scholarly journals Study of Molecular Docking of Chalcone Analoque Compound as Inhibitors for Liver Cancer Cells HepG2

2018 ◽  
Vol 7 (2) ◽  
pp. 147-158
Author(s):  
Neni Frimayanti ◽  
Enda Mora ◽  
Rizki Anugrah
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Liver Cancer ◽  
Docking Study ◽  
Positive Control ◽  
Crystallographic Structure ◽  
Amino Acid Residues ◽  
Autodock Vina ◽  
Molecular Docking Study ◽  
Liver Cancer Cells

Molecular docking study using chalcone analogue compounds with proteins target from modeling crystallographic structure of Tyrosine kinase enzymes with code 1T46 was carried out with the aid of a computer using the AutoDock Vina program. The aim this study to determine the activity of 5 chalcone analogue compounds obtained from previous studies and 3 chalcone analogues which were modified as inhibitors of liver cancer using 5-fluorouracil as a positive control. Based on the docking results, it has been carried out and shown those compounds 1, 2, and 3 have the potential as the active inhibitors againts HepG2 liver cancer with a successive affinity of -10.1 kcal/mol, -9.7 kcal/mol, and - 9.6 kcal/mol, respectively. For the modified chalcone analogue compounds, compound 8 has the best results with an affinity value of -8.3 kcal/mol and this compound also has six amino acid residues which are the same as 5-flourouracyl (i.e. positive control).

scholarly journals A Combined Spectroscopic and Molecular Modeling Study on Structure-Function-Dynamics under Chemical Modification: Alpha-Chymotrypsin with Formalin Preservative

2021 ◽  
Author(s):  
Pritam Biswas ◽  
Aniruddha Adhikari ◽  
Uttam Pal ◽  
Susmita Mondal ◽  
Dipanjan Mukherjee ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Molecular Docking ◽  
Amino Acid ◽  
Large Scale ◽  
Docking Study ◽  
Product Formation ◽  
Amino Acid Residues ◽  
Acid Modification ◽  
Molecular Docking Study ◽  
Ans Binding

Enzyme conformations can be altered via modification of its amino acid residues, side chains and large-scale domain modifications, which are closely linked to its function. Herein, we have addressed the role of residue modification in catalytic activity and molecular recognition of an enzyme alpha-chymotrypsin (CHT) in presence of covalent cross-linker formalin. Optical spectroscopy studies exhibit reduced catalytic activity of the enzyme with increased formalin concentration. Polarization gated anisotropy studies of a fluorophore 8-anilino-1-napthelenesulfonic acid (ANS) in CHT show a dip rise pattern in presence of formalin which is consistent with the generation of multiple ANS binding sites in the enzyme owing to modifications of its local amino acid residues. Molecular docking study on minimal local residue modifications in CHT reveals formation of a stable enzyme-substrate complex even with the serine-histidine cross-linked enzyme which prohibits product formation giving rise to reduced catalytic activity. Keywords: amino acid modification; chymotrypsin; formalin; cross-linking; spectroscopy; molecular docking

scholarly journals Synthesis and Molecular Docking Studies of Coumarinyl Thiazole as Cell Division Protein Kinase 2 Inhibitor

2019 ◽  
Vol 31 (11) ◽  
pp. 2453-2456
Author(s):  
J. Brindha ◽  
T.F. Abbs Fen Reji
Keyword(s):  
Molecular Docking ◽  
Cell Division ◽  
Protein Kinase ◽  
Screening Tool ◽  
Docking Study ◽  
Docking Studies ◽  
Autodock Vina ◽  
Molecular Docking Study ◽  
Molecular Docking Studies ◽  
Cell Division Protein

A series of 2-alkylamino-4-(3-coumarinyl)thiazoles were synthesized, characterized and evaluated their anticancer activity through molecular docking studies. Cell division protein kinase 2 (PDB code: 1KE9) is selected as a target and the compounds which obeys Lipinski rule of five is selected as a ligand. Molecular docking study is carried out using AutoDock Vina in PyRx virtual screening tool. This study revealed that all the compounds are active against the molecular target and compounds 5a and 5c have the highest docking score.

scholarly journals Isoniazid-Isatin Hydrazone Derivatives: Synthesis, Antitubercular Activity and Molecular Docking Studies

2021 ◽  
Vol 18 (21) ◽  
pp. 39
Author(s):  
Mardi Santoso ◽  
Muhammad Riza Ghulam Fahmi ◽  
Yehezkiel Steven Kurniawan ◽  
Taslim Ersam ◽  
Sri Fatmawati ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Mycobacterium Tuberculosis ◽  
Molecular Docking ◽  
Active Site ◽  
Antitubercular Activity ◽  
Docking Study ◽  
Positive Control ◽  
Tuberculosis H37rv ◽  
Molecular Docking Study

