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Diana Lousa [F] is currently a Researcher at the Protein Modelling Lab, ITQB NOVA. She obtained her PhD in Biochemistry, with a specialization in Computational Biology 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 is the co-author of 29 published articles in peer-reviewed scientific journals (8 as first author, 3 of which as co-corresponding author and 2 as corresponding author) and 2 peer-reviewed book chapters (1 as first and co-corresponding author). She has supervised 2 Postdocs, 3 PhD and 7 Master students, and co-supervised 1 Postdoc and 2 Master students: Currently she supervises 2 PhD students and 2 Master students and co-supervises 1 PhD and 2 Master students. She is the co-author of 34 oral (20 as presenter) and 33 poster presentations in scientific meetings. She has been a member of the executive committee of the ITQB NOVA Postdoctoral Association and has organized/is organizing several scientific meetings, including the 2022 FEBS Young Scientists Forum. She is the assistant-coordinator of the Master in Computational Biology and Bioinformatics of the NOVA University.
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Identification

Personal identification

Full name
Diana Andreia Pereira Lousa

Citation names

  • Lousa, Diana

Author identifiers

Ciência ID
061D-9BE6-C638
ORCID iD
0000-0002-2309-0980

Knowledge fields

  • Exact Sciences - Chemical Sciences - Physical Chemistry
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Natural sciences - Biological Sciences - Biophysics

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Beginner (A1) Intermediate (B1) Beginner (A1) Beginner (A1)
Portuguese Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2014/08/01 - 2018/10/31
Concluded
 Postdoc in Computational Biology (Pós-doutoramento)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007/01/01 - 2013/03/22
Concluded
 PhD in Biochemistry (Doutoramento)
Major in Computational Biology
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
"Molecular determinants of nonaqueous biocatalysis: A computational analysis" (THESIS/DISSERTATION)
 n/a
2004/09/01 - 2005/06/30
Concluded
 Post-graduation in Bioinformatics (Pós-Graduação)
Universidade de Lisboa Faculdade de Ciências, Portugal

Instituto Gulbenkian de Ciência, Portugal
16
1999/09/01 - 2004/07/31
Concluded
 Degree in Applied Chemistry (5 year course) (Licenciatura)
Major in Biotechnoloy
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
"n/a" (THESIS/DISSERTATION)
 15
Affiliation

Science

Category
Host institution 		Employer
2018/11/01 - 2024/10/31 Researcher (Research) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2014/08/01 - 2018/10/31 Postdoc (Research) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2014 - 2018 Postdoc (Research) Universidade Nova de Lisboa Microbiologia Molecular Estrutural e Celular, Portugal
2004/02/01 - 2004/07/28 Research Trainee (Research) Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2003/07/01 - 2003/09/30 Research Trainee (Research) National Center for Scientific Research "Demokritos", Greece
National Center for Scientific Research "Demokritos", Greece

Others

Category
Host institution 		Employer
2013/10/01 - 2016/06/30 Visiting researcher at Professor Alessandro Laio Lab This included 3 short visits (of 2weeks each) and permanent collaboration during this period. Scuola Internazionale Superiore di Studi Avanzati, Italy
2013/12/01 - 2014/07/31 Research fellow (BI) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2007 - 2013 PhD student Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2006/05/15 - 2006/11/15 Research fellow (BI) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Projects

Grant

Designation Funders
2024/01 - 2029/12 EvaMobs: Evolvable and rapidly adaptable monobodies: a broad-spectrum antiviral platform - co PI
HORIZON-HLTH-2023-DISEASE-03-04, ID 101137419
 Horizon 2020
2022/11/01 - 2025/10/31 The BioPlaTTAR Platform for the Tailored and Rapid Development of Antiviral Biopharmaceuticals - Co-PI - "la Caixa" Foundation HR22-00722
HR22-00722
Co-Principal Investigator (Co-PI)
Universidade Nova de Lisboa, Portugal
 "la Caixa" Foundation
Ongoing
2019/01 - 2022/12 SHIKIFACTORY100 - Modular cell factories for the production of 100 compounds from the shikimate pathway
Call: H2020 BIOTEC-03-2018, grant agreement number 814408
 Horizon 2020 Framework Programme
2018/10 - 2021/09 Using computational and experimental methods to provide a global characterization of viral fusion peptides - PI of the project
PTDC/CCI-BIO/28200/2017
 Fundação para a Ciência e a Tecnologia
2020/12/01 - 2021/05/31 CPCA/A0/7305/2020: "Design of protein chimeras targeting SARS-CoV-2"
CPCA/A0/7305/2020
Principal investigator
Fundação para a Ciência e a Tecnologia, Portugal
Ongoing
2014/08 - 2018/10 Molecular mechanisms of viral membrane fusion: A computational analysis - Postdoc Grant
SFRH/BPD/92537/2013
 Fundação para a Ciência e a Tecnologia
2015/02 - 2015/04 Probing the pH-induced conformational change of influenza hemagglutinin using micro-second long MD simulations
2010PA3220/2015
 Partnership for Advanced Computing In Europe
2010/12 - 2014/07 Membrane fusion mechanism of Influenza Hemagglutinin: a simulation and biophysical approach.
PTDC/QUI-BIQ/114774/2009
 Fundação para a Ciência e a Tecnologia, I.P. (Lisbon, Portugal)
2014/02 - 2014/04 Analysing the effect of mutations on the energy landscape of influenza fusion peptide using bias-exchange metadynamics simulations
2010PA2071/2013
 PRACE (Partnership for Advanced Computing in Europe)
2007/01 - 2010/12 Engenharia de proteínas aplicada a enzimas em solventes não aquosos: Um contributo da bioinformática estrutural - PhD Grant
SFRH/BD/28269/2006
 Fundação para a Ciência e Tecnologia
Outputs

