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Pedro M.F. Sousa is a Senior Scientist at the Structural Biology for Drug Discovery Unit (Merck Healthcare Lab) from the Health & Pharma Division at the iBET. Pedro M.F. Sousa graduated in Biology at the Universidade Lusófona de Humanidades e Tecnologias (Lisbon), and holds a PhD in Biochemistry from Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa. During his PhD, from 2009 to 2013, Pedro contributed for the characterization of the supramolecular assemblies of Escherichia coli and Bacillus subtilis aerobic respiratory chains and for the kinetic characterization of a novel NhaE-type Na+/H+ antiporter from Neisseria meningitidis. He became highly skilled in biochemical and biophysical methodologies with special focus on proteomic analysis and enzyme kinetic characterization. After a short early-stage postdoc internship at the European Molecular Biology Laboratory (EMBL, Hamburg, Germany), Pedro enrolled in an intensive training on Surface Plasmon Resonance Spectroscopy at the Department of Molecular Interactions and Biophysics (Merck KGaA, Darmstadt, Germany) and has joined iBET in 2014. Current Research is focused on the management of the Molecular Interactions Platform at the Structural Biology for Drug Discovery Unit (iBET). Molecular interactions with selected drug targets are evaluated in a combination of different cutting edge biophysical methods such as Surface Plasmon Resonance, Differential Scanning Fluorimetry and Bio-Layer interferometry. This research is developed on the scope of the collaboration with Merck KGaA.
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Identification

Personal identification

Full name
Pedro Sousa
Date of birth
1984/11/03
Gender
Male

Citation names

  • Sousa, Pedro M. F.

Author identifiers

Ciência ID
C615-6E7D-6ABB
ORCID iD
0000-0002-6672-3610
Researcher Id
AAG-5206-2019

Email addresses

  • pedrosousa@ibet.pt (Professional)

Telephones

Telephone
  • 214469757 (Professional)

Addresses

  • Instituto de Biologia Experimental e Tecnológica. Av. da República, Estação Agronómica Nacional (EAN), 2780-157, Oeiras, Oeiras, Portugal (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences - Biochemistry

Languages

Language Speaking Reading Writing Listening Peer-review
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Portuguese (Mother tongue)
French Elementary (A2) Upper intermediate (B2) Elementary (A2) Upper intermediate (B2)
Spanish; Castilian Elementary (A2) Upper intermediate (B2) Elementary (A2) Upper intermediate (B2)
Education
Degree Classification
2009/01/01 - 2013/12/13
Concluded
 Bioquímica (Doutoramento)
Major in Especialidade: Bioenergética
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
"Supercomplexes of Prokaryotic Aerobic Respiratory Chains – Escherichia coli and Bacillus subtilis supramolecular assemblies" (THESIS/DISSERTATION)
 Approved by Unanimity
2002/10/01 - 2008/10/01
Concluded
 Biologia (Licenciatura)
Universidade Lusófona de Humanidades e Tecnologias, Portugal
"Study of Escherichia coli Aerobic Respiratory Chain: Identification of a NADH:Oxygen oxidoreductase supercomplex" (THESIS/DISSERTATION)
 17/20
Affiliation

Others

Category
Host institution 		Employer
2018/05/01 - Current Senior Scientist at Merck Healthcare Lab Instituto de Biologia Experimental e Tecnológica, Portugal
Instituto de Biologia Experimental e Tecnológica, Portugal
2014/10/01 - 2018/04/30 Associate Researcher at Merck Healthcare Lab Instituto de Biologia Experimental e Tecnológica, Portugal
Instituto de Biologia Experimental e Tecnológica, Portugal
2009/03/01 - 2013/03/01 PhD Student (SFRH/BD/46553/2008) Fundação para a Ciência e a Tecnologia, Portugal
Projects

