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Postdoc Position - CNB-CSIC

Three-dimensional reconstruction, using cryo-EM data, of complexes between different viral receptors and synthetic antiviral proteins

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Postdoc Position - IMROH, Zagreb, Croatia

Initial assessment of monobodies' (Mobs) effects on human cells

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Matea Kurtović Kodžoman

PhD student/assistant
Linkedin

Matea is a postdoctoral researcher on the EvaMobs project at the Institute for Medical Research and Occupational Health in Zagreb, Croatia. She holds a PhD in Biotechnology in Biomedicine and a Master’s degree in Chemistry, with over eight years of experience in cancer research and therapeutic development. Her doctoral work focused on mutation-driven tumor biology and immune-related receptor polymorphisms associated with disease risk, using advanced in vitro models and a wide range of molecular and biochemical approaches. This background provided her with a strong foundation in target validation, drug development principles, and safety assessment of novel biologics. Her work employed a diverse set of experimental methods, including cell-based assays, protein analysis, and genome editing techniques. In the EvaMobs project, she applies this expertise to a new antiviral strategy, focusing on evaluating the toxicological safety of evolvable monobodies (Mobs).

Key Publications

Kurtović M, Piteša N, Bartoniček N, Ozretić P, Musani V, Čonkaš J, Petrić T, King C, Sabol M. RNA-seq and ChIP-seq Identification of Unique and Overlapping Targets of GLI Transcription Factors in Melanoma Cell Lines. Cancers (Basel). 2022 Sep 19;14(18):4540. doi: 10.3390/cancers14184540. PMID: 36139698; PMCID: PMC9497141.

Kurtović M, Piteša N, Čonkaš J, Hajpek H, Vučić M, Musani V, Ozretić P, Sabol M. GLI Transcriptional Targets S100A7 and KRT16 Show Upregulated Expression Patterns in Epidermis Overlying the Tumor Mass in Melanoma Samples. Int J Mol Sci. 2024 May 31;25(11):6084. doi: 10.3390/ijms25116084. PMID: 38892279; PMCID: PMC11172526.

Piteša N, Kurtović M, Bartoniček N, Gkotsi DS, Čonkaš J, Petrić T, Musani V, Ozretić P, Riobo-Del Galdo NA, Sabol M. Signaling Switching from Hedgehog-GLI to MAPK Signaling Potentially Serves as a Compensatory Mechanism in Melanoma Cell Lines Resistant to GANT-61. Biomedicines. 2023 May 3;11(5):1353. doi: 10.3390/biomedicines11051353. PMID: 37239024; PMCID: PMC10216463.

Baranašić J, Šutić M, Catalano C, Drpa G, Huhn S, Majhen D, Nestić D, Kurtović M, Rumora L, Bosnar M, Vukić Dugac A, Sokolović I, Popovic-Grle S, Oršolić N, Škrinjarić-Cincar S, Jakopović M, Samaržija M, Weber ANR, Försti A, Knežević J. TLR5 Variants Are Associated with the Risk for COPD and NSCLC Development, Better Overall Survival of the NSCLC Patients and Increased Chemosensitivity in the H1299 Cell Line. Biomedicines. 2022 Sep 9;10(9):2240. doi: 10.3390/biomedicines10092240. PMID: 36140341; PMCID: PMC9496592.

Trnski D, Sabol M, Tomić S, Štefanac I, Mrčela M, Musani V, Rinčić N, Kurtović M, Petrić T, Levanat S, Ozretić P. SHH-N non-canonically sustains androgen receptor activity in androgen-independent prostate cancer cells. Sci Rep. 2021 Jul 21;11(1):14880. doi: 10.1038/s41598-021-93971-6. PMID: 34290270; PMCID: PMC8295376.

Maria Benedita Ferreira Moço Rodrigues Pereira

Former Master Student
Linkedin

Benedita Pereira developed her master thesis in Biotechnology at ITQB NOVA, where she aimed to computationally design novel antiviral proteins that target and bind to the Zika virus envelope protein, using state-of-the-art protein design computational tools. Additionally, she evaluated the stability of the designs through computational methods such as molecular dynamics and participated in the experimental production of the top designs to assess their binding affinity to the target.

Antonio Zandona

Scientific Associate
Linkedin

Antonio Zandona, PhD in Chemistry – Biochemistry and Medicinal Chemistry, is an expert in the enzyme kinetics and cell based research, with specific training in flow cytometry and molecular biology techniques. His fields of interest include influence of oxime reactivators and potential drugs on cell level, mechanisms of toxicity on cell level and activation and/or inhibition of signaling pathways with an aim to determine specific mechanisms of toxicity and dependence of compounds structure and toxicity. In addition to being a collaborator on several national and bilateral projects, he was PI of three projects supported by Croatian Academy of Science and Art. As the recipient of EMBO scientific exchange grants he had opportunities to collaborate with leading experts in his field and gain exposure to cutting-edge techniques. His role in the EvaMobs project will be formation and maintenance of the cell bank and performance of specific assays used as a safety assessment in preclinical evaluation of Mobs.

Key Publications

Zandona, Antonio; Madunić, Josip; Miš, Katarina; Maraković, Nikola; Dubois-Goeffroy, Pierre; Cavaco, Marco; Mišetić, Petra; Padovan, Jasna; Castanho, Miguel; Jean, Ludovic et al. Biological response and cell death signaling pathways modulated by tetrahydroisoquinoline-based aldoximes in human cells. Toxicology, 494 (2023) str. 153588-1536. doi: 10.1016/j.tox.2023.153588

Žunec, S.; Vadlja, D.; Ramić, A.; Zandona, A.; Maraković, N.; Brekalo, I.; Primožič, I.; Katalinić, M. Profiling Novel Quinuclidine-Based Derivatives as Potential Anticholinesterase Drugs: Enzyme Inhibition and Effects on Cell Viability. Int. J. Mol. Sci. 2024, 25, 155. https://doi.org/10.3390/ijms25010155

Zandona, Antonio; Jagić, Karla; Dvoršćak, Marija; Madunić, Josip; Klinčić, Darija; Katalinić, Maja. PBDEs found in house dust impact human lung epithelial cell homeostasis. Toxics, 10 (2022), 97-112 doi:10.3390/toxics10020097.

