venglustat   Click here for help

GtoPdb Ligand ID: 11550

Synonyms: Genz-682452 | GZ/SAR402671 | ibiglustat | SAR402671
PDB Ligand
Compound class: Synthetic organic
Comment: Venglustat is a clinical stage oral glucosylceramide synthase (GCS) inhibitor. GCS is encoded by the UGCG gene. It was developed for potential to treat diseases in which the glycolipid glucosylceramide accumulates and leads to lysosomal dysfunction and organ damage [3-4]. Venglustat inhibits glucosylceramide synthesis. Its chemical structure is claimed in Genzyme's patent WO2012129084A2 [1]. It has subsequently been reported to act as a substrate-competitive inhibitor of N-terminal Xaa-Pro-Lys N-methyltransferase 1 (NTMT1; Q9BV86; IC50 420 nM) [2].

The venglustat analogue GENZ-667161 and the eliglustat analogue GENZ-123346 have been shown to inhibit replication of SARS-CoV-2 in vitro [5], potentially by disrupting the host cell membrane dynamics which the virions depend upon for infection.
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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.

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View interactive charts of activity data across species
2D Structure
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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.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. 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.

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Hydrogen bond acceptors 5
Hydrogen bond donors 1
Rotatable bonds 6
Topological polar surface area 82.7
Molecular weight 389.16
XLogP 3.27
No. Lipinski's rules broken 0
SMILES / InChI / InChIKey
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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.

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Canonical SMILES O=C(NC(c1csc(n1)c1ccc(cc1)F)(C)C)O[C@@H]1CN2CCC1CC2
Isomeric SMILES O=C(NC(c1csc(n1)c1ccc(cc1)F)(C)C)O[C@@H]1CN2CCC1CC2
InChI InChI=1S/C20H24FN3O2S/c1-20(2,17-12-27-18(22-17)14-3-5-15(21)6-4-14)23-19(25)26-16-11-24-9-7-13(16)8-10-24/h3-6,12-13,16H,7-11H2,1-2H3,(H,23,25)/t16-/m1/s1
InChI Key YFHRCLAKZBDRHN-MRXNPFEDSA-N
References
1. Bourque E, Celatka C, Hirth B, Metz M, Zhao Z, Skerlj R, Xiang Y, Jancisics K, Marshall J, Cheng S et al.. (2014)
Glucosylceramide synthase inhibitors.
Patent number: WO2012129084A2. Assignee: Genzyme Corporation. Priority date: 18/03/2011. Publication date: 24/04/2014.
2. Dong G, Deng Y, Yasgar A, Yadav R, Talley D, Zakharov AV, Jain S, Rai G, Noinaj N, Simeonov A et al.. (2022)
Venglustat Inhibits Protein N-Terminal Methyltransferase 1 in a Substrate-Competitive Manner.
J Med Chem, 65 (18): 12334-12345. [PMID:36074125]
3. Schneider SA, Alcalay RN. (2020)
Precision medicine in Parkinson's disease: emerging treatments for genetic Parkinson's disease.
J Neurol, 267 (3): 860-869. [PMID:31974807]
4. van der Veen SJ, Hollak CEM, van Kuilenburg ABP, Langeveld M. (2020)
Developments in the treatment of Fabry disease.
J Inherit Metab Dis, 43 (5): 908-921. [PMID:32083331]
5. Vitner EB, Achdout H, Avraham R, Politi B, Cherry L, Tamir H, Yahalom-Ronen Y, Paran N, Melamed S, Erez N et al.. (2021)
Glucosylceramide synthase inhibitors prevent replication of SARS-CoV-2 and influenza virus.
J Biol Chem, 296: 100470. [PMID:33639165]
6. Wilson MW, Shu L, Hinkovska-Galcheva V, Jin Y, Rajeswaran W, Abe A, Zhao T, Luo R, Wang L, Wen B et al.. (2020)
Optimization of Eliglustat-Based Glucosylceramide Synthase Inhibitors as Substrate Reduction Therapy for Gaucher Disease Type 3.
ACS Chem Neurosci, 11 (20): 3464-3473. [PMID:33035424]