Cysteine proteases from ReFrame Library Repurposing Screen

Recently released paper is here https://www.biorxiv.org/content/10.1101/2020.04.16.044016v1.full.pdf

Compounds are as follows:

ONO 5334
C[C@@H]1CS/C(=N\\NC(=O)C(=O)[C@H](C2CCOCC2)NC(=O)C3CCCCCC3)/N1C
Available in Molport!
https://www.molport.com/shop/moleculelink/BTZCSXIUAFVRTE-LHMVCHPVSA-N/42665823?searchtype=smiles-search

image

VBY-825
CC[C@@H](C(=O)C(=O)NC1CC1)NC(=O)[C@H](CS(=O)(=O)CC2CC2)N[C@@H](c3ccc(cc3)F)C(F)(F)F
Available in Molport
https://www.molport.com/shop/moleculelink/about-this-molecule/46418263?searchtype=smiles-search&searchkey=55E7VC86AH2T21E6CNLU63

image

Human cysteinyl cathepsins, including cathepsin B, cathepsin L, and cathepsin K, are required for the proteolytic processing of virally encoded proteins during
infection77-79. Cathepsin activity seems to be required for proper processing of the SARS-CoV-1 S protein within the endosome in order to activate its fusogenic acitivity78. Inhibition of cathepsin L activity has been previously shown to efficiently suppress SARS-CoV-1 infection78. We found ONO 5334 (a cathepsin K inhibitor) and VBY-825 (a reversible cathepsin protease inhibitor) to inhibit SARS-CoV-2 infection in a dosedependent manner, however additional studies will be required to determine if their antiviral activities are due to inhibiting proteolysis of viral or host cellular proteins.

MDL28170
CC(C)[C@H](NC(=O)OCc1ccccc1)C(=O)NC(Cc1ccccc1)C=O
Available in Molport
https://www.molport.com/shop/moleculelink/benzyl-N-1S-2-methyl-1-1-oxo-3-phenylpropan-2-yl-carbamoyl-propyl-carbamate/6822458?searchtype=text-search&searchkey=6FNT3UTP70QLA1E6CMA1B3

image

Z LVG CHN2
[H]N(CC(=O)C=[N+]=[N-])C(=O)[C@@H](N([H])C(=O)[C@H](CC(C)C)N([H])C(=O)OCC1=CC=CC=C1)C(C)C
Not available in Molport, but synthesis is reported in https://patentimages.storage.googleapis.com/ee/63/d3/4069d347483844/US5037957.pdf


Z LVG CHN2, a preclinical tripeptide
derivative that displays a broad-spectrum bactericidal activity. Specifically, this molecule has been previously shown to suppress herpes simplex virus (HSV) replication by inhibiting the enzymatic activity of HSV-encoded cysteine protease68, which may indicate that the antiviral function of Z LVG CHN2 occurs through inhibition of SARSCOV-2 3CLpro protease. Another preclinical molecule that exhibits strong antiviral activity, MDL 28170, is a potent cell permeable calpain I and II inhibitor. Interestingly, MDL 28170 was previously found to impair infection by SARS-COV-1 and Ebola virus (EBOV)

All four “were found to inhibit viral replication at EC50 concentration <500 nM”

More info in the paper

@RGlen also brought up an interesting point mentioned in the paper regarding the difference between vero cells and the cells of interest in the lung:

Of note, one potential limitation of Vero cells is that, due to species differences, pro-drugs that require the human host cell machinery for processing into their active form, such as some nucleoside inhibitors, may not harbor the same potency as in human cells. Consistently, we found that remdesivir inhibits SARS-CoV-2 replication ~60-fold more potently in human cells in comparison to Vero E6 cells

great find; some of these compounds are “less beautiful” than other though! The Z LVG CHN2 diazo looks more like a covalent tag for proteomics than a drug lead and the ONO is quite an apt name “oh no!”… Looks like a metal chelator all day long and unstable. Middle 2 look good though!

1 Like

Interesting. I think many would say the same, but the compound inducing an interjection is actually the farthest along!

From the paper:

ONO 5334 harbored an antiviral EC50 of ~500 nM, which is in range of a previously reported 85 % activity observed at 100 nM in an osteoclast-mediated bone resorption assay80. Importantly, the Cmax of this compound is 1.6 µM (300 mg QD), and treatment with ONO-5334 was well tolerated up to daily doses of 300 mg and for up to 12 months without any clinically relevant safety concerns. ONO5334 reached phase II clinical trials for the treatment of osteoporosis in postmenopausal women, but development was discontinued due to an unfavorable competitive landscape

And I agree that the warhead of Z LVG CHN2 is troublesome. Apparently some diazomethylketones were trialed in the 60s as chemotherapy drugs

Perhaps we can try https://en.wikipedia.org/wiki/Odanacatib vs the main protease?

So just checked and Odanacatib was actually included in the ReFrame library, so I’m not sure if it is worth trying if it is already failing in viral assays.

Agree some look a bit funky but I’m not sure I’d be too concerned about looks given these come from the REFRAME library. all 12,000 compounds have already progressed to the clinic at some point or another so a lot of the potential issues such as stability, off target potential tox etc will have already been either ironed out or throughly investigated and deemed acceptable for whatever indication they were initially pitched… at least that’s the theory.

I think ONO 5334 could be quite interesting despite it being riddled with things I wouldnt touch if I saw them in a HTS hit!

1 Like