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Author Angelica Mazzolari

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MetaClass, a Comprehensive Classification System for Predicting the Occurrence of Metabolic Reactions Based on the MetaQSAR Database.

Angelica Mazzolari, Alice Scaccabarozzi, Giulio Vistoli, Alessandro Pedretti,

(1) Background: Machine learning algorithms are finding fruitful applications in predicting the ADME profile of new molecules, with a particular focus on metabolism predictions. However, the development of comprehensive metabolism predictors is hampered by the lack of highly accurate metabolic resources. Hence, we recently proposed a manually curated metabolic database ... Read more >>

Molecules (Molecules (Basel, Switzerland))
[2021, 26(19):]

Cited: 0 times

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The VEGA suite of programs: an versatile platform for cheminformatics and drug design projects.

Alessandro Pedretti, Angelica Mazzolari, Silvia Gervasoni, Laura Fumagalli, Giulio Vistoli,

The purpose of the article is to offer an overview of the latest release of the VEGA suite of programs. This software has been constantly developed and freely released during the last 20 years and has now reached a significant diffusion and technology level as confirmed by the about 22 500 registered ... Read more >>

Bioinformatics (Bioinformatics (Oxford, England))
[2021, 37(8):1174-1175]

Cited: 7 times

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MetaTREE, a Novel Database Focused on Metabolic Trees, Predicts an Important Detoxification Mechanism: The Glutathione Conjugation.

Angelica Mazzolari, Luca Sommaruga, Alessandro Pedretti, Giulio Vistoli,

(1) Background: Data accuracy plays a key role in determining the model performances and the field of metabolism prediction suffers from the lack of truly reliable data. To enhance the accuracy of metabolic data, we recently proposed a manually curated database collected by a meta-analysis of the specialized literature (MetaQSAR). ... Read more >>

Molecules (Molecules (Basel, Switzerland))
[2021, 26(7):]

Cited: 1 time

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What Makes a Paper Be Highly Cited? 60 Years of the Journal of Chemical Information and Modeling.

Ariane Nunes-Alves, Angelica Mazzolari, Kenneth M Merz,

J Chem Inf Model (Journal of chemical information and modeling)
[2020, 60(12):5866-5867]

Cited: 0 times

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Repositioning Dequalinium as Potent Muscarinic Allosteric Ligand by Combining Virtual Screening Campaigns and Experimental Binding Assays.

Angelica Mazzolari, Silvia Gervasoni, Alessandro Pedretti, Laura Fumagalli, Rosanna Matucci, Giulio Vistoli,

Structure-based virtual screening is a truly productive repurposing approach provided that reliable target structures are available. Recent progresses in the structural resolution of the G-Protein Coupled Receptors (GPCRs) render these targets amenable for structure-based repurposing studies. Hence, the present study describes structure-based virtual screening campaigns with a view to repurposing ... Read more >>

Int J Mol Sci (International journal of molecular sciences)
[2020, 21(17):]

Cited: 1 time

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GLORYx: Prediction of the Metabolites Resulting from Phase 1 and Phase 2 Biotransformations of Xenobiotics.

Christina de Bruyn Kops, Martin Šícho, Angelica Mazzolari, Johannes Kirchmair,

Predicting the structures of metabolites formed in humans can provide advantageous insights for the development of drugs and other compounds. Here we present GLORYx, which integrates machine learning-based site of metabolism (SoM) prediction with reaction rule sets to predict and rank the structures of metabolites that could potentially be formed ... Read more >>

Chem Res Toxicol (Chemical research in toxicology)
[2021, 34(2):286-299]

Cited: 4 times

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Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry.

Angelica Mazzolari, Ariane Nunes-Alves, Habibah A Wahab, Rommie E Amaro, Zoe Cournia, Kenneth M Merz,

In this Viewpoint, we provide a commentary on the impact of the <i>Journal of Chemical Information and Modeling</i> Special Issue on Women in Computational Chemistry published in May 2019 and the feedback we received. ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, 60(7):3328-3330]

Cited: 1 time

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Carbachol dimers with primary carbamate groups as homobivalent modulators of muscarinic receptors.

