Understanding molecular recognition by small proteins, nucleic acids, and other proteins is a vital process in biological systems, and understanding these events provides us with a rational route for their practical manipulation.
My research focuses on understanding the energetic and structural factors of molecular recognition of pharmacologically relevant proteins. I use theoretical tools, such as molecular modeling and dynamics, to identify small organic molecules with pharmacological properties. These techniques allow us to study the behavior of our study systems in the presence or absence of inhibitors, as well as to explore their conformational behavior in response to mutations and high-temperature conditions. To enhance our study of complex biomolecules, we employ advanced techniques, such as MARTINI 3 protein description and single-molecule force spectroscopy data, leveraging the GōMARTINI computational model. Our study model systems include ATP synthase in eukaryotic organisms and bacterial pathogens. We focus on structural characterization and the search for drugs based on their structure. We also investigate the molecular basis of antimicrobial resistance in Mycobacterium tuberculosis pyrazinamidase. In response to the challenges posed by the SARS-CoV-2 pandemic, we have formed a multidisciplinary research team. Our main objective is to produce, structurally characterize and design strategies for the inhibition of key proteins in the life cycle of COVID-19, both for prophylactic and therapeutic purposes. In particular, we studied the molecular interaction of the SARS-CoV-2 spike protein with the human angiotensin-converting enzyme 2 receptors and neutralizing antibodies. We aspire to contribute to the development of innovative approaches to combat this disease. In addition, another line of research covers the study of protein-sugar interactions in viruses, especially in the case of SARS-CoV-2 and the human papillomavirus, key events in the initial molecular recognition between the virus and the host cell.
Current activity
PostDoc Position at Department of Biosystems and Soft Matter, Institute of Fundamental Technological Research, Polish Academy of Sciences
Supervisor: Dr. Adolfo Poma Bernaola
Education
PhD in Biochemical Sciences
National Autonomous University of Mexico
Thesis: Exploring the pharmacobility of the binding site of aurovertin, an exogenous inhibitor of FOF1-ATP synthase.
Supervisor: Dr. Enrique García-Hernández
MS in Biochemical Sciences
National Autonomous University of Mexico
Thesis: Exploring the pharmacological potential of FOF1-ATP synthase: comparative structural study of the binding sites of natural inhibitors of the F1 sector from different species.
Supervisor: Dr. Enrique García-Hernández
Bachelor's degree: Industrial Biochemical Engineering
Metropolitan Autonomous University
Project: Pre-feasibility study to establish a carminic acid production company.
Publications
2023
Titaux-Delgado, G., Lopez-Giraldo, A.E., Carrillo, E., Cofas-Vargas,L.F., Carranza, L.E., López-Vera, E., García-Hernández,E. and del Rio-Portilla, F. Beta-KTx14.3, a scorpion toxin, blocks the human potassium channel KCNQ1. BBA - Proteins and Proteomics 2023. DOI:10.1016/j.bbapap.2023.140906
https://www.sciencedirect.com/science/article/abs/pii/S1570963923000201?via%3Dihub
Open access: No
2022
Cofas-Vargas, L.F, Mendoza-Espinosa, P., Avila-Barrientos, L.P., Prada-Gracia, D., Riveros-Rosas, H., and Enrique García-Hernández. Exploring the druggability of the binding site of aurovertin, an exogenous allosteric inhibitor of FOF1-ATP synthase. Frontiers in Pharmacology 2022, DOI: 10.3389/fphar.2022.1012008
https://www.frontiersin.org/articles/10.3389/fphar.2022.1012008/full
Open access: Yes
Avila-Barrientos, L.P.; Cofas-Vargas, L.F.; Agüero-Chapin, G.; Hernández-García, E.; Ruiz-Carmona, S.; Valdez-Cruz, N.A.; Trujillo-Roldán, M.; Weber, J.; Ruiz-Blanco, Y.B.; Barril, X.; García-Hernández, E. Computational Design of Inhibitors Targeting the Catalytic β Subunit of Escherichia coli FOF1-ATP Synthase. Antibiotics 2022, 11, 557. DOI:10.3390/antibiotics11050557
https://www.mdpi.com/2079-6382/11/5/557
Open access: Yes
2021
Valdez-Cruz, N.A., García-Hernández, E., Espitia, C., Cobos-Marín, L., Altamirano, C., Bando-Campos, C.G., Cofas-Vargas, L.F., Coronado-Aceves, E.W., González-Hernández, R.A., Hernández-Peralta, P., Juárez-López, D., Ortega-Portilla, P.A., Restrepo-Pineda, S., Zelada-Cordero, P. & Trujillo-Roldán, M.A. Integrative overview of antibodies against SARS-CoV-2 and their possible applications in COVID-19 prophylaxis and treatment. Microbial Cell Factories 20, 88. 2021. DOI: 10.1186/S12934-021-01576-5
https://microbialcellfactories.biomedcentral.com/articles/10.1186/s12934-021-01576-5
Open access: Yes
Labra-Núñez, A., Cofas-Vargas, L.F., Gutiérrez-Magdaleno, G., Gómez-Velasco, H., Rodríguez-Hernández, A., Rodríguez-Romero, A., García-Hernández, E. Energetic and structural effects of the Tanford transition on ligand recognition of bovine β-lactoglobulin. Arch Biochem Biophys. 2021, mar 15;699:108750. DOI: 10.1016/j.abb.2020.108750.
https://www.sciencedirect.com/science/article/abs/pii/S000398612030758X
Open access: No