Zandona, Antonio; Maraković, Nikola; Mišetić, Petra; Madunić, Josip; Miš, Katarina; Padovan, Jasna; Pirkmajer, Sergej; Katalinić, Maja. Activation of (un)regulated cell death as a new perspective for bispyridinium and imidazolium oximes. Archives of toxicology, 95 (2021), 2737-2754. doi:10.1007/s00204-021-03098-w

Zandona, Antonio; Lihtar, Gabriela; Maraković, Nikola; Miš, Katarina; Bušić, Valentina; Gašo- Sokač, Dajana; Pirkmajer, Segej; Katalinić, Maja. Vitamin B3-Based Biologically Active Compounds as Inhibitors of Human Cholinesterases. International journal of molecular sciences, 21 (2020), 21; 8088, 19. doi:10.3390/ijms21218088

Neha Dalvi

Research Associate
Linkedin

Neha Dalvi joined the Formulation and Stability Group at NIBRT in February 2024. She obtained her bachelor’s in engineering degree in Biotechnology from Savitribai Phule Pune University, India in 2020. She moved to Ireland in 2021 to pursue her Master’s in Biological and Biomolecular Science at University College Dublin, Ireland. She has studied mammalian stem cells, microbial cells and hydrophobin production using Pleoretus ostreatus culture. Her Thesis was an investigation into the tissue-specific expression of aquaporins and big brain homolog in the common bed bug. She worked as a research associate in the Cell Technology Group with senior scientist, Dr Elizabeth Matthews and Prof. Michael Butler from September 2022 to January 2024. The purpose of her research was to selectively modify the glycosylation of monoclonal antibodies and other recombinant biotherapeutic proteins. Currently, she is working with Dr. Caio Henrique Barros under the guidance of Prof. Elizabeth Topp to develop a pipeline to accelerate the stability testing of Monobodies for lead selection. The stable leads will be formulated after being validated by various analytical techniques to assess physical and chemical properties of the monobodies.

Caio Henrique Barros

Senior Research Scientist
Linkedin

Caio is a Research Scientist working in the Formulation and Stability research group since 2020, under the supervision of Dr. Elizabeth Topp. His work is focused on the formulation and assessment of stability of lyophilised formulations containing mRNA and proteins, while working in industry-facing projects and collaborations. Caio graduated with a BSc and a Msc in Chemistry at the State University of Campinas, Brazil (2011-2017) followed by a PhD degree (2017-2020) in the field of bionanotechnology completed at the UCD Chemical and Bioprocess Engineering School. Within the EvaMobs project, Caio is responsible for managing the laboratory research activities at NIBRT related to the screening of monomody candidates regarding their stability and formulation.

Key Publications

Barros CHN et al. Effect of Atomic Layer Coating on the Stability of Solid Myoglobin Formulations (2023) Molecular Pharmaceutics (20) 4086-4099.

Arda Deniz Tugrul

PhD Researcher
Linkedin

In the EvaMobs consortium, Arda Deniz Tugrul’s role centers on the formulation and stability enhancement of novel monobody fragments, with a specific focus on mitigating aggregation and boosting therapeutic efficacy through targeted post-translational modifications, primarily PEGylation. His responsibilities include exploring how these modifications, along with sequence changes, influence the stability and aggregation propensity of monobodies. Some of the primary techniques he utilizes include Circular Dichroism (CD), Liquid Chromatography-Mass Spectrometry (LC-MS), Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis (SDS-PAGE), Microfluidic Capillary Electrophoresis, and a FITC-specific fluorescence plate reader, optimized for quantifying the degree of substitution and assessing product loss to aggregation. Additionally, he employs molecular modeling with PyMol to conduct computational simulations and optimize monobody behavior under various conditions. This role supports the consortium’s goal of advancing pandemic preparedness by enhancing the development of stable and effective antiviral monobodies through innovative biotechnological approaches.

David Gil Cantero

Post-doctoral researcher
Linkedin

David is a postdoctoral researcher at the National Center for Biotechnology (CNB-CSIC) in Madrid. He obtained his PhD in Microbiology from the Autonomous University of Madrid, specializing in structural biology. David’s research focuses on elucidating protein-protein interactions and macromolecular complexes using cutting-edge techniques such as cryo-electron microscopy (cryo-EM). David contributes to various disease-focused research projects at José María Valpuesta’s group, including structural studies of viral proteins aimed at understanding the mechanisms of action of newly developed neutralizing antibodies.

Key Publications

Vaccines | Free Full-Text | Immunogenicity of Multi-Target Chimeric RHDV Virus-Like Particles Delivering Foreign B-Cell Epitopes (mdpi.com)

 

Modifying the Catalytic Activity of Lipopeptide Assemblies with Nucleobases – Vela‐Gallego – 2024 – Chemistry – A European Journal – Wiley Online Library

César Santiago

Head of the X-ray Facility at CNB

César Santiago is a member of the macromolecules structure team at CNB-CSIC. Their primary objective is to elucidate the structure of the Mobs in complex with the antigens selected for study and to understand their neutralization mechanisms. To achieve this, they will employ both X-ray crystallography and cryo-EM microscopy techniques.

Key Publications

Cesar Santiago; Angela Ballesteros; Cecilia Tami; Laura Martinez-Munoz; Gerardo G. Kaplan; Jose M. Casasnovas. Structures of T cell immunoglobulin mucin receptors 1 and 2 reveal mechanisms for regulation of immune responses by the TIM receptor family. Immunity. 26 – 3, pp. 299 – 310. 2007. ISSN 1074-7613.

Cesar Santiago; Angela Ballesteros; Laura Martinez-Munoz; Mario Mellado; Gerardo G. Kaplan; Gordon J. Freeman; Jose M. Casasnovas. Structures of T cell immunoglobulin mucin protein 4 show a metal-ion-dependent ligand binding site where phosphatidylserine binds. Immunity. 27 – 6, pp. 941 – 951. 2007. ISSN 1074-7613

Juan Reguera; Cesar Santiago; Gaurav Mudgal; Desiderio Ordono; Luis Enjuanes; Jose M. Casasnovas. Structural Bases of Coronavirus Attachment to Host Aminopeptidase N and Its Inhibition by Neutralizing Antibodies. Plos Pathogens. 8 – 8, 2012. ISSN 1553-7374.

