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New molecule holds promise of therapies for cancer and rare diseases

April 05, 2022

Irvine, Calif. — Researchers at the University of California, Irvine and the Italian Institute of Technology have developed a new molecular compound, ALY101, that shows promising anti-cancer activity against a wide range of tumor cell types and a common type of melanoma in mouse models. The findings, “Structure-based Design of CDC42 Effector Interaction Inhibitors for the Treatment of Cancer,” are published in Cell Reports.

The collaboration integrated computational chemistry approaches and wet biology assay systems between Marco De Vivo, PhD, director of the Molecular Modeling and Drug Discovery Laboratory at IIT, and the UCI laboratory of Anand K. Ganesan, MD, PhD, a professor of dermatology and biological chemistry and co-director of the Chao Family Comprehensive Cancer Center’s Biotechnology, Imaging & Drug Discovery program.

This resulted in a unique way to develop drugs that block the protein-protein interactions underpinning basic cellular processes, including tumor initiation, growth, metastasis and blood vessel formation. These interactions are part of the cellular machinery that can become dysregulated in cancers and diseases such as neurofibromatosis type 2. 

Their work focused initially on blocking the interaction of members of the CDC42 family of GTPases with a key kinase, PAK1, which is amplified in breast, colon and other cancers and also is active in the pathology of neurofibromatosis and other rare diseases such as Ewing sarcoma.    

“We identified a previously unknown PAK1 binding pocket present only in CDC42 and we used this pocket at the interface between both proteins to disrupt the interaction that would normally lead to PAK1 activation," said De Vivo.

"By blocking this interaction, we can inhibit the excessive PAK1 activity that drives cellular changes that lead to cancer and other diseases. We used computer simulations of both proteins to design compounds able to bind to that pocket and modeled blockade of the interaction between both proteins using a range of simulated compounds that we ‘screened’ for in silico and then synthesized the most promising ones for further experimental tests.”

Specifically, ALY101, the primary compound discovered in the collaboration, works by blocking the interaction that normally converts PAK1 from an inactive to an active state. Other researchers have demonstrated that suppressing or inhibiting PAK1 activity in tumor cells sensitizes them to a broad range of different anticancer agents, enhancing their antitumor activity.

This rational approach for structure-based drug design has been fully integrated with wet biology assay workflows in the Ganesan lab at UCI.

“This compound and the effects of the drug on the tumor and its microenvironment has potential applications both as monotherapy or in combination regimens to reduce dose-limiting toxicities of existing agents, or as a treatment for tumors that have developed resistance to other agents,” said Ganesan, who serves as vice-chair of research for the UCI School of Medicine's Department of Dermatology. “In a broader context, these studies provide a roadmap for the rational structure-based design of drugs targeting GTPase family member proteins, known to be important but difficult-to-target to treat cancer.”

Their research has been funded by foundations such as the Italian Association for Cancer Research in Italy and the U.S. National Institutes of Health, including NIH awards R01CA244571 and U54CA217378. Their findings also led to the launch of a start-up, Alyra Therapeutics, which is dedicated to expanding the platform developed by De Vivo and Ganesan to further develop ALY101 and other compounds as potential new treatments for cancer, neurofibromatosis and other diseases where small GTPases and their signaling interactions play a role in disease pathology.

Alyra Therapeutics’ lead program, ALY101, was developed from this work and it acts to restore normal cell signaling processes that may become dysregulated in patients with certain cancers and rare diseases such as neurofibromatosis type 2.   

“We are extremely pleased to see the publication of Drs. De Vivo and Ganesan’s work outlining the activity of ALY101,” said Mark Benedyk, PhD, president and CEO of Alyra Therapeutics.

“The integrated approach pursued by both labs has efficiently generated multiple compounds that block the CDC42/PAK1 interaction, validating our platform, and similar projects are underway to address other small GTPase proteins outside of the CDC42 family. The significance of their discovery with regards to the potential treatment of cancer and neurofibromatosis type 2 cannot be underestimated.”

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Each year, the UCI School of Medicine educates more than 400 medical students and nearly 150 doctoral and master’s degree students. More than 700 residents and fellows are trained at UCI Medical Center and affiliated institutions. The School of Medicine offers an MD; a dual MD/PhD medical scientist training program; and PhDs and master’s degrees in anatomy and neurobiology, biomedical sciences, genetic counseling, epidemiology, environmental health sciences, pathology, pharmacology, physiology and biophysics, and translational sciences. Medical students also may pursue an MD/MBA, an MD/master’s in public health, or an MD/master’s degree through one of three mission-based programs: the Health Education to Advance Leaders in Integrative Medicine (HEAL-IM), the Leadership Education to Advance Diversity-African, Black and Caribbean (LEAD-ABC), and the Program in Medical Education for the Latino Community (PRIME-LC). The UCI School of Medicine is accredited by the Liaison Committee on Medical Accreditation and ranks among the top 50 nationwide for research. For more information, visit som.uci.edu.