Design, synthesis and evaluation of inhibitors of the SARS-CoV-2 nsp3 macrodomain

Sherrill, Lavinia M; Joya, Elva E.; Walker, AnnMarie; Roy, Anuradha; Alhammad, Yousef M O; Atobatele, Moriama; Wazir, Sarah; Abbas, George; Keane, Patrick; Zhuo, Junlin; Leung, Anthony Kwan; Johnson, David K.; Lehtiö, L.; Ferraris, Dana

doi:10.1016/j.bmc.2022.116788

Cited by 19 publications

(26 citation statements)

References 40 publications

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“…Promisingly, inactivation of Mac1 by single-point mutations in the ADPr-binding site demonstrated significant reduction in lethality and pathogenicity in mice after SARS-CoV infection (8). Small molecule inhibitors of SARS-CoV-2 Mac1 might therefore offer novel therapeutics to mitigate COVID-19 (9,10). A challenge for the development of such inhibitors has been the lack of small molecule modulators of macrodomain activity, other than ADPr.…”

Section: Introductionmentioning

confidence: 99%

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Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2

Gahbauer

Correy

Schuller

et al. 2022

Preprint

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The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for pathogenesis and lethality. While small molecule inhibitors of Mac1 have great therapeutic potential, few have been described. Here, we report the structure-based development of several chemical scaffolds exhibiting low- to sub-micromolar affinity for Mac1 through iterations of computer-aided design, structural characterization by ultra-high resolution X-ray protein crystallography, and binding evaluation with in-solution assays. Potent scaffolds were designed with in silico linkage of previously obtained fragment hits and ultra-large library docking screens of more than 450 million molecules. In total, 160 hits comprising 119 different scaffolds were discovered and 152 Mac1-ligand complex crystal structures were determined, typically to 1 Å resolution or better. The structure-activity-relationships emerging from this study may template future drug development against Mac1.

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Section: Introductionmentioning

confidence: 99%

“…Promisingly, inactivation of Mac1 by single-point mutations in the ADPr-binding site significantly reduced lethality and pathogenicity in mice after SARS-CoV infection (8). Small molecule inhibitors of SARS-CoV-2 Mac1 should therefore offer novel therapeutics to mitigate COVID-19 (9, 10).…”

Section: Introductionmentioning

confidence: 99%

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2

Gahbauer

Correy

Schuller

et al. 2022

Preprint

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“…The importance of ADP-ribosylation-dependent systems in the antiviral response is highlighted by the fact that several viruses, such as alphaviruses and coronaviruses, have evolved macrodomains to counter hosts’ defensive processes controlled by ADP-ribosylation [ 33 , 53 , 60 , 195 , 196 , 197 , 198 ]. Viral macrodomains represent potential targets of antiviral drugs [ 69 , 70 , 71 , 199 , 200 , 201 ]. The role of ADP-ribosylation in antiviral and stress response, for instance, involving the ADP-ribosylation of viral genetic material, are reminiscent of the DNA modifications observed in lower organisms, where the transfer of ADP-ribose on nucleic acids results in the defence mechanism’s response.…”

Section: Discussionmentioning

confidence: 99%

The DarT/DarG Toxin–Antitoxin ADP-Ribosylation System as a Novel Target for a Rational Design of Innovative Antimicrobial Strategies

2023

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The chemical modification of cellular macromolecules by the transfer of ADP-ribose unit(s), known as ADP-ribosylation, is an ancient homeostatic and stress response control system. Highly conserved across the evolution, ADP-ribosyltransferases and ADP-ribosylhydrolases control ADP-ribosylation signalling and cellular responses. In addition to proteins, both prokaryotic and eukaryotic transferases can covalently link ADP-ribosylation to different conformations of nucleic acids, thus highlighting the evolutionary conservation of archaic stress response mechanisms. Here, we report several structural and functional aspects of DNA ADP-ribosylation modification controlled by the prototype DarT and DarG pair, which show ADP-ribosyltransferase and hydrolase activity, respectively. DarT/DarG is a toxin–antitoxin system conserved in many bacterial pathogens, for example in Mycobacterium tuberculosis, which regulates two clinically important processes for human health, namely, growth control and the anti-phage response. The chemical modulation of the DarT/DarG system by selective inhibitors may thus represent an exciting strategy to tackle resistance to current antimicrobial therapies.

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“…These combined studies have prompted several groups to begin screening for and developing SARS-CoV-2 Mac1 inhibitors that could potentially be used therapeutically to treat patients infected with SARS-CoV-2 or other emerging CoVs (34)(35)(36)(37)(38)(39)(40)(41). However, before testing any of these inhibitors for their antiviral activity, it is imperative to determine the role and functions of Mac1 in SARS-CoV-2 replication, pathogenesis, and the host immune response.…”

Section: Introductionmentioning

confidence: 99%

SARS-CoV-2 Mac1 is required for IFN antagonism and efficient virus replication in mice

Alhammad

Parthasarathy

Ghimire

et al. 2023

Preprint

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Several coronavirus (CoV) encoded proteins are being evaluated as targets for antiviral therapies for COVID-19. Included in this set of proteins is the conserved macrodomain, or Mac1, an ADP-ribosylhydrolase and ADP-ribose binding protein. Utilizing point mutant recombinant viruses, Mac1 was shown to be critical for both murine hepatitis virus (MHV) and severe acute respiratory syndrome (SARS)-CoV virulence. However, as a potential drug target, it is imperative to understand how a complete Mac1 deletion impacts the replication and pathogenesis of different CoVs. To this end, we created recombinant bacterial artificial chromosomes (BACs) containing complete Mac1 deletions (ΔMac1) in MHV, MERS-CoV, and SARS-CoV-2. While we were unable to recover infectious virus from MHV or MERS-CoV ΔMac1 BACs, SARS-CoV-2 ΔMac1 was readily recovered from BAC transfection, indicating a stark difference in the requirement for Mac1 between different CoVs. Furthermore, SARS-CoV-2 ΔMac1 replicated at or near wild-type levels in multiple cell lines susceptible to infection. However, in a mouse model of severe infection, ΔMac1 was quickly cleared causing minimal pathology without any morbidity. ΔMac1 SARS-CoV-2 induced increased levels of interferon (IFN) and interferon-stimulated gene (ISG) expression in cell culture and mice, indicating that Mac1 blocks IFN responses which may contribute to its attenuation. ΔMac1 infection also led to a stark reduction in inflammatory monocytes and neutrophils. These results demonstrate that Mac1 only minimally impacts SARS-CoV-2 replication, unlike MHV and MERS-CoV, but is required for SARS-CoV-2 pathogenesis and is a unique antiviral drug target.

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Design, synthesis and evaluation of inhibitors of the SARS-CoV-2 nsp3 macrodomain

Cited by 19 publications

References 40 publications

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2

Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 Macrodomain of SARS-CoV-2

The DarT/DarG Toxin–Antitoxin ADP-Ribosylation System as a Novel Target for a Rational Design of Innovative Antimicrobial Strategies

SARS-CoV-2 Mac1 is required for IFN antagonism and efficient virus replication in mice

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