María Teresa Bueno-Carrasco; Jorge Cuéllar; Marte I. Flydal; César Santiago; Trond-André Kråkenes; Runne Kleppe; José R. López-Blanco; Miguel Marcilla; Knut Teigen; Sara Alvira; Aurora Martínez; José M. Valpuesta. Structural mechanism for tyrosine hydroxylase inhibition by dopamine and reactivation by Ser40 phosphorylation. Nature Communications. 17/11/2021.

Dante Barreda; César Santiago; Juan R. Rodríguez; José F. Rodríguez; José María Casasnovas; Isabel Mérida; Antonia Ávila-Flores. SARS-CoV-2 Spike Protein and Its Receptor Binding Domain Promote a Proinflammatory Activation Profile on Human Dendritic Cells. CELLS. MDPI, 19/11/2021.

André Rafael Ferreira Salgueiro

Former Master Student
Linkedin
During the Evamobs project, Rafael Salgueiro participated in the computational design of Monobodies, as well as testing different pipelines to be utilized for the design of these proteins. In particular, he applied several computational tools and pipelines for Monobody sequence generation and refinement for specific viral targets.

Madalena de Castro Marques

Master Student
Linkedin

Madalena Marques’ master thesis project aims to computationally design Virus-Targeting Antibody-like scaffolds (ViTAls) to bind to hemagglutinin glycoprotein present on the surface of the influenza A virus. She is also studying the stability and conformational dynamics of the best designs through molecular dynamics simulations. In addition, she will work on the purification and characterization of the best ViTAls.

Suzana Žunec

Senior scientific associate
Linkedin

Suzana žunec, PhD in Chemistry – Biochemistry and Medicinal Chemistry, has profiled herself in the field of toxicology. She is experienced in human and animal tissue based research, analysis of  biochemical and molecular mechanisms of toxicity of xenobiotics and natural compounds and enzyme kinetics with 18 years of research work. Also, she is trained in chromatographic techniques and analysis of samples. Her research areas include effects of various inorganic and organic pollutants on human health and the environment, protection against chemical weapons and interactions of conventional drugs and herbal products. Her expertise and rich background in toxicology and biochemistry, will contribute to early toxicological evaluation of Mobs – identification of possible toxicities and likelihood of potential adverse events or undesirable effects to allow deciding when it is reasonably safe to proceed to in vivo studies and clinical investigation.

Key Publications

Žunec, S.; Vadlja, D.; Ramić, A.; Zandona, A.; Maraković, N.; Brekalo, I.; Primožič, I.; Katalinić, M. Profiling Novel Quinuclidine-Based Derivatives as Potential Anticholinesterase Drugs: Enzyme Inhibition and Effects on Cell Viability. Int. J. Mol. Sci. 2024, 25, 155. https://doi.org/10.3390/ijms25010155

Matošević, Ana; Opsenica, Dejan; Spasić, Marta; Maraković, Nikola; Zandona, Antonio; Žunec, Suzana; Bartolić, Marija; Kovarik, Zrinka; Bosak, Anita. Evaluation of 4-aminoquinoline derivatives with an n-octylamino spacer as potential multi-targeting ligands for the treatment of Alzheimer’s disease. Chemico-Biological Interactions, 382 (2023), 110620, 13 doi:10.1016/j.cbi.2023.110620

Žunec S, Brčić Karačonji I, Čatalinac M, Jurič A, Katić A, Kozina G, Micek V, Neuberg M, Lucić Vrdoljak A. Effects of concomitant use of THC and irinotecan on tumour growth and biochemical markers in a syngeneic mouse model of colon cancer. Arh Hig Rada Toksikol 2023;74:198-206 doi.org/10.2478/aiht-2023-74-3765

Jurič A, Brčić Karačonji I, Žunec S, Katić A, Gašić U, Milojković Opsenica D, Kopjar N. Protective role of strawberry tree (Arbutus unedo L.) honey against cyto/genotoxic effects induced by ultraviolet B radiation in vitro. Journal of apicultural research (2022) DOI: 10.1080/00218839.2022.2047421

Zorbaz T, Malinak D, Hofmanova T, Maraković N, Žunec S, Maček Hrvat N, Andrys R, Psotka M, Zandona A, Svobodova J, Prchal L, Fingler S, Katalinić M, Kovarik Z, Musilek K. Halogen substituents enhance oxime nucleophilicity for reactivation of cholinesterases inhibited by nerve agents, European Journal of Medicinal Chemistry,Volume 238, 2022, 114377 doi.org/10.1016/j.ejmech.2022.114377

Diogo Silva

Research Fellow
During the Evamobs project, Diogo Silva will be participating in the computational design of antiviral proteins, as well as testing different pipelines to be utilized for the design of these proteins. Additionally, he will be working on the in silico characterization of the designs through computational methods like molecular dynamics, to study aspects of the designs such as oligomerization and stability.
 
During the second work package, he will also participate in the production and purification of the computationally designed protein antivirals.

Pedro Moreira

PhD Student
Linkedin

Pedro possesses an academic background in Biomedical Engineering and Bioinformatics. Commencing his PhD. Programme at ITQB NOVA in 2022, he has gathered significant expertise in computational protein design employing state-of-the-art structural-based artificial intelligence methodologies, alongside developing his capabilities in analysis of protein structures and protein-protein interfaces through the use of methodologies like molecular dynamics.

His principal task within the project entails the development of computational frameworks tailored to engineer monobodies with predicted high affinity towards specific epitopes. Following this, he aims to validate these pipelines by designing monobody binders against an extensive array of pertinent viral targets.

Key Publications

Moreira, Pedro; Sequeira, Ana Marta; Pereira, Sara; Rodrigues, Rúben; Lousa, Diana; Rocha, Miguel. “ViralFP: A web application of viral fusion proteins”. Fronteirs in Medical Technology 3 (2021).

