New molecules block activity of disease-related proteins

A research team of Ca' Foscari, École Polytechnique Fédérale de Lausanne (EPFL) and the University of Padua has developed a method to rapidly and sustainably synthesize and isolate large collections of macrocyclic compounds, an emerging class of pharmaceutical molecules for the treatment of severe diseases such as cancer. This result was achieved by miniaturising chemical reactions in tiny droplets using acoustic dispensing technology for reagent transfer. The study, Synthesis and direct assay of large macrocycle diversities by combinatorial late-stage modification at picomole scale has been published in the Nature Communications journal.

Most drug discovery research programmes begin with a combinatorial process in which large numbers of structurally diverse chemical compounds collected over many years are tested against a given protein target of interest. These experiments are usually performed in plates containing hundreds of microwells each, in which each single well contains a chemical compound to be analysed, ultimately resulting in thousands of plates to be examined. This is a laborious procedure which usually takes multiple days and requires large amount of chemicals, and which often does not lead to the identification of promising molecules.

To overcome this painstaking and expensive process, a new method has been established to synthesise large collections of compounds in tiny volumes by rapidly transferring the reagents using acoustic waves. Through the miniaturisation and the high speed, it has been possible to sustainably generate a collection of more than ten thousand different compounds at picomole scale in only half a day.

The technology has been applied to synthesise small macrocyclic compounds, a class of emerging molecules capable of selectively targeting disease-related proteins. These compounds mimic some naturally occurring molecules, such as the immunosuppressive cyclosporine, the antibiotic vancomycin and the antitumor dactinomycin, and possess numerous qualities that have raised great interest in the pharmaceutical industry. For example, they have a low molecular weight, a property that allows them to cross the cell membrane and reach intracellular disease targets. Furthermore, their compact and rigid structure favors a high binding affinity with the target protein, ultimately enabling the use of a smaller amount of molecule to obtain the desired effect.

"Our contribution was crucial in understating the binding mode of these novel macrocyclic compounds to a protein target of interest and further validated the approach of screening large macrocyclic libraries with diversified peripheral groups," explained Alessandro Angelini, professor at the Department of Molecular Sciences and Nanosystems at Ca’ Foscari University of Venice and member of the European Centre for Living Technology (ECLT).

"The determination of the three-dimensional X-ray structure of an inhibitor bound to the protein target revealed that both moieties, the macrocyclic ring and the appended carboxylic acids made critical contributions to the binding," explained Laura Cendron, professor at the Department of Biology at the University of Padua.

"Given the small size and the limited polar surface of macrocyclic compounds, they have a high chance of being passing through cell membranes, which means that they can be used to developing drugs for intracellular targets or even drugs that are taken orally." explained Christian Heinis, professor at Institute of Chemical Sciences and Engineering of the École Polytechnique Fédérale de Lausanne.