COV-DOCK server: A web server for COVID-19 ligand-target docking

Singh, Prashant K.; Sinha, Robin; Nath, Swarsat Kaushik; P, Preeti; Kumari, Priya; Garg, Naveen

doi:10.31219/osf.io/x2ky5

Cited by 2 publications

(1 citation statement)

References 11 publications

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“…Here we performed the docking of trypanocidal drugs (Bz and Nf), control drugs (orlistat and aspirin), and 1500 FDA-approved drugs with T. cruzi network proteins (4905), as well as with the whole human proteome (19,523). We used our new drug repurposing pipeline to conduct large-scale docking [ 86 ]. Based on our prediction, we propose that the trypanocidal drugs show a preferential binding with T. cruzi proteins, as compared to the control drugs.…”

Section: Discussionmentioning

confidence: 99%

A Data-Driven Approach to Construct a Molecular Map of Trypanosoma cruzi to Identify Drugs and Vaccine Targets

et al. 2023

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Chagas disease (CD) is endemic in large parts of Central and South America, as well as in Texas and the southern regions of the United States. Successful parasites, such as the causative agent of CD, Trypanosoma cruzi have adapted to specific hosts during their phylogenesis. In this work, we have assembled an interactive network of the complex relations that occur between molecules within T. cruzi. An expert curation strategy was combined with a text-mining approach to screen 10,234 full-length research articles and over 200,000 abstracts relevant to T. cruzi. We obtained a scale-free network consisting of 1055 nodes and 874 edges, and composed of 838 proteins, 43 genes, 20 complexes, 9 RNAs, 36 simple molecules, 81 phenotypes, and 37 known pharmaceuticals. Further, we deployed an automated docking pipeline to conduct large-scale docking studiesinvolving several thousand drugs and potential targets to identify network-based binding propensities. These experiments have revealed that the existing FDA-approved drugs benznidazole (Bz) and nifurtimox (Nf) show comparatively high binding energies to the T. cruzi network proteins (e.g., PIF1 helicase-like protein, trans-sialidase), when compared with control datasets consisting of proteins from other pathogens. We envisage this work to be of value to those interested in finding new vaccines for CD, as well as drugs against the T. cruzi parasite.

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Section: Discussionmentioning

confidence: 99%

A Data-Driven Approach to Construct a Molecular Map of Trypanosoma cruzi to Identify Drugs and Vaccine Targets

et al. 2023

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Review of Novel Corona Virus Disease (Covid-19) in India

Sevak

Chauhan

Parihar

et al. 2022

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Novel coronavirus also known as severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) was emerged from Wuhan, China and have taken catastrophic form globally. India being a dense populated country is also affected by it’s deadly infection. Bats were considered as its primary host but COVID-19 disease became pandemic via human to human transmission by droplet nuclei. The incubation period ranges upto 14 days and main symptoms of disease were noticed as atypical pneumonia, fever, difficult breathing, decreased SPO2 level and ultimately death due to respiratory failure depending upon immune status of the patients. Coronaviruses are positive-sense, single-stranded RNA viruses and harbour a genome (30 kb) consisting of two terminal untranslated regions and twelve putative functional open reading frames (ORFs), encoding for non-structural and structural proteins. There are sixteen putative non-structural proteins, including proteases, RNA-dependent RNA polymerase, helicase, other proteins involved in the transcription and replication of SARS-CoV-2, and four structural proteins, including spike protein (S), envelope (E), membrane (M), and nucleocapsid (N). SARS-CoV-2 infection, with a heavy viral load in the body, destroys the human lungs through cytokine storm, especially in elderly persons and people with immunosuppressed disorders. A number of drugs have been repurposed and employed, but still, no specific antiviral medicine has been approved by the FDA to treat this disease. This review provides a current status of the COVID-19, epidemiology, an overview of phylogeny, mode of action, diagnosis, and possible treatment methods and vaccines.

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COV-DOCK server: A web server for COVID-19 ligand-target docking

Cited by 2 publications

References 11 publications

A Data-Driven Approach to Construct a Molecular Map of Trypanosoma cruzi to Identify Drugs and Vaccine Targets

A Data-Driven Approach to Construct a Molecular Map of Trypanosoma cruzi to Identify Drugs and Vaccine Targets

Review of Novel Corona Virus Disease (Covid-19) in India

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