Meet The Team

Miguel Machuqueiro

Lab's Head

Miguel Machuqueiro is an Assistant Researcher at BioISI – BioSystems and Integrative Sciences Institute and the Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa (FCUL). He got his degree in Biochemistry from FCUL and a Ph.D. in Bioorganic Chemistry from the University of Bern, Switzerland. During his post-doc at ITQB-UNL, he started his research about the pH and redox potential effects on the structure and dynamics of biomolecules.

In 2009, he moved back to FCUL as an independent researcher, founded the Machuqueiro Lab, and started his actual research lines. There is a special emphasis on studies involving the influence of pH and redox potential on biomolecules in confined environments, in particular, in protein’s active sites and at the water/membrane interface.

Nuno Oliveira

PhD Student

Nuno Oliveira is a PhD student developing new and highly efficient computational methods to tackle and revert multi-drug resistance. He will characterize the tumor resistance mechanisms that are specific for several Lewis base-containing chemotherapeutics and propose drug modifications to revert them.

Filipe Rodrigues

PhD Student

Filipe Rodrigues is a PhD student studying the molecular details of peptide dendrimers and how these molecules can be tailored to help transfect DNA and/or RNA-based vectors into cells, a strategy that is nowadays being used in vaccine development. This work is done under the co-supervision of Prof. Tamis Darbre (Univ. Bern, CH).

João Vitorino

PhD Student

João Vitorino is a PhD student working on an extension of the PypKa-MD method to use the CHARMM36m force field and study the details of the pH effects in GPCRs activation mechanisms. He will explore the role of protonation in the activation, molecular recognition, and binding of these receptors with their interacting partners. This work is done with the co-supervision of Prof. Irina Moreira (CNC, Univ. Coimbra).

João Sequeira

PhD Student

João Sequeira is a PhD student working on the extension of our PypKa-MD method to the most recent AMBER force fields. He also plans using this methodology to study the pH-dependent mechanism of cation transport by the acid-sensing ion channels (ASICs). This work is done with the co-supervision of Prof. Adrian Roitberg (Univ. Florida, USA).

Sara Ferreira

PhD Student

Sara Ferreira is a PhD student (BioSYS2 Program @BioISI) studying the role of knots in the mechanical stability and self-association of proteins. She is developing methodologies to estimate the free energy profiles of knot formation, stability, and impact on self-association of UCH-L1, one of the most abundant proteins in the brain, whose misfolding has been associated with the onset of Parkinson’s and Alzheimer’s diseases. This work is co-supervised by Prof. Patrícia Faísca (DF@FCUL).

Mohannad Yousef

PhD Student

Mohannad Yousef is a PhD student studying the pH effects on protein-ligand binding using protonation-dependent molecular docking and CpHMD simulations. He will also study these same effects on protein-protein interactions using CpHMD simulations coupled with enhanced sampling techniques.

Pedro Suzano

PhD Student Candidate

Pedro Suzano is a PhD Candidate studying heme systems and predicting their redox potential values taking in consideration the effects of pH. He is updating, calibrating, and benchmarking a C(pH,E)MD method which will be applied to increasingly complex porphyrinic systems from the literature or provided by our experimental collaborators at the Anderson Lab (Bristol, UK). This work is done with the co-supervision of Dr. Paulo J. Costa (DQB@FCUL).

Inês Pires

PhD Student Candidate

Inês Pires has finished her Masters’ degree in Biochemistry focused on the research of metal-based drugs for cancer therapy. She is studying how modifications on TM34, a Ru-based antitumor agent, can improve the compound’s overall antitumor performance and help circumvent multi-drug resistance. This work is in close collaboration with Dr. Tânia Morais' group (DQB@FCUL).

André Gomes

MsC Student

André Gomes is a Masters student studying the interaction of several small drug-like molecules with membranes at the molecular level. He is developping computational methods to estimate the impact of protonation/deprotonation events and noncovalent interactions (hydrogen or halogen bonds) in membrane permeability. This work is done in co-supervision with Dr. Paulo J. Costa (DQB@FCUL).

Rita Guerra

MsC Student

Rita Guerra is a Masters’s student in Bioinformatics and Computational Biology and is working on molecular docking protocols to study the impact of modifying several tyrosine kinase inhibitors (TKI) on their anti-cancer activity. This work is done in co-supervision with Dr. Bruno L. Victor (DQB@FCUL).

Francisco Duarte

BsC Student

Francisco Duarte is a BSc. student in Chemistry and is starting a computational chemistry project focused on designing new isoniazid derivatives aiming to circumvent drug resistance in tuberculose treatments.

Group Photos

May 19, 2022


Pedro Reis (MSc. and PhD)

Tomás F. Silva (MSc. and PhD)

Telmo Silva (MsC.)

J. Ricardo Dias (MSc.)

Diogo Reis (MSc.)

Pedro Lopes (PosDoc)

Pedro Magalhães (PosDoc)

Diogo Vila Viçosa (MSc., PhD, and PosDoc)

Bruno Victor (PosDoc)

Vitor Teixeira (PosDoc)

Rafael Nunes (MSc.)

Bruno Calçada (MSc.)

Tomás J. Silva (MSc.)

Hugo Santos (MSc.)

Ana Sofia Capacho (MSc.)

João Henriques (MSc.)

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