
==== Front
bioRxiv
BIORXIV
bioRxiv
2692-8205
Cold Spring Harbor Laboratory

10.1101/2024.08.25.609621
preprint
1
Article
Extensive exploration of structure activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment merging and active learning
Correy Galen J. http://orcid.org/0000-0001-5155-7325

Rachman Moira http://orcid.org/0000-0003-3671-8885

Togo Takaya http://orcid.org/0000-0003-0243-0760

Gahbauer Stefan http://orcid.org/0000-0002-3115-9757

Doruk Yagmur U. http://orcid.org/0000-0002-3388-7803

Stevens Maisie http://orcid.org/0009-0004-9732-0349

Jaishankar Priyadarshini http://orcid.org/0009-0005-2013-8941

Kelley Brian http://orcid.org/0000-0003-3615-2818

Goldman Brian http://orcid.org/0009-0006-6465-6959

Schmidt Molly http://orcid.org/0000-0002-8535-6764

Kramer Trevor http://orcid.org/0009-0002-5932-7406

Ashworth Alan http://orcid.org/0000-0003-1446-7878

Riley Patrick http://orcid.org/0000-0003-0797-0272

Shoichet Brian K. http://orcid.org/0000-0002-6098-7367

Renslo Adam R. http://orcid.org/0000-0002-1240-2846

Walters W. Patrick http://orcid.org/0000-0003-2860-7958

Fraser James S. http://orcid.org/0000-0002-5080-2859

26 8 2024
2024.08.25.609621https://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License, which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
http://biorxiv.org/lookup/doi/10.1101/2024.08.25.609621
nihpp-2024.08.25.609621.pdf
Abstract

The macrodomain contained in the SARS-CoV-2 non-structural protein 3 (NSP3) is required for viral pathogenesis and lethality. Inhibitors that block the macrodomain could be a new therapeutic strategy for viral suppression. We previously performed a large-scale X-ray crystallography-based fragment screen and discovered a sub-micromolar inhibitor by fragment linking. However, this carboxylic acid-containing lead had poor membrane permeability and other liabilities that made optimization difficult. Here, we developed a shape- based virtual screening pipeline - FrankenROCS - to identify new macrodomain inhibitors using fragment X-ray crystal structures. We used FrankenROCS to exhaustively screen the Enamine high-throughput screening (HTS) collection of 2.1 million compounds and selected 39 compounds for testing, with the most potent compound having an IC 50 value equal to 130 μM. We then paired FrankenROCS with an active learning algorithm (Thompson sampling) to efficiently search the Enamine REAL database of 22 billion molecules, testing 32 compounds with the most potent having an IC 50 equal to 220 μM. Further optimization led to analogs with IC 50 values better than 10 μM, with X-ray crystal structures revealing diverse binding modes despite conserved chemical features. These analogs represent a new lead series with improved membrane permeability that is poised for optimization. In addition, the collection of 137 X-ray crystal structures with associated binding data will serve as a resource for the development of structure-based drug discovery methods. FrankenROCS may be a scalable method for fragment linking to exploit ever-growing synthesis-on- demand libraries.
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pmc
