Ikerbasque Research Fellow Ramón y Cajal (RyC) Programme
0000-0002-7813-8216Francesca Peccati obtained her BSc and MSc in Chemistry from the Università degli Studi di Torino and continued her scientific pursuits by completing her PhD in Chemistry from the Autonomous University of Barcelona (UAB), Spain.
In 2018, Dr. Peccati joined the laboratory of Prof. Dr. Contreras at the Chimie Théorique Sorbonne Université/CNRS where she developed a new method to obtain quick quantification of non-covalent interactions in biomolecular systems, implemented in the popular NCIPLOT program.
In 2020, Dr. Peccati became a postdoctoral researcher in the Computational Chemistry Lab at CIC bioGUNE. She was awarded a Juan de la Cierva (2021) and a Ramón y Cajal Fellowship (2023), and she currently holds the position of Emerging Scientist.
Her primary research interests focus on protein design and engineering, biomolecular recognition, protein aggregation, and materials. Computational chemistry serves as a powerful tool to explore mechanistic effects at the molecular level, offering insights into life sciences, biotechnology, and medicine. By integrating quantum mechanics, molecular dynamics, and data-driven technologies, computational chemistry enables the optimization of biomolecules for custom functions, driving advancements in biotechnology and therapeutic design.
Research line 1: Protein Misfolding and Aggregation
The misfolding and aggregation of amyloidogenic proteins into insoluble fibrils is a hallmark of several neurodegenerative diseases. The structural characterization of these fibrillar structures at atomic resolution is challenging due to their inherent heterogeneity and polymorphism. Computational modeling is used to investigate the aggregation propensity of amyloidogenic proteins, considering sequence variations, structural differences, and post-translational modifications.
Research line 2: Optimization of Protein Function
The development of artificial intelligence tools for protein structure and sequence sampling opens new opportunities to design proteins with tailored properties. Combining classical protein design methods with AI-driven approaches, the team develops computational pipelines to optimize thermal stability, conformational preferences, and luminescence properties in both natural and synthetic proteins.
She co-supervises the PhD theses of Cristina María Segovia Martín and Milagros Muriel Olaya and also co-supervises and co-funds postdoc Reyes Núñez Franco, alongside Gonzalo Jiménez-Osés.
Awards & recognitions
R3 Certificate (2024). Ikerbasque Research Fellow (2024). Ramón y Cajal Fellowship (2023). Juan de la Cierva Fellowship (2021). Best Computational Chemistry Article Award from the Specialized Group in Chemistry and Computation (RSEQ) (2020). Extraordinary PhD Award from the Autonomous University of Barcelona (2019).
Collaborations
A. Jean-Luc Ayitou (University of Illinois Chicago), D. A. Mitchell (University of Illinois Urbana-Champaign), R. Buller (ZHAW), S. Boxer (Stanford), J. Castilla, L. Unione (CIC bioGUNE), E. Vázquez (USC-CIQUS), S. Ventura (IBB).
Personal and group social networks
Latest Publications
2024
2023
2022
Computational Chemical Biology is a cross-disciplinary area devoted to the accurate atomistic simulation of chemical and biochemical phenomena, from small-molecule reactions and recognition to protein folding, dynamics, and function. It is at the core of the structure-activity relationship and uses cutting edge technology and algorithms, from quantum mechanics to artificial intelligence.
Research line 1: Protein design and engineering
We use deep-learning models for backbone and sequence design, either to improve the properties of existing proteins related to metabolic diseases and biosensors, or to create new proteins de novo with tailored functions. Our approaches allow the design and experimental validation of enzymes for unnatural reactions, engineered antibodies and therapeutic protein binders with enhanced expression levels.
Research line 2: Bioorthogonal chemistry
We develop new concepts and methods based on fundamental chemical processes for the site-selective modification of proteins and antibodies, with strong emphasis on improving stability, bioavailability, and spatiotemporal control of therapeutic Antibody-Drug Conjugates (ADCs) with potential clinical applications.
Research line 3: Drug discovery
We use in silico tools to accelerate the discovery of small molecules, peptides, small proteins with therapeutic potential for neurodegenerative disorders, cancer, and infectious diseases.
Research line 4: Glycobiology
We provide detailed insights on the mechanisms of glycosylation processes and glycan recognition, developing methods for the structural modeling of complex glycoproteins and lectins.
