An overview of recent molecular dynamics applications as medicinal chemistry tools for the undruggable site challenge

Complexation of NAC-Derived Peptide Ligands with the C-Terminus of α-Synuclein Accelerates Its Aggregation

(2018) Narendra Nath Jha et al.   BIOCHEMISTRY

KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks

(2018) José Jiménez et al.   Journal of Chemical Information and Modeling

Molecular-Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors

(2018) Gerard Martinez-Rosell et al.   Journal of Chemical Information and Modeling

Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs

(2018) Noelia Ferruz et al.   Scientific Reports

2-methoxyestradiol impacts on amino acids-mediated metabolic reprogramming in osteosarcoma cells by its interaction with NMDA receptor

(2017) Magdalena Gorska-Ponikowska et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Identification of Potential Small Molecule Binding Pockets in p38α MAP Kinase

(2017) Patricia Gomez-Gutierrez et al.   Journal of Chemical Information and Modeling

Steered molecular dynamics simulation of the binding of the bovine auxilin J domain to the Hsc70 nucleotide-binding domain

(2017) You-Lin Xue et al.   JOURNAL OF MOLECULAR MODELING

A structural perspective on the interactions of TRAF6 and Basigin during the onset of melanoma: A molecular dynamics simulation study

(2017) Ria Biswas et al.   JOURNAL OF MOLECULAR RECOGNITION

Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV NTAIL through Enhanced Sampling Simulations

(2017) Mattia Bernetti et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Single or Multiple Access Channels to the CYP450s Active Site? An Answer from Free Energy Simulations of the Human Aromatase Enzyme

(2017) Alessandra Magistrato et al.   Journal of Physical Chemistry Letters

Solution NMR Spectroscopy in Target-Based Drug Discovery

(2017) et al.   MOLECULES

Supporting the Identification of Novel Fragment-Based Positive Allosteric Modulators Using a Supervised Molecular Dynamics Approach: A Retrospective Analysis Considering the Human A2A Adenosine Receptor as a Key Example

(2017) et al.   MOLECULES

Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

(2017) Nuria Plattner et al.   Nature Chemistry

Allosteric-activation mechanism of BK channel gating ring triggered by calcium ions

(2017) Ronghua Guan et al.   PLoS One

Computational investigation of conformational variability and allostery in cathepsin K and other related peptidases

(2017) Marko Novinec   PLoS One

AnchorQuery: Rapid online virtual screening for small-molecule protein-protein interaction inhibitors

(2017) David R. Koes et al.   PROTEIN SCIENCE

Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme

(2017) M. J. Latallo et al.   Chemical Science

An allosteric ligand-binding site in the extracellular cap of K2P channels

(2017) Qichao Luo et al.   Nature Communications

Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics

(2017) Nicolas E Martin et al.   PLoS Computational Biology

Probing protein flexibility reveals a mechanism for selective promiscuity

(2017) Nicolas A Pabon et al.   eLife

Computational methods in drug discovery

(2016) Sumudu P Leelananda et al.   Beilstein Journal of Organic Chemistry

Evaluating the stability of pharmacophore features using molecular dynamics simulations

(2016) Marcus Wieder et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Basigin-2 upregulated by receptor activator of NF-κB ligand enhances lung cancer-induced osteolytic lesions

(2016) Cheng-Gong Liao et al.   Cancer Cell International

Protein-protein interaction and molecular dynamics analysis for identification of novel inhibitors in Burkholderia cepacia GG4

(2016) Money Gupta et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Interplay between Two Allosteric Sites and Their Influence on Agonist Binding in Human μ Opioid Receptor

(2016) Damian Bartuzi et al.   Journal of Chemical Information and Modeling

Deciphering the Complexity of Ligand–Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations

(2016) Alberto Cuzzolin et al.   Journal of Chemical Information and Modeling

Role of Molecular Dynamics and Related Methods in Drug Discovery

(2016) Marco De Vivo et al.   JOURNAL OF MEDICINAL CHEMISTRY

Kinetic and Structural Insights into the Mechanism of Binding of Sulfonamides to Human Carbonic Anhydrase by Computational and Experimental Studies

