High-throughput virtual molecular docking with AutoDockCloud

2012 ◽  
Vol 26 (4) ◽  
pp. 907-916 ◽  
Author(s):  
Sally R. Ellingson ◽  
Jerome Baudry
Keyword(s):  
Molecular Docking ◽  
High Throughput

Inhibition Profiling of Urease and Carbonic Anhydrase II by High- Throughput Screening and Molecular Docking Studies of Structurally Diverse Organic Compounds

2020 ◽  
Vol 17 ◽  
Author(s):  
Majid Ali ◽  
Syed Majid Bukhari ◽  
Asma Zaidi ◽  
Farhan A. Khan ◽  
Umer Rashid ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Carbonic Anhydrase ◽  
Metal Complexes ◽  
Organic Compounds ◽  
High Throughput ◽  
High Throughput Screening ◽  
Docking Studies ◽  
Carbonic Anhydrase Ii ◽  
Molecular Docking Studies ◽  
Ic50 Values

Background:: Structurally diverse organic compounds and available drugs were screened against urease and carbonic anhydrase II in a formulation acceptable for high-throughput screening. Objective: The study was conducted to find out potential inhibitors of urease and carbonic anhydrase II. Methods:: Quantification of the possible HITs was carried out by determining their IC50 values. Results and Discussion:: of several screened compounds including derivatives of oxadiazole, coumarins, chromane-2, 4- diones and metal complexes of cysteine-omeprazole showed promising inhibitory activities with IC50 ranging from 47 μM to 412 μM against the urease. The interactions of active compounds with active sites of enzymes were investigated through molecular docking studies which revealed that (R)-1-(4-amino-4-(5-(thiophen-2-yl)-1,3,4-oxadiazol-2-yl) butyl) guanidine possessing IC50 of 47 μM, interacts with one of the nickel metal atom of urease besides further interactions as predictable hydrogen bonds with KCX490, Asp633, His492, His407 and His409 along with Ala440 and 636. Bi-ligand metal complexes of 4-aminoantipyrine based Schiff bases showed activation of urease with AC50 ranging from 68 μM to 112 μM. Almost 21 compounds with varying functional groups including pyrimidines, oxadiazoles, imidazoles, hydrazides and tin based compounds were active carbonic anhydrase II inhibitors presenting 98 μM to 390 μM IC50 values. Several N-substituted sulfonamide derivatives were inactive against carbonic anhydrase II. Conclusion:: Among all the screened compounds, highly active inhibitor of carbonic anhydrase II was (4-(3- hydroxyphenyl)-6-phenyl-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl)phenyl) methanone with IC50 of 98.0 μM. This particular compound showed metallic interaction with Zn ion of carbonic anhydrase II through hydroxyl group of phenyl ring.

scholarly journals ANALYSIS OF MOLECULAR DOCKING EFFICIENCY OF CLEISTANTHIN-A, AS AN ALTERNATIVE FOR NICOTINE ADDICTION

2018 ◽  
Vol 10 (4) ◽  
pp. 98
Author(s):  
A. Amala Lourthuraj ◽  
M. Masilamani Selvam ◽  
Bharathi Ravikrishnan ◽  
M. Vinoth ◽  
Waheeta Hopper
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
Protein Data Bank ◽  
Acetylcholine Receptor ◽  
Nicotinic Acetylcholine Receptor ◽  
High Throughput ◽  
In Silico ◽  
Data Bank ◽  
Tobacco Consumption ◽  
Nicotinic Acetylcholine

Objective: The present research was aimed to understand the molecular docking efficiency of a plant-derived compound cleistanthin-A and a common ingredient in tobacco consumption nicotine with nicotinic acetylcholine receptor (nAChR).Methods: The 3-D structure of nAChR was retrieved from the protein data bank (ID 5AFH). Ligand was obtained from the PUBCHEM. The in silico protocol comprised of three steps: high-throughput virtual screening (HTVS), standard preci­sion (SP) and extra precision (XP). The screened molecules were ranked accordingly using glide score. Schrödinger tool was used to perform the docking analysis.Results: The binding efficiency of the nicotine and cleistanthin-A was found to be docked at the cys-cys loop of the receptor. Based upon the glide score and glide energy it can be reported that, nicotine binding can be inhibited by the binding of cleistanthin-A to the nAChR.Conclusion: The docking efficiency of cleistanthin-A was good compared to nicotine towards nAChR. Hence, cleistanthin–A was derived as a better choice as an alternative for nicotine in smoke therapy.

