Cargando…

The rise of molecular simulations in fragment-based drug design (FBDD): an overview

Fragment-based drug discovery (FBDD) is an innovative approach, progressively more applied in the academic and industrial context, to enhance hit identification for previously considered undruggable biological targets. In particular, FBDD discovers low-molecular-weight (LMW) ligands (<300 Da) abl...

Descripción completa

Detalles Bibliográficos
Autores principales:	Bissaro, Maicol, Sturlese, Mattia, Moro, Stefano
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	The Author(s). Published by Elsevier Ltd. 2020
Materias:	Review
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7314695/ https://www.ncbi.nlm.nih.gov/pubmed/32592867 http://dx.doi.org/10.1016/j.drudis.2020.06.023

Ejemplares similares

Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules?
por: Bissaro, Maicol, et al.
Publicado: (2020)

Inspecting the Mechanism of Fragment Hits Binding on SARS‐CoV‐2 M(pro) by Using Supervised Molecular Dynamics (SuMD) Simulations
por: Bissaro, Maicol, et al.
Publicado: (2021)

Comparing Fragment Binding PosesPrediction Using HSP90 as a Key Study: When Bound Water Makes the Difference
por: Bolcato, Giovanni, et al.
Publicado: (2020)

HT-SuMD: making molecular dynamics simulations suitable for fragment-based screening. A comparative study with NMR
por: Ferrari, Francesca, et al.
Publicado: (2020)

New Insights into Key Determinants for Adenosine 1 Receptor Antagonists Selectivity Using Supervised Molecular Dynamics Simulations
por: Bolcato, Giovanni, et al.
Publicado: (2020)

Revisiting the Allosteric Regulation of Sodium Cation on the Binding of Adenosine at the Human A(2A) Adenosine Receptor: Insights from Supervised Molecular Dynamics (SuMD) Simulations
por: Bissaro, Maicol, et al.
Publicado: (2019)

Shedding Light on the Molecular Recognition of Sub-Kilodalton Macrocyclic Peptides on Thrombin by Supervised Molecular Dynamics
por: Hassankalhori, Mahdi, et al.
Publicado: (2021)

Can We Still Trust Docking Results? An Extension of the Applicability of DockBench on PDBbind Database
por: Bolcato, Giovanni, et al.
Publicado: (2019)

Targeting the coronavirus SARS-CoV-2: computational insights into the mechanism of action of the protease inhibitors lopinavir, ritonavir and nelfinavir
por: Bolcato, Giovanni, et al.
Publicado: (2020)

A Computational Workflow for the Identification of Novel Fragments Acting as Inhibitors of the Activity of Protein Kinase CK1δ
por: Bolcato, Giovanni, et al.
Publicado: (2021)

C–H functionalisation tolerant to polar groups could transform fragment-based drug discovery (FBDD)
por: Chessari, Gianni, et al.
Publicado: (2021)

Deciphering the Molecular Recognition Mechanism of Multidrug Resistance Staphylococcus aureus NorA Efflux Pump Using a Supervised Molecular Dynamics Approach
por: Palazzotti, Deborah, et al.
Publicado: (2019)

Rethinking to riluzole mechanism of action: the molecular link among protein kinase CK1δ activity, TDP-43 phosphorylation, and amyotrophic lateral sclerosis pharmacological treatment
por: Bissaro, Maicol, et al.
Publicado: (2019)

Investigating RNA–protein recognition mechanisms through supervised molecular dynamics (SuMD) simulations
por: Pavan, Matteo, et al.
Publicado: (2022)

Qualitative Estimation of Protein–Ligand Complex Stability through Thermal Titration Molecular Dynamics Simulations
por: Pavan, Matteo, et al.
Publicado: (2022)

Fighting Antimicrobial Resistance: Insights on How the Staphylococcus aureus NorA Efflux Pump Recognizes 2-Phenylquinoline Inhibitors by Supervised Molecular Dynamics (SuMD) and Molecular Docking Simulations
por: Palazzotti, Deborah, et al.
Publicado: (2023)