Rita Teixeira

PhD Student
Linkedin

Rita Teixeira is a Ph.D. student supervised by the Head of the Protein Modelling Laboratory at ITQB NOVA, Professor Cláudio M. Soares, Doctor Diana Lousa, and Bruno Correia from EPFL, in Lausanne. Her current research focuses on leveraging the knowledge of viral fusion proteins (VFPs) essential for the entry of potential pandemic viruses to develop new therapeutics capable of neutralizing infection.

Within the scope of the project, she will contribute to the computational framework to generate antiviral biologics tailor-made for specific epitopes, which will be experimentally screened and validated by the team collaborator. Prior to binder design, she will also study the VFPs of the pathogenic viruses, including the effect of glycan shielding, to identify neutralizable epitopes using molecular dynamics simulations.

Catarina Carmo

Project Manager
Linkedin
 

Catarina Carmo is EvaMobs’ Project Manager and is responsible for overseeing various aspects of the project’s execution, including financial, administrative, and legal management, guaranteeing that the project is running according to plan and there is effective communication between partners and with the European Commission. She was previously a researcher both at EMBL-Heidelberg and Instituto Gulbenkian de Ciência, Portugal, investigating Microbiology and Infection. She did her PhD in Clinical Medicine Research at Imperial College London, UK. Currently, she is in the final stages of completing a postgraduate program in Project Management in Healthcare at the NOVA University. She really enjoys science communication and takes initiatives to make it engaging for all.

Name

Title at Institution
Linkedin

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Cláudio M. Soares

Project Coordinator EvaMobs and Full Professor
Linkedin

Cláudio M. Soares is Full Professor of Biochemistry at ITQB NOVA and Pro-Rector for the NOVAHealth Platform of NOVA University Lisbon. He is also the PI of the Protein Modelling Laboratory of ITQB NOVA and the Coordinator of the Molecular, Structural and Cellular Microbiology – MOSTMICRO-ITQB Research Unit of ITQB NOVA since 2015.  He is co-author of 129 papers and has participated in 37 competitively funded projects since 1996. He is a member of the Directive Board of  the Portuguese Biophysical Society and President of the Scientific Council of TAGUSPARK – Parque de Ciência e Tecnologia. He was member of the International Union for Pure and Applied Biophysics (IUPAB) council (2011-2017), and member of the Federation of European Biochemical Societies (FEBS) Advanced Courses Committee (2015-2018). Cláudio M. Soares was Dean of ITQB NOVA from 2013 to 2023 and Vice-Dean during 2005-2008 and 2011-2013.

Key Publications

Valério, M, Borges-Araújo, L, Melo, MN, Lousa, D, Soares*, CM (2022) “SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility”, Front. Med. Technol., 4:1009451.

Abreu, B, Cruz, C, Oliveira, ASF, Soares, CM (2020) “ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK2E importer”, Sci.Rep., 11, 10591

Lousa, D, Pinto, ART, Campos, SRR, Baptista, AM, Veiga, AS, Castanho, MARB, Soares, CM (2020) “Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment”, Sci.Rep., 10, 20082

Barbosa, TM, Baltazar, CSA, Cruz, DR, Lousa, D, Soares, CM (2020) “Studying O2 pathways in [NiFe]- and [NiFeSe]-hydrogenases”, Sci.Rep., 10, 10540

Oliveira, ASF, Campos, SRR, Baptista, AM, Soares, CM (2016) “Coupling between protonation and conformation in cytochrome c oxidase: Insights from Constant-pH MD simulations”, BBA Bioenergetics, 1857, 759-771.

Victor, BL, Lousa, D, Antunes, J, Soares, CM (2015) “Self-assembly molecular dynamics simulations shed light into the interaction of the influenza fusion peptide with a membrane bilayer”, J.Chem. Infor. Model., 55, 795–805

Oliveira, ASF, Damas, JM, Baptista, AM, Soares, CM (2014) “Exploring O2 diffusion in A-type Cytochrome c Oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site, PLoS Comp.Biol., 10, e1004010

Damas, JM, Baptista, AM, Soares, CM (2014) “The Pathway for O-2 Diffusion inside CotA Laccase and Possible Implications on the Multicopper Oxidases Family”, J Chem Theor Comp, 10, 3525–3531

Name

Title at Institution
Linkedin

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.

Key Publications

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Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.

Maja Katalinić

Scientific Advisor
Linkedin

Maja Katalinić, PhD, has 20 years of experience in the field of drug discovery research and excellent insight into its high demands. She possesses invaluable experience in enzyme kinetics and enzyme biochemistry in general, as well as in evaluating drugs’ effects on the cell level in the early phase of studies. She has passed several trainings in molecular biology as well as training for lab management/leadership. She was a leader and collaborator on national and international projects involving research on antidotes development for the treatment of organophosphorus compounds poisoning, while in 2017 she establish her research group focusing on the molecular mechanisms underlying the toxicity of antidotes and potential drugs. As a leading researcher of IMI team, Dr Katalinić will be responsible for the overall implementation of cell-based in vitro toxicology assays as a safety assessment to evaluate Mobs toxicity.

Key Publications

Žunec, Suzana; Vadlja, Donna; Ramić, Alma; Zandona, Antonio; Maraković, Nikola; Brekalo, Iva; Primožič, Ines; Katalinić, Maja. Profiling Novel Quinuclidine-Based Derivatives as Potential Anticholinesterase Drugs: Enzyme Inhibition and Effects on Cell Viability. International journal of molecular sciences, 25 (2024), 1; 155, 19. doi: doi.org/10.3390/ijms25010155

Zandona, Antonio; Madunić, Josip; Miš, Katarina; Maraković, Nikola; Dubois-Goeffroy, Pierre; Cavaco, Marco; Mišetić, Petra; Padovan, Jasna; Castanho, Miguel; Jean, Ludovic et al. Biological response and cell death signaling pathways modulated by tetrahydroisoquinoline-based aldoximes in human cells. Toxicology, 494 (2023), 153588-153602. doi: 10.1016/j.tox.2023.153588

Miš, Katarina ; Lulić, Ana-Marija ; Marš, Tomaž ; Pirkmajer, Sergej ; Katalinić, Maja. Insulin, dibutyryl-cAMP, and glucose modulate expression of patatin-like domain containing protein 7 in cultured human myotubes. Frontiers in endocrinology (Lausanne), 14 (2023), 1139303, 13. doi: 10.3389/fendo.2023.1139303

Zandona, Antonio; Maraković, Nikola; Mišetić, Petra; Madunić, Josip; Miš, Katarina; Padovan, Jasna; Pirkmajer, Sergej; Katalinić, Maja. Activation of (un)regulated cell death as a new perspective for bispyridinium and imidazolium oximes. Archives of Toxicology 95, (2021) 2737-2754.

