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2,150 results on '"Luchinat, Claudio"'

1. NMR-Based Metabolomics to Evaluate Individual Response to Treatments

Author

Vignoli, Alessia, Meoni, Gaia, Ghini, Veronica, Di Cesare, Francesca, Tenori, Leonardo, Luchinat, Claudio, Turano, Paola, Michel, Martin C., Editor-in-Chief, Barrett, James E., Editorial Board Member, Centurión, David, Editorial Board Member, Flockerzi, Veit, Editorial Board Member, Geppetti, Pierangelo, Editorial Board Member, Hofmann, Franz B., Editorial Board Member, Meier, Kathryn Elaine, Editorial Board Member, Page, Clive P., Editorial Board Member, Wang, KeWei, Editorial Board Member, Ghini, Veronica, editor, Stringer, Kathleen A., editor, and Luchinat, Claudio, editor

Published
2023
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2. Cerebrospinal fluid lipoproteins inhibit α-synuclein aggregation by interacting with oligomeric species in seed amplification assays

Author

Bellomo, Giovanni, Paciotti, Silvia, Concha-Marambio, Luis, Rizzo, Domenico, Wojdaƚa, Anna Lidia, Chiasserini, Davide, Gatticchi, Leonardo, Cerofolini, Linda, Giuntini, Stefano, De Luca, Chiara Maria Giulia, Ma, Yihua, Farris, Carly M., Pieraccini, Giuseppe, Bologna, Sara, Filidei, Marta, Ravera, Enrico, Lelli, Moreno, Moda, Fabio, Fragai, Marco, Parnetti, Lucilla, and Luchinat, Claudio

Published
2023
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3. Biomolecular NMR at 1.2 GHz

Author

Banci, Lucia, Barbieri, Letizia, Calderone, Vito, Cantini, Francesca, Cerofolini, Linda, Ciofi-Baffoni, Simone, Felli, Isabella C., Fragai, Marco, Lelli, Moreno, Luchinat, Claudio, Luchinat, Enrico, Parigi, Giacomo, Piccioli, Mario, Pierattelli, Roberta, Ravera, Enrico, Rosato, Antonio, Tenori, Leonardo, and Turano, Paola

Subjects
Physics - Chemical Physics, Physics - Biological Physics
Abstract

The development of new superconducting ceramic materials, which maintain the superconductivity at very intense magnetic fields, has prompted the development of a new generation of highly homogeneous high field magnets that has trespassed the magnetic field attainable with the previous generation of instruments. But how can biomolecular NMR benefit from this? In this work, we review a few of the notable applications that, we expect, will be blooming thanks to this newly available technology., Comment: 17 pages, 13 figures

Published
2019

6. Using Simple Algebraic Concepts to Understand Chemical Composition Problems

Author

Ravera, Enrico and Luchinat, Claudio

Abstract

Problems involving the composition of mixtures are common in chemical practice and are thus part of introductory Chemistry courses at the early undergraduate level. However, they are often perceived by students as a rather obscure matter, which may be due to poor familiarity with algebraic manipulations. Furthermore, to increase the distaste of students, these problems are susceptible to large errors arising from minor rounding errors, which is an intrinsic feature of the underlying operations. In this manuscript, we show how these problems can be easily solved with matrix algebra and, from this formulation, explain where the standard approaches for solving these problems come from, and how to reduce the numerical errors.

Published
2022
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11. Pseudocontact shifts and paramagnetic susceptibility in semiempirical and quantum chemistry theories

Author

Parigi, Giacomo, Benda, Ladislav, Ravera, Enrico, Romanelli, Maurizio, and Luchinat, Claudio

Subjects
Physics - Chemical Physics
Abstract

Pseudocontact shifts are traditionally described as a function of the anisotropy of the paramagnetic susceptibility tensor, according to the semiempirical theory mainly developed by Kurland and McGarvey (R.J. Kurland and B.R. McGarvey, J. Magn. Reson. 2, 286 (1970)). The paramagnetic susceptibility tensor is required to be symmetric. Applying point-dipole approximation to the quantum chemistry theory of hyperfine shift, pseudocontact shifts are found to scale with a non-symmetric tensor that differs by a factor g/ge from the paramagnetic susceptibility tensor derived within the semiempirical framework. We analyze the foundations of the Kurland-McGarvey pseudocontact shift expression and recall that it is inherently based on the Russell-Saunders (LS) coupling approximation for the spin-orbit coupling. We show that the difference between the semiempirical and quantum chemistry pseudocontact shift expressions arises directly from the different treatment of the orbital contribution to the hyperfine coupling.

