PrankWeb: web server for ligand binding-site prediction and visualization

Jendele, Lukáš; Krivák, Radoslav; Škoda, Petr; Novotný, Marián; Hoksza, David

doi:10.1101/590877

Cited by 10 publications

(10 citation statements)

References 35 publications

(20 reference statements)

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“…PrankWeb [54] was used to check the binding site coordinate and specify the amino acids in the SARS-CoV-2 proteins and pockets. Couplings were carried out using Auto Dock vina version 4.2.6 [55], configuring a box with dimensions x: 24, y: 24, z: 24, this for each simulation carried out with the viral proteins using exhaustiveness of 20.…”

Section: Methodsmentioning

confidence: 99%

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Atorvastatin effectively inhibits late replicative cycle steps of SARS-CoV-2in vitro

Flórez-Álvarez

Zapata

et al. 2021

Preprint

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Introduction: SARS-CoV-2 has caused a pandemic of historic proportions and continues to spread worldwide. Currently, there is no effective therapy against this virus. This article evaluated the in vitro antiviral effect of Atorvastatin against SARS-CoV-2 and also identified the interaction affinity between Atorvastatin and three SARS-CoV-2 proteins, using in silico structure-based molecular docking approach. Materials and methods: The antiviral activity of Atorvastatin against SARS-CoV-2 was evaluated by three different treatment strategies using a clinical isolate of SARS-CoV-2. The interaction of Atorvastatin with Spike, RNA-dependent RNA polymerase (RdRp) and 3C-like protease (3CLpro) was evaluated by molecular docking. Results: Atorvastatin showed anti-SARS-CoV-2 activity of 79%, 54.8%, 22.6% and 25% at 31.2, 15.6, 7.9, and 3.9 µM, respectively, by pre-post-treatment strategy. In addition, atorvastatin demonstrated an antiviral effect of 26.9% at 31.2 µM by pre-infection treatment. This compound also inhibited SARS-CoV-2 in 66.9%, 75%, 27.9% and 29.2% at concentrations of 31.2, 15.6, 7.9, and 3.9 µM, respectively, by post-infection treatment. The interaction of atorvastatin with SARS-CoV-2 Spike, RdRp and 3CL protease yielded a binding affinity of -8.5 Kcal/mol, -6.2 Kcal/mol, and -7.5 Kcal/mol, respectively. Conclusion: Our study demonstrated the in vitro anti-SARS-CoV-2 activity of Atorvastatin, mainly against the late steps of the viral replicative cycle. A favorable binding affinity with viral proteins by bioinformatics methods was also shown. Due to its low cost, availability, well-established safety and tolerability, and the extensive clinical experience of atorvastatin, it could prove valuable in reducing morbidity and mortality from COVID-19.

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Section: Methodsmentioning

confidence: 99%

“…PrankWeb [54] was used to check the binding site coordinate and specify the amino acids in the SARS-CoV-2 proteins and pockets. Couplings were carried out using Auto Dock vina version 4.…”

Section: Molecular Dockingmentioning

confidence: 99%

Atorvastatin effectively inhibits late replicative cycle steps of SARS-CoV-2in vitro

Flórez-Álvarez

Zapata

et al. 2021

Preprint

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“…The interaction of ligands with these active residues halt substrate processing, which results in protein inhibition. By keeping this strategy in mind, DogSite Scorer [9] and Prank Web [10] were used to predict the active site residues within these receptors to direct these ligands toward these areas in the screening analysis.…”

Section: Active Site Predictionmentioning

confidence: 99%

Do fever-relieving Medicines have anti-COVID Activity: an in silico Insight

2021

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Aim: The present study was performed to determine the inhibitory interaction of fever-relieving medicines with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) essential proteins. Materials & methods: Structure-based drug repositioning was performed using PYRX 0.9 and these drugs were directed toward the predicted active site of SARS-CoV-2 spike glycoprotein receptor-binding domain, main protease and RNA-dependent RNA polymerase. Results: Results showed that acetaminophen and naproxen have considerable inhibitory activity and show a high affinity for active residues of these proteins. The prediction of activity spectra for substances (PASS) studies showed that these drugs are anti-inflammatory, antiviral and immunostimulant. Conclusion: Hence, it is proven that these drugs have antiviral activity against SARS-CoV-2 and can stimulate the immune and anti-inflammatory response against this disease.

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“…We draw a Ramachandran plot using the RAMPAGE program to validate the predicted structures by measuring backbone psi (Ψ) and dihedral phi ( ) angles (Lovell et al, 2003). We also used P2Rank in PrankWeb software (Jendele et al, 2019) and CASTp tool (Tian et al, 2018) to analyze the refined structure of GASA proteins to predict protein pockets and cavities. Finally, PyMOL (DeLano, 2002) was used to visualize results.…”

Section: Three-dimensional Protein Modeling and Molecular Dockingmentioning

confidence: 99%

TheGASAGene Family inTheobroma cacao: Genome wide Identification and Expression Analysis

Abdullah

Faraji

Mehmood

et al. 2021

Preprint

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The gibberellic acid-stimulated Arabidopsis (GASA/GAST) gene family is widely distributed in plants. The role of the GASA gene family has been reported previously in various physiological and biological processes, such as cell division, root and seed development, stem growth, and fruit ripening. These genes also provide resistance to abiotic and biotic stresses including antimicrobial, antiviral, and antifungal. Here, we report 17 tcGASA genes in Theobroma cacao L. distributed on six chromosomes. The gene structure, promoter-region sequences, protein structure, and biochemical properties, expression, and phylogenetics of all tcGASAs were analyzed. Phylogenetic analyses divided tcGASA proteins into five groups. The nine segmentally duplicating genes form four pairs and cluster together in phylogenetic tree. Purifying selection pressure was recorded on tcGASA, including duplicated genes. Several stress/hormone-responsive cis-regulatory elements were also recognized in the promoter region of tcGASAs. Differential expression analyses revealed that most of the tcGASA genes showed elevated expression in the seeds (cacao food), implying their role in seed development. The black rod disease of genus Phytophthora caused up to 20–25% loss (700,000 metric tons) in world cacao production. The role of tcGASA genes in conferring fungal resistance was also explored based on RNAseq data against Phytophthora megakarya. The differential expression of tcGASA genes was recorded between the tolerant and susceptible cultivars of cacao plants, which were inoculated with the fungus for 24h and 72h. This differential expression indicating possible role of tcGASA genes to fungal resistant in cacao. Our findings provide new insight into the function, evolution, and regulatory system of the GASA family genes in T. cacao and provide new target genes for development of fungi-resistant cacao varieties in breeding programs.

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PrankWeb: web server for ligand binding-site prediction and visualization

Cited by 10 publications

References 35 publications

Atorvastatin effectively inhibits late replicative cycle steps of SARS-CoV-2in vitro

Atorvastatin effectively inhibits late replicative cycle steps of SARS-CoV-2in vitro

Do fever-relieving Medicines have anti-COVID Activity: an in silico Insight

TheGASAGene Family inTheobroma cacao: Genome wide Identification and Expression Analysis

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