Zandona, Antonio; Katalinić, Maja; Šinko, Goran; Radman Kastelic, Andreja; Primožič, Ines; Kovarik, Zrinka. Targeting organophosphorus compounds poisoning by novel quinuclidine-3 oximes: development of butyrylcholinesterase-based bioscavengers. Archives of Toxicology (2020)  94(9): 3157-3171.

Xavier Saelens

Group Leader

Xavier Saelens obtained his PhD degree from the University of Ghent under the supervision of professor Walter Fiers. After postdoctoral training in the influenza research group of Willy Min Jou, and in the Molecular Signaling and Cell Death group of Peter Vandenabeele, both at Ghent University, he became an assistant professor in Molecular Virology in 2008. Currently, he is a full professor in the Department of Biochemistry and Microbiology at Ghent University and a group leader at the VIB-UGent Center for Medical Biotechnology.

His research team applies modern biotechnology methods to develop new vaccines and antivirals against human respiratory viruses such as influenza virus, respiratory syncytial virus, and coronaviruses. In addition, his group uses interactomics tools to gain new insights in the molecular interplay between host and viral factors.

He leads EvaMobs WP3: Preclinical antiviral and safety evaluation of monobodies.

Key Publications

Rossey I, et al., Potent single-domain antibodies that arrest respiratory syncytial virus fusion protein in its prefusion state. Nat Commun, 2017, (PMID: 28194013).

Schepens B, et al., An affinity-enhanced, broadly neutralizing heavy chain-only antibody protects against SARS-CoV-2 infection in animal models. Sci Transl Med, 2021, (PMID: 34609205).

Catani JPP, et al., Pre-existing antibodies directed against a tetramerizing domain enhance the immune response against artificially stabilized soluble tetrameric influenza neuraminidase. npj Vaccines, 2022, (PMID: 35087067).

Lucija Marcelić

PhD student/assistant
Linkedin

I am a doctoral research assistant at the Institute for Medical Research and Occupational Health in Zagreb, pursuing a PhD in Chemistry. My research focuses on enhancing synaptic function and neurotransmission using newly synthesized compounds with potential applications in neurodegenerative disease treatment. My work combines in vitro cytotoxicity assays across multiple cell lines with enzymatic studies targeting monoamine oxidases and cholinesterases, as well as investigations of ligand activity at neuronal receptor systems including nAChRs, NMDA, AMPA, and 5-HT receptors. I am also involved in the Horizon Europe project EvaMobs, evaluating the cytotoxic and immunomodulatory properties of novel antiviral monobodies. I hold a Master’s degree in Experimental Biology and have international research experience in molecular medicine and blood–brain barrier models.

Key Publications

Effects of N-alkyl quaternary quinuclidines on oxidative stress biomarkers in SH-SY5Y cells

DOI: 10.2478/aiht-2025-76-4007

Cholinesterase activity modulators: Evaluation of dodecylaminoquinuclidines as inhibitors of human AChE and BChE

DOI: 10.1016/j.cbi.2025.111567

André Filipe Miranda Bagão

Master Student
Linkedin

André is currently a second-year Master’s student in Biochemistry for Health, conducting his thesis research at ITQB NOVA. His work focuses on the computational design of novel antiviral proteins targeting the Respiratory Syncytial Virus (RSV) Fusion protein. Using advanced computational tools for protein design, he aims to create proteins that specifically bind to this viral target. To ensure the stability and functionality of these designs, he utilizes molecular dynamics simulations and other computational methods to evaluate their structural integrity. Following this, he will experimentally produce the top candidates and assess their binding affinity to the RSV Fusion protein. Additionally, he will perform biophysical characterization of the designed proteins to gain further insights into their properties and potential as antiviral agents.

María-Jesús Rodríguez

Post-doctoral researcher at CNB-CSIC
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María-Jesús completed her PhD at CNB-CSIC in 2024, where she investigated the mechanical and structural properties of the human picobirnavirus capsid. As a postdoctoral researcher, she set up a new electron micro-diffraction (MicroED) data-collection workflow for atomic-resolution structure determination. She brings broad expertise across electron microscopy and image processing, including single-particle cryo-EM, MicroED, and analysis pipelines. Within the CNB-CSIC team for EvaMobs, she contributes to the structural characterization of targets and to method development aimed at accelerating high-resolution structure determination.

Vera van de Donk

Science Communication Advisor at Catalyze
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Vera leads the communication and dissemination activities across multiple Horizon-funded projects. With a background in biomedical sciences and experience in communication roles at various organizations, she enjoys translating complex research into clear, accessible content tailored to diverse audiences. By combining her scientific knowledge and creativity, she is keen on helping research projects maximize their impact.

Carolina Vieira

Senior Science Communication Advisor at Catalyze
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Carolina Vieira is a Senior Science Communication Advisor at Catalyze. Her background combines Multimedia Design and Nutrition Sciences and she has a 4 – year track record in coordinating communication and dissemination activities for various EU – funded research projects. Currently, Carolina oversees science communication and patient/end – user/advocate engagement tasks across over 8 EU projects and proficiently ensures that comp lex scientific topics are conveyed simply and strategically to diverse audiences. 

