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Carlos José Vieira Simões concluiu licenciatura em Ciências Farmacêuticas e doutoramento em Química pela Universidade de Coimbra. É co-fundador e Chief Technology Officer da empresa BSIM Therapeutics, anteriormente designada BSIM², com sede em Instituto Pedro Nunes. Mantém funções como colaborador externo do Centro de Química de Coimbra. É inventor de 2 patentes concedidas nos EUA e Europa. É autor de artigos científicos relacionados com a descoberta de novos fármacos e publicados em revistas nacionais e internacionais com arbitragem científica. Foi co-orientador em 2 dissertações de mestrado e em 2 teses de doutoramento na área de Biotecnologia Médica na Universidade de Coimbra e na Universidade de Leeds. Participa em 2 projectos de investigação académica. Actua nas áreas de Ciências Médicas com ênfase em Ciências da Saúde, Ciências Médicas com ênfase em Biotecnologia Médica e Ciências Médicas. Nas suas actividades profissionais interagiu com mais de 50 colaboradores na co-autorias de trabalhos científicos.
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Identification

Personal identification

Full name
Carlos José Vieira Simões

Citation names

  • Simões, Carlos J. V.

Author identifiers

Ciência ID
F316-4650-B228
ORCID iD
0000-0001-5994-9104

Websites

Knowledge fields

  • Medical and Health Sciences - Medical Biotechnology
  • Medical and Health Sciences - Other Medical Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Portuguese Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2007 - 2012/10/01
Concluded
 Química (Doutoramento)
Major in Química Biológica
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
"Virtual Screening with Sense and Sensibility in the Search of New Amyloid Inhibitors" (THESIS/DISSERTATION)
 Distinção e Louvor, por Unanimidade
2007 - 2007
Concluded
 International Computational Drug Discovery Course (Outros)
Centre for Molecular and Biomolecular Informatics - Radboud University, Netherlands
2006 - 2007
Concluded
 PhD Program in Computational Biology (Pós-Graduação)
Instituto Gulbenkian de Ciência (Oeiras), Portugal
 NA
1999 - 2005
Concluded
 Ciências Farmacêuticas (Licenciatura)
Universidade de Coimbra, Portugal
"Protein folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom Molecular Dynamics" (THESIS/DISSERTATION)
 15
Affiliation

Science

Category
Host institution 		Employer
2012/01 - Current Coordinating Researcher (Research) BSIM² - Biomolecular Simulations, Portugal
2007 - 2013 Researcher (Research) Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
2011/01 - 2012/01 Researcher (Research) Universidade de Coimbra, Portugal
2011/01/01 - 2011/12/31 Researcher (Research) Partnership for Advanced Computing In Europe, Belgium
2005/10 - 2011/12 Research Assistant (Research) Centro de Neurociências e Biologia Celular, Portugal
2007/10/22 - 2010/12/31 Visiting Researcher (Research) University of Leeds, United Kingdom
2007/10 - 2010/12 Research Assistant (Research) Institute of Molecular and Cellular Biology, University of Leeds, United Kingdom
2004/02 - 2005/07 Research Assistant (Research) Centro de Estudos Farmacêuticos da Universidade de Coimbra, Portugal
2004/10 - 2005/05 Research Assistant (Research) Consiglio Nazionale delle Ricerche, Italy

Others

Category
Host institution 		Employer
2012/02/01 - Current CTO e Fundador BSIM² - Biomolecular Simulations, Portugal
2012/02/01 - Current Research Collaborator Universidade de Coimbra Centro de Química de Coimbra, Portugal
2004/11/01 - 2006/03/24 Young Researcher Istituto di Chimica del Riconoscimento Molecolare Consiglio Nazionale delle Ricerche, Italy
Projects

Contract

Designation Funders
2018/08/01 - 2021/07/31 Novos antivirais contra Influenza: validação do alvo NS1 e descoberta de compostos líder
PTDC/QUI-OUT/32572/2017
Universidade de Coimbra, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/06/22 - 2021/06/21 Técnicas deep na descoberta e desenvolvimento de fármacos
PTDC/CCI-BIO/29266/2017
Universidade de Coimbra, Portugal

