Bioinformatics focusing on the development of new methodologies and tools Dr. Chasapis Christos | Associate Researcher, Group Leader
Our activities lie at the interface of computational structure and systems biology. Our lab is a multi-disciplinary group comprising researchers with expertise in various fields, including biochemistry, biotechnology, molecular biology, data analysis, and artificial intelligence: machine learning (ML) and deep learning (DL).
Research activities
Structural bioinformatics: modeling and molecular dynamics of organic compounds and biomolecules (proteins and protein-ligand/drug complexes)
Analysis of Organic spectroscopy and NMR data
Computational Systems Biology
Biological Big Data Analysis
Inter- and Intra- Species Protein-Protein Interaction (PPI) networks
Network-based drug repurposing and side effect indications
Modeling of human disease networks
Development of ML and DL algorithms for biological network analysis
Goal
Computational design of Next-Generation Antiviral Therapeutics.
Development of novel personalized medicine strategies based on Human-microbiome interplay modeling.
Acceleration the implementation of innovative non-animal approaches for drug development and repurposing via AI algorithm.
Prediction of side effects for drugs in clinical trials and postmarketing via AI algorithm implementation.
Development of novel computational methodologies for functional plasticity prediction of protein drug targets.
Group Structure and Personnel
Dr. Christos T. Chasapis, Research Assistant Professor
Head of the Laboratory of Bioinformatics focusing on the development of new methodologies and tools.
Ph.D. candidates
MSc Despoina P. Kiouri, PhD in Bioinformatics, NHRF/ICB and Department of Chemistry, NKUA
MSc Georgios Batsis, NHRF/ICB
MSc students
Ms. Aikaterini Oikonomidi, MSc in Medicinal Chemistry and Chemical Biology, NHRF/ICB and University of Patras
Undergraduate students
Ms. Athanasia K. Georgiopoulou, Department of Biosystems & Agricultural Engineering of the University of Patras
Laboratory Alumni
Charalampos Ntallis, MSc in Medicinal Chemistry and Chemical Biology, NHRF/ICB and University of Patras (2022-2023)
Collaborations
National academic
Dr. Maria Klapa, Research Director, FORTH/ICE-HT, Patras, Greece
Prof. Ioannis Matsoukas, NewDrug PC, Patras Science Park, 265 04 Platani, Greece
Prof. Thomas Mavromoustakos, Department of Chemistry, National and Kapodistrian University of Athens, Greece
Prof. Sotirios Tsiodras, National and Kapodistrian University of Athens Medical School, Greece
Associate Prof. Irene Margiolaki, Department of Biology, University of Patras, Greece
Prof. Maria Stefanidou, National and Kapodistrian University of Athens Medical School
Assistant Prof. Alexios Vlamis, Department of Chemistry, University of Patras, Greece
Prof. Spyros Perlepes, Department of Chemistry, University of Patras, Greece
International academic
Dr. Alessandro Giuliani, Environment and Health Department, Istituto Superiore di Sanità, 00161 Rome, Italy
Dr. Harry Ridgway, AquaMem Scientific Consultants, Rodeo, NM 88056, USA
Prof. Vasso Apostolopoulos, Institute for Health and Sport, Victoria University, Melbourne, VIC 3030, Australia
Associate Prof., Massimiliano Peana, Department of Chemical, Physics, Mathematics and Natural Sciences, University of Sassari, Italy
Dr. Geir Bjørklund, President of the Council for Nutritional and Environmental, Medicine (CONEM), Mo i Rana, Norway
Associate Prof. Antonio Rosato, NMR center, CERM, University of Florence
Associate Prof. Ioannis Gelis, Department of Chemistry, University of South Florida, Tampa USA
Ntallis C., Tzoupis H., Tselios T., Chasapis C. T., Vlamis A. G, Distinct or Overlapping Areas of Mitochondrial Thioredoxin 2 May Be Used for Its Covalent and Strong Non-Covalent Interactions with Protein Ligands, Antioxidants, 2024, 13(1), 15
doi: 10.3390/antiox13010015
Kiouri DP, Ntallis C, Kelaidonis K, Peana M, Tsiodras S, Mavromoustakos T, Giuliani A, Ridgway H, Moore GJ, Matsoukas JM, Chasapis CT*. Network-Based Prediction of Side Effects of Repurposed Antihypertensive Sartans against COVID-19 via Proteome and Drug-Target Interactomes. Proteomes.2023 Jun 8;11(2):21.
