RG9. Computational Biochemistry

Principal investigator

Research Overview

The BioComp group is devoted to the computational description of catalysis phenomena in biological systems, mostly enzyme catalyzed processes. For this purpose, theories, methods and techniques of theoretical and computational chemistry are developed, implemented and used. Computational algorithms and protocols, based on hybrid QM/MM potentials, are created and this new knowledge is exploited in designing new materials with properties to be used in biomedicine and biotechnology. In particular, these applications are focused on elucidating enzyme reaction mechanisms including fundamental new quantum and dynamical perspectives, to design new pharmacological agents to inhibit enzyme activity, or new catalysts mimicking the catalytic efficiency and features of natural enzymes.

Group's research interests

Development of QM/MM methods, combined with ML techniques, for the study of biochemical processes.
Deciphering the mode of action of enzymes.
Predicting enzymatic properties by computational simulations.(rate constants, Michaelis constants, inhibition constants, kinetic isotope effects, etc).
Design of new enzymes.
Design of new enzyme-inhibitors.
Development of new biological materials with specific properties.

Members

Vicent Moliner

Principal Investigator

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Katarzyna Świderek

Senior Researcher

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Raquel Castillo

Senior Researcher

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Sergio Martí

Senior Researcher

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María Teresa Roca Moliner

Senior Researcher

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Kemel Arafet Cruz

Research Scientist

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Victor Batista

Research Scientist

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Álvaro Serrano López de la Vieja

Doctoral Candidate

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Adrián Fernández de la Pradilla Ibáñez

Doctoral Candidate

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Publications

2025

Catalysis Science & Technology, 2025, 15, 6486-6498.

Pacheco, S.Fernando C.; Świderek, K.; Moran, M.Jesus; Oliden-Sánchez, A.; Moliner, V.; Salassa, L.; López-Gallego, F.

Overcoming Flavin-Driven Inactivation of Alcohol Dehydrogenases Through Enzyme Immobilization.

Article page: https://pubs.rsc.org/en/content/articlelanding/2025/cy/d5cy00964b
Nature Methods, 2025, 22, 641.

Amaro, R.E.; Åqvist, J.; Bahar, I.; Battistini, F.; Bellaiche, A.; Beltran, D.; Biggin, P.C.; Bonomi, M.; Bowman, G.R.; Bryce, R.; Bussi, G.; Carloni, P.; Case, D.; Cavalli, A.; Chang, C.E.A.; Cheung, M.S.; Chipot, C.; Chong, L.T.; Choudhary, P.; Cisneros, G.A.; Clementi, C.; Collepardo-Guevara, R.; Coveney, P.; Covino, R.; Crawford, T.D.; Peraro, M.D.; de Groot, B.; Delemotte, L.; Vivo, M.D.; Essex, J.; Fraternali, F.; Gao, J.; Gelpí, J.L.; Gervasio, F.L.; Gonzalez-Nilo, F.D.; Grubmüller, H.; Guenza, M.; Guzman, H.V.; Harris, S.; Head-Gordon, T.; Hernandez, R.; Hospital, A.; Huang, N.; Huang, X.; Hummer, G.; Iglesias-Fernández, J.; Jensen, J.H.; Jha, S.; Jiao, W.; Jorgensen, W.L.; Kamerlin, S.C.L.; Khalid, S.; Laughton, C.; Levitt, M.; Limongelli, V.; Lindahl, E.; Lindorff-Larsen, K.; Loverde, S.; Lundborg, M.; Luo, Y.L.; Luque, F.J.; Lynch, C.I.; MacKerell, A.; Magistrato, A.; Marrink, S.J.; Martin, H.; McCammon, J.A.; Merz, K.; Moliner, V.; Mulholland, A.; Murad, S.; Naganathan, A.N.; Nangia, S.; Noe, F.; Noy, A.; Oláh, J.; O’Mara, M.; Ondrechen, M.J.; Onuchic, J.N.; Onufriev, A.; Osuna, S.; Panchenko, A.R.; Pantano, S.; Parish, C.; Parrinello, M.; Perez, A.; Perez-Acle, T.; Perilla, J.R.; Pettitt, B.M.; Pietropalo, A.; Piquemal, J.P.; Poma, A.; Praprotnik, M.; Ramos, M.J.; Ren, P.; Reuter, N.; Roitberg, A.; Rosta, E.; Rovira, C.; Roux, B.; Röthlisberger, U.; Sanbonmatsu, K.Y.; Schlick, T.; Shaytan, A.K.; Simmerling, C.; Smith, J.C.; Sugita, Y.; Świderek, K.; Taiji, M.; Tao, P.; Tikhonova, I.G.; Tirado-Rives, J.; Tuñón, I.; Kamp, M.W.V. d.; der Spoel, D.V.; Velankar, S.; Voth, G.A.; Wade, R.; Warshel, A.; Welborn, V.V.; Wetmore, S.; Wong, C.F.; Yang, L.W.; Zacharias, M.; Orozco, M.

The need to implement FAIR principles in biomolecular simulations.

Article page: https://www.nature.com/articles/s41592-025-02635-0
Chemistry - A European Journal, 2025, 31, e202403735.

Grajales-Hernández, D.A.; Roca, M.; Moliner, V.; López-Gallego, F.

Active Site Engineering of a Glycerol Dehydrogenase Improves its Oxidative Activity and Scope Toward Glycerol Derivatives.
ACS Synthetic Biology, 2025, 14, 3721–3733.

Bemelmans, M.; Wetzel, B.; Neusius, F.; Tieves, F.; Schwarz, C.; Mateljak, I.; Świderek, K.; Moliner, V.; Alcalde, M.; Sieber, V.

Engineering the Tobacco Etch Virus Protease toward a Platform for Traceless Cleavage Using Distal Site Prediction and Smart Library Design.

Article page: https://pubs.acs.org/doi/full/10.1021/acssynbio.5c00423
Chemical Science, 2025, 16, 14509.

Gabirondo, E.; Maiz-Iginitz, A.; Ximenis, M.; Świderek, K.; Andrés-Sanz, D.; Moliner, V.; Cabedo, L.; Westlie, A.H.; Chen, E.Y.X.; Cerrón-Infantes, A.; Unterlass, M.M.; Gallego, L.; Etxeberria, A.; Sardon, H.

Selective chemical recycling of polyhydroxybutyrate into high-value hydroxy acid using Taurine organocatalyst.

Article page: https://pubs.rsc.org/en/content/articlelanding/2025/sc/d5sc02196k#!divAbstract
The Journal of Physical Chemistry Letters, 2025, 16, 3249.

Casalino, L.; Ramos-Guzmán, C.A.; Amaro, R.E.; Simmerling, C.; Lodola, A.; Mulholland, A.J.; Świderek, K.; Moliner, V.

A Reflection on the Use of Molecular Simulation to Respond to SARS-CoV-2 Pandemic Threats.

Article page: https://pubs.acs.org/doi/full/10.1021/acs.jpclett.4c03654
WIREs Computational Molecular Science , 2025, 15, e70003.

Świderek, K.; Bertran, J.; Zinovjev, K.; Tuñón, I.; Moliner, V.

Advances in the Simulations of Enzyme Reactivity in the Dawn of the Artificial Intelligence Age.

Article page: https://wires.onlinelibrary.wiley.com/doi/10.1002/wcms.70003