Non-covalent interactions are of great importance in biology, chemistry, and material sciences. Although much information about different types of non-covalent interactions is available, incorporating them in a molecular design to generate a molecule that can undergo association to form a molecular assembly with bulk properties of interest is a challenge. To understand and harness intermolecular interactions, we have designed an indane 2,5-diketopiperazine (DKP) scaffold. Crystal engineering studies with this scaffold show that the molecules assemble into one dimensional tapes via reciprocal amide hydrogen bonds, tapes assemble into two dimensional sheets via arene-arene interactions, and sheets assemble into three dimensional solids via van der Waals contacts. A series of tetraalkoxy-substituted DKPs previously investigated exhibited liquid crystalline behavior. A new class of DKPs with one alkoxy substituent, rather than two, on each benzene ring has been synthesized. Thermochemical studies of the new DKPs by differential scanning calorimetry and polarized optical microscopy show that they are not liquid crystalline as expected. However, in the process of making the DKPs, conformationally constrained tyrosine analogues, (R)- and (S)-5-hydroxy-2-aminoindan- 2-carboxylic acids, were prepared by chromatographic separation of diastereomeric dipeptide derivatives formed from N-Boc-L-phenylalanine. Absolute configurations were assigned by X-ray crystallographic analysis. The series of tetraalkoxy-substituted DKPs showed a remarkable trend in freezing point. The freezing point for the series decreases with an increase in alkyl chain length. To understand the relationship between the crystal packing interactions and the freezing point trend, a study of the association of DKPs in solution by NMR was initiated. An Nmethylated 2,5-diketopiperazine was previously synthesized and studied by NMR using chloroform as solvent to obtain equilibrium constants for self association. Attempted multi-step syntheses of a more lipophilic N-3,7-dimethyloctyl 2,5-diketopiperazine, which was expected to have solubility in non-interfering solvents such as carbon disulfide, benzene, and carbon tetrachloride, failed. In response, a direct and concise method for accessing N-alkyl DKPs was developed, and an N-decyl 2,5-diketopiperazine was synthesized. X-ray crystallographic analysis of the N-decyl 2,5-diketopiperazine reveals formation of dimers via hydrogen bonding in the solid state.

Progress towards the design and the application of small molecules as inhibitors of angiogenesis is reported. First, the regulation of hypoxia inducible transcription with epipolythiodioxopiperazine (ETP) natural products is discussed, beginning with the exploration of the physical and chemical properties of ETP skeletal analogs, xylylene-linked bis-diketopiperazines (1,4-piperazine-2,5-diones, DKPs).The design, synthesis and solid-state structures of a new class of xylylene-linked bis(1,4-piperazine-2,5-diones) are reported in an effort to extend the molecular framework of piperazine-2,5-diones. These compounds were derived from piperazine-2,5-dione as the core structure, synthesized via a new efficient route, and their crystal structures were determined. We examined the effects of side chain substitution on conformations of the linked bis-DKPs in the solid state. The results suggested that the interplay between the attractive intermolecular interactions and repulsive steric interactions of the substituents at the C6 and C6' positions of the diketopiperazine rings is important in determining the solid-state conformations of xylylene-linked bis(piperazine-2,5-diones).Asymmetric alpha-sulfenylation reactions were designed and performed as a potential route to the synthesis of epipolythiodioxopiperazine natural products. First, a chiral auxiliary approach is reported, sulfenylating chiral azomethines of alpha-amino acids as epipolythiodiketopiperazine precursors in yields of 55% with de as high as 74%. Asymmetric organocatalytic alpha-sulfenylation of substituted piperazine-2,5-diones is also reported, with chiral cinchona alkaloids as bases and benzyl-substituted electrophilic sulfur transfer reagents. The reaction was investigated with varied catalyst loading, type of sulfenylating agent, temperature and solvent. The effects of ring substitution and type of catalyst on yield and enantioselectivity of the reaction are reported. The synthetic utility of the asymmetric alpha-sulfenylation in context of the synthesis of epipolythiodioxopiperazine fungal metabolites is discussed.Finally, chemical approach towards the inhibition of angiogenesis by targeting alpha v beta 3 integrin antagonists with synthetic multifunctional boron neutron capture therapy (BNCT) integrin ligands is presented. The novel synthesis of an alpha v beta 3 integrin antagonist containing a free amine group for peripheral modification is reported, along with the preparation of a bifunctional BNCT integrin ligand and a trifunctional BNCT integrin ligand containing a fluorescent dye. Synthetic challenges and potential therapeutic applications of these ligands are discussed.

Malgré l’intérêt et la diversité des propriétés pharmacologiques des 2,5-dicétopipérazines (DKP), les voies de biosynthèse de ces molécules d’origine microbienne sont très peu connues. L’objectif de mes travaux de thèse a été i) de documenter de nouvelles voies de biosynthèse de DKP qui se caractérisent par la présence d’une synthase de cyclodipeptides (CDPS) travaillant souvent de concert avec une ou plusieurs enzymes de modification des cyclodipeptides et ii) d’explorer la diversité chimique codée par ces voies. Dans un premier temps, je me suis intéressée aux CDPS. Après la sélection par bioinformatique de candidats dans les bases de données génomiques, j’ai pu identifier 51 nouvelles CDPS actives et montrer que ces enzymes peuvent incorporer 17 des 20 acides aminés naturels. Par ailleurs, ce travail a permis de mieux caractériser la famille des CDPS, de définir l’existence de plusieurs sous-familles aux signatures fonctionnelles spécifiques et d’établir les premiers éléments d’un code de spécificité pour la synthèse de cyclodipeptides. Dans un second temps, je me suis attachée à caractériser les enzymes de modification associées aux nouvelles CDPS et, en particulier, les dioxygénases dépendant du Fe(II) et du 2-oxoglutarate (OG) qui sont très représentées dans ces voies. J’ai ainsi pu détecter une activité in vivo pour 11 OG et poursuivre la caractérisation in vitro pour l’une de ces OG, ce qui a permis de caractériser les DKP qu’elle synthétise et d’ainsi montrer la complexité des modifications chimiques introduites. L’ensemble de ces travaux a donc permis d’identifier et de caractériser de nouvelles voies de biosynthèse qui donnent accès à une diversité accrue de DKP. / Despite the interest and diversity of the pharmacological properties of 2,5-diketopiperazines (DKPs), the biosynthetic pathways of these microbial molecules are poorly documented. The aim of my doctoral work was i) to identify new DKP biosynthetic pathways that are characterized by the presence of a cyclodipeptide synthase (CDPS) often associated with one or more cyclodipeptide-tailoring enzymes and ii) to explore the chemical diversity encoded by these pathways. First of all, my study focused on CDPSs. After the bioinformatics-based selection of candidates, 51 novel CDPS were characterized, revealing the incorporation of 17 of the 20 proteinogenic amino acids. Moreover, this work has allowed a better characterization of the CDPS family, by showing the existence of several subfamilies with specific functional signatures and laying the foundations of a specificity conferring code for the synthesis of cyclodipeptides. Second, I characterized the tailoring enzymes associated with the newly identified CDPSs and, in particular, the Fe(II) and oxoglutarate dependent dioxygenases (OGs) that are highly represented in these pathways. I detected the in vivo activity for 11 OGs and characterized the in vitro activity for one of them, showing the complexity of the chemical modifications introduced into the cyclodipeptide. This work has led to identify and characterize novel biosynthetic pathways that provide access to a greater diversity of DKPs.