Publications

Book chapter
  1. Sequeira, A.M.; Lousa, D.; Rocha, M.. "ProPythia: A Python Automated Platform for the Classification of Proteins Using Machine Learning". In PACBB 2020. Advances in Intelligent Systems and Computing. 2021.
    10.1007/978-3-030-54568-0_4
  2. Lousa, Diana. "Hydration effects on enzyme properties in nonaqueous media analyzed by MD simulations". 501-521. 2016.
    10.4032/9789814669337
Journal article
  1. Mariana Valério; Luís Borges-Araújo; Manuel N. Melo; Diana Lousa; Cláudio M. Soares. Corresponding author: Diana Lousa. "SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility". Frontiers in Medical Technology 4 (2022): http://dx.doi.org/10.3389/fmedt.2022.1009451.
    10.3389/fmedt.2022.1009451
  2. Mariana Valério; Diogo A. Mendonça; João Morais; Carolina C. Buga; Carlos H. Cruz; Miguel A.R.B. Castanho; Manuel N. Melo; et al. Corresponding author: Diana Lousa. "Parainfluenza Fusion Peptide Promotes Membrane Fusion by Assembling into Oligomeric Porelike Structures". ACS Chemical Biology (2022): https://doi.org/10.1021/acschembio.2c00208.
    10.1021/acschembio.2c00208
  3. Marta C. Marques; Diana Lousa; Patrícia M. Silva; André F. Faustino; Claudio M. Soares; Nuno C. Santos. "The Importance of Lipid Conjugation on Anti-Fusion Peptides against Nipah Virus". Biomedicines (2022): https://www.mdpi.com/2227-9059/10/3/703.
    10.3390/biomedicines10030703
  4. Margarida Saramago; Vanessa G. Costa; Caio S. Souza; Cátia Bárria; Susana Domingues; Sandra C. Viegas; Diana Lousa; et al. "The nsp15 Nuclease as a Good Target to Combat SARS-CoV-2: Mechanism of Action and Its Inactivation with FDA-Approved Drugs". Microorganisms 10 2 (2022): 342-342. https://doi.org/10.3390/microorganisms10020342.
    10.3390/microorganisms10020342
  5. Diana Lousa; Cláudio M. Soares. "Molecular mechanisms of the influenza fusion peptide: insights from experimental and simulation studies". FEBS Open Bio (2021): https://doi.org/10.1002/2211-5463.13323.
    10.1002/2211-5463.13323
  6. Sequeira, A.M.; Lousa, D.; Rocha M.. Corresponding author: Rocha M.. "ProPythia: A Python package for protein classification based on machine and deep learning". Neurocomputing (2021): http://dx.doi.org/10.1016/j.neucom.2021.07.102.
    10.1016/j.neucom.2021.07.102
  7. Moreira P.; Sequeira, A.M.; Pereira S.; Rodrigues R.; Rocha M.; Lousa D. "ViralFP: A Web Application of Viral Fusion Proteins". Frontiers in Medical Technology 3 (2021): http://dx.doi.org/10.3389/fmedt.2021.722392.
    10.3389/fmedt.2021.722392
  8. Maria C. Martins; Susana F. Fernandes; Bruno A. Salgueiro; Jéssica C. Soares; Célia V. Romão; Cláudio M. Soares; Diana Lousa; Filipe Folgosa; Miguel Teixeira. "The Amino Acids Motif -32GSSYN36- in the Catalytic Domain of E. coli Flavorubredoxin NO Reductase Is Essential for Its Activity". Catalysts 11 8 (2021): 926-926. https://doi.org/10.3390/catal11080926.
    10.3390/catal11080926
  9. Saramago, Margarida; Bárria, Cátia; Costa, Vanessa G.; Souza, Caio S.; Viegas, Sandra C.; Domingues, Susana; Lousa, Diana; et al. "New targets for drug design: Importance of nsp14/nsp10 complex formation for the 3’-5’ exoribonucleolytic activity on SARS-CoV-2". The FEBS Journal (2021): http://dx.doi.org/10.1111/febs.15815.
    10.1111/febs.15815
  10. Pavlu-Pereira H; Lousa D; Tomé CS; Florindo C; Silva MJ; de Almeida IT; Leandro P; Rivera I; Vicente JB. "Structural and functional impact of clinically relevant E1a variants causing pyruvate dehydrogenase complex deficiency.". Biochimie (2021): http://europepmc.org/abstract/med/33588022.
    10.1016/j.biochi.2021.02.007
  11. Faustino, M.M.; Fonseca, B.M.; Costa, N.L.; Lousa, D.; Louro, R.O.; Paquete, C.M.. "Crossing the wall: Characterization of the multiheme cytochromes involved in the extracellular electron transfer pathway of Thermincola ferriacetica". Microorganisms 9 2 (2021): 1-14. http://www.scopus.com/inward/record.url?eid=2-s2.0-85100048839&partnerID=MN8TOARS.
    10.3390/microorganisms9020293
  12. Alenquer, M.; Ferreira, F.; Lousa, D.; Valério, M.; Medina-Lopes, M.; Bergman, M.-L.; Gonçalves, J.; et al. "Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies". PLoS Pathogens 17 8 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85112329556&partnerID=MN8TOARS.
    10.1371/journal.ppat.1009772
  13. Rebelo, B.A.; Santos, R.B.; Ascenso, O.S.; Nogueira, A.C.; Lousa, D.; Abranches, R.; Ventura, M.R.. "Synthesis and biological effects of small molecule enhancers for improved recombinant protein production in plant cell cultures". Bioorganic Chemistry 94 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85076599041&partnerID=MN8TOARS.
    10.1016/j.bioorg.2019.103452
  14. Barbosa, T.M.; Baltazar, C.S.A.; Cruz, D.R.; Lousa, D.; Soares, C.M.. "Studying O2 pathways in [NiFe]- and [NiFeSe]-hydrogenases". Scientific Reports 10 1 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85087025960&partnerID=MN8TOARS.
    10.1038/s41598-020-67494-5
  15. Lousa, D.; Pinto, A.R.T.; Campos, S.R.R.; Baptista, A.M.; Veiga, A.S.; Castanho, M.A.R.B.; Soares, C.M.. "Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment". Scientific Reports 10 1 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85096181420&partnerID=MN8TOARS.