This study examined the synthesis of isoniazid-isatin hydrazone derivatives 5-7, followed by an investigation on the in vitro antitubercular activity against Mycobacterium tuberculosis H37Rv, and molecular docking. A yield of 81 - 92 % of these compounds was achieved, with structural characterization by spectroscopic methods (FTIR, NMR, HRMS). The in vitro antitubercular activity was evaluated against M. tuberculosis H37Rv, and the highest effect was observed in compound 7, with a minimum inhibitory concentration (MIC) of 0.017 mM, lower than rifampicin (MIC 0.048 mM), which served as the positive control. In addition, the molecular docking of 5-7 was performed to visualize the interaction of isoniazid-isatin hydrazone derivatives with the active site of InhA receptor, which was in agreement with the experimental data. The hydrogen bonding with Ser94 and pi-pi interaction with Phe41 and/or Phe97 on the InhA active site was pivotal for the antitubercular activity. HIGHLIGHTS Tuberculosis caused by Mycobacterium tuberculosis is one of the top ten leading causes of death globally The first and second lines of antituberculosis drugs are the prevalent treatment for this disease, but they show several drawbacks and are exacerbated by the occurrence of drug resistance The isoniazid-isatin hydrazone derivatives were designed through molecular hybridization and synthesized effectively and exhibited moderate to high activity against tuberculosis H37Rv Molecular docking study demonstrated that the hydrogen bonding with Ser94 and the pi-pi interaction with Phe41 and/or Phe97 are important for antitubercular activity GRAPHICAL ABSTRACT

scholarly journals Antilymphoma Effect of Incomptine A: In Vivo, In Silico, and Toxicological Studies

Molecules ◽  
2021 ◽  
Vol 26 (21) ◽  
pp. 6646
Author(s):  
Fernando Calzada ◽  
Elihú Bautista ◽  
Sergio Hidalgo-Figueroa ◽  
Normand García-Hernández ◽  
Elizabeth Barbosa ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Acute Toxicity ◽  
In Silico ◽  
Docking Study ◽  
Positive Control ◽  
Oral Toxicity ◽  
Molecular Docking Study ◽  
Toxicological Studies ◽  
Species Production

Incomptine A (IA) is a sesquiterpene lactone isolated from Decachaeta incompta that induces apoptosis, reactive oxygen species production, and a differential protein expression on the U-937 (diffuse histiocytic lymphoma) cell line. In this work, the antitumor potential of IA was investigated on Balb/c mice inoculated with U-937 cells and through the brine shrimp lethality (BSL) test. Furthermore, IA was subjected to molecular docking study using as targets proteins associated with processes of cancer as apoptosis, oxidative stress, and glycolytic metabolism. In addition to determining the potential toxicity of IA in human, its acute toxicity was performed in mice. Results reveals that IA showed high antilymphoma activity and BSL with an EC50 of 2.4 mg/kg and LC50 16.7 µg/mL, respectively. The molecular docking study revealed that IA has strong interaction on all targets used. In the acute oral toxicity, IA had a LD50 of 149 mg/kg. The results showed that the activities of IA including antilymphoma activity, BSL, acute toxicity, and in silico interactions were close to the methotrexate, an anticancer drug used as positive control. These findings suggest that IA may serve as a candidate for the development of a new drug to combat lymphoma.

scholarly journals Potential Phytochemical Inhibitors of the Coronavirus RNA Dependent RNA Polymerase: A Molecular Docking Study

2020 ◽  
Author(s):  
Ardra. P ◽  
Prachi Singh ◽  
Hariprasad VR ◽  
Babu UV ◽  
Mohamed Rafiq ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Rna Polymerase ◽  
Metal Ion ◽  
Docking Study ◽  
Nucleoside Triphosphate ◽  
Root Extract ◽  
Amino Acid Residues ◽  
Molecular Docking Study ◽  
Rna Dependent Rna Polymerase ◽  
Phytochemical Compounds

Abstract The COVID-19 disease that originated in China by the end of 2019 has now become a pandemic and has affected 216 countries as on 08 June 2020. RNA dependent RNA polymerase (RdRp), the core enzyme in the multiprotein replicase-transcriptase complex of coronaviruses, serves as a classical target for inhibiting the coronavirus infectivity. In this study we performed molecular docking of sixty-nine different phytochemical compounds from various herbs with RdRp of both SARS-CoV-2 and its predecessor SARS-CoV. Our results show that various phytochemical constituents from Withania somnifera root extract, Hyssopus officinalis and Camellia sinensis leaf extract have high binding affinity towards RdRps and are comparable to the small molecule drug remdesivir. Their binding interactions reveal that they bind to the amino acid residues involved in nucleoside triphosphate (NTP) entry and recognition site and metal ion cofactor chelating site of both SARS-CoV-2 and SARS-CoV. Hence they are different from the classical nucleotide analog inhibitors of RdRp. This study paves a quick platform for development of targeted therapy using phytochemicals for COVID-19 and other potential SARS coronavirus related outbreaks in future.

