André Pina
Fullstack Developer @ LabOrders • Biochemist • PhD in Biomedicine
Porto e Região
493 seguidores
494 conexões
Sobre
𝐋𝐢𝐬𝐭𝐞𝐧 𝐮𝐩, 𝐰𝐨𝐫𝐥𝐝! Here's the deal: I'm a biochemist turned into a coding warrior.
I spent four strenuous years doing a PhD in Computational Biochemistry, where I made science my playground and had a blast experimenting with some mind-bending techniques like Molecular Dynamics simulations, Quantum Mechanics/Molecular Mechanics calculations, and HPC systems. I even became a Linux system pro and a Vim text editor master. But, you know what? That wasn't enough for me. I wanted more. So, I said goodbye to the lab and hello to <Academia de Código_>'s 14-week bootcamp where I'm mastering my programming skills like a boss.
Science was my first love, but coding stole my heart. Watch out, tech world, here I come!
If you are looking for a partner in crime, look no further - 𝐚𝐝𝐝 𝐦𝐞 𝐚𝐧𝐝 𝐥𝐞𝐭'𝐬 𝐦𝐚𝐤𝐞 𝐭𝐡𝐢𝐧𝐠𝐬 𝐡𝐚𝐩𝐩𝐞𝐧.
Experiência
Formação acadêmica
-
<Academia de Código_>
-
-
A 14-Week Intensive && Immersive Full Stack Programming Bootcamp
// Programming in Java
Introduction to Computer Science and Programming
Version Control Systems
Java Programming Language
Object-Oriented Programming
// Advanced Concepts and Tools
Documentation and Code Conventions
Network Programming
Concurrent Programming
Software Engineering
Build Systems
Testing
Debugging
// Databases, Frameworks and Web Development
Relational Database…A 14-Week Intensive && Immersive Full Stack Programming Bootcamp
// Programming in Java
Introduction to Computer Science and Programming
Version Control Systems
Java Programming Language
Object-Oriented Programming
// Advanced Concepts and Tools
Documentation and Code Conventions
Network Programming
Concurrent Programming
Software Engineering
Build Systems
Testing
Debugging
// Databases, Frameworks and Web Development
Relational Database Management Systems
Java Database Connectivity
Java Persistence
Spring Framework
Java Web Programming
// JavaScript
JS Fundamentals
Frontend Web Development
jQuery Library -
-
Universidade do Porto
Master's degree Biochemistry 18
-
Final grade: 18/20 corresponding to grade B on the European grading scale
-
Stockholms universitet
Erasmus Student Biochemical Toxicology
-
Erasmus Student at the Department of Biochemistry and Biophysics during the second semester of the third year of the Biochemistry Bachelor's degree.
Completed the course of "Biochemical Toxicology" (15 ECTS) with a final grade of A.
Performed a traineeship at the Department of Neurochemistry under the supervision of Bengt Mannervik. Final grade: 19/20 -
Instituto CRIAP
Intensive Course in Legal Medicine Legal Medicine
-
Lectured by Professor José Pinto da Costa, MD
Recognized by the Portuguese Association of Criminology
Duration: 16 hours -
Universidade do Porto
Bachelor's degree Biochemistry 15
-
Final grade: 15/20 corresponding to grade C on the European grading scale
-
Escola Secundária Felismina Alcântara
High School Diploma Science and Technology
-
Licenças e certificados
Publicações
-
[Journal Article] Non-B DNA conformations analysis through molecular dynamics simulations
Biochimica et Biophysica Acta - General Subjects
## Background
Non-B DNA conformations are molecular structures that do not follow the canonical DNA double helix. Mutagenetic instability in nuclear and mitochondrial DNA (mtDNA) genomes has been associated with simple non-B DNA conformations, as hairpins or more complex structures, as G-quadruplexes. One of these structures is Structure A, a cloverleaf-like non-B conformation predicted for a 93-nt (nucleotide) stretch of the mtDNA control region 5′-peripheral domain. Structure A is embedded…## Background
Non-B DNA conformations are molecular structures that do not follow the canonical DNA double helix. Mutagenetic instability in nuclear and mitochondrial DNA (mtDNA) genomes has been associated with simple non-B DNA conformations, as hairpins or more complex structures, as G-quadruplexes. One of these structures is Structure A, a cloverleaf-like non-B conformation predicted for a 93-nt (nucleotide) stretch of the mtDNA control region 5′-peripheral domain. Structure A is embedded in a hot spot for the 3′ end of human mtDNA deletions revealing its importance in influencing the mutational instability of the mtDNA genome.
