The molecular docking simulation encircles that the carisoprodol behaves as a good inhibitor with the target protein, Tyrosine-protein kinase ABL.

Download Full-text

Molecular Docking Approaches to Suggest the Anti-Mycobacterial Targets of Natural Products

10.26434/chemrxiv.13325690.v1 ◽

2020 ◽

Author(s):

Rafael Baptista ◽

Sumana Bhowmick ◽

Shen Jianying ◽

Luis Mur

Keyword(s):

Natural Products ◽

Molecular Docking ◽

Free Energies ◽

Antibiotic Resistant ◽

Drug Lead ◽

Bisbenzylisoquinoline Alkaloids ◽

Docking Approach ◽

Global Threat ◽

Physicochemical And Structural Properties

Tuberculosis (TB) is a major global threat mostly due to the development of antibiotic resistant forms of Mycobacterium tuberculosis, the causal agent of the disease. Driven by the pressing need for new anti-mycobacterial agents, several natural products (NPs) have been shown to have in vitro activities against M. tuberculosis. The utility of any NP as a drug lead is augmented when the anti-mycobacterial target(s) is unknown. To suggest these, we used a molecular docking approach to predict the interactions of 53 selected anti-mycobacterial NPs against known ‘druggable’ mycobacterial targets ClpP1P2, DprE1, InhA, KasA, PanK, PknB and Pks13. The docking scores / binding free energies were predicted and calculated using AutoDock Vina along with physicochemical and structural properties of the NPs, using PaDEL descriptors. These were compared to the established inhibitor (control) drugs for each mycobacterial target. The specific interactions of the bisbenzylisoquinoline alkaloids 2-nortiliacorinine, tiliacorine and 13’-bromotiliacorinine against the targets PknB and DprE1 (-11.4, -10.9 and -9.8 kcal.mol-1 ; -12.7, -10.9 and -10.3 kcal.mol-1 , respectively) and the lignan αcubebin and Pks13 (-11.0 kcal.mol-1 ) had significantly superior docking scores compared to controls. Our approach can be used to suggest predicted targets for the NP to be validated experimentally but these in silico steps are likely to facilitate drug optimisation.

Download Full-text

Current Advances in the Biological Activity of Polysaccharides in Dendrobium with Intriguing Therapeutic Potential

Current Medicinal Chemistry ◽

10.2174/0929867324666170227114648 ◽

2018 ◽

Vol 25 (14) ◽

pp. 1663-1681 ◽

Cited By ~ 9

Author(s):

Chun-Ting Lee ◽

Heng-Chun Kuo ◽

Yung-Hsiang Chen ◽

Ming-Yen Tsai

Keyword(s):

Biological Activity ◽

Therapeutic Potential ◽

Biological Activities ◽

Biological Effects ◽

Herbal Medicines ◽

Research Field ◽

Protective Effects ◽

Pharmacological Effects ◽

The Family ◽

Anti Tumor Activity

The polysaccharides in many plants are attracting worldwide attention because of their biological activities and medical properties, such as anti-viral, anti-oxidative, antichronic inflammation, anti-hypertensive, immunomodulation, and neuron-protective effects, as well as anti-tumor activity. Denodrobium species, a genus of the family orchidaceae, have been used as herbal medicines for hundreds of years in China due to their pharmacological effects. These effects include nourishing the Yin, supplementing the stomach, increasing body fluids, and clearing heat. Recently, numerous researchers have investigated possible active compounds in Denodrobium species, such as lectins, phenanthrenes, alkaloids, trigonopol A, and polysaccharides. Unlike those of other plants, the biological effects of polysaccharides in Dendrobium are a novel research field. In this review, we focus on these novel findings to give readers an overall picture of the intriguing therapeutic potential of polysaccharides in Dendrobium, especially those of the four commonly-used Denodrobium species: D. huoshanense, D. offininale, D. nobile, and D. chrysotoxum.

Download Full-text

Discovery of Camptothecin Based Topoisomerase I Inhibitors: Identification Using an Atom Based 3D-QSAR, Pharmacophore Modeling, Virtual Screening and Molecular Docking Approach

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207319666160810154346 ◽

2016 ◽

Vol 19 (9) ◽

pp. 752-763 ◽

Cited By ~ 4

Author(s):

Sanal Dev ◽

Sunil Dhaneshwar ◽

Bijo Mathew

Keyword(s):

Molecular Docking ◽

Virtual Screening ◽

Topoisomerase I ◽

3D Qsar ◽

Pharmacophore Modeling ◽

Topoisomerase I Inhibitors ◽

Docking Approach

Download Full-text

In Silico Studies on Anti-Stress Compounds of Ethanolic Root Extract of Hemidesmus indicus L.

Current Pharmaceutical Biotechnology ◽

10.2174/1389201021666191211152754 ◽

2020 ◽

Vol 21 (6) ◽

pp. 502-515

Author(s):

Jayasimha R. Daddam ◽

Basha Sreenivasulu ◽

Katike Umamahesh ◽

Kotha Peddanna ◽

Dowlathabad M. Rao

Keyword(s):

Conventional Medicine ◽

Herbal Medicines ◽

Ethanolic Extract ◽

Data Bank ◽

Docking Studies ◽

Dynamics Simulation ◽

Alternative Methods ◽

Root Extract ◽

Hemidesmus Indicus ◽

In Silico Studies

Background: Alternative medicine is available for those diseases which cannot be treated by conventional medicine. Ayurveda and herbal medicines are important alternative methods in which the treatment is done with extracts of different medicinal plants. This work is concerned with the evaluation of anti-stress bioactive compounds from the ethanolic root extract of Hemidesmus indicus. Methods: Gas chromatography and Mass Spectrum studies are used to identify the compounds present in the ethanolic extract based on the retention time, area. In order to perform docking studies, Vasopressin model is generated using modeling by Modeller 9v7. Vasopressin structure is developed based on the crystal structure of neurophysin-oxytocin from Bos taurus (PDB ID: 1NPO_A) collected from the PDB data bank. Using molecular dynamics simulation methods, the final predicted structure is obtained and further analyzed by verifying 3D and PROCHECK programs, confirmed that the final model is reliable. The identified compounds are docked to vasopressin for the prediction of anti-stress activity using GOLD 3.0.1 software. Results: The predicted model of Vasopressin structure is stabilized and confirmed that it is a reliable structure for docking studies. The results indicated ARG4, THR7, ASP9, ASP26, ALA32, ALA 80 in Vasopressin are important determinant residues in binding as they have strong hydrogen bonding with phytocompounds. Among the 21 phytocompounds identified and docked, molecule Deoxiinositol, pentakis- O-(trimethylsilyl) showed the best docking results with Vasopressin. Conclusion: The identified compounds were used for anti-stress activity by insilico method with Vasopressin which plays an important role in causing stress and hence selected for inhibitory studies with phytocompounds. The phytocompounds are inhibiting vasopressin through hydrogen bodings and are important in protein-ligand interactions. Docking results showed that out of twenty-one compounds, Deoxiinositol, pentakis-O-(trimethylsilyl) showed best docking energy to the Vasopressin.

Download Full-text