Published
2018
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15. HTS by NMR for the Identification of Potent and Selective Inhibitors of Metalloenzymes

Author

Baggio, Carlo, Cerofolini, Linda, Fragai, Marco, Luchinat, Claudio, and Pellecchia, Maurizio

Subjects
Biotechnology, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, HTS by NMR, FBDD, FBLD, MMP, focused positional scanning libraries, Medicinal and Biomolecular Chemistry, Organic Chemistry, Pharmacology and Pharmaceutical Sciences
Abstract

We have recently proposed a novel drug discovery approach based on biophysical screening of focused positional scanning libraries in which each element of the library contained a common binding moiety for the given target or class of targets. In this Letter, we report on the implementation of this approach to target metal containing proteins. In our implementation, we first derived a focused positional scanning combinatorial library of peptide mimetics (of approximately 100,000 compounds) in which each element of the library contained the metal-chelating moiety hydroxamic acid at the C-terminal. Screening of this library by nuclear magnetic resonance spectroscopy in solution allowed the identification of a novel and selective compound series targeting MMP-12. The data supported that our general approach, perhaps applied using other metal chelating agents or other initial binding fragments, may result very effective in deriving novel and selective agents against metalloenzyme.

Published
2018

18. A geroscience approach for Parkinson’s disease: Conceptual framework and design of PROPAG-AGEING project

Author

Adarmes-Gómez, Astrid, Azevedo, Tiago, Bacalini, Maria Giulia, Baldelli, Luca, Bartoletti-Stella, Anna, Bhatia, Kailash P., Bonilla-Toribio, Marta, Boninsegna, Claudia, Broli, Marcella, Buiza-Rueda, Dolores, Calandra-Buonaura, Giovanna, Capellari, Sabina, Carrión-Claro, Mario, Cilea, Rosalia, Clayton, Robert, Cortelli, Pietro, Molin, Alessandra Dal, De Luca, Silvia, De Massis, Patrizia, Dimitri, Giovanna Maria, Doykov, Ivan, Escuela-Martin, Rocio, Fabbri, Giovanni, Franceschi, Claudio, Gabellini, Anna, Garagnani, Paolo, Giuliani, Cristina, Gómez-Garre, Pilar, Guaraldi, Pietro, Hägg, Sara, Hällqvist, Jenny, Halsband, Claire, Heywood, Wendy, Houlden, Henry, Huertas, Ismae, Jesús, Silvia, Jylhävä, Juulia, Labrador-Espinosa, Miguel A., Licari, Cristina, Liò, Pietro, Luchinat, Claudio, Macias, Daniel, Macrì, Stefania, Magrinelli, Francesca, Rodríguez, Juan Francisco Martín, Delledonne, Massimo, Maturo, Maria Giovanna, Mengozzi, Giacomo, Meoni, Gaia, Mignani, Francesco, Milazzo, Maddalena, Mills, Kevin, Mir, Pablo, Mollenhauer, Brit, Nardini, Christine, Nassetti, Stefania Alessandra, Pedersen, Nancy L., Periñán-Tocino, Maria Teresa, Pirazzini, Chiara, Provini, Federica, Ravaioli, Francesco, Sala, Claudia, Sambati, Luisa, Scaglione, Cesa Lorella Maria, Schade, Sebastian, Schreglmann, Sebastian, Spasov, Simeon, Strom, Stephen, Tejera-Parrado, Cristina, Tenori, Leonardo, Trenkwalder, Claudia, Turano, Paola, Valzania, Franco, Ortega, Rosario Vigo, Williams, Dylan, Xumerle, Luciano, Zago, Elisa, Dal Molin, Alessandra, and Kwiatkowska, Katarzyna Malgorzata

