Peptide transporters occur ubiquitiously in Nature. The Escherichia coli dipeptide permease (Dpp) shares some common substrate specificities with the intestinal Pep Tl transporter involved in oral absorption of peptide-based drugs. Structural features determining the uptake of natural peptide substrates and peptide-based drugs, e.g. angiotensin-converting enzyme (ACE) inhibitors, by Dpp were investigated using isoelectric focusing (IEF), agar plate competition assays and radioligand competition filter binding assays. Computer-based conformational analysis was used to determine the conformer distribution profiles of natural peptides, peptidomimetics, ACE inhibitors and antimicrobial smugglins. Correlation of activity data with the conformer distribution profiles of natural peptides identified molecular recognition templates (MR.Ts) for substrates for effective uptake by peptide transporters. The established MR.Ts were applied to evaluate the putative ability of dipeptide mimetics to be transported by Dpp. The majority of peptidomimetics had conformer distribution profiles outside the MR.Ts. Systematic modifications in mimetic structure produced compounds with conformers within Dpp' s MRT. The structural modifications described can be applied to the rational design of peptidomimetics for improved oral bioavailability. ACE inhibitors are used for the treatment of hypertension and predictions of their oral bioavailability were determined by assessing whether their conformer distribution profiles matched the MR.Ts. ACE inhibitors had a low percentage of conformers distributed in the MR T sectors. Correlation of molecular modelling data with results from competition filter binding assay, using purified dipeptide-binding protein (DppA), revealed additional features involved in molecular recognition. Knowledge gained from molecular modelling of peptidomimetics and peptides was applied to the rational design of ACE inhibitors. This produced a set of theoretical compounds that matched the MR.Ts required for effective oral delivery by intestinal peptide transporters. Natural antimicrobial smugglins had the majority of their conformers distributed in the MRT sectors. This confirmed the established MR.Ts for peptide transporters, and revealed how these compounds had optimised structural and conformational features for efficient delivery by the peptide permeases. This study has shown how the established MR.Ts for peptide transporters may be used to determine the oral bioavailability of peptidomimetics and peptide-based therapeutics, and this requires verification by experimentation. The application of the MR.Ts for the rational design of peptide drugs in silico for improved oral delivery has also been illustrated. Results obtained in this study also indicate comparable recognition processes for transporters and peptidases, and provide evidence that the MR.Ts for peptide transporters may be applied for the design of substrates of peptidases for therapeutic use.