Collaborations
Donald Hilvert (ETH Zürich), David Baker (University of Washington), Frances Arnold, Brian Stoltz (Caltech), Wilfred van der Donk (University of Illinois Urbana-Champaign), Yi Tang, Ken Houk (UCLA), A. Jean-Luc Ayitou (University of Illinois Chicago), Gonçalo Bernardes, (University of Cambridge), Rebecca Buller (ZHAW), Josiel Domingos (Federal University of Santa Catarina), Jesús Jiménez-Barbero, Óscar Millet, Joaquín Castilla, Asís Palazón, Juan Anguita, Alberto Fernández-Tejada, Malu Martínez-Chantar, Nicola Abrescia, Mikel Valle (CIC bioGUNE), Fernando López-Gallego (CIC biomaGUNE), Francisco Corzana (University of La Rioja), Antonio J Moreno-Vargas (University of Sevilla), José Luis Mascareñas, Eugenio Vázquez (USC-CIQUS).
Links
Webpage: http://www.gonzalojimenezoses.com
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Group Leader
Gonzalo Jiménez-Osés
Ikerbasque Research Professor POSTDOCTORAL RESEARCHER -
Reyes Nuñez Franco
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Claudio Daniel Navo Najera
TECHNICIANS / DOCTORAL CANDIDATES -
Cristina María Segovia Martín
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Milagros Muriel Olaya
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Sara Alunno Rufini
Members
Latest Publications
Host-Guest Dynamic Behavior of Melatonin Encapsulated in β-Cyclodextrin Nanosponges
Ferrero, R; Pantaleone, S; Brunella, V; Corno, M; Jiménez-Osés, G; Peccati, F;
ACS OMEGA
2025-01-28
Doublet Spin State Mediated Photoluminescence Upconversion in Organic Radical Donor-Triplet Acceptor Dyads
OShea, JM; Yun, YJ; Jamhawi, AM; Peccati, F; Jiménez-Osés, G; Ayitou, AJL;
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2024-12-19
Exploring Glycan-Lectin Interactions in Natural-Like Environments: A View Using NMR Experiments Inside Cell and on Cell Surface
Bertuzzi, S; Lete, MG; Franconetti, A; Diercks, T; Delgado, S; Oyenarte, I; Moure, MJ; Nuñez-Franco, R; Valverde, P; Lenza, MP; Sobczak, K; Jiménez-Osés, G; Paulson, JC; Ardá, A; Ereño-Orbea, ...
CHEMISTRY-A EUROPEAN JOURNAL
2024-12-11
Mechanistic Insights into Chloride-Dependent Uncaging Reaction of Propargyl and Allene-Protected Substrates by Pd-Complexes
Ferreira, TM; Navo, CD; Agnes, JP; Cardozo, F; de Oliveira, DC; Zanotto, A; Jimenez-Osés, G; Domingos, JB;
CHEMISTRY-A EUROPEAN JOURNAL
2024-12-10
Unveiling the GT114 family: Structural characterization of A075L, a glycosyltransferase from Paramecium bursaria chlorella virus-1 (PBCV-1)
Laugieri, ME; Speciale, I; Gimeno, A; Lin, SC; Byers, BW; Poveda, A; Nunez-Franco, R; Iturrioz, I; Moure, MJ; Jimenez-Oses, G; Russo-Krauss, I; Notaro, A; Van Etten, JL; Lowary, TL; Jimenez-Barbero, ...
PROTEIN SCIENCE
2024-12-01
Enriching productive mutational paths accelerates enzyme evolution
Patsch, D; Schwander, T; Voss, M; Schaub, D; Hüppi, S; Eichenberger, M; Stockinger, P; Schelbert, L; Giger, S; Peccati, F; Jiménez-Osés, G; Mutny, M; Krause, A; Bornscheuer, UT; Hilvert, D; ...
