VBY-825   Click here for help

GtoPdb Ligand ID: 10746

Synonyms: VBY825
Compound class: Synthetic organic
Comment: VBY-825 is a reversible cysteine protease inhibitor with high potency against cathepsins B, L, S and V [1]. Human cysteinyl cathepsins are required for proteolytic processing of virally encoded proteins during infection [2-3,5], including a likely requirement for proper processing of the SARS-CoV-2 S protein within the endosome (activating its fusogenic acitivity) [5]. Experimental evidence indicates that VBY-825 has some antiviral activity against SARS-CoV-2 [4]. In in vitro experiments VBY-825 inhibits SARS-CoV-2 entry. It does not inhibit the viral 3C-like protease (3CLpro) or papain-like protease (PLpro), which suggests that its antiviral activity is associated with inhibition of host proteases.

In the oncology setting, a pre-clinical model of pancreatic islet cancer revealed that VBY-825 exhibits significant anti-tumour activity.
Click here for help

Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

✖

View interactive charts of activity data across species
2D Structure
Click here for help

2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

✖
Hydrogen bond acceptors 8
Hydrogen bond donors 3
Rotatable bonds 16
Topological polar surface area 129.82
Molecular weight 535.18
XLogP 3.24
No. Lipinski's rules broken 1

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
SMILES / InChI / InChIKey
Click here for help

SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

✖
Canonical SMILES CC[C@@H](C(=O)C(=O)NC1CC1)NC(=O)[C@H](CS(=O)(=O)CC1CC1)N[C@H](C(F)(F)F)c1ccc(cc1)F
Isomeric SMILES CC[C@@H](C(=O)C(=O)NC1CC1)NC(=O)[C@H](CS(=O)(=O)CC1CC1)N[C@H](C(F)(F)F)c1ccc(cc1)F
InChI InChI=1S/C23H29F4N3O5S/c1-2-17(19(31)22(33)28-16-9-10-16)30-21(32)18(12-36(34,35)11-13-3-4-13)29-20(23(25,26)27)14-5-7-15(24)8-6-14/h5-8,13,16-18,20,29H,2-4,9-12H2,1H3,(H,28,33)(H,30,32)/t17-,18-,20-/m0/s1
InChI Key PPUXXDKQNAHHON-BJLQDIEVSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
References
1. Elie BT, Gocheva V, Shree T, Dalrymple SA, Holsinger LJ, Joyce JA. (2010)
Identification and pre-clinical testing of a reversible cathepsin protease inhibitor reveals anti-tumor efficacy in a pancreatic cancer model.
Biochimie, 92 (11): 1618-24. [PMID:20447439]
2. Marzi A, Reinheckel T, Feldmann H. (2012)
Cathepsin B & L are not required for ebola virus replication.
PLoS Negl Trop Dis, 6 (12): e1923. [PMID:23236527]
3. Mori Y, Yamashita T, Tanaka Y, Tsuda Y, Abe T, Moriishi K, Matsuura Y. (2007)
Processing of capsid protein by cathepsin L plays a crucial role in replication of Japanese encephalitis virus in neural and macrophage cells.
J Virol, 81 (16): 8477-87. [PMID:17553875]
4. Riva L, Yuan S, Yin X, Martin-Sancho L, Matsunaga N, Pache L, Burgstaller-Muehlbacher S, De Jesus PD, Teriete P, Hull MV et al.. (2020)
Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing.
Nature, [Epub ahead of print]. DOI: 10.1038/s41586-020-2577-1
5. Simmons G, Gosalia DN, Rennekamp AJ, Reeves JD, Diamond SL, Bates P. (2005)
Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry.
Proc Natl Acad Sci USA, 102 (33): 11876-81. [PMID:16081529]