Roche, Stephane P.

In this study, we developed a new peptide motif called β-strap (strap = strand + cap) used to fold β-hairpins of varying length. β-Straps are mean to be short sequences (4 to 8 a-amino acids) forming β-sheets using a judicious combination of non-covalent interactions (NCI) to overcome the entropic penalty inherent to long loop closure. Among those, we proved that a couple of CH-π / NH-π interactions from a tryptophan zipper motif were critical to create a stable packing of the structure. To optimize these interactions, we incorporated unnatural tryptophan derivatives having functionalized indole side chains. Finally, the innate ability of the β-strap to bring β-stand in close contact was exploited to promote macrocyclization of long coiled peptides (up to 16 residues).
Then, we studied a more complex β-hairpin loop mimics found at the apex of monoclonal antibodies (mAb) complementary determining region 3 (CDR-H3). Using a set of bioinformatics tools, a search of PDB crystal structures revealed that a large set of mAb crystals possess a β-bulge, located at the edge of CDR-H3 loops. A cluster analysis revealed it has an impressive adaptability towards different H3-loop sizes and conformations. In order to evaluate its function in antibodies, we synthesized several β-hairpin models bearing a prototypical β-bulge. By combining short β-straps and the β-bulge, we were able to design β-hairpin peptides mimic of mAb with a variety of lengths and rigidity while retaining a high degree of folding. Starting from pembrolizumab, the most outstanding blocker of the PD-1/PD-L1 checkpoint currently available in clinic, we scoped ~30 CDR-H3 mAb mimics (H3 loop). As a result, several novel β-hairpin peptide inhibitors of the PD-1/PD-L1 pathway were identified (IC50 <0.3 μM).

Published Content: Jeedimalla, N.; Jacquet, C.; Bahneva, D.; Youte Tendoung, J.-J.; Roche, S. P. J. Org. Chem. 2018, 83, 12357.
The present thesis will be focused on the study of House-Meinwald Rearrangement (HMR) reactions for the congested trisubstituted spiro-epoxide molecules. Including their regio-selective, chemo-selective, enantio- selective selective and stereo-selectivity’s will be discussed in detailed by the mechanistic study approach of HMR reaction of trisubstituted spiro-epoxides.
Chapter 1 will present the efforts towards the biomimetic total synthesis of meroterpenoid natural product (+)-liphagal, which possess a recognizable biological activity. The shortcomings associated with its stereochemical assignment, and also the revision of stereochemical assignment of siphonodictyal B, through which the biosynthesis of (+)-liphagal was proposed were discussed.
Chapter 2 will focus on the study of regio and chemoselective HMR reaction. In addition, a three-step sequence for the synthesis of α-arylated cyclohexanones and the most challenging cycloheptanones is reported. First, an efficient one-pot synthesis of β, β’-disubstituted benzylidene cycloalkanes using the palladium-catalyzed Barluenga reaction from readily available feedstock chemicals is described. Second, an epoxidation followed by the HMR of spiro-epoxides is reported to produce a number of α -arylated cycloalkanones upon the ring expansion. Reactions catalyzed by bismuth triflate underwent quasi-exclusively ring expansion for all substrates (electronically poor and rich), demonstrating the difficulty to achieve the ring enlargement for electron deficient spiro-epoxides. On the other hand, via catalysis with aluminium trichloride the rearrangement proceeded typically in high yields and with remarkable regioselectivity. In this case, a switch of regioselectivity was achieved for spiro-epoxides with electron-withdrawing substituents which enabled this method to be successfully extended to some chemo specific arene shifts and it can also synthesize aldehydes derivatives bearing a α-quaternary carbon.