Published
2021
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23. Exploring the Effects of Probiotic Treatment on Urinary and Serum Metabolic Profiles in Healthy Individuals

Author

Di Cesare, Francesca, primary, Calgaro, Matteo, additional, Ghini, Veronica, additional, Squarzanti, Diletta Francesca, additional, De Prisco, Annachiara, additional, Visciglia, Annalisa, additional, Zanetta, Paola, additional, Rolla, Roberta, additional, Savoia, Paola, additional, Amoruso, Angela, additional, Azzimonti, Barbara, additional, Vitulo, Nicola, additional, Tenori, Leonardo, additional, Luchinat, Claudio, additional, and Pane, Marco, additional

Published
2023
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24. COVID-19: A complex disease with a unique metabolic signature

Author

Ghini, Veronica, primary, Vieri, Walter, additional, Celli, Tommaso, additional, Pecchioli, Valentina, additional, Boccia, Nunzia, additional, Alonso-Vásquez, Tania, additional, Pelagatti, Lorenzo, additional, Fondi, Marco, additional, Luchinat, Claudio, additional, Bertini, Laura, additional, Vannucchi, Vieri, additional, Landini, Giancarlo, additional, and Turano, Paola, additional

Published
2023
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25. Accurate, fully-automated NMR spectral profiling for metabolomics

Author

Ravanbakhsh, Siamak, Liu, Philip, Bjorndahl, Trent, Mandal, Rupasri, Grant, Jason R., Wilson, Michael, Eisner, Roman, Sinelnikov, Igor, Hu, Xiaoyu, Luchinat, Claudio, Greiner, Russell, and Wishart, David S.

Subjects
Computer Science - Artificial Intelligence, Computer Science - Computational Engineering, Finance, and Science, Quantitative Biology - Quantitative Methods
Abstract

Many diseases cause significant changes to the concentrations of small molecules (aka metabolites) that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile". This information can be extracted from a biofluid's NMR spectrum. Today, this is often done manually by trained human experts, which means this process is relatively slow, expensive and error-prone. This paper presents a tool, Bayesil, that can quickly, accurately and autonomously produce a complex biofluid's (e.g., serum or CSF) metabolic profile from a 1D1H NMR spectrum. This requires first performing several spectral processing steps then matching the resulting spectrum against a reference compound library, which contains the "signatures" of each relevant metabolite. Many of these steps are novel algorithms and our matching step views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures, show that Bayesil can autonomously find the concentration of all NMR-detectable metabolites accurately (~90% correct identification and ~10% quantification error), in <5minutes on a single CPU. These results demonstrate that Bayesil is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively -- with an accuracy that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of NMR in clinical settings. Available at http://www.bayesil.ca.

Published
2014
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27. A framework for validating AI in precision medicine: considerations from the European ITFoC consortium

Author

Tsopra, Rosy, Fernandez, Xose, Luchinat, Claudio, Alberghina, Lilia, Lehrach, Hans, Vanoni, Marco, Dreher, Felix, Sezerman, O.Ugur, Cuggia, Marc, de Tayrac, Marie, Miklasevics, Edvins, Itu, Lucian Mihai, Geanta, Marius, Ogilvie, Lesley, Godey, Florence, Boldisor, Cristian Nicolae, Campillo-Gimenez, Boris, Cioroboiu, Cosmina, Ciusdel, Costin Florian, Coman, Simona, Hijano Cubelos, Oliver, Itu, Alina, Lange, Bodo, Le Gallo, Matthieu, Lespagnol, Alexandra, Mauri, Giancarlo, Soykam, H.Okan, Rance, Bastien, Turano, Paola, Tenori, Leonardo, Vignoli, Alessia, Wierling, Christoph, Benhabiles, Nora, and Burgun, Anita

Published
2021
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32. Machine Learning-Enhanced Quantum Chemistry-Assisted Refinement of the Active Site Structure of Metalloproteins