Rosanna Matucci, Cristina Bellucci, Maria Vittoria Martino, Marta Nesi, Dina Manetti, Jessica Welzel, Ulrike Bartz, Janine Holze, Christian Tränkle, Klaus Mohr, Angelica Mazzolari, Giulio Vistoli, Silvia Dei, Elisabetta Teodori, Maria Novella Romanelli,

Although agonists and antagonists of muscarinic receptors have been known for long time, there is renewed interest in compounds (such as allosteric or bitopic ligands, or biased agonists) able to differently and selectively modulate these receptors. As a continuation of our previous research, we designed a new series of dimers ... Read more >>

Eur J Pharmacol (European journal of pharmacology)
[2020, 883:173183]

Cited: 1 time

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Unveiling the molecular mechanisms underpinning biorecognition of early-glycated human serum albumin and receptor for advanced glycation end products.

Anna Tramarin, Marina Naldi, Genny Degani, Loredana Lupu, Pascal Wiegand, Angelica Mazzolari, Alessandra Altomare, Giancarlo Aldini, Laura Popolo, Giulio Vistoli, Michael Przybylski, Manuela Bartolini,

Serum levels of early-glycated albumin are significantly increased in patients with diabetes mellitus and may play a role in worsening inflammatory status and sustaining diabetes-related complications. To investigate possible pathological recognition involving early-glycated albumin and the receptor for advanced glycation end products (RAGE), an early-glycated human serum albumin (HSAgly), with ... Read more >>

Anal Bioanal Chem (Analytical and bioanalytical chemistry)
[2020, 412(18):4245-4259]

Cited: 0 times

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FAME 3: Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes.

Martin Šícho, Conrad Stork, Angelica Mazzolari, Christina de Bruyn Kops, Alessandro Pedretti, Bernard Testa, Giulio Vistoli, Daniel Svozil, Johannes Kirchmair,

In this work we present the third generation of FAst MEtabolizer (FAME 3), a collection of extra trees classifiers for the prediction of sites of metabolism (SoMs) in small molecules such as drugs, druglike compounds, natural products, agrochemicals, and cosmetics. FAME 3 was derived from the MetaQSAR database ( Pedretti ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2019, 59(8):3400-3412]

Cited: 13 times

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Rescoring and Linearly Combining: A Highly Effective Consensus Strategy for Virtual Screening Campaigns.

Alessandro Pedretti, Angelica Mazzolari, Silvia Gervasoni, Giulio Vistoli,

The study proposes a novel consensus strategy based on linear combinations of different docking scores to be used in the evaluation of virtual screening campaigns. The consensus models are generated by applying the recently proposed Enrichment Factor Optimization (EFO) method, which develops the linear equations by exhaustively combining the available ... Read more >>

Int J Mol Sci (International journal of molecular sciences)
[2019, 20(9):]

Cited: 5 times

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Prediction of UGT-mediated Metabolism Using the Manually Curated MetaQSAR Database.

Angelica Mazzolari, Avid M Afzal, Alessandro Pedretti, Bernard Testa, Giulio Vistoli, Andreas Bender,

Even though glucuronidations are the most frequent metabolic reactions of conjugation, both in quantitative and qualitative terms, they have rather seldom been investigated using computational approaches. To fill this gap, we have used the manually collected MetaQSAR metabolic reaction database to generate two models for the prediction of UGT-mediated metabolism, ... Read more >>

ACS Med Chem Lett (ACS medicinal chemistry letters)
[2019, 10(4):633-638]

Cited: 4 times

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Prediction of the Formation of Reactive Metabolites by A Novel Classifier Approach Based on Enrichment Factor Optimization (EFO) as Implemented in the VEGA Program.

Angelica Mazzolari, Giulio Vistoli, Bernard Testa, Alessandro Pedretti,

The study is aimed at developing linear classifiers to predict the capacity of a given substrate to yield reactive metabolites. While most of the hitherto reported predictive models are based on the occurrence of known structural alerts (e.g., the presence of toxophoric groups), the present study is focused on the ... Read more >>

Molecules (Molecules (Basel, Switzerland))
[2018, 23(11):]

Cited: 5 times

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WarpEngine, a Flexible Platform for Distributed Computing Implemented in the VEGA Program and Specially Targeted for Virtual Screening Studies.

