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List of works by Alessandro Pedretti

5-(2-Pyrrolidinyl)oxazolidinones and 2-(2-pyrrolidinyl)benzodioxanes: synthesis of all the stereoisomers and alpha4beta2 nicotinic affinity

scientific article

A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0.

scientific article published on 21 July 2020

A molecular modelling approach to rationalize the stereochemical outcome of the Burkholderia cepacia lipase-catalyzed transesterification of aromatic primary alcohols with vinyl esters with different chain lengths in chloroform

An integrated high resolution mass spectrometric and informatics approach for the rapid identification of phenolics in plant extract.

scientific article published on 3 March 2011

Analysis of the full-length integrase–DNA complex by a modified approach for DNA docking

article

Approaching Pharmacological Space: Events and Components

scientific article published on 01 January 2018

Assessing drug-likeness--what are we missing?

scientific article published on 16 January 2008

Atomic diversity, molecular diversity, and chemical diversity: the concept of chemodiversity

scientific article published in August 2009

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

scientific article published on 20 June 2017

Binding site analysis of full-length alpha1a adrenergic receptor using homology modeling and molecular docking.

scientific article

Chemodiversity and molecular plasticity: recognition processes as explored by property spaces

scientific article published on June 2011

Combining Molecular Dynamics and Docking Simulations to Develop Targeted Protocols for Performing Optimized Virtual Screening Campaigns on The hTRPM8 Channel

scientific article published on 25 March 2020

Comparative modeling of the quaternary structure for the human TRPM8 channel and analysis of its binding features

scientific article

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

scientific article published on September 2016

Construction of human ghrelin receptor (hGHS-R1a) model using a fragmental prediction approach and validation through docking analysis

scientific article published on June 2006

Design, synthesis, ADME properties, and pharmacological activities of β-alanyl-D-histidine (D-carnosine) prodrugs with improved bioavailability

scientific article published in June 2011

Design, synthesis, and evaluation of carnosine derivatives as selective and efficient sequestering agents of cytotoxic reactive carbonyl species

scientific article published in June 2009

Docking analyses on human muscarinic receptors: unveiling the subtypes peculiarities in agonists binding

scientific article published on 7 January 2008

Enhanced activity or resistance of adenosine derivatives towards adenosine deaminase-catalyzed deamination: Influence of ribose modifications

scientific article

Enhancing the Reliability of GPCR Models by Accounting for Flexibility of Their Pro-Containing Helices: the Case of the Human mAChR1 Receptor

scientific article published on 20 March 2015

Exploring the activation mechanism of TRPM8 channel by targeted MD simulations

article published in 2011

Exploring the space of histidine containing dipeptides in search of novel efficient RCS sequestering agents

scientific article published on 30 May 2013

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

scientific article published on 30 July 2019

Fragmental modeling of hPepT2 and analysis of its binding features by docking studies and pharmacophore mapping

scientific article published on 16 June 2011

Fragmental modeling of human glutamate transporter EAAT1 and analysis of its binding modes by docking and pharmacophore mapping

scientific article published in January 2008

Homology Modeling of Human Serum Carnosinase, a Potential Medicinal Target, and MD Simulations of Its Allosteric Activation by Citrate

article

Homology modeling and metabolism prediction of human carboxylesterase-2 using docking analyses by GriDock: a parallelized tool based on AutoDock 4.0.

scientific article published on 11 July 2010

Homology modelling of human DHCR24 (seladin-1) and analysis of its binding properties through molecular docking and dynamics simulations

scientific article published on 23 February 2008

In silico prediction of human carboxylesterase-1 (hCES1) metabolism combining docking analyses and MD simulations

scientific article published in 2010

Influence of ionization state on the activation of temocapril by hCES1: a molecular-dynamics study

scientific article published in November 2009

Key factors regulating protein carbonylation by α,β unsaturated carbonyls: A structural study based on a retrospective meta-analysis.