## Methods
To better characterize Structure A, we predicted its 3D conformation using state-of-art methods and algorithms. The methodologic workflow consisted in the prediction of non-B conformations using molecular dynamics simulations. The conservation scores of alignments of the Structure A region in humans, primates, and mammals, was also calculated.
## Results
Our results show that these computational methods are able to measure the stability of non-B conformations by using the level of base pairing during molecular dynamics. Structure A showed high stability and low flexibility correlated with high conservation scores in mammalian, more specifically in primate lineages.
##Conclusions
We showed that 3D non-B conformations can be predicted and characterized by our methodology. This allowed the in-depth analysis of the structure A, and the main results showed the structure remains stable during the simulations.
## General significance
The fine-scale atomic molecular determination of this type of non-B conformation opens the way to perform computational molecular studies that can show their involvement in mtDNA cellular mechanisms.Outros autoresVer publicação -
[Journal Article] Identification of novel aptamers targeting cathepsin B-overexpressing prostate cancer cells
Molecular Systems Design and Engineering
Increased levels of cathepsin B (CatB), a cysteine protease, have been associated with different types of tumors, including prostate cancer. Hence, the identification of novel targeting ligands homing CatB may be a promising approach for the development of CatB-targeted therapies. In this work, a methodology called systematic evolution of ligands by EXponential enrichment (SELEX) was used to generate and isolate new aptamers targeting CatB. After 8 rounds of selection, the pool was sequenced…
Increased levels of cathepsin B (CatB), a cysteine protease, have been associated with different types of tumors, including prostate cancer. Hence, the identification of novel targeting ligands homing CatB may be a promising approach for the development of CatB-targeted therapies. In this work, a methodology called systematic evolution of ligands by EXponential enrichment (SELEX) was used to generate and isolate new aptamers targeting CatB. After 8 rounds of selection, the pool was sequenced, and the 10 most prevalent sequences, along with their corresponding reverse complementary sequences, were further analyzed. In order to assess the binding affinity of the aptamers towards the CatB, bioinformatics tools were used. After generating the 3D structures for each aptamer, the HADDOCK software was used for the docking studies between them and CatB. Molecular dynamics simulations and free binding energy calculations by molecular mechanics-generalized born surface area (MM-GBSA) allowed selection of a new aptamer with potential to target CatB. Cell binding assays against the PC-3 prostate cancer cell line confirmed the in silico predictions, further validating the newly discovered aptamer as a promising targeting ligand for CatB-overexpressing cancer cells.