Universidade de Aveiro, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2016/07/01 - 2019/12/31 Ao Encontro das Regras para a Permeação Passiva através da Barreira Hemato-Encefálica
PTDC/DTP-FTO/2784/2014
Universidade de Coimbra, Portugal

Universidade de Évora, Portugal

Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal

Universidade do Porto Faculdade de Ciências, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2012/03/01 - 2015/08/31 Fibrilas Interrompidas: Inibição de interacções aberrantes proteína-proteína em Amilóides
PTDC/QUI-QUI/122900/2010
Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2008/01/01 - 2010/12/31 Procura de regras de alto nível em dobragem e desdobragem de proteínas: das doenças amiloidogénicas à previsão da estrutura proteica
PTDC/BIA-PRO/72838/2006
Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal

Universidade do Minho, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2007/06/01 - 2010/12/31 P-found: computação GRID e armazenamento distribuído de dados de simulações de dobragem e desdobragem de proteínas
GRID/GRI/81809/2006
Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal

Universidade do Minho, Portugal

Universidade de Coimbra, Portugal
Fundação para a Ciência e a Tecnologia
Concluded

Other

Designation Funders
2010/07 - Current IBERCIVIS: Uma Plataforma de Computação Voluntária para a Ciência
NA
Centro de Neurociências e Biologia Celular, Portugal

UMIC - Agência para a Sociedade do Conhecimento, Portugal

Laboratório de Instrumentação e Física Experimental de Partículas, Portugal

Ciência Viva - Agência Nacional para a Cultura Científica e Tecnológica, Portugal
UMIC - Agência para a Sociedade do Conhecimento

Fundação para a Ciência e a Tecnologia
Ongoing
2009/01 - Current Rumo a novos inibidores de amilóide-beta e toxicidade associados à doença de Alzheimer: das estatinas, como potenciais compostos-líder, ao desenho de fármacos eficazes
III/BIO/40/2008
Researcher
Centro de Neurociências e Biologia Celular, Portugal
 Instituto de Investigação Interdisciplinar da Universidade de Coimbra
Ongoing
2006 - Current Protein conformation, plasticity and amyloid formation: molecular simulations in parallel computer environment
PTDC/BIA-PRO/72838/2006
Researcher
Centro de Neurociências e Biologia Celular, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2006 - Current P-found: computação GRID e armazenamento distribuído de dados de simulações de dobragem e desdobragem de proteínas
GRID/GRI/81809/2006
Researcher
Centro de Neurociências e Biologia Celular, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2004 - Current Protein Folding, Misfolding and Aggregation: A Computational Biophysics Approach
NA
Researcher
Consiglio Nazionale delle Ricerche, Italy
Concluded
2002 - Current Green Processes in Pharmaceutical Chemistry: Oxidative and Chemoenzymatic Transformations
NA
Centro de Estudos Farmacêuticos da Universidade de Coimbra, Portugal
Concluded
2003 - 2004 Bioactive Steroids: Synthesis, Biological and Toxicological Evaluation
NA
Researcher
Centro de Estudos Farmacêuticos da Universidade de Coimbra, Portugal
Concluded
Outputs

