PublicationsLatest articles in international journals
2023 Sérgio M. Marques, Petr Kouba, Anthony Legrand, Jiri Sedlar, Lucas Disson, Joan Planas-Iglesias, Zainab Sanusi, Antonin Kunka, Jiri Damborsky, Tomas Pajdla, Zbynek Prokop, Stanislav Mazurenko, Josef Sivic, David Bednar. Effects of Alzheimer’s Disease Drug Candidates on Disordered Aβ42 Dissected by Comparative Markov State Analysis (CoVAMPnet). Preprints at BioRxiv, DOI: 10.1101/2023.01.06.523007 2022 Michal Nemergut, Sergio Marques, Lukas Uhrik, Tereza Vanova, Marketa Nezvedova, Darshak Chandulal Gadara, Durga Jha, Jan Tulis, Veronika Blechova, Joan Iglesias-Planas, Antonin Kunka, Anthony Legrand, Hana Hribkova, Veronika Pospisilova, Jiri Sedmik, Jan Raska, Zbynek Prokop, Jiri Damborsky, Dasa Bohaciakova, Zdenek Spacil, Lenka Hernychova, David Bednar, Martin Marek. Domino-like Effect of C112R Mutation on APOE4 Aggregation and Its Suppression by Alzheimer’s Disease Drug Candidate. Preprints at BioRxiv, DOI: 10.1101/2022.10.09.511473 Pavol Ulbrich, Manuela Waldner, Katarina Furmanova, Sérgio M, Marques, David Bednar, Barbora Kozlikova, Jan Byska. sMolBoxes: Dataflow Model for Molecular Dynamics Exploration. IEEE Trans. Vis. Comput. Graph. 2022. ASAP article. DOI: 10.1109/tvcg.2022.3209411 [full text] Sérgio M. Marques, Michaela Slanska, Klaudia Chmelova, Radka Chaloupkova, Martin Marek, Spencer Clark, Jiri Damborsky, Eric T. Kool, David Bednar, Zbynek Prokop. Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling. JACS Au. 2022, 2, 1324−1337. DOI: 10.1021/jacsau.2c00002 [full text] Michal Vasina, Jan Velecký, Joan Planas-Iglesias, Sergio M. Marques, Jana Skarupova, Jiri Damborsky, David Bednar, Stanislav Mazurenko, Zbynek Prokop. Tools for Computational Design and High-Throughput Screening of Therapeutic Enzymes. Adv. Drug Deliv. Rev. 2022, 114143. DOI: 10.1016/j.addr.2022.114143. [full text] Lea R. Rapp, Sérgio M. Marques, Bernd Nebel, Jiri Damborsky, Bernhard Hauer. "Engineering CYP153AM.aq to Oxyfunctionalize its Inhibitor Dodecylamine Using a LC/MS Based Rapid Flow Analysis Screening". ChemCatChem, 2022. e202101648. DOI: 10.1002/cctc.202101648. [full text] 2021 Klara Markova, Antonin Kunka, Klaudia Chmelova, Martin Havlasek, Petra Babkova, Sérgio M. Marques, Michal Vasina, Joan Planas-Iglesias, Radka Chaloupkova, David Bednar, Zbynek Prokop, Jiri Damborsky, Martin Marek. "Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers". ACS Catalysis 2021. 11, 12864–12885. DOI: 10.1021/acscatal.1c03343 [full text] Preprints at: ChemRxiv. 2021. DOI: 10.26434/chemrxiv.13634021 Gaspar P. Pinto, Ondrej Vavra, Sergio M. Marques, Jiri Filipovic, David Bednar, Jiri Damborsky. "Screening of World Approved Drugs against Highly Dynamical Spike Glycoprotein of SARS-CoV-2 using CaverDock and Machine Learning". Comput. Struct. Biotechnol. J. 2021. 19, 3187-3197. DOI: 10.1016/j.csbj.2021.05.043 [full text] Preprints at: ChemRxiv. 