Protein-protein interactions represent the largest untapped opportunity for therapeutic development. The number of protein-protein interactions in human cells has been estimated to exceed 100,000, well above the ~30,000 human genes. This multitude of protein-protein interactions constitutes a tremendous opportunity for therapeutic innovation as the field has languished due to lack of promising technological approaches. To address the shortcomings in existing technologies, Carmot is developing an innovative lead finding technology called Chemotype Evolution. Chemotype Evolution is a proprietary technology based on the well- validated approach of making and screening target-directed compound libraries, but uses fragment-based concepts to take this approach to a new level. Chemotype Evolution enables an evolutionary screening paradigm that is unprecedented in small molecule drug discovery and provides rapid and inexpensive access to novel and target-relevant chemical diversity that is not easily accessed by other technologies. The long-term objective of this proposal is to develop small molecule drugs that stimulate tumor cell apoptosis and inhibit inflammatory signaling in the tumor environment. The NF-kB pathway is a key signaling node in the communication between tumors and the inflammatory microenvironment. The activities of anticancer drugs bortezomib and thalidomide have in part been attributed to indirect inhibition of NF-kB. Despite intensive efforts, viable drug-leads that directly target NF-kB activation have not been identified. The protein-protein interaction between IkB Kinase (IKK) and Nf-kB Essential Modulator (NEMO), referred to as NEMO/IKK, has emerged as a promising target for inhibiting NF-kB activation: Peptides that encompass the NEMO binding domain (NBD) of IKK can block IKK binding to NEMO and inhibit NF-kB activation in vivo. The specific objective of this Phase I proposal is to discover drug-like inhibitors of NF-kB activation. To achieve this, Carmot will use Chemotype Evolution to evolve NBD peptides into small molecule inhibitors of NEMO/IKK. In the first aim, Chemotype Evolution will be used to discover hybrid molecules of NBD peptides and drug fragments that bind to NEMO. In the second aim, Chemotype Evolution will be used to evolve these hybrids into drug-like inhibitors of IKK binding to NEMO. In the third aim, the best inhibitors will be characterized in more detail to lay the foundation for a Phase II proposal to advance select inhibitors towards drug candidates for treating human cancers. The proposed research will validate Chemotype Evolution as a transformative technology for targeting protein-protein interactions and has high potential both for scientific innovation and for development or products that have significant economic and societal benefits.

Public Health Relevance

Localized inflammation plays an essential role in the progression of human cancer and is a promising target for therapeutic intervention. This proposal offers an innovative strategy for targeting inflammation in tumor tissue. The objective is to identify lead compounds with the potential to become drug candidates for treating human cancers.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Small Business Innovation Research Grants (SBIR) - Phase I (R43)
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Special Emphasis Panel (ZRG1-IMST-G (11))
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Haim, Todd E
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Carmot Therapeutics, Inc.
San Francisco
United States
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