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Identification

Personal identification

Full name
Rafael de Santana Nunes

Citation names

  • Nunes, Rafael
  • Nunes, Rafael Santana
  • Nunes, Rafael S.

Author identifiers

Ciência ID
D31F-119C-44C5
ORCID iD
0000-0002-9014-0570
Google Scholar ID
1dYmV_EAAAAJ&hl
Researcher Id
H-8983-2016
Scopus Author Id
56973529200

Email addresses

  • rsnunes@fc.ul.pt (Professional)
  • rafaelnunes@campus.ul.pt (Professional)

Addresses

  • Biosystems & Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016, Lisboa, Lisboa, Portugal (Professional)
  • Centro de Química Estrutural - Institute of Molecular Sciences, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, Ed. C8, 1749-016, Lisboa, Lisboa, Portugal (Professional)

Websites

Knowledge fields

  • Exact Sciences - Chemical Sciences - Organic Chemistry
  • Medical and Health Sciences - Basic Medicine - Medicinal Chemistry
  • Natural sciences - Biological Sciences - Biochemistry
  • Natural sciences - Biological Sciences - Biophysics
  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Elementary (A2) Intermediate (B1) Elementary (A2) Upper intermediate (B2)
Education
Degree Classification
2017/03/01 - 2024
Ongoing
 Chemistry (Doctor of Philosophy)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Molecular modeling of halogen bonds towards applications in drug design" (THESIS/DISSERTATION)
2015/10/27
Concluded
 Chemistry (Master)
Major in Chemistry
Universidade de Lisboa Faculdade de Ciências, Portugal
"Synthesis of new antibiotic glycosides and computational studies on their interaction with model lipid bilayers" (THESIS/DISSERTATION)
 19/20
2012/09/18
Concluded
 Biochemistry (Bachelor)
Universidade de Lisboa Faculdade de Ciências, Portugal
 14/20
2010/12/21
Concluded
 University Extension Course - Research Integration (Outros)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
 18/20
Affiliation

Others

Category
Host institution 		Employer
2023/05 - Current R&D Chemist Cipan, Portugal
Projects

Grant

Designation Funders
2017/03/01 - 2021/06/30 Molecular modeling of halogen bonds towards applications in drug design
SFRH/BD/116614/2016
COVID/BD/151785/2021
PhD Student Fellow
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal

Universidade de Lisboa Centro de Química Estrutural, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2009/10 - 2010/10 Synthesis of sugar derivatives for protein stabilisation studies
034/BII/2009
Integration into Research Grant Fellow
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded

Contract

Designation Funders
2022/01/01 - 2024/12/31 Monosaccharide analogues as novel therapeutic agents to block glycan-driven cancer cell metastasis
PTDC/MED-QUI/2335/2021
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal

FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Universidade de Lisboa Centro de Química Estrutural, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2022/01/02 - 2023/07/01 Development of novel nucleotide and sugar diphosphate mimetics as potential antibacterial agents targeting the peptidoglycan biosynthetic pathway
EXPL/MED-QUI/1017/2021
Researcher
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Universidade de Lisboa Centro de Química Estrutural, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2018/07/01 - 2021/12/31 Uncovering blind spots in halogen bonding applications
PTDC/QUI-QFI/28455/2017
LISBOA-01- 0145-FEDER-028455
Researcher
Universidade de Lisboa Faculdade de Ciências, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2017/03/01 - 2020/04 Halogen bonds in (bio)chemical systems: a theoretical approach for ‘real world’ applications
IF/00069/2014/CP1216/CT0006
Researcher
Universidade de Lisboa Faculdade de Ciências, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book chapter
  1. Costa, Paulo J.; Nunes, Rafael (D31F-119C-44C5). "Advances in the Computational Modeling of Halogen Bonds in Biochemical Systems". In Frontiers in Computational Chemistry: Volume 4, edited by Ul-Haq, Z.; Wilson, A. K., 144-183. Sharjah, United Arab Emirates: BENTHAM SCIENCE PUBLISHERS, 2018.
    Published • 10.2174/97816810844111180401
  2. Xavier, Nuno M.; Nunes, Rafael (D31F-119C-44C5). "Recent Advances in the Synthesis of N-Glycosyl Compounds". In Advances in Organic Synthesis: Volume 10, edited by Atta-ur-Rahman, 99-138. Sharjah, United Arab Emirates: BENTHAM SCIENCE PUBLISHERS, 2018.
    Published • 10.2174/9781681087436118100005
  3. de Matos, Ana Marta ; Nunes, Rafael (D31F-119C-44C5); Dias, Catarina; Rauter, Amélia P.. "Cyclic acetals for regiosselective protection in carbohydrate synthesis: A comparative experiment". In Comprehensive Organic Chemistry Experiments for the Laboratory Classroom, edited by Afonso, Carlos A. M.; Franzén, Robert; Tan, Bin; Coelho, Jaime A. S.; Simão, Dulce Pereira; Candeias, Nuno R.; Trindade, Alexandre F., 188-193. United Kingdom: Royal Society of Chemistry, 2017.
    Published
Conference abstract
  1. Nunes, Rafael de Santana; Vila-Viçosa, Diogo; Costa, Paulo J.. "Halogen bonding in membrane-ligand recognition: Insights from computational biophysics". Paper presented in 20th IUPAB International Congress, 45th SBBf Congress and 50th Annual Meeting of SBBq, virtual event, 2021.
    Published • 10.1007/s12551-021-00845-2
  2. Vila-Viçosa, Diogo; Nunes, Rafael; Costa, Paulo J.. "Folding of cyclic peptides stabilized by halogen bonds". Paper presented in JOINT 12th EBSA congress and 10th ICBP – IUPAP congress, Madrid, 2019.
    Published • 10.1007/s00249-019-01373-4
  3. Nunes, Rafael (D31F-119C-44C5); Xavier, Nuno M.; Costa, Paulo J.. "In silico design of halogenated carbohydrate mimetics as potential halogen-bonding ligands". Paper presented in MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition, Sciforum Electronic Conference Series, 2019.
    Published • 10.3390/mol2net-04-06125
  4. Costa, Paulo J.; Vila-Vicosa, Diogo; Nunes, Rafael. "Tackling halogenated species in biomolecular systems with force field methods: MD sampling and PBSA solvation energies". Paper presented in JOINT 12th EBSA congress and 10th ICBP - IUPAP congress, Madrid, 2019.
    Published • 10.1007/s00249-019-01373-4
  5. Nunes, Rafael; Vila-Vicosa, Diogo; Machuqueiro, Miguel; Costa, Paulo J.. "Improved modeling of halogen-protein interactions in biomolecular simulations using a GROMOS force field". Paper presented in JOINT 12th EBSA congress and 10th ICBP – IUPAP congress, Madrid, 2019.
    Published • 10.1007/s00249-019-01373-4
  6. Nunes, Rafael (D31F-119C-44C5); Costa, Paulo J. (1A1B-A2B9-8D44); Vila-Viçosa, Diogo; Machuqueiro, Miguel. "T4 Lysozyme/Halobenzene: A Test System for Modeling Biomolecular Halogen Bonds". Paper presented in MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition, Sciforum Electronic Conference Series, 2017.
    Published • 10.3390/mol2net-03-05075
Conference poster
