APPLICATIONS OF NANOMATERIALS FOR BIOMATERIALS: DEVELOPING NANOMATERIAL-ENHANCED BIOMATERIALS USING COMPUTATIONAL DOCKING OF PROTEIN-LIGAND PAIRS

Biotechnology

The integration of nanotechnology with protein-ligand interactions offers a promising avenue for developing advanced biomaterials for therapeutic and diagnostic applications. This project investigates the role of protein-ligand interactions in designing nanomaterial-based systems, focusing on their potential to address challenges in precision medicine, targeted therapies, and diagnostics. Using AutoDock Vina, a computational molecular docking tool, we evaluated the binding affinities and interaction mechanisms of ten therapeutically relevant protein-ligand pairs: Cyclooxygenase-2 (COX-2) with Celecoxib (PDB ID: 3LN1), HIV Reverse Transcriptase (HIV RT) with Nevirapine (1RT1), EGFR Kinase with Erlotinib (1M17), Aldose Reductase with Fidarestat (1US0), Acetylcholinesterase (AChE) with Donepezil (4EY6), Human Cyclin Kinase 2 with Roscovitine (1HCK), Human Epidermal Growth Factor Receptor 2 (HER2) with Lapatinib (3PP0), Human Tyrosinase with Kojic Acid (5M8P), Alpha-Synuclein with Dopamine (2KKW), and Cytochrome P450 3A4 (CYP3A4) with Midazolam (1WOE). Binding affinities ranged from -6.5 to -10.0 kcal/mol, with HER2-Lapatinib and COX-2-Celecoxib exhibiting the strongest interactions at -10.0 and -9.0 kcal/mol, respectively, indicating high specificity for targeted cancer therapies, while Alpha-Synuclein-Dopamine showed the weakest affinity at -6.5 kcal/mol, suggesting challenges in Parkinson’s treatment.Nanomaterials, including silica nanoparticles, gold nanorods, liposomes, magnetic nanoparticles, and polymeric nanocarriers, were integrated with these protein-ligand pairs to develop innovative biomaterials. Applications included targeted drug delivery (e.g., silica nanoparticles with Celecoxib for anti-inflammatory therapy), photothermal therapy (e.g., gold nanorods with Lapatinib for HER2-positive breast cancer), controlled release systems (e.g., lipid-based nanoparticles with Nevirapine for HIV treatment), and diagnostics (e.g., magnetic nanoparticles with Erlotinib for cancer imaging). The study also explored nanomaterial-enhanced solutions for crossing biological barriers, such as liposomes delivering Donepezil across the blood-brain barrier for Alzheimer’s treatment. Results highlight the synergy between protein-ligand docking and nanotechnology, with strong binding affinities correlating with effective nanomaterial applications, such as Aldose Reductase-Fidarestat (-9.5 kcal/mol) for diabetes management and AChE-Donepezil (-8.75 kcal/mol) for cognitive improvement in Alzheimer’s. Despite challenges like weak affinities in certain pairs and the need for experimental validation, this project underscores the potential of nanomaterial-based biomaterials in advancing precision medicine, offering a foundation for future research in targeted therapies and diagnostics for cancer, HIV, neurodegenerative diseases, and metabolic disorders.

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