Cheminformatics Tools to Evaluate Drug-Protein Interactions and Observe Structure-Activity Relationships to Identify New Molecular Entities for The Treatment of Ocular Diseases

• Author(s): Ruchika Jaral
• Paper ID: 1711606
• Page: 2040-2051
• Published Date: 26-11-2025
• Published In: Iconic Research And Engineering Journals
• Publisher: IRE Journals
• e-ISSN: 2456-8880
• Volume/Issue: Volume 9 Issue 5 November-2025

Abstract

Ocular diseases are those diseases that affect the eyes, according to recent data, globally 2.2 billion people have vision impairment and half of them have a type which was preventable or is yet to be addressed. Ocular diseases are categorised into two types on the basis of their target regions in the eyes: Anterior segment ocular diseases that affect the anterior portion of the eye which includes the cornea, iris, ciliary body and lens, such as dry eye, conjunctivitis, blepharitis, cataract, glaucoma etc & Posterior segment eye diseases that affect the retina, choroid and optic nerve such as optic neuritis, macular degeneration, retinal detachment, intravenous haemorrhage etc. While some types are milder ones that do not cause much harm to the eyes, many of these pose serious threats which may also include the permanent loss of vision along with other complications such as damage to the optic nerve, deformation of lens, damage to the retina etc. Uveitis is a rare disease that affects the uvea part of the eye, its possible causes include infection injury or an autoimmune or inflammatory disease, in a paediatric case study extraocular Staphylococcus aureus infection was shown to have triggered the reactivation of autoimmune ocular inflammation thereby causing autoimmune uveitis. Hence, there is ongoing research to come out with solutions that could help to treat or prevent this disease. Oxazolidinones are a class of drugs that treat bacterial infections, its first compound is Linezolid which was approved by FDA in 1999. It targets diseases caused by gram-positive bacteria; it works by inhibiting the process of translation after binding to the rRNA. Several other drugs are available worldwide whose potential effects for other diseases apart from the ones that they mainly treat are yet to be discovered. In recent times, Computer Aided Drug Design has provided an efficient tool for drug designing and discovery within the shortest time span and with reliable results. One can screen a large library of compounds in a short stretch of time and get the work done efficiently. Simulations such as molecular docking can help to arrive at conclusions regarding the various possible uses of a compound against several diseases. Softwares such as Autodock, Pyrx aid in performing molecular docking. Docking can be done between protein-ligand, ligand-ligand and protein-DNA/rna, it can be rigid or flexible docking. It occurs in two steps: binding of the ligand in the active sites of protein and then the different conformations of ligand are ranked using a scoring function that computes the binding energies of the conformations. The results can further be analysed using software such as Discovery studio, Swissadme etc.

Keywords

Computer-Aided Drug Designing, Molecular Docking, Protein, Ligand, Antibiotics, Translation, Rrna, Autoimmune Diseases, Uveitis, Ocular Inflammation, Binding Energy, Scoring Function.

Citations

IRE Journals:
Ruchika Jaral "Cheminformatics Tools to Evaluate Drug-Protein Interactions and Observe Structure-Activity Relationships to Identify New Molecular Entities for The Treatment of Ocular Diseases" Iconic Research And Engineering Journals Volume 9 Issue 5 2025 Page 2040-2051 https://doi.org/10.64388/IREV9I5-1711606

IEEE:
Ruchika Jaral "Cheminformatics Tools to Evaluate Drug-Protein Interactions and Observe Structure-Activity Relationships to Identify New Molecular Entities for The Treatment of Ocular Diseases" Iconic Research And Engineering Journals, 9(5) https://doi.org/10.64388/IREV9I5-1711606