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Faris J, Adaligil E, Popovych N, Ono S, Takahashi M, Nguyen H, Plise E, Taechalertpaisarn J, Lee HW, Koehler MFT, Cunningham CN, Lokey RS. Membrane Permeability in a Large Macrocyclic Peptide Driven by a Saddle-Shaped Conformation. J Am Chem Soc 2024; 146:4582-4591. [PMID: 38330910 PMCID: PMC10885153 DOI: 10.1021/jacs.3c10949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/10/2024] [Accepted: 01/17/2024] [Indexed: 02/10/2024]
Abstract
The effort to modulate challenging protein targets has stimulated interest in ligands that are larger and more complex than typical small-molecule drugs. While combinatorial techniques such as mRNA display routinely produce high-affinity macrocyclic peptides against classically undruggable targets, poor membrane permeability has limited their use toward primarily extracellular targets. Understanding the passive membrane permeability of macrocyclic peptides would, in principle, improve our ability to design libraries whose leads can be more readily optimized against intracellular targets. Here, we investigate the permeabilities of over 200 macrocyclic 10-mers using the thioether cyclization motif commonly found in mRNA display macrocycle libraries. We identified the optimal lipophilicity range for achieving permeability in thioether-cyclized 10-mer cyclic peptide-peptoid hybrid scaffolds and showed that permeability could be maintained upon extensive permutation in the backbone. In one case, changing a single amino acid from d-Pro to d-NMe-Ala, representing the loss of a single methylene group in the side chain, resulted in a highly permeable scaffold in which the low-dielectric conformation shifted from the canonical cross-beta geometry of the parent compounds into a novel saddle-shaped fold in which all four backbone NH groups were sequestered from the solvent. This work provides an example by which pre-existing physicochemical knowledge of a scaffold can benefit the design of macrocyclic peptide mRNA display libraries, pointing toward an approach for biasing libraries toward permeability by design. Moreover, the compounds described herein are a further demonstration that geometrically diverse, highly permeable scaffolds exist well beyond conventional drug-like chemical space.
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Affiliation(s)
- Justin
H. Faris
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Emel Adaligil
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Nataliya Popovych
- Department
of Early Discovery Biochemistry, Genentech, South San Francisco, California 94080, United States
| | - Satoshi Ono
- Innovative
Research Division, Mitsubishi Tanabe Pharma
Corporation, Kanagawa 227-0033, Japan
| | - Mifune Takahashi
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, South
San Francisco, California 94080, United States
| | - Huy Nguyen
- Department
of Analytical Research, Genentech, South San Francisco, California 94080, United States
| | - Emile Plise
- Department
of Drug Metabolism and Pharmacokinetics, Genentech, South
San Francisco, California 94080, United States
| | - Jaru Taechalertpaisarn
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Hsiau-Wei Lee
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
| | - Michael F. T. Koehler
- Department
of Medicinal Chemistry, Genentech, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - R. Scott Lokey
- Department
of Chemistry and Biochemistry, University
of California, Santa
Cruz, California 95064, United States
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