In silico screening

Last updated: 2022 May 14
Total hit(s): 118
Select item(s)
Key Findings
Comments
(You can add your comments too!)
Original Article
(hover to see details)
U. tomentosa can be used as a herbal supplement with the safety and efficacy parameters at both preclinical and clinical stages to evaluate its effectiveness in the treatment of novel coronavirus disease. All components discovered in U. tomentosa may work together to prevent the transmission of SARS-CoV-2 through several processes.
✍
 		33118480
(J Biomol Struct Dyn)
PMID
33118480
Date of Publishing: 2020 Oct 29
Title Uncaria tomentosa (cat's claw): a promising herbal medicine against SARS-CoV-2/ACE-2 junction and SARS-CoV-2 spike protein based on molecular modeling
Author(s) name Yepes-Pérez AF, Herrera-Calderon O, Quintero-Saumeth J.
Journal J Biomol Struct Dyn
Impact factor
3.22
Citation count: 8
Date of Entry 2022 May 14

Quantitative in-silico analysis of 14 treat-medicine candidates showed they did not inhibit omicron S-RBD and ACE-2 binding, but got adsorbed at the ACE-2 contact site and blocked enzyme activity. Modified gallocatechin gallate and modified PF-07321332 repulsed from ACE-2 contact site. The candidate inhibitors for blocking the Spike-RBD and ACE-2 binding should be acidic compounds, so that they are repulsed from ACE-2, as several acidic amino acids exist at the ACE-2 contact site. The practical medical treatment compounds should not block the ACE-2 activity adsorbing at the contact site. The proposed medicines may need modification to be repulsed from adsorption on to the active site of ACE-2.
✍
 		35026638
(Talanta)
PMID
35026638
Date of Publishing: 2022 Apr 1
Title Quantitative in silico analysis of SARS-CoV-2 S-RBD omicron mutant transmissibility
Author(s) name Hanai T.
Journal Talanta
Impact factor
10.5
Citation count: 5
Date of Entry 2022 Feb 23

2466 drugs from DrugBank were used to computationally target against RBD of Spike protein in SARS-CoV-2 to obtain 18 favourable drugs with top docking scores, 6 of them formed stable complex by MD simulation, with 3 of them showing enhanced binding Residues in the predicted binding pocket exhibit conformational variability at the side-chain level. Flavin adenine dinucleotide (FAD), fondaparinux and atorvastatin showed RMSD 5 and low conformational fluctuations.
✍
 		34256255
(Comput Biol Med)
PMID
34256255
Date of Publishing: 2021 Aug
Title Drug repurposing against SARS-CoV-2 receptor binding domain using ensemble-based virtual screening and molecular dynamics simulations
Author(s) name Kumar V, Liu H, Wu C.
Journal Comput Biol Med
Impact factor
2.93
Citation count: 2
Date of Entry 2021 Sep 5

Virtual Screening of 6218 compounds against MPro (Main Protease) and RdRp (RNA dependant RNA polymerase) identified 15 and 23 potential repurposed drugs, respectively. At least three promising drug combinations (omipalisib/remdesivir, tipifarnib/omipalisib, and tipifarnib/remdesivir) could be obtained with high efficacy of SARS-CoV-2 inhibition at their clinically achievable concentrations.
The virtual screening strategy for drug repurposing reported here could be used for for rapid identification of drug candidates for any known target protein. doseresponse curve (DRC) was generated for each compound, and three key drug performance values, the 50% inhibitory concentration (IC50), the 50% cytotoxicity concentration (CC50), and selective index (SI) defined as (CC50)/(IC50), were determined for each compound.
✍
 		34234012
(Proc Natl Acad Sci U S A)
PMID
34234012
Date of Publishing: 2021 Jul 27
Title Drugs repurposed for COVID-19 by virtual screening of 6,218 drugs and cell-based assay
Author(s) nameJang WD, Jeon S et al.
Journal Proc Natl Acad Sci U S A
Impact factor
9.35
Citation count: 28
Date of Entry 2021 Sep 5

