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Zeppilli D, Aldinio-Colbachini A, Ribaudo G, Tubaro C, Dalla Tiezza M, Bortoli M, Zagotto G, Orian L. Antioxidant Chimeric Molecules: Are Chemical Motifs Additive? The Case of a Selenium-Based Ligand. Int J Mol Sci 2023; 24:11797. [PMID: 37511560 PMCID: PMC10380222 DOI: 10.3390/ijms241411797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
We set up an in silico experiment and designed a chimeric compound integrating molecular features from different efficient ROS (Reactive Oxygen Species) scavengers, with the purpose of investigating potential relationships between molecular structure and antioxidant activity. Furthermore, a selenium centre was inserted due to its known capacity to reduce hydroperoxides, acting as a molecular mimic of glutathione peroxidase; finally, since this organoselenide is a precursor of a N-heterocyclic carbene ligand, its Au(I) carbene complex was designed and examined. A validated protocol based on DFT (Density Functional Theory) was employed to investigate the radical scavenging activity of available sites on the organoselenide precursor ((SMD)-M06-2X/6-311+G(d,p)//M06-2X/6-31G(d)), as well as on the organometallic complex ((SMD)-M06-2X/SDD (Au), 6-311+G(d,p)//ZORA-BLYP-D3(BJ)/TZ2P), considering HAT (Hydrogen Atom Transfer) and RAF (Radical Adduct Formation) regarding five different radicals. The results of this case study suggest that the antioxidant potential of chemical motifs should not be considered as an additive property when designing a chimeric compound, but rather that the relevance of a molecular topology is derived from a chemical motif combined with an opportune chemical space of the molecule. Thus, the direct contributions of single functional groups which are generally thought of as antioxidants per se do not guarantee the efficient radical scavenging potential of a molecular species.
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Affiliation(s)
- Davide Zeppilli
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Anna Aldinio-Colbachini
- CNRS, Aix Marseille Université, BIP, IMM, IM2B, 31 Chemin J. Aiguier, 13009 Marseille, France
| | - Giovanni Ribaudo
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Cristina Tubaro
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Marco Dalla Tiezza
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Marco Bortoli
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, University of Oslo, 0315 Oslo, Norway
| | - Giuseppe Zagotto
- Dipartimento di Scienze del Farmaco, Università degli Studi di Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Laura Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
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2
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Zeppilli D, Ribaudo G, Pompermaier N, Madabeni A, Bortoli M, Orian L. Radical Scavenging Potential of Ginkgolides and Bilobalide: Insight from Molecular Modeling. Antioxidants (Basel) 2023; 12:antiox12020525. [PMID: 36830083 PMCID: PMC9952587 DOI: 10.3390/antiox12020525] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/12/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The reactive oxygen species (ROS) scavenging capacities of ginkgolides and bilobalide, which are the peculiar constituents of the extract of Ginkgo biloba, are investigated in silico (level of theory: (SMD)-M06-2X/6-311+G(d,p)//M06-2X/6-31G(d)). Unlike other popular antioxidant natural substances, the carbon backbones of these compounds are entirely aliphatic and exclusively single C-C bonds are present. The selectivity for alkoxyl radicals via hydrogen-atom transfer (HAT) is assessed; importantly, the scavenging of peroxyl radicals is also possible from a peculiar site, here labeled C10 both for ginkgolides and bilobalide. The energetics are described in detail, and the analysis discloses that the studied compounds are powerful scavengers, with thermodynamic and kinetic properties similar to those of Trolox and melatonin, and that, in addition, they display selectivity for peroxyl radicals. These are all chemical-reactivity features contributing to the therapeutic action of the extract of G. biloba.
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Affiliation(s)
- Davide Zeppilli
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35129 Padova, Italy
| | - Giovanni Ribaudo
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Nicola Pompermaier
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35129 Padova, Italy
| | - Andrea Madabeni
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35129 Padova, Italy
| | - Marco Bortoli
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, 0315 Oslo, Norway
| | - Laura Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35129 Padova, Italy
- Correspondence:
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3
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Ribaudo G, Orian L. From a Molecule to a Drug: Chemical Features Enhancing Pharmacological Potential. Molecules 2022; 27:molecules27134144. [PMID: 35807388 PMCID: PMC9268219 DOI: 10.3390/molecules27134144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 06/27/2022] [Indexed: 02/05/2023] Open
Abstract
Health is a fundamental human right and is a global goal to which extensive research effort is devoted in all fields [...]
