Search Results - "Coimbra, João T. S"

The importance of intramolecular hydrogen bonds on the translocation of the small drug piracetam through a lipid bilayer by Coimbra, João T. S, Feghali, Ralph, Ribeiro, Rui P, Ramos, Maria J, Fernandes, Pedro A

“…The number of hydrogen bond donors and acceptors is a fundamental molecular descriptor to predict the oral bioavailability of small drug candidates. In fact,…”
Get full text

Transmembrane Protease Serine 2 Proteolytic Cleavage of the SARS-CoV‑2 Spike Protein: A Mechanistic Quantum Mechanics/Molecular Mechanics Study to Inspire the Design of New Drugs To Fight the COVID-19 Pandemic by Teixeira, Luís M. C., Coimbra, João T. S., Ramos, Maria João, Fernandes, Pedro Alexandrino

“…Despite the development of vaccines against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, there is an urgent need for efficient drugs…”
Get full text

Different Enzyme Conformations Induce Different Mechanistic Traits in HIV‐1 Protease by Coimbra, João T. S., Neves, Rui P. P., Cunha, Ana V., Ramos, Maria J., Fernandes, Pedro A.

“…The influence of the dynamical flexibility of enzymes on reaction mechanisms is a cornerstone in biological sciences. In this study, we aim to 1) study the…”
Get full text

New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein–Protein Interfaces by Simões, Inês C. M, Costa, Inês P. D, Coimbra, João T. S, Ramos, Maria J, Fernandes, Pedro A

“…Knowing how proteins make stable complexes enables the development of inhibitors to preclude protein–protein (P:P) binding. The identification of the specific…”
Get full text

Beyond the TPP "gold standard": a new generation mitochondrial delivery vector based on extended PN frameworks by Ong, How Chee, Coimbra, João T. S, Ramos, Maria J, Xing, Bengang, Fernandes, Pedro A, García, Felipe

“…Mitochondrial targeting represents an attractive strategy for treating metabolic, degenerative and hyperproliferative diseases, since this organelle plays key…”
Get full text

Enabling Mitochondrial Uptake of Lipophilic Dications Using Methylated Triphenylphosphonium Moieties by Ong, How Chee, Hu, Zhang, Coimbra, João T. S, Ramos, Maria J, Kon, Oi Lian, Xing, Bengang, Yeow, Edwin K. L, Fernandes, Pedro A, García, Felipe

“…Triphenylphosphonium (TPP+) species comprising multiple charges, i.e., bis-TPP+, are predicted to be superior mitochondrial-targeting vectors and are expected…”
Get full text

Revisiting Partition in Hydrated Bilayer Systems by Coimbra, João T. S, Fernandes, Pedro A, Ramos, Maria J

“…We discuss potential-of-mean force convergence issues involving the methods for generating starting structures of umbrella sampling simulations for the study…”
Get full text

Diffusion of the small, very polar, drug piracetam through a lipid bilayer: an MD simulation study by Ribeiro, Rui P., Coimbra, João T. S., Ramos, Maria J., Fernandes, Pedro A.

“…One of the major goals to improve drug discovery is to understand the molecular properties that influence oral bioavailability. Molecular dynamics-based…”
Get full text

Relevant Interactions of Antimicrobial Iron Chelators and Membrane Models Revealed by Nuclear Magnetic Resonance and Molecular Dynamics Simulations by Coimbra, João T. S, Moniz, Tânia, Brás, Natércia F, Ivanova, Galya, Fernandes, Pedro A, Ramos, Maria J, Rangel, Maria

“…The dynamics and interaction of 3-hydroxy-4-pyridinone fluorescent iron chelators, exhibiting antimicrobial properties, with biological membranes were…”
Get full text

Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations by Coimbra, João T. S., Fernandes, Pedro A., Ramos, Maria J.

