Osuna, Sílvia

Computational design of proficient enzymes: exploring the molecular basis of biocatalysis

Contact info:
Dr. Sílvia Osuna
silvia.osuna@udg.edu
Tel. (+34) 972 41 93 21
Website

osuna-team

Selected publications


Miguel A. Maria-Solano, Javier Iglesias-Fernández, Sílvia Osuna
Deciphering the Allosterically Driven Conformational Ensemble in Tryptophan Synthase Evolution
J. Am. Chem. Soc., 2019, 141, 13049-13056
DOI: 10.1021/jacs.9b03646

Christian Curado-Carballada, Ferran Feixas, Javier Iglesias-Fernández, Sílvia Osuna
Hidden Conformations inAspergillus niger Monoamine Oxidase are Key for Catalytic Efficiency
Angew. Chem. Int. Ed., 2019, 58, 3097-3101
DOI: 10.1002/anie.201812532

Xi Chen, Hongliu Zhang, Miguel A. Maria-Solano, Weidong Liu, Juan Li, Jinhui Feng, Xiangtao Liu, Sílvia Osuna, Rey-Ting Guo, Qiaqing Wu, Dunming Zhu, Yanhe Ma
Efficient reductive desymmetrization of bulky 1,3-cyclodiketones enabled by structure-guided directed evolution of a carbonyl reductase
Nat Catal, 2019, 2, 931-941
DOI: 10.1038/s41929-019-0347-y

Xavier Arqué, Adrian Romero-Rivera, Ferran Feixas, Tania Patiño, Sílvia Osuna, Samuel Sánchez
Intrinsic enzymatic properties modulate the self-propulsion of micromotors
Nat Commun, 2019, 10, 2826
DOI: 10.1038/s41467-019-10726-8

Antonia Tomás-Loba, Elisa Manieri, Bárbara González-Terán, Alfonso Mora, Luis Leiva-Vega, Ayelén M. Santamans, Rafael Romero-Becerra, Elena Rodríguez, Aránzazu Pintor-Chocano, Ferran Feixas, Juan Antonio López, Beatriz Caballero, Marianna Trakala, Óscar Blanco, Jorge L. Torres, Lourdes Hernández-Cosido, Valle Montalvo-Romeral, Nuria Matesanz, Marta Roche-Molina, Juan Antonio Bernal, Hannah Mischo, Marta León, Ainoa Caballero, Diego Miranda-Saavedra, Jesús Ruiz-Cabello, Yulia A. Nevzorova, Francisco Javier Cubero, Jerónimo Bravo, Jesús Vázquez, Marcos Malumbres, Miguel Marcos, Sílvia Osuna & Guadalupe Sabio
p38Υ is essential for cell cycle progression and liver tumorigenesis
Nature, 2019, 568, 557-560
DOI: 10.1038/s41586-019-1112-8

+ Publications

Dr. Sílvia Osuna

Sílvia Osuna received her PhD in 2010 from the University of Girona (UdG) at the Institut de Química Computacional (IQC). In 2010, she moved to the group of Prof. Houk at the University of California, Los Angeles (UCLA) with a Marie Curie postdoctoral fellowship. She obtained a JdC postdoctoral contract at the UdG, a 5-year RyC contract (RYC-2014-16846), and in 2018 an ICREA Research position.

The group of Dr. Osuna was established thanks to the awarded 2015 European Research Council project – Starting grant project (ERC-2015-StG-679001) and focuses on the development of new computational tools and approaches for computational enzyme design. Her group is currently funded by a European Research Council project – Consolidator Grant, two ERC- Proof of Concept grants, and two I+D Spanish MINECO projects.

She been recently awarded the 2023 Young Spanish National Award in Chemistry (María Teresa Toral), 2021 EuChemS lecture award, the Catalan National Research Award – Young Talent 2019 from Fundació Catalana de Recerca i Innovació (FCRi), the Young Researcher award by the Royal Spanish Society of Chemistry (RSEQ 2016), Research award by the Fundación Princesa de Girona (FPdGi 2016- Science category), among many others.

Research overview

Billions of years of evolution have made enzymes superb catalysts capable of accelerating reactions by several orders of magnitude. The underlying physical principles of their extraordinary catalytic power still remains highly debated, which makes the alteration of natural enzyme activities towards synthetically useful targets a tremendous challenge for modern chemical biology. The routine design of enzymes will, however, have large socio-economic benefits, as because of the enzymatic advantages the production costs of many drugs will be reduced and will allow industries to use environmentally friendly alternatives. The goal of our group is to make the routine design of proficient enzymes possible.

Billions of years of evolution have made enzymes superb catalysts capable of accelerating reactions by as many as seventeen orders of magnitude. This rate acceleration is achieved by decreasing the activation barriers of reactions, making them possible at lower temperatures and pressures. Enzymes (i.e. biocatalysts) are indeed the most efficient, specific and selective catalysts known. They operate under biological conditions, are biodegradable, non-toxic, their high selectivities and efficiencies reduce the number of work- up steps, and provide product in higher yields. These characteristics make enzyme-catalyzed processes an attractive alternative for chemical manufacturing. However, the use of enzymes in industry is limited, as most of processes do not present a biocatalyst to catalyze and accelerate the corresponding reactions. The ability of routinely designing enzymes for any target process will have large socio-economic impacts, as the production costs of many drugs will be reduced and will allow industries to use environmentally friendly alternatives. However, the routine design of enzymes for any target reaction has not yet been achieved. This is in part motivated by the imprecise knowledge of the underlying physical principles of biocatalysis, which makes the alteration of the natural activity of enzymes towards synthetically relevant targets a tremendous challenge for biochemistry. Current computational and experimental approaches are able to confer natural enzymes new functionalities but are economically unviable and the catalytic efficiencies lag far behind their natural counterparts.

