Discovery of a Direct Ras Inhibitor by Screening a Combinatorial Library of Cell-Permeable Bicyclic Peptides

• Published in: ACS combinatorial science Vol. 18; no. 1; pp. 75 - 85
• Main Authors: Trinh, Thi B, Upadhyaya, Punit, Qian, Ziqing, Pei, Dehua
• Format: Journal Article
• Language: English
• Published: WASHINGTON American Chemical Society 11.01.2016; Amer Chemical Soc
• Subjects: Antineoplastic Agents - chemical synthesis; Antineoplastic Agents - chemistry; Antineoplastic Agents - pharmacology; Cell Line, Tumor; Cell-Penetrating Peptides - chemical synthesis; Cell-Penetrating Peptides - chemistry; Cell-Penetrating Peptides - pharmacology; Chemistry; Chemistry, Applied; Chemistry, Medicinal; Chemistry, Multidisciplinary; Humans; Life Sciences & Biomedicine; Lung - drug effects; Lung - metabolism; Lung Neoplasms - drug therapy; Lung Neoplasms - genetics; Lung Neoplasms - metabolism; Peptide Library; Peptides, Cyclic - chemical synthesis; Peptides, Cyclic - chemistry; Peptides, Cyclic - pharmacology; Pharmacology & Pharmacy; Physical Sciences; Point Mutation; ras Proteins - antagonists & inhibitors; ras Proteins - genetics; ras Proteins - metabolism; Science & Technology; Signal Transduction - drug effects; cell-penetrating peptide; anticancer agent; Ras inhibitor; bicyclic peptide; peptide library; NUCLEOTIDE EXCHANGE; ONCOGENIC KRAS; KINASE; EFFECTOR INTERACTIONS; K-RAS; PATHWAY; SURFACE; BLOCKING; BINDING; EFFICIENT
• ISSN: 2156-8952; 2156-8944
• DOI: 10.1021/acscombsci.5b00164

Cyclic peptides have great potential as therapeutic agents and research tools. However, their applications against intracellular targets have been limited, because cyclic peptides are generally impermeable to the cell membrane. It was previously shown that fusion of cyclic peptides with a cyclic cell-penetrating peptide resulted in cell-permeable bicyclic peptides that are proteolytically stable and biologically active in cellular assays. In this work, we tested the generality of the bicyclic approach by synthesizing a combinatorial library of 5.7 × 106 bicyclic peptides featuring a degenerate sequence in the first ring and an invariant cell-penetrating peptide in the second ring. Screening of the library against oncoprotein K-Ras G12V followed by hit optimization produced a moderately potent and cell-permeable K-Ras inhibitor, which physically blocks the Ras-effector interactions in vitro, inhibits the signaling events downstream of Ras in cancer cells, and induces apoptosis of the cancer cells. Our approach should be generally applicable to developing cell-permeable bicyclic peptide inhibitors against other intracellular proteins.