Publications

Book chapter
  1. Pereira, Max; Costa, Vítor Santos; Camacho, Rui; Fonseca, Nuno A.; Simões, Carlos; Brito, Rui M. M.. "Comparative Study of Classification Algorithms Using Molecular Descriptors in Toxicological DataBases". In Advances in Bioinformatics and Computational Biology, 121-132. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009.
    Published • 10.1007/978-3-642-03223-3_11
Conference paper
  1. Vaz, Daniela C.; Brito, Rui M. M.; Mata, Ana I.; Alves, Nuno G.; Simões, Carlos J. V.; Vaz, João Pereira; Duque, Vitor. "Use of molecular interaction fields to understand drug resistance in HIV 1 protease caused by single point mutations". 2018.
    10.4172/0974-276X-C3-119
  2. Silvério, Rita; Rocha, Miguel; Simões, Carlos J. V.; Brito, Rui M. M.; Couto, Bráulio R. G. M.; Santos, Marcos A. dos. "Prediction of drug targets in human pathogens". 2015.
  3. Simões, Carlos J. V.; Rivero, Alejandro; Tarancón, Alfonso; Sanz, Fermín S.; Romero, Javier L; Abreu, Pedro; Manuel, Carlos; et al. "Running faster and further together: the AMILOIDE project, the onset of the Portuguese participation on the Ibercivis volunteer computing network". Paper presented in Ibergrid 2010, Braga, 2010.
    Published
  4. Silva, Cândida G.; Palma, Rui; Simões, José R.; Loureiro-Ferreira, Nuno; Simões, Carlos J. V.; Swain, Martin; Dubitzky, Werner; Brito, Rui M. M.. "P-found GRID: A Grid-enabled repository prototype for protein simulation data". Paper presented in Ibergrid 2009, Valencia, 2009.
    Published
Journal article
  1. João P. Luís; Ana I. Mata; Carlos J. V. Simões; Rui M. M. Brito. "Analysis of the Conformational Dynamics of the Soluble and Membrane-Bound Forms of Interleukin-1 Receptor Type-1: Insights into Linker Flexibility and Domain Rearrangements". International Journal of Molecular Sciences 23 5 (2022): 2599-2599. https://doi.org/10.3390/ijms23052599.
    10.3390/ijms23052599
  2. João P. Luís; Carlos J. V. Simões; Rui M. M. Brito. "The Therapeutic Prospects of Targeting IL-1R1 for the Modulation of Neuroinflammation in Central Nervous System Disorders". International Journal of Molecular Sciences (2022): https://doi.org/10.3390/ijms23031731.
    10.3390/ijms23031731
  3. Simões, Carlos J. V.. "Synthesis and structure-activity relationships of new chiral spiro-ß-lactams highly active against HIV-1 and Plasmodium". European Journal of Medicinal Chemistry 219 (2021): 113439-113439. http://dx.doi.org/10.1016/j.ejmech.2021.113439.
    10.1016/j.ejmech.2021.113439
  4. Simões, Carlos J. V.. "Spiro-ß-lactam BSS-730A Displays Potent Activity against HIV and Plasmodium". ACS Infectious Diseases 7 2 (2021): 421-434. http://dx.doi.org/10.1021/acsinfecdis.0c00768.
    10.1021/acsinfecdis.0c00768
  5. Alves, Nuno G.; Mata, Ana I.; Luís, João P.; Brito, Rui M. M.; Simões, Carlos J. V.. "An Innovative Sequence-to-Structure-Based Approach to Drug Resistance Interpretation and Prediction: The Use of Molecular Interaction Fields to Detect HIV-1 Protease Binding-Site Dissimilarities". Frontiers in Chemistry 8 (2020): http://dx.doi.org/10.3389/fchem.2020.00243.
    Open access • Published • 10.3389/fchem.2020.00243
  6. Simões, Carlos J. V.; Almeida, Zaida L.; Cardoso, Ana L.; Bezerra, Filipa; Almeida, Maria R.; Beirão, João; Pinho e Melo, Teresa M. V. D.; Saraiva, Maria J.; Brito, Rui M. M.. "Lead optimization of resilient next-generation transthyretin stabilizers for multiple target-product profiles: approaching the CNS". Amyloid 26 sup1 (2019): 77-78. http://dx.doi.org/10.1080/13506129.2019.1583195.
    Published • 10.1080/13506129.2019.1583195
  7. Bezerra, Filipa; Simões, Carlos J. V.; Beirão, João M.; Saraiva, Maria João; Brito, Rui M. M.; Almeida, Maria Rosário. "Targeting transthyretin amyloidosis in the eye with next-generation stabilizers: AT40 displays potent TTR stabilization in the human vitreous". Amyloid 26 sup1 (2019): 73-74. http://dx.doi.org/10.1080/13506129.2019.1583193.