NATURE CHEMICAL BIOLOGY
2024-09-11
AlphaFold2 Predicts Alternative Conformation Populations in Green Fluorescent Protein Variants
Núñez-Franco, R; Muriel-Olaya, MM; Jiménez-Osés, G; Peccati, F;
JOURNAL OF CHEMICAL INFORMATION AND MODELING
2024-09-03
Gold(III)-Induced Amide Bond Cleavage In Vivo: A Dual Release Strategy via π-Acid Mediated Allyl Substitution
Unnikrishnan, VB; Sabatino, V; Amorim, F; Estrada, MF; Navo, CD; Jimenez-Oses, G; Fior, R; Bernardes, GJL;
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2024-08-08
Different roles of the heterodimer architecture of galectin-4 in selective recognition of oligosaccharides and lipopolysaccharides having ABH antigens
Quintana, JI; Massaro, M; Cagnoni, AJ; Nuñez-Franco, R; Delgado, S; Jiménez-Osés, G; Mariño, KV; Rabinovich, GA; Jiménez-Barbero, J; Ardá, A;
JOURNAL OF BIOLOGICAL CHEMISTRY
2024-08-01
Interplay Between Substrate Polarity and Protein Dynamics in Evolved Kemp Eliminases
Peccati, F; Noey, EL; Houk, KN; Osuna, S; Jiménez-Osés, G;
CHEMCATCHEM
2024-06-05
Darobactin Substrate Engineering and Computation Show Radical Stability Governs Ether versus C-C Bond Formation
Woodard, AM; Peccati, F; Navo, CD; Jiménez-Osés, G; Mitchell, DA;
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2024-05-10
Interplay of chloride levels and palladium(ii)-catalyzed O-deallenylation bioorthogonal uncaging reactions
Dal Forno, GM; Latocheski, E; Navo, CD; Albuquerque, BL; St John, AL; Avenier, F; Jiménez-Osés, G; Domingos, JB;
CHEMICAL SCIENCE
2024-03-20
A Protein Misfolding Shaking Amplification-based method for the spontaneous generation of hundreds of bona fide prions
Erana, H; Sampedro-Torres-Quevedo, C; Charco, JM; Diaz-Dominguez, CM; Peccati, F; San-Juan-Ansoleaga, M; Vidal, E; Goncalves-Anjo, N; Perez-Castro, MA; Gonzalez-Miranda, E; Pineiro, P; Fernandez-Veiga, ...
NATURE COMMUNICATIONS
2024-03-08
Improving Protein Expression, Stability, and Function with ProteinMPNN
Sumida, KH; Núñez-Franco, R; Kalvet, I; Pellock, SJ; Wicky, BIM; Milles, LF; Dauparas, J; Wang, J; Kipnis, Y; Jameson, N; Kang, AL; De La Cruz, J; Sankaran, B; Bera, AK; Jiménez-Osés, G; Baker, ...
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
2024-01-09
Experimental and Theoretical Analysis of the Thiol-Promoted Fragmentation of 2-Halo-3-tosyl-oxanorbornadienes
Carranza, M; Carmona, AT; Navo, CD; Robina, I; Fratta, S; Newburn, C; Jiménez-Osés, G; Moreno-Vargas, AJ;
ORGANIC LETTERS
2023-10-10
Merging the Isonitrile-Tetrazine (4+1) Cycloaddition and the Ugi Four-Component Reaction into a Single Multicomponent Process
Méndez, Y; Vasco, AV; Ivey, G; Dias, AL; Gierth, P; Sousa, BB; Navo, CD; Torres-Mozas, A; Rodrigues, T; Jiménez-Osés, G; Bernardes, GJL;
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
2023-09-20
Unraveling the Photophysical Characteristics, Aromaticity, and Stability of π-Extended Acene-Quinodimethyl Thioamides†
Yang, G; Yun, YJ; Peccati, F; Jamhawi, AM; Kamatham, N; Jockusch, S; Jiménez-Osés, G; Ayitou, AJL;
CHEMPHYSCHEM
2023-09-19
The catalytic role of glutathione transferases in heterologous anthocyanin biosynthesis
Eichenberger, M; Schwander, T; Hüppi, S; Kreuzer, J; Mittl, PRE; Peccati, F; Jimenez-Osés, G; Naesby, M; Buller, RM;
NATURE CATALYSIS
2023-08-31
Expanding the Substrate Scope of Acyltransferase LovD9 for the Biosynthesis of Statin Analogues
García-Marquina, G; Núñez-Franco, R; Grajales-Hernández, D; Jiménez-Osés, G; López-Gallego, F;
CHEMISTRY-A EUROPEAN JOURNAL
2023-06-05
Molecular Recognition of Glycan-Bearing Glycomacromolecules Presented at Membrane Surfaces by Lectins: An NMR View
Lete, MG; Hoffmann, M; Schomann, N; Martínez-Castillo, A; Peccati, F; Konietzny, PB; Delgado, S; Snyder, NL; Jiménez-Oses, G; Abrescia, NGA; Ardá, A; Hartmann, L; Jiménez-Barbero, J;
ACS OMEGA
2023-05-03