João B. Vicente

Auxiliary Investigator

João has a background in protein biochemistry and biophysics, with research dedicated to investigating the molecular mechanisms of proteins related to human disease. He leads the APB lab at ITQB NOVA, which specializes in the production of recombinant proteins and their functional and structural characterization using biophysical methods.

In EvaMobs, the APB lab is responsible for bringing the computationally designed Mobs to life. The lab has been implementing screening approaches based on small-scale Mobs production and purification, followed by analysis of thermal stability and binding affinity. Selected hit Mobs are then produced on a larger scale, their biophysical and functional properties analyzed, and sent to consortium partners for further evaluation in other work packages.

Key Publications

CHEK2 germline variants identified in familial nonmedullary thyroid cancer lead to impaired protein structure and function. Pires C, Marques IJ, Valério M, Saramago A, Santo PE, Santos S, Silva M, Moura MM, Matos J, Pereira T, Cabrera R, Lousa D, Leite V, Bandeiras TM, Vicente JB, Cavaco BM. J Biol Chem. 2024 Mar;300(3):105767. doi: 10.1016/j.jbc.2024.105767

Structural and functional impact of clinically relevant E1α variants causing pyruvate dehydrogenase complex deficiency. Pavlu-Pereira H, Lousa D, Tomé CS, Florindo C, Silva MJ, de Almeida IT, Leandro P, Rivera I, Vicente JB. Biochimie. 2021 Apr;183:78-88. doi: 10.1016/j.biochi.2021.02.007.

Structure of full-length wild-type human phenylalanine hydroxylase by small angle X-ray scattering reveals substrate-induced conformational stability. Tomé CS, Lopes RR, Sousa PMF, Amaro MP, Leandro J, Mertens HDT, Leandro P, Vicente JB. Sci Rep. 2019 Sep 20;9(1):13615. doi: 10.1038/s41598-019-49944-x.

Screening Pyridine Derivatives against Human Hydrogen Sulfide-synthesizing Enzymes by Orthogonal Methods. Zuhra K, Sousa PMF, Paulini G, Lemos AR, Kalme Z, Bisenieks I, Bisenieks E, Vigante B, Duburs G, Bandeiras TM, Saso L, Giuffrè A, Vicente JB. Sci Rep. 2019 Jan 24;9(1):684. doi: 10.1038/s41598-018-36994-w.

S-Adenosyl-l-methionine Modulates CO and NO• Binding to the Human H2S-generating Enzyme Cystathionine β-Synthase. Vicente JB, Colaço HG, Sarti P, Leandro P, Giuffrè A. J Biol Chem. 2016 Jan 8;291(2):572-81. doi: 10.1074/jbc.M115.681221. Epub 2015 Nov 18.

Raquel Domingues

MSc Student
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Raquel Domingues is a second-year Master’s student in Computational Biology and Bioinformatics, currently working on her thesis at ITQB NOVA. Her research focuses on the computational design of novel antiviral proteins that target and bind to the F protein of Respiratory Syncytial Virus (RSV). Future steps of the project will involve assessing the stability of the designed proteins through molecular dynamics simulations and evaluating their binding affinity in vitro.

Manuel N. Melo

Auxiliary Researcher

Manuel is the head of the Multiscale Modeling lab at ITQB NOVA. His work is centered on elucidating the molecular-level details of lipid-lipid, lipid-protein, and protein-protein interactions. Recent collaborations also focus on modeling nanomaterials and bacterial structures. Manuel’s research employs coarse-grained, atomistic, and hybrid molecular dynamic simulations, alongside active development of simulation and analysis software.

Manuel is a representative for the community of Portuguese structural computational biology researchers within the BioData.pt infrastructure, towards the development and implementation of good data stewardship practices.

Manuel contributes to the EvaMobs project in both these scopes: with expertise in structural modelling (WP1) and data management (WP6).

Carolina C. Buga

PhD Student
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Carolina C. Buga is a PhD student interested in understanding the mechanisms underlying viral entry and leveraging this knowledge in developing broad-spectrum viral inhibitors. In the EvaMobs project, she is involved in the design, production and biophysical characterization of viral inhibitors. Carolina also evaluates the efficacy of the viral inhibitors in a pre-clinical stage. With her expertise, she aims to bridge the computational and experimental realms contributing to the development of a novel generation of antivirals.

Key Publications

Valério M, Mendonça DA, Morais J, Buga CC, Cruz CH, Castanho MARB, Melo MN, Soares CM, Veiga AS, Lousa D. Parainfluenza Fusion Peptide Promotes Membrane Fusion by Assembling into Oligomeric Porelike Structures. ACS Chem Biol. 2022 Jul 15;17(7):1831-1843.
doi: 10.1021/acschembio.2c00208.

Mariana Parada

Researcher
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Mariana is a researcher both at the Applied Protein Biochemistry Lab and at the Proteome Regulation in Plants Lab, in ITQB NOVA. She holds a bachelor’s degree in Biochemistry (2021), and a master’s degree in Biotechnology (2023). Mariana has previously worked in the production of computationally designed therapeutic proteins, such as Fabs and miniproteins, and in their structural and functional characterization. She also has experience in cell culture, both in BSL2 and BSL3 labs.

Recently, Mariana did an internship at EPFL to learn how to perform Yeast Display. Her role in EvaMobs will be implementing Yeast Display to screen the computationally designed Mobs, and she will also be involved in the production and characterization of the best leads.

Iebe Rossey

Postdoctoral researcher
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Iebe Rossey obtained her PhD degree at the University of Ghent under supervision of professor Xavier Saelens. Her PhD research focused on the development of single-domain antibodies against the human Respiratory Syncytial Virus (hRSV). This research continued during her postdoctoral training, which also took place in the group of professor Saelens. Currently, she studies the development of single-domain antibodies targeting the human parainfluenzaviruses.

Iebe will contribute to EvaMobs WP3: Preclinical antiviral and safety evaluation of monobodies, evaluating the efficacy of the monobodies against hRSV and SARS-Cov-2 both in vitro and in vivo.

Key Publications

Rossey I, et al., Potent single-domain antibodies that arrest respiratory syncytial virus fusion protein in its prefusion state. Nat Commun, 2017, (PMID: 28194013).

