Abstract
Members of the solute carrier 15 family (SLC15) transport di- and tripeptides as well as peptidomimetic drugs across the cell membrane. Structures of bacterial homologues have provided valuable information on the binding and transport of their natural substrates, but many do not transport medically relevant drugs. In contrast, a homologue from Escherichia coli, DtpA (dipeptide and tripeptide permease), shows a high similarity to human PepT1 (SLC15A1) in terms of ligand selectivity and transports a similar set of drugs. Here, we present the crystal structure of DtpA in ligand-free form (at 3.30 Å resolution) and in complex with the antiviral prodrug valganciclovir (at 2.65 Å resolution) supported by biochemical data. We show that valganciclovir unexpectedly binds with the ganciclovir moiety mimicking the N-terminal residue of a canonical peptide substrate. On the basis of a homology model we argue that this binding mode also applies to the human PepT1 transporter. Our results provide new insights into the binding mode of prodrugs and will assist the rational design of drugs with improved absorption rates.
Highlights
The proton-dependent oligopeptide transporters (POTs) constitute a subfamily of the major facilitator superfamily (MFS), transporting di/tripeptides and peptide-like compounds coupled to cotransport of protons
The bacterial homologue of PepT1, DtpA, provides an excellent prototype to understand the molecular mechanism of peptide and drug transport due to the high conservation of the binding site as well as the highly similar substrate specificity profile compared to PepT1.4,5 like for their human homologues, structural insights into relevant drug binding are missing for bacterial peptide transporters
We find that DtpA, in contrast to most characterized bacterial POTs to date, prefers to bind and transport tripeptides over dipeptides, which appears to relate to the presence of a characteristic intrahelical loop in TM10
Summary
The proton-dependent oligopeptide transporters (POTs) constitute a subfamily of the major facilitator superfamily (MFS), transporting di/tripeptides and peptide-like compounds coupled to cotransport of protons. The bacterial homologue of PepT1, DtpA (dipeptide and tripeptide permease), provides an excellent prototype to understand the molecular mechanism of peptide and drug transport due to the high conservation of the binding site as well as the highly similar substrate specificity profile compared to PepT1.4,5 like for their human homologues, structural insights into relevant drug binding are missing for bacterial peptide transporters. We combined biochemical, biophysical, and structural approaches to obtain molecular insights into binding and transport of peptides and drugs of the prototypic DtpA transporter, which provided the basis for structural modeling of the human PepT1 transporter
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