Molecular Biotechnology and Protein Engineering

Isaura Simões

PhD, Group Leader

The Molecular Biotechnology and Protein Engineering Group general objectives are to contribute to a better understanding of mechanisms of disease and pathogenicity in the context of infection, facilitate the identification of new factors/molecular pathways that may constitute pathogen- or host-directed targets for therapeutic intervention, and contribute for the development of new biological drugs as well as for the rational design of drugs for new enzyme targets. By the recent integration of two outstanding young investigators through the prestigious FCT-Investigator Programme, the group is composed by a highly multi- and interdisciplinary team with solid expertise in the areas of enzymology and protein biochemistry; structural biology; computational biochemistry and enzyme design; as well as antibody engineering and production.

With a common focus on research and development of alternative strategies to combat infectious diseases, our research is organized in the following topics:

  1. Understanding proteolysis/proteostasis in the context of infection, both on the relevance of these mechanisms for bacterial pathogenesis and for modulating host-pathogen interactions;
  2. Understanding the molecular basis for species-specific patterns of spotted fever group Rickettsia cellular tropism and their relevance for rickettsial pathogenesis;
  3. Rational structure-based design, engineering and production of recombinant immunogens (e.g. surface-exposed bacterial virulence factors), optimizing its potential for the production and selection of highly specific and functional antibodies and antibody fragments, for immunoresearch and immunotherapies;
  4. Rational design of new enzymes and drugs using our own developed protocols based on state-of-the-art computational biochemistry methods.

Rational design of new enzymes and drugs using our own developed protocols based on state-of-the-art computational biochemistry methods.

Group Members

Group Members

Group members are: Isaura Simões (PhD, Group Leader), Alexandra Carvalho (PhD), Andreia Barro, André Simões, Bárbara Teixeira, Carlos Faro (PhD), Euclides Pires (PhD), Paula Veríssimo (PhD), Pedro Curto (PhD), Rafaela Seabra, Ricardo Vieira-Pires (PhD), Tiago Ôchoa-Pires.

Selected Publications

Barata SL, Cunha PR, Vieira-Pires RS. I Rest My Case! The Possibilities and Limitations of Blockchain-Based IP Protection. In: Siarheyeva A., Barry C., Lang M., Linger H. SC, ed. Springer, Cham; 2020:57-73. doi:10.1007/978-3-030-49644-9_4.

Ôchoa-Pires T, Rosa M, Laranjeira J, Francisco R, Silva D, Vieira-Pires RS. Antibody discovery using Japanese quail: towards new anti-infective strategies. Ecronicon Microbiol. 2020. https://www.ecronicon.com/ecmi/pdf/ECMI-16-00936.pdf.

Barata S, Cunha PR, Vieira-Pires RS. I Rest My Case! The Possibilities and Limitations of Blockchain-Based IP Protection. In: Information Systems Development (ISD). ; 2019:http://aisel.aisnet.org/isd2014/proceedings2019.

Thirumalai D, Visaga Ambi S, Vieira-Pires RS, Xiaoying Z, Sekaran S, Krishnan U. Chicken egg yolk antibody (IgY) as diagnostics and therapeutics in parasitic infections – A review. Int J Biol Macromol. 2019;136:755-763. doi:10.1016/j.ijbiomac.2019.06.118.

Harley C, Vieira-Pires RS. Antibody fragment technology and avian IgY antibodies: a powerful combination. Drug Target Rev. 2016;3:4-8. https://www.drugtargetreview.com/article/33086/antibody-fragment-technology-and-avian-igy-antibodies-a-powerful-combination/.

Szollosi A, Vieira-Pires RS, Teixeira-Duarte CM, Rocha R, Morais-Cabral JH. Dissecting the Molecular Mechanism of Nucleotide-Dependent Activation of the KtrAB K+ Transporter. Dutzler R, ed. PLOS Biol. 2016;14(1):e1002356. doi:10.1371/journal.pbio.1002356.

Vieira-Pires RS, Szollosi A, Morais-Cabral JH. The structure of the KtrAB potassium transporter. Nature. 2013;496(7445):323-328. doi:10.1038/nature12055.

Selected Projects

BYDRUG: Immunotargeting efflux systems for therapeutic modulation of multidrug resistant bacteria. FCT - Fundação para a Ciência e Tecnologia (2018-2021). PI: Isaura Simões.

Hijack the host or get killed: delineating Rickettsia survival strategies for development of targeted therapeutic strategies. FCT - Fundação para a Ciência e Tecnologia (2018-2021). PI: Isaura Simões

POLYREP: An intriguing mycobacterial polysaccharide: recycling, replication and beyond. FCT - Fundação para a Ciência e Tecnologia (2018-2021). PI: Isaura Simões.

Rational design of a thermostable esterase for the production of high-value bioplastics for biomedical applications (FCT/MIT Portugal). (2018-1019). PI: Alexandra T. P. Carvalho.

The retropepsin-like enzyme RC1339/APRick from Rickettsiae as a potential therapeutic target for rickettsial disease. 1R21-AI111086 (NIH) (2015-2017). PI: Juan Martinez.

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