Alessandro Pedretti, Angelica Mazzolari, Giulio Vistoli,

The manuscript describes WarpEngine, a novel platform implemented within the VEGA ZZ suite of software for performing distributed simulations both in local and wide area networks. Despite being tailored for structure-based virtual screening campaigns, WarpEngine possesses the required flexibility to carry out distributed calculations utilizing various pieces of software, which ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2018, 58(6):1154-1160]

Cited: 2 times

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Approaching Pharmacological Space: Events and Components.

Giulio Vistoli, Alessandro Pedretti, Angelica Mazzolari, Bernard Testa,

With a view to introducing the concept of pharmacological space and its potential applications in investigating and predicting the toxic mechanisms of xenobiotics, this opening chapter describes the logical relations between conformational behavior, physicochemical properties and binding spaces, which are seen as the three key elements composing the pharmacological space. ... Read more >>

Methods Mol Biol (Methods in molecular biology (Clifton, N.J.))
[2018, 1800:245-274]

Cited: 0 times

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MetaQSAR: An Integrated Database Engine to Manage and Analyze Metabolic Data.

Alessandro Pedretti, Angelica Mazzolari, Giulio Vistoli, Bernard Testa,

The study describes the MetaQSAR tool, a new database engine specifically tailored to collect and analyze metabolic data. This is a plug-in embedded in the VEGA suite of programs (freely downloadable at www.vegazz.net ) and takes advantage from all cheminformatics features implemented in the software with additional tools aimed to ... Read more >>

J Med Chem (Journal of medicinal chemistry)
[2018, 61(3):1019-1030]

Cited: 7 times

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Quenching activity of carnosine derivatives towards reactive carbonyl species: Focus on α-(methylglyoxal) and β-(malondialdehyde) dicarbonyls.

Giulio Vistoli, Mara Colzani, Angelica Mazzolari, Ettore Gilardoni, Carola Rivaletto, Marina Carini, Giancarlo Aldini,

The study combines HPLC-based with MS-based competitive analyses to evaluate the quenching activity of a set of carnosine derivatives towards methylglyoxal (MGO) and malondialdehyde (MDA) chosen as representative of α- and β-dicarbonyls, respectively. The obtained results underline that these derivatives are moderately reactive towards MDA with which they form the ... Read more >>

Biochem Biophys Res Commun (Biochemical and biophysical research communications)
[2017, 492(3):487-492]

Cited: 9 times

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Binding Space Concept: A New Approach To Enhance the Reliability of Docking Scores and Its Application to Predicting Butyrylcholinesterase Hydrolytic Activity.

Giulio Vistoli, Angelica Mazzolari, Bernard Testa, Alessandro Pedretti,

Docking simulations are very popular approaches able to assess the capacity of a given ligand to interact with a target. Docking simulations are usually focused on a single best complex even though many studies showed that ligands retain a significant mobility within a binding pocket by assuming different binding modes ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2017, 57(7):1691-1702]

Cited: 10 times

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Data from docking simulations to develop an efficient strategy able to evaluate the interactions between RAGE and MDA-induced albumin adducts.

Angelica Mazzolari, Crescenzo Coppa, Alessandra Altomare, Genny Degani, Giulio Vistoli,

This data article contains the results of docking simulations performed in order to develop a suitable in silico strategy able to assess the stability of the putative complexes between RAGE and MDA induced adducts on human albumin as experimentally determined doi: 10.1016/j.redox.2016.12.017, (Degani et al., 2017) [1]. The docking simulations ... Read more >>

Data Brief (Data in brief)
[2017, 12:656-661]

Cited: 0 times

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Structural Effects of Some Relevant Missense Mutations on the MECP2-DNA Binding: A MD Study Analyzed by Rescore+, a Versatile Rescoring Tool of the VEGA ZZ Program.

Alessandro Pedretti, Cinzia Granito, Angelica Mazzolari, Giulio Vistoli,

DNA methylation plays key roles in mammalian cells and is modulated by a set of proteins which recognize symmetrically methylated nucleotides. Among them, the protein MECP2 shows multifunctional roles repressing and/or activating genes by binding to both methylated and unmethylated regions of the genome. The interest for this protein markedly ... Read more >>

Mol Inform (Molecular informatics)
[2016, 35(8-9):424-433]

Cited: 8 times

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Computational approaches in the rational design of improved carbonyl quenchers: focus on histidine containing dipeptides.