Outros autoresVer publicação -
[Journal Article] The catalytic mechanism of Pdx2 glutamine driven by a Cys‐His‐Glu triad: a computational study
ChemBioChem
The catalytic mechanism of Pdx2 was herein studied with atomic detail employing the computational ONIOM hybrid QM/MM methodology. Pdx2 employs a Cys-His-Glu catalytic triad to deaminate glutamine to glutamate and ammonia–the source of the nitrogen of pyridoxal 5’-phosphate(PLP). This enzyme is, therefore, a rate-limiting step in the PLP biosynthetic pathway of Malaria and Tuberculosis pathogens. For this reason,Pdx2 is considered a novel and promising drug target to treat these diseases. The…
The catalytic mechanism of Pdx2 was herein studied with atomic detail employing the computational ONIOM hybrid QM/MM methodology. Pdx2 employs a Cys-His-Glu catalytic triad to deaminate glutamine to glutamate and ammonia–the source of the nitrogen of pyridoxal 5’-phosphate(PLP). This enzyme is, therefore, a rate-limiting step in the PLP biosynthetic pathway of Malaria and Tuberculosis pathogens. For this reason,Pdx2 is considered a novel and promising drug target to treat these diseases. The results herein obtained show that the catalytic mechanism of Pdx2 occurs in six steps that can be divided into four stages: (i) activation of Cys87, (ii) deamination of glutamine with the formation of the glutamyl-thioester intermediate, (iii) hydrolysis of the formed intermediate, and (iv) enzymatic turnover. The kinetic data available in the literature(19.1–19.5 kcal mol-1) agrees very well with the calculated free energy barrier of the hydrolytic step(18.2 kcal.mol-1), which is the rate-limiting step of the catalytic process when substrate is readily available in the active site. This catalytic mechanism differs from other known amidases in three main points: i)it requires the activation of the nucleophile Cys87 to a thiolate; ii)the hydrolysis occurs in a single step and therefore does not require the formation of a second tetrahedral reaction intermediate, as it is proposed, and iii)Glu198 does not have a direct role in the catalytic process.
Outros autoresVer publicação -
[Conference Poster] Pyridoxine/pyridoxamine 5'-phosphate oxidase: a computational study
7º Encontro de Jovens Investigadores de Biologica Computacional Estrutural
FCUL, Lisbon, Portugal
André F. Pina, Sérgio F. Sousa, Nuno M. F. S. A. Cerqueira -
[Conference Poster] Application of molecular dynamics simulations in the study of the PLP synthase macrocomplex
BImBS 2019 – BioInformatics meets BioSimulations in protein and DNA studies: from theory to practice
October 5-12
Università della Svizzera italiana, Lugano, Switzerland
André F. Pina, Sérgio F. Sousa, Nuno M. F. S. A. Cerqueira
-
[Journal Article] PLP-dependent Enzymes as Important Biocatalysts for the Pharmaceutical and Chemical Industries
Catalysis Science & Technology
Enzymes catalyze a plethora of chemical reactions in nature. These biocatalysts offer a variety of benefits that no other synthetic catalyst can offer: high catalytic power, regio- and stereo-selectivity, ability to work at mild conditions, and to react in environmentally friendly manufacturing processes. However, enzymes are not normally optimally suited for industrial applications. It is important to improve their properties to favor a more efficient application of enzymes in an industrial…
Enzymes catalyze a plethora of chemical reactions in nature. These biocatalysts offer a variety of benefits that no other synthetic catalyst can offer: high catalytic power, regio- and stereo-selectivity, ability to work at mild conditions, and to react in environmentally friendly manufacturing processes. However, enzymes are not normally optimally suited for industrial applications. It is important to improve their properties to favor a more efficient application of enzymes in an industrial setting while also expanding the range of potential chemical reactions that they can catalyze. Problems like the scarce nature of oil reserves, together with increasing concerns on man-made environmental damage, have led to a boost in the need for the development and optimization of new and improved tailor-made enzymes for industrial applications. In this review, we focus our analysis on different enzymes, containing a pyridoxal-5’-phosphate (PLP) cofactor, that have great potential as biocatalysts in a variety of industries and applications. The selected PLP enzymes are the ω-transaminases, lysine decarboxylase, threonine aldolase, L-tyrosine phenol-lyase, α-amino-ϵ-caprolactam racemases, and cystathionine β-lyases. For each of these enzymes, the catalytic mechanism, industrial application, as well as, the advantages and disadvantages of their application is reviewed in detail. In general, this review highlights the immense biocatalytic potential, rich chemistry and diverse set of applications that different enzymes sharing a common element (PLP) can have.
