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 Emerging Scientist -
Francesca Peccati
Ikerbasque Research Fellow - Ramón y Cajal (RyC) Programme SPECIALIST -
Claudio Daniel Navo Najera
POSTDOCTORAL RESEARCHER -
Reyes Nuñez Franco
TECHNICIANS / DOCTORAL CANDIDATES -
Sara Alunno Rufini
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Milagros Muriel Olaya
Members
Latest Publications
Effect of primary structural variation on cervid prion protein in flexibility, stability, and spontaneous misfolding propensity
Díaz-Domínguez, CM; Eraña, H; Peccati, F; Vidal, E; Charco, JM; Sampedro-Torres-Quevedo, C; Pérez-Castro, MA; Lorenzo, NL; Giler, S; Tellingg, GC; Geijo, M; Requena, JR; Jiménez-Osés, G; Castilla, ...
NEUROBIOLOGY OF DISEASE
2025-09-01
Glycans and Chirality: Stereoselectivity at the Core of DC-SIGN's Recognition. A Novel View of the Optimum Minimal Ligand Epitope
Martínez, JD; Núñez-Franco, R; Valverde, P; Delgado, S; Ardá, A; Jiménez-Barbero, J; Jiménez-Oses, G; Cañada, FJ;
CHEMISTRY-A EUROPEAN JOURNAL
2025-05-22
The disease-linked R336C mutation in cystathionine β-synthase disrupts communication with the PLP cofactor, yet maintains the enzyme's overall structural integrity
Conter, C; Núñez-Franco, R; Al-Sadeq, DW; Fernández-Rodríguez, C; Goikoetxea-Usandizaga, N; Nasrallah, GK; Nomikos, M; Martinez-Chantar, ML; Astegno, A; Jiménez-Osés, G; Martínez-Cruz, LA;
FEBS JOURNAL
2025-05-06
Bis-CF3-bipyridine Ligands for the Iridium-Catalyzed Borylation of N-Methylamides
Marcos-Atanes, D; Jiménez-Osés, G; Mascareñas, JL;
ACS CATALYSIS
2025-04-16
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