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Affiliation(s)
- Giovanni Ribaudo
- Dipartimento di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy;
| | - Laura Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131 Padova, Italy
- Correspondence:
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4
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Analytical and Theoretical Studies of Antioxidant Properties of Chosen Anthocyanins; A Structure-Dependent Relationships. Int J Mol Sci 2022; 23:ijms23105432. [PMID: 35628243 PMCID: PMC9141991 DOI: 10.3390/ijms23105432] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/08/2022] [Accepted: 05/11/2022] [Indexed: 02/04/2023] Open
Abstract
The relationship between the structure and the antiradical and antioxidant activities of three anthocyanidins, namely peonidin, petunidin, and delphinidin, and their glucosides was investigated in this study. The ability of anthocyanins to scavenge free radicals was determined using DPPH● assay, whereas the inhibition of peroxidation in liposomes in relation to a model membrane that imitated the composition of a lipid membrane in tumor cells was specified using the fluorimetric method. To explore this issue at the atomistic level, density functional theory studies were applied. It was shown that glycosides performed better than anthocyanidins in protecting membranes against oxidation. The highest redox potential was demonstrated by anthocyanidins with the highest number of hydroxyl groups in the B ring in the order as follows: (Dp > Pt > Pn), and the same relationship was proven for their glucosides. The majority of the compounds studied here proved to be better antioxidants than ascorbic acid. They showed consistent electrodonating properties and though the f-HAT mechanism became more feasible with each consecutive deprotonation. Glycosylation did not have a direct impact on reactivity, apart from peonidin and petunidin in the study of which it was found that this process was responsible for lifting off steric hindrance between B and C rings and rendering certain pathways more feasible. Kinetic and molecular dynamics are essential to properly describe the membrane’s lipid oxidation.
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Spiegel M. Current Trends in Computational Quantum Chemistry Studies on Antioxidant Radical Scavenging Activity. J Chem Inf Model 2022; 62:2639-2658. [PMID: 35436117 PMCID: PMC9198981 DOI: 10.1021/acs.jcim.2c00104] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
The antioxidative
nature of chemicals is now routinely studied
using computational quantum chemistry. Scientists are constantly proposing
new approaches to investigate those methods, and the subject is evolving
at a rapid pace. The goal of this review is to collect, consolidate,
and present current trends in a clear, methodical, and reference-rich
manner. This paper is divided into several sections, each of which
corresponds to a different stage of elaborations: preliminary concerns,
electronic structure analysis, and general reactivity (thermochemistry
and kinetics). The sections are further subdivided based on methodologies
used. Concluding remarks and future perspectives are presented based
on the remaining elements.
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Affiliation(s)
- Maciej Spiegel
- Department of Pharmacognosy and Herbal Medicines, Wroclaw Medical University, Borowska 211A, 50-556 Wroclaw, Poland
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6
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Ribaudo G, Bortoli M, Witt CE, Parke B, Mena S, Oselladore E, Zagotto G, Hashemi P, Orian L. ROS-Scavenging Selenofluoxetine Derivatives Inhibit In Vivo Serotonin Reuptake. ACS OMEGA 2022; 7:8314-8322. [PMID: 35309454 PMCID: PMC8928538 DOI: 10.1021/acsomega.1c05567] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
While the neurochemistry that underpins the behavioral phenotypes of depression is the subject of many studies, oxidative stress caused by the inflammation comorbid with depression has not adequately been addressed. In this study, we described novel antidepressant-antioxidant agents consisting of selenium-modified fluoxetine derivatives to simultaneously target serotonin reuptake (antidepressant action) and oxidative stress. Excitingly, we show that one of these agents (1-F) carries the ability to inhibit serotonin reuptake in vivo in mice. We therefore present a frontier dual strategy that paves the way for the future of antidepressant therapies.
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Affiliation(s)
- Giovanni Ribaudo
- Dipartimento
di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Marco Bortoli
- Dipartimento
di Scienze Chimiche, Università degli
Studi di Padova Via Marzolo 1, 35131 Padova, Italy
- Institut
de Química Computacional i Catàlisi and Departament
de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Catalonia, Spain
| | - Colby E. Witt
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia South Carolina 29201, United States
| | - Brenna Parke
- Department
of Bioengineering, Imperial College London, London SW7 2AZ, U.K.
| | - Sergio Mena
- Department
of Bioengineering, Imperial College London, London SW7 2AZ, U.K.
| | - Erika Oselladore
- Dipartimento
di Medicina Molecolare e Traslazionale, Università degli Studi di Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Giuseppe Zagotto
- Dipartimento
di Scienze del Farmaco, Università
degli Studi di Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Parastoo Hashemi
- Department
of Bioengineering, Imperial College London, London SW7 2AZ, U.K.
