clofazimine   Click here for help

GtoPdb Ligand ID: 9184

Synonyms: Lamprene®
Approved drug Immunopharmacology Ligand
clofazimine is an approved drug (FDA (1986))
Compound class: Synthetic organic
Comment: Clofazimine is a phenazine dye with antimycobacterial properties [3]. It has both antibacterial and anti-inflammatory activities. State-dependent block of Kv1.3 channels by clofazimine offers therapeutic potential for selective immunosuppression in the context of autoimmune diseases in which Kv1.3-expressing T cells play a significant role [4].

SARS-CoV-2: A report in Nature has identified that clofazimine has anti-coronavirus activity, and that this is synergistic with the antiviral activity of remdesivir [7]. The drug was found to inhibit viral spike-mediated cell fusion and viral helicase activity in vitro, which translated to reduced pulmonary viral load, gut viral shedding and inflammation in an in vivo infection model. The authors suggest that their data supports the use of clofazimine in an outpatient setting for those infected with SARS-CoV-2, or for hospitalised COVID-19 patients if combined with remdesivir. Based on this evidence it is planned to progress clofazimine + remdesivir directly into Phase 2 clinical trial. A trial of clofazimine + interferon-1β is already underway.
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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 3
Hydrogen bond donors 1
Rotatable bonds 4
Topological polar surface area 41.69
Molecular weight 472.12
XLogP 8.81
No. Lipinski's rules broken 1
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 Clc1ccc(cc1)Nc1cc2nc3ccccc3n(c2cc1=NC(C)C)c1ccc(cc1)Cl
Isomeric SMILES Clc1ccc(cc1)Nc1cc2nc3ccccc3n(c2cc1=NC(C)C)c1ccc(cc1)Cl
InChI InChI=1S/C27H22Cl2N4/c1-17(2)30-24-16-27-25(15-23(24)31-20-11-7-18(28)8-12-20)32-22-5-3-4-6-26(22)33(27)21-13-9-19(29)10-14-21/h3-17,31H,1-2H3
InChI Key WDQPAMHFFCXSNU-UHFFFAOYSA-N
References
1. Alcedo KP, Thanigachalam S, Naser SA. (2016)
RHB-104 triple antibiotics combination in culture is bactericidal and should be effective for treatment of Crohn's disease associated with Mycobacterium paratuberculosis.
Gut Pathog, 8: 32. [PMID:27307791]
2. Arbiser JL, Moschella SL. (1995)
Clofazimine: a review of its medical uses and mechanisms of action.
J Am Acad Dermatol, 32 (2 Pt 1): 241-7. [PMID:7829710]
3. Barry VC, Belton JG, Conalty ML, Denneny JM, Edward DW, O'Sullivan JF, Twomey D, Winder F. (1957)
A new series of phenazines (rimino-compounds) with high antituberculosis activity.
Nature, 179 (4568): 1013-5. [PMID:13430770]
4. Faouzi M, Starkus J, Penner R. (2015)
State-dependent blocking mechanism of Kv 1.3 channels by the antimycobacterial drug clofazimine.
Br J Pharmacol, 172 (21): 5161-73. [PMID:26276903]
5. HRSA. 
National Hansen's Disease (Leprosy) Program.
Accessed on 04/07/2016. Modified on 04/07/2016. HRSA- Health Resources and Services Administration, http://www.hrsa.gov/hansensdisease/
6. Savarino E, Bertani L, Ceccarelli L, Bodini G, Zingone F, Buda A, Facchin S, Lorenzon G, Marchi S, Marabotto E et al.. (2019)
Antimicrobial treatment with the fixed-dose antibiotic combination RHB-104 for Mycobacterium avium subspecies paratuberculosis in Crohn's disease: pharmacological and clinical implications.
Expert Opin Biol Ther, 19 (2): 79-88. [PMID:30574820]
7. Yuan S, Yin X, Meng X, Chan JF, Ye ZW, Riva L, Pache L, Chan CC, Lai PM, Chan CC et al.. (2021)
Clofazimine broadly inhibits coronaviruses including SARS-CoV-2.
Nature, 593 (7859): 418-423. [PMID:33727703]