2020. DOI: 10.26434/chemrxiv.13168883 Sérgio M. Marques, Lucie Šupolíková, Lenka Molčanová, Karel Šmejkal, David Bednar, Iva Slaninová. "Screening of Natural Compounds as P-Glycoprotein Inhibitors Against Multidrug Resistance". Biomedicines 2021, 9, 357. DOI: 10.3390/biomedicines9040357 [full text] Lea R. Rapp, Sérgio M. Marques, Erna Zukic, Benjamin Rowlinson, Mahima Sharma, Gideon Grogan, Jiri Damborsky, Bernhard Hauer. "Substrate anchoring and flexibility reduction in CYP153AM.aq leads to highly improved efficiency towards octanoic acid". ACS Catalysis 2021. 11, 3182-3189. DOI: 10.1021/acscatal.0c05193 [full text] Sérgio M. Marques, Joan Planas-Iglesias, Jiri Damborsky. "Web-based Tools for Computational Enzyme Design". Curr. Opin. Struct. Biol. 2021. 69, 19-34. DOI: 10.1016/j.sbi.2021.01.010 [full text] Preprints at: Preprints 2020, 2020120089. DOI: 10.20944/preprints202012.0089 Joan Planas-Iglesias, Sérgio M. Marques, Gaspar P. Pinto, Milos Musil, Jan Stourac, Jiri Damborsky, David Bednar. "Computational Design of Enzymes for Biotechnological Applications". Biotechnol. Adv. 2021, 47, 107696. DOI: 10.1016/j.biotechadv.2021.107696 [full text] 2020 Klara Markova, Klaudia Chmelova, Sérgio M. Marques, Philippe Carpentier, David Bednar, Jiri Damborsky, Martin Marek. "Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst". Chem. Sci., 2020, 11, 11162-11178. DOI: 10.1039/D0SC03367g [full text] Jiri Filipovic, Ondrej Vávra, Jan Plhák, David Bednar, Sérgio M. Marques, Jan Brezovsky, Ludek Matyska, Jiri Damborsky. "CaverDock: A Novel Method for the Fast Analysis of Ligand Transport". IEEE/ACM Trans. Comput. Biol. Bioinform. 2020, 5, 1625-1638. DOI: 10.1109/TCBB.2019.2907492 [full text] 2019 Jiří Černý, Paulína Božíková, Aleš Balík, Sérgio M. Marques, Ladislav Vyklický. "NMDA Receptor Opening and Closing-Transitions of a Molecular Machine Revealed by Molecular Dynamics". Biomolecules. 2019, 9, 546. DOI: 10.3390/biom9100546 [full text] Ondrej Vavra, Jiri Filipovic, Jan Plhak, David Bednar, Sergio M. Marques, Jan Brezovsky, Jan Stourac, Ludek Matyska, Jiri Damborsky. "CaverDock: A Molecular Docking-Based Tool to Analyse Ligand Transport through Protein Tunnels and Channels". Bioinformatics 2019, btz386. DOI: 10.1093/bioinformatics/btz386 [full text] Jan Byška, Thomas Trautner, Sergio M. Marques, Jiri Damborský, Barbora Kozlíková, Manuela Waldner. “Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization,” Comput. Graph. Forum 2019, 38, 441–453. DOI: 10.1111/cgf.13701 [full text here] Sérgio M. Marques, David Bednar, Jiri Damborsky. "Computational study of protein-ligand unbinding for enzyme engineering". Front. Chem., 2019, 6, 650. DOI: 10.3389/fchem.2018.00650 [full text] 2018 Shubhangi Kaushik, Sérgio M. Marques, Prashant Khirsariya, Kamil Paruch, Lenka Libichova, Jan Brezovsky, Zbynek Prokop, Radka Chaloupkova, Jiri Damborsky. "Impact of the access tunnel engineering on catalysis is strictly ligand-specific", FEBS J. 2018, 285, 1456-1476. DOI: 10.1111/febs.14418 [full text] Adam Jurcik, David Bednar, Jan Byska, Sergio M. Marques, Katarina Furmanova, Lukas Daniel, Piia Kokkonen, Jan rezovsky, Ondrej Strnad, Jan Stourac, Antonin Pavelka, Martin Manak, Jiri Damborsky, Barbora Kozlikova. "CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories", Bioinformatics 2018, 34, 3586-3588. DOI: 10.1093/bioinformatics/bty386 [full text here] Koen Beerens, Stanislav Mazurenko, Antonin Kunka, Sergio M. Marques, Niels Hansen, Milos Musil, Radka Chaloupkova, Jitka Waterman, Jan Brezovsky, David Bednar, Zbynek Prokop, and Jiri Damborsky. "Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization". ACS Catalysis 2018, 8, 9420–9428. DOI: 10.1021/acscatal.8b01677 [full text] 2017 Sérgio M. Marques, Zuzana Dunajova, Zbynek Prokop, Radka Chaloupkova, Jan Brezovsky, Jiri Damborsky, "Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling", J. Chem. Inf. Model. 