Maria João Ramos

Computational Biochemistry, University of Porto

Maria João Ramos

Research Areas

Enzyme Catalysis:
We have been performing the study of catalytic and inhibition mechanisms of several enzymes, such as Class I Ribonucleotide Reductase, Pyruvate Formate Lyase, Farnesyltransferase, Fumarate Reductase, Cox-2, Uroporphyrinogen III Decarboxylase, Glutathione Transferase, Superoxide Dismutase, Thioredoxin, HIV-1 Protease, Reverse Transcriptase and Integrase, PLP-dependent enzymes, HMG-CoA-Reductase, Asparaginase, Renin, ACE-II and several glucosidades, among others. We have been using QM/MM methodologies with the QM part described at the DFT level with large basis sets, embedded in complete enzyme models described at the MM level. 

Molecular Dynamics of Proteins
We have been addressing many aspects of enzyme catalysis via molecular dynamics simulations. These include conformational changes, detection of water channels and water hydration sites, evaluation of protein flexibility, or refinement of enzyme:substrate complexes obtained from docking/modelling studies. Cu, Zn Superoxide Dismutase, Farnesyltransferase, Gluthatione Transferase or HIV-1 Reverse Transcriptase are some of the studied systems. Parameter Development is also an area in which we have been working on, e.g. we have developed molecular mechanics parameters for  metal enzymes in several ligand environments. The parameters have been obtained by fitting to DFT potential energy surfaces and are committed to the Amber force field. Parameters for biological membranes have also been developed.

omputational Mutagenesis:

Protein complexation regulates a large number of cellular events, and to interfere with protein:protein complexes is of the utmost therapeutic importance. Alanine scanning mutagenesis of protein-protein interfacial residues is currently performed to detect the hot spots for protein complexation. These are the regions that must be drug-targeted.
We have developed a computational protocol, based on MM-PBSA calculations, that predicts differences in binding free energies between the wild-type and alanine mutated complexes with an average unsigned error of 0.80 kcal/mol, and a maximum error of 2.5 kcal/mol. It was benchmarked with a set of 46 mutations, and permits a systematic scanning mutagenesis of protein-protein interfaces. We have recently shown that the method is as accurate as TI but at a fraction of the computational cost.

Drug Transport Across Cell Membranes:
In addition to therapeutic effect, drugs need to exhibit favourable absorption, distribution, metabolism and excretion (ADME) characteristics to produce a desirable response in vivo. For absorption and tissue distribution, a drug must be absorbed through a succession of lipid bilayers before reaching its target. This makes cell membrane permeation of paramount importance, and a clear understanding of this process is crucial for rational drug design. 

Drug Discovery:
Drug discovery is an area in which we have been working on. Basically, we have been exploring ways of optimizing lead compounds. Usually we start from a structure of a receptor and try to find hit compounds that bind the receptor with virtual screening techniques. After experimental validation, we try to perform subtle modifications in the drug which improve its affinity (calculated with FEP/TI techniques) without compromising its ADME properties.