Feature Breakdown,100-million-membered macrocyclic libraries

The field of drug discovery is constantly seeking innovative approaches to tackle challenging biological targets. Among the most promising avenues is the exploration of macrocyclic peptides. These molecules, characterized by their ring-like structures formed from a chain of amino acids, offer a unique blend of biological properties akin to larger biologics, yet with the potential for oral administration. At the forefront of this endeavor lies the development and application of macrocyclic peptide libraries, vast collections of these molecules designed to accelerate the identification of novel therapeutic agents.

Macrocyclic peptides are not a new concept, but their potential as drugs has been significantly amplified by advancements in library synthesis and screening. Unlike linear peptides, the cyclic nature of macrocyclic peptides confers increased stability against enzymatic degradation and often leads to enhanced binding affinity and selectivity for their targets. This makes them particularly attractive for inhibiting intracellular protein-protein interactions (PPIs) or for use as peptide-drug conjugates for targeted therapies. Merck scientists are exploring macrocyclic peptides as a new way to combine the properties of a biologic in a pill, highlighting the significant industry interest in this therapeutic modality.

The power of macrocyclic peptide libraries lies in their sheer scale and diversity. Researchers are creating collections with billions of members, such as the 2.4 x 10^12 members synthesized in one study, composed of both natural and non-natural amino acids. This extensive chemical space allows for the exploration of a wide range of structural possibilities, increasing the probability of discovering molecules with desired therapeutic properties. Technologies like DNA-encoded chemical libraries (DELs) have revolutionized the creation and screening of these vast collections. DNA-encoded macrocyclic peptide libraries enable the efficient synthesis and selection of billions of unique compounds, where each macrocycle is tagged with a DNA barcode that encodes its structure. This allows for rapid and high-throughput screening, as demonstrated by the discovery of a neutral nonapeptide, UNP-6457, that inhibits the MDM2–p53 interaction with an IC50 of 8.9 nM using DNA-encoded cyclic peptide libraries.

The design of these libraries is crucial for their success. Various strategies are employed, including the proprietary BRiTeCycle™ platform, which enables the creation of structurally diverse, non-canonical macrocyclic peptides. Other approaches focus on specific cyclization methods, such as disulfide-cyclised peptides generated through yeast display, or the synthesis of macrocyclic peptides containing multiple N-alkylated units. The goal is to create large libraries of macrocyclic peptides that are not only diverse but also synthetically accessible and amenable to screening.

The utility of macrocyclic peptides extends to various therapeutic areas. Macrocycles are discovery tools for targets with shallow or extended binding sites, making them ideal for targets that have been historically difficult to drug with small molecules. This includes a broad range of protein targets, and the ability to optimize macrocyclic leads from various display technology libraries like mRNA and display libraries is critical. The development of tailored DEL libraries is proving to be a practical technology for the discovery of macrocyclic DELs, enabling researchers to directly yield macrocyclic peptides that benefit from low molecular weight, TPSA, and HBD/HBA counts, characteristics often associated with improved pharmacokinetic profiles.

The creation of these libraries is an active area of research. Current approaches for generating macrocyclic peptide libraries often involve techniques like mRNA display, which allows for the generation of peptide libraries. The Prestwick Peptidic Macrocycle Library, for instance, offers a unique collection of 400 peptidic macrocycles, including more complex structures. Furthermore, the development of linearizable macrocyclic peptide libraries is addressing limitations in the application of combinatorial library selection for therapeutic development. These large-scale macrocyclic libraries are expected to catalyze therapeutic peptide discovery and development.

Beyond DNA-encoded approaches, other display technologies are also being leveraged. Bacterial display of genetically encoded macrocyclic peptides is emerging as a robust approach for generating diverse cyclic peptide libraries, expanding the scope of cell-surface display for macrocyclic drug discovery. Methods used for the creation of cyclic peptide libraries are continually being refined to increase diversity and efficiency. For example, 100-million-membered macrocyclic libraries containing natural and non-natural amino acids are being produced, with near-quantitative intramolecular disulfide formation.

The ongoing innovation in macrocyclic peptide libraries is paving the way for a new era in drug discovery. The ability to make rather large cyclic peptide structures that can still function as drugs, combined with high-throughput screening capabilities, promises to unlock therapies for diseases that were previously considered intractable. The continuous development of methods for the creation of cyclic peptide libraries and the exploration of diverse chemical scaffolds will undoubtedly lead to the identification of novel peptides with significant therapeutic potential.