“…Due to the emergence of antibiotic resistance, the need to explore novel antibiotics and/or novel strategies to counter antibiotic resistance is of utmost…”
Get full text

Biomolecular structure manipulation using tailored electromagnetic radiation: a proof of concept on a simplified model of the active site of bacterial DNA topoisomerase by Jarukanont, Daungruthai, Coimbra, João T S, Bauerhenne, Bernd, Fernandes, Pedro A, Patel, Shekhar, Ramos, Maria J, Garcia, Martin E

“…We report on the viability of breaking selected bonds in biological systems using tailored electromagnetic radiation. We first demonstrate, by performing…”
Get more information

Membrane partition of bis-(3-hydroxy-4-pyridinonato) zinc(ii) complexes revealed by molecular dynamics simulations by Coimbra, João T S, Brás, Natércia F, Fernandes, Pedro A, Rangel, Maria, Ramos, Maria J

“…The class of 3-hydroxy-4-pyridinone ligands is widely known and valuable for biomedical and pharmaceutical purposes. Their chelating properties towards…”
Get full text

Alkyl vs. aryl modifications: a comparative study on modular modifications of triphenylphosphonium mitochondrial vectors by Ong, How Chee, Coimbra, João T S, Kwek, Germain, Ramos, Maria J, Xing, Bengang, Fernandes, Pedro A, García, Felipe

“…Triphenylphosphonium (TPP ) moieties are commonly conjugated to drug molecules to confer mitochondrial selectivity due to their positive charge and high…”
Get full text

A computational study on the redox properties and binding affinities of iron complexes of hydroxypyridinones by Coimbra, João T. S., Brás, Natércia F., Fernandes, Pedro A., Rangel, Maria, Ramos, Maria J.

“…The potential of hydroxypyridinones for in vivo iron sequestration, in both biological and medical contexts, has been extensively discussed in the literature…”
Get full text

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes by Sousa, Sérgio F., Pinto, Gaspar R. P., Ribeiro, António J. M., Coimbra, João T. S., Fernandes, Pedro A., Ramos, Maria João

“…In this study, a set of 50 transition‐metal complexes of Cu(I) and Cu(II), were used in the evaluation of 18 density functionals in geometry determination. In…”
Get full text

Properties that rank protein:protein docking poses with high accuracy by Simões, Inês C M, Coimbra, João T S, Neves, Rui P P, Costa, Inês P D, Ramos, Maria J, Fernandes, Pedro A

“…The development of docking algorithms to predict near-native structures of protein:protein complexes from the structure of the isolated monomers is of…”
Get more information

A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy by Moreira, Irina S, Martins, João M, Coimbra, João T S, Ramos, Maria J, Fernandes, Pedro A

“…Protein-protein (P-P) 3D structures are fundamental to structural biology and drug discovery. However, most of them have never been determined. Many docking…”
Get more information

Molecular dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif by Sousa, Sérgio F., Coimbra, João T. S., Paramos, Diogo, Pinto, Rita, Guimarães, Rodrigo S., Teixeira, Vitor, Fernandes, Pedro A., Ramos, Maria J.

“…Protein farnesyltransferase (FTase) is an important target in many research fields, more markedly so in cancer investigation since several proteins known to be…”
Get full text

Crosstalk of Nucleic Acid Mimics with Lipid Membranes: A Multifaceted Computational and Experimental Study by T. Magalhães, Beatriz, S. Coimbra, João T., M. Silva, Raquel, Ferreira, Mariana, S. Santos, Rita, Gameiro, Paula, Azevedo, Nuno F., Fernandes, Pedro A.

“…Nucleic acid mimics (NAMs) have demonstrated high potential as antibacterial drugs. However, very few studies have assessed their possible diffusion across the…”
Get full text

Passive Diffusion of Ciprofloxacin and its Metalloantibiotic: A Computational and Experimental study by Sousa, Carla F., Coimbra, João T.S., Ferreira, Mariana, Pereira-Leite, Catarina, Reis, Salette, Ramos, Maria J., Fernandes, Pedro A., Gameiro, Paula

“…[Display omitted] •Comparison of the translocation of ciprofloxacin and its metalloantibiotic across the membrane.•The net charge of the lipid bilayer…”
Get full text