Pharmaceutical sciences and phytopharmacology are being reshaped by artificial intelligence, computational pharmacology, multimodal evidence integration, and increasingly connected molecular data. However, discovery acceleration alone cannot establish mechanistic validity, safety, clinical utility, sustainability, or regulatory readiness. This article proposes a future research agenda for integrating AI-era pharmaceutical sciences with responsible natural product-based therapeutic research. The agenda is organized around high-integrity data ecosystems, molecular intelligence, natural product identity and characterization, multimodal discovery methods, mechanistic validation, safety-aware design, exposure and response modeling, translational evidence, regulatory science, sustainability, ethical sourcing, benefit-sharing, and accountable governance. It emphasizes benchmarking, reproducibility, uncertainty estimation, bias assessment, model documentation, external validation, and multidisciplinary human oversight as foundational research capabilities rather than optional additions. Molecular intelligence is positioned as a means of connecting chemical structures, phytochemical profiles, assays, omics, textual knowledge, and supported clinical signals while maintaining provenance and evidence-level distinctions. Responsible translation is framed as a stage-gated research process requiring empirical validation, safety evaluation, exposure feasibility, clinical evidence where relevant, and regulatory assessment where applicable. Strategic priorities include interoperable infrastructures, natural product knowledge graphs, validation pipelines, federated collaboration, causal and digital-twin research where justified, sustainability safeguards, and workforce development. The principal contribution is an evidence-bounded agenda that links discovery innovation with validation and governance while maintaining a clear separation between research prioritization and therapeutic decision-making.