  1. Szilagyi, Jennifer; Nunes, Rafael S.; Joana Silva; Celso Alves; Alice I. Martins; René Csuk; Nuno M. Xavier. "Synthesis and biological evaluation of novel guanidino and guanidinopurine-containing nucleosides". Paper presented in CQE Days 2024, 2024.
  2. Szilagyi, Jennifer; Nunes, Rafael S.; Joana Silva; Alice I. Martins; Nuno M. Xavier. "Synthesis of potentially bioactive azido nucleosides". Paper presented in IUPAC World Chemistry Congress (IUPAC Chains 23), 2023.
  3. Szilagyi, Jennifer; Nunes, Rafael S.; Nuno M. Xavier. "Synthesis of potentially anticancer azido/guanidino nucleosides". Paper presented in European carbohydrate Simposim (Eurocarb 21), 2023.
  4. Szilagyi, Jennifer; Nunes, Rafael S.; Nuno M. Xavier. "Synthesis and study of potentially bioactive azido/guanidino nucleosides". Paper presented in International Meeting of the Portuguese Carbohydrate Group (Glupor 14), 2023.
  5. Tânia Moreira; Rita G. Pereira; Nunes, Rafael; Frias, Maria João; Filipe, Sérgio; Jorda, Radek; Nunes, Rafael (D31F-119C-44C5); Xavier, Nuno M.. "Synthesis of Novel Potentially Bioactive D-Glucuronamide-based Nucleosides and (Triazolyl)methyl Amide-linked Pseudodisaccharide Derivatives". Paper presented in 14th International Meeting of the Portuguese Carbohydrate Group - GLUPOR 14, Caparica, Portugal, 2023.
  6. Domingos M. Manuel; Joana Rosa; Nunes, Rafael; Nuno M. Xavier. "Synthesis of Novel D-Glucuronamide-based Nucleoside Analogs Containing 1,2,3-Triazole Units". Paper presented in 14th International Meeting of the Portuguese Carbohydrate Group - GLUPOR 14, Caparica, Portugal, 2023.
  7. Jennifer Szilagyi; Nunes, Rafael; Nuno M. Xavier. "Synthesis of novel 5'-azido/guanidino xylofuranosyl nucleosides". Paper presented in 14th International Meeting of the Portuguese Carbohydrate Group - GLUPOR 14, Caparica, Portugal, 2023.
  8. Nunes, Rafael; Costa, Paulo. J.; Nuno M. Xavier. "In silico studies and synthesis of halogenated sugar mimetics as potential modulators of protein-carbohydrate recognition". Paper presented in 14th International Meeting of the Portuguese Carbohydrate Group - GLUPOR 14, Caparica, Portugal, 2023.
  9. Tânia Moreira; Domingos, Manuel ; Neto, Euclydes; Nunes, Rafael S.; Nuno M. Xavier. "Synthesis of nucleoside analogs based on D-glucuronamide moieties as potential antibacterial agent". Paper presented in 2nd Chem &Biochem Students Meeting, 2022.
  10. Moreira, Tânia; Manuel, Domingos M; Neto, Euclydes P; Nunes, Rafael S.; Frias, Maria João; Filipe, Sérgio; Xavier, Nuno M.. "Synthesis of novel potentially bioactive D-glucuronamide-based nucleoside and nucleotide analogs containing 1,2,3-triazole units". Paper presented in 5th Meeting of the CQUL (5EQCUL) - Forging Bonds, Lisboa, Portugal, 2022.
  11. Nunes, Rafael; Costa, Paulo. J.; Xavier, Nuno M.. "Synthesis of halogen-bonding glycomimetics as potential modulators of protein-carbohydrate recognition events". Paper presented in 30th International Carbohydrate Symposium, virtual event, 2022.
  12. Nunes, Rafael; Costa, Paulo. J.; Xavier, Nuno M.. "Design and synthesis of halogenated glycomimetics targeting carbohydrate-binding proteins". Paper presented in 2nd Chem & Biochem Students Meeting, Lisboa, Portugal, 2022.
  13. Moreira, Tânia; Manuel, Domingos; Neto, Euclydes; Nunes, Rafael; Frias, Maria; Filipe, Sérgio; Xavier, Nuno. "Synthesis of nucleoside analogs based on D-glucoronamide moieties as potential antibacterial agents". Paper presented in 2nd Chem & Biochem Students Meeting, Lisboa, Portugal, 2022.
  14. Nunes, Rafael; Costa, Paulo. J.; Xavier, Nuno M.. "Molecular design of halogenated glycosides as tools to study protein-carbohydrate interactions". Paper presented in CQE Days 2022, Lisboa, Portugal, 2022.
  15. Tânia, Moreira; Domingos, Manuel ; Neto, Euclydes; Nunes, Rafael S.; Nuno M. Xavier. "Synthesis of potentially bioactive 1,2,3-triazole-containing nucleoside and nucleotide analogs based on D-glucuronamide moietie". Paper presented in CQE Days 2022, 2022.
  16. Szilagyi, Jennier; Nunes, Rafael; Xavier, Nuno M.. "Synthesis of potentially bioactive azido/guanidino nucleosides". Paper presented in CQE Days 2022, Lisboa, Portugal, 2022.