Schepens B, et al., An affinity-enhanced, broadly neutralizing heavy chain-only antibody protects against SARS-CoV-2 infection in animal models. Sci Transl Med, 2021, (PMID: 34609205).

Rossey I, et al., A vulnerable, membrane-proximal site in human respiratory syncytial virus F revealed by a prefusion-specific single-domain antibody. J Virol, 2021 (PMID: 33692208)

Liana De Plasencia Mascuñana

Clinical Operations Director
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Liana De Plasencia Mascuñana is a graduate in Pharmacy by the Complutense University of Madrid and Master in Clinical Research.

She developed her professional career always linked to clinical research, occupying different positions in pharmaceutical companies and CROs.

Since her beginnings as a clinical trial monitor, she has been consolidating her knowledge and experience, growing professionally from the ground up, to currently occupy the Clinical Operations Director position.

For this project, she will be coordinating the clinical research activities to develop a phase I clinical trial, from the protocol elaboration, going through the monitoring of the trial and release of study results.

Pedro Andrade

Country Manager
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Pedro Andrade is Graduate in Management and in Nutrition Science and with a Master degree in Clinical Research.

He has developed his professional career always linked to clinical research, occupying different positions in the biggest hospital in Portugal (Hospital de Santa Maria) and in Academic Institutes (iMM) and in pharmaceutical companies and CROs.

He started as a Clinical Research Study Coordinator in Rheumatology and Oncology departments, being responsible for the major international clinical trials (Phase I to Phase III), and he also developed strong know-how in translational oncology studies by being part of a team responsible for a innovative project with Liquid byopsis. After he acted as a Clinical Research Associate, in CROs and dedicated to several Pharma companies where he was able to consolidate his knowledge and experience, growing professionally from the ground up, to a position of managing CRAs as a Clinical Team Leader. In the past years, he has been acting as a Business Development in Portugal, being responsible to improve and get new clinical research projects. Since October 2023, he is the Country Manager in Portugal, responsible for managing Evidenze in its severals dimensions.

For this project, he will be managing the interaction between Evamobs’ team and Evidenze’s operational team from the protocol elaboration phase, going through the monitoring of the trial and release of study results.

Javier Collado

PhD Student
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Javier is a researcher currently in the second year of his doctoral thesis, focusing on the study of membrane proteins. His background includes valuable experience of over three years as a member of a cryo-electron microscopy service, where he developed a solid knowledge in advanced imaging techniques at the molecular level. During his time in the service, he acquired specialized skills in sample preparation, operation of state-of-the-art electron microscopes, and processing complex data. He played an important role in establishing and refining the electron microdiffraction technique, expanding the service’s repertoire of tools for atomic-scale structural analysis.

Rocío Arranz

Head of the Cryo-EM Facility at the Centro Nacional de Biotecnología
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Dr. Rocío Arranz received her PhD in Molecular Biology from the Univ. Autónoma de Madrid in 2013. With more than 20 years of scientific experience, she has been extensively involved in the structural determination of macromolecules by cryo-EM, particularly in studies related to influenza. She is currently the head of the Cryo-EM Facility at the Centro Nacional de Biotecnología, where she develops studies using techniques such as: cryo-EM single particle analysis, cryo-electron tomography, cryocorrelative microscopy and micro-electron diffraction.

José María Valpuesta

Full Professor at the Centro Nacional de Biotecnología
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José María Valpuesta holds a PhD in Biochemistry from the Universidad del País Vasco (Bilbao, Spain) and trained as a postdoctoral at the Laboratory of Molecular Biology (LMB-MRC) in Cambridge, under the supervision of Dr. Richard Henderson (Nobel Prize in Chemistry, 2017) and John E. Walker (Nobel Prize in Chemistry, 1997). He’s currently Full Professor at the National Center for Biotechnology (Centro Nacional de Biotecnología, CNB), the largest institute of the Spanish Research Council (CSIC). He’s been Vicedirector (206-2007) and Director (2007-2013) of the CNB, where he’s currently Head of its Department of Macromolecular Structures. He’s co-author of more than 180 papers, some in journals such as Nature, Science, Mol Cell, Nat Cell Biol, Nat Struct Mol Biol, Nat Commun, J Exp Med, Proc Natl Acad Sci USA, EMBO J… He’s also author of three books (in Spanish) on science dissemination. He has been President of the European Microscopy Society (EMS; 2020-2024), of the Spanish Microscopy Society (SME; 2005-2009) and he’s currently President of the Spanish Biophysical Society (SBE; 2022-).

Marta Alenquer

Staff Scientist
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Marta Alenquer is a virologist with longstanding expertise in herpesviruses, influenza A virus and, more recently, in SARS-CoV-2. Her scientific career has been dedicated to understanding virus-host interactions at both the cellular and organismal levels, identifying host factors and pathways essential for viral replication, as well as viral proteins and virulence factors that impact viral disease in animal models of infection. Since the COVID-19 pandemic, Marta has also been actively involved in the study of antivirals, including anti-SARS-CoV-2 and anti-influenza A virus biopharmaceuticals. In this project, she is involved in in vitro virus-neutralization studies and in vivo antiviral studies of Mobs.

