List of works - Francesca Spyrakis

4-Amino-1,2,4-triazole-3-thione as a Promising Scaffold for the Inhibition of Serine and Metallo-β-Lactamases

scientific article published on 24 March 2020

A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins.

scientific article published on 10 September 2015

A novel Bim-BH3-derived Bcl-XL inhibitor: biochemical characterization, in vitro, in vivo and ex-vivo anti-leukemic activity

scientific article published on 20 October 2008

Allosteric communication between alpha and beta subunits of tryptophan synthase: modelling the open-closed transition of the alpha subunit

scientific article published on 18 April 2006

BioGPS: The Music for the Chemo- and Bioinformatics Walzer

scientific article

Bound water at protein-protein interfaces: partners, roles and hydrophobic bubbles as a conserved motif

scientific article (publication date: 2011)

CO Rebinding Kinetics and Molecular Dynamics Simulations Highlight Dynamic Regulation of Internal Cavities in Human Cytoglobin

scientific article

Can We Exploit β-Lactamases Intrinsic Dynamics for Designing More Effective Inhibitors?

scientific article published on 21 November 2020

Chemogenomics of pyridoxal 5'-phosphate dependent enzymes

scientific article published on 19 December 2011

Comparing Drug Images and Repurposing Drugs with BioGPS and FLAPdock: The Thymidylate Synthase Case.

scientific article published on 12 July 2016

Complexity in modeling and understanding protonation states: computational titration of HIV-1-protease-inhibitor complexes

scientific article

Computational titration analysis of a multiprotic HIV-1 protease-ligand complex.

scientific article

Correct protonation states and relevant waters = better computational simulations?

scientific article published on January 2013

Correction: Recent advances in the synthesis of analogues of phytohormones strigolactones with ring-closing metathesis as a key step

scientific article published on 21 September 2017

Cryo-EM structures of staphylococcal IsdB bound to human hemoglobin reveal the process of heme extraction

scientific article published on 31 March 2022

Design of O -Acetylserine Sulfhydrylase Inhibitors by Mimicking Nature

scientific article

Different roles of protein dynamics and ligand migration in non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana

article

Discovering New Casein Kinase 1d Inhibitors with an Innovative Molecular Dynamics Enabled Virtual Screening Workflow

scientific article published on 13 December 2018

Energetics of the protein-DNA-water interaction

scientific article

Energy-based prediction of amino acid-nucleotide base recognition

scientific article published on 01 September 2008

Expanding the chemical space of human serine racemase inhibitors

scientific article published on 4 August 2015

FADB: a food additive molecular database for in silico screening in food toxicology

scientific article

Fine tuning of the active site modulates specificity in the interaction of O-acetylserine sulfhydrylase isozymes with serine acetyltransferase

scientific article published on 19 September 2012

First virtual screening and experimental validation of inhibitors targeting GES-5 carbapenemase

scientific article published on 02 January 2019

Folic Acid-Peptide Conjugates Combine Selective Cancer Cell Internalization with Thymidylate Synthase Dimer Interface Targeting

scientific article published on 12 March 2021

From Experiments to a Fast Easy-to-Use Computational Methodology to Predict Human Aldehyde Oxidase Selectivity and Metabolic Reactions.

scientific article published on 14 December 2017

Geminate rebinding in R-state hemoglobin: kinetic and computational evidence for multiple hydrophobic pockets

scientific article

Getting it right: modeling of pH, solvent and "nearly" everything else in virtual screening of biological targets

scientific article

Histidine E7 Dynamics Modulates Ligand Exchange between Distal Pocket and Solvent in AHb1 fromArabidopsis thaliana

scientific article published on 14 April 2011

How computational methods try to disclose the estrogen receptor secrecy--modeling the flexibility.

scientific article published on January 2009

Interaction of human hemoglobin and semi-hemoglobins with the Staphylococcus aureus hemophore IsdB: a kinetic and mechanistic insight

scientific article published on 09 December 2019

Iron Metabolism at the Interface between Host and Pathogen: From Nutritional Immunity to Antibacterial Development

scientific article published on 20 March 2020

Isozyme-specific ligands for O-acetylserine sulfhydrylase, a novel antibiotic target

scientific article

Ligand migration and hexacoordination in type 1 non-symbiotic rice hemoglobin

scientific article

Ligand migration in nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana

scientific article

Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations.

scientific article

Ligand migration through the internal hydrophobic cavities in human neuroglobin

scientific article published on 22 October 2009

Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules

scientific article published on 2 February 2006

Modulating Ligand Dissociation through Methyl Isomerism in Accessory Sites: Binding of Retinol to Cellular Carriers

scientific article published on 14 November 2019

NO release regulated by doxorubicin as the green light-harvesting antenna

scientific article published on 21 May 2020

Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description.

scientific article published on 10 August 2015

Oxygen and nitric oxide rebinding kinetics in nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana

scientific article

Oxygen binding to Arabidopsis thaliana AHb2 nonsymbiotic hemoglobin: evidence for a role in oxygen transport

article

Paracetamol-Galactose Conjugate: A Novel Prodrug for an Old Analgesic Drug

scientific article published on 12 September 2019

Rational Design of a User-Friendly Aptamer/Peptide-Based Device for the Detection of Staphylococcus aureus

scientific article published on 02 September 2020

Recent advances in the synthesis of analogues of phytohormones strigolactones with ring-closing metathesis as a key step

scientific article published on 7 September 2017

Robust Classification of “Relevant” Water Molecules in Putative Protein Binding Sites

scientific article published on 31 January 2008

Serine racemase: a key player in neuron activity and in neuropathologies

scientific article published on June 2013

Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 3. The Free Energy Contribution of Structural Water Molecules in HIV-1 Protease Complexes

article

Strigolactone Analogs Are Promising Antiviral Agents for the Treatment of Human Cytomegalovirus Infection

scientific article published on 10 May 2020

Structural insight into the interaction of O-acetylserine sulfhydrylase with competitive, peptidic inhibitors by saturation transfer difference-NMR.

scientific article

Structural plasticity and functional implications of internal cavities in distal mutants of type 1 non-symbiotic hemoglobin AHb1 from Arabidopsis thaliana.

scientific article

Structure-Based Virtual Screening for the Discovery of Novel Inhibitors of New Delhi Metallo-β-lactamase-1.

scientific article published on 26 November 2017

Structure-activity relationships of strigolactones via a novel, quantitative in planta bioassay

scientific article published on 15 March 2018

Target flexibility: an emerging consideration in drug discovery and design

scientific article published on 12 September 2008

Targeting cystalysin, a virulence factor of treponema denticola-supported periodontitis

scientific article

Ten Years with New Delhi Metallo-β-lactamase-1 (NDM-1): From Structural Insights to Inhibitor Design

scientific article published on 28 November 2018

The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery.

scientific article

The consequences of scoring docked ligand conformations using free energy correlations

scientific article

The inhibition of extended spectrum β-lactamases: hits and leads

scientific article published on January 2014

The multifaceted pyridoxal 5'-phosphate-dependent O-acetylserine sulfhydrylase

scientific article published on 28 April 2011

The reactivity with CO of AHb1 and AHb2 from Arabidopsis thaliana is controlled by the distal HisE7 and internal hydrophobic cavities

scientific article published on 14 February 2007

Tools for building a comprehensive modeling system for virtual screening under real biological conditions: The Computational Titration algorithm

scientific article

Tuning the Hydrophobicity of a Mitochondria-Targeted NO Photodonor

scientific article published on 08 May 2018

Unintended consequences? Water molecules at biological and crystallographic protein-protein interfaces

scientific article

Water: How to evaluate its contribution in protein-ligand interactions

article by Pietro Cozzini et al published 2005 in International Journal of Quantum Chemistry

List of works by Francesca Spyrakis

4-Amino-1,2,4-triazole-3-thione as a Promising Scaffold for the Inhibition of Serine and Metallo-β-Lactamases

A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins.

A novel Bim-BH3-derived Bcl-XL inhibitor: biochemical characterization, in vitro, in vivo and ex-vivo anti-leukemic activity

Allosteric communication between alpha and beta subunits of tryptophan synthase: modelling the open-closed transition of the alpha subunit

BioGPS: The Music for the Chemo- and Bioinformatics Walzer

Bound water at protein-protein interfaces: partners, roles and hydrophobic bubbles as a conserved motif

CO Rebinding Kinetics and Molecular Dynamics Simulations Highlight Dynamic Regulation of Internal Cavities in Human Cytoglobin

Can We Exploit β-Lactamases Intrinsic Dynamics for Designing More Effective Inhibitors?

Chemogenomics of pyridoxal 5'-phosphate dependent enzymes

Comparing Drug Images and Repurposing Drugs with BioGPS and FLAPdock: The Thymidylate Synthase Case.

Complexity in modeling and understanding protonation states: computational titration of HIV-1-protease-inhibitor complexes

Computational titration analysis of a multiprotic HIV-1 protease-ligand complex.

Correct protonation states and relevant waters = better computational simulations?