Thermal Titration Molecular Dynamics (TTMD): Not Your Usual Post-Docking Refinement
por: Menin, Silvia, et al.
Publicado: (2023)

A Deep-Learning Approach toward Rational Molecular Docking Protocol Selection
por: Jiménez-Luna, José, et al.
Publicado: (2020)

DockBench: An Integrated Informatic Platform Bridging the Gap between the Robust Validation of Docking Protocols and Virtual Screening Simulations
por: Cuzzolin, Alberto, et al.
Publicado: (2015)

Supervised Molecular Dynamics (SuMD) Insights into the mechanism of action of SARS-CoV-2 main protease inhibitor PF-07321332
por: Pavan, Matteo, et al.
Publicado: (2021)

Drugging the Undruggable Trypanosoma brucei Monothiol Glutaredoxin 1
por: Favaro, Annagiulia, et al.
Publicado: (2023)

Thermal titration molecular dynamics (TTMD): shedding light on the stability of RNA-small molecule complexes
por: Dodaro, Andrea, et al.
Publicado: (2023)

The Multifaceted Role of GPCRs in Amyotrophic Lateral Sclerosis: A New Therapeutic Perspective?
por: Bassani, Davide, et al.
Publicado: (2022)

Implementing a Scoring Function Based on Interaction Fingerprint for Autogrow4: Protein Kinase CK1δ as a Case Study
por: Pavan, Matteo, et al.
Publicado: (2022)

Bat coronaviruses related to SARS-CoV-2: what about their 3CL proteases (MPro)?
por: Pavan, Matteo, et al.
Publicado: (2022)

Sodium or Not Sodium: Should Its Presence Affect the Accuracy of Pose Prediction in Docking GPCR Antagonists?
por: Bassani, Davide, et al.
Publicado: (2022)

From the Wuhan-Hu-1 strain to the XD and XE variants: is targeting the SARS-CoV-2 spike protein still a pharmaceutically relevant option against COVID-19?
por: Pavan, Matteo, et al.
Publicado: (2022)

Chronic Pelvic Pain in Endometriosis: An Overview
por: Triolo, Onofrio, et al.
Publicado: (2013)

Concepts and Core Principles of Fragment-Based Drug Design
por: Kirsch, Philine, et al.
Publicado: (2019)

Re-Exploring the Ability of Common Docking Programs to Correctly Reproduce the Binding Modes of Non-Covalent Inhibitors of SARS-CoV-2 Protease M(pro)
por: Bassani, Davide, et al.
Publicado: (2022)

Ribose and Non-Ribose A2A Adenosine Receptor Agonists: Do They Share the Same Receptor Recognition Mechanism?
por: Bolcato, Giovanni, et al.
Publicado: (2022)

On the mechanism of tumor cell entry of aloe‐emodin, a natural compound endowed with anticancer activity
por: Pecere, Teresa, et al.
Publicado: (2021)

Solvents to Fragments to Drugs: MD Applications in Drug Design
por: Defelipe, Lucas A., et al.
Publicado: (2018)

NMR-Fragment Based Virtual Screening: A Brief Overview
por: Singh, Meenakshi, et al.
Publicado: (2018)

Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview
por: Salmaso, Veronica, et al.
Publicado: (2018)

Fragment-Based Ligand-Protein Contact Statistics: Application to Docking Simulations
por: Macari, Gabriele, et al.
Publicado: (2019)

Past, Present, and Future Perspectives on Computer-Aided Drug Design Methodologies
por: Bassani, Davide, et al.
Publicado: (2023)

Docking, virtual high throughput screening and in silico fragment-based drug design
por: Zoete, Vincent, et al.
Publicado: (2009)

An overview to process design, simulation and sustainability evaluation of biodiesel production
por: Pasha, Mustafa Kamal, et al.
Publicado: (2021)

Integrating Protein Interaction Surface Prediction with a Fragment-Based Drug Design: Automatic Design of New Leads with Fragments on Energy Surfaces
por: Torielli, Luca, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_kldtup7v89kaj9e1bn6oa49hm6