Developing and applying computer simulation methods to enhance the molecular understanding to engineer functionalized biomaterials

• Grant number: 20/07158-2
• Support Opportunities: Regular Research Grants
• Start date: March 01, 2021
• End date: August 31, 2025
• Field of knowledge: Engineering - Biomedical Engineering
• Agreement: ANR
• Principal Investigator: Fernando Luis Barroso da Silva
• Grantee: Fernando Luis Barroso da Silva
• Principal researcher abroad: ETCHEBEST
• Institution abroad: Université Paris Diderot - Paris 7, France
• Host Institution: Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Associated researchers: Alexandre de Brevern ; Frédéric Guyon ; Jean-Christophe Gelly ; Julien Diharce

Abstract

The central theme here is the engineering of new biomolecular materials. An essential aspect is the understanding and control of biomolecular interactions particularly the pH dependence. This topic is highly challenging and extremely important in many bioprocesses. Based on our joined experience and the development of novel theoretical methods, we want to enhance the knowledge of the fundamental physical interactions responsible for the formation and stability of molecular complexes as the basis for the understanding, diagnosis and treatment of infectious diseases; developments in the pharmaceutical and food industries; design of new (bio) functionalized materials and processes of bioseparation in general. Studied systems will include proteins from flaviviruses and relatated to SARS-CoV-2, and the design of new antibodies due to their global health importance. Our proposal benefits from our expertise on computer simulations, electrostatic models and the deep knowledge of biomolecular dynamics and interactions. (AU)

Scientific publications

(9)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

DA SILVA, FERNANDO LUIS BARROSO; PACO, KAREN; LAAKSONEN, AATTO; RAY, ANIMESH. Biophysics of SARS-CoV-2 spike protein's receptor-binding domain interaction with ACE2 and neutralizing antibodies: from computation to functional insights. BIOPHYSICAL REVIEWS, v. N/A, p. 25-pg., 2025-03-08. (20/07158-2)

NEAMTU, ANDREI; MOCCI, FRANCESCA; LAAKSONEN, AATTO; DA SILVA, FERNANDO L. BARROSO. Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants. COLLOIDS AND SURFACES B-BIOINTERFACES, v. 221, p. 10-pg., 2023-01-01. (20/07158-2)

DA SILVA, FERNANDO L. BARROSO; GIRON, CAROLINA CORREA; LAAKSONEN, AATTO. Electrostatic Features for the Receptor Binding Domain of SARS-COV-2 Wildtype and Its Variants. Compass to the Severity of the Future Variants with the Charge-Rule. Journal of Physical Chemistry B, v. 126, n. 36, p. 18-pg., 2022-09-06. (20/07158-2)

GIRON, CAROLINA CORREA; LAAKSONEN, AATTO; DA SILVA, FERNANDO LUIS BARROSO. Up State of the SARS-COV-2 Spike Homotrimer Favors an Increased Virulence for New Variants. FRONTIERS IN MEDICAL TECHNOLOGY, v. 3, p. 20-pg., 2021-06-30. (20/07158-2)

POVEDA-CUEVAS, SERGIO A.; BARROSO DA SILVA, FERNANDO LUIS; ETCHEBEST, CATHERINE. How the Strain Origin of Zika Virus NS1 Protein Impacts Its Dynamics and Implications to Their Differential Virulence. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 61, n. 3, p. 1516-1530, MAR 22 2021. (15/16116-3, 20/07158-2)

LUNKAD, RAJU; BARROSO DA SILVA, FERNANDO L.; KOSOVAN, PETER. Both Charge-Regulation and Charge-Patch Distribution Can Drive Adsorption on the Wrong Side of the Isoelectric Point. Journal of the American Chemical Society, v. 144, n. 4, p. 13-pg., 2022-01-20. (20/07158-2)

PRATES-SYED, WASIM A.; CHAVES, LORENA C. S.; CREMA, KARIN P.; VUITIKA, LARISSA; LIRA, ALINE; CORTES, NELSON; KERSTEN, VICTOR; GUIMARAES, FRANCISCO E. G.; SADRAEIAN, MOHAMMAD; BARROSO DA SILVA, FERNANDO L.; et al. LP-Based COVID-19 Vaccines: An Adaptable Technology against the Threat of New Variant. VACCINES, v. 9, n. 12, DEC 2021. (20/05146-7, 20/07158-2, 17/10910-5, 19/14526-0)

LUNKAD, RAJU; BARROSO DA SILVA, FERNANDO L.; KOSOVAN, PETER. oth Charge-Regulation and Charge-Patch Distribution Can Drive Adsorption on the Wrong Side of the Isoelectric Poin. Journal of the American Chemical Society, v. 144, n. 4, p. 1813-1825, FEB 2 2022. (20/07158-2)

CUEVAS, SERGIO ALEJANDRO POVEDA; DA SILVA, FERNANDO L. BARROSO; ETCHEBEST, CATHERINE. NS1 from Two Zika Virus Strains Differently Interact with a Membrane: Insights to Understand Their Differential Virulence. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. N/A, p. 15-pg., 2023-02-13. (20/07158-2, 15/16116-3)