  17. Moreira, Tânia; Manuel, Domigos M. ; Pretti, Euclydes; Nunes, Rafael S.; Frias, Maria João; Filipe, Sérgio; Xavier, Nuno M.. "Synthesis of potentially bioactive 1,2,3-triazole-containing nucleoside and nucleotide analogs based on D-glucuronamide moieties". Paper presented in CQE Days 2022, Lisboa, Portugal, 2022.
  18. Xavier, Nuno M.; Moreira, Tânia; Fortuna, Andreia; Nunes, Rafael; Gonçalves-Pereira, Rita; Frias, Maria João; Filipe, Sérgio; Jorda, Radek. "Synthesis of potentially bioactive triazole-containing nucleoside, sugar diphosphate and nucleotide analogs". Paper presented in 14th Nacional Organic Chemistry Meeting & 7th Nacional Therapeutic Chemistry Meeting, Caparica, Portugal, 2022.
  19. Nunes, Rafael de Santana; Vila-Vicosa, Diogo; Costa, Paulo J.. "Halogen bonding in membrane-ligand recognition: Insights from computational biophysics". Paper presented in 20th IUPAB International Congress, 45th SBBf Congress and 50th Annual Meeting of SBBq, virtual event, 2021.
  20. Nunes, Rafael; Vila-Vicosa, Diogo; Costa, Paulo J.. "Molecular modeling studies of halogen bonding in drug-membrane recognition". Paper presented in EJIBCE 2109 – 7o Encontro de Jovens Investigadores de Biologia Computacional Estrutural (7th Meeting of Young Researchers in Structural Computational Biology), Lisboa, Portugal, 2019.
  21. Nunes, Rafael; Vila-Vicosa, Diogo; Costa, Paulo J.. "Estimation of hydration free energies involving halogenated ligands for applications in drug design". Paper presented in EUROPIN Vienna Summer School on Drug Design, Vienna, Austria, 2019.
  22. Vila-Vicosa, Diogo; Nunes, Rafael; Costa, Paulo J.. "Folding of cyclic peptides stabilized by noncovalent interactions". Paper presented in 1st International Conference on Noncovalent Interactions (ICNI2019), Lisboa, Portugal, 2019.
  23. Šivickyte, Ona; Nunes, Rafael; Costa, Paulo J.. "Potential C-X...pi halogen bonds in halogenated sugar mimetics: a DFT study". Paper presented in 1st International Conference on Noncovalent Interactions (ICNI2019), Lisboa, Portugal, 2019.
  24. Nunes, Rafael; Vila-Vicosa, Diogo; Machuqueiro, Miguel; Costa, Paulo J.. "Improved modeling of halogen-protein interactions in biomolecular simulations using a GROMOS force field". Paper presented in Joint 12th EBSA – 10th ICBP-IUPAP Biophysics Congress, Madrid, Spain, 2019.
  25. Vila-Vicosa, Diogo; Nunes, Rafael; Costa, Paulo J.. "Folding of cyclic peptides stabilized by halogen bonds". Paper presented in Joint 12th EBSA – 10th ICBP-IUPAP Biophysics Congress, Madrid, Spain, 2019.
  26. Costa, Paulo J.; Vila-Vicosa, Diogo; Nunes, Rafael. "Tackling halogenated species in biomolecular systems with force field methods: MD sampling and PBSA solvation energies". Paper presented in Joint 12th EBSA – 10th ICBP-IUPAP Biophysics Congress, Madrid, Spain, 2019.
  27. Nunes, Rafael; Xavier, Nuno M.; Costa, Paulo J.. "Theoretical investigation of carbohydrate mimetics as potential halogen-bonding ligands". Paper presented in 4th Meeting of the CQUL (4EQCUL) - Chemistry: Shaping the Future & 2019 Summer School, Lisboa, Portugal, 2019.
  28. Nunes, Rafael; Xavier, Nuno M.; Costa, Paulo J.. "In silico design of halogenated carbohydrate mimetics as potential halogen-bonding ligands". Paper presented in 6o Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE 2018), Porto, Portugal, 2018.
  29. Šivickyte, Ona; Nunes, Rafael; Costa, Paulo J.. "Carbohydrate-aromatic interactions in halogenated sugar mimetics: The role of C-Br...pi bonds". Paper presented in 29th International Carbohydrate Symposium (ICS 2018), Lisboa, Portugal, 2018.
  30. Nunes, Rafael; Costa, Paulo J.. "Estimation of solvation free energies by continuum methods: How to tackle halogenated species?". Paper presented in 11th International Conference on Chemical Structures, Noordwijkerhout, The Netherlands, 2018.
  31. Nunes, Rafael; Costa, Paulo J.. "Tuning ion-pair halogen bonds towards efficient anion receptors in solution". Paper presented in 1o Encontro do Colégio de Química da Universidade de Lisboa (1ECQUL), Lisboa, Portugal, 2017.