Key Publications

Goncalves J, Melro M, Alenquer M, Araujo C, Castro-Neves J, Amaral-Silva D, Ferreira F, Ramalho J, Charepe N, Serrano F, Pontinha C, Amorim MJ, Soares H (2023) “Balance between maternal antiviral response and placental transfer of protection in gestational SARS-CoV-2 infection” JCI Insight e167140. doi: 10.1172/jci.insight.167140

Etibor TA, Sridharan S, Vale-Costa S, Brás S, Becher I, Mello I, Ferreira F, Alenquer M, Savitski M, Amorim MJ (2023) “Defining basic rules for hardening influenza A virus liquid condensates” eLife 12:e85182. doi: 10.7554/eLife.85182

Alenquer M, Milheiro Silva T, Akpogheneta O, Ferreira F, Vale-Costa S, Medina-Lopes M, Batista F, Garcia AM, Barreto VM, Paulino C, Costa J, Sobral J, Diniz-da-Costa M, Ladeiro S, Corte-Real R, Delgado Alves J, Leite RB, Demengeot J, Rocha Brito MJ, Amorim MJ (2022) “Saliva molecular testing bypassing RNA extraction is suitable for monitoring and diagnosing SARS-CoV-2 infection in children” PLOS One 17(6): : e0268388 . doi: 10.1371/journal.pone.0268388

Gonçalves J, Juliano AM*, Charepe N*, Alenquer M*, Athayde D, Ferreira F, Archer M, Amorim MJ, Serrano F, Soares M (2021) “Non-neutralizing secretory IgA and T cells targeting SARS-CoV-2 spike protein are transferred to the breastmilk upon BNT162b2 vaccination” Cell Reports Medicine 2(12):100468. doi: 10.1016/j.xcrm.2021.100468 *equal contribution

Alenquer M, Ferreira F, Lousa D, Valério M, Medina-Lopes M, Bergman ML, Gonçalves J, Demengeot J, Leite BL, Lilue J, Ning Z, Penha-Gonçalves C, Soares H, Soares CM, Amorim MA (2021) “Signatures in SARS-CoV-2 spike protein conferring escape to neutralizing antibodies” PLoS Pathogens 17(8):e1009772. doi: 10.1371/journal.ppat.1009772

Ho JSY, Angel M, Ma Y, Sloan E, Wang G, Martinez-Romero C, Alenquer M, Roudko V, Chung L, Zheng S, Chang M, Fstkchyan Y, Clohisey S, Dinan AM, Gibbs J, Gifford R, Shen R, Gu Q, Irigoyen N, Campisi L, Huang C, Zhao N, Jones JD, van Knippenberg I, Zhu Z, Moshkina N, Meyer L, Noel J, Peralta Z, Rezelj V, Kaake R, Rosenberg B, Wang B, Wei J, Paessler S, Wise HM, Johnson J, Vannini A, Amorim MJ, Baillie JK, Miraldi ER, Benner C, Brierley I, Digard P, Łuksza M, Firth AE, Krogan N, Greenbaum BD, MacLeod MK, van Bakel H, Garcìa-Sastre A, Yewdell JW, Hutchinson E, Marazzi I (2020) “Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection”. Cell 2181(7):1502-1517.e23. doi: 10.1016/j.cell.2020.05.035

Alenquer M*, Vale-Costa S*, Etibor TA, Ferreira F, Sousa AL, Amorim MJ “Influenza A virus ribonucleoproteins form liquid organelles at endoplasmic reticulum exit sites”. (2019) Nature Communications 10: 1629. doi: 10.1038/s41467-019-09549-4

Maria João Amorim

Associate Professor
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Maria João Amorim serves as an Associate Professor at the Medical School of Universidade Católica Portuguesa, and is a group leader and vice-director at the Católica Biomedical Research Centre since 2022. Trained in the United Kingdom as a virologist, she earned her PhD from the University of Cambridge, followed by postdocs at the National Institute for Medical Research and at the University of Cambridge. She became a group leader at Instituto Gulbenkian de Ciência in 2012, in Portugal. Her group focuses on host-viral interactions using mostly influenza A virus as model. In EvaMobs, her Lab will conduct in vitro, in cellula and in vivo work on influenza A virus. Her research is supported by the ERC-CoG, La Caixa, Horizon 2023 and FCT. Amorim is committed to public engagement and education, participating in many outreach actions, representing the virology/scientific community, including in TV and Radio broadcasts, documentaries, press releases, and published pieces.

Diana Lousa

Co-coordinator of EvaMobs and
Assistant Reseracher
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Diana Lousa is currently a Researcher at the Protein Modelling Lab, ITQB NOVA. She obtained her PhD in Biochemistry in 2013. The main goal of her current research focuses on the application of computational biophysics to develop tailor-made biopharmaceuticals against viral pathogens such as influenza, zika, HIV, and SARS-CoV-2. She is the co-coordinator of the projects EvaMobs, funded by Horizon Europe (HORIZON-HLTH-2023-DISEASE-03-04), and BioPlaTTAR, funded by the La Caixa Foundation (HR22-00722). She has co-authored 29 articles in peer-reviewed scientific journals, 2 peer-reviewed book chapters, and 34 oral presentations (20 as presenter) in scientific meetings. She has supervised/co-supervised 3 Postdocs, 8 PhD, and 11 Master students, and is the assistant coordinator of the Master in Computational Biology and Bioinformatics at NOVA University. In EvaMobs, she will co-supervise WP1 (computational design of Mobs) and WP6 (project management).

Key Publications

Valério M., Mendonça D. A., Morais J., Buga C. C., Cruz C. H., Castanho M. A R. B., Melo M. N., Soares C. M., Veiga A. S. and Lousa D. (2022), Parainfluenza Fusion Peptide Promotes Membrane Fusion by Assembling into Oligomeric Porelike Structures, ACS Chemical Biology, 17(7), 1831-1843; doi: 10.1021/acschembio.2c00208

Valério M., Borges-Araújo L., Melo M. N., Lousa D., Soares C. M. (2022) SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility. Front Med Technol. Pharmaceutical innovation, vol. 4:1009451. doi: 10.3389/fmedt.2022.1009451. PMID: 36277437; PMCID: PMC9581196

Lousa, D., & Soares, C. M. (2021). Molecular mechanisms of the influenza fusion peptide: Insights from experimental and simulation studies. FEBS Open Bio, vol. 11(12): 3253-3261. doi:10.1002/2211-5463.13323 –Joint corresponding author

Lousa D., Pinto A. R. T., Campos S. R. R., Baptista A. M., Veiga A. S., Castanho M. A. R. B., Soares C. M. (2020), Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment, Scientific Reports, vol. 10: 20082; doi: 10.1038/s41598-020-77040-y

Sequeira, A. M., Lousa D., Rocha M. (2022) ProPythia: A Python package for protein classification based on machine and deep learning, Neurocomputing, vol. 484: 172-182; doi: 10.1016/j.neucom.2021.07.102