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Article

Structural Similarities between Some Common Fluorophores Used in Biology, Marketed Drugs, Endogenous Metabolites, and Natural Products

by 1,2 and 3,4,*
1
Department of Chemistry, The University of Manchester, Manchester M13 9PT, UK
2
Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
3
Department of Biochemistry and Systems Biology, Institute of Molecular, Integrative and Systems Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
4
Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kongens Lyngby, Denmark
*
Author to whom correspondence should be addressed.
Mar. Drugs 2020, 18(11), 582; https://doi.org/10.3390/md18110582
Received: 8 November 2020 / Revised: 16 November 2020 / Accepted: 20 November 2020 / Published: 23 November 2020
(This article belongs to the Special Issue Fighting Antimicrobial Resistance with Marine Antibacterial Compounds)
It is known that at least some fluorophores can act as ‘surrogate’ substrates for solute carriers (SLCs) involved in pharmaceutical drug uptake, and this promiscuity is taken to reflect at least a certain structural similarity. As part of a comprehensive study seeking the ‘natural’ substrates of ‘orphan’ transporters that also serve to take up pharmaceutical drugs into cells, we have noted that many drugs bear structural similarities to natural products. A cursory inspection of common fluorophores indicates that they too are surprisingly ‘drug-like’, and they also enter at least some cells. Some are also known to be substrates of efflux transporters. Consequently, we sought to assess the structural similarity of common fluorophores to marketed drugs, endogenous mammalian metabolites, and natural products. We used a set of some 150 fluorophores along with standard fingerprinting methods and the Tanimoto similarity metric. Results: The great majority of fluorophores tested exhibited significant similarity (Tanimoto similarity > 0.75) to at least one drug, as judged via descriptor properties (especially their aromaticity, for identifiable reasons that we explain), by molecular fingerprints, by visual inspection, and via the “quantitative estimate of drug likeness” technique. It is concluded that this set of fluorophores does overlap with a significant part of both the drug space and natural products space. Consequently, fluorophores do indeed offer a much wider opportunity than had possibly been realised to be used as surrogate uptake molecules in the competitive or trans-stimulation assay of membrane transporter activities. View Full-Text
Keywords: drugs; natural products; fluorophores; fingerprinting; similarity; cheminformatics; rdkit; Tanimoto distance drugs; natural products; fluorophores; fingerprinting; similarity; cheminformatics; rdkit; Tanimoto distance
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MDPI and ACS Style

O’Hagan, S.; Kell, D.B. Structural Similarities between Some Common Fluorophores Used in Biology, Marketed Drugs, Endogenous Metabolites, and Natural Products. Mar. Drugs 2020, 18, 582. https://doi.org/10.3390/md18110582

AMA Style

O’Hagan S, Kell DB. Structural Similarities between Some Common Fluorophores Used in Biology, Marketed Drugs, Endogenous Metabolites, and Natural Products. Marine Drugs. 2020; 18(11):582. https://doi.org/10.3390/md18110582

Chicago/Turabian Style

O’Hagan, Steve, and Douglas B. Kell 2020. "Structural Similarities between Some Common Fluorophores Used in Biology, Marketed Drugs, Endogenous Metabolites, and Natural Products" Marine Drugs 18, no. 11: 582. https://doi.org/10.3390/md18110582

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