Molecular Dynamics Simulations and Current Trends in Designing NewAntivirals Targeting Proteases: A Review from 2018 to 2025

In recent years, Molecular Dynamics (MD) simulations have emerged as a cornerstone in molecular biology and antiviral drug discovery, driven by the growing demand for high-resolution insights into biomolecular behaviour. This surge in relevance stems from the need to understand complex molecular mechanisms at an atomic scale, an area where traditional experimental techniques often face limitations. MD simulations offer a powerful computational framework capable of capturing the dynamic behaviour of proteases and other biomolecules with unparalleled spatial and temporal resolution. As a result, they have become instrumental in elucidating protein inhibition mechanisms, unveiling the molecular basis of various diseases, and guiding the rational design and optimization of therapeutic agents. In this review, we synthesize recent advances in the application of MD simulations to the study of protease inhibitors, highlighting their transformative impact on drug discovery and structural biology.