scientific article

Lack of enantioselectivity in the SULT1A3-catalyzed sulfoconjugation of normetanephrine enantiomers: an in vitro and computational study

scientific article published on 24 September 2012

Mechanisms and pharmaceutical consequences of processes of stereoisomerisation - A didactic excursion

scientific article published on 7 April 2016

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

scientific article published on 15 December 2017

Modeling of binding modes and inhibition mechanism of some natural ligands of farnesyl transferase using molecular docking

scientific article published in March 2002

Modeling of human ghrelin receptor (hGHS-R1a) in its close state and validation by molecular docking

scientific article published in 2007

Modeling of the intestinal peptide transporter hPepT1 and analysis of its transport capacities by docking and pharmacophore mapping

scientific article

Modelling of full-length human alpha4beta2 nicotinic receptor by fragmental approach and analysis of its binding modes

scientific article

Modelling of the Interactions of Some Inhibitors with the PGHS-1 by BIODOCK - a Stochastic Approach to the Automated Docking of Ligands to Biomacromolecules

Molecular dynamics studies of the full-length integrase-DNA complex

scientific article published in November 2005

Muscarinic receptors: A comparative analysis of structural features and binding modes through homology modelling and molecular docking

article

Musings on ADME predictions and structure-activity relations

scientific article published on November 2005

Novel selective, potent naphthyl TRPM8 antagonists identified through a combined ligand- and structure-based virtual screening approach

scientific article published on 8 September 2017

Organic Stereochemistry. Part 1. Symmetry Elements and Operations, Classification of Stereoisomers

article

Organic Stereochemistry. Part 4

article

Organic Stereochemistry. Part 5

article

Organic Stereochemistry. Part 6

article

Partition Coefficient and Molecular Flexibility: The Concept of Lipophilicity Space

scholarly article by Giulio Vistoli published in August 2009

Peptidomimetic inhibitors of farnesyltransferase with high in vitro activity and significant cellular potency

scientific article published on 8 September 2007

Predicting the physicochemical profile of diastereoisomeric histidine-containing dipeptides by property space analysis

scientific article published on 8 May 2012

Prediction and mechanism elucidation of analyte retention on phospholipid stationary phases (IAM-HPLC) by in silico calculated physico-chemical descriptors

scientific article

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

scientific article published on 12 February 2019

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

Publisher Correction: Novel selective, potent naphthyl TRPM8 antagonists identified through a combined ligand- and structure-based virtual screening approach.

scientific article

QSAR study for a novel series of ortho monosubstituted phenoxy analogues of alpha1-adrenoceptor antagonist WB4101.

scientific article

Range and Sensitivity as Descriptors of Molecular Property Spaces in Dynamic QSAR Analyses

Reactions and enzymes in the metabolism of drugs and other xenobiotics

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

scientific article published on 19 August 2020

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

scientific article published on 26 April 2019

SPILLO-PBSS: detecting hidden binding sites within protein 3D-structures through a flexible structure-based approach

scientific article

Small molecules as exemplars of emergent properties and diversification into the 'adjacent possible'.

scientific article

Solvent constraints on the property space of acetylcholine. 2. Ordered media

scientific article

Solvent constraints on the property space of acetylcholine. I. Isotropic solvents

scientific article

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

scientific article published on 14 July 2016

Structure and dynamics of the full-length M1 muscarinic acetylcholine receptor studied by molecular dynamics simulations

scientific article published on 15 September 2007

Structure-affinity studies for a novel series of homochiral naphtho and tetrahydronaphtho analogues of alpha 1 antagonist WB-4101.

scientific article published in September 2004

Synthesis and molecular modeling of 1H-pyrrolopyrimidine-2,4-dione derivatives as ligands for the α1-adrenoceptors

scientific article published on 21 June 2011

The Approach of Conformational Chimeras to Model the Role of Proline-Containing Helices on GPCR Mobility: the Fertile Case of Cys-LTR1

article

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

scientific article published on 10 September 2020

The conformational and property space of acetylcholine bound to muscarinic receptors: an entropy component accounts for the subtype selectivity of acetylcholine

scientific article published on 15 May 2007

The solute-solvent system: solvent constraints on the conformational dynamics of acetylcholine

scientific article

Towards the Inhibition of Protein-Protein Interactions (PPIs) in STAT3: Insights into a New Class of Benzothiadiazole Derivatives

scientific article published on 31 July 2020

Type 2 Diabetes Mellitus: A Review of Multi-Target Drugs

scientific article published on 23 April 2020

VEGA – An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming

scientific article

VEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs.

scientific article published in August 2002

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

scientific article published on 21 May 2018

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