We work in the design of new enzymes for distinct processes important for their potential applications in medicine. We explore the structural basis of improved catalysis achieved by the experimental directed evolution (DE) technique through computational modeling, and are currently developing a new computational protocol based on Molecular Dynamics and network models that reduce the complexity of the enzyme design paradigm. Our computational predictions are tested in the lab to finally elucidate the potential of this genuinely new computational approach for mimicking Nature’s rules of evolution.
We collaborate with many groups, being the most relevant ones: Prof. K. N. Houk (UCLA, USA), Prof. Y. Tang (UCLA, USA), Dr. G. Huisman (Codexis).

SilviaOsuna_RL_1

We additionally work on the computational exploration of the chemical reactivity and properties of carbon-based materials. This topic is related to Dr. Osuna’s PhD thesis and she has collaborations with the groups of Prof. L. Echegoyen (UTEP), Dr. Y. Yamakoshi (ETH Zurich), Prof. J. M. Poblet (URV), and Prof. N. Martín (UCM).

People

Principal Investigator

Sílvia Osuna

ICREA Research Professor


Staff and Postdocs

Alexander Swoboda

Postdoc

Supervisor:
- S. Osuna

Eduard Masferrer

Postdoc

Supervisor:
- S. Osuna

Guillem Casadevall

Postdoc

Supervisor:
- S. Osuna

Miquel Estévez

Postdoc

Supervisor:
- S. Osuna


PhD and MACMoM students

Akram Doustmohammadi

PhD student

Supervisor:
- S. Osuna

Cristina Duran

PhD Student (FPI)

Supervisor:
- S. Osuna

Esther Pruna

PhD student

Supervisor:
- S. Osuna

Janet Sánchez

PhD (FPI) student

Supervisor:
- S. Osuna

Javier Moreno

PhD student

Supervisor:
- S. Osuna

Jonnely Rissell Luizaga

PhD student

Supervisor:
- S. Osuna

Laia Ramoneda Giralt

PhD student

Supervisor:
- S. Osuna


Funding

ERC


Project: Fast yet accurate routine rational design of novel enzymes (FASTEN)
Researcher: Dr. Sílvia Osuna
Reference: ERC-2022-CoG-101088032
Funding: 1.996.250 €
Period: 01/10/2023 – 30/09/2028
Project: Computational design of industrial enzymes for green chemistry (GREENZYME)
Researcher: Dr. Sílvia Osuna
Reference: ERC-2022-PoC2-101112805
Funding: 150.000 €
Period: 01/05/2023 – 31/10/2025

ERC Proof of concept


Project: Development of rationally designed enzyme kits (KITZYME)
Researcher: Dr Sílvia Osuna
Reference: ERC-2023-POC-101158166
Funding: 150.000 €
Period: 01/07/2024– 31/12/2025

Juan de la Cierva


Project: Juan de la Cierva
Researcher: Dr. Eduard Masferrer (S. Osuna))
Reference: JDC2023-052689-I
Funding: – €
Period: –

MCIU Proyectos I+D

Project: Evolución computacional de nuevos (bio)catalizadores
Researcher: Dr. Sílvia Osuna
Reference: PDC2022-133950-100
Funding: 143.750 €
Period: 01/12/2022 – 31/12/2024
Project: Diseño computacional de enzimas conformacionalmente dirigido para mejorar la actividad aislada o en complejo
Researcher: Dr. Sílvia Osuna
Reference: PID2021-129034NB-100
Funding: 157.300 €
Period: 01/09/2022 – 31/08/2025

AGAUR. Suport a grups de recerca.

Project: Theoretical Chemistry of Biosystems (TCBioSys)
Researcher: Dr. Sílvia Osuna
Reference: 2021 SGR 00487
Funding: 60.000 €
Period: 01/01/2022 – 31/12/2024

Collaborations

Nobu TokurikiUniversity of British Columbia (Canada), collaboration with Sílvia Osuna.
Manfred ReetzMax-Planck-Institut für Kohlenforschung (Germany), collaboration with Sílvia Osuna.
News

New Full Professors: Prof. Sílvia Osuna and Prof. Marcel Swart

In the last weeks, two PIs of the Institut de Químicia Computacional i

Jordi Soler receives PhD theses in Chemistry award of RSEQ-JIQ

Jordi Soler won the II edition of the best PhD in Chemistry award

Sílvia Osuna recives Chemitry Europe Lecture Award (JIQ-RSEQ)

Last week the Jóvenes Investigadores Químicos (JIQ-RSEQ) announced that Prof. Sílvia Osuna, ICREA researcher at the Institut de

Alexander Swoboda, new Erwin Schrödinger postdoc fellow at IQCC

Dr. Alexander Swoboda has recently become a new member of the Institute of Computational