Biomolecular recognition is based on collective and specific non-covalent interactions between discrete biological molecules. Our laboratory studies a variety of protein systems, for instance antibody-antigen and receptor-ligand complexes, to understand quantitatively how these coordinated non-covalent interactions contribute to their specific recognition in biological and artificial systems. We seek to elucidate the molecular mechanisms by which biological molecules obtain high-specificity and affinity from multiple angles using advanced instrumentation. Our approaches include biophysical techniques such as isothermal titration calorimetry (ITC), surface plasmon resonance (SPR), and differential scanning calorimetry (DSC), spectroscopic analysis like circular dichroism (CD), high-resolution structural techniques like X-ray crystallography, and protein manipulation strategies using arginine co-solvents and site-directed mutagenesis. We aim to produce functional molecules with higher performance and better properties, to build a solid foundation from which to develop drugs that modulate specific interactions between biomolecules, and ultimately to understand the principles of molecular interactions in our lives.
Living organisms are fundamentally based on sophisticated interactions at the molecular level between a variety of biomolecules such as proteins, nucleic acids, lipids, sugar, and organic compounds. Thus, to understand the basis of life, we need first to characterize the general principles governing their communication at the molecular level. Our laboratory elucidates the mechanisms of interaction between biomolecules by quantitative approaches using a combination of thermodynamic, kinetic, and structural techniques. Our current efforts are directed towards three key groups of interactions: protein-protein, protein-lipid, and protein-nucleic acids interactions.
Protein dysregulation is one of the hallmarks of disease at the cellular level, such as in cancer. Key regulatory proteins must work in a coordinated fashion to keep the cells in a healthy state. However, when this system breaks-down, they elicit cascades of defective signals resulting in the abnormal proliferation of cells, altering biological function, and leading to metastasis and severe disease. Therefore, the artificial modulation of disease-specific protein-protein interactions is increasingly considered an attractive strategy to repair faulty networks, thus tackling disease. In our laboratory we target some of the critical protein-protein interaction networks involved in carcinogenesis, such as regulatory proteins belonging to signal transduction cascades, or the essential components of the cell-cell adhesion machinery.
Our laboratory also focuses on diseases caused by pathogenic microorganisms. Whole-genome sequencing have identified numerous pathogenic factors in bacteria, many of them of unknown function. To find novel and effective therapeutic agents is essential to first have a clear understanding of the mechanism of action of the target protein under study. In our laboratory we have focused on the human pathogens Staphylococcus aureus (the most dangerous microorganism in a hospital setting), and Streptococcus pyogenes (causing severe hemolytic infections). We aim to elucidate the mechanism of action of proteins activated during pathogenesis, such as the heme scavenging Isd system of S. aureus, and to employ these data to mount an effective antimicrobial strategy using small-molecule inhibitors.
Protein-based biomaterials are increasingly employed not only for biomedical applications, but also in the energy industry and for the preparation of high-performance applications. We investigate the underlying interactions between proteins of various model systems inspired from Nature such as human hair, a biological material consisting of multiple proteins and showing a sophisticated mechanism of self-assembly. Other example is the nanometer-scale thin fimbriae from bacteria (termed pili) composed of polymerized proteins and synthesized on their cell surface. Our laboratory aims to design Nature-inspired functional molecules with high-performance and good quality relying on the higher-order architecture of these types of proteins, and on the basis of their biophysical analysis.
Antibodies are employed in large-scale therapeutic and diagnostic applications, being the best-selling pharmaceutical products for the last few years. Antibody success relies on their unsurpassed ability to recognize virtually every class of antigens with high affinity and specificity. For the development of the next generation of antibodies with better physicochemical properties (bio-better) and superior functions (bio-superior), our group employs multi-dimensional analysis and protein engineering. We approach antibodies from three points of view: characterization, selection, and modification.
Characterization : the key residues for molecular recognition are analyzed and described based on physicochemical, structural, and cell-based approaches.
Selection : phage-display technologies select antibodies with optimal physiochemical properties.
Modification : Reduction of size, fusion to shift targeting abilities, and functionalization by chemical conjugation are routinely employed. In favorable cases, the design of antibodies with higher affinity is performed with in silico techniques.
To regulate target biomolecular interactions, we perform the drug screening and the characterization of drugs (small molecules) binding to the target proteins. The development of small molecule drug discovery is recently stopped at the primary step (target validation, 1st screening) due to the hard manipulation of the target proteins and its unique targets (Membrane proteins, Protein-protein interactions, Intrinsically disordered proteins et al.). These high level target proteins do not be covered by traditional methods of drug discovery and design. Therefore, we must exploit the next generation methods and approaches of drug discovery base on the quantitative and physicochemical analyses of proteins with their structural information.
In our Laboratory, we perform the screening, hit validation, lead optimization in drug discovery of small molecules using biophysical methods (SPR, ITC, DSC, DSF, etc.). This approach can provide the information for the specificity of the interaction between small molecules and target proteins. The target types are enzymes, membrane proteins and PPIs and so on. In addition, we use various types of libraries such as fragment library, PPI library and natural product library. Our group is collaborated with Drug Discovery Initiative, The University of Tokyo to make a platform of open innovation in drug discovery in Japan. Our project contributes to not only a development of drug designs but also life science.