  32. Nunes, Rafael; Costa, Paulo J.. "The Key Role of Solvent in Ion-Pair Halogen Bonds: Building Efficient Receptors for Halide Recognition in Solution". Paper presented in XXV Encontro Nacional da Sociedade Portuguesa de Química, Lisboa, Portugal, 2017.
  33. Cachatra, Vasco; Nunes, Rafael; Vila-Vicosa, Diogo; Calhorda, Maria José; Rauter, Amélia P.. "Studies on Wittig olefination towards branched chain sugars". Paper presented in Chem&Biochem Postgraduate Students Meeting 2017, Lisboa, Portugal, 2017.
  34. Dias, Catarina; Pais, João P.; Nunes, Rafael; Pelerito, Ana; DE ALMEIDA, RODRIGO F.M.; Rauter, Amélia P.. "Structural optimization of alkyl deoxy glycosides as innovative antibacterial agents". Paper presented in Chem&Biochem Postgraduate Students Meeting 2017, Lisboa, Portugal, 2017.
  35. Nunes, Rafael; Pais, João; Vila-Vicosa, Diogo; Machuqueiro, Miguel; Rauter, Amélia P.. "Synthesis of new antibiotic glycosides and computational studies on their interaction with model lipid bilayers". Paper presented in CQB Day 2016, Lisboa, Portugal, 2016.
  36. Nunes, Rafael; Vila-Vicosa, Diogo; Rauter, Amélia P.; Machuqueiro, Miguel. "Sugar-based surfactants as antibacterial agents targeting lipid bilayers: Insights from molecular dynamics simulations". Paper presented in 3o Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE 2015), Coimbra, Portugal, 2015.
  37. Nunes, Rafael; Pais, João; Vila-Vicosa, Diogo; Machuqueiro, Miguel; Rauter, Amélia P.. "Novel antibacterial glycosides: synthesis and computational studies on their interaction with model membranes". Paper presented in 11th International Meeting of the Portuguese Carbohydrate Group and 6th Iberian Carbohydrate Meeting, Viseu, Portugal, 2015.
  38. Nunes, Rafael; Pais, João; Vila-Vicosa, Diogo; Machuqueiro, Miguel; Rauter, Amélia P.. "New sugar-based surfactants targetting lipid bilayers: Synthesis and molecular dynamics study". Paper presented in CQB Day 2015, Lisboa, Portugal, 2015.
  39. Nunes, Rafael; Pais, João; Vila-Vicosa, Diogo; Machuqueiro, Miguel; Rauter, Amélia P.. "Synthesis and molecular dynamics study of new membrane-active antibacterial glycosides". Paper presented in 19th European Symposium on Organic Chemistry, Lisboa, Portugal, 2015.
  40. Nunes, Rafael; Vila-Vicosa, Diogo; Rauter, Amélia P.; Machuqueiro, Miguel. "New insights into the interaction of sugar-based surfactants with lipid bilayers from molecular dynamics simulations". Paper presented in 2o Encontro de Jovens Investigadores de Biologia Computacional Estrutural, Lisboa, Portugal, 2014.
  41. Nunes, Rafael; Pais, João P.; Dias, Catarina. "Towards the efficient production of antibiotics from sugars: Synthesis of new alkyl glycosides and their antimicrobial activity". Paper presented in 1st EFMC Young Medicinal Chemistry Symposium, Lisboa, Portugal, 2014.
  42. Serra, Patrícia; Almeida, Andreia; Cachatra, Vasco; Dias, Catarina; Nunes, Rafael; Pais, João; Martins, Alice; et al. "Exploiting alkyl deoxy glycosides as antimicrobial agents: Synthesis, bioactivity and surface properties". Paper presented in CQB Day 2014, Lisboa, Portugal, 2014.
  43. Nunes, Rafael; Vila-Vicosa, Diogo; Rauter, Amélia P.; Machuqueiro, Miguel. "A molecular view on the interaction of antibiotic deoxy glycosides with model phospholipid bilayers". Paper presented in MultyGlycoNano 2014 - COST Action CM1102 Meeting, Siena, Italy, 2014.
  44. Nunes, Rafael; Vila-Vicosa, Diogo; Rauter, Amélia P.; Machuqueiro, Miguel. "Interaction of antibacterial sugar-based surfactants with model lipid membranes: Insights from molecular dynamics simulations". Paper presented in Dynamic nano- and glyco-sciences, COST Action CM1102 spring training school, University of Namur, Belgium, 2014.
  45. Nunes, Rafael; Vila-Viçosa, Diogo; Rauter, Amélia P.; Machuqueiro, Miguel. "Molecular dynamics simulations of antimicrobial deoxy glycoside-based surfactants: Micellization and structural insights". Paper presented in 1o Encontro de Jovens Investigadores de Biologia Computacional Estrutural, Porto, Portugal, 2013.
