Projects 13430-13437

Cause: covid-19

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 protease

SARS-CoV-2 main viral potease (Mpro) with ligand bound, from the RCSB

List of Contributors

This project is managed by Prof. John Chodera at Memorial Sloan Kettering Cancer Center.


The Chodera lab uses computation and experiment to develop quantitative, multiscale models of the effects of small molecules on biomolecular macromolecules and cellular pathways. To do this, the group utilizes physical models and rigorous statistical mechanics, with overall goals of engineering novel therapeutics and tools for chemical biology, as well as understanding the physical driving forces behind the evolution of resistance mutations. The group makes use of advanced algorithms for molecular dynamics simulations on GPUs and distributed computing platforms, in addition to robot-driven high-throughput experiments focusing on characterizing biophysical interactions between proteins and small molecules.

A main focus of the lab is on the engineering of highly selective targeted small molecule inhibitors in cancer.

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