Contract

Designation Funders
2014/01/01 - 2019/12/31 Structure and Function of a Dodecameric Molecular Machine: the human RuvBL1/RuvBL2 Complex and its Role in Disease
PTDC/BBB-BEP/1463/2014
Researcher
Instituto de Biologia Experimental e Tecnológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2018/02/01 - 2019/07/31 Bypassing Protein Purification in Drug Discovery
P1-700
Principal investigator
Instituto de Biologia Experimental e Tecnológica, Portugal
 Instituto de Biologia Experimental e Tecnológica
Concluded
2008/01/01 - 2013/12/13 Identification and characterization of the supercomplexes from the bacterial aerobic respiratory chain of Escherichia coli and Bacillus subtilis
PTDC/BIA-PRO/67105/2006
Researcher
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Instituto de Investigação Científica Tropical, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Conference abstract
  1. Sousa, Pedro M. F.. "An integrated perspective of the Escherichia coli aerobic respiratory chain". Paper presented in European Bioenergetics Conference, Friburgo, 2012.
    Published • https://doi.org/10.1016/j.bbabio.2012.06.372
  2. Sousa, Pedro M. F.. "The succinate oxidase supercomplex of the Bacillus subtilis aerobic respiratory chain". Paper presented in European Bioenergetics Conference, Friburgo, 2012.
    Published
  3. Sousa, Pedro M. F.. "Identification and characterization of a new Na+/H+ antiporter in Neisseria meningitidis". Paper presented in European Bioenergetics Conference, Friburgo, 2012.
    Published
  4. Sousa, Pedro M. F.. "Supramolecular organization of the aerobic respiratory chain of Escherichia coli". Paper presented in European Bioenergetics Conference, Varsóvia, 2010.
    Published • https://doi.org/10.1016/j.bbabio.2010.04.350
  5. Sousa, Pedro M. F.. "Characterization of the supramolecular structure of Bacillus subtilis aerobic respiratory chain". Paper presented in European Bioenergetics Conference, Varsóvia, 2010.
    Published • https://doi.org/10.1016/j.bbabio.2010.04.349
Journal article
  1. Sousa, Pedro M. F.. "The HSP90/R2TP Quaternary Chaperone Scaffolds Assembly of the TSC Complex". Journal of Molecular Biology 436 23 (2024): https://www.sciencedirect.com/science/article/pii/S0022283624004698?via%3Dihub.
    Open access • Published
  2. Ana C. F. Paiva; Ana Rita Lemos; Philipp Busse; Madalena T. Martins; Diana O. Silva; Micael Freitas; Sandra Isabel Pereira dos Santos; et al. "Extract2Chip—Bypassing Protein Purification in Drug Discovery Using Surface Plasmon Resonance". Biosensors (2023): https://www.mdpi.com/2079-6374/13/10/913.
    10.3390/bios13100913
  3. Gabriela Silva; Ana F. Rodrigues; Susana Ferreira; Carolina Matos; Rute P. Eleutério; Gonçalo Marques; Khrystyna Kucheryava; et al. "Novel scFv against Notch Ligand JAG1 Suitable for Development of Cell Therapies toward JAG1-Positive Tumors". Biomolecules (2023): https://doi.org/10.3390/biom13030459.
    10.3390/biom13030459
