RESEARCH: COVID-19
FOLDING PROJECT #13434 PROFILE

This project uses computer simulations to study how potential drugs might work against the main enzyme of the SARS-CoV-2 virus. The goal is to help researchers quickly identify promising drug candidates for testing. You can even support this open science project by donating!

Note: This TLDR is a simplication and may not be 100% accurate.

https://www.youtube.com/watch?v=VnyaAmM1nhE These projects are to assist rapid sprints of relative alchemical free energy calculations for prioritizing compound designs from chemists from the COVID Moonshot for synthesis. This series of projects simulates the SARS-CoV-2 main viral protease. These projects collectively cover the entire set of X-ray structures collected by the COVID Moonshot, and more RUNs will be added as new structures are collected. To learn more about what the Moonshot is and how it came about, you can read our blog post or watch this video. In addition to helping us prioritize compounds, you can help us purchase more compounds for synthesis at cost from Enamine by sponsoring our GoFundMe page for patent-free open science COVID-19 drug discovery! This is a radical new approach to drug discovery that aims to rapidly produce inexpensive new therapies. SARS-CoV-2 main viral potease (Mpro) with ligand bound, from the RCSB.

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alchemical free energy calculations

Calculations that estimate the energy changes associated with chemical reactions.

Alchemical free energy calculations are a type of computer simulation used in drug discovery to predict how well a molecule will bind to a target protein. This information can be used to prioritize compounds for further testing.

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compound design

The process of creating new molecules with desired biological activity.

Compound design is a crucial step in drug discovery, where chemists use their knowledge of molecular structures and biological targets to create new molecules that can interact with specific proteins or pathways in the body. This involves designing compounds that have the right shape, charge, and functional groups to bind effectively to their target.

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SARS-CoV-2

The virus that causes COVID-19.

SARS-CoV-2 is a type of coronavirus that emerged in late 2019 and rapidly spread worldwide, causing the COVID-19 pandemic. This virus primarily infects the respiratory system and can lead to severe illness, pneumonia, and death.

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viral protease

An enzyme produced by viruses that cleaves viral proteins to enable replication.

Viral proteases are essential enzymes for the life cycle of many viruses, including SARS-CoV-2. They cleave (cut) specific viral proteins, which allows the virus to assemble new viral particles and spread infection.

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X-ray structures

3D representations of molecules obtained using X-ray crystallography.

X-ray structures are detailed 3D models of molecules determined by shining X-rays through crystallized samples. These structures reveal the arrangement of atoms within a molecule, providing crucial insights into its function and interactions with other molecules.

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Mpro

Main protease of SARS-CoV-2.

Mpro, also known as 3CL protease, is a key enzyme produced by the SARS-CoV-2 virus. It plays a crucial role in viral replication by cleaving viral proteins, which are necessary for assembling new viral particles and spreading infection.

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RCSB

Research Collaboratory for Structural Bioinformatics.

The RCSB Protein Data Bank (PDB) is a comprehensive global database of experimentally determined 3D structures of proteins and nucleic acids. It provides researchers with access to a vast collection of structural data, which is essential for understanding the function and interactions of biomolecules.