Giulio Vistoli, Mara Colzani, Angelica Mazzolari, Danilo De Maddis, Giovanni Grazioso, Alessandro Pedretti, Marina Carini, Giancarlo Aldini,

<h4>Aim</h4>The inhibition of protein carbonylation can play therapeutic roles in several oxidative-based diseases and direct carbonyl quenching appears the most effective inhibition strategies. l-carnosine derivatives are effective and selective quenchers toward 4-hydroxy-2-nonenal even though their activity was never investigated in a fully comparable way.<h4>Results</h4>The reported results revealed that anserine, homocarnosine ... Read more >>

Future Med Chem (Future medicinal chemistry)
[2016, 8(14):1721-1737]

Cited: 11 times

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Serum albumin as a probe for testing the selectivity of irreversible cysteine protease inhibitors: The case of vinyl sulfones.

Luca Regazzoni, Simone Colombo, Angelica Mazzolari, Giulio Vistoli, Marina Carini,

Vinyl sulfones are used for drug design of irreversible inhibitors of cysteine proteases since they are able to alkylate cysteine thiols inside the catalytic pocket of this class of enzymes. Some authors have reported the lack of reactivity towards glutathione as sufficient evidence of the selectivity of such a mechanism. ... Read more >>

J Pharm Biomed Anal (Journal of pharmaceutical and biomedical analysis)
[2016, 124:294-302]

Cited: 2 times

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A capture method based on the VC1 domain reveals new binding properties of the human receptor for advanced glycation end products (RAGE).

Genny Degani, Alessandra A Altomare, Mara Colzani, Caterina Martino, Angelica Mazzolari, Guenter Fritz, Giulio Vistoli, Laura Popolo, Giancarlo Aldini,

The Advanced Glycation and Lipoxidation End products (AGEs and ALEs) are a heterogeneous class of compounds derived from the non-enzymatic glycation or protein adduction by lipoxidation break-down products. The receptor for AGEs (RAGE) is involved in the progression of chronic diseases based on persistent inflammatory state and oxidative stress. RAGE ... Read more >>

Redox Biol (Redox biology)
[2017, 11:275-285]

Cited: 6 times

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The replacement of the 2-methoxy substituent of N-((6,6-diphenyl-1,4-dioxan-2-yl)methyl)-2-(2-methoxyphenoxy)ethan-1-amine improves the selectivity for 5-HT1A receptor over α1-adrenoceptor and D2-like receptor subtypes.

Fabio Del Bello, Alessandro Bonifazi, Mario Giannella, Gianfabio Giorgioni, Alessandro Piergentili, Riccardo Petrelli, Carlo Cifani, Maria Vittoria Micioni Di Bonaventura, Thomas M Keck, Angelica Mazzolari, Giulio Vistoli, Antonio Cilia, Elena Poggesi, Rosanna Matucci, Wilma Quaglia,

N-((6,6-diphenyl-1,4-dioxan-2-yl)methyl)-2-(2-methoxyphenoxy)ethan-1-amine (3) is a potent 5-HT<sub>1A</sub> receptor and α<sub>1d</sub>-adrenoceptor (α<sub>1d</sub>-AR) ligand. Analogues 5-10 were rationally designed and prepared to evaluate whether electronic and/or lipophilic properties of substituents in the ortho position of its phenoxy moiety exert any favorable effects on the affinity/activity at 5-HT<sub>1A</sub> receptor and improve selectivity over α<sub>1</sub>-ARs. ... Read more >>

Eur J Med Chem (European journal of medicinal chemistry)
[2017, 125:233-244]

Cited: 4 times

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Carbachol dimers as homobivalent modulators of muscarinic receptors.

Rosanna Matucci, Marta Nesi, Maria Vittoria Martino, Cristina Bellucci, Dina Manetti, Elisa Ciuti, Angelica Mazzolari, Silvia Dei, Luca Guandalini, Elisabetta Teodori, Giulio Vistoli, Maria Novella Romanelli,

A series of homodimers of the well-known cholinergic agonist carbachol have been synthesized, showing the two agonist units symmetrically connected through a methylene chain of variable length. The new compounds have been tested on the five cloned muscarinic receptors (hM1-5) expressed in CHO cells by means of equilibrium binding studies, ... Read more >>

Biochem Pharmacol (Biochemical pharmacology)
[2016, 108:90-101]

Cited: 4 times

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