  4. Raphael Dos Santos Morais; Paulo Espírito Santo; Marie Ley; Cédric Schelcher; Yoann Abel; Laura Plassart; Evolène Deslignière; et al. "Deciphering cellular and molecular determinants of human DPCD protein in complex with RUVBL1/RUVBL2 AAA-ATPases". Journal of Molecular Biology 434 19 (2022): 167760-167760. http://dx.doi.org/10.1016/j.jmb.2022.167760.
    10.1016/j.jmb.2022.167760
  5. Timo Heinrich; Carl Peterson; Richard Schneider; Sakshi Garg; Daniel Schwarz; Jakub Gunera; Anita Seshire; et al. "Optimization of TEAD P-Site Binding Fragment Hit into In Vivo Active Lead MSC-4106". Journal of Medicinal Chemistry (2022): http://dx.doi.org/10.1021/acs.jmedchem.2c00403.
    10.1021/acs.jmedchem.2c00403
  6. Sales-Dias, Joana; Ferreira, Andreia; Lamy, Márcia; Domenici, Giacomo; Monteiro, Sandra M.S.; Pires, António; Lemos, Ana R.; et al. "Development of antibodies against the notch ligand Delta-Like-1 by phage display with activity against breast cancer cells". New Biotechnology 64 (2021): 17-26. http://dx.doi.org/10.1016/j.nbt.2021.05.003.
    10.1016/j.nbt.2021.05.003
  7. Gabriela Silva; Joana Sales-Dias; Diogo Casal; Sara Alves; Giacomo Domenici; Clara Barreto; Carolina Matos; et al. "Development of Dl1.72, a Novel Anti-DLL1 Antibody with Anti-Tumor Efficacy against Estrogen Receptor-Positive Breast Cancer". Cancers (2021): https://www.mdpi.com/2072-6694/13/16/4074.
    10.3390/cancers13164074
  8. Raquel R. Lopes; Catarina S. Tomé; Roberto Russo; Roberta Paterna; João Leandro; Nuno R. Candeias; Lídia M. D. Gonçalves; et al. "Modulation of Human Phenylalanine Hydroxylase by 3-Hydroxyquinolin-2(1H)-One Derivatives". Biomolecules 11 3 (2021): 462-462. https://doi.org/10.3390/biom11030462.
    10.3390/biom11030462
  9. Abel, Yoann; Paiva, Ana C F; Bizarro, Jonathan; Chagot, Marie-Eve; Santo, Paulo E; Robert, Marie-Cécile; Quinternet, Marc; et al. "NOPCHAP1 is a PAQosome cofactor that helps loading NOP58 on RUVBL1/2 during box C/D snoRNP biogenesis". Nucleic Acids Research 49 2 (2021): 1094-1113. http://dx.doi.org/10.1093/nar/gkaa1226.
    Published • 10.1093/nar/gkaa1226
  10. Seixas, João D.; Sousa, Bárbara B.; Marques, Marta C.; Guerreiro, Ana; Traquete, Rui; Rodrigues, Tiago; Albuquerque, Inês S.; et al. "Structural and biophysical insights into the mode of covalent binding of rationally designed potent BMX inhibitors". RSC Chemical Biology 1 4 (2020): 251-262. http://dx.doi.org/10.1039/d0cb00033g.
    Published • 10.1039/d0cb00033g
  11. Tomé, Catarina S.; Lopes, Raquel R.; Sousa, Pedro M. F.; Amaro, Mariana P.; Leandro, João; Mertens, Haydyn D. T.; Leandro, Paula; Vicente, João B.. "Structure of full-length wild-type human phenylalanine hydroxylase by small angle X-ray scattering reveals substrate-induced conformational stability". Scientific Reports 9 1 (2019): http://dx.doi.org/10.1038/s41598-019-49944-x.
    10.1038/s41598-019-49944-x
  12. Zuhra, Karim; Sousa, Pedro M. F.; Paulini, Giulia; Lemos, Ana Rita; Kalme, Zenta; Bisenieks, Imants; Bisenieks, Egils; et al. "Screening Pyridine Derivatives against Human Hydrogen Sulfide-synthesizing Enzymes by Orthogonal Methods". Scientific Reports 9 1 (2019): http://dx.doi.org/10.1038/s41598-018-36994-w.
