Virtually screening antiviral compounds against SARS-CoV-2 structure may speed up drug and vaccine D

June 24, 2020

Virtually screening antiviral compounds to model their interactions with the SARS-CoV-2 virus may enable scientists to more easily identify antiviral drugs that work against the virus while informing the search for viable vaccine candidates, according to a new study. By screening for interactions with certain structural domains and active sites on the virus, this structure-based approach may help scientists identify existing drugs that can be repurposed, including therapies developed to treat MERS-CoV, SARS-CoV, Ebola, and HIV. This approach may also assist with the development of new drugs and protein-based SARS-CoV-2 vaccines with fewer experiments and higher reliability than traditional methods. Information about SARS-CoV-2 reported from its recent genome sequencing has revealed key targets for drugs and vaccines, including the spike protein complex, which helps mediate viral entry into host cells, as well as the main protease, an enzyme that enables viral replication and transcription. To test how these elements of the virus' structure may be used to search virtually for prospective drugs, Pritam Kumar Panda and colleagues computationally screened 640 antiviral compounds from a database against the spike protein and main protease using AutoDock Vina, an open-source program for identifying the "best fit" orientation of a molecule that binds to a protein. The researchers then used two additional programs, UCSF Chimera and Discovery Studio Visualizer, to analyze these molecular orientations. The researchers found that an antiviral polymerase inhibitor PC786 targets several SARS-CoV-2 receptors with high affinity, making it a standout among the antiviral drugs they studied. Panda et al. also identified several additional antiviral drugs with strong binding affinities to the spike protein and main protease, revealing a number of drugs that may be candidates for further research in efforts to fight SARS-CoV-2.

American Association for the Advancement of Science

Related Protein Articles from Brightsurf:

The protein dress of a neuron
New method marks proteins and reveals the receptors in which neurons are dressed

Memory protein
When UC Santa Barbara materials scientist Omar Saleh and graduate student Ian Morgan sought to understand the mechanical behaviors of disordered proteins in the lab, they expected that after being stretched, one particular model protein would snap back instantaneously, like a rubber band.

Diets high in protein, particularly plant protein, linked to lower risk of death
Diets high in protein, particularly plant protein, are associated with a lower risk of death from any cause, finds an analysis of the latest evidence published by The BMJ today.

A new understanding of protein movement
A team of UD engineers has uncovered the role of surface diffusion in protein transport, which could aid biopharmaceutical processing.

A new biotinylation enzyme for analyzing protein-protein interactions
Proteins play roles by interacting with various other proteins. Therefore, interaction analysis is an indispensable technique for studying the function of proteins.

Substituting the next-best protein
Children born with Duchenne muscular dystrophy have a mutation in the X-chromosome gene that would normally code for dystrophin, a protein that provides structural integrity to skeletal muscles.

A direct protein-to-protein binding couples cell survival to cell proliferation
The regulators of apoptosis watch over cell replication and the decision to enter the cell cycle.

A protein that controls inflammation
A study by the research team of Prof. Geert van Loo (VIB-UGent Center for Inflammation Research) has unraveled a critical molecular mechanism behind autoimmune and inflammatory diseases such as rheumatoid arthritis, Crohn's disease, and psoriasis.

Resurrecting ancient protein partners reveals origin of protein regulation
After reconstructing the ancient forms of two cellular proteins, scientists discovered the earliest known instance of a complex form of protein regulation.

Sensing protein wellbeing
The folding state of the proteins in live cells often reflect the cell's general health.

Read More: Protein News and Protein Current Events is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to