Successful in silico discovery of natural inhibitors for human rhinovirus coat protein

Planta Medica ◽  
2007 ◽  
Vol 73 (09) ◽  
Author(s):  
JM Rollinger ◽  
TM Steindl ◽  
K Anrain ◽  
EP Ellmerer ◽  
M Schmidtke ◽  
...  
Keyword(s):  
Coat Protein ◽  
In Silico ◽  
Human Rhinovirus ◽  
Natural Inhibitors

Structure-Based Virtual Screening for the Discovery of Natural Inhibitors for Human Rhinovirus Coat Protein

2008 ◽  
Vol 51 (4) ◽  
pp. 842-851 ◽  
Author(s):  
Judith M. Rollinger ◽  
Theodora M. Steindl ◽  
Daniela Schuster ◽  
Johannes Kirchmair ◽  
Kathrin Anrain ◽  
...  
Keyword(s):  
Coat Protein ◽  
Virtual Screening ◽  
Human Rhinovirus ◽  
Natural Inhibitors

In silico comparisons between natural inhibitors of ABCB1/P-glycoprotein to overcome doxorubicin-resistance in the NCI/ADR-RES cell line

2018 ◽  
Vol 112 ◽  
pp. 87-94 ◽  
Author(s):  
Mohamed A. Morsy ◽  
Azza A.K. El-Sheikh ◽  
Ahmed R.N. Ibrahim ◽  
Mohammed A. Khedr ◽  
Abdulla Y. Al-Taher
Keyword(s):  
Cell Line ◽  
In Silico ◽  
Doxorubicin Resistance ◽  
P Glycoprotein ◽  
Natural Inhibitors

Insight into virus encapsulation mechanism through in silico interaction study between coat protein and RNA operator loops of Sesbania mosaic virus

2016 ◽  
Vol 12 (6) ◽  
pp. 1996-2009 ◽  
Author(s):  
Chetan Kumar Meena ◽  
Subhomoi Borkotoky ◽  
Ayaluru Murali
Keyword(s):  
Coat Protein ◽  
Mosaic Virus ◽  
In Silico ◽  
Interaction Study ◽  
Inhibitor Development ◽  
Insight Into

Viruses are parasite by nature and they are responsible for many diseases. Inhibitor development is very difficult for viruses due to their rapid mutative nature.

scholarly journals In Silico Identification and in Vitro Activity of Novel Natural Inhibitors of Trypanosoma brucei Glyceraldehyde-3-phosphate-dehydrogenase

Molecules ◽  
2015 ◽  
Vol 20 (9) ◽  
pp. 16154-16169 ◽  
Author(s):  
Fabian Herrmann ◽  
Mairin Lenz ◽  
Joachim Jose ◽  
Marcel Kaiser ◽  
Reto Brun ◽  
...  
Keyword(s):  
Trypanosoma Brucei ◽  
In Silico ◽  
Vitro Activity ◽  
In Vitro Activity ◽  
In Silico Identification ◽  
Natural Inhibitors

scholarly journals Novel Natural Inhibitors of CYP1A2 Identified by in Silico and in Vitro Screening

2011 ◽  
Vol 12 (5) ◽  
pp. 3250-3262 ◽  
Author(s):  
Ruixin Zhu ◽  
Liwei Hu ◽  
Haiyun Li ◽  
Juan Su ◽  
Zhiwei Cao ◽  
...  
Keyword(s):  
In Silico ◽  
In Vitro Screening ◽  
Natural Inhibitors

scholarly journals Identifying potential natural inhibitors of Brucella melitensis Methionyl-tRNA synthetase through an in-silico approach

2021 ◽  
Author(s):  
Adekunle Babjide Rowaiye ◽  
Akwoba Joseph Ogugua ◽  
Gordon Ibeanu ◽  
Doofan Bur ◽  
Osaretin Benjamin Ogbeide ◽  
...  
Keyword(s):  
In Silico ◽  
Brucella Melitensis ◽  
Trna Synthetase ◽  
Dynamics Simulation ◽  
List Type ◽  
Lead Compounds ◽  
Long Term Treatment ◽  
Methionyl Trna Synthetase ◽  
Natural Inhibitors