2017, 57, 1970–1989. DOI: 10.1021/acs.jcim.7b00070 [full text] Sergio M. Marques, Lukas Daniel, Tomas Buryska, Zbynek Prokop, Jan Brezovsky, Jiri Damborsky, “Enzyme Tunnels and Gates as Relevant Targets in Drug Design”, Med. Res. Rev. 2017, 37, 1095–1139. DOI: 10.1002/med.21430 [full text] 2015 Catarina Quintanova, Rangappa S. Keri, Sérgio M. Marques, Maria G. Fernandes, Sandra M. Cardoso, M. Luísa Serralheiro and M. Amélia Santos, "Design, synthesis and bioevaluation of tacrinehybrids with cinnamate and cinnamylidene acetate derivatives as potential anti-Alzheimer drug candidates", Med. Chem. Commun. 2015, 6, 1969-1977. DOI: 10.1039/c5md00236b [full text here] Olayiwola A. Adekoya, Stian Sjøli, Yimingjiang Wuxiuer, Irina Biltoa, Sérgio M. Marques, M. Amélia Santos, Elisa Nuti, Giovanni Cercignani, Armando Rossello, Jan-Olof Winberg, Ingebrigt Sylte, "Inhibition of pseudolysin and thermolysin by hydroxamate-based MMP inhibitors", Eur. J. Med. Chem. 2015, 89, 340-348. DOI: 10.1016/j.ejmech.2014.10.009 [full text here] 2014 Valeria M. Nurchi, Guido Crisponi, Massimiliano Arca, Miriam Alonso-Crespo, Joanna I. Lachowicz, Delara Mansoor, Leonardo Toso, Giuseppina Pichiri, M. Amelia Santos, Sergio M. Marques, Juan Niclós-Gutierrez, Joseph M. González-Pérez, Alicia Domínguez-Martín, Duane Choquesillo-Lazare, Zbigniew Szewczuk, M. Antonietta Zoroddu, Massimiliano Pean, "A new bis-3-hydroxy-4-pyrone as a potential therapeutic iron chelating agent. Effect of connecting and side chains on the complex structures and metal ion selectivity", J. Inorg. Biochem. 2014, 141, 132-143. DOI: 10.1016/j.jinorgbio.2014.09.002 [full text here] Leonardo Toso, Guido Crisponi, Valeria M. Nurchi, Miriam Crespo-Alonso, Joanna I. Lachowicz, Delara Mansoori, Massimiliano Arca, M. Amélia Santos, Sérgio M. Marques, Lurdes Gano, Juan Niclós-Gutíerrez, Josefa M. González-Pérez, Alicia Domínguez-Martín, Duane Choquesillo-Lazarte, Zbigniew Szewczuk, “Searching for new aluminium chelating agents: A family of hydroxypyrone ligands”, J. Inorg. Biochem. 2014, 130, 112-121. DOI: 10.1016/j.jinorgbio.2013.09.022 [full text here] 2013 Sérgio M. Marques, Claudia Abate, Sílvia Chaves, Fernanda Marques, Isabel Santos, Elisa Nuti, Armando Rossello, M. Amélia Santos, "New bifunctional metalloproteinase inhibitors: an integrated approach towards biological improvements and cancer therapy", J. Inorg. Biochem. 2013, 127, 188–202. DOI: 10.1016/j.jinorgbio.2013.03.003 [full text here] Leonardo Toso, Guido Crisponi, Valeria M. Nurchi, Miriam Crespo-Alonso, Joanna I. Lachowicz, M. Amelia Santos, Sergio M. Marques, Juan Niclos-Gutierrez, Josefa M. Gonzalez-Perez, Alicia Dominguez-Martin, Duane Choquesillo-Lazarte, Zbigniew Szewczuk, "A family of hydroxypyrone ligands designed and synthesized as iron chelators", J. Inorg. Biochem. 