    10.1038/s41598-020-77040-y
  16. Pereira, F.C.; Nunes, F.; Cruz, F.; Fernandes, C.; Isidro, A.L.; Lousa, D.; Soares, C.M.; et al. "A LysM Domain intervenes in sequential protein-protein and protein-peptidoglycan interactions important for spore coat assembly in bacillus subtilis". Journal of Bacteriology 201 4 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85061486186&partnerID=MN8TOARS.
    10.1128/JB.00642-18
  17. Duarte, A.G.; Catarino, T.; White, G.F.; Lousa, D.; Neukirchen, S.; Soares, C.M.; Sousa, F.L.; Clarke, T.A.; Pereira, I.A.C.. "An electrogenic redox loop in sulfate reduction reveals a likely widespread mechanism of energy conservation". Nature Communications 9 1 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85058913300&partnerID=MN8TOARS.
    10.1038/s41467-018-07839-x
  18. Jeremias, H.F.; Lousa, D.; Hollmann, A.; Coelho, A.C.; Baltazar, C.S.; Seixas, J.D.; Marques, A.R.; et al. "Study of the interactions of bovine serum albumin with a molybdenum(II) carbonyl complex by spectroscopic and molecular simulation methods". PLoS ONE 13 9 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85053913626&partnerID=MN8TOARS.
    10.1371/journal.pone.0204624
  19. Velada, I.; Grzebelus, D.; Lousa, D.; Soares, C.M.; Macedo, E.S.; Peixe, A.; Arnholdt-Schmitt, B.; Cardoso, H.G.. "AOX1-subfamily gene members in olea europaea cv. “Galega vulgar”—gene characterization and expression of transcripts during IBA-induced in vitro adventitious rooting". International Journal of Molecular Sciences 19 2 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85042233401&partnerID=MN8TOARS.
    10.3390/ijms19020597
  20. Lousa, D.; Pinto, A.R.T.; Victor, B.L.; Laio, A.; Veiga, A.S.; Castanho, M.A.R.B.; Soares, C.M.. "Fusing simulation and experiment: The effect of mutations on the structure and activity of the influenza fusion peptide". Scientific Reports 6 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84975041212&partnerID=MN8TOARS.
    10.1038/srep28099
  21. Nobre, L.S.; Lousa, D.; Pacheco, I.; Soares, C.M.; Teixeira, M.; Saraiva, L.M.. "Insights into the structure of the diiron site of RIC from Escherichia coli". FEBS Letters 589 4 (2015): 426-431. http://www.scopus.com/inward/record.url?eid=2-s2.0-84964273503&partnerID=MN8TOARS.
    10.1016/j.febslet.2014.12.028
  22. Victor, B.L.; Lousa, D.; Antunes, J.M.; Soares, C.M.. "Self-assembly molecular dynamics simulations shed light into the interaction of the influenza fusion peptide with a membrane bilayer". Journal of Chemical Information and Modeling 55 4 (2015): 795-805. http://www.scopus.com/inward/record.url?eid=2-s2.0-84928686003&partnerID=MN8TOARS.
    10.1021/ci500756v
  23. Fernandes, C.G.; Plácido, D.; Lousa, D.; Brito, J.A.; Isidro, A.; Soares, C.M.; Pohl, J.; et al. "Structural and Functional Characterization of an Ancient Bacterial Transglutaminase Sheds Light on the Minimal Requirements for Protein Cross-Linking". Biochemistry 54 37 (2015): 5723-5734. http://www.scopus.com/inward/record.url?eid=2-s2.0-84942100927&partnerID=MN8TOARS.
    10.1021/acs.biochem.5b00661
  24. Lousa, D.; Baptista, A.M.; Soares, C.M.. "A molecular perspective on nonaqueous biocatalysis: Contributions from simulation studies". Physical Chemistry Chemical Physics 15 33 (2013): 13723-13736. http://www.scopus.com/inward/record.url?eid=2-s2.0-84881248110&partnerID=MN8TOARS.
    10.1039/c3cp51761f
  25. Damas, J.M.; Filipe, L.C.S.; Campos, S.R.R.; Lousa, D.; Victor, B.L.; Baptista, A.M.; Soares, C.M.. "Predicting the thermodynamics and kinetics of helix formation in a cyclic peptide model". Journal of Chemical Theory and Computation 9 11 (2013): 5148-5157. http://www.scopus.com/inward/record.url?eid=2-s2.0-84887835236&partnerID=MN8TOARS.
    10.1021/ct400529k
  26. Lousa, D.; Baptista, A.M.; Soares, C.M.. "Analyzing the molecular basis of enzyme stability in ethanol/water mixtures using molecular dynamics simulations". Journal of Chemical Information and Modeling 52 2 (2012): 465-473. http://www.scopus.com/inward/record.url?eid=2-s2.0-84857583770&partnerID=MN8TOARS.
    10.1021/ci200455z
  27. Lousa, D.; Cianci, M.; Helliwell, J.R.; Halling, P.J.; Baptista, A.M.; Soares, C.M.. "Interaction of counterions with subtilisin in acetonitrile: Insights from molecular dynamics simulations". Journal of Physical Chemistry B 116 20 (2012): 5838-5848. http://www.scopus.com/inward/record.url?eid=2-s2.0-84862279541&partnerID=MN8TOARS.
    10.1021/jp303008g
  28. Lousa, D.; Baptista, A.M.; Soares, C.M.. "Structural determinants of ligand imprinting: A molecular dynamics simulation study of subtilisin in aqueous and apolar solvents". Protein Science 20 2 (2011): 379-386. http://www.scopus.com/inward/record.url?eid=2-s2.0-79251557782&partnerID=MN8TOARS.
    10.1002/pro.569
  29. Garcia, S.; Lourenço, N.M.T.; Lousa, D.; Sequeira, A.F.; Mimoso, P.; Cabral, J.M.S.; Afonso, C.A.M.; Barreiros, S.. "A comparative study of biocatalysis in non-conventional solvents: Ionic liquids, supercritical fluids and organic media". Green Chemistry 6 9 (2004): 466-470. http://www.scopus.com/inward/record.url?eid=2-s2.0-8144227149&partnerID=MN8TOARS.
    10.1039/b405614k