Author

Gigli, Lucia, Silva, José Malanho, Cerofolini, Linda, Macedo, Anjos L., Geraldes, Carlos F. G. C., Suturina, Elizaveta A., Calderone, Vito, Fragai, Marco, Parigi, Giacomo, Ravera, Enrico, and Luchinat, Claudio

Abstract

Understanding the fine structural details of inhibitor binding at the active site of metalloenzymes can have a profound impact on the rational drug design targeted to this broad class of biomolecules. Structural techniques such as NMR, cryo-EM, and X-ray crystallography can provide bond lengths and angles, but the uncertainties in these measurements can be as large as the range of values that have been observed for these quantities in all the published structures. This uncertainty is far too large to allow for reliable calculations at the quantum chemical (QC) levels for developing precise structure–activity relationships or for improving the energetic considerations in protein-inhibitor studies. Therefore, the need arises to rely upon computational methods to refine the active site structures well beyond the resolution obtained with routine application of structural methods. In a recent paper, we have shown that it is possible to refine the active site of cobalt(II)-substituted MMP12, a metalloprotein that is a relevant drug target, by matching to the experimental pseudocontact shifts (PCS) those calculated using multireference ab initio QC methods. The computational cost of this methodology becomes a significant bottleneck when the starting structure is not sufficiently close to the final one, which is often the case with biomolecular structures. To tackle this problem, we have developed an approach based on a neural network (NN) and a support vector regression (SVR) and applied it to the refinement of the active site structure of oxalate-inhibited human carbonic anhydrase 2 (hCAII), another prototypical metalloprotein target. The refined structure gives a remarkably good agreement between the QC-calculated and the experimental PCS. This study not only contributes to the knowledge of CAII but also demonstrates the utility of combining machine learning (ML) algorithms with QC calculations, offering a promising avenue for investigating other drug targets and complex biological systems in general.

Published
2024
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33. Dependence of apparent diffusion coefficient measurement on diffusion gradient direction and spatial position – A quality assurance intercomparison study of forty-four scanners for quantitative diffusion-weighted imaging

Author

Fedeli, Luca, Belli, Giacomo, Ciccarone, Antonio, Coniglio, Angela, Esposito, Marco, Giannelli, Marco, Mazzoni, Lorenzo Nicola, Nocetti, Luca, Sghedoni, Roberto, Tarducci, Roberto, Altabella, Luisa, Belligotti, Eleonora, Benelli, Matteo, Betti, Margherita, Caivano, Rocchina, Carni', Marco, Chiappiniello, Andrea, Cimolai, Sara, Cretti, Fabiola, Fulcheri, Christian, Gasperi, Chiara, Giacometti, Mara, Levrero, Fabrizio, Lizio, Domenico, Maieron, Marta, Marzi, Simona, Mascaro, Lorella, Mazzocchi, Silvia, Meliado', Gabriele, Morzenti, Sabrina, Noferini, Linhsia, Oberhofer, Nadia, Quattrocchi, Maria Grazia, Ricci, Alessandra, Taddeucci, Adriana, Tenori, Leonardo, Luchinat, Claudio, Gobbi, Gianni, Gori, Cesare, and Busoni, Simone

Published
2018
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35. The NMR tube bioreactor

Author

Chatzikonstantinou, Alexandra V., primary, Tsiailanis, Antonis D., additional, Gerothanassis, Ioannis P., additional, Stamatis, Haralambos, additional, Ravera, Enrico, additional, Fragai, Marco, additional, Luchinat, Claudio, additional, Parigi, Giacomo, additional, and Tzakos, Andreas G., additional

Published
2020
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36. Theoretical analysis of the long-distance limit of NMR chemical shieldings.

