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André Rafael Ferreira Salgueiro

Master Student
Linkedin
During the Evamobs project, Rafael Salgueiro will be participating in the computational design of Monobodies, as well as testing different pipelines to be utilized for the design of these proteins. In particular, he will be applying several computational tools and pipelines for Monobody sequence generation and refinement for specific viral targets.

Maria Benedita Ferreira Moço Rodrigues Pereira

Master Student
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Benedita Pereira is a second-year Master student in Biotechnology. Currently, she is developing her master thesis at ITQB NOVA, where she aims to computationally design novel antiviral proteins that target and bind to the Zika virus envelope protein, using state-of-the-art protein design computational tools. Additionally, she will be evaluating the stability of the designs through computational methods such as molecular dynamics and will participate in the experimental production of the top designs to assess their binding affinity to the target.

Madalena de Castro Marques

Master Student
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Madalena Marques’ master thesis project aims to computationally design Virus-Targeting Antibody-like scaffolds (ViTAls) to bind to hemagglutinin glycoprotein present on the surface of the influenza A virus. She is also studying the stability and conformational dynamics of the best designs through molecular dynamics simulations. In addition, she will work on the purification and characterization of the best ViTAls.

Diogo Silva

Research Fellow
During the Evamobs project, Diogo Silva will be participating in the computational design of antiviral proteins, as well as testing different pipelines to be utilized for the design of these proteins. Additionally, he will be working on the in silico characterization of the designs through computational methods like molecular dynamics, to study aspects of the designs such as oligomerization and stability.
 
During the second work package, he will also participate in the production and purification of the computationally designed protein antivirals.

Pedro Moreira

PhD Student
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Pedro possesses an academic background in Biomedical Engineering and Bioinformatics. Commencing his PhD. Programme at ITQB NOVA in 2022, he has gathered significant expertise in computational protein design employing state-of-the-art structural-based artificial intelligence methodologies, alongside developing his capabilities in analysis of protein structures and protein-protein interfaces through the use of methodologies like molecular dynamics.

His principal task within the project entails the development of computational frameworks tailored to engineer monobodies with predicted high affinity towards specific epitopes. Following this, he aims to validate these pipelines by designing monobody binders against an extensive array of pertinent viral targets.

Key Publications

Moreira, Pedro; Sequeira, Ana Marta; Pereira, Sara; Rodrigues, Rúben; Lousa, Diana; Rocha, Miguel. “ViralFP: A web application of viral fusion proteins”. Fronteirs in Medical Technology 3 (2021).

Rita Teixeira

PhD Student
Linkedin

Rita Teixeira is a Ph.D. student supervised by the Head of the Protein Modelling Laboratory at ITQB NOVA, Professor Cláudio M. Soares, Doctor Diana Lousa, and Bruno Correia from EPFL, in Lausanne. Her current research focuses on leveraging the knowledge of viral fusion proteins (VFPs) essential for the entry of potential pandemic viruses to develop new therapeutics capable of neutralizing infection.

Within the scope of the project, she will contribute to the computational framework to generate antiviral biologics tailor-made for specific epitopes, which will be experimentally screened and validated by the team collaborator. Prior to binder design, she will also study the VFPs of the pathogenic viruses, including the effect of glycan shielding, to identify neutralizable epitopes using molecular dynamics simulations.

Catarina Carmo

Project Manager
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Catarina Carmo is EvaMobs’ Project Manager and is responsible for overseeing various aspects of the project’s execution, including financial, administrative, and legal management, guaranteeing that the project is running according to plan and there is effective communication between partners and with the European Commission. She was previously a researcher both at EMBL-Heidelberg and Instituto Gulbenkian de Ciência, Portugal, investigating Microbiology and Infection. She did her PhD in Clinical Medicine Research at Imperial College London, UK. Currently, she is in the final stages of completing a postgraduate program in Project Management in Healthcare at the NOVA University. She really enjoys science communication and takes initiatives to make it engaging for all.

Name

Title at Institution
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Cláudio M. Soares

Project Coordinator EvaMobs and Full Professor
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Cláudio M. Soares is Full Professor of Biochemistry at ITQB NOVA and Pro-Rector for the NOVAHealth Platform of NOVA University Lisbon. He is also the PI of the Protein Modelling Laboratory of ITQB NOVA and the Coordinator of the Molecular, Structural and Cellular Microbiology – MOSTMICRO-ITQB Research Unit of ITQB NOVA since 2015.  He is co-author of 129 papers and has participated in 37 competitively funded projects since 1996. He is a member of the Directive Board of  the Portuguese Biophysical Society and President of the Scientific Council of TAGUSPARK – Parque de Ciência e Tecnologia. He was member of the International Union for Pure and Applied Biophysics (IUPAB) council (2011-2017), and member of the Federation of European Biochemical Societies (FEBS) Advanced Courses Committee (2015-2018). Cláudio M. Soares was Dean of ITQB NOVA from 2013 to 2023 and Vice-Dean during 2005-2008 and 2011-2013.

Key Publications

Valério, M, Borges-Araújo, L, Melo, MN, Lousa, D, Soares*, CM (2022) “SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility”, Front. Med. Technol., 4:1009451.

Abreu, B, Cruz, C, Oliveira, ASF, Soares, CM (2020) “ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK2E importer”, Sci.Rep., 11, 10591

Lousa, D, Pinto, ART, Campos, SRR, Baptista, AM, Veiga, AS, Castanho, MARB, Soares, CM (2020) “Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment”, Sci.Rep., 10, 20082

Barbosa, TM, Baltazar, CSA, Cruz, DR, Lousa, D, Soares, CM (2020) “Studying O2 pathways in [NiFe]- and [NiFeSe]-hydrogenases”, Sci.Rep., 10, 10540

Oliveira, ASF, Campos, SRR, Baptista, AM, Soares, CM (2016) “Coupling between protonation and conformation in cytochrome c oxidase: Insights from Constant-pH MD simulations”, BBA Bioenergetics, 1857, 759-771.

Victor, BL, Lousa, D, Antunes, J, Soares, CM (2015) “Self-assembly molecular dynamics simulations shed light into the interaction of the influenza fusion peptide with a membrane bilayer”, J.Chem. Infor. Model., 55, 795–805

Oliveira, ASF, Damas, JM, Baptista, AM, Soares, CM (2014) “Exploring O2 diffusion in A-type Cytochrome c Oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site, PLoS Comp.Biol., 10, e1004010

Damas, JM, Baptista, AM, Soares, CM (2014) “The Pathway for O-2 Diffusion inside CotA Laccase and Possible Implications on the Multicopper Oxidases Family”, J Chem Theor Comp, 10, 3525–3531

Name

Title at Institution
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Key Publications

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Diana Lousa

Co-coordinator of EvaMobs and
Assistant Reseracher
Linkedin

Diana Lousa is currently a Researcher at the Protein Modelling Lab, ITQB NOVA. She obtained her PhD in Biochemistry in 2013. The main goal of her current research focuses on the application of computational biophysics to develop tailor-made biopharmaceuticals against viral pathogens such as influenza, zika, HIV, and SARS-CoV-2. She is the co-coordinator of the projects EvaMobs, funded by Horizon Europe (HORIZON-HLTH-2023-DISEASE-03-04), and BioPlaTTAR, funded by the La Caixa Foundation (HR22-00722). She has co-authored 29 articles in peer-reviewed scientific journals, 2 peer-reviewed book chapters, and 34 oral presentations (20 as presenter) in scientific meetings. She has supervised/co-supervised 3 Postdocs, 8 PhD, and 11 Master students, and is the assistant coordinator of the Master in Computational Biology and Bioinformatics at NOVA University. In EvaMobs, she will co-supervise WP1 (computational design of Mobs) and WP6 (project management).

Key Publications

Valério M., Mendonça D. A., Morais J., Buga C. C., Cruz C. H., Castanho M. A R. B., Melo M. N., Soares C. M., Veiga A. S. and Lousa D. (2022), Parainfluenza Fusion Peptide Promotes Membrane Fusion by Assembling into Oligomeric Porelike Structures, ACS Chemical Biology, 17(7), 1831-1843; doi: 10.1021/acschembio.2c00208

Valério M., Borges-Araújo L., Melo M. N., Lousa D., Soares C. M. (2022) SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility. Front Med Technol. Pharmaceutical innovation, vol. 4:1009451. doi: 10.3389/fmedt.2022.1009451. PMID: 36277437; PMCID: PMC9581196

Lousa, D., & Soares, C. M. (2021). Molecular mechanisms of the influenza fusion peptide: Insights from experimental and simulation studies. FEBS Open Bio, vol. 11(12): 3253-3261. doi:10.1002/2211-5463.13323 –Joint corresponding author

Lousa D., Pinto A. R. T., Campos S. R. R., Baptista A. M., Veiga A. S., Castanho M. A. R. B., Soares C. M. (2020), Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment, Scientific Reports, vol. 10: 20082; doi: 10.1038/s41598-020-77040-y

Sequeira, A. M., Lousa D., Rocha M. (2022) ProPythia: A Python package for protein classification based on machine and deep learning, Neurocomputing, vol. 484: 172-182; doi: 10.1016/j.neucom.2021.07.102