    Published • 10.1080/13506129.2019.1583193
  8. Carlos J.V. Simões; Zaida L. Almeida; Dora Costa; Catarina S.H. Jesus; Ana L. Cardoso; Maria R. Almeida; Maria J. Saraiva; Teresa M.V. D. Pinho e Melo; Rui M.M. Brito. "A novel bis-furan scaffold for transthyretin stabilization and amyloid inhibition". European Journal of Medicinal Chemistry 121 (2016): 823-840. https://doi.org/10.1016%2Fj.ejmech.2016.02.074.
    10.1016/j.ejmech.2016.02.074
  9. Cândida G. Silva; Carlos J.V. Simoes; Pedro Carreiras; Rui M.M. Brito. "Enhancing Scoring Performance of Docking-Based Virtual Screening Through Machine Learning". Current Bioinformatics 11 4 (2016): 408-420. https://doi.org/10.2174%2F1574893611666160212234816.
    10.2174/1574893611666160212234816
  10. Miguel Jorge; Nuno M. Garrido; Carlos J. V. Simões; Cândida G. Silva; Rui M. M. Brito. "Predicting hydrophobic solvation by molecular simulation: 1. Testing united-atom alkane models". Journal of Computational Chemistry 38 6 (2016): 346-358. https://doi.org/10.1002%2Fjcc.24690.
    10.1002/jcc.24690
  11. Camacho, Rui; Pereira, Max; Costa, Vitor S.; Fonseca, Nuno A.; Adriano, Carlos; Simões, Carlos J. V.; Brito, Rui M. M.. "A relational learning approach to structure-activity relationships in drug design toxicity studies". Journal of Integrative Bioinformatics 1 (2011): 1-17. http://journal.imbio.de/index.php?paper_id=182.
    Published • 10.2390/biecoll-jib-2011-182
  12. Faculdade de Engenharia; Faculdade de Ciências. "A relational learning approach to Structure-Activity Relationships in drug design toxicity studies.". (2011): https://repositorio-aberto.up.pt/handle/10216/67124.
    10.2390/biecoll-jib-2011-182
  13. Rodrigues, J. Rui; Simões, Carlos J. V.; Silva, Cândida G.; Brito, Rui M. M.. "Potentially amyloidogenic conformational intermediates populate the unfolding landscape of transthyretin: insights from molecular dynamics simulations". Protein Science 19 2 (2010): 202-219. http://www3.interscience.wiley.com/journal/123188796/abstract.
    Published • 10.1002/pro.289
  14. Simões, Carlos J. V.; Mukherjee, Trishna; Brito, Rui M. M.; Jackson, Richard M. "Toward the discovery of functional transthyretin amyloid inhibitors: application of virtual screening methods". Journal of Chemical Information and Modeling 10 50 (2010): 1806-1820. http://pubs.acs.org/doi/abs/10.1021/ci100250z.
    Published • 10.1021/ci100250z
  15. Monticelli, Luca; Simões, Carlos; Belvisi, Laura; Colombo, Giorgio. "Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides". Journal of Physics: Condensed Matter 18 14 (2006): 329-345. stacks.iop.org/JPhysCM/18/S329.
    Published • 10.1088/0953-8984/18/14/S15
Magazine article
  1. Simões, Carlos J. V.; Jesus, Catarina J. H.; Jackson, Richard M; Brito, Rui M. M.. "Solubility meets Specificity: Evaluation of virtual screening methods towards the discovery of functional transthyretin amyloid inhibitors.", Revista Portuguesa de Farmácia, 2010
  2. Simões, Carlos J. V.; Rivero, Alejandro; Brito, Rui M. M.. "Searching for Anti-Amyloid Drugs with the Help of Citizens: the “AMILOIDE” Project on the IBERCIVIS Platform", ERCIM News, 2010, http://ercim-news.ercim.eu/images/stories/EN82/EN82-web.pdf.
Manual
  1. Simões, Carlos J. V.; Brito, Rui M. M.. À procura dos mecanismos moleculares das doenças amilóides. Portugal. 2011.
Working paper
  1. Simões, Carlos J. V.; Brito, Rui M. M.. 2011. "AMILOIDE, "trailer" em estilo "A Origem"". https://educast.fccn.pt/vod/clips/2hs3vyrnok.
  2. Simões, Carlos J. V.; Brito, Rui M. M.. 2011. "AMILOIDE, O Filme". https://educast.fccn.pt/vod/clips/q934wm2sb.

