My past research focused on the understanding of protein structure, stability, interactions and functions with a focus on biomedically relevant proteins such as β2 microglobulin and influenza NS1 using different types of computational methodologies. Indeed, in my PhD, I characterized the early phase of the aggregation mechanism of protein β2 microglobulin in amyloid disease using molecular simulations (protein-protein docking and molecular dynamics). In particular, I developed a Monte Carlo ensemble docking (MC-ED) method with a scoring function based on shape, hydrophobic and electrostatic complementarity, which is actually an upgraded version of the MC-ED method developed by Faísca and co-workers that optimized dimer interfaces exclusively for shape complementarity, and adapted it to the prediction of the structure of tetramers. This allowed me to predict and characterize the structures and association interfaces of early oligomers (i.e. dimers and tetramers) on the β2 microglobulin aggregation pathway and key molecular events driving this process. Later, in my first post-doc position at the Protein Biophysical Chemistry Group of the Chemistry Department, University of Coimbra, I characterized the structure, stability and interactions with several host proteins of influenza A NS1 protein and validated NS1 as a biological target in influenza antiviral therapy using molecular dynamics and druggability predictions. Currently, I'm working towards the optimization of a new technology to stabilize proteins for biotechnological and biomedical applications using Monte Carlo simulations in the framework of the European Innovation Council (EIC) INCYPROnext project at the Janusz Bujnicki's Laboratory of Bioinformatics and Protein Engineering at the IIMCB, Warsaw.
Rui J. Loureiro, Andreia Cunha, Nícia Rosário-Ferreira, Rui M. M. Brito, "Non-structural protein 1 (NS1) as a drug target for seasonal and pandemic Influenza", Biophysics Festival - 2nd Meeting of Young Biophysicists, Aveiro, Portugal, June 3, 2022.
Rui J. Loureiro, Andreia Cunha, Rui M. M. Brito, "Non-structural protein 1 (NS1) interaction with TRIM25 as a target for influenza antiviral therapy", EJIBCE 2021, Coimbra, Portugal, December 20, 2021.
Rui J. Loureiro, Andreia Cunha, Rui M. M. Brito, "Non-structural protein 1 (NS1) interaction with PI3K as a target for influenza antiviral therapy", 7th International Iberian Biophysics Congress, Coimbra, Portugal, June 14-16, 2021.
Rui J. Loureiro, Diogo Vila-Viçosa, Miguel Machuqueiro, Eugene I. Shakhnovich, Patrícia F.N. Faísca, “The early phase of the β2m aggregation mechanism: an integrative computational analysis framed on the D76N mutant and ΔN6 variant”, 1st BioSIM Cycle of Conferences, Porto, Portugal, February 17, 2020.
Rui J. Loureiro, Diogo Vila-Viçosa, Miguel Machuqueiro, Eugene I. Shakhnovich, Patrícia F.N. Faísca, “The early phase of the β2m aggregation mechanism: an integrative computational analysis based on the D76N mutant and ΔN6 variant”, EJIBCE 2019, Lisboa, Portugal, December 20, 2019.
Rui J. Loureiro, Diogo Vila-Viçosa, Miguel Machuqueiro, Eugene I. Shakhnovich, Patrícia F.N. Faísca, “The dimerization phase of the β2m aggregation mechanism: An integrative computational analysis based on the D76N mutant and ΔN6 variant”, Workshop on Integrative Approaches to Protein Folding & Aggregation, Lisboa, Portugal, June 11-12, 2019.
Rui J. Loureiro, Diogo Vila-Viçosa, Miguel Machuqueiro, Eugene I. Shakhnovich, Patrícia F.N. Faísca, “The importance of unstructured termini in the aggregation cascade of beta-2-microglobulin: Insights from molecular simulations of D76N mutant”, Biophysics Party, Oeiras, Portugal, July 6, 2018.
Rui J. Loureiro, Eugene I. Shakhnovich, Patrícia F.N. Faísca, “A novel docking method for protein-protein interactions offers new insights into the aggregation mechanism of β2m in amyloid disease”, BioSys Retreat 2017, Beja, Portugal, October 6-7, 2017.
Rui J. Loureiro, Diogo Vila-Viçosa, Miguel Machuqueiro, Eugene I. Shakhnovich, Patrícia F.N. Faísca, "The importance of unstructured termini in the aggregation cascade of beta-2-microglobulin: Insights from molecular simulations of D76N mutant", Biomolecules and Nanostructures 6, Podlesice, Poland, May 10-14, 2017.
Rui J. Loureiro, Diogo Vila-Viçosa, Miguel Machuqueiro, Patrícia F.N. Faísca, "The importance of unstructured termini in the aggregation cascade of beta-2-microglobulin: Insights from molecular simulations of D76N mutant", Chemistry and Biochemistry Postgraduate Students Meeting, Lisboa, Portugal, February 9, 2017.
Rui J. Loureiro, Patrícia F. N. Faísca, Diogo Vila-Viçosa, Miguel Machuqueiro, "The importance of unstructured termini in the aggregation cascade of beta-2-microglobulin: Insights from molecular simulations of D76N mutant", EJIBCE 2016, Oeiras, Portugal, December 21, 2016.
Rui J. Loureiro, Diogo Vila-Viçosa, Miguel Machuqueiro, Patrícia F.N. Faísca, "Novel insights into beta-2-microglobulin amyloidogenesis from molecular simulations: the importance of unstructured termini in the aggregation cascade", Conférence Jacques Monod "Protein misfolding in disease - Toxic aggregation-prone proteins in aging and age-related diseases: from structure to pathology and spreading", Roscoff, France, September 12-16, 2016.
Rui J. Loureiro, Diogo Vila-Viçosa, Miguel Machuqueiro, Patrícia F.N. Faísca, "The importance of unstructured termini in the aggregation cascade of beta-2-microglobulin: insights from molecular simulations of D76N mutant", EMBO Practical Course on Integrative modelling of biomolecular interactions, Barcelona, Spain, July 4-9, 2016.
Rui J. Loureiro, Patrícia F.N. Faísca, “Molecular events triggering the aggregation cascade in ß2-microglobulin amyloidosis”, EJIBCE 2015, Instituto Pedro Nunes, Coimbra, Portugal, December 18, 2015.
Rui J. Loureiro, Patrícia F.N. Faísca, Eugene Shakhnovich, “Disclosing the aggregation mechanism of β2-microglobulin in amyloid disease”, 1st BioISI Annual Meeting, Lisboa, Portugal, December 11, 2015.
Participation in schools, conferences and meetings
1st BioSIM Cycle of Conferences, BioSIM, Centro de Investigação Médica, Faculdade de Medicina da Universidade do Porto, Porto, Portugal, February 17, 2020.
