List of works - Vittorio Limongelli

Accelerating the Calculation of Protein-Ligand Binding Free Energy and Residence Times Using Dynamically Optimized Collective Variables

scientific article published on 28 December 2018

Acetic acid aldose reductase inhibitors bearing a five-membered heterocyclic core with potent topical activity in a visual impairment rat model.

scientific article published on 2 May 2008

Binding mechanism of the farnesoid X receptor marine antagonist suvanine reveals a strategy to forestall drug modulation on nuclear receptors. Design, synthesis, and biological evaluation of novel ligands.

scientific article

Breaking the dogma of the metal-coordinating carboxylate group in integrin ligands: introducing hydroxamic acids to the MIDAS to tune potency and selectivity

scientific article

Calmodulin-dependent kinase II mediates vascular smooth muscle cell proliferation and is potentiated by extracellular signal regulated kinase

scientific article

Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations

scientific article

DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis

scientific article published on 01 December 2019

Design, synthesis and biological evaluation of carboxy analogues of arginine methyltransferase inhibitor 1 (AMI-1).

scientific article published in March 2010

Design, synthesis, and biological evaluation of novel aminobisphosphonates possessing an in vivo antitumor activity through a gammadelta-T lymphocytes-mediated activation mechanism.

scientific article published on 21 October 2008

Design, synthesis, and biological evaluation of potent dual agonists of nuclear and membrane bile acid receptors.

scientific article published on 17 January 2014

Discovery of ((1,2,4-oxadiazol-5-yl)pyrrolidin-3-yl)ureidyl derivatives as selective non-steroidal agonists of the G-protein coupled bile acid receptor-1

scientific article published on 21 February 2019

Disruption of TFGβ-SMAD3 pathway by the nuclear receptor SHP mediates the antifibrotic activities of BAR704, a novel highly selective FXR ligand

scientific article published on 9 March 2018

Energetics and structural characterization of the large-scale functional motion of adenylate kinase

scientific article

Ensemble-docking approach on BACE-1: pharmacophore perception and guidelines for drug design

scientific article published in May 2007

Ethyl 8-fluoro-6-(3-nitrophenyl)-4H-imidazo[1,5-a][1,4]benzodiazepine-3-carboxylate as novel, highly potent, and safe antianxiety agent

scientific article published on 19 July 2008

Funnel metadynamics as accurate binding free-energy method

scientific article

Funnel-metadynamics and solution NMR to estimate protein-ligand affinities

scientific article published on 14 January 2015

G-triplex structure and formation propensity

scientific article

Gamma-glutamyl 16-diaminopropane derivative of vasoactive intestinal peptide: a potent anti-oxidative agent for human epidermoid cancer cells.

scientific article

Homology modeling of NR2B modulatory domain of NMDA receptor and analysis of ifenprodil binding

scientific article published on October 2007

Hyodeoxycholic acid derivatives as liver X receptor α and G-protein-coupled bile acid receptor agonists

scientific article

Incisterols, highly degraded marine sterols, are a new chemotype of PXR agonists.

scientific article

Indolylarylsulfones carrying a heterocyclic tail as very potent and broad spectrum HIV-1 non-nucleoside reverse transcriptase inhibitors

scientific article published on 24 November 2014

Insights on pregnane-X-receptor modulation. Natural and semisynthetic steroids from Theonella marine sponges.

scientific article

Introduction of Nonacidic Side Chains on 6-Ethylcholane Scaffolds in the Identification of Potent Bile Acid Receptor Agonists with Improved Pharmacokinetic Properties

scientific article published on 16 March 2019

Investigating the mechanism of substrate uptake and release in the glutamate transporter homologue Glt(Ph) through metadynamics simulations

scientific article

Investigation around the Oxadiazole Core in the Discovery of a New Chemotype of Potent and Selective FXR Antagonists

scientific article published on 10 January 2019

Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps

scientific article

Ligand Binding, Unbinding, and Allosteric Effects: Deciphering Small-Molecule Modulation of HSP90

scientific article published on 08 October 2019

Ligand binding free-energy calculations with funnel metadynamics

scientific article published on 19 August 2020

Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations

scientific article published on 23 February 2017

Marine and semi-synthetic hydroxysteroids as new scaffolds for pregnane X receptor modulation

scientific article

Mechanistic insight into ligand binding to G-quadruplex DNA

scientific article

Membrane charge dependent states of the beta-amyloid fragment Abeta (16-35) with differently charged micelle aggregates

scientific article published on 4 January 2010

Modeling of Cdc25B Dual Specifity Protein Phosphatase Inhibitors: Docking of Ligands and Enzymatic Inhibition Mechanism