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2024/10/19 Lousa D., Preparing for the Next Pandemic: Targeting viral fusion proteins – Current Topics in Biochemistry 2023, Florianópolis, Braszil, 19-20 October 2023. Invited keynote lecture by Diana Lousa. Current Topics in Biochemistry 2023
(Florianópolis, Brazil)
2023/11/28 Lousa D., Valério M., Buga C. C., Sequeira A. M., Victor B. L., Laio A., Mendonça D. A., Morais J., Melo M. N., Rocha M., Castanho M. A. R. B. Castanho, Veiga A. S., Soares C. M, Fusion peptides: Scenes from the lives of key players in viral infections ¿ XVIII Iberian Peptide Meeting, 27-29 November 2023, Sesimbra, Portugal. Invited Keynote lecture by Diana Lousa. XVIII Iberian Peptide Meeting
(Sesimbra, Portugal)
2023/11/21 Lousa D. and Soares C.M., EvaMobs: A multidisciplinary approach to design the antiviral biologics of the future ¿ Nova Science and Innovation Day, 21 November 2023, Lisbon, Portugal. Invited talk by Diana Lousa. Nova Science and Innovation Day
(Lisbon, Portugal)
2023/10/25 Lousa D., Preparing for the Next Pandemic: Targeting viral fusion proteins – Seminar Cycle Antônio Luiz Vianna, Universidade Federal do Rio de Janeir0, Brazil. 25 October 2023. Invited talk by Diana Lousa. Seminar Cycle Antônio Luiz Vianna
(Rio de Janeiro, Brazil)
2023/07/26 Saramago M. and Lousa D., Tailor-made Replication-inhibitory Proteins to combat COVID-19, ITQB Day, July 2023. Invited talk by Diana Lousa and Margarida Saramago. ITQB Day
(Oeiras, Portugal)
2022/10/01 Valério M, Borges-Araújo L, Teixiera R, Melo MN, Soares CM and Lousa D, The SARS-CoV-2 receptor binding domain in motion: how dynamics evolved across variants – BPS Sponsored Networking Conference on Computational Biophysics, Kenya, October 2022. Invited virtual talk by Diana Lousa BPS Sponsored Networking Conference on Computational Biophysics
(Kenya)
2022/07/09 Valério M, Borges-Araújo L, Teixiera R, Melo MN, Soares CM and Lousa D, The SARS-Cov-2 receptor binding domain: characterizing and inactivating a moving target – 25th IUBMB 46th FEBS and 15th PABMB Congress, Lisbon, Portugal, 9-14 July 2022. Invited talk by Diana Lousa 25th IUBMB 46th FEBS and 15th PABMB Congress
(Lisbon, Portugal)
2022/06/20 Valério M, et al., Lousa D, Targeting the SARS-CoV-2 spike protein: from fundamental research to tailor-made biopharmaceuticals , 8th International Iberian Biophysics Congress, Bilbao, Spain, 20-21 June 2022. Invited talk by Diana Lousa in the "New and Notable" 8th International Iberian Biophysics Congress
(Bilbao, Spain)
2021/12/20 Lousa D, Valério M, Buga CC, Sequeira A;, Victor BL, Laio A, Mendonça DA, Morais J, Melo MN, Rocha M, Castanho MARB, Veiga AS, Soares CM (2021) "Viral membrane fusion: characterizing and inactivating a crucial step of the infection by devastating pathogens. " - keynote lecture by Lousa D. EJIBCE 2021
(Coimbra, Portugal)
2021/12/20 Valério MF, Mendonça D, Morais J, Cruz CH, Castanho MARB, Veiga AS, Melo MN, Soares CM, Lousa D (2021) "Parainfluenza fusion peptide promotes membrane fusion by assembling into oligomeric pore-like structures", selected presentation by Valério MF EJIBCE 2021
(Coimbra, Portugal)
2021/12/20 Araújo LB, Valério MF, Melo MN, Lousa D, Soares CM, "SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility.", selected oral presentation by Araújo LB
2021/10/14 Saramago, M., Bárria, C., Costa, V., Souza, C.S., Viegas, S.C., Domingues, S., Lousa, D., Soares, C.M., Arraiano, C.M. & Matos, R.G.. "New targets for drug design: Importance of nsp14/nsp10 complex formation for the 3'-5' exoribonucleolytic activity on SARS-CoV-2." XXI SPB National Congress of Biochemistry 2020
(Évora, Portugal)
2021/07/04 Saramago, M., Bárria, C., Costa, V., Souza, C.S., Viegas, S.C., Domingues, S., Lousa, D., Soares, C.M., Arraiano, C.M. & Matos, R.G. , "New targets for drug design: Importance of nsp14/nsp10 complex formation for the 3'-5' exoribonucleolytic activity on SARS-CoV-2", selected oral presentation by M. Saramago 45th FEBS Congress / Molecules of Life: Towards New Horizons / RNA function symposium
(Ljubljana, Slovenia)
2021/07/01 Saramago, M., Bárria, C., Costa, V., Souza, C.S., Viegas, S.C., Domingues, S., Lousa, D., Soares, C.M., Arraiano, C.M. & Matos, R.G.. "Importance of nsp14/nsp10 complex formation for the 3¿-5¿ exoribonucleolytic activity on SARS-CoV-2", Presented by Costa, VG II International Meeting of The Portuguese Society of Genetics
(online, Slovenia)
2021/05/07 Cruz C, Buga CC, Parreiras S, Valério M, Soares CM, Vicente JB and Lousa D (2021). "Protein Engineering of Mini Therapeutic Proteins against SARS-CoV-2" - selected oral presentation by Cruz C. 10th Bioinformatics Open Days
(Braga - online conference, Portugal)
2021/05/06 Valério MF, Mendonça D, Morais J, Cruz CH, Castanho MARB, Veiga AS, Melo MN, Soares CM, Lousa D (2021). "MD Simulation reveals that the Parainfluenza FP forms Oligomeric Pore-like Structures." - selected oral presentation by Valério MF 10th Bioinformatics Open Days
(Braga - online conference, Portugal)
2019/10/14 Lousa D., “Influenza virus fusion analysed through the computational microscope”, invited oral presentation by D. Lousa in the II International Conference NOVAsaúde Chronicle Disease and Infection
(Lisbon, Portugal)
