Design and synthesis of engineered peptides to target undruggable PPIs: from in silico to in vitro studies

Abstract

Major unsolved diseases such as Cancer, cardiopathies or neurodegenerative disorders are frequently related with the malunction of complex protein networks. These networks are integrated by the interaction of multiple proteins that in case of a misregulation can trigger an undesired effect. Therefore, disruption of protein-protein interactions (PPIs), that are involucrated in a protein signalling cascade which is relevant for a particular diseases, is a hot topic in pharmaceutical industry. Unfortunately, traditional small molecules have been found to not be the most suitable inhibitiors of these therapeutic targets as PPI interfaces are characterized by a flat area with a lack of cavities that can fit a small molecule. In this scenario, peptides has called the attention in the drug discovery field for be a more appropiate candidates to target PPIs. Peptides are found in the chemical space between small molecules and antibodies, usullay contain between 2-50 amino acids and have an approximated weight of 250-10.000 Da. Then, their medium size allows a efficient recognition of the target protein without the need of well formed cavieties on the protein surface. However, peptides are characterized by a poor permeability and low stability in blood stream which had limited their therapeutic application in the past. Opportunately, introduction of non-natural amino acids and D-amino acids, N-alkylations of peptide backbone, cyclization and N-terminal and C-terminal modified cappings improve the biophysical properties along with the affinity for the receptor protein. Then, the use of engineered peptides, so-called peptidomimetics, is a promissing approach to target PPIs that can improve the binding potency of natural peptides and overcoming their major drawbacks at the same time. This thesis was carried out at Iproteos, a biotech company positioned in the use of peptidomimetics to target intracellular PPIs. The company has developed an in-house technology coined IPROTech, which is a platform that applys different in silico tools that are focused in the design of peptidomimetics, which are synthesized manually, quantified and finally evaluated in vitro. The experimental results are reintroduced in the platform and the process is repeated iteratively until achieve a final lead candidate. Hence, in the present work, IPROTech was applied to found de novo peptidomimetic molecules that inhibit the interaction of 4 different PPIs that are considered of therapeutic importance, Talin- Vinculin (Cancer), Rad51-BRCA2 (Cancer), Ras-Effectors (Cancer) and Retromer-L2 (HPVs infection). For each PPI, a collabration project with an academic group expert in field was setted up. Iproteos was in charge of the in silico studies of the target protein in order to design and synthesized a set peptidomimetic sequences that were predicted to disrupt the PPI of interest. On the other hand, the collaborators were responsible of the experimental evualtion of the synthesized compounds. In this terms, at least 1 hit was found for each PPI when evaluated in vitro, demonstrating an outsanding overall succes-rate of 31 % when all synthesized peptidomimetics were evaluated in vitro. Additinoally, the inclusion of new fancy builduing blocks into the compounds sintheysis, N-alkylation of the peptidomimetics backbone, pearmeability across biological barriers or the use of cyclodextrins as solvating excipient were other points studied as well.

Trobar nous fàrmacs capaços de trencar interaccions proteïna-proteïna, que d’alguna manera estan involucrades amb una malaltia, és de gran interès en el camp de la indústria farmacèutica. No obstant això, aquest tipus de diana terapèutica normalment no presenten cap cavitat ben definida a la seva superfície, característica necessària per albergar les tradicionals molècules petites. Per aquest motiu, la utilització de pèptids com a possibles fàrmacs és una aproximació molt prometedora perquè en tenir una mida molecular superior poden establir més interaccions amb la proteïna receptora afavorint així la seva unió. Però, aquesta aproximació està limitada per les propietats bioquímiques dels pèptids, ja que normalment són poc permeables i amb una baixa estabilitat un cop administrats. Afortunadament, els avanços fets en la síntesi de pèptids ha permès afegir modificacions sobre la seqüència dels pèptids per tal de millora les seves propietats, això inclou amino àcids no naturals, N-alquilacions, diferent tipus de N-terminals i C-terminals, entre altres. Els compostos obtinguts quan s’aplica aquesta enginyeria es coneixen com a peptidomimetics. Aquesta tesi es va realitzar a Iproteos. Iproteos és una petita empresa biotecnològica, focalitzada en l’ús de peptidomimetics per tal d’inhibir IPPs relacionades amb alguna malaltia. Per fer possible aquesta tasca, Iproteos ha creat una tecnologia, IPROTech, que agrupa tècniques computacionals per tal de cribrar la proteïna d’interès i genera estructures peptidometiques que més tard són sintetitzades, purificades i quantificades. Per aquesta tesi, es va aplicar la tecnologia IPROTech per trobar peptidomimetics amb la capacitat d’inhibir quatre IPP de rellevància terapèutica, Talina-Vinculina (càncer), Rad51- BRCA2 (càncer), Ras-Effectors (càncer) i Retromer-L2 (HPVs). Per cadascuna d’aquestes dianes, a Iproteos es va realitzar els estudis in silico i la síntesi dels peptidomimetics mentre que l'avaluació experimental la van fer grups acadèmics experts en cada camp. En tots els casos es va trobar almenys un compost capaç de trencar amb la interacció. Addicionalment propietats com la solubilitat, permeabilitat o estabilitat van ser avaluades per aquells compostos actius. Finalment, gràcies a les dades generades, alguns d’aquests compostos es van poder optimitzar obtenint un candidat final més potent encara.