High-Throughput Screening by In silico Molecular Docking of Eryngium Foetidum (Linn.) Bioactives for Cylcooxygenase-2 Inhibition

2016 ◽  
Vol 6 (4) ◽  
pp. 232-237 ◽  
Author(s):  
Pavan Rangahanumaiah ◽  
Ravishankar Vittal Rai ◽  
Asma Saqhib ◽  
Lydia Jothi ◽  
Marula Siddha Swamy ◽  
...  
Keyword(s):  
Molecular Docking ◽  
High Throughput ◽  
In Silico ◽  
High Throughput Screening ◽  
Eryngium Foetidum ◽  
In Silico Molecular Docking

scholarly journals Molecular docking of resveratrol with known protein structures as well as high-throughput meta-data analyses uncork the “French Paradox” and its potential “Druggable” targets in humans

BMC Genomics ◽  
2014 ◽  
Vol 15 (S2) ◽  
Author(s):  
Peter Natesan Pushparaj ◽  
Zeenat Mirza ◽  
Sajjad Karim ◽  
Kalamegam Gauthaman ◽  
Kothandaraman Narasimhan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
High Throughput ◽  
Protein Structures ◽  
Meta Data ◽  
Data Analyses ◽  
Druggable Targets ◽  
French Paradox

scholarly journals High throughput screening of tubulin inhibitors from parasitic fungi

1970 ◽  
pp. 319-322
Author(s):  
P. A. Karpov ◽  
O. M. Demchuk ◽  
S. P. Ozheriedov ◽  
S. I. Spivak ◽  
O. V. Raievskyi ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
High Throughput ◽  
High Throughput Screening ◽  
Protein Structures ◽  
Pathogenic Fungi ◽  
Tubulin Inhibitors ◽  
Parasitic Fungi ◽  
High Throughput Virtual Screening

Aim. Implementation of 3D-modeling, molecular dynamics, high-throughput screening and molecular docking for search of new inhibitors of parasitic fungi tubulin. Methods. Protein structures were constructed using I-TASSER server and optimized by Gromacs. Ligands library was prepared in Mopac7 program and screened using UCSF Dock 6. Best ligands were docked in CCDC Gold. Results. It was reconstructed spatial molecular structure for 93 α-, 95 β- and 78 γ-tubulins from 76 species of pathogenic fungi genus: Microsporum, Arthroderma, Histoplasma, Blastomyces, Emmonsia, Uncinocarpus, Coccidioides, Paracoccidioides, Aspergillus, Botrytis cinerea, Sclerotinia, Rhynchosporium, Marssonina, Scedosporium, Fusarium, Gibberella, Candida, Ceraceosorus, Malassezia, Anthracocystis, Melanopsichium, Sporisorium, Ustilago, Cryptococcus, Trichosporon, Mucor, Rhizopus and Lichtheimia. Libraries of 3D-models of parasitic fungi tubulins and perspective ligands were created. Based on results of high-throughput virtual screening, 200 perspective agents were selected from more than 7 million compounds. After resulting molecular docking in CCDC GOLD, we specify 19 leading compounds. We propose these compounds as potent tubulin inhibitors and recommend them for in vitro testing as new fungicides. Conclusions. Based on results of high-throughput virtual screening in Grid, 19 new imidazole inhibitors of parasitic fungi tubulin were selected.Keywords: microtubule, tubulins, fungicides, imidazole derivatives, virtual screening, molecular docking.

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