Projects

Quantum and molecular mechanics QM/MM

Quantum treatment of the reactive region coupled to a classical force field for the rest of the system, for mechanisms that molecular mechanics alone cannot describe.

2 projects

Computational study on the location of molecular orbitals in the HOMO-LUMO frontier region in enzyme reaction sites: Application in drug planning.

Computational study on the location of molecular orbitals in the HOMO-LUMO frontier region in enzyme reaction sites: Application in drug planning.

Aloisio Almeida de SouzaBSc.

Mechanisms of enzymatic reactions are widely studied, and catalytic cycles with several steps involving proton transfer have been proposed. However, delocalization and electronic transfer effects are almost always neglected, especially in the context of planning new drugs. With this project we aim to develop a protocol for drug prospecting, taking into account the grouping of frontier orbitals and their neighborhood in catalytic sites of enzymes. We evaluate the delocalization of molecular orbitals in polymer systems of polyacetylenes, polyglycines and polyalanines as simplified models to help understand electronic processes that occur in catalytic sites of enzymes.

Team: Pedro Geraldo Pascutti (oritentador), Mariana Simões Ferreira (coorientadora) e José de Anchieta de Oliveira Filho (coorientador)

In silico study of the evolution of quantum properties in the antibody affinity maturation process toward HIV epitopes

Lilian Mendonça Alves de OliveiraMSc.

B lymphocytes produce antibodies, molecules able to recognise and neutralise antigens. Antibodies carry a complementarity-determining region (CDR) that binds the epitopes of the antigen, and that binding is what neutralises the pathogen. Computational biology now makes it possible to model those interactions in three dimensions at different stages of affinity maturation, with molecular dynamics and hybrid quantum mechanics/molecular mechanics (QM/MM) approaches, which give a sharper account of structure, chemical reactivity and binding affinity, and support the design of better immunotherapies and vaccines against viruses such as HIV. Work in quantum biology suggests that natural selection acts on the three-dimensional location of electronic orbitals in protein structures, and this project investigates that phenomenon under a simplified evolutionary model: somatic hypermutation, which effectively selects progressively more efficient antibodies over the course of an infection. The aim is to study how somatic hypermutation and affinity maturation of anti-HIV antibodies shape the antigen-antibody complex and its molecular reactivity, measuring how adaptive mutations change electronic reactivity indices such as the Fukui function.

Team: Pedro Henrique Monteiro Torres

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