scholarly journals IDENTIFICATION OF NOVEL 5-STYRYL-1,2,4-OXADIAZOLE/TRIAZOLE DERIVATIVES AS THE POTENTIAL ANTI-ANDROGENS THROUGH MOLECULAR DOCKING STUDY

2016 ◽  
Vol 8 (10) ◽  
pp. 72 ◽  
Author(s):  
Paranjeet Kaur ◽  
Gopal L. Khatik
Keyword(s):  
Molecular Docking ◽  
Androgen Receptor ◽  
Binding Affinity ◽  
Docking Study ◽  
Molecular Structures ◽  
The Novel ◽  
Autodock Vina ◽  
Molecular Docking Study ◽  
Triazole Derivatives ◽  
Better Than

<p class="Default"><strong>Objective: </strong>To identify the novel and simple bioactive antiandrogens, that can overcome to side effects as well as drug resistance.</p><p class="Default"><strong>Methods: </strong>The AutoDock Vina (ADT) 1.5.6 software is used for molecular docking purposes. The molecular structures were drawn in ChemBiodraw ultra and by the help of ChemBiodraw 3D, all structures were energy minimized by MM2 method and converted to pdb extension file which is readable at the ADT interface.</p><p class="Default"><strong>Results: </strong>Total ten compounds from both series were shown better binding affinity than <em>R</em>-bicalutamide including oxadiazole and triazole series. Among these pk42 and pk46 were studied in-depth which showed best binding affinity to the androgen receptor. The <em>cis</em>-isomers were found better than their <em>trans</em>-isomer.</p><p><strong>Conclusion: </strong>Novel 5-styryl-1,2,4-oxadiazole/triazole derivatives were studied through molecular modeling using Autodock Vina. The potent compounds which showed better binding affinity than <em>R</em>-bicalutamide like pk24 and 46 were further analyzed for their interactions. The conformational effect also found significant in binding to the androgen receptor.</p>

Molecular docking study of flavonoid compounds for possible matrix metalloproteinase-13 inhibition

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Amir Taherkhani ◽  
Shirin Moradkhani ◽  
Athena Orangi ◽  
Alireza Jalalvand ◽  
Zahra Khamverdi
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Matrix Metalloproteinase ◽  
Bone Development ◽  
Bone Mineralization ◽  
Docking Study ◽  
Oral Diseases ◽  
Molecular Docking Study ◽  
Flavonoid Compounds ◽  
Matrix Metalloproteinase 13

AbstractObjectivesMatrix metalloproteinase-13 (MMP-13) has been reported to be involved in different biological processes such as degradation of extracellular matrix proteins, activating or degrading some significant regulatory proteins, wound healing, tissue remodeling, cartilage degradation, bone development, bone mineralization, ossification, cell migration, and tumor cell invasion. Further, MMP-13 participates in many oral diseases such as tooth decay, gingivitis, and degradation of enamel and tissue around the implant. In addition, inhibition of MMP-13 has shown therapeutic properties for Alzheimer’s disease (AD). We performed molecular docking to assess the binding affinity of 29 flavonoid compounds with the MMP-13. Additionally, pharmacokinetic and toxicity characteristics of the top-ranked flavonoids were studied. The current study also intended to identify the most important amino acids involved in the inhibition of MMP-13 based on topological feature (degree) in the ligand-amino acid network for MMP-13.MethodsMolecular docking and network analysis were studied using AutoDock and Cytoscape software, respectively. Pharmacokinetic and toxicity characteristics of compounds were predicted using bioinformatics web tools.ResultsThe results revealed that nine of the studied flavonoids had considerable estimated free energy of binding and inhibition constant: Rutin, nicotiflorin, orientin, vitexin, apigenin-7-glucoside, quercitrin, isoquercitrin, quercitrin-3-rhamnoside, and vicenin-2. Proline-242 was found to be the most important amino acid inhibiting the enzyme.ConclusionsThe results of the current study may be helpful in the prevention and therapeutic procedures of many disorders such as cancer, tooth caries, and AD. Nevertheless, validation tests are required in the future.

scholarly journals COUMARIN ANALOGUES AS A POTENTIAL INHIBITOR OF LEISHMANIASIS: A MULTI-TARGETING PROTEIN INHIBITION APPROACH BY MOLECULAR DOCKING