  46. Nunes, Rafael S. (D31F-119C-44C5); Lourenço, Eva C.; Ventura, M. Rita. "Synthesis of glycoside derived compatible solutes for protein stabilization". Paper presented in Ciência 2010 - Encontro com a Ciência e Tecnologia em Portugal, Lisboa, Portugal, 2010.
Journal article
  1. Tânia Moreira; Domingos M. Manuel; Joana Rosa; Rafael Santana Nunes; Veronika Vojácková; Radek Jorda; M. Conceição Oliveira; Nuno M. Xavier. "Synthesis and Antiproliferative Evaluation of d-Glucuronamide-Based Nucleosides and (Triazolyl)methyl Amide-Linked Pseudodisaccharide Nucleosides**". ChemMedChem (2024): https://doi.org/10.1002/cmdc.202300608.
    10.1002/cmdc.202300608
  2. Nunes, Rafael Santana (D31F-119C-44C5); Vila-Viçosa, Diogo; Costa, Paulo J.. "Halogen Bonding: An Underestimated Player in Membrane–Ligand Interactions". Journal of the American Chemical Society 143 11 (2021): 4253-4267. http://dx.doi.org/10.1021/jacs.0c12470.
    Published • 10.1021/jacs.0c12470
  3. Ana M. de Matos; M. Teresa Blázquez-Sánchez; Andreia Bento-Oliveira; Rodrigo F. M. de Almeida; Rafael Nunes; Pedro E. M. Lopes; Miguel Machuqueiro; et al. "Glucosylpolyphenols as Inhibitors of Aß-Induced Fyn Kinase Activation and Tau Phosphorylation: Synthesis, Membrane Permeability, and Exploratory Target Assessment within the Scope of Type 2 Diabetes and Alzheimer’s Disease". Journal of Medicinal Chemistry 63 20 (2020): 11663-11690. https://doi.org/10.1021/acs.jmedchem.0c00841.
    Published • 10.1021/acs.jmedchem.0c00841
  4. Nunes, Rafael; Vila-Viçosa, Diogo; Costa, Paulo J.. "Tackling Halogenated Species with PBSA: Effect of Emulating the s-Hole". Journal of Chemical Theory and Computation 15 7 (2019): 4241-4251. http://dx.doi.org/10.1021/acs.jctc.9b00106.
    Published • 10.1021/acs.jctc.9b00106
  5. Costa, Paulo J.; Nunes, Rafael; Vila-Viçosa, Diogo. "Halogen bonding in halocarbon-protein complexes and computational tools for rational drug design". Expert Opinion on Drug Discovery 14 8 (2019): 805-820. http://dx.doi.org/10.1080/17460441.2019.1619692.
    Published • 10.1080/17460441.2019.1619692
  6. Dias, Catarina; Pais, João P.; Nunes, Rafael; Blázquez-Sánchez, Maria-Teresa; Marquês, Joaquim T.; Almeida, Andreia F.; Serra, Patrícia; et al. "Sugar-based bactericides targeting phosphatidylethanolamine-enriched membranes". Nature Communications 9 1 (2018): https://doi.org/10.1038/s41467-018-06488-4.
    Open access • Published • 10.1038/s41467-018-06488-4
  7. Nunes, Rafael; Diogo Vila-Viçosa; Miguel Machuqueiro; Paulo J. Costa. "Biomolecular Simulations of Halogen Bonds with a GROMOS Force Field". Journal of Chemical Theory and Computation 14 10 (2018): 5383-5392. https://doi.org/10.1021/acs.jctc.8b00278.
    Published • 10.1021/acs.jctc.8b00278
  8. Nunes, Rafael (D31F-119C-44C5); Costa, Paulo J.. "Ion-pair halogen bonds in 2-halo-functionalized imidazolium chloride receptors: Substituent and solvent effects". Chemistry - An Asian Journal 12 5 (2017): 586-594. http://www.scopus.com/inward/record.url?eid=2-s2.0-85012146169&partnerID=MN8TOARS.
    Published • 10.1002/asia.201601690
  9. Cachatra, V.; Almeida, A.; Sardinha, J.; Lucas, S.D.; Gomes, A.; Vaz, P.D.; Florêncio, M.H.; et al. "Wittig Reaction: Domino Olefination and Stereoselectivity DFT Study. Synthesis of the Miharamycins' Bicyclic Sugar Moiety". Organic Letters 17 22 (2015): 5622-5625. http://www.scopus.com/inward/record.url?eid=2-s2.0-84947996973&partnerID=MN8TOARS.
    Published • 10.1021/acs.orglett.5b02849
  10. Monteiro, A.S.; Almeida, J.; Cabral, G.; Severino, P.; Videira, P.A.; Sousa, A.; Nunes, Rafael; et al. "Synthesis and evaluation of N-acylamino acids derivatives of triazenes. Activation by tyrosinase in human melanoma cell lines". European Journal of Medicinal Chemistry 70 (2013): 1-9. http://www.scopus.com/inward/record.url?eid=2-s2.0-84885368654&partnerID=MN8TOARS.
    Published • 10.1016/j.ejmech.2013.09.040
Thesis / Dissertation
  1. Nunes, Rafael de Santana. "Synthesis of new antibiotic glycosides and computational studies on their interaction with model lipid bilayers". Master, Universidade de Lisboa Faculdade de Ciências, 2015. http://hdl.handle.net/10451/20827.