2013, 127, 220–231. DOI: 10.1016/j.jinorgbio.2013.06.009 [full text here] Rangappa S. Keri, Catarina Quintanova, Sérgio M. Marques, A. Raquel Esteves, Sandra M. Cardoso, M. Amélia Santos, "Design, synthesis and neuroprotective evaluation of novel tacrine-benzothiazole hybrids as multi-targeted compounds against Alzheimer's disease", Bioorg. Med. Chem. 2013, 21, 4559-4569. DOI: 10.1016/j.bmc.2013.05.028 [full text here] Andreia Nunes, Sérgio M. Marques, Catarina Quintanova, Diana F. Silva, Sandra M. Cardoso, Sílvia Chaves, M. Amélia Santos, "Multifunctional iron-chelators with protective roles against neurodegenerative diseases", Dalton Trans. 2013, 42, 6058–6073. DOI: 10.1039/c3dt50406a [full text here] Ana C. Mendonça, André F. Martins, Andrea Melchior, Sérgio M. Marques, Sílvia Chaves, Sandrine Villette, Stéphane Petoud, Pier Luigi Zanonato, Marilena Tolazzi, Célia S. Bonnet, Éva Tóth, Plinio Di Bernardo, Carlos F.G.C. Geraldes, M. Amélia Santos, "New tris-3,4-HOPO lanthanide complexes as potential imaging probes: complex stability and magnetic properties", Dalton Trans. 2013, 42, 6046-6057. DOI: 10.1039/C2DT32237D [full text here] Sílvia Chaves, Anabela Capelo, Laurinda Areias,Sérgio M. Marques, Lurdes Gano, M. Alexandra Esteves, M. Amélia Santos, "A novel tripodal tris-hydroxypyrimidinone sequestering agent for trivalent hard metal ions: synthesis, complexation and in vivo studies", Dalton Trans. 2013, 42, 6033-6045. DOI: 10.1039/C2DT32361C [full text here] -->> Earlier publications are listed on Publons and ORCID <<-- Conference papers 2017 1) Viktor Vad, Jan Byška, Adam Jurcík, Ivan Viola, Eduard Gröller, Helwig Hauser, Sérgio M. Marques, Jiří Damborský, Barbora Kozlíková, "Watergate: Visual Exploration of Water Trajectories in Protein Dynamics". In Eurographics Workshop on Visual Computing for Biology and Medicine; Eds. Bruckner, S., Hennemuth, A., Kainz, B., Hotz, I., Merhof, D., Rieder, C.; The Eurographics Association, 2017; pp 33–42. DOI: 10.2312/vcbm.20171235 [full text here] Book chapters 2016 1) Sérgio M . Marques, Jan Brezovsky and Jiri Damborsky, "Role of Tunnels and Gates in Enzymatic Catalysis". In Understanding Enzymes: Function, Design, Engineering, and Analysis, Ed. Allan Svendsen, Pan Stanford Publishing: Singapore, 2016, 421–463. DOI: 10.1201/b19951-15 [full text here] Patents 1) M. Amélia Santos, Sérgio M. Marques, Marco Gil, Matteo Tegoni, Sílvia Chaves, “Set of medicinal metal enzyme high capacity inhibitors comprises succinic and iminodiacetic acids giving high zinc and nickel ion complexing capacity”, PT 103003, 2005. 2) Sérgio M. Marques, Armando Rossello, M. Amélia Santos, “New inhibitors of metalo-enzymes with potential clinical application: 1-hydroxy-piperazino-2,6-dione derivatives as a new zinc-binding group”, PT 103897, 2008. [full text here] |
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56 articles 1 book chapter 2 patents 3 conference proceedings with refereeing Times cited: 1,314 h-index: 23 (last updated: Feb. 2023) ORCID: 0000-0002-6281-7505 Web of Science: H-8685-2012 ResearchGate: link here |
