Publications

2021

Structure-Based Virtual Screening for Ligands of G Protein–Coupled Receptors: What Can Molecular Docking Do for You?

Ballante, Flavio; Kooistra, Albert J; Kampen, Stefanie; de Graaf, Chris; Carlsson, Jens

Structure-Based Virtual Screening for Ligands of G Protein–Coupled Receptors: What Can Molecular Docking Do for You? Journal Article

In: Pharmacological Reviews, 73 , pp. 527-565, 2021, ISSN: 1521-0081.

Abstract | Links | BibTeX | Tags: GPCR, Molecular Docking, Review, Structure-Based Drug Design, Virtual Screening

Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

Kapla, Jon; Espigares, Ismael Rodriguez; Ballante, Flavio; Selent, Jana; Carlsson, Jens

Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models? Journal Article

In: PLOS Computational Biology, 2021.

Links | BibTeX | Tags: GPCR, Molecular Docking, Molecular Dynamics, Molecular Modeling

Protein-Ligand Interactions and Drug Design

Methods in Molecular Biology book series (MIMB, volume 2266)

Protein-Ligand Interactions and Drug Design Book

Humana, New York, NY, 2021.

Abstract | Links | BibTeX | Tags: Book, Chemoinformatics, Molecular Modeling, Protocol

2020

Identification of histone deacetylase inhibitors with (arylidene)aminoxy scaffold active in uveal melanoma cell lines

Nencetti, Susanna; Cuffaro, Doretta; Nuti, Elisa; Ciccone, Lidia; Rossello, Armando; Fabbi, Marina; Ballante, Flavio; Ortore, Gabriella; Carbotti, Grazia; Campelli, Francesco; Banti, Irene; Gangemi, Rosaria; Marshall, Garland R.; Orlandini, Elisabetta

Identification of histone deacetylase inhibitors with (arylidene)aminoxy scaffold active in uveal melanoma cell lines Journal Article

In: Journal of Enzyme Inhibition and Medicinal Chemistry, 36 (1), pp. 34–47, 2020.

Abstract | Links | BibTeX | Tags: Biochemistry, HDAC, Molecular Docking, Molecular Modeling

2019

Docking finds GPCR ligands in dark chemical matter

Ballante, Flavio; Rudling, Axel; Zeifman, Alexey; Luttens, Andreas; Vo, Duy Duc; Irwin, John; Kihlberg, Jan; Brea, José; Loza, Maria; Carlsson, Jens

Docking finds GPCR ligands in dark chemical matter Journal Article

In: Journal of Medicinal Chemistry, Just accepted manuscript , 2019.

Abstract | Links | BibTeX | Tags: Biochemistry, Dark Chemical Matter, GPCR, Molecular Docking, Virtual Screening

2018

Structural characterization of agonist binding to protease-activated receptor 2 through mutagenesis and computational modeling

Kennedy, Amanda J.; Ballante, Flavio; Johansson, Johan R.; Milligan, Graeme; Sundström, Linda; Nordqvist, Anneli; Carlsson, Jens

Structural characterization of agonist binding to protease-activated receptor 2 through mutagenesis and computational modeling Journal Article

In: ACS Pharmacology & Translational Science, 1 (2), pp. 119-133, 2018, ISSN: 2575-9108.

Abstract | Links | BibTeX | Tags: Biochemistry, Clusterizer, Homology Modeling, Molecular Docking

Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection

Ballante, Flavio

Protein-Ligand Docking in Drug Design: Performance Assessment and Binding-Pose Selection Book Chapter

In: Mavromoustakos, Thomas; Kellici, Tahsin F. (Ed.): 1824 , Chapter 5, pp. 67-88, Springer Nature, 2018, ISBN: 978-1-4939-8630-9.

Links | BibTeX | Tags: Docking Assessment, Molecular Docking, Molecular Modeling

2017

Limiting Assumptions in the Design of Peptidomimetics

Marshall, Garland R.; Ballante, Flavio

Limiting Assumptions in the Design of Peptidomimetics Journal Article

In: Drug Development Research, 78 (6), pp. 245–267, 2017, ISSN: 1098-2299.

