Designing a new drug often begins with finding the right molecules to hit the right protein targets and disable important mechanisms in disease-causing cells. However, when the ideal target sits inside a cell rather than on its surface, many prospective drugs run into a Goldilocks-like conundrum of being too small or too big for their chosen beds.
“Most biological pathways are mediated by protein-protein interactions (PPIs) inside cells,” explained Chandra Verma, a Senior Principal Investigator at the A*STAR Bioinformatics Institute (A*STAR BII). “These PPIs have been undruggable by today’s two main drug modalities: small molecules, which have trouble targeting the large, flat binding surfaces on most PPIs; and antibodies, which are too large to enter cells at all.”
Stapled peptides may be a ‘just right’ solution. This emerging class of therapeutic molecules consists of short, linear chains of amino acids—the building blocks of protein—braced by chemical “staples” that hold them in a specific shape.
“Being proteins themselves, stapled peptides can mimic the surfaces of target proteins, boosting their specificity,” said Verma. “Stapling also reorganises peptides into the most efficient shapes to bind target proteins; protects them against degrading enzymes; and helps them permeate membranes.”
To understand the molecular mechanics behind how staples enable peptides to slip into cells, Verma and joint first author, Jianguo Li, worked with pharmaceutical company Merck & Co, US and MSD, Singapore, to explore the trans-membrane journey of ATSP-7041M, a modified version of a stapled peptide known to inhibit tumour growth. Using solid state nuclear magnetic resonance (ssNMR) imaging, the team measured the peptide’s shapes and interactions with cell membranes, then used their resulting data to guide molecular dynamics (MD) simulations of its entry into cells.
The team found that when ATSP-7041M came in contact with cell membranes, it coiled into a corkscrew-shaped α-helix structure, turning its hydrogen bonds inward. The affinity for the membrane was enhanced by a special interaction called cation-π between the peptide’s phenylalanine side chain and the positively charged atoms on the surface of the membrane. This enables the peptide to enter the membrane where the shapeshifting is further enhanced by the hydrophobic interior of the membrane.
“Peptide chains are normally polar, which cause the lipid (fat)-based membranes of cells to repel them,” said Verma. “However, we found that ATSP-7041M’s helical conformation basically buries its polar groups inside the peptide, allowing it to more easily pass through membranes.”
The team plans to further study the mechanics of membrane permeation by stapled peptides, which could support the design of future therapeutics aided by artificial intelligence platforms.
“The ATSP-7041M story signifies the importance of understanding detailed molecular mechanisms for drug discovery,” Verma added. “We’d like to also acknowledge the research groups of David Lane and Christopher Brown of the A*STAR Institute of Molecular and Cell Biology (A*STAR IMCB); and Charles Johannes of the A*STAR Institute of Sustainability for Chemicals, Energy and Environment (A*STAR ISCE2) for their contributions to this work.”
The A*STAR-affiliated researchers contributing to this research are from the A*STAR Bioinformatics Institute (A*STAR BII).