1018 Brown algal (Phaeophyceae) natural compounds were screened against MPro as potential Main protease inhibitors in SARS-CoV-2, out of which 7 favourable compounds were shown to have good binding affinities. Lopinavir and Remdesivir were used as comparative standards for docking studies. For virtual screening, crystal structure of main protease in complex with 6-(ethylamino) pyridine-3-carbonitrile (RZS) was used as a template.
✍
 		34226782
(S Afr J Bot)
PMID
34226782
Date of Publishing: 2021 Jul 1
Title Docking-based virtual screening and identification of potential COVID-19 main protease inhibitors from brown algae
Author(s) nameRauf A, Rashid U et al.
Journal S Afr J Bot
Impact factor
N/A
Citation count: 2
Date of Entry 2021 Sep 5

The aim of this study was to compare viral load, clinical presentation at diagnosis and type of exposure among vaccinated (with BNT162b2) and non-vaccinated health care workers (HCWs). Prospective cohort of HWCs diag nosed with COVID-19 by nasopharyngeal PCR from 4 January to 14 April. Viral loads were expressed by the cycle threshold (Ct) in PCR. During the study period 55 HCWs were found positive for SARS-CoV-2. This study found a similar viral load in vaccinated and non-vaccinat ed HCWs infected by SARS-CoV-2 variant B.1.1.7, sugg esting potentially reduced efficacy of BNT162b2 in preve nting transmission of B.1.1.7.
✍
 		34176397
(Infect Dis (Lond))
PMID
34176397
Date of Publishing: 2021 Jun 26
Title Transmission of SARS-CoV-2 variant B.1.1.7 among vaccinated health care workers
Author(s) nameIoannou P, Karakonstantis S et al.
Journal Infect Dis (Lond)
Impact factor
1.23
Citation count: 14
Date of Entry 2021 Sep 5

Structural modelling and binding site analysis of human host cell transmembrane protease serine 2 (TMPRSS2), a protease involved in cleaving a spike protein domain of SARS-CoV-2 to facilitate membrane fusion, was done, followed by structure-based screening of drug-like compounds for it's inhibition. Compounds Otamixaban and NCGC00386945 were shown to exhibit potent activity against TMPRSS2 with an efficient activity in the viral entry assay whereas the compound UKI-1 showed promising activity against the serine protease but was inactive in the SARS-CoV-2 PP entry assay. Out of 20,000 potential drug-like compounds, 350 were selected for experimental validation.
based on binding model analysis with known inhibitors( nafamostat, camostat, and gabexate), 4 pharmacophores were developed.
Virtual screening was done on the basis of pharmacophore based searching, 3 dimensional shape based mapping and structure band docking. Out of the 20,000 drug like compounds, only those matching atleast 2 pharmacophores were extracted.
Activity of TMPRSS2 Inhibitors in the Enzyme Assay and the SARS-COV-2 PP Entry Assay was recorded.
it was observed that most of the inhibitors possessed a benzoamidiniumhead headgroup, playing a key role in effective binding and inhibition.
✍
 		34136758
(ACS Pharmacol Transl Sci)
PMID
34136758
Date of Publishing: 2021 Jun 11
Title Discovery of TMPRSS2 Inhibitors from Virtual Screening as a Potential Treatment of COVID-19
Author(s) nameHu X, Shrimp JH et al.
Journal ACS Pharmacol Transl Sci
Impact factor
14.357
Citation count: 10
Date of Entry 2021 Sep 5

Activity of catechins as an entry-inhibitory agent against viral activity of SARS-CoV-2 and its UK variant (VUI 202012/01) was analysed using molecular docking followed by molecular dynamic simulations. The study showed that catechins formed favourable interactions with the S-protein of the virus, which would potentially block its function. Epigallocatechin gallate (EGCG) was shown to have the best binding amongst the 8 catechins studied against the virus. EGCG showed poor bioavailability but has high levels of maximum tolerance. Active site was located using the native ligand NAG and ligand interactions as mentioned in the primary citation of the spike protein. In the active site, only a change from THR to ILE at position 716 was seen in the mutated variant when compared to the wild spike protein. The active binding scores for the actives sites of the native and mutated spike protein are 66.64 and 63.68 respectively. This mutation was not shown to alter stability, volume or conformation of the active site. Key amino acids observed in a majority of the interactions are AGN919 and THR716 in the wild strain and ILE716 in the mutated strain and TYR1110, PHE1109, GLN1071 and GLU918. It was computationally predicted that clearance of EGCG was relatively faster than what was reported experimentally previously. The maximum tolerance of EGCG was also found to be high.
✍
 		34147855
(Comput Biol Med)
PMID
34147855
Date of Publishing: 2021 Jun 10
Title Entry-inhibitory role of catechins against SARS-CoV-2 and its UK variant
Author(s) nameMhatre S, Gurav N et al.
Journal Comput Biol Med
Impact factor
2.93
Citation count: 5
Date of Entry 2021 Sep 5