Author

Lang, Lucas, Ravera, Enrico, Parigi, Giacomo, Luchinat, Claudio, and Neese, Frank

Subjects
CHEMICAL shift (Nuclear magnetic resonance), QUADRUPOLE moments, SPIN-orbit interactions, DIRAC equation, GAUGE invariance, NUCLEAR charge
Abstract

After some years of controversy, it was recently demonstrated how to obtain the correct long-distance limit [point-dipole approximation (PDA)] of pseudo-contact nuclear magnetic resonance chemical shifts from rigorous first-principles quantum mechanics [Lang et al., J. Phys. Chem. Lett. 11, 8735 (2020)]. This result confirmed the classical Kurland–McGarvey theory. In the present contribution, we elaborate on these results. In particular, we provide a detailed derivation of the PDA both from the Van den Heuvel–Soncini equation for the chemical shielding tensor and from a spin Hamiltonian approximation. Furthermore, we discuss in detail the PDA within the approximate density functional theory and Hartree–Fock theories. In our previous work, we assumed a relatively crude effective nuclear charge approximation for the spin–orbit coupling operator. Here, we overcome this assumption by demonstrating that the derivation is also possible within the fully relativistic Dirac equation and even without the assumption of a specific form for the Hamiltonian. Crucial ingredients for the general derivation are a Hamiltonian that respects gauge invariance, the multipolar gauge, and functional derivatives of the Hamiltonian, where it is possible to identify the first functional derivative with the electron number current density operator. The present work forms an important foundation for future extensions of the Kurland–McGarvey theory beyond the PDA, including induced magnetic quadrupole and higher moments to describe the magnetic hyperfine field. [ABSTRACT FROM AUTHOR]

Published
2022
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44. Combining Solid‐State NMR with Structural and Biophysical Techniques to Design Challenging Protein‐Drug Conjugates

Author

Cerofolini, Linda, primary, Vasa, Kristian, additional, Bianconi, Elisa, additional, Salobehaj, Maria, additional, Cappelli, Giulia, additional, Bonciani, Alice, additional, Licciardi, Giulia, additional, Pérez‐Ràfols, Anna, additional, Padilla‐Cortés, Luis, additional, Antonacci, Sabrina, additional, Rizzo, Domenico, additional, Ravera, Enrico, additional, Viglianisi, Caterina, additional, Calderone, Vito, additional, Parigi, Giacomo, additional, Luchinat, Claudio, additional, Macchiarulo, Antonio, additional, Menichetti, Stefano, additional, and Fragai, Marco, additional

Published
2023
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47. Exploration of Blood Metabolite Signatures of Colorectal Cancer and Polyposis through Integrated Statistical and Network Analysis

Author

Di Cesare, Francesca, Vignoli, Alessia, Luchinat, Claudio, Tenori, Leonardo, Saccenti, Edoardo, Di Cesare, Francesca, Vignoli, Alessia, Luchinat, Claudio, Tenori, Leonardo, and Saccenti, Edoardo

Abstract

Colorectal cancer (CRC), one of the most prevalent and deadly cancers worldwide, generally evolves from adenomatous polyps. The understanding of the molecular mechanisms underlying this pathological evolution is crucial for diagnostic and prognostic purposes. Integrative systems biology approaches offer an optimal point of view to analyze CRC and patients with polyposis. The present study analyzed the association networks constructed from a publicly available array of 113 serum metabolites measured on a cohort of 234 subjects from three groups (66 CRC patients, 76 patients with polyposis, and 92 healthy controls), which concentrations were obtained via targeted liquid chromatography-tandem mass spectrometry. In terms of architecture, topology, and connectivity, the metabolite-metabolite association network of CRC patients appears to be completely different with respect to patients with polyposis and healthy controls. The most relevant nodes in the CRC network are those related to energy metabolism. Interestingly, phenylalanine, tyrosine, and tryptophan metabolism are found to be involved in both CRC and polyposis. Our results demonstrate that the characterization of metabolite–metabolite association networks is a promising and powerful tool to investigate molecular aspects of CRC.

Published
2023

48. Plasma metabolome and cognitive skills in Down syndrome

Author

Antonaros, Francesca, Ghini, Veronica, Pulina, Francesca, Ramacieri, Giuseppe, Cicchini, Elena, Mannini, Elisa, Martelli, Anna, Feliciello, Agnese, Lanfranchi, Silvia, Onnivello, Sara, Vianello, Renzo, Locatelli, Chiara, Cocchi, Guido, Pelleri, Maria Chiara, Vitale, Lorenza, Strippoli, Pierluigi, Luchinat, Claudio, Turano, Paola, Piovesan, Allison, and Caracausi, Maria

Published
2020
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