Links | BibTeX | Tags: Beta-sheet mimetics, Helix mimetics reverse-turn mimetics, Peptidomimetics, Semi-rigid analogs

Structural Insights of SmKDAC8 Inhibitors: Targeting Schistosoma Epigenetics Through a Combined Structure-Based 3D QSAR, in vitro and Synthesis Strategy

Ballante, Flavio; Reddy, D. Rajasekhar; Zhou, Nancy J.; Marshall, Garland R.

Structural Insights of SmKDAC8 Inhibitors: Targeting Schistosoma Epigenetics Through a Combined Structure-Based 3D QSAR, in vitro and Synthesis Strategy Journal Article

In: Bioorganic & Medicinal Chemistry, 2017.

Links | BibTeX | Tags: 3D QSAR, Biochemistry, COMBINEr, Molecular Docking, Molecular Modeling, Organic Chemistry, PLS, Schistosoma mansoni, Virtual Screening

2016

Design and synthesis of benzodiazepine analogs as isoform-selective human lysine deacetylase inhibitors

Reddy, D. Rajasekhar; Ballante, Flavio; Zhou, Nancy J.; Marshall, Garland R.

Design and synthesis of benzodiazepine analogs as isoform-selective human lysine deacetylase inhibitors Journal Article

In: European Journal of Medicinal Chemistry, 127 , pp. Pages 531–553, 2016.

Abstract | Links | BibTeX | Tags: Biochemistry, HDAC, Molecular Docking

2015

An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design

Flavio, Ballante; Marshall, Garland R.

An Automated Strategy for Binding-Pose Selection and Docking Assessment in Structure-Based Drug Design Journal Article

In: Journal of Chemical Information and Modeling, 56 (1), pp. 54-72, 2015.

Abstract | Links | BibTeX | Tags: Chemoinformatics, Clusterizer, DockAccessor, Docking Assessment, Molecular Docking, Molecular Modeling

Design and Synthesis of Simplified Largazole Analogs as Isoform-Selective Human Lysine Deacetylase Inhibitors

Damodara, Reddy Nandarapu; Flavio, Ballante; Timothy, Chuang; Adele, Pirolli; Biagina, Marrocco; Garland R, Marshall

Design and Synthesis of Simplified Largazole Analogs as Isoform-Selective Human Lysine Deacetylase Inhibitors Journal Article

In: Journal of Medicinal Chemistry, in press , 2015.

Abstract | Links | BibTeX | Tags: Biochemistry, HDAC, Molecular Docking, Organic Chemistry

Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand-and structure-based approaches

Rino, Ragno; Flavio, Ballante; Adele, Pirolli; Richard B, Wickersham III; Alexandros, Patsilinakos; Stéphanie, Hesse; Enrico, Perspicace; Gilbert, Kirsch

Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand-and structure-based approaches Journal Article

In: Journal of Computer-Aided Molecular Design, 29 (8), pp. 757-776, 2015.

Abstract | Links | BibTeX | Tags: 3-D QSAutogrid/R, 3D QSAR, Ligand-Based Design, Molecular Docking, Molecular Modeling, Pharmacophoric Model, PLS, VEGFR-2

2014

Exploring the Role of 2 ‑ Chloro-6- fluoro Substitution in 2 ‑ Alkylthio-6- benzyl-5-alkylpyrimidin-4(3 H ) ‑ ones: Effects in HIV-1-Infected Cells and in HIV ‑ 1 Reverse Transcriptase Enzymes

Dante, Rotili; Domenico, Tarantino; Maxim B, Nawrozkij; Alexandre S, Babushkin; Giorgia, Botta; Biagina, Marrocco; Roberto, Cirilli; Sergio, Menta; Roger, Badia; Emmanuele, Crespan; Flavio, Ballante; Rino, Ragno; José A, Esté; Giovanni, Maga; Antonello, Mai

Exploring the Role of 2 ‑ Chloro-6- fluoro Substitution in 2 ‑ Alkylthio-6- benzyl-5-alkylpyrimidin-4(3 H ) ‑ ones: Effects in HIV-1-Infected Cells and in HIV ‑ 1 Reverse Transcriptase Enzymes Journal Article

In: Journal of Medicinal Chemistry, 57 (12), pp. 5212-5225, 2014.

