Research Area

A major focus of our laboratory is the identification and characterization of protein–protein interactions involved in cancer and other complex diseases. Using a combination of biochemical assays and molecular biology techniques, we investigate disease-associated signaling networks and regulatory hubs at both molecular and cellular levels. To achieve high-resolution structural and mechanistic insights, we employ advanced technologies including X-ray crystallography, mass spectrometry, Cryo-EM, and hydrogen–deuterium exchange (HDX)-based approaches. The integration of these platforms allows us not only to identify protein interaction partners, but also to map interaction interfaces and reveal dynamic conformational changes that are critical for disease progression and therapeutic targeting. In particular, our studies focus on ER-associated degradation (ERAD) mechanisms as well as proliferative and apoptotic signaling pathways, with the aim of identifying critical regulatory nodes that can be therapeutically targeted in cancer and other diseases.

Building on these findings, our laboratory actively develops therapeutic strategies aimed at regulating or inhibiting key oncogenic hubs. We design and synthesize novel peptide-based therapeutics and perform extensive physicochemical and biophysical characterization of these molecules. In addition to peptide therapeutics, we also develop small-molecule candidates targeting disease-related pathways. To enhance therapeutic efficacy and bioavailability, we also develop and utilize carrier-based delivery systems for the controlled release and targeted delivery of our candidate molecules.
One of our recent achievements includes the development of an innovative purification platform that offers a promising alternative for Fab purification in both academic and industrial settings (Tatlı et al., 2023). To evaluate the therapeutic potential of our candidates, we conduct pathway analyses, cytotoxicity assays, and dose optimization studies by screening multiple cell lines. Promising candidates are further evaluated through pre-clinical animal studies and early-stage translational investigations. Currently, our peptide candidates are undergoing advanced preclinical evaluation for their therapeutic efficacy (Tatlı et al., 2025).

Beyond therapeutic discovery, our laboratory actively contributes to the pharmaceutical and biotechnology sectors through collaborative research and development projects. By leveraging our advanced infrastructure and expertise, we support the development of biosimilar products, peptide-based therapeutics, and diagnostic applications in partnership with industrial stakeholders. These collaborations strengthen the translational impact of our research and facilitate the transfer of scientific innovation into practical healthcare solutions.
As a biochemistry-oriented laboratory, we also produce and characterize a wide range of proteins and enzymes for both research and industrial applications. Through our systematic production platforms and extensive expertise in protein science, many routinely used biomolecules are developed and optimized within our laboratory. In addition to therapeutic proteins, we work on industrially relevant enzymes such as PETase and β-glucuronidase. These biomolecules undergo rigorous biophysical and structural characterization using high-resolution analytical techniques including circular dichroism spectroscopy and mass spectrometry, ensuring stability, functionality, and industrial applicability.
At the genetic level, we collaborate with hospitals and clinical research centers to perform next-generation sequencing (NGS)-based germline mutation analyses. By screening panels composed of cancer predisposition genes, we generate population-level datasets and identify variants classified as pathogenic, benign, or variants of uncertain significance (VUS). A particularly important aspect of our work involves the functional reclassification of VUS variants. To support clinical interpretation and improve diagnostic decision-making, we investigate the effects of these variants at both protein and cellular levels. By integrating biochemical characterization, structural analysis, and cellular functional assays, we generate experimental evidence that contributes to the reclassification of variants as pathogenic or benign, thereby facilitating more accurate diagnosis and treatment strategies for clinicians and patients.