Structural Biology of Host-Pathogen Interactions

The Structural Biology of Host-Pathogen Interactions group is interested in the understanding the protein-protein interactions that mediate the communication between humans and the bacterial communities to which we are continually exposed. These interactions often involve bacterial pathogens, which attempt to evade the constant surveillance of human innate immunity and, specifically, the activated branch of the complement system. Our group studies other processes that are vital for bacterial cell survival in the human body as well as in environmental reservoirs, including enzymes of sugar and amino acid metabolism and sulfur mobilization and trafficking. To this end, we use a combination of advanced protein production techniques, X-ray diffraction, biochemical, biophysical and computational chemistry methods to analyze snapshots of protein complex interactions, as well as their associated dynamic behavior, both underlying the functional results of those interactions.

As a result of our participation in the European consortium ComplexINC and Complemento I (CM), recently we confounded a CSIC spin-off, Abvance, to offer innovative antibody-based medicines for the treatment of immunological disorders, inflammatory and neurodegenerative diseases.

The Structural Biology of Host-Pathogen Interactions group participates in the Interdisciplinary Platform (PTI) “Global Health” del Consejo Superior de Investigaciones Científicas (CSIC). Our laboratory is working on two research projects, DeCOV-DT and DALI5, aimed at the development of therapeutic and diagnostic antibodies, and specific biologics for the prevention of acute lung damage induced by COVID-19. With the TwinKidz project (CPP2022-009838) we are developing together with Abvance and the Fundación para la Invest. Biomedical Hospital Univ. 12 de Octubre a molecule for medical imaging diagnosis of kidney disease.

Complement System

The interactions that occur at the interface between the human host and the countless microorganisms with which we come into contact daily constitute a topic of profound importance, both at a fundamental biological level and in an area of growing medical interest. The complement system of innate immunity constitutes one of the first defense barriers against pathogens. The complement system includes soluble and membrane-associated proteins that monitor blood and tissue interstitial fluids for pathogens, apoptotic cells, and immune complexes. Pathogens have evolved a sophisticated molecular arsenal that allows them to escape the surveillance of the complement system, a strategy known as immunoevasion. In this context, we focused on elucidating the structures and mechanistic details of the components of the complement system and its protein complexes with virulence factors with immunoevasive properties.

Protein Interactions at the Heart of Defense Against Pathogens

The central component of the complement system is a large multidomain protein called C3, one of the most abundant proteins in the blood and a central player in the defense of the innate immune system. When complement is activated on the surface of pathogens, C3 undergoes a series of transformations that lead to the covalent attachment of thousands of activated C3 molecules on the surface of the pathogen (opsonization). The main binding protein or opsonin is iC3b, one of the activated C3 molecules with a radically different structural organization. C3 deposition occurs so rapidly and so completely that within minutes the pathogen is surrounded by a maze of iC3b molecules. iC3b is recognized by CR3, a cell surface receptor present on most immune cells, including macrophages and neutrophils responsible for eliminating pathogens by phagocytosis. The structure of the complex between iC3b and the αI domain of CR3 (Figure below) illustrates how the modular structure of iC3b plays a crucial role in creating the surfaces required for CR3 binding (Fernández et al. Nat Comm 2022). Since iC3b is bound to the surface of the pathogen and CR3 to the surface of the immune cell, the complex models the dense cell-cell interactions required for efficient recognition and destruction of pathogens by the immune system.

Bacterial Immunoevasive Factors Against the Human Complement System

GAPDH, an essential glycolytic enzyme central to carbon and energy metabolism, stands out as a multifunctional protein with the ability to function as a virulence factor (Fernandez et al. Sem Cell Dev 2019). In this pathogenic role, GAPDH can bind to various human complement factors, thereby interfering with the natural defense barriers established by human innate immunity. Our group has contributed to establishing the immunoevasive role of bacterial GAPDH in several Gram-positive pathogens (e.g., S. pyogenes, A. vaginae, C. perfringens) (Querol et al. Front Microbiol 2018, 2019). More recently, we have established that GAPDH from Leptospira interrogans, the Gram-negative bacteria responsible for one of the most important zoonoses, leptospirosis, can also sequester C5a. These studies have paved the way for the discovery of new antimicrobial agents designed to disrupt the interaction between GAPDH and anaphyllotoxin C5a and C3. Increasing our understanding of these processes at the atomic level is crucial for the development of potential treatments against bacterial infectious diseases.

Improvement of Methods for the Production of Therapeutic Molecules

We are interested in the development and improvement of new technologies and production tools for complex protein biologics using expression methodologies in yeast and other eukaryotic expression systems. The ultimate goal of these toolkits, including two yeast-based kits developed in our laboratory, is to facilitate micro- and large-scale production of high-quality protein biologics for drug discovery and as biopharmaceuticals. The knowledge generated led to the creation of the spin-off company Abvance.

Carbohydrate and Amino Acid Metabolism

Bacteria and fungi contain an impressive repertoire of enzymes capable of synthesizing and metabolizing amino acids, carbohydrates and sulfur. In this line of research we have studied: i) Sulfur trafficking is important for cellular fitness and organisms have developed complex protein systems that interact with the task of mobilizing sulfur atoms from the amino acid L-cysteine in the form of highly persulfides. reagents (-S-S-). We established the reaction mechanism for the transfer of sulfur atoms through protein-protein interfaces (Fernandez, et al. ACS Catal 2017); ii) We also focused on the de novo synthesis of pyrimidine nucleotides studying the still controversial reaction mechanism of the synthesis of the OMP precursor catalyzed by OPRT. These are vital reactions conserved between all divisions of life (Roca et al. ACS Catal 2021); iii) We used yeast peroxidases as a model of the resistance mechanisms of pathogenic yeasts to the phagocytic oxidative burst (Gómez et al. Free Rad Biol Med 2019).