Abstract | Links | BibTeX | Tags: Biochemistry, COMBINEr, DABO, HIV-1, HIV-RT, Molecular Docking, Molecular Modeling, NNRTIs, Organic Chemistry, PLS

Hsp90 inhibitors, part 1: definition of 3-D QSAutogrid/R models as a tool for virtual screening

Flavio, Ballante; Antonia, Caroli; Richard B, Wickersham III; Rino, Ragno

Hsp90 inhibitors, part 1: definition of 3-D QSAutogrid/R models as a tool for virtual screening Journal Article

In: Journal of Chemical Information and Modeling, 54 (3), pp. 956-969, 2014.

Abstract | Links | BibTeX | Tags: 3-D QSAutogrid/R, 3D QSAR, HSP90, Ligand-Based Design, Molecular Docking, Pharmacophoric Model, PLS, Virtual Screening

Hsp90 Inhibitors, Part 2: Combining Ligand-Based and Structure-Based Approaches for Virtual Screening Application

Antonia, Caroli; Flavio, Ballante; Richard B, Wickersham III; Federico, Corelli; Rino, Ragno

Hsp90 Inhibitors, Part 2: Combining Ligand-Based and Structure-Based Approaches for Virtual Screening Application Journal Article

In: Journal of Chemical Information and Modeling, 54 (3), pp. 970-977, 2014.

Abstract | Links | BibTeX | Tags: 3-D QSAutogrid/R, 3D QSAR, HSP90, Ligand-Based Design, Molecular Docking, Molecular Modeling, MPGRS, Pharmacophoric Model, PLS, Virtual Screening

Application of Medicinal Chemistry Methods on Different Classes of Drugs

Flavio, Ballante

Application of Medicinal Chemistry Methods on Different Classes of Drugs PhD Thesis

Sapienza University of Rome, 2014.

Abstract | Links | BibTeX | Tags: 3-D QSAutogrid/R, 3D QSAR, Biochemistry, BSAO, Chemoinformatics, Chemometrics, COMBINEr, CoMFA, DABO, DockAccessor, Docking Assessment, HCV NS5B, HDAC, HIV-1, HIV-RT, HSP90, HUVEC, Ligand-Based Design, Molecular Docking, Molecular Modeling, MPGRS, NNRTIs, Opioid-Receptor Antagonists, Organic Chemistry, Pharmacophoric Model, PLS, Tuberculosis, VEGFR-2, Virtual Screening

2013

Computational strategies to design new highly potential BSAO polyamine substrates - Abstracts presented at the 13th International Congress on Amino acids, peptides and proteins

Flavio, Ballante; Giampiero, Tempera; Enzo, Agostinelli; Rino, Ragno

Computational strategies to design new highly potential BSAO polyamine substrates - Abstracts presented at the 13th International Congress on Amino acids, peptides and proteins Proceeding

Amino Acids, 45 (3), 2013.

Abstract | Links | BibTeX | Tags: 3-D QSAutogrid/R, 3D QSAR, Biochemistry, BSAO, Molecular Docking, Molecular Modeling, MPGRS

Design, synthesis and biological evaluation of new classes of thieno [3, 2-d] pyrimidinone and thieno [1, 2, 3] triazine as inhibitor of vascular endothelial growth factor receptor-2 (VEGFR-2)

Enrico, Perspicace; Valérie, Jouan-Hureaux; Rino, Ragno; Flavio, Ballante; Stefania, Sartini; Concettina, La Motta; Federico, Da Settimo; Binbin, Chen; Gilbert, Kirsch; Serge, Schneider; Béatrice, Faivre; Stéphanie, Hesse

Design, synthesis and biological evaluation of new classes of thieno [3, 2-d] pyrimidinone and thieno [1, 2, 3] triazine as inhibitor of vascular endothelial growth factor receptor-2 (VEGFR-2) Journal Article

In: European Journal of Medicinal Chemistry, 63 , pp. 765-781, 2013.