2019 ◽  
Author(s):  
Kapish Kapoor
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Active Compound ◽  
Active Site ◽  
Therapeutic Potential ◽  
Docking Study ◽  
Developed Countries ◽  
Molecular Docking Study

Leishmaniasis is one of the most dreadful diseases as a leading cause of death in most of the developed countries. In the given study molecular docking study was performed on the library of coumarin analogues as anti-leishmaniasis agents. Total 300 coumarins analogues were taken from Pubmed and were studied using a molecular docking study on trypanothione reductase from Leishmania infantum (PDB code: 2JK6 and 2P18) and Leishmania mexicana (PDB code: 3PP7). Molecular docking result revealed that most active compound COU-130 and COU-220 bind to the active site of the protein with amino acids present in the various proteins. In PDB 2JK6 the active compound binds to the amino acid thr-51 and ser-14 were binding to the active site, and in PDB 3PP7 the active compound binds amino acid thr-26 and in PDB 2P18 the active compound binds to the amino acid phe-219 and try-212. Further in vitro and in vivo study of selected coumarin analogues can be studied for their therapeutic potential in treating leishmaniasis.

scholarly journals In Silico Designing and Interaction of Coumarin-Amino Acid(s) Conjugates with Integrin Like Protein of Cryptococcus neoformans: Insights on Antifungal Drug Design

2020 ◽  
Vol 11 (2) ◽  
pp. 8587-8598
Keyword(s):  
Amino Acid ◽  
Cryptococcus Neoformans ◽  
In Silico ◽  
Homology Model ◽  
Docking Study ◽  
Binding Energies ◽  
Crystallographic Structure ◽  
Molecular Docking Study ◽  
Coumarin Amino Acid

In the present work, a library of 117 coumarin-amino acid(s) conjugates was designed, and molecular docking study was performed to investigate their possible role as fungal integrin like receptor antagonists. The objective of this study is in-silico designing and docking of coumarin-amino acid conjugates against integrin like protein of Cryptococcus neoformans. In the absence of a crystallographic structure of integrin of the fungal pathogen, a homology model of protein OXH63806.1 of Cryptococcus neoformans was developed using the currently available X-ray structure of human integrin as a template. The quality of the 3D model obtained by homology modeling was evaluated by the PROCHECK program. A docking study using coumarin-amino acid(s) conjugates as ligands on the binding site of the modeled receptor was carried out to understand the protein-ligand binding interactions. Some of the compounds have shown very good binding energies ranging from -10.32 to -10.94 Kcal/mol towards the target receptor. These results may be helpful in the designing and development of new antifungal agents as integrin like protein antagonists.

scholarly journals Synthesis, Molecular Docking and Pharmacological Investigation of Some 4-Methylphenylsulphamoyl Carboxylic Acid Analogs

2020 ◽  
Vol 11 (4) ◽  
pp. 5357-5366
Author(s):  
Melford C Egbujor ◽  
Uchechukwu C Okoro ◽  
Sunday N Okafor ◽  
Ifeanyi S Amasiatu ◽  
Ugochukwu B Amadi ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Analytical Data ◽  
Methyl Chloride ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Binding Interaction ◽  
Sulfa Drug ◽  
Lipinski’S Rule ◽  
Anti Oxidant

Compounds bearing and amino acid moieties are considered the basis for sulfa drug development. The synthesis of 4-methylphenylsulphamoyl acids and the evaluation of their pharmacological activities are reported. The synthesis of these compounds was accomplished by the reaction of various acids and 4-methyl chloride in basic aqueous solution. Structures were confirmed by FTIR, 1HNMR, 13CNMR spectra and elemental analytical data. Molecular docking interactions of the analogues were determined using PyRx. In the in antimicrobial activity analysis, compounds 1, 3, 5and 7 had antimicrobial inhibitory concentration range of 0.5-1.0mg/ml comparable with 0.1-2.0mg/ml of and . In the in anti-oxidant activity study compounds 1, 2and 6displayed half-maximal inhibitory concentrations (IC50) of 1.104±0.001 /ml, 1.159±0.002µg/ml and1.240±0.001µg/ml respectively comparable with 0.999±0.002µg/ml of acid. In the molecular docking study, compound 4 had a strong 2D binding interaction with II amino acid residue and compounds 1, 3, 4, 5, 6 and 7 had in antimicrobial, anti-oxidant, and antimalarial properties similar to their standard drugs. Considering the outstanding pharmacological properties and their strict compliance with Lipinski’s rule, the synthesized 4-methylphenylsulphamoyl analogues could be considered as antimicrobial, antimalarial, and anti-oxidant drug candidates.

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