AbstractBackgroundBrucellosis is an infectious disease caused by bacteria of the genus Brucella. Although it is the most common zoonosis worldwide, there are increasing reports of drug resistance and cases of relapse after long term treatment with the existing drugs of choice. This study therefore aims at identifying possible natural inhibitors of Brucella melitensis Methionyl-tRNA synthetase through an in-silico approach.MethodsUsing PyRx 0.8 virtual screening software, the target was docked against a library of natural compounds obtained from edible African plants. The compound, 2-({3-[(3,5-dichlorobenzyl) amino] propyl} amino) quinolin-4(1H)-one (OOU) which is a co-crystallized ligand with the target was used as the reference compound. Screening of the molecular descriptors of the compounds for bioavailability, pharmacokinetic properties, and bioactivity was performed using the SWISSADME, pkCSM, and Molinspiration web servers respectively. The Fpocket and PLIP webservers were used to perform the analyses of the binding pockets and the protein ligand interactions. Analysis of the time-resolved trajectories of the Apo and Holo forms of the target was performed using the Galaxy and MDWeb servers. The lead compounds, Strophanthidin and Isopteropodin are present in Corchorus olitorius and Uncaria tomentosa (cat-claw) plants respectively.ResultsIsopteropodin had a binding affinity score of -8.9 kcal / ml with the target and had 17 anti-correlating residues in pocket 1 after molecular dynamics simulation. The complex formed by Isopteropodin and the target had a total RMSD of 4.408 and a total RMSF of 9.8067. However, Strophanthidin formed 3 hydrogen bonds with the target at ILE21, GLY262 and LEU294, and induced a total RMSF of 5.4541 at Pocket 1.ConclusionOverall, Isopteropodin and Strophanthidin were found to be better drug candidates than OOU and they showed potentials to inhibit the Brucella melitensis Methionyl-tRNA synthetase at Pocket 1, hence abilities to treat brucellosis. In vivo and in vitro investigations are needed to further evaluate the efficacy and toxicity of the lead compounds.Author SummaryStrophanthidin and Isopteropodin showed potentials to inhibit the Brucella melitensis Methionyl-tRNA synthetase at Pocket 1Both compounds can be used to treat brucellosis.Both compounds showed potentials of being safe to use in humans.

scholarly journals In Silico Exploration of Potential Natural Inhibitors against SARS-Cov-2 nsp10

Molecules ◽  
2021 ◽  
Vol 26 (20) ◽  
pp. 6151
Author(s):  
Ibrahim H. Eissa ◽  
Mohamed M. Khalifa ◽  
Eslam B. Elkaeed ◽  
Elsayed E. Hafez ◽  
Aisha A. Alsfouk ◽  
...  
Keyword(s):  
In Silico ◽  
Density Functional ◽  
Nonstructural Protein ◽  
Structural Similarity ◽  
Docking Studies ◽  
Similarity Analysis ◽  
Selection Methods ◽  
Functional Theory ◽  
Adenosyl Methionine ◽  
Natural Inhibitors

In continuation of our previous effort, different in silico selection methods were applied to 310 naturally isolated metabolites that exhibited antiviral potentialities before. The applied selection methods aimed to pick the most relevant inhibitor of SARS-CoV-2 nsp10. At first, a structural similarity study against the co-crystallized ligand, S-Adenosyl Methionine (SAM), of SARS-CoV-2 nonstructural protein (nsp10) (PDB ID: 6W4H) was carried out. The similarity analysis culled 30 candidates. Secondly, a fingerprint study against SAM preferred compounds 44, 48, 85, 102, 105, 182, 220, 221, 282, 284, 285, 301, and 302. The docking studies picked 48, 182, 220, 221, and 284. While the ADMET analysis expected the likeness of the five candidates to be drugs, the toxicity study preferred compounds 48 and 182. Finally, a density-functional theory (DFT) study suggested vidarabine (182) to be the most relevant SARS-Cov-2 nsp10 inhibitor.

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