Discovery of Drug-like Ligands for the Mac1 Domain of SARS-CoV-2 Nsp3

Virdi, Rajdeep S; Bavisotto, Robert; Hopper, Nicholas C; Vuksanovic, Nemanja; Melkonian, Trevor R; Silvaggi, N.R.; Frick, David N.

doi:10.1101/2020.07.06.190413

Cited by 7 publications

(7 citation statements)

References 27 publications

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“…Because of their ready availability in useful amounts, most of these experiments focused on the docking hits. For DSF, in agreement with previous reports for this domain ( 24 ), we observed substantial elevation of the apparent melting temperature (Tm a ) of Nsp3 Mac1 upon addition of its known binding partner, ADP-ribose ( Fig. 9 C,D,G).…”

Section: Resultssupporting

confidence: 92%

“…While this inhibitor showed on-target activity in cells, its unique allosteric binding site is difficult to translate to other macrodomains. While potential Mac1 inhibitors have emerged with the advent of SARS-CoV-2 (23)(24)(25)(26)(27), their binding mechanisms and efficacy remain unclear. The lack of a biochemical assay specific for Mac1 has hindered their development.…”

Section: Introductionmentioning

confidence: 99%

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Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking

Schuller¹,

Correy²,

Gahbauer³

et al. 2020

Preprint

102

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The SARS-CoV-2 macrodomain (Mac1) within the non-structural protein 3 (Nsp3) counteracts host-mediated antiviral ADP-ribosylation signalling. This enzyme is a promising antiviral target because catalytic mutations render viruses non-pathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of diverse fragment libraries resulted in 214 unique macrodomain-binding fragments, out of 2,683 screened. An additional 60 molecules were selected from docking over 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several crystallographic and docking fragment hits were validated for solution binding using three biophysical techniques (DSF, HTRF, ITC). Overall, the 234 fragment structures presented explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.

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Section: Resultssupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking

Schuller¹,

Correy²,

Gahbauer³

et al. 2020

Preprint

102

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show abstract

“…The structural (Figure 4) and functional perspectives of the SARS-CoV-2 protein mutations reported here provide some useful information for the therapeutics. The PL-pro domain and macrodomain of NSP3 can be potential drug targets as they are comparatively resistant to mutations 67 . Occurrence of S25L and S26F in NSP7 are at the proximity of NSP8 interface, NSP8 mutations M129I (at the interface of NSP8-NSP12) and R51C/L (at the RNA interacting region) and proximity of P323L-NSP12 to the NSP8 binding site indicate a possible modulation in the viral replication mechanism.…”

Section: Discussionmentioning

confidence: 99%

Global variation in the SARS-CoV-2 proteome reveals the mutational hotspots in the drug and vaccine candidates

Patro

Sathyaseelan

Uttamrao

et al. 2020

Preprint

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To accelerate the drug and vaccine development against the severe acute respiratory syndrome virus 2 (SARS-CoV-2), a comparative analysis of SARS-CoV-2 proteome has been performed in two phases by considering manually curated 31389 whole genome sequences from 84 countries. Among the 9 mutations that occur at a high significance (T85I-NPS2, L37F-NSP6, P323L-NSP12, D614G-spike, Q57H-ORF3a, G251V-ORF3a, L84S-ORF8, R203K-nucleocapsid and G204R-nucleocapsid), R203K-nucleocapsid and G204R-nucleocapsid are co-occurring mutations and P323L-NSP12 and D614G-spike often appear simultaneously. Other notable variations that appear with a moderate to low significance are, M85-NSP1 deletion, D268-NSP2 deletion, 112 amino acids deletion in ORF8, a phenylalanine insertion amidst F34-F36 (NSP6) and several co-existing substitution/deletion (I559V & P585S in NSP2, P504L & Y541C in NSP13, G82 & H83 deletions in NSP1 and K141, S142 & F143 deletions in NSP2) mutations. P323L-NSP12, D614G-spike, L37F-NSP6, L84S-ORF8 and the sequences deficient of the high significant mutations has led to 4 major SARS-CoV-2 clades. The top 5 countries bearing all the high significant and majority of the moderate significant mutations are: USA, England, Wales, Australia and Scotland. Further, the majority of the significant mutations has evolved in the first phase and has already transmitted around the globe indicating the positive selection pressure. Among the 26 SARS-CoV-2 proteins, nucleocapsid protein, ORF3a, ORF8, RNA dependent RNA polymerase and spike exhibit a higher heterogeneity compared with the rest of the proteins. However, NSP9, NSP10, NSP8, the envelope protein and NSP4 are highly resistant to mutations and can be exploited for drug/vaccine development.

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“…Since the role of macrodomains in pathogenesis is essential, it appears that their inhibition may help to reduce the viral load and facilitate recovery. Therefore, these proteins might be attractive targets for the development of small-molecule antivirals, assuming that highly selective compounds could be found that discriminate between viral and human macrodomains (Virdi et al, 2020). As a step towards this goal, we have determined the crystal structure of SARS-CoV-2 ADRP in multiple states: in the apo form and in complexes with 2-(N-morpholino)ethanesulfonic acid (MES), AMP and ADPr.…”

Section: Introductionmentioning

confidence: 99%

Crystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes

Michalska

Kim

Jedrzejczak

et al. 2020

IUCrJ

106

131

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Among 15 nonstructural proteins (Nsps), the newly emerging Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) encodes a large, multidomain Nsp3. One of its units is the ADP-ribose phosphatase domain (ADRP; also known as the macrodomain, MacroD), which is believed to interfere with the host immune response. Such a function appears to be linked to the ability of the protein to remove ADP-ribose from ADP-ribosylated proteins and RNA, yet the precise role and molecular targets of the enzyme remain unknown. Here, five high-resolution (1.07–2.01 Å) crystal structures corresponding to the apo form of the protein and its complexes with 2-(N-morpholino)ethanesulfonic acid (MES), AMP and ADP-ribose have been determined. The protein is shown to undergo conformational changes to adapt to the ligand in the manner previously observed in close homologues from other viruses. A conserved water molecule is also identified that may participate in hydrolysis. This work builds foundations for future structure-based research on ADRP, including the search for potential antiviral therapeutics.

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Discovery of Drug-like Ligands for the Mac1 Domain of SARS-CoV-2 Nsp3

Cited by 7 publications

References 27 publications

Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking

Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking

Global variation in the SARS-CoV-2 proteome reveals the mutational hotspots in the drug and vaccine candidates

Crystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes

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