Computational characterization of the structural determinants of antibody stability in the humanization process

• Grant number: 24/10665-4
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: January 01, 2025
• End date: July 31, 2027
• Field of knowledge: Biological Sciences - Biochemistry - Chemistry of Macromolecules
• Principal Investigator: Paulo Sergio Lopes de Oliveira
• Grantee: Amauri Donadon Leal Junior
• Host Institution: Centro Nacional de Pesquisa em Energia e Materiais (CNPEM). Ministério da Ciência, Tecnologia e Inovação (Brasil). Campinas , SP, Brazil

Abstract

The design of therapeutic antibodies involves optimizing their characteristics such as affinity and specificity for antigens. This process begins with obtaining the complementarity-determining regions (CDRs), usually from murine models, and inserting them into human frameworks to avoid adverse reactions. However, during the humanization stage, negative impacts on antibodies' production and stability have been reported. Indeed, the structural effect of grafting CDRs into human frameworks is still insufficiently understood. Therefore, in this project, we aim to computationally investigate the relationship between the variable and constant regions, specifically CDRs and frameworks, to evaluate antibody stability during humanization. To achieve this, we will start with a dataset of over 80 structural and experimental stability data points from different framework combinations retrieved from the literature. These antibodies will be modeled or obtained from databases and submitted to structural analyses, artificial intelligence tools, and molecular dynamics simulations to characterize the structural determinants of their stability. As a preliminary result, we evaluated the permutation of CDRs between two clinically used antibodies, Pertuzumab and Trastuzumab, with identical frameworks and observed that the CDRs impact the flexibility of the constant and variable domains, which, to our knowledge, is an unprecedented finding. Thus, with this promising step, we hope that our discoveries can be used as a descriptive tool for the efficiency of antibody design, aiming to optimize the humanization stage and expand the range of available immunotherapeutics.