2017 flavone analogs was prepared and screened against SARS-CoV-2 Mpro using the molecular docking technique. 371 flavone analogs exhibited good potency towards Mpro with docking scores less than 9.0 kcal/mol. Molecular dynamics (MD) simulations, followed by molecular mechanics-generalized Born surface area (MM/GBSA) binding energy calculations, were performed for the top potent analogs in complex with Mpro. A comparison of the binding affinities demonstrated that the MM/GBSA binding energies of the identified flavone analogs were approximately three and two times less than those of lopinavir and baicalein, respectively.
✍
 		33798836
(J Mol Graph Model)
PMID
33798836
Date of Publishing: 2021 Jun
Title Rutin and flavone analogs as prospective SARS-CoV-2 main protease inhibitors: In silico drug discovery study
Author(s) nameIbrahim MAA, Mohamed EAR et al.
Journal J Mol Graph Model
Impact factor
1.93
Citation count: 17
Date of Entry 2021 Sep 5

11,000 compounds out of this library was chosen for target-specific virtual screening based on Lipinskis rule of 5. The natural screening suggested two efficient compounds (PubChem ID: 95372568 and 1776037) with dihydroxyphenyl region of the compound, found to be important in the interaction with the viral protein showing promising activity which may act as a potent lead inhibitory molecule against the virus. In combina tion with virtual screening, modelling, drug like liness, molecular docking, and 500 ns cumulative molecular dynamics simulations (100 ns for each complex) along with the decomposition analysis to calculate and confirm the stability and fold, we propose 95372568 and 1776037 as novel compo unds of natural origin capable of getting develop ed into potent lead molecules against SARS-CoV- 2 target protein NSP15.
✍
 		33963942
(J Mol Model)
PMID
33963942
Date of Publishing: 2021 May 8
Title Analysis of natural compounds against the activity of SARS-CoV-2 NSP15 protein towards an effective treatment against COVID-19: a theoretical and computational biology approach
Author(s) name Motwalli O, Alazmi M.
Journal J Mol Model
Impact factor
2.9
Citation count: 4
Date of Entry 2021 Sep 5

Different potential repurposed drugs, including hydroxychloroquine, remdesivir, Lopinavir and Affatinib..etc, i.e total 131 drugs were screened in the present study. Molecular docking of these drugs with different SARS-CoV-2 target proteins, including main protease of the virus MPro, Papain-like Protease from SARS-COV-2PLPro, N-terminal RNA binding domain of Nucleocapsid protein of SARS-COV-2 and RNA dependent RNA Polymerase from SARS-COV-2 was performed. Molecular dynamics simulation and MM-PBSA calculation were also conducted. This study showed that among tested drugs in the present in silico study, Afatinib has the highest binding potential to the main protease of SARS-CoV-2, which is higher than HCQ and remdesivir, respectively.
✍
 		34032180
(J Biomol Struct Dyn)
PMID
34032180
Date of Publishing: 2021 May 25
Title Virtual screening of quinoline derived library for SARS-COV-2 targeting viral entry and replication
Author(s) nameAnju A, Chaturvedi S et al.
Journal J Biomol Struct Dyn
Impact factor
3.22
Citation count: 1
Date of Entry 2021 Sep 5