Intellectual property

Patent
  1. 2021. "2-thioxothiazolidin-4-one derivatives active as transthyretin ligands and uses thereof". United States.
    Granted/Issued
  2. Simões, Carlos J. V.. 2020. "BIS-FURAN DERIVATIVES AS TRANSTHYRETIN (TTR) STABILIZERS AND AMYLOID INHIBITORS FOR THE TREATMENT OF FAMILIAL AMYLOID POLYNEUROPATHY (FAP)".
  3. Simões, Carlos J. V.. 2019. "Bis-furan derivatives as transthyretin (TTR) stabilizers and amyloid inhibitors for the treatment of Familial Amyloid Polyneuropathy (FAP)". United States.
    Granted/Issued

Other

Other output
  1. Assessing the Effect of 2D Fingerprint Filtering on ILP-Based Structure-Activity Relationships Toxicity Studies in Drug Design. 2011. Rui Camacho; Max Pereira; Vítor Santos Costa; Nuno A. Fonseca; Carlos J. V. Simões; Rui M. M. Brito. https://doi.org/10.1007%2F978-3-642-19914-1_46.
    10.1007/978-3-642-19914-1_46
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2010 Running faster and further together: The AMILOIDE project, the onset of the Portuguese participation on the Ibercivis volunteer computing network IBERGRID'2010
Universidade do Minho (Braga, Portugal)
2010 Solubility meets Specificity: Evaluation of virtual screening methods towards the discovery of functional transthyretin amyloid inhibitors. 2nd National Meeting on Medicinal Chemistry
Faculty of Pharmacy, University of Coimbra (Coimbra, Portugal)
2010 Towards the discovery of novel and safer transthyretin amyloid inhibitors: application of “in silico” screening methods. XVII National Congress of Biochemistry
Biochemistry Portuguese Society (Porto, Portugal)
2006 Experimentally-driven in silico screening of new lead compounds wtih enhanced transthyretin tetramer stabilizing effects XV National Congress of Biochemistry
Universidade de Aveiro (Aveiro, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2008 - 2008 Inhibiting Protein-Protein Interaction through Tetramer Stabilization in Transthyretin
Co-supervisor
 Bioinformatics and Computational Biology (Master)
Faculty of Biological Sciences, University of Leeds, United Kingdom

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2010 - 2010 Running faster and further together: the AMILOIDE project, the onset of the Portuguese participation on the Ibercivis volunteer computing network
Conference
 IBERGRID'2010 - Bridging the gap between European e-Science and Iberian America
Universidade do Minho, Portugal
2010 - 2010 Evaluation of virtual screening methods towards the discovery of new functional transthyretin amyloid inhibitors
Meeting
 240th ACS National Meeting & Exposition Fall 2010
American Chemical Society, Portugal
2009 - 2009 Transthyretin amyloid as a model target for the modulation of protein-protein interactions
Symposium
 VIII European Symposium of the Protein Society
Protein Society, Switzerland
2009 - 2009 New challenges from old problems: Transthyretin amyloid as a model target for the modulation of protein-protein interactions
Workshop
 Leeds Annual Statistical Research
University of Leeds, United Kingdom
2007 - 2007 Experimentally-driven in silico screening for high-affinity transthyretin amyloid inhibitors
Workshop
 International Workshop New Approaches in Drug Design & Discovery 2007
Philipps-Universität Marburg, Germany
2006 - 2006 Experimentally-driven in silico screening of new lead compounds wtih enhanced transthyretin tetramer stabilizing effects
Congress
 XV National Congress of Biochemistry
Universidade de Aveiro, Portugal
2006 - 2006 Probing the conformational pathways leading to transthyretin amyloidosis: insights from multiple molecular dynamics unfolding simulations
Congress
 VI Ibero-American Congress of Biophysics

Association member

Society Organization name Role
2010/04 - Current American Chemical Society
2007/01 - Current Ordem dos Farmacêuticos
2006/08 - Current Sociedade Portuguese de Biofísica
Distinctions

Other distinction

2010 Prémio Connecting Science to People
Portuguese Biochemistry Society and Take The Wind, Portugal
2007 START - Prémio Nacional de Empreendedorismo
BPI, Portugal

Microsoft Portugal, Portugal