article

Modification on ursodeoxycholic acid (UDCA) scaffold. discovery of bile acid derivatives as selective agonists of cell-surface G-protein coupled bile acid receptor 1 (GP-BAR1)

scientific article published on 07 September 2014

Molecular Modeling for Nanomaterial-Biology Interactions: Opportunities, Challenges, and Perspectives

scientific article published on 17 October 2019

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

scientific article

New insight into the central benzodiazepine receptor-ligand interactions: design, synthesis, biological evaluation, and molecular modeling of 3-substituted 6-phenyl-4H-imidazo[1,5-a][1,4]benzodiazepines and related compounds

scientific article published on 27 July 2011

Novel Isoxazole Derivatives with Potent FXR Agonistic Activity Prevent Acetaminophen-Induced Liver Injury

scientific article published on 06 December 2018

Novel N2-substituted pyrazolo[3,4-d]pyrimidine adenosine A3 receptor antagonists: inhibition of A3-mediated human glioblastoma cell proliferation.

scientific article published on May 2010

Potent arylsulfonamide inhibitors of tumor necrosis factor-alpha converting enzyme able to reduce activated leukocyte cell adhesion molecule shedding in cancer cell models

scientific article

Protein-ligand binding with the coarse-grained Martini model

scientific article published on 24 July 2020

Sampling protein motion and solvent effect during ligand binding

scientific article published on 11 January 2012

Steroidal scaffolds as FXR and GPBAR1 ligands: from chemistry to therapeutical application

scientific article published on July 2015

Stop Fitan: antispasmodic effect of natural extract of chestnut wood in guinea pig ileum and proximal colon smooth muscle

scientific article published on October 2010

Structural Insight into the Binding Mode of FXR and GPBAR1 Modulators

scientific article published on 01 January 2019

Structural and conformational requisites in DNA quadruplex groove binding: another piece to the puzzle

scientific article

Structure-based drug design targeting the cell membrane receptor GPBAR1: exploiting the bile acid scaffold towards selective agonism

scientific article published on 16 November 2015

Tailoring of Integrin Ligands: Probing the Charge Capability of the Metal Ion-Dependent Adhesion Site

scientific article published on 09 January 2012

Targeting Bile Acid Receptors: Discovery of a Potent and Selective Farnesoid X Receptor Agonist as a New Lead in the Pharmacological Approach to Liver Diseases

scientific article published on 30 March 2017

The Free Energy Landscape of GABA Binding to a Pentameric Ligand-Gated Ion Channel and Its Disruption by Mutations

scientific article published on 26 May 2016

The G-Triplex DNA

The Molecular Mechanism Underlying Ligand Binding to the Membrane-Embedded Site of a G-Protein-Coupled Receptor

scientific article published on 27 April 2018

The glycan role in the glycopeptide immunogenicity revealed by atomistic simulations and spectroscopic experiments on the multiple sclerosis biomarker CSF114(Glc)

scientific article

Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations

scientific article published on 14 March 2017

List of works by Vittorio Limongelli

Accelerating the Calculation of Protein-Ligand Binding Free Energy and Residence Times Using Dynamically Optimized Collective Variables

Acetic acid aldose reductase inhibitors bearing a five-membered heterocyclic core with potent topical activity in a visual impairment rat model.

Binding mechanism of the farnesoid X receptor marine antagonist suvanine reveals a strategy to forestall drug modulation on nuclear receptors. Design, synthesis, and biological evaluation of novel ligands.

Breaking the dogma of the metal-coordinating carboxylate group in integrin ligands: introducing hydroxamic acids to the MIDAS to tune potency and selectivity

Calmodulin-dependent kinase II mediates vascular smooth muscle cell proliferation and is potentiated by extracellular signal regulated kinase

Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations

DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis

Design, synthesis and biological evaluation of carboxy analogues of arginine methyltransferase inhibitor 1 (AMI-1).

Design, synthesis, and biological evaluation of novel aminobisphosphonates possessing an in vivo antitumor activity through a gammadelta-T lymphocytes-mediated activation mechanism.

Design, synthesis, and biological evaluation of potent dual agonists of nuclear and membrane bile acid receptors.