Correction: Recent advances in the synthesis of analogues of phytohormones strigolactones with ring-closing metathesis as a key step

Cryo-EM structures of staphylococcal IsdB bound to human hemoglobin reveal the process of heme extraction

Design of O -Acetylserine Sulfhydrylase Inhibitors by Mimicking Nature

Different roles of protein dynamics and ligand migration in non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana

Discovering New Casein Kinase 1d Inhibitors with an Innovative Molecular Dynamics Enabled Virtual Screening Workflow

Energetics of the protein-DNA-water interaction

Energy-based prediction of amino acid-nucleotide base recognition

Expanding the chemical space of human serine racemase inhibitors

FADB: a food additive molecular database for in silico screening in food toxicology

Fine tuning of the active site modulates specificity in the interaction of O-acetylserine sulfhydrylase isozymes with serine acetyltransferase

First virtual screening and experimental validation of inhibitors targeting GES-5 carbapenemase

Folic Acid-Peptide Conjugates Combine Selective Cancer Cell Internalization with Thymidylate Synthase Dimer Interface Targeting

From Experiments to a Fast Easy-to-Use Computational Methodology to Predict Human Aldehyde Oxidase Selectivity and Metabolic Reactions.

Geminate rebinding in R-state hemoglobin: kinetic and computational evidence for multiple hydrophobic pockets

Getting it right: modeling of pH, solvent and "nearly" everything else in virtual screening of biological targets

Histidine E7 Dynamics Modulates Ligand Exchange between Distal Pocket and Solvent in AHb1 fromArabidopsis thaliana

How computational methods try to disclose the estrogen receptor secrecy--modeling the flexibility.

Interaction of human hemoglobin and semi-hemoglobins with the Staphylococcus aureus hemophore IsdB: a kinetic and mechanistic insight

Iron Metabolism at the Interface between Host and Pathogen: From Nutritional Immunity to Antibacterial Development

Isozyme-specific ligands for O-acetylserine sulfhydrylase, a novel antibiotic target

Ligand migration and hexacoordination in type 1 non-symbiotic rice hemoglobin

Ligand migration in nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana

Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations.

Ligand migration through the internal hydrophobic cavities in human neuroglobin

Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules

Modulating Ligand Dissociation through Methyl Isomerism in Accessory Sites: Binding of Retinol to Cellular Carriers

NO release regulated by doxorubicin as the green light-harvesting antenna

Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description.

Oxygen and nitric oxide rebinding kinetics in nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana

Oxygen binding to Arabidopsis thaliana AHb2 nonsymbiotic hemoglobin: evidence for a role in oxygen transport

Paracetamol-Galactose Conjugate: A Novel Prodrug for an Old Analgesic Drug

Rational Design of a User-Friendly Aptamer/Peptide-Based Device for the Detection of Staphylococcus aureus

Recent advances in the synthesis of analogues of phytohormones strigolactones with ring-closing metathesis as a key step

Robust Classification of “Relevant” Water Molecules in Putative Protein Binding Sites

Serine racemase: a key player in neuron activity and in neuropathologies

Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 3. The Free Energy Contribution of Structural Water Molecules in HIV-1 Protease Complexes

Strigolactone Analogs Are Promising Antiviral Agents for the Treatment of Human Cytomegalovirus Infection

Structural insight into the interaction of O-acetylserine sulfhydrylase with competitive, peptidic inhibitors by saturation transfer difference-NMR.

Structural plasticity and functional implications of internal cavities in distal mutants of type 1 non-symbiotic hemoglobin AHb1 from Arabidopsis thaliana.

Structure-Based Virtual Screening for the Discovery of Novel Inhibitors of New Delhi Metallo-β-lactamase-1.

Structure-activity relationships of strigolactones via a novel, quantitative in planta bioassay

Target flexibility: an emerging consideration in drug discovery and design

Targeting cystalysin, a virulence factor of treponema denticola-supported periodontitis

Ten Years with New Delhi Metallo-β-lactamase-1 (NDM-1): From Structural Insights to Inhibitor Design

The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery.

The consequences of scoring docked ligand conformations using free energy correlations

The inhibition of extended spectrum β-lactamases: hits and leads

The multifaceted pyridoxal 5'-phosphate-dependent O-acetylserine sulfhydrylase

The reactivity with CO of AHb1 and AHb2 from Arabidopsis thaliana is controlled by the distal HisE7 and internal hydrophobic cavities

Tools for building a comprehensive modeling system for virtual screening under real biological conditions: The Computational Titration algorithm

Tuning the Hydrophobicity of a Mitochondria-Targeted NO Photodonor

Unintended consequences? Water molecules at biological and crystallographic protein-protein interfaces

Water: How to evaluate its contribution in protein-ligand interactions