Revealed by molecular docking the profound binding affinity of 14 selected phenolics and terpenes present in honey and propolis (bees glue) against the main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) enzymes of the novel SARS-CoV-2 virus (the causative agent of COVID-19) using AutoDock Vina software. "The bioactive compounds, ellagic acid, hesperetin, and kaempferol, are the most promising compounds on COVID-19 RdRp, while artepillin C, ellagic acid, hesperetin, kaempferol, and quercetin were the most active on the main protease (Mpro)."
✍
 		33934306
(Environ Sci Pollut Res Int)
PMID
33934306
Date of Publishing: 2021 May 2
Title In silico screening of potent bioactive compounds from honeybee products against COVID-19 target enzymes
Author(s) nameShaldam MA, Yahya G et al.
Journal Environ Sci Pollut Res Int
Impact factor
N/A
Citation count: 13
Date of Entry 2021 Sep 5

In this Study the work aims to find molecules that can inhibit the attraction between the Spike proteins of the SARS-COV-2 virus and human ACE2. The results of molecular docking positioned four molecules at the interaction site Tyr-491(Spike)-Glu-37(ACE2) and one at the site Gly-488(Spike)-Lys-353(ACE2).
✍
 		33583954
(J Mol Struct)
PMID
33583954
Date of Publishing: 2021 May 15
Title Computational search for drug repurposing to identify potential inhibitors against SARS-COV-2 using Molecular Docking, QTAIM and IQA methods in viral Spike protein - Human ACE2 interface
Author(s) name Faria SHDM, Teleschi JG.
Journal J Mol Struct
Impact factor
2.19
Citation count: 2
Date of Entry 2021 Sep 5

✍
 		33986405
(Sci Rep)
PMID
33986405
Date of Publishing: 2021 May 13
Title Repurposing potential of posaconazole and grazoprevir as inhibitors of SARS-CoV-2 helicase
Author(s) nameAbidi SH, Almansour NM et al.
Journal Sci Rep
Impact factor
4.12
Citation count: 2
Date of Entry 2021 Sep 5

In-silico screening of 11 FDA approved drugs were performed for drug repurposing against Main protease of SARS-CoV-2 TNF-, IL-6, and IL-1. 2 suitable candidates Rifampicin and Letermovir, were found, based on their binding affinity with the targets and MD simulation. Lopinavir and Ritonavir were used as positive control compounds against Mpro. Rifampicin showed a good binding affinity with inflammatory cytokines : TNF- ( 43.51 kJ/mol), IL-6 ( 34.98 kJ/mol) , and IL-1( 29.54 kJ/mol) During toxicity analysis, most of the selected FDA-approved drugs did not show any potential cytotoxicity, carcinogenicity, and mutagenicity including Rifampicin and Letermovir.
✍
 		33970450
(Pharmacol Rep)
PMID
33970450
Date of Publishing: 2021 May 10
Title Rifampicin and Letermovir as potential repurposed drug candidate for COVID-19 treatment: insights from an in-silico study
Author(s) namePathak Y, Mishra A et al.
Journal Pharmacol Rep
Impact factor
5.1
Citation count: 6
Date of Entry 2021 Sep 5

We used DFT calculation studies for structural elucidation and optimization of the molecules and molecular docking studies on several Covid-19 related proteins and it was found that Vtocdea and VXn molecules are seem to be good candidates for further studies as antiviral agents.
✍
 		33553857
(Comput Toxicol)
PMID
33553857
Date of Publishing: 2021 May
Title Screening possible drug molecules for Covid-19. The example of vanadium (III/IV/V) complex molecules with computational chemistry and molecular docking
Author(s) name Vlasiou MC, Pafti KS.
Journal Comput Toxicol
Impact factor
2.11
Citation count: 5
Date of Entry 2021 Sep 5

