Docking and Molecular Dynamics Analysis of Gold Nanoparticle–Ligand Interactions for Targeted Antimicrobial Therapy: A Bioinformatics Perspective
DOI:
https://doi.org/10.70749/ijbr.v4i5.3196Keywords:
Antimicrobial Resistance, Docking and Molecular Dynamics, Antimicrobial Therapy, Gold Nanoparticle–Ligand.Abstract
There is a global rise in antimicrobial resistance (AMR), hence the need for new drugs that surpass conventional antibiotic treatments. There are no doubts about the tremendous potentials of AuNPs as effective antimicrobial materials because of their physicochemical properties and compatibility with biomolecules. Nevertheless, designing AuNP-ligand based antimicrobials necessitates knowledge on the molecular basis of AuNPs. In this study, we have proposed a combined computational approach involving molecular docking, molecular dynamic (MD) simulation, artificial intelligence, and nano-bioinformatics that will guide the rational design of AuNP-based antimicrobials. This review focuses on the methods of docking for nanoparticles, particularly in parameterization of metal surfaces, ligand flexibility, and solvent considerations. The MD simulation of AuNPs is also covered in this work. The focus is placed on cutting-edge techniques such as nanotherapeutic design using artificial intelligence, personalized medicine using the concept of the digital twin, quantum mechanics and nano-immunoinformatics. Combining these advances in computer science, we offer a perspective on implementing in-silico design strategies for nanomedical AuNP-based anti-microbial agents. We highlight potential shortcomings concerning the lack of standardization, experimental verification, force fields' accuracy, long-term molecular dynamics simulation, database creation, and regulation. The future of anti-microbial therapy is within computational nanomedicine, while the use of docking, MD, and AI combined with experimental validation will provide rationally designed AuNPs to fight AMR.
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