    10.1038/s41598-018-36994-w
  13. Maurizy, Chloé; Quinternet, Marc; Abel, Yoann; Verheggen, Céline; Santo, Paulo E.; Bourguet, Maxime; C.F. Paiva, Ana; et al. "The RPAP3-Cterminal domain identifies R2TP-like quaternary chaperones". Nature Communications 9 1 (2018): http://dx.doi.org/10.1038/s41467-018-04431-1.
    Open access • Published • 10.1038/s41467-018-04431-1
  14. Sousa, P.M.F.; Videira, M.A.M.; Santos, F.A.S.; Hood, B.L.; Conrads, T.P.; Melo, A.M.P.. "The bc:caa3 supercomplexes from the Gram positive bacterium Bacillus subtilis respiratory chain: A megacomplex organization?". Archives of Biochemistry and Biophysics 537 1 (2013): 153-160. http://www.scopus.com/inward/record.url?eid=2-s2.0-84881120335&partnerID=MN8TOARS.
    10.1016/j.abb.2013.07.012
  15. Sousa, P.M.F.; Videira, M.A.M.; Vorburger, T.; Silva, S.T.N.; Moir, J.W.; Steuber, J.; Melo, A.M.P.. "The novel NhaE-type Na+/H+ antiporter of the pathogenic bacterium Neisseria meningitidis". Archives of Microbiology 195 3 (2013): 211-217. http://www.scopus.com/inward/record.url?eid=2-s2.0-84875841445&partnerID=MN8TOARS.
    10.1007/s00203-012-0856-4
  16. Sousa, P.M.F.; Videira, M.A.M.; Melo, A.M.P.. "The formate: Oxygen oxidoreductase supercomplex of Escherichia coli aerobic respiratory chain". FEBS Letters 587 16 (2013): 2559-2564. http://www.scopus.com/inward/record.url?eid=2-s2.0-84881476538&partnerID=MN8TOARS.
    10.1016/j.febslet.2013.06.031
  17. Sousa, P.M.F.; Videira, M.A.M.; Bohn, A.; Hood, B.L.; Conrads, T.P.; Goulao, L.F.; Melo, A.M.P.. "The aerobic respiratory chain of Escherichia coli: From genes to supercomplexes". Microbiology (United Kingdom) 158 9 (2012): 2408-2418. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865675123&partnerID=MN8TOARS.
    10.1099/mic.0.056531-0
  18. Sousa, P.M.F.; Silva, S.T.N.; Hood, B.L.; Charro, N.; Carita, J.N.; Vaz, F.; Penque, D.; Conrads, T.P.; Melo, A.M.P.. "Supramolecular organizations in the aerobic respiratory chain of Escherichia coli". Biochimie 93 3 (2011): 418-425. http://www.scopus.com/inward/record.url?eid=2-s2.0-79951517273&partnerID=MN8TOARS.
    10.1016/j.biochi.2010.10.014
Thesis / Dissertation
  1. Sousa, Pedro M. F.. "Supercomplexes of Prokaryotic Aerobic Respiratory Chains – Escherichia coli and Bacillus subtilis supramolecular assemblies". PhD, Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, 2013. https://run.unl.pt/bitstream/10362/12026/1/PhD%20Thesis%20Pedro%20Miguel%20Sousa.pdf.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2023/11/29 Biophysical characterisation of binary and ternary drug-target complexes using the BRUKER SPR-32 PRO platform Biophysical characterisation of binary and ternary drug-target complexes using the BRUKER SPR-32 PRO platform
Drug Target Review
2021/06/29 Extract2Chips: Bypassing protein purification in drug discovery. Latin Biacore System User Days 2021 - Virtual Event
Cytiva