2019/07/20 Lousa D., Pinto A. R. T., Campos S. R. R., Baptista A. M., Veiga A. S., Castanho M. A. R. B. and Soares C. M., “Effect of pH on the influenza fusion peptide structure and activity: A constant-pH molecular dynamics approach”, selected oral presentation by D. Lousa in the 12th EBSA-10th ICBP-IUPAP Biophysics Congress
(Madrid, Spain)
2019/02/21 Lousa D., Pinto A. R. T., Victor B. L., Laio A., Campos S. R. R., Baptista A. M., Veiga A. S., Castanho M. A. R. B. and Soares C. M., “Structural Bioinformatics studies on the Influenza virus fusion machinery”, selected oral presentation by D. Lousa in the Bioinformatics Open Days 2019
(Braga, Portugal)
2019/02/08 Lousa D., Pinto A. R. T., Victor B. L., Laio A., Campos S. R. R., Baptista A. M., Veiga A. S., Castanho M. A. R. B. and Soares C. M., “Characterizing the influenza virus fusion machinery: A computational approach”, invited oral presentation by D. Lousa in the JORTEC Bioquímca 2019, FCT NOVA
(Almada, Portugal)
2019/01/30 Lousa D., Pinto A. R. T., Victor B. L., Laio A., Campos S. R. R., Baptista A. M., Veiga A. S., Castanho M. A. R. B. and Soares C. M., “Influenza fusion peptide: Dissecting the molecular properties of a key player in the infectious process”, invited oral presentation by D. Lousa in the SCAN seminars, ITQB NOVA
(Oeiras, Portugal)
2018/05/28 Soares C. M., Lousa D.; Victor B. L., Laio A., Veiga A. S., Castanho M. A. R. B., “Molecular properties of the influenza fusion peptide: Combining simulation and experiment”, invited oral presentation by C. M. Soares in 47th Annual Meeting of the Brazilian Society for Biochemistry and Molecular Biology (SBBq)
(Joinville, Brazil)
2016/06/16 Lousa D., Pinto A. R. T., Victor B. L., Laio A., Veiga A. S., Castanho M. A. R. B. and Soares C. M., “Structure and activity of the influenza fusion peptide: A combined simulation and experimental approach”, selected oral presentation by D. Lousa in the 5th Iberian Biophysics Congress
(Porto, Portugal)
2016/02/10 Lousa D., Pinto A. R. T., Veiga A. S., Laio A., Castanho M. A. R. B. and Soares C. M., “When simulation and experiment fuse: Analysing the interaction of the influenza fusion peptide with model membranes”, selected oral presentation by D. Lousa in the XV Iberic Peptide Meeting
(Porto, Portugal)
2016/01/06 Lousa D., Pinto A. R. T., Victor B. L., Laio A., Veiga A. S., Castanho M. A. R. B. and Soares C. M., “Fusing simulation and experiment: Structure and activity studies on the influenza fusion peptide”, SCAN seminar by D. Lousa at ITQB NOVA
(Oeiras, Portugal)
2015/12/18 Lousa D., Pinto A. R. T., Veiga A. S., Laio A., Castanho M. A. R. B. and Soares C. M., “When simulation and experiment fuse: Analysing the interaction of the influenza fusion peptide with model membranes”, selected oral presentation by D. Lousa in EJIBCE III
(Coimbra, Portugal)
2014/08/29 Lousa D.; Victor B. L., Fernandez C. and Soares C. M., “Molecular insights into the role of the fusion peptide from influenza virus: A computational analysis”, selected oral presentation by D. Lousa in FEBS Young Scientists
(Paris, France)
2014/08/05 Soares C. M., Lousa D.; Victor B. L., Antunes J., “Molecular dynamics simulation studies of the interaction of the influenza hemagglutinin fusion peptide with membranes”, invited oral presentation by C. M. Soares
(Brisbaine, Australia)
2014/05/18 Lousa D.; Victor B. L., Demmelhuber L.,.Baptista A. M. and Soares C. M, “Interaction of influenza hemagglutinin with membranes: a molecular simulation analysis”, Invited oral presentation by C. M. Soares
(Iguaçu, Brazil)
2014/03/12 Lousa, D., Cianci, M., Helliwell, J. R., Halling, P. J., Baptista, A. M., Soares,C. M., “Simulation of proteins in nonaqueous media”. Invited oral presentation by C. M. Soares in the Stuttgart, Germany, March 10-12, 2014 CECAM meeting “Biological Molecules under non-natural conditions”,
(Stuttgart, Germany)
2014/03/11 Cianci, M., Tomaszewski, B., Lousa, D., Baptista, A. M., Soares,C. M., Helliwell, J. R., Halling, P. J. (2014) “Analysis of counter-ion effects in nonaqueous enzymology of subtilisin”. Invited oral presentation by M. Cianci CECAM meeting “Biological Molecules under non-natural conditions”,
(Stuttgard, Germany)
2012/09/02 Cianci M., Tomaszewski M., Lousa D., Baptista A. M., Soares C. M., Helliwell J. R., Halling P. J. “Analysis of counter-ion effects in nonaqueous enzymology of subtilisin”. Oral presentation by M. Cianci 6th International Congress on Biocatalysis
(Hamburg, Germany)
2012/05/08 Simulating the unusual properties of enzymes in nonaqueous media: basic knowledge approaching rational engineering In silico enzyme design and screening
(Trieste, Italy)
2012/04/16 Cianci M., Llamas M., Lousa D., Baptista A. M., Soares C. M., Halling P. J., Helliwell J. R., (2012) “Crystallographic analysis of weaker counter-ion interactions with proteins correlated with enzyme activity”,, presented by M. Llamas 30th annual BCA spring meeting at the University of Warwick
(Coventry, United Kingdom)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2024/01/01 - Current Small biologics discovery: unlocking new antivirals for pandemic preparedness
Co-supervisor
 Biociências Moleculares (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

