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A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing
TLDR
A human–SARS-CoV-2 protein interaction map highlights cellular processes that are hijacked by the virus and that can be targeted by existing drugs, including inhibitors of mRNA translation and predicted regulators of the sigma receptors.
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ZINC - A Free Database of Commercially Available Compounds for Virtual Screening
TLDR
This paper has prepared a library of 727,842 molecules, each with 3D structure, using catalogs of compounds from vendors, and hopes that this database will bring virtual screening libraries to a wide community of structural biologists and medicinal chemists.
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Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
TLDR
An improved benchmarking set that includes more diverse targets such as GPCRs and ion channels, totaling 102 proteins with 22886 clustered ligands drawn from ChEMBL, each with 50 property-matched decoys drawn from ZINC, is described.
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Benchmarking sets for molecular docking.
TLDR
A directory of useful decoys (DUD), with 2950 ligands for 40 different targets, leading to a database of 98,266 compounds, which allowed 40x40 cross-docking, where the enrichments of each ligand set could be compared for all 40 targets, enabling a specificity metric for the docking screens.
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Relating protein pharmacology by ligand chemistry
TLDR
This work began with 65,000 ligands annotated into sets for hundreds of drug targets, and found that methadone, emetine and loperamide (Imodium) may antagonize muscarinic M3, α2 adrenergic and neurokinin NK2 receptors, respectively.
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ZINC ? A Free Database of Commercially Available Compounds for Virtual Screening.
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The Global Phosphorylation Landscape of SARS-CoV-2 Infection
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A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing
TLDR
The identification of host dependency factors mediating virus infection may provide key insights into effective molecular targets for developing broadly acting antiviral therapeutics against SARS-CoV-2 and other deadly coronavirus strains.
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Predicting new molecular targets for known drugs
TLDR
Compared 3,665 US Food and Drug Administration (FDA)-approved and investigational drugs against hundreds of targets, defining each target by its ligands, chemical similarities between drugs and ligand sets predicted thousands of unanticipated associations.
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Automated docking with grid‐based energy evaluation
The ability to generate feasible binding orientations of a small molecule within a site of known structure is important for ligand design. We present a method that combines a rapid, geometric docking…
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