Structural determinants of Mac1 inhibition: Lessons from ligand binding patterns

International Journal of Biological Macromolecules, vol. 382, pp. 154249

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 adenine-analogue 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 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. However, 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 2 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.

Authors 5

1. Verena Weber Aachen Faculty of Mathematics, Computer Science and Natural Sciences

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52062, Aachen, Germany; Computational Biomedicine, Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany

2. Sarah Knapp Aachen Institute of Biochemistry and Molecular Biology Medical School Institute of Pharmacology, Medical School

   RWTH Aachen University

   Affiliation as printed

   Institute of Biochemistry and Molecular Biology, Medical School of the RWTH Aachen University, 52074, Aachen, Germany; Institute of Pharmacology, Medical School of the RWTH Aachen University, 52074, Aachen, Germany

3. Patricia Korn Aachen Institute of Biochemistry and Molecular Biology Medical School Department of Cardiac Surgery Medical Faculty

   RWTH Aachen University

   Affiliation as printed

   Institute of Biochemistry and Molecular Biology, Medical School of the RWTH Aachen University, 52074, Aachen, Germany; Department of Cardiac Surgery, Medical Faculty, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany

4. Bernhard Lüscher Aachen Institute of Biochemistry and Molecular Biology Medical School

   RWTH Aachen University

   Affiliation as printed

   Institute of Biochemistry and Molecular Biology, Medical School of the RWTH Aachen University, 52074, Aachen, Germany

5. Giulia Rossetti corresponding Aachen Department of Neurology, Medical Faculty

   Forschungszentrum Jülich · Jülich Supercomputing Centre · RWTH Aachen University

   Affiliation as printed

   Computational Biomedicine, Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428, Jülich, Germany; Department of Neurology, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany; Jülich Supercomputing Center (JSC), Forschungszentrum Jülich, 52425, Jülich, Germany. Electronic address: g.rossetti@fz-juelich.de