Outros autoresVer publicação -
[Conference Poster] Application of QM/MM Methods in the Study of PNPOx
6º Encontro de Jovens Investigadores de Biologica Computacional Estrutural
CIM-FMUP, Porto, Portugal
André Pina, Sérgio F. Sousa, Nuno M. F. S. A. Cerqueira -
[Conference Poster] Computational studies addressed to the catalytic mechanism of PNPOx
UCIBIO Annual Meeting 2018
FCT/UNL, Lisbon, Portugal
André F. Pina, Sérgio F. Sousa, Nuno M. F. S. A. Cerqueira -
[Journal Article] Antitumor Activity of Quinazolinone Alkaloids Inspired by Marine Natural Products
Marine Drugs
Long, S., Resende, D. I., Kijjoa, A., Silva, A. M., Pina, A., Fernández-Marcelo, T., Vasconcelos, M. H., Sousa, E., Pinto, M. M. (2018)
-
[Conference Poster] Synthesis and tumor cell growth inhibitory effects of the marine products analogues of Fiscalin B
12th YES Meeting
Faculty of Medicine of the University of Porto (FMUP), Porto, Portugal
Lopes, N., Long, S., Resende, D., Kijjoa, A., Silva, A., Pina, A., Fernández-Marcelo, T., Vasconce-
los, M. H., Pinto, M., Sousa, E. -
[Conference Poster] Antitumor Activity of Quinazolinone Alkaloids-Inspired in Marine Products
XXV Encontro Nacional da Sociedade Portuguesa de Química
Faculty of Pharmacy of the University of Lisbon (FFUL), Lisbon, Portugal
Long, S., Resende, D., Kijjoa, A., Silva, A., Pina, A., Fernández-Marcelo, T., Vasconcelos, M. H., Sousa, E., Pinto, M. -
[Conference Poster] Expression of the drug efflux pump P-glycoprotein (P-gp) may be associated with the release of larger extracellular vesicles (EVs) in multidrug resistant cells
IJUP ’17 (10th edition)
Faculty of Medicine of the University of Porto (FMUP), Porto, Portugal
Castro, I., Pina, A., Sousa, D., Lopes-Rodrigues, V., Caires, H., Xavier, C. P. R., Vasconcelos, M. H.
Idiomas
-
Portuguese
Nível nativo ou bilíngue
-
English
Nível avançado
Organizações
-
EJIBCE 2018 - 6º Encontro de Jovens Investigadores em Biologia Computacional Estrutural
Organizing Committee
-O Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE) tem como objectivo reunir a comunidade científica portuguesa nesta área num encontro livre de encargos, de forma a proporcionar um espaço de discussão e partilha sem compromissos. Esta sexta edição alimenta-se do sucesso das edições anteriores, que têm reunido cada vez mais participantes ao longo dos anos. A sexta edição decorreu no dia 21 de Dezembro de 2018, e teve lugar no CIM - Centro de Investigação Médica…
O Encontro de Jovens Investigadores de Biologia Computacional Estrutural (EJIBCE) tem como objectivo reunir a comunidade científica portuguesa nesta área num encontro livre de encargos, de forma a proporcionar um espaço de discussão e partilha sem compromissos. Esta sexta edição alimenta-se do sucesso das edições anteriores, que têm reunido cada vez mais participantes ao longo dos anos. A sexta edição decorreu no dia 21 de Dezembro de 2018, e teve lugar no CIM - Centro de Investigação Médica da Faculdade de Medicina da Universidade do Porto.
-
Workshop "Utilização de software na simulação molecular" no âmbito do V Encontro Internacional da Casa das Ciências
Instructor
-As tecnologias de informação e comunicação são nos dias de hoje uma ferramenta apelativa para o ensino da química. Neste contexto, salientam-se os programas de computador utilizados em modelação molecular que permitem visualizar e interpretar vários fenómenos químicos e que são normalmente difíceis de lecionar ou entendidos pelos alunos. Este workshop teve por objetivo a apresentação de vários programas de modelação molecular (como o Avogadro ou o VMD) que permitem a visualização e edição de…
As tecnologias de informação e comunicação são nos dias de hoje uma ferramenta apelativa para o ensino da química. Neste contexto, salientam-se os programas de computador utilizados em modelação molecular que permitem visualizar e interpretar vários fenómenos químicos e que são normalmente difíceis de lecionar ou entendidos pelos alunos. Este workshop teve por objetivo a apresentação de vários programas de modelação molecular (como o Avogadro ou o VMD) que permitem a visualização e edição de estruturas moleculares, bem como o cálculo de propriedades químicas de algumas moléculas. Todas as ferramentas apresentadas foram de acesso livre e por isso poderão ser instaladas e usadas pelos professores e alunos sem qualquer custo. Os exemplos abordados poderão ser mais tarde utilizados na sala de aula e permitir a construção de um ambiente de aprendizagem mais dinâmico e interativo, tornando o conteúdo lecionado mais estimulante e elucidativo para os alunos.
