Ribonucleic acid
Combining the best of small molecules and biologics Drug development is an increasingly complex challenge, as researchers seek to modulate novel biological targets. Professor Tom Grossmann tells us about the PEP-PRO-RNA project’s work in identifying principles for the design of peptide-based drugs, laying the foundations for the future development of novel macrocyclic compounds targeting biological processes The majority of approved drugs in the past were small molecules addressing defined pockets on a protein target. However, over recent decades, the pace of small molecule-based drug discovery has slowed, as researchers have faced difficulties in identifying novel biological targets that expose appropriate binding pockets and can be modulated with small molecular scaffolds. Since biologics such as antibodies exhibit improved surface recognition properties, they have been exploited successfully to address such targets. However, biologics are very poor cell penetrators, which restricts their use to extracellular targets. For these reasons, it has proven extremely challenging to address intracellular biomolecules which lack defined binding pockets. This holds particularly true for intracellular proteinRNA interactions (PRI) and proteinprotein interactions (PPI). “If you want to modulate a PPI inside a cell, then you hope that there is a small pocket in the binding interface. Otherwise there are basically no suitable molecular scafolds with sufficient cell permeability,” outlines Professor Tom Grossmann. Based at the VU University of Amsterdam, Professor Grossmann is the Principal Investigator of the PEP-PRO-RNA project, an EC-backed initiative developing a new approach, using peptide binding epitopes.
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“If you start with a peptide originating from the protein of a PPI, there is a good chance of getting a high-affinity binder for that site,” he explains. “A key challenge is to make sure that these peptides, or related molecules, actually go into the cell. We aim to develop a technology that combines high affinity for the biological target with good cellular uptake.” A number of peptides are known to be able to penetrate cells, yet the precise mechanisms behind this are not fully understood, meaning there is not a solid foundation for continued development. It is known that linear and flexible peptides are particularly poor cell penetrators and that reduced flexibility can support uptake, says Professor Grossmann. In addition, such constrained peptides also show an increased tendency to bind their target with high affinity. This is due to the fact that the flexibility of a peptide decreases upon binding, leading to entropic penalty and reduced overall affinity. “If a system gains order upon binding, that costs a certain form of energy, so we pay a penalty for binding a flexible peptide. The idea is to pre-organise the peptide in solution, in the same state as it wants to be bound,” continues Professor Grossmann. “In this process, we focus
on the identification of basic design principles. We want to provide tools that enable scientists to identify and optimize structures to address a given problem.”
Peptide organisation The first step in this work is to identify suitable peptide-binding epitopes. “We have defined some clear parameters for their selection. In terms of size, we don’t want a huge peptide, but also there’s no point in producing something very tiny that would not provide enough energy when binding the target. Taking this into consideration, we searched for potential starting points,” says Professor Grossmann. The researchers use a computational approach to analyse available structural data that identifies potential starting points for the development of agents to inhibit PPI or PRI. The next step in development involves macrocyclisation, meaning the formation of a large molecular ring system, where researchers aim to improve the affinity for the biological target. Professor Grossmann says there are two key parameters that need to be considered in this step. “One is – where do you choose the two attachment points for cyclization? It could be head-to-tail, or anywhere within the peptide sequence,”
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