Powered by OpenAIRE graph
Found an issue? Give us feedback
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODOarrow_drop_down
image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
ZENODO
Article . 2026
License: CC BY
Data sources: ZENODO
https://doi.org/10.26434/chemr...
Article . 2026 . Peer-reviewed
Data sources: Crossref
ZENODO
Article . 2026
License: CC BY
Data sources: Datacite
ZENODO
Article . 2026
License: CC BY
Data sources: Datacite
versions View all 3 versions
addClaim

Structural Determinants of Mac1 Inhibition: Lessons from Ligand Binding Patterns

Authors: Weber, Verena; Rossetti, Giulia; Lüscher, Bernhard; Korn, Patricia; Knapp, Sarah;

Structural Determinants of Mac1 Inhibition: Lessons from Ligand Binding Patterns

Abstract

This study comprehensively analyzes how various inhibitors bind to the SARS-CoV-2 macrodomain Mac1, a key protein implicated in hampering the host's immune response following viral infection. In this study we used volume-based metadynamics simulations to investigate the binding mechanisms of ADP-ribose and two Mac1 inhibitors: the adenineanalogue GS-441524 and the non-adenine-analogue S09. By combining free-energy simulations with a bioinformatic analysis, we aimed at determining whether the binding patterns observed for the selected ligands are conserved can be generalized across Mac1 inhibitors and can be exploited to guide a rational design for future therapeutics. Our simulations show the pivotal role of the adenosine moiety in Mac1 recognition. Notably, for small molecules, like S09 and GS-441524, the oxyanion hole also emerged as an alternative and essential stabilizing region. This site, which preferentially accommodates electronegative groups, is engaged by approximately 76% of reported Mac1 inhibitors, making it a key target for Mac1 inhibition. In addition, we demonstrate that the unstructured loops 1 and 2 shape ligand entry, with loop 1 functioning as a dynamic gateway. Within this loop, Leu126, part of the virus-specific P-L-L-S motif, serves as a key anchoring residue for potent inhibitors. Collectively, these findings suggest that targeting both the oxyanion hole and Leu126 may enhance both the specificity and affinity of next-generation Mac1 inhibitors.

  • BIP!
    Impact byBIP!
    selected citations
    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    0
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Average
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Average
Powered by OpenAIRE graph
Found an issue? Give us feedback
selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
0
Average
Average
Average
Related to Research communities