-
CHEMTECH DQB – Chemistry Technology Events at DQB
Collaborator
-Realizou-se no Departamento de Química e Bioquímica da Faculdade de Ciências da Universidade do Porto uma mini feira de ciência onde se mostraram os softwares desenvolvidos no grupo de Bioquímica Teórica e Computacional. Os softwares são todos eles extensões para o VMD (Visual Molecular Dynamics) um visualizador molecular gratuito desenvolvido pela Universidade Illinois. Os participantes tiveram a oportunidade de falar com os desenvolvedores e experimentar os softwares, que sendo gratuitos…
Realizou-se no Departamento de Química e Bioquímica da Faculdade de Ciências da Universidade do Porto uma mini feira de ciência onde se mostraram os softwares desenvolvidos no grupo de Bioquímica Teórica e Computacional. Os softwares são todos eles extensões para o VMD (Visual Molecular Dynamics) um visualizador molecular gratuito desenvolvido pela Universidade Illinois. Os participantes tiveram a oportunidade de falar com os desenvolvedores e experimentar os softwares, que sendo gratuitos podem ser mais tarde instalados e usados por cada um dos participantes.
-
IJUP'18 | 11ª edição - Encontro de Investigação Jovem da Universidade do Porto
Collaborator
- -
V AEICBAS Biomedical Congress
Coordinator of the Biochemistry Department
-O ABC reúne alunos de Medicina, Medicina Veterinária, Ciências do Meio Aquático, Bioquímica e Bioengenharia durante 4 dias, nos quais são abordados temas emergentes na comunidade científica, quer de caráter transversal quer específicos a cada um dos cinco cursos. Conta com uma programação diversa e inovadora, incluindo workshops, palestras, conferências, roundtables e apresentação de posters. Ao longo de todo o congresso, o ABC fomenta o convívio e partilha de experiências e ideias, através da…
O ABC reúne alunos de Medicina, Medicina Veterinária, Ciências do Meio Aquático, Bioquímica e Bioengenharia durante 4 dias, nos quais são abordados temas emergentes na comunidade científica, quer de caráter transversal quer específicos a cada um dos cinco cursos. Conta com uma programação diversa e inovadora, incluindo workshops, palestras, conferências, roundtables e apresentação de posters. Ao longo de todo o congresso, o ABC fomenta o convívio e partilha de experiências e ideias, através da construção de um primoroso programa social, recebido com grande entusiasmo pelos participantes. Tal como o progresso científico não tem barreiras, também a nossa ambição e vontade de fazer o ABC sempre maior e melhor não tem limites.
-
NEBQUP - Núcleo de Estudantes de Bioquímica da Universidade do Porto
Coordinator of the Scientific Department
- -
NEBQUP - Núcleo de Estudantes de Bioquímica da Universidade do Porto
Member
- -
II AEICBAS Biomedical Congress
Organizing Committee
-
Outros perfis semelhantes
Outras pessoas chamadas André Pina em Portugal
-
André Pina
-
André P.
Incident Responder | Vulnerability Analyst | CTI
-
André Pina
PhD Candidate (Sociology)
-
André Pina
Psicólogo no CLDS 4G SER Sardoal
Mais 36 pessoas chamadas André Pina fazem parte do LinkedIn em Portugal
Veja mais pessoas chamadas André Pina