École Polytechnique Fédérale de Lausanne, Switzerland
2023/09/01 - Current Design of next-generation antiviral biologics targeting Zika virus
Supervisor
 Biotecnologia (Master)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2023/09/01 - Current Artificial Intelligence-Based Design of Antibody-like Engineered Protein Scaffolds
Supervisor
 Biologia Computacional e Bioinformática (Master)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2023/09/01 - Current Computationally designed antiviral proteins targeting Influenza A hemagglutinin: design, production and characterization
Co-supervisor
 Biotecnologia (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal

Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2023/02/01 - Current Co-supervision of the PhD student Susana Parreiras, enrolled in the ITQB NOVA PhD Program in Molecular Biosciences (FCT fellowship 2022.13172.BD). Title “Oxidative modifications of human hydrogen sulfide-synthesizing enzymes in cancer chemoresistance”
Co-supervisor of Susana Parreiras
 Biociências Moleculares (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2022/11/01 - Current Supervision of the PhD student Ana Carolina Buga, enrolled in the ITQB NOVA PhD Program in Molecular Biosciences (FCT fellowship 2022.13959.BD). Title “Exploring new targets on the Spike glycoprotein for broad-spectrum therapies against coronaviruses”
Supervisor
 Biociências Moleculares (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2022/09/01 - Current Co-supervision of the Master thesis of the student João Correia, ITQB NOVA, Master in Computational Biology and Bioinformatics. Thesis title: An in silico enzyme engineering approach to optimize the production of shikimate derived compounds”.
Co-supervisor
 Biologia Computacional e Bioinformática (Master)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2022/01/01 - Current Supervision of the PhD student Pedro Moreira, enrolled in the ITQB NOVA PhD Program in Molecular Biosciences (FCT fellowship 2021.09343.BD). Title “A computational pipeline for the development of tailored biopharmaceuticals targeting viral fusion peptides”
Supervisor of Pedro Daniel Martins Moreira
 Biociências Moleculares (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2020/03/01 - Current Computational mining for phage lytic enzymes against antibiotic resistant bacteria
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2019/05/15 - Current Building an automated platform for enzyme selection and engineering - Postdoc
Co-supervisor
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2017/10/01 - Current Viral Membrane Fusion: Structural determinants and dynamical behaviour
Co-supervisor
 Biociências Moleculares (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2017/09/01 - Current The effect of pH on the conformation of the influenza hemagglutinin hinge peptide
Supervisor
2014/01/01 - Current Membrane altering proteins: a computational study of viral membrane fusion and antimicrobial peptides
Co-supervisor
 Biochemistry (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2020/01/01 - 2023/12/14 Dengue fusion peptide:: from molecular properties to the design of therapeutic applications
Co-supervisor
 Biochemistry (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2021/09/01 - 2023/02/02 Developing broad-spectrum antiviral proteins against SARS-CoV-2 and its variants
Supervisor of Rita Teixeira
 Bioquímica para a Saúde (Master)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2021/09/01 - 2022/12/22 Structure and function of designed and engineered proteins targeting SARS-CoV-2
Co-supervisor of Bárbara Fernandes
 Bioquímica para a Saúde (Master)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2020/06/01 - 2022/03/31 Molecular determinants of the SARS-CoV-2 fusion peptide activity
Supervisor
 Biochemistry for Health (Master)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2020/09/01 - 2022/03/24 Rationally designed antiviral proteins targeting SARS-CoV-2
Supervisor
 Biochemistry (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2019/12/01 - 2022/02/28 Using computational and experimental methods to provide a global characterization of viral fusion peptides - Postdoc
Supervisor
 Computational Biology (Other)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019/09/01 - 2021/03/11 Implementing a webserver for managing and detecting viral fusion proteins.
Co-supervisor
 Bioinformatics (Master)
2018/09/01 - 2019/11/11 Building an automated platform for the classification of peptides/proteins using machine learning (score 19/20)
Co-supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2018/02/01 - 2019/03/22 Structural and dynamic properties of the Dengue fusion peptide in a membrane bilayer: A computational approach (score 18/20)
Supervisor
 Bioquímica para a Saúde (Master)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018/02/01 - 2019/03/21 Building a database and development of a machine learning algorithm to identify and characterize viral fusion peptides (score 18/20)
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2019/01/01 - 2021/07/08 Member of the organzing committee of the FEBS Young Scientists Forum, Lisbon, 2021 (2019/01/01 - 2021/07/08)
Congress (Member of the Organising Committee)
2016/09/01 - 2018/06/30 Member of the organizing committee of the 1st Career Opportunities for Postdoctoral Researchers in Life Sciences, Hotel Baía, Cascais (2017/11/22 - 2017/11/24)
2015/12/01 - 2017/12/31 Co-chair of the organizing committee of the IV Encontro de Jovens Investigadores de Biologia Computacional Estrutural, ITQB NOVA, Oeiras, Portugal (2016/12/19 - 2019/12/19)
Meeting (Co-organisor)
2015/09/01 - 2016/09/30 Member of the organizing committee of the 1st Summer Science @ ITQB NOVA, ITQB NOVA. Oeiras, Portugal (2016/07/25 - 2016/07/29)
2016/06/15 - 2016/06/17 Member or the organizing staff of the 5th Iberian Biophysical Congress, Porto, Portugal (2016/06/15 - 2016/06/17)
Conference (Other)
2015/06/01 - 2016/01/31 Member of the organizing committee of the 1st ITQB Alumni gathering, ITQB NOVA, Oeiras, Portugal (2015/12/22 - 2015/12/22)
Meeting (Co-organisor)
2014/06/01 - 2015/11/30 Member of the organizing committee of the ITQB Open Day an exhibition for the general public (2015/10/10 - 2015/10/10)
Exhibition
2013/07/01 - 2013/07/31 Member of the organizing staff 9th European Biophysical Congress, Pavilhão Meo Arena, Lisboa (2013/07/13 - 2013/07/17)
Congress (Other)
2009/09/01 - 2011/02/28 Member of the organizing committee of the 1st ITQB PhD Students’ Meeting (2010/10/21 - 2010/10/22)
2003/01/02 - 2003/12/31 Member of the organizing committee of the 1st Applied-Chemistry Forum, at FCT-UNL (2003/10/16 - 2003/10/17)
Symposium (Other)

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2024/02/15 A Study of Machine Learning for Artificial Intelligence-Based Enzyme Classification
President of the jury
 Ana Patrícia Fernandes Brás da Silva (Master)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2024/02/12 Experiments in the use of ddG predictions for de novo in silico protein design
(Thesis) Main arguer
 Rodrigo António Correia Tavares Bernardino (Master)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2024/01/11 Poking holes in membranes with coarse-grained simulations
President of the jury
 Ana Carolina Borges Araújo (Master)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2023/12/21 Structural Characterization and identification of novel inhibitors of respiratory proteins from human bacterial pathogens
(Thesis) Main arguer
 Bárbara Sofia Valente Almeida (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2023/04/14 Interacções proteína-proteína e proteína-RNA na proteína não-estrutural 1 (NS1) do vírus influenza
(Thesis) Main arguer
 Nícia Filipa Rosário Ferreira (PhD)
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
2022/03/28 Aquaporin inhibitors with anticancer properties - computational screening and functional validation
(Thesis) Main arguer
 Jéssica Marques Lopes (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022/01/19 PhageDPO: Phage Depolymerase Finder
(Thesis) Main arguer
 José Alexandre Graça Duarte (Master)
Universidade do Minho, Portugal
2021/11/02 Pyruvate dehydrogenase complex deficiency: mutational spectrum in Portugal, molecular mechanisms underlying pathogenic variants and potential therapeutic effect of arginine
(Thesis) Arguer
 Hana Pavlu Pereira (PhD)
Universidade de Lisboa Faculdade de Farmácia, Portugal
2021/04/05 Bacteriophage-host determinants: identification of bacteriophage receptors through machine learning techniques
(Thesis) Main arguer
 Pedro Henrique Matela Aidos Manso de Araújo (Master)
Universidade do Minho, Portugal
2020/10/01 Tumor microenvironment models: ex vivo, in vitro and in silico approaches to address targeted therapies
(Thesis) Arguer
 Ana Luísa Pécurto Cartaxo (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019/06/05 Targeting enveloped virus entry into cells
(Thesis) Arguer
 Tiago Nascimento Figueira (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal

Committee member

Activity description
Role 		Institution / Organization
2020/10/01 - 2024/09/30 Member of the Thesis Committee of Bruno Salgueiro
Member
 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019/10/01 - 2023/11/30 Member of the Thesis Committee of Lucie Rocha
Member
 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2017/01/01 - 2018/01/10 Member of the executive committee and treasurer of the ITQB NOVA Postdoctoral Association (PdA). The PdA executive committee mediates the interaction between postdoctoral researchers the ITQB direction and the Rectory of Universidade Nova de Lisboa, and coordinates professional enrichment and career development activities, as well as networking events
Other
 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2021/10/08 - 2022/01/14 Perspectives in Computational biology Biologia Computacional e Bioinformática (Mestrado integrado) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2021/11/25 - 2022/01/06 Fundamentals of Computational Biology Biologia Computacional e Bioinformática (Mestrado integrado) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2006/02/01 - 2019/10/31 Co-tutor in the practical classes on Molecular Visualization and Protein Structure Prediction in the ITQB NOVA PhD Program Biociências Moleculares (Doutoramento) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2014/03/01 - 2019/07/15 Co-tutor in the practical classes on Molecular Visualization, Molecular Mechanics/Dynamics, Molecular Docking and Protein Structure Prediction in the ITQB NOVA Master Program in Biochemistry for Health Bioquímica para a Saúde (Mestrado) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019/04/10 - 2019/04/10 Theoretical Class on Applications of Simulation Methods, Master in Biomolecular Engineering, IST-UL Engenharia Biomolecular (Mestrado) Universidade de Lisboa Instituto Superior Técnico, Portugal
2019/02/19 - 2019/02/19 Protein structure prediction workshop, Bioinformatics Open Days 2019, Universidade do Minho Bioinformática (Licenciatura) Instituto Politécnico de Setúbal Escola Superior de Saúde, Portugal
2018/04/25 - 2018/04/25 Theoretical Class on Applications of Simulation Methods, Master in Biomolecular Engineering, IST-UL Engenharia Biomolecular (Mestrado) Universidade de Lisboa Instituto Superior Técnico, Portugal
2017/04/24 - 2017/04/24 Theoretical Class on Applications of Simulation Methods, Master in Biomolecular Engineering, IST-UL Engenharia Biomolecular (Mestrado) Universidade de Lisboa Instituto Superior Técnico, Portugal
2006/02/01 - 2009/06/30 Co-tutor in the practical classes on Molecular Visualization, Molecular Mechanics/Dynamics, and Molecular Docking in the IGC PhD Program in Computational Biology PhD in computational biology Instituto Gulbenkian de Ciência, Portugal

Journal scientific committee

Journal title (ISSN) Publisher
2019/10/01 - Current Frontiers in Medical Technology (2673-3129) Frontiers Media SA