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2021/01/01 - Current Understanding box HACA snoRNP biogenesis: The role of DKC1 and SHQ1 proteins in cancer
Supervisor of Philipp Busse
 Biociências Moleculares (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal
2019/09/01 - Current Structure and Function of a molecular machine: Human RuvBL1/2 complex and its role in human disease
Co-supervisor of Ana Catarina Fernandes Paiva
 Biociências Moleculares (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2017/01/01 - 2017/07/01 Biotinilação in vivo no desenvolvimento de novos fármacos
Co-supervisor of Madalena Tropa Martins
 Biologia (Degree)
Universidade de Lisboa Instituto Superior de Agronomia, Portugal
2016/11/01 - 2017/02/28 Biochemical and biophysical methods in drug discovery
Co-supervisor of Philipp Busse
 Biochemistry (Master)
Goethe-Universität Frankfurt am Main, Germany

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2019/03/20 - 2019/03/22 Participation in the 6th NovAliX Conference "Biophysics in Drug Discovery". Cannes, France. This edition intended to bring together biophysicists and medicinal chemists, the synergy between their disciplines being key to deliver better drugs on a shorter timeline.
Conference
 6th NovAliX Conference "Biophysics in Drug Discovery
NovAliX, France
2018/11/22 - 2018/11/23 Participation in the "Biacore User Symposium 2018" Cologne, Germany. SPR-related research and applications in biomolecular interactions.
Meeting
 Biacore User Symposium 2018
GE Healthcare AB, Sweden
2018/06/06 - 2018/06/08 Participation in the "switchSENSE User Meeting: interACT!" Munich, Germany
Meeting
 switchSENSE User Meeting: interACT!
Dynamic Biosensors, Germany
2017/03/05 - 2017/03/07 Participation in the "6th RSC-BMCS Fragment-based Drug Discovery Meeting" Vienna, Austria
Meeting
Royal Society of Chemistry, United Kingdom
2016/11/13 - 2016/11/15 Participation in the "24th Protein Structure Determination in Industry (PSDI)" Conference. Malmo, Sweden. For three days, speakers addressed a range of topics, including fragment screening, biophysical characterization of biosimilars and structural approaches to improving pharmacokinetics, highlighting the role of structural biology throughout the drug discovery process.
Conference
 24th Protein Structure Determination in Industry
Novo Nordisk Scandinavia AB, Sweden
2016/06/12 - 2016/06/15 Participation in the "Developments in Protein Interaction Analysis (DIPIA) 2016" Berlin, Germany. Conference topics included: - Biophysical characterization of biotherapeutics - Low molecular weight drug discovery and characterization - From basic research to advanced applications - Comparability and quality control of biologics
Conference
 Developments in Protein Interaction Analysis (DIPIA) 2016
GE Healthcare AB, Sweden
2015/03/22 - 2015/03/24 Participation in the "5th RSC-BMCS Fragment-based Drug Discovery meeting", Cambridge, United Kingdom. The aim of the 5th RSC-BMCS Fragment-based Drug Discovery meeting was to continue the focus on case studies in Fragment-based Drug Discovery that have delivered compounds to late stage medicinal chemistry, preclinical or clinical programmes.
Workshop
Royal Society of Chemistry, United Kingdom
2012/09/15 - 2012/09/20 Bioenergetics Conference in Freiburg, Germany. Participation with posters "The succinate oxidase supercomplex of the Bacillus subtilis aerobic respiratory chain", "Identification and characterization of a new Na+/H+ antiporter in Neisseria meningitidis" and "An integrated perspective of the Escherichia coli aerobic respiratory chain"
Conference
 European Bioenergetics Conference (EBEC)
Albert-Ludwigs-Universitat Freiburg Fakultat fur Chemie und Pharmazie, Germany
2011 - 2011 Participation in the "7th European Workshop on Bacterial Respiratory Chain". Lund, Sweden.
Workshop
 7th European Workshop on Bacterial Respiratory Chain
2010/07/17 - 2010/07/22 Bioenergetics Conference in Warsaw, Poland. Participation with posters "Supramolecular organization of the aerobic respiratory chain of Escherichia coli" and "Characterization of the supramolecular structure of Bacillus subtilis aerobic respiratory chain"
Conference
 European Bioenergetics Conference (EBEC)
2009/06/02 - 2009/06/03 Participation in the "1st CERMAX practical course on basic NMR" - a two day course with theoretical and practical sessions covering basic aspects of NMR, oriented towards both beginners and current users of the technique.
Workshop
 1st CERMAX practical course on basic NMR
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2009/03/19 - 2009/03/19 Participation in the "Protein Folding Diseases: from metabolic disorders to neurodegeneration" workshop, which gathered specialists that overviewed the state of the art in our understanding of many of these diseases. The talks illustrated the importance of combining different experimental approaches to understand the molecular and cellular biology of protein folding diseases.
Workshop
 Protein Folding Diseases: from metabolic disorders to neurodegeneration
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2009 - 2009 Participation in FEBS course "Chemistry of Metals in Biological Systems". Louvain-la-Neuve, Belgium.
Workshop
 FEBS course "Chemistry of Metals in Biological Systems"
2008/07/10 - 2008/07/13 Participation in the 1st Portuguese-Spanish-British Joint Congress of Biophysics
Conference
 1st Portuguese-Spanish-British Joint Congress of Biophysics
2008 - 2008 Participation in the 1st international forum for Pathway Analysis in Proteomics (PathProt)
Conference
 The international forum on Pathway Analysis in Proteomics
Instituto Gulbenkian de Ciência, Portugal

Journal scientific committee

Journal title (ISSN) Publisher
2017/07 - 2017/07 Journal of Biotechnology (0168-1656) Elsevier
Distinctions

Other distinction

2014 Instruct Fellowship at EMBL (Hamburg)
European Molecular Biology Laboratory Hamburg, Germany

Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2009 PhD Fellowship
Fundação para a Ciência e a Tecnologia, Portugal