Meet The Team

Miguel Machuqueiro

Lab's Head


Miguel Machuqueiro is an Assistant Professor 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.
Email: machuque@ciencias.ulisboa.pt

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.
Email: nfoliveira@ciencias.ulisboa.pt

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).
Email: ferodrigues@ciencias.ulisboa.pt

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).
Email: jnvitorino@ciencias.ulisboa.pt

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).
Email: jgsequeira@ciencias.ulisboa.pt

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).
Email: sferreira@ciencias.ulisboa.pt

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.
Email: mjyousef@ciencias.ulisboa.pt

Inês Pires

PhD Student

Inês Pires is working on her PhD project focused on studying the movement of protons in Cytochrome c Oxidase against their concentration gradient and overall electrochemical potential. This work is co-supervised by Dr. António M. Baptista (ITQB@UNL).
Email: idpires@ciencias.ulisboa.pt

Marta Batista

PhD Student

Marta Batista is working on her PhD project where she will combine constant-pH molecular dynamics methodologies with a metadynamics scheme to correctly model pH and study the permeation process of water and glycerol in aquaporins. Marta is also supervised by Dr. Bruno L. Victor (DQB@FCUL & AccelBio CoLAB).
Email: martaspbat@ciencias.ulisboa.pt

Francisco Duarte

MSc Student

Francisco Duarte is a MSc. student in Chemistry, working on an in silico protocol to evaluate and optimize cyclodextrins for drug delivery. This work is done in co-supervision with Prof. Paulo J. Costa (DQB@FCUL).
Email: fpduarte@ciencias.ulisboa.pt

Ana Figueiredo

MSc Student

Ana Figueiredo is a MSc. student in Biochemistry, working on a computational study of phosphatidylinositol protonation in different membrane environments with biological relevance.
Email: atfigueiredo@ciencias.ulisboa.pt

Maria João Pintassilgo

BSc Student

Maria João Pintassilgo is a BSc. student in Chemistry, working on a computational study of cobalt-containing antitumor drugs, optimizing their structures and studying the interaction of these compounds with biological membrane models. This work is done in co-supervision with Dr. Tânia Morais (DQB@FCUL).
Email: fc60086@alunos.fc.ul.pt

Group Photos

June 11, 2024


June 20, 2023


May 19, 2022

Alumni

Rita Guerra (MsC.)

André Gomes (MsC.)

Pedro Suzano (MsC.)

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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