Discovery of ((1,2,4-oxadiazol-5-yl)pyrrolidin-3-yl)ureidyl derivatives as selective non-steroidal agonists of the G-protein coupled bile acid receptor-1

Disruption of TFGβ-SMAD3 pathway by the nuclear receptor SHP mediates the antifibrotic activities of BAR704, a novel highly selective FXR ligand

Energetics and structural characterization of the large-scale functional motion of adenylate kinase

Ensemble-docking approach on BACE-1: pharmacophore perception and guidelines for drug design

Ethyl 8-fluoro-6-(3-nitrophenyl)-4H-imidazo[1,5-a][1,4]benzodiazepine-3-carboxylate as novel, highly potent, and safe antianxiety agent

Funnel metadynamics as accurate binding free-energy method

Funnel-metadynamics and solution NMR to estimate protein-ligand affinities

G-triplex structure and formation propensity

Gamma-glutamyl 16-diaminopropane derivative of vasoactive intestinal peptide: a potent anti-oxidative agent for human epidermoid cancer cells.

Homology modeling of NR2B modulatory domain of NMDA receptor and analysis of ifenprodil binding

Hyodeoxycholic acid derivatives as liver X receptor α and G-protein-coupled bile acid receptor agonists

Incisterols, highly degraded marine sterols, are a new chemotype of PXR agonists.

Indolylarylsulfones carrying a heterocyclic tail as very potent and broad spectrum HIV-1 non-nucleoside reverse transcriptase inhibitors

Insights on pregnane-X-receptor modulation. Natural and semisynthetic steroids from Theonella marine sponges.

Introduction of Nonacidic Side Chains on 6-Ethylcholane Scaffolds in the Identification of Potent Bile Acid Receptor Agonists with Improved Pharmacokinetic Properties

Investigating the mechanism of substrate uptake and release in the glutamate transporter homologue Glt(Ph) through metadynamics simulations

Investigation around the Oxadiazole Core in the Discovery of a New Chemotype of Potent and Selective FXR Antagonists

Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps

Ligand Binding, Unbinding, and Allosteric Effects: Deciphering Small-Molecule Modulation of HSP90

Ligand binding free-energy calculations with funnel metadynamics

Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations

Marine and semi-synthetic hydroxysteroids as new scaffolds for pregnane X receptor modulation

Mechanistic insight into ligand binding to G-quadruplex DNA

Membrane charge dependent states of the beta-amyloid fragment Abeta (16-35) with differently charged micelle aggregates

Modeling of Cdc25B Dual Specifity Protein Phosphatase Inhibitors: Docking of Ligands and Enzymatic Inhibition Mechanism

Modification on ursodeoxycholic acid (UDCA) scaffold. discovery of bile acid derivatives as selective agonists of cell-surface G-protein coupled bile acid receptor 1 (GP-BAR1)

Molecular Modeling for Nanomaterial-Biology Interactions: Opportunities, Challenges, and Perspectives

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

New insight into the central benzodiazepine receptor-ligand interactions: design, synthesis, biological evaluation, and molecular modeling of 3-substituted 6-phenyl-4H-imidazo[1,5-a][1,4]benzodiazepines and related compounds

Novel Isoxazole Derivatives with Potent FXR Agonistic Activity Prevent Acetaminophen-Induced Liver Injury

Novel N2-substituted pyrazolo[3,4-d]pyrimidine adenosine A3 receptor antagonists: inhibition of A3-mediated human glioblastoma cell proliferation.

Potent arylsulfonamide inhibitors of tumor necrosis factor-alpha converting enzyme able to reduce activated leukocyte cell adhesion molecule shedding in cancer cell models

Protein-ligand binding with the coarse-grained Martini model

Sampling protein motion and solvent effect during ligand binding

Steroidal scaffolds as FXR and GPBAR1 ligands: from chemistry to therapeutical application

Stop Fitan: antispasmodic effect of natural extract of chestnut wood in guinea pig ileum and proximal colon smooth muscle

Structural Insight into the Binding Mode of FXR and GPBAR1 Modulators

Structural and conformational requisites in DNA quadruplex groove binding: another piece to the puzzle

Structure-based drug design targeting the cell membrane receptor GPBAR1: exploiting the bile acid scaffold towards selective agonism

Tailoring of Integrin Ligands: Probing the Charge Capability of the Metal Ion-Dependent Adhesion Site

Targeting Bile Acid Receptors: Discovery of a Potent and Selective Farnesoid X Receptor Agonist as a New Lead in the Pharmacological Approach to Liver Diseases

The Free Energy Landscape of GABA Binding to a Pentameric Ligand-Gated Ion Channel and Its Disruption by Mutations

The G-Triplex DNA

The Molecular Mechanism Underlying Ligand Binding to the Membrane-Embedded Site of a G-Protein-Coupled Receptor

The glycan role in the glycopeptide immunogenicity revealed by atomistic simulations and spectroscopic experiments on the multiple sclerosis biomarker CSF114(Glc)

Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations