Sara Alunno Rufini
Sara Alunno Rufini
DOCTORAL CANDIDATE
Computational Chemistry Lab
Address: Bizkaia Science and Technology Park, building 800, Derio (Bizkaia)

Computational Chemistry is a cross-disciplinary area devoted to the accurate atomistic simulation of chemical and biochemical phenomena, from small-molecule reactions and metal-catalyzed processes to protein folding, dynamics and function. It is at the core of the structure-activity relationship and uses cutting edge technology based on state-of-the art supercomputing, nearly-exact quantum mechanics and multiscale molecular mechanics and dynamics simulations, with strong validation and feedback from experiments.

The Computational Chemistry Group (CCG) at CIC bioGUNE aims to create a solid platform for the theoretical prediction of chemical reactions for bioconjugation, designing and simulation of therapeutic peptides and proteins, and understanding Glycochemistry processes. A strong emphasis is also made on the Computer-Aided Enzyme Engineering and Directed Evolution. These are the main research lines developed at our group:

  • Enzyme engineering and evolution: we use computational mutagenesis tools to predict and understand the structure-activity role of mutations in the catalytic performance of enzymes, both for biologically relevant processes and unnatural reactions with potential industrial application. We collaborate with leading biochemistry labs to guide and/or explain laboratory evolution towards stable, selective and highly active biocatalysts.
  • 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.
  • Drug Discovery: we use synthetic chemistry and in silico tools to generate small molecules and peptides with therapeutic potential for neurodegenerative disorders (amyloidogenesis inhibitors) and infectious diseases (antimicrobial agents).
  • Glycobiology: we provide detailed insights on the mechanisms of chemical and biochemical glycosylation processes and develop methods for the structural elucidation of complex glycocalyx components.
Latest Publications

Immobilization of Biantennary N-Glycans Leads to Branch Specific Epitope Recognition by LSECtin

Bertuzzi, S;Peccati, F;Serna, S;Artschwager, R;Notova, S;Thepaut, M;Jimenez-Oses, G;Fieschi, F;Reichardt, NC;Jimenez-Barbero, J;Arda, A

ACS CENTRAL SCIENCE

2022-09-20

Stereoselective alpha-Deuteration of Serine, Cysteine, Selenocysteine, and 2,3-Diaminopropanoic Acid Derivatives

Navo, CD;Oroz, P;Mazo, N;Blanco, M;Peregrina, JM;Jimenez-Oses, G

ORGANIC LETTERS

2022-09-09

Controlled masking and targeted release of redox-cycling ortho-quinones via a C-C bond-cleaving 1,6-elimination

Dunsmore, L;Navo, CD;Becher, J;de Montes, EG;Guerreiro, A;Hoyt, E;Brown, L;Zelenay, V;Mikutis, S;Cooper, J;Barbieri, I;Lawrinowitz, S;Siouve, E;Martin, E;Ruivo, PR;Rodrigues, T;da Cruz, FP;Werz, ...

NATURE CHEMISTRY

2022-06-27

Synthesis of beta(2,2)-Amino Acids by Stereoselective Alkylation of Isoserine Derivatives Followed by Nucleophilic Ring Opening of Quaternary Sulfamidates

Tovillas, P;Navo, CD;Oroz, P;Avenoza, A;Corzana, F;Zurbano, MM;Jimenez-Oses, G;Busto, JH;Peregrina, JM

JOURNAL OF ORGANIC CHEMISTRY

2022-06-22

Platform for Orthogonal N-Cysteine-Specific Protein Modification Enabled by Cyclopropenone Reagents

Istrate, A;Geeson, MB;Navo, CD;Sousa, BB;Marques, MC;Taylor, RJ;Journeaux, T;Oehler, SR;Mortensen, MR;Deery, MJ;Bond, AD;Corzana, F;Jimenez-Oses, G;Bernardes, GJL

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

2022-06-05

Assessing the Mobility of Severe Acute Respiratory Syndrome Coronavirus-2 Spike Protein Glycans by Structural and Computational Methods

Stagnoli, S;Peccati, F;Connell, SR;Martinez-Castillo, A;Charro, D;Millet, O;Bruzzone, C;Palazon, A;Arda, A;Jimenez-Barbero, J;Ereno-Orbea, J;Abrescia, NGA;Jimenez-Oses, G

FRONTIERS IN MICROBIOLOGY

2022-04-15

Triplet photodynamic and up-conversion luminescence in donor-acceptor dyads with slip-stacked vs. co-facial arrangement

Yun, YJ;Peccati, F;Wiederrecht, GP;Gosztola, DJ;Diroll, BT;Jimenez-Oses, G;Ayitou, AJL

JOURNAL OF MATERIALS CHEMISTRY C

2022-04-04

Single Mutation on Trastuzumab Modulates the Stability of Antibody-Drug Conjugates Built Using Acetal-Based Linkers and Thiol-Maleimide Chemistry

Ferhati, X;Jimenez-Moreno, E;Hoyt, EA;Salluce, G;Cabeza-Cabrerizo, M;Navo, CD;Companon, I;Akkapeddi, P;Matos, MJ;Salaverri, N;Garrido, P;Martinez, A;Laserna, V;Murray, TV;Jimenez-Oses, G;Ravn, ...

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

2022-03-30

Deconvoluting the Directed Evolution Pathway of Engineered Acyltransferase LovD

Garcia-Marquina, G;Nunez-Franco, R;Peccati, F;Tang, Y;Jimenez-Oses, G;Lopez-Gallego, F

CHEMCATCHEM

2022-01-10

A Computational Perspective on Molecular Recognition by Galectins

Nunez-Franco, R;Peccati, F;Jimenez-Oses, G

CURRENT MEDICINAL CHEMISTRY

2022-01-01