Using computational tools to screen a library of marine seaweed compounds against the Spike protein RBD of the SARS-CoV-2 UK variant (VUI 202012/01). Dieckol cannot be used as a lead inhibitor against RBD. 1.Dieckol derivative, i.e., DK07 most potent inhibitor of RBD and was found to possess acceptable physicochemical, pharmacokinetic, drug-likeness, and ADMET properties. 2.The IUPAC name of DK07 is 8-{3-hydroxy-4-[(7-hydroxynaphthalen-2-yl)oxy]phenoxy}-1,4-benzodioxin-5-ol. DK07 binds to the RBD at the ACE2RBD interface and interacts with key amino acid residues. 3.In vitro and in vivo experiments to validate the potential of DK07 to bind UK strain of SARS-CoV-2 Spike protein RBD and prevent its interaction with ACE2.
✍
 		33922914
(Mar Drugs)
PMID
33922914
Date of Publishing: 2021 Apr 25
Title Dieckol and Its Derivatives as Potential Inhibitors of SARS-CoV-2 Spike Protein (UK Strain: VUI 202012/01): A Computational Study
Author(s) nameAatif M, Muteeb G et al.
Journal Mar Drugs
Impact factor
8
Citation count: 5
Date of Entry 2021 Sep 5

Computational screening of Neem compounds by molecular docking and MD-simulation studies indicates Azadirachta Indica a potential inhibitor against PLpro of SARS-CoV-2. DCG causes a huge impact on PLpro upon binding with the latter.
✍
 		33041371
(J Mol Struct)
PMID
33041371
Date of Publishing: 2021 Mar 5
Title Screening of potential drug from Azadiractha Indica (Neem) extracts for SARS-CoV-2 : An insight from molecular docking and MD-simulation studies
Author(s) nameBaildya N, Khan AA et al.
Journal J Mol Struct
Impact factor
2.19
Citation count: 22
Date of Entry 2021 Sep 5

A total of 3639 drugs from SuperDRUG2 database and additionally 14 potential drugs reported against COVID-19 proteins were selected. Molecular docking analyses revealed that nine drugs can bind the active site of M-protein with desirable molecular interactions. We there fore applied molecular dynamics simulations and binding free energy calculation using MM-PBSA to analyze the stability of the compounds.The binding mode of the drugs with M-protein was analyzed and it was observed that Colchicine, Remdesivir, Bafilomycin A1 from COVID-19 suggested drugs and Temozolomide from SuperDRUG2 database displayed desirable molecular interactions and higher binding affinity towards M-protein. Interestingly, Colchicine was found as the top most binder among tested drugs against M-protein.
✍
 		33684397
(J Pharm Sci)
PMID
33684397
Date of Publishing: 2021 Mar 5
Title Insilico drug repurposing using FDA approved drugs against Membrane protein of SARS-CoV-2
Author(s) namePeele KA, Kumar V et al.
Journal J Pharm Sci
Impact factor
- n/a -
Citation count: 4
Date of Entry 2021 Sep 5

In the present study, we perform an in silico screening of 100 compounds isolated from the most commonly used Mexican plants, against the SARS-CoV-2 virus. As results, we identify ten compounds that meet leadlikeness criteria (emodin anthrone, kaempferol, quercetin, aesculin, cichoriin, luteolin, matricin, riolozatrione, monocaffeoyl tartaric acid, aucubin). According to the docking analysis, only three compounds target the key proteins of SARS-CoV-2 (quercetin, riolozatrione and cichoriin), but only one appears to be safe (cichoriin).
✍
 		33557097
(Biomolecules)
PMID
33557097
Date of Publishing: 2021 Feb 4
Title In Silico Screening of Natural Products Isolated from Mexican Herbal Medicines against COVID-19
Author(s) name Rivero-Segura NA, Gomez-Verjan JC.
Journal Biomolecules
Impact factor
4.65
Citation count: 6
Date of Entry 2021 Sep 5

An application of a deep neural network based drug screening method, validating it using a docking algorithm on approved drugs for drug repurposing efforts, and extending the screen to a large library of 750,000 compounds for de novo drug discovery effort. The results of large library screens are incorporated into an open-access web interface to allow researchers from diverse fields to target molecules of interest. Our combined approach allows for both the identification of existing drugs that may be able to be repurposed and de novo design of ACE2-regulatory compounds.
✍
 		33557253
(Int J Mol Sci)
PMID
33557253
Date of Publishing: 2021 Feb 4
Title Predicting Potential SARS-COV-2 Drugs-In Depth Drug Database Screening Using Deep Neural Network Framework SSnet, Classical Virtual Screening and Docking
Author(s) nameKarki N, Verma N et al.
Journal Int J Mol Sci
Impact factor
4.21
Citation count: 11
Date of Entry 2021 Sep 5