- Department
of Chemistry and Biochemistry, University
of South Carolina, Columbia South Carolina 29201, United States
| | - Laura Orian
- Dipartimento
di Scienze Chimiche, Università degli
Studi di Padova Via Marzolo 1, 35131 Padova, Italy
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Writing assistant scoring system for English second language learners based on machine learning. JOURNAL OF INTELLIGENT SYSTEMS 2022. [DOI: 10.1515/jisys-2022-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
To reduce the workload of paper evaluation and improve the fairness and accuracy of the evaluation process, a writing assistant scoring system for English as a Foreign Language (EFL) learners is designed based on the principle of machine learning. According to the characteristics of the data processing process and the advantages and disadvantages of the Browser/Server (B/S) structure, the equipment structure design of the project online evaluation teaching auxiliary system is further optimized. The panda method is used to read the data, the clean method is used to realize the data preprocessing, the model test is carried out, the cross validation method is selected, the data is divided in advance, and the process of programming the problem scoring system is further optimized, the automatic scoring technology is constructed by English teaching recognition module, feature extraction module and scoring module, the table structure of programming problems is designed, the auxiliary evaluation program of English writing is designed, and the design of writing auxiliary scoring system is completed. The analysis of the experimental results shows that the accuracy of the system is close to 90%, and the total average difference is 0.56. The system can normally take out a variety of test papers. Considering the subjectivity of manual scoring and the impact of key code setting on scoring, the carefully set key code can effectively improve the scoring accuracy of the system. The scoring strategy of the automatic scoring system is effective and the scoring effect is good, and it can be used in practical application.
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Liu BB. Design of Golfer’s Heart Rate Data Transmission System Based on Machine Learning. IOT AND BIG DATA TECHNOLOGIES FOR HEALTH CARE 2022:105-118. [DOI: 10.1007/978-3-030-94185-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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9
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Dalla Tiezza M, Hamlin TA, Bickelhaupt FM, Orian L. Radical Scavenging Potential of the Phenothiazine Scaffold: A Computational Analysis. ChemMedChem 2021; 16:3763-3771. [PMID: 34536069 PMCID: PMC9292796 DOI: 10.1002/cmdc.202100546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/05/2021] [Indexed: 01/05/2023]
Abstract
The reactivity of phenothiazine (PS), phenoselenazine (PSE), and phenotellurazine (PTE) with different reactive oxygen species (ROS) has been studied using density functional theory (DFT) in combination with the QM‐ORSA (Quantum Mechanics‐based Test for Overall Free Radical Scavenging Activity) protocol for an accurate kinetic rate calculation. Four radical scavenging mechanisms have been screened, namely hydrogen atom transfer (HAT), radical adduct formation (RAF), single electron transfer (SET), and the direct oxidation of the chalcogen atom. The chosen ROS are HO., HOO., and CH3OO.. PS, PSE, and PTE exhibit an excellent antioxidant activity in water regardless of the ROS due to their characteristic diffusion‐controlled regime processes. For the HO. radical, the primary active reaction mechanism is, for all antioxidants, RAF. But, for HOO. and CH3OO., the dominant mechanism strongly depends on the antioxidant: HAT for PS and PSE, and SET for PTE. The scavenging efficiency decreases dramatically in lipid environment and remains only significant (via RAF) for the most reactive radical (HO.). Therefore, PS, PSE, and PTE are excellent antioxidant molecules, especially in aqueous, physiological environments where they are active against a broad spectrum of harmful radicals. There is no advantage or significant difference in the scavenging efficiency when changing the chalcogen since the reactivity mainly derives from the amino hydrogen and the aromatic sites.
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Affiliation(s)
- Marco Dalla Tiezza
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Trevor A Hamlin
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Amsterdam Center for Multiscale Modeling (ACMM), Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Institute for Molecules and Materials (IMM), Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Laura Orian
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Via Marzolo 1, 35131, Padova, Italy
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Ceriotti M, Clementi C, Anatole von Lilienfeld O. Machine learning meets chemical physics. J Chem Phys 2021; 154:160401. [PMID: 33940847 DOI: 10.1063/5.0051418] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Over recent years, the use of statistical learning techniques applied to chemical problems has gained substantial momentum. This is particularly apparent in the realm of physical chemistry, where the balance between empiricism and physics-based theory has traditionally been rather in favor of the latter. In this guest Editorial for the special topic issue on "Machine Learning Meets Chemical Physics," a brief rationale is provided, followed by an overview of the topics covered. We conclude by making some general remarks.
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Affiliation(s)
- Michele Ceriotti
- Laboratory of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Cecilia Clementi
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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Castro-González LM, Galano A, Alvarez-Idaboy JR. Free radical scavenging activity of newly designed sesamol derivatives. NEW J CHEM 2021. [DOI: 10.1039/d1nj02225c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Recently proposed derivatives of sesamol as better oxidants than the parent molecule are predicted to react faster, with several orders larger rate constants than sesamol itself.
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Affiliation(s)
- Laura M. Castro-González
- Department of Biological Sciences
- Centre for Molecular Simulation
- University of Calgary
- Calgary
- Canada
| | - Annia Galano
- Departamento de Química
- Universidad Autónoma Metropolitana-Iztapalapa
- Mexico
| | - Juan Raúl Alvarez-Idaboy
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México
- Mexico
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