CycPeptMPDB: A Database Aimed at Promoting Drug Design Using Cyclic Peptides

CycPeptMPDB, a novel database—created by Tokyo Tech researchers—focused on the membrane permeability of cyclic peptides, could accelerate the development of drugs based on these promising compounds. This database was created by gathering published information on thousands of cyclic peptides and organizing it neatly in an online-accessible platform. Thanks to its search and visualization capabilities, CycPeptMPDB could pave the way to new computational and machine learning methods for screening and designing drugs with cyclic peptides. One of the greatest challenges in modern drug design is to find compounds that satisfy somewhat contradictory requirements—they need to be small enough to permeate human cell membranes, while being large enough to target various protein surfaces and protein–protein interactions. This is a fine balance to achieve—if the compounds are too large, they may not pass through the cell membrane, and their bioavailability would be affected; if they are too small, they would not retain high specificity to the target protein (or proteins). Scientists estimate that over 80% of all known proteins associated with diseases cannot be targeted by conventional small-molecule drugs or antibody-based drugs. That is why, in recent years, cyclic peptides have become a very active research area. In principle, these compounds can achieve the fine balance required of modern drugs.

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