In this dissertation, we discuss the development of a synthetic method to functionalize various α-haloglycine esters, as key precursors to a large variety of non-proteinogenic α-amino acids (Xaas). At first, we discovered a very practical and high yielding acetyl chloride-mediated cascade reaction to synthesize α-arylated amino esters in one-pot. In this multicomponent reaction (MCR), a primary carbamate was condensed with a glyoxylate, followed by an in situ halogenation which proved essential to trigger the final Friedel−Crafts functionalization. After careful reaction optimization, a plethora of arene nucleophiles were reacted with high regioselectively in CHCl3 at low temperatures (Method A) while less activated arenes reacted more cleanly in CH3CN and at higher temperatures (Method B). To broaden the scope of this reaction to acid sensitive nucleophiles, a one-pot reaction was designed via evaporation of all acid by-products at the α-haloglycine stage. The anion-binding Schreiner’s thiourea catalyst proved to be extremely efficient to promote this complementary approach (Method C) which relies on the chloride leaving group activation by the catalyst to assist the functionalization stage and deliver the α-amino ester product.
In the second chapter, some highly practical and efficient preparations of α-haloglycine esters in one-pot have been developed to generate useful precursors of non-proteinogenic α-amino esters. Also, a mild and unique AcOH(cat.)/AcCl system was found to promote an autocatalytic-like condensation/deoxy halogenation and facilitate the multicomponent assembly of non-proteinogenic α-amino esters. Friedel–Crafts reaction between α-chloroglycine and N-methylindole have been studied in details to understand the mechanistic intricacy of this reaction. Our findings through the initial kinetic profiling support that the arylation likely proceeds via a SN1-like (or SN2C+) mechanism.
In third chapter, we discuss the development of the most challenging α,α-disubstituted amino esters in a multicomponent fashion. Our results highlight that the MCR proceeds via the formation of an enamide intermediate, which is further tautomerized to corresponding iminium to produce the desired product. In collaboration with Eli Lilly at the Automated Synthesis Laboratory (ASL), we have developed silver (I) salts mediated Friedel–Crafts reaction for synthesis of α-trifluoromethylated α-amino esters on a fully automatized robot.

Peptides and proteins with photochemical sensors
are valuable tools when analyzing biochemical processes
and peptide properties. Recent work on
fluorescent α-amino acids (FlAAs) proved extremely
useful in studying protein folding, conformational
changes and reactivity. When fluorescent tags are
appropriately attached to proteins they allow for the
detection of their environment and changes therein.
Research on the topic of site-specific fluorescent
molecules is in its early stages. Several challenges
face the topic of selectively excitable fluorescent
probes. These include limits on the size and lifetime of synthesized proteins and enzymes, attaching the
tag at the target location on a peptide chain which
will take advantage of the photochemical properties
of the tag, and developing molecules that will readily
exhibit environment-sensitive fluorescence.

In order to keep up with the high demand for
biologically active molecules, chemists devised
several synthetic strategies to access novel chemical
spaces. The two main strategies to construct new
scaffolds are to revisit underexploited or forgotten
reactions or to devise new transformations. We are
exploring a unique and underexploited reaction, the
Himbert–Henn cycloaddition, to produce complex
molecular scaffolds in a single step (strategy 1). In a
second novel approach, we are modifying the
Hantzsch 4-component reaction (4CR) by
incorporating an α-amino ester residue to construct
new molecules (strategy 2). Both of these reactions
have great potential to synthesize novel and chiral
molecules from proteinogenic α-amino esters. These
unprecedented and complex polycyclic molecules
have potential application in medicinal chemistry and
natural product synthesis. 4-aza-podophyllotoxins
obtained by the Hantzsch-4CR have been proven to
be potent as anti-leukemia, anti-colon cancer, and
vascular disrupting agents (with nanomolar activity).

Podophyllotoxin is a natural aryltetralin lignan compound isolated from plants within the genus Podophyllum. Podophyllotoxin has been under extensive biochemical investigation since the discovery of its biological activity as a strong microtubule destabilizing mitotic agent. Although these antineoplastic compounds have shown significant activity as cancerous cell growth inhibitors, they lack selectivity and are thus extremely toxic to healthy cells. This has led to a recent interest in the synthesis of Podophyllotoxin analogues in hopes of optimizing the biological selectivity and potency of these semi-synthetic derivatives. The objective of my research in the Roche group is to generate a library of these derivatives for subsequent biological assays to determine their potential as chemotherapeutic agents. In total I have synthesized 22 Podophyllotoxin analogues. Of these 22 derivatives, 14 have been biologically evaluated and 4 were observed to possess promising anti-cancer activity and are currently undergoing further evaluation.