Other

Other output
  1. Synthesis and Antiproliferative Evaluation of Novel D-Glucuronamide-based Nucleosides and (Triazolyl)methyl Amide-linked Pseudodisaccharide Nucleosides. ChemRxiv (Preprint). 2023. Nunes, Rafael. https://publons.com/wos-op/publon/62845030/.
    10.26434/CHEMRXIV-2023-RH8CK
  2. Halogen Bonding: An Underestimated Player in Membrane-Ligand Interactions. ChemRxiv (preprint). 2020. Nunes, Rafael Santana (D31F-119C-44C5); Vila-Vicosa, Diogo; Costa, Paulo J.. https://doi.org/10.26434/chemrxiv.11894547.
    10.26434/chemrxiv.11894547.v1
  3. Tackling Halogenated Species with PBSA: Effect of Emulating the s-Hole. ChemRxiv (preprint). 2019. Nunes, Rafael; Vila-Vicosa, Diogo; Costa, Paulo J.. https://doi.org/10.26434/chemrxiv.7660550.
    10.26434/chemrxiv.7660550
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2022/04/20 Design and synthesis of halogenated glycomimetics targeting carbohydrate-binding proteins [Flash presentation] 14th Nacional Organic Chemistry Meeting & 7th Nacional Therapeutic Chemistry Meeting
(Caparica, Portugal)
2021/09/01 Biomolecular simulations of halogen bonding in membrane-ligand recognition events 2021 IUPAB-SBBq-SBBf Young Scientist Program Webinar series (virtual event)
SBBq-Brazilian Society for Biochemistry and Molecular Biology
2020/11/03 Prediction of hydration free energies involving halogenated ligands for applications in drug discovery 4th International Symposium on Halogen Bonding (ISXB-4 virtual)
Department of Chemical and Polymer Science at Stellenbosch University, South Africa
2019/09/05 Molecular dynamics simulations of halogen bond-mediated biomolecular recognition events 1st International Conference on Noncovalent Interactions (ICNI2019)
(Lisboa, Portugal)
2019/06/28 Treatment and application of halogen bonding in biological systems: MD sampling and PBSA hydration free energies 1st BioISI PhD Symposium
Universidade de Lisboa Faculdade de Ciências (Lisboa, Portugal)
2018/07/14 In silico design of halogenated carbohydrate mimetics as potential halogen-bonding ligands [Flash presentation] ICS Iberian Day – satellite event of the 29th International Carbohydrate Symposium (ICS 2018)
(Lisboa, Portugal)
2018/06/13 Halogen bonds in (bio)molecular systems: A deeper look into force field methods [Invited oral communication] 3rd International Symposium on Halogen Bonding
(Greenville, United States)
2017/12/22 T4 lysozyme/halobenzene: A test system for modeling biomolecular halogen bonds EJIBCE 2017 - 5º Encontro de Jovens Investigadores de Biologia Computacional Estrutural (5th Meeting of Young Researchers in Structural Computational Biology)
(Coimbra, Portugal)
2017/12/05 Molecular dynamics simulations of biomolecular halogen bonds: application to phage T4 lysozyme/halobenzene systems [Flash presentation] UL Chemistry PhD Meeting – 2nd Meeting of the CQUL (College of Chemistry of ULisboa)
(Lisboa, Portugal)
2016/07/21 An efficient synthetic route to byciclic sugars: Tuning regio- and stereoselectivity on Wittig olefination by solvent and steric effects XXVIII International Carbohydrate Symposium
(New Orleans, United States)