Abstract | Links | BibTeX | Tags: 3-D QSAutogrid/R, 3D QSAR, Biochemistry, HUVEC, Organic Chemistry, PLS, VEGFR-2

Pharmacophore assessment through 3-D QSAR: Evaluation of the predictive ability on new derivatives by the application on a series of antitubercular agents

Laura, Friggeri; Flavio, Ballante; Rino, Ragno; Ira, Musmuca; Daniela, De Vita; Fabrizio, Manetti; Mariangela, Biava; Luigi, Scipione; Roberto, Di Santo; Roberta, Costi; Marta, Feroci; Silvano, Tortorella

Pharmacophore assessment through 3-D QSAR: Evaluation of the predictive ability on new derivatives by the application on a series of antitubercular agents Journal Article

In: Journal of Chemical Information and Modeling, 53 (6), pp. 1463-1474, 2013.

Abstract | Links | BibTeX | Tags: 3-D QSAutogrid/R, 3D QSAR, Ligand-Based Design, MPGRS, Organic Chemistry, Pharmacophoric Model, PLS, Tuberculosis

2012

Comprehensive model of wild-type and mutant HIV-1 reverse transciptases

Flavio, Ballante; Ira, Musmuca; Marshall, Garland R; Rino, Ragno

Comprehensive model of wild-type and mutant HIV-1 reverse transciptases Journal Article

In: Journal of Computer-Aided Molecular Design, 26 (8), pp. 907-919, 2012.

Abstract | Links | BibTeX | Tags: 3D QSAR, COMBINEr, DABO, HIV-1, HIV-RT, PLS

Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction

Laura, Silvestri; Flavio, Ballante; Antonello, Mai; Garland R, Marshall; Rino, Ragno

Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction Journal Article

In: Journal of Chemical Information and Modeling, 52 (8), pp. 2215-2235, 2012.

Abstract | Links | BibTeX | Tags: 3D QSAR, COMBINEr, HDAC, Molecular Docking, Molecular Modeling, PLS

3-D QSAutogrid/R: An Alternative Procedure To Build 3-D QSAR Models. Methodologies and Applications

Flavio, Ballante; Rino, Ragno

3-D QSAutogrid/R: An Alternative Procedure To Build 3-D QSAR Models. Methodologies and Applications Journal Article

In: Journal of Chemical Information and Modeling, 52 (6), pp. 1674, 2012.

Abstract | Links | BibTeX | Tags: 3-D QSAutogrid/R, 3D QSAR, Chemoinformatics, Chemometrics, CoMFA, HCV NS5B, Molecular Modeling, MPGRS, Opioid-Receptor Antagonists, PLS

2-(Alkyl/aryl) amino-6-benzylpyrimidin-4 (3H)-ones as inhibitors of wild-type and mutant HIV-1: enantioselectivity studies

Dante, Rotili; Alberta, Samuele; Domenico, Tarantino; Rino, Ragno; Ira, Musmuca; Flavio, Ballante; Giorgia, Botta; Ludovica, Morera; Marco, Pierini; Roberto, Cirilli; Maxim B, Nawrozkij; Emmanuel, Gonzalez; Bonaventura, Clotet; Marino, Artico; José A, Esté; Giovanni, Maga; Antonello, Mai

2-(Alkyl/aryl) amino-6-benzylpyrimidin-4 (3H)-ones as inhibitors of wild-type and mutant HIV-1: enantioselectivity studies Journal Article

In: Journal of Medicinal Chemistry, 55 (7), pp. 3558-3562, 2012.

Abstract | Links | BibTeX | Tags: Biochemistry, COMBINEr, DABO, HIV-1, Molecular Docking, Molecular Modeling, NNRTIs, Organic Chemistry