A computational approach for the molecular recognition of novel ophthalmic prodrugs and molecular modelling of sigma receptor ligands in ocular diseases

In full compliance with the project financed by the European Social Fund, Action I.1 “Innovative Doctorates with Industrial Characterization”, some strategies have been adopted for the targeted delivery of ophthalmic drugs through the design and synthesis of prodrugs. The physicochemical, pharmacokinetic, and pharmacodynamic properties represent, in many cases, a limitation of drugs, regardless of the pharmacological activity. For this reason, the need arises to use the prodrug approach to overcome these gaps. Ophthalmic drug administration is generally the most common in treating many eye diseases, although the ocular bioavailability of topically applied drugs is <5%. Transporters play an important role in arranging many drugs and their metabolites in other parts of the body. Although the role of active transporters has been known for a long time, in recent years, they have drawn the attention of researchers to improve drug recognition by transporters and elucidate complex transport mechanisms. After an overview of prodrugs (Chapter 1), ophthalmic prodrugs were designed based on the molecular recognition by two different active transporters: sodium-dependent multivitamin transporter (SMVT) for timolol transport (Chapter 2) and concentrative nucleoside transporter (CNT) for the transport of acyclovir (Chapter 3). The SMVT transporter structure was reconstructed using a homology modeling approach. This method allowed to evaluate, in-silico, the stability, and the new self-immolative prodrugs’ recognition quality. This study highlights for the first time the likely binding site of biotin and other physiological ligands for the SMVT transporter, detailing key interaction residues at the binding site. Furthermore, the molecular dynamics simulation (MD simulation) allowed us to evaluate the stability of every single complex with prodrugs. The synthesized prodrugs show a better partition coefficient (logP) than timolol, with consistent corneal permeability values. Conjugated acyclovir-uridine prodrugs have been designed and synthesized to study and evaluate the potential of these cellular transport systems that have never been considered to date. Furthermore, computational studies were carried out to evaluate the stability of the interactions between prodrugs and the recognition site of the CNT transporter. Computational analyzes revealed interesting mechanistic interactions on uridine-drug reuptake for the rational design of prodrugs recognized by CNT. In Chapter 4, the sigma (σ) receptors were treated for their biological activity in some eye diseases. Ligands of the σ receptors were synthesized. The new hybrid inhibitors allow having both a σ1 ligand and a NO donor fraction in the same scaffold. In this preliminary phase, the synthesized compounds were evaluated both for their ability to bind sigma receptors and for the release of NO. Furthermore, a computational method that could predict the agonist/antagonist activity of the σ1 receptor ligands has been shown in this chapter. This computational approach could facilitate pharmaceutical chemists’ task for the rational synthesis of new drugs with σ1activity. This is the first prodrug design study for molecular recognition from transporters (SMVT and CNT) based on a comprehensive computational approach. Unfortunately, the COVID-19 pandemic interfered with the period in the company (translated into smart working), slowing down both the in vivo experiments on cell lines to demonstrate the uptake of the newly synthesized prodrugs and the ophthalmic formulation tests.