doi: 10.3390/proteomes11020021
Kiouri, D. P., Tsoupra, E., Peana, M., Perlepes, S. P., Stefanidou, M. E., & Chasapis, C. T*. (2023). Multifunctional role of zinc in human health: an update. EXCLI Journal, 2023, 22, 809–827.
doi: 10.17179/excli2023-6335
Ridgway H*, Orbell JD, Matsoukas MT, Kelaidonis K, Moore GJ, Tsiodras S, Gorgoulis VG, Chasapis CT*, Apostolopoulos V, Matsoukas JM*. W254 in furin functions as a molecular gate promoting anti-viral drug binding: Elucidation of putative drug tunneling and docking by non-equilibrium molecular dynamics. Comput Struct Biotechnol J. 2023 Sep 9;21:4589-4612.
doi: 10.1016/j.csbj.2023.09.003
Kelaidonis K, Ligielli I, Letsios S, Vidali VP, Mavromoustakos T, Vassilaki N, Moore GJ, Hoffmann W, Węgrzyn K, Ridgway H, Chasapis CT*, Matsoukas JM*. Computational and Enzymatic Studies of Sartans in SARS-CoV-2 Spike RBD-ACE2 Binding: The Role of Tetrazole and Perspectives as Antihypertensive and COVID-19 Therapeutics. Int J Mol Sci.2023 May 8;24(9):8454.
doi: 10.3390/ijms24098454
Chasapis CT*, Perlepes SP, Bjørklund G, Peana M., Structural modeling of protein ensembles between E3 RING ligases and SARS-CoV-2: The role of zinc binding domains, J.Trace Elem Med Biol, 2023 Jan:75:127089.
doi: 10.1016/j.jtemb.2022.127089
Mpekoulis, G.; Kalliampakou, K.I.; Milona, R.S.; Lagou, D.; Ioannidis, A.; Jahaj, E.; Chasapis, C.T. ;Kefallinos, D.; Karakasiliotis, I.; Kotanidou, A.; et al. Significance of Catecholamine Biosynthetic/Metabolic Pathway in SARS-CoV-2 Infection and COVID-19 Severity. Cells2023, 12, 12. https://doi.org/10.3390/cells12010012
Triandafillidis, D. P., Karavassili, F., Spiliopoulou, M., Valmas, A., Athanasiadou, M., Nikolaras, G., Fili, S., Kontou, P., Bowler, M. W., Chasapis, C. T., Von Dreele, R. B., Fitch, A. N. & Margiolaki, I. The T2 structure of polycrystalline cubic human insulin, Acta Cryst. 2023, D79, 374-386.
Podzimek S, Himmlova L, Janatova T, Bjørklund G, Vrbova R, Janovska M, Peana M, Chasapis CT, Vinsu A, Prochazkova J, Duskova J., Metal hypersensitivity and pro-inflammatory cytokine production in patients with failed orthopedic implants: A case-control study, Clin Immunol. 2022 245:109152.
doi: 10.1016/j.clim.2022.109152
Bjørklund G, Zou L, Peana M, Chasapis CT, Hangan T, Lu J, Maes M., The Role of the Thioredoxin System in Brain Diseases., Antioxidants (Basel). 2022, 11(11):2161.
doi: 10.3390/antiox11112161
Oulas A, Zachariou M, Chasapis CT, Tomazou M, Ijaz UZ, Schmartz GP, Spyrou GM, Vlamis-Gardikas A., Putative Antimicrobial Peptides Within Bacterial Proteomes Affect Bacterial Predominance: A Network Analysis Perspective, Front Microbiol 2021 12:752674.
doi: 10.3389/fmicb.2021.752674
Bjørklund G, Zou L, Wang J, Chasapis CT, Peana M., Thioredoxin reductase as a pharmacological target., Pharmacol Res. 2021, 174:105854.
doi: 10.1016/j.phrs.2021.105854
Chasapis CT, Makridakis M, Damdimopoulos AE, Zoidakis J, Lygirou V, Mavroidis M, Vlahou A, Miranda-Vizuete A, Spyrou G, Vlamis-Gardikas A. Implications of the mitochondrial interactome of mammalian thioredoxin 2 for normal cellular function and disease, Free Radic Biol Med 2019, 137: 59-73.
doi: 10.1016/j.freeradbiomed.2019.04.018
