The Role of Aromatic Moieties in Modulating Biomedical Properties of Small Molecules: Synthetic Organic Chemistry Meets Process Development

From naturally occurring biomolecules to modern pharmaceuticals, aromatic moieties consistently emerge as central structural elements shaping molecular recognition and biological response. A wide range of bioactive secondary metabolites derived from plants, microbes, and marine organisms feature aromatic scaffolds as core pharmacophores, a structural motif that is equally important in approved drugs across many therapeutic areas. The planar structure of the aromatic systems, together with their tunable electronic properties and ability to participate in − and other noncovalent interactions, enables effective binding with biological targets. Within this framework, substitution on aromatic rings remains one of the powerful and versatile strategies for modulating their biological activity. Subtle changes in the nature and position of substituents on an aromatic scaffold can profoundly influence electronic distribution, steric hindrance, lipophilicity, metabolic stability, and target selectivity, often transforming weakly active molecules into potent and selective drug candidates. This principle has been consistently and largely explored across synthetic organic chemistry and medicinal chemistry, underscoring that aromatic substitution is not a peripheral modification but a central design element linking molecular structure to biological performance. However, the successful translation of such molecular design strategies into viable therapeutics ultimately depends on the development of robust, scalable, and industrially feasible synthetic processes, making process development a critical bridge between chemical innovation and real-world pharmaceutical application. This thesis, titled “Aromatic Substitutions Modulating Biological Activities: Synthetic Organic Chemistry Meets Process Development,” explores a multidisciplinary interface between structure- activity relationships and practical chemical synthesis, highlighting how rational aromatic functionalization must be accompanied by scalable, robust, and industrially viable synthetic routes. By integrating synthetic organic chemistry with process development, this work aims to demonstrate how molecular design and manufacturing strategy are inherently interconnected in the successful translation of small-molecule therapeutics. The research presented in this thesis was carried out in the research group of Prof. Enrico Marcantoni at the University of Camerino between December 2022 and November 2025. As part of the mandatory PhD research and training mobility program, the work included a seven- month research period abroad from November 2024 to May 2025 at Thermo Fisher Scientific, Cork, Ireland, which was closely aligned with the scope and objectives of the research topic. The thesis is organized into four chapters, each divided into an introduction section and an experimental section. Chapter 1 describes the synthesis of a novel anhydrous cerium(III) catalyst and its application in the Michael addition of indoles, an important aromatic motif widely found in bioactive natural products and small-molecule drugs. Chapter 2 focuses on the design and synthesis of a benzothiazoline analogue as a cleavable linker for fluorescence image-guided surgery, combining tumor-responsive behavior with fluorescence activation. Chapter 3 addresses the design and synthesis of a new analogue of climacostol, a bioactive secondary metabolite produced by freshwater eukaryotic microorganisms, achieved through the introduction of a hydroxyl group at the 4-position of the aromatic ring. The modulation of biological activity toward prokaryotes, free-living protists, and non-target cells, particularly with respect to cytotoxic effects, was evaluated through collaborations with the Department for Innovation in Biological, Agro-food and Forest Systems (DIBAF), University of Tuscia, and the Laboratory of Protistology and Biology Education, Department of Education, Cultural Heritage, and Tourism (ECHT), University of Macerata. Part of this work has been published in Bioorganic & Medicinal Chemistry under the title “Chemical modification for improving drug-like molecular properties of climacostol, a natural resorcinolic lipid” in February 2025. Chapter 4 is dedicated to technical and process development aspects of small-molecule drugs and includes two experimental projects assisted during the research period at Thermo Fisher Scientific, Cork, Ireland, together with a theoretical review of quality system frameworks relevant to the active pharmaceutical ingredient (API) industry.