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Bioorthogonal Metal-Peptide Catalysis

Periodic Reporting for period 1 - BioMPCat (Bioorthogonal Metal-Peptide Catalysis)

Reporting period: 2017-03-01 to 2019-02-28

In recent years, the development of bioorthogonal reactions has had a profound impact on several research areas such as imaging, drug development, biochemistry, and biotechnology. However, further advances in this topic are hindered by the limited number of biocompatible chemical transformations and by their rather modest reaction rate. BioMPCat (Bioorthogonal Metal-Peptide Catalysis) aims at overcoming the current limitations by establishing metal-peptide complexes as a novel and powerful class of bioorthogonal catalysts capable of promoting unprecedented transformations with remarkable efficiency under physiological conditions.
Naturally occurring peptides are ideally suited ligands for metals and, due to the inherent large structural and functional diversity, the chemical properties of their metal-complexes can be tuned to display optimal catalytic features: reactivity, selectivity, stability, and biocompatibility. Using simple and rationally designed combinatorial assays, the BioMPCat project focuses on the identification of lead catalysts structures for biomolecules ligations and as well as for site-selective cleavage of native proteins under physiological conditions.

The objectives of the action are the exploration on novel catalytic concepts: (1) identifying a non-toxic and highly effective Cu-peptide catalyst for the alkyne-azide cycloaddition reaction, which could render such important transformation compatible with the cellular environment; (2) developing a general approach to site-selective cleavage of native proteins. This research aims to investigate the interface between chemistry and biology: new perspectives in biochemistry and cell biology will be opened, as well as novel avenues in medicinal chemistry and therapeutics.

On this basis, from 1st March 2017 to 30th September 2017, the investigations within BioMPCat have focused on the identification of a new peptide ligand capable of stabilizing Cu(I) species under aerobic conditions and promoting the Cu-AAC with remarkable efficiency. Using split-and-mix peptidic libraries, convenient screening methods for the identification of functional peptides were designed. These experiments allowed the simultaneous testing of thousands of peptidic ligands and the identification of catalyst candidates. This process allowed the identification of a promising class of peptidic ligand for the desired transformation. The results constitute a milestone-proof of concept for the BioMPCat project and demonstrate the possible use of peptidic ligands in biorthogonal chemistry.

In conclusion, these initial results set the ground for future exploration in the field of bioorthogonal metal-peptide catalysis and constitute an interesting starting point for a thorough optimization of such peptidic ligands, which could lead to the identification of an optimal catalyst candidate.
Combinatorial screening.
Using a chemically encoded two-strand one-bead-one-compound peptidic library, combinatorial screenings were performed by using two different approaches.
1) In a first, unsuccessful, approach, the library was first incubated with Cu(I) salts, aiming at the direct generation of stable Cu(I)-acetylides on resin beads, and then with a solution of the dye-labelled organic azide. Unfortunately, in all experiments performed by using this approach, most of the resin beads showed a red coloration with almost no colour difference, thus suggesting that a very poor selectivity was obtained.
2) Gratifyingly, a very different outcome was obtained when the combinatorial screenings were performed using Cu(II) salts. This second approach selects the most stable Cu(II)-peptide precatalysts and allows the identification of active catalysts by investigating the desired cycloaddition in the presence of sodium ascorbate as an external reducing agent. Under these conditions, few beads showed a remarkable red coloration, thus allowing their isolation and the sequence decoding. We carefully tuned the reaction time, the solvent mixture and the concentration of the reagents in order to achieve optimal selectivity. The decoding of the peptidic sequences allowed the identification of a new class of peptides as promising ligands for the transformation.

Evaluation of metal-peptide catalysis.
The ligand candidates were prepared using standard Fmoc-based solid-phase-peptide-synthesis (SPPS) and conveniently used in a two-step preparation of the Cu(II) precatalysts: the peptides were converted into the corresponding Ag-salts, which were then used for the straightforward preparation of the Cu(II)-peptide salts in a metal-exchange reaction. We then focused on evaluating the activity of these precatalysts under homogeneous conditions. Different reaction parameters were screened (concentration, catalyst amount, solvent mixtures) and the results confirmed the activity previously observed in the combinatorial screening and also indicated the current limits of the methodology.
The initial investigations of BioMPCat set the ground for future studies and developments. The use of combinatorial chemistry allowed obtaining an important proof of concept for bioorthogonal metal-peptide catalysis: the identification of a novel class of peptidic ligands capable of promoting the Cu-AAC. However, the catalysts explored so far are not as active as desired for applications in chemical biology and therefore additional studies are needed to further enhance such activity.
Development of a peptidic catalyst for Cu-AAC