In silico screening of 100 compounds isolated from Mexican plants against SARS-CoV-2 was done to identify 10 compounds that meet the leadlikeness and Lipinskis rules. Further docking and toxicoinformatic analysis showed that cichoriin was the best natural product against some of the main proteins in SARS-CoV-2. Pharmacokinetic potential of cichoriin against COVID-19 was done by building PBPK model simulations using data from other coumarins with similar structure. Of the three potential doses of 1, 10, and 100 mg/kg of cichoriin administered IV to a 60-year-old male Mexican American in simulation, cichoriin reaches a higher concentration in the lungs intracellular compared to other compartments with 100mg/kg considered the best dosage.
✍
 		33557097
(Biomolecules)
PMID
33557097
Date of Publishing: 2021 Feb 4
Title In Silico Screening of Natural Products Isolated from Mexican Herbal Medicines against COVID-19
Author(s) name Rivero-Segura NA, Gomez-Verjan JC.
Journal Biomolecules
Impact factor
4.65
Citation count: 6
Date of Entry 2021 Sep 5

Virulence protein factor Nsp1 was targeted by in silico virtual screening of ligand libraries. Molecular docking simulations of the top6 screened ligands with Nsp1 were used and the ligand-Nsp1 complexes were subjected to molecular dynamics simulations to analyze the behaviours of the ligands in a virtual cell From the analyses, it could be safely concluded that the ligands, viz., ligand1, ligand4 and ligand6 had the maximum binding affinities to the Nsp1 apoprotein. All these ligands could bind to the key amino acid residues, Lys164 and His165, which are vital to exert the activity of the Nsp1 apoprotein.
✍
 		33612076
(J Biomol Struct Dyn)
PMID
33612076
Date of Publishing: 2021 Feb 22
Title Identification of the binding interactions of some novel antiviral compounds against Nsp1 protein from SARS-CoV-2 (COVID-19) through high throughput screening.
Author(s) name Chowdhury N, Bagchi A.
Journal J Biomol Struct Dyn
Impact factor
3.22
Citation count: 1
Date of Entry 2021 Sep 5

Computational screening of 84 renin inhibitors by molecular docking and MD-simulation studies indicates remikiren (Ro 425892) of HoffmannLa Roche can be repurposed against the main protease SARS-CoV-2. Renin inhibitors downregulate ACE2 receptor which is a first target for SARS-COV-2 infection, as well as their inhibitory activity on proteases. Remikiren was identified to fulfill the pharmacophore query and showed promising results in both molecular docking and molecular dynamics studies and is recommended for further clinical studies.
✍
 		33370597
(Virology)
PMID
33370597
Date of Publishing: 2021 Feb
Title Repurposing of renin inhibitors as SARS-COV-2 main protease inhibitors: A computational study
Author(s) name Refaey RH, El-Ashrey MK, Nissan YM.
Journal Virology
Impact factor
2.819
Citation count: 5
Date of Entry 2021 Sep 5

Virtual screening of 22 plant bioactive compounds from Azadirachta indica, Mangifera indica, and Moringa oleifera using molecular docking techniques and ADMET studies show top 5 compounds (kaempferol, mangiferin, myrecitin, nimbolide, and quercetin) against SARS-CoV-2 Mpro The docking outputs revealed that catechin, chlorogenic acid, ellagic acid, epicatechin, gedunin, kaempferol, lupeol, mangiferin, myricetin, nimbandiol, nimbinene, nimbolide, and quercetin had better binding positions with Mpro than with hydroxychloroquine. The control drug, hydroxychloroquine, has a binding energy of 6.4 kcal/mol.
✍
 		33437230
(J Taibah Univ Med Sci)
PMID
33437230
Date of Publishing: 2021 Jan 6
Title In-silico analysis of the inhibition of the SARS-CoV-2 main protease by some active compounds from selected African plants
Author(s) nameUmar HI, Josiah SS et al.
Journal J Taibah Univ Med Sci
Impact factor
2.4
Citation count: 10
Date of Entry 2021 Sep 5