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2019/12/20 - 2019/12/20 EJIBCE 2109 – 7º Encontro de Jovens Investigadores de Biologia Computacional Estrutural (7th Meeting of Young Researchers in Structural Computational Biology) (2019/12/20 - 2019/12/20)
Meeting (Other)
 Universidade de Lisboa Faculdade de Ciências, Portugal
2019/06/28 - 2019/06/28 1st BioISI PhD Symposium (post-graduate meeting of the BioISI research unit), Auditório do Caleidoscópio da Universidade de Lisboa (2019/06/28 - 2019/06/28)
Meeting (Co-organisor)
 Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2018/07/14 - 2018/07/19 29th International Carbohydrate Symposium (ICS 2018) and satellite events ICS Iberian Day, ICS Young Researcher Workshop and Glycoinformatics Masteclass (2018/07/14 - 2018/07/19)
Symposium (Member of the Organising Committee)
 Universidade de Lisboa Faculdade de Ciências, Portugal
2015/07/12 - 2015/07/16 19th European Symposium on Organic Chemistry (2015/07/12 - 2015/07/16)
Symposium (Member of the Organising Committee)
 Universidade de Lisboa Faculdade de Ciências, Portugal
2014/12/18 - 2014/12/19 2º Encontro de Jovens Investigadores de Biologia Computacional Estrutural (2nd Meeting of Young Researchers in Structural Computational Biology) (2014/12/18 - 2014/12/19)
Meeting (Member of the Organising Committee)
 Universidade de Lisboa Faculdade de Ciências, Portugal
2014/07/08 - 2014/07/11 Protein Electrostatics - Satellite Meeting of the 18th European Bioenergetics Conference (EBEC 2014) (2014/07/08 - 2014/07/11)
Conference (Member of the Organising Committee)
 Universidade de Lisboa Faculdade de Ciências, Portugal
2012/07/18 - 2012/07/20 6th Spanish-Portuguese-Japanese Organic Chemistry Symposium (2012/07/18 - 2012/07/20)
Symposium (Member of the Organising Committee)
 Universidade de Lisboa Faculdade de Ciências, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2024/05/26 - 2024/05/29 International School of Process Chemistry - Advanced Edition
Other
Università degli Studi di Milano Dipartimento di Chimica, Italy
2024/03/18 - 2024/03/20 Process Scale-up, Validation & Technology Transfer
Other
Symmetric Training, Slovakia
2023/09/04 - 2023/09/05 Grignard Chemistry Short Course
Other
Scientific Update Ltd, United Kingdom
2019/09/15 - 2019/09/20 EUROPIN Vienna Summer School on Drug Design, organised by the group of Prof. Gerhard Ecker at the Department of Pharmaceutical Chemistry, University of Vienna
Other
 EUROPIN Summer School on Drug Design
Universität Wien, Austria
2014/04/07 - 2014/04/09 Spring training school organized by Prof. Stéphane Vincent in the framework of COST Action CM1102 MultiGlycoNano (Multivalent Glycosystems for Nanoscience)
Other
 Dynamic nano- and glyco-sciences
Université de Namur, Belgium
2011/02/23 - 2011/02/25 Specialization course lectured by Prof. Jesús Jiménez Barbero, Dr. Ana Ardá and Dr. Filipa Marcelo (CIB-CSIC Madrid, Spain)
Other
 Structure and conformation of carbohydrate molecules: NMR and molecular recognition
Universidade de Lisboa Faculdade de Ciências, Portugal

Association member

Society Organization name Role
2012 - Current Sociedade Portuguesa de Química (Portuguese Society of Chemistry) Member
Distinctions

Award

2020 Best oral presentation award at the 4th International Symposium on Halogen Bonding (ISXB-4, virtual conference)
CrystEngComm, United Kingdom
2017 Best flash communication award at UL Chemistry PhD Meeting – 2nd Meeting of the CQUL (College of Chemistry of ULisboa)
Sociedade Portuguesa de Química, Portugal

Other distinction

2020 IUCr bursary to attend the 4th International Symposium on Halogen Bonding
International Union of Crystallography, United Kingdom
2020 IUPAB-SBBq bursary to attend the Joint 20th IUPAB - 45th SBBq - 50th SBBf (IUPAB 2021) Congress and Young Scientists Program
International Union for Pure and Applied Biophysics, Singapore
2019 EBSA bursary to attend the Joint 12th EBSA – 10th ICBP-IUPAP Biophysics Congress
European Biophysical Societies' Association, United Kingdom
2018 ICCS bursary to attend the 11th International Conference on Chemical Structures
11th International Conference on Chemical Structures, Netherlands