Adding to the Wiki Background Section of Other Nsp13 Inhibitors

[mattodd]

Hi @lindapatio. We were talking the other day about the need to improve the wiki in terms of its coverage of molecules known to inhibit Nsp13, and in particular to focus on any other molecules known to bind at site C-terminus-B.

I added the paper found by @TomkUCL here, though obviously this does not contain info about binding location. Could you add some more over the coming weeks, based on your reading? This is important for your UCL project, but also important that we understand all and any relevant known binders.

Obviously anyone else should feel free to add links to that section of the wiki too.

[lindapatio]

Sure, I'll try to find more relevant papers to add! This is the study I mentioned yesterday: https://pubs.acs.org/doi/10.1021/acs.jpclett.0c02421

[lindapatio]

https://www.tandfonline.com/doi/full/10.1080/13543776.2021.1884224

This study identified patented small molecules that are able to inhibit nsp13. The most potent molecule identified was SSYA10-001 which is a 1,2,4-triazole compound. It exerts a noncompetitive inhibition effect with respect to ATP and nucleic acid substrate. Further studies have shown its ability to also inhibit SARS-COv, MERS-CoV and MHV with comparable IC50. Heat maps were also produced to compare seven compounds of similar structure/physicochemical properties.

[lindapatio]

This study utilised a molecular dynamic simulation to examine the protein's binding site and interaction with ligands. Cordycepin (https://en.wikipedia.org/wiki/Cordycepin) and pritelivir (https://en.wikipedia.org/wiki/Pritelivir) showed favourable pharmacokinetics. Here is the link to the short description: https://www.tandfonline.com/doi/full/10.1080/07391102.2021.1970024?scroll=top&needAccess=true

[lindapatio]

A study that outlined class of compounds that would be able to inhibit helicase enzymes in pathogens belonging to the Flaviviridae, Coronaviridae, and Picornaviridae families. The compound classes are as follows: benzotriazole, imidazole, imidazo-diazepine, phenothiazine, quinoline, anthracycline, triphenylmethane, tropolone, pyrrole, acridone, small peptide, and Bananin derivatives https://doi.org/10.1155/2011/213135

another study tested the effectiveness of bananin derivatives in sars-cov helicase inhibition: https://pubmed.ncbi.nlm.nih.gov/15797214/ "Bananin, iodobananin, vanillinbananin, and eubananin were effective inhibitors of the ATPase activity of the SCV helicase with IC50 values in the range 0.5-3 microM"

[TomkUCL]

Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of nsp13 helicase

https://doi.org/10.1042/BCJ20210201

Maybe some interesting points here?

"We validated suramin, suramin-like compounds and FPA-124 as nsp13 inhibitors that could be subjected to careful structural optimization to generate clinically more useful compounds in the hope of increasing antiviral potency and reducing cytotoxicity"

"Suramin, originally synthesized by Bayer in 1916, is a clinically approved drug mainly used to treat river blindness and sleeping sickness [43,64]. We show that suramin and several of its structurally similar compounds are novel inhibitors of SARS-CoV-2 nsp13. Suramin inhibited nsp13 in vitro with an IC50 of 1 mM and inhibited viral growth in cell-based assays with an EC50 of ∼10 mM. A wide range of antiviral effects have been reported for suramin, as it inhibits Zika virus, dengue virus, chikungunya virus, HIV, hepatitis C virus, herpes simplex type-1 virus and recently SARS-CoV-2 [43,65]. Suramin seems to inhibit multiple steps in viral infection and replication: it interferes with virus-receptor interaction and hence viral–host cell binding and uptake [66,67], it interferes with viral helicase activities ([48] and this work) and it interferes with viral RNA polymerase activity [49,68]. Suramin is a large symmetrical molecule carrying two polysulfonated naphthyl urea groups containing six negative charges at physiological pH and therefore, the basis for its many targets is likely to be its ability to strongly bind positively charged regions in proteins such as polymerases [44,46]."

Sumarin:

"Notably, a kinase inhibitor, FPA-124, inhibited nsp13 with a micromolar IC50 of ∼9 mM, and its IC50 value was not affected by the addition of the non-ionic detergents Tween-20 or Triton X-100 (Supplementary Figures S8 and S9), suggesting its nsp13 inhibition was unlikely to be due to aggregation"

[TomkUCL]

@lindapatio @mattodd Apologies I meant to add my additions here, but see some of the recent papers added to issue #10

Of particular interest is the following from DOI 10.1016/j.chembiol.2005.01.006: "Bananin acted as a noncompetative inhibitor with respect to both ATP and nucleic acid, suggesting this class of inhibitors binds to a site distinct from the ATP and nucleic acid binding sites."

Could this suggest binding to the third site that we are interested in? Maybe worth docking bananin? I though it was worth a look considering the close similarity in the SARS and SARS-CoV-2 helicase sequences.

[TomkUCL]

Hi @lindapatio, just curious, did you try docking any of the non-competitive inhibitors mentioned in this thread? It would be interesting to know if any of these score well in site 16 :)

[TomkUCL]

@mattodd @tmw20653 @kipUNC @H-agha A micromolar inhibitor of nsp13 was sourced from an in-house library in May 2022 with low micromolar inhibition activity, however, no mode of action has been indicated as of yet...

Discovery of 2-Phenylquinolines with Broad-Spectrum Anti-coronavirus Activity ACS Medicinal Chemistry Letters 2022 13 (5), 855-864 DOI: 10.1021/acsmedchemlett.2c00123 https://pubs.acs.org/doi/10.1021/acsmedchemlett.2c00123

My own short docking session of the ligand in question (compound 6g) in AutoDock Vina suggests binding in a hydrophobic pocket between domains Rec2A, Rec1A, and 1B, so not in our pocket of interest. My grid was based on the B chain of the APO-state homodimer of nsp13 (PDB ID: 7NIO) taking the 5 top scoring poses. The lowest scoring pose (-7.2) is highlighted in green in the images below; this score is comparable to our current fragment scores, however, I would take that with a big pinch of salt.