Substrate space analysis of the bacterial proton-coupled oligopeptide transporter YdgR by cheminformatics

Salvia Sajid, Marcus M.K. Nielsen, Ruqaiya Khalil, Paul R. Hansen, Henrik Franzyk, Mikkel Girke Jørgensen, Lars P. Christensen, Osman Mirza, Bala Krishna Prabhala*


Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review


Proton-dependent oligopeptide transporters (POTs) are recognized for their substrate promiscuity due to their ability to transport a wide range of substrates. POTs are conserved in all forms of life ranging from bacteria to humans. A dipeptide-fluorophore conjugate, H-(β-Ala)-Lys(AMCA)-OH, is a well-known substrate of the transporter YdgR that is commonly used as a fluorescent reporter. In order to understand the substrate space of YdgR, we used this dipeptide as a bait reference, when screening an ensemble of compounds (previously tested in PEPT/PTR/NPF space) via a cheminformatic analysis based on the Tanimoto similarity index. Eight compounds (sinalbin, abscisic acid, carnosine, jasmonic acid, N-acetyl-aspartate, N-acetyl-lysine, aspartame, and N-acetyl-aspartylglutamate), covering a wide range on the Tanimoto scale, were tested for YdgR-mediated transport. Carnosine was the only compound observed to be a YdgR substrate based on cell-based transport assays and molecular docking. The other compounds tested were neither inhibitors nor substrates. Thus, we found that neither the Tanimoto similarity index nor ADME (absorption, distribution, metabolism, and excretion) properties appear useful for the identification of substrates (e.g., dipeptides) in YdgR-mediated drug transport.

TidsskriftFEMS Microbiology Letters
Antal sider9
StatusUdgivet - 10. jun. 2023

Bibliografisk note

Funding Information:
We acknowledge the Carlsberg Foundation for supporting the purchase of the BMG CLARIO star Labtech plate reader used in the study. We are also thankful to the Higher Education Commission (HEC, Islamabad, Pakistan) for supporting the PhD study of Salvia Sajid. We also wish to acknowledge Carsten Uhd Nielsen for fruitful discussions.

Publisher Copyright:
© The Author(s) 2023. Published by Oxford University Press on behalf of FEMS. All rights reserved.


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