Recent advancements in 3D drug design and nanotechnology have opened new avenues for targeted therapy and precision medicine. Functionalized nanoparticles (NPs) offer enhanced specificity, controlled drug release, and the potential for theranostic applications. This presentation explores three cutting-edge approaches leveraging nanotechnology for drug delivery and antiviral strategies. First, allele-specific small interfering RNA (siRNA) therapy, delivered via human recombinant ferritin nanoparticles, demonstrates a promising strategy to selectively silence mutant FGFR2 in Crouzon syndrome, mitigating pathological osteogenic differentiation. Second, Nano-Immuno-Probes (NIPs), a novel biotechnological device based on polymeric NPs conjugated with antibody fragments, show potential for early detection and treatment of Herpes Simplex Virus 2. Finally, a groundbreaking strategy against SARS-CoV-2 utilizes PLGA-based nanoparticles functionalized with the PDZ2 domain of the ZO-1 protein, effectively acting as intracellular molecular sponges to sequester viral E-proteins and disrupt viral pathogenesis. These studies highlight the transformative potential of nanoparticle-based platforms in both therapeutic and diagnostic applications, paving the way for more effective, personalized, and minimally invasive treatments.