(2016) Roberto Gaspari et al.   JOURNAL OF MEDICINAL CHEMISTRY

Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design

(2016) Yaw Sing Tan et al.   Journal of Physical Chemistry Letters

Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations

(2016) Marcus Wieder et al.   MONATSHEFTE FUR CHEMIE

Systematic Targeting of Protein–Protein Interactions

(2016) Ashley E. Modell et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Understanding allosteric interactions in G protein-coupled receptors using Supervised Molecular Dynamics: A prototype study analysing the human A3 adenosine receptor positive allosteric modulator LUF6000

(2015) Giuseppe Deganutti et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Progress in discovery of small-molecule modulators of protein–protein interactions via fragment screening

(2015) Thomas V. Magee   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Allosteric Effects of Sodium Ion Binding on Activation of the M3 Muscarinic G-Protein-Coupled Receptor

(2015) Yinglong Miao et al.   BIOPHYSICAL JOURNAL

Molecular dynamics and functional studies define a hot spot of crystal contacts essential for PcTx1 inhibition of acid-sensing ion channel 1a

(2015) Natalie J Saez et al.   BRITISH JOURNAL OF PHARMACOLOGY

KRAS as a Therapeutic Target

(2015) F. McCormick   CLINICAL CANCER RESEARCH

Nicotinamide Adenine Dinucleotide Based Therapeutics, Update

(2015) K.W. Pankiewicz et al.   CURRENT MEDICINAL CHEMISTRY

Alternative modulation of protein–protein interactions by small molecules

(2015) Gerhard Fischer et al.   CURRENT OPINION IN BIOTECHNOLOGY

Allosteric Modulation of Alpha7 Nicotinic Receptors: Mechanistic Insight through Metadynamics and Essential Dynamics

(2015) Giovanni Grazioso et al.   Journal of Chemical Information and Modeling

Molecular Dynamics Simulations and Structural Analysis of Giardia duodenalis 14-3-3 Protein–Protein Interactions

(2015) Ylenia Cau et al.   Journal of Chemical Information and Modeling

Activation and Allosteric Modulation of Human μ Opioid Receptor in Molecular Dynamics

(2015) Damian Bartuzi et al.   Journal of Chemical Information and Modeling

The Application of Ligand-Mapping Molecular Dynamics Simulations to the Rational Design of Peptidic Modulators of Protein–Protein Interactions

(2015) Yaw Sing Tan et al.   Journal of Chemical Theory and Computation

A Collective Variable for the Rapid Exploration of Protein Druggability

(2015) Rémi Cuchillo et al.   Journal of Chemical Theory and Computation

Extracting ligands from receptors by reversed targeted molecular dynamics

(2015) Romain M. Wolf   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors

(2015) Rushikesh Sable et al.   MOLECULES

Virtual Screening and Molecular Dynamics Study of Potential Negative Allosteric Modulators of mGluR1 from Chinese Herbs

(2015) Ludi Jiang et al.   MOLECULES

The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins

(2015) Dima Kozakov et al.   Nature Protocols

Understanding the conformation transition in the activation pathway of β2 adrenergic receptor via a targeted molecular dynamics simulation

(2015) Xiuchan Xiao et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Conformational processing of oncogenic v-Src kinase by the molecular chaperone Hsp90

(2015) Edgar E. Boczek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Investigation of the conformational dynamics of the apo A2Aadenosine receptor

(2015) Alisha D. Caliman et al.   PROTEIN SCIENCE

The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning

(2015) Sergio Decherchi et al.   Nature Communications

Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations

(2015) Luca Mollica et al.   Scientific Reports

Identification and Characterization of an Allosteric Inhibitory Site on Dihydropteroate Synthase

(2014) Dalia I. Hammoudeh et al.   ACS Chemical Biology

Mechanistic Insights into the Allosteric Modulation of Opioid Receptors by Sodium Ions

(2014) Yi Shang et al.   BIOCHEMISTRY

Antibody informatics for drug discovery

(2014) Hiroki Shirai et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Statistical allosteric coupling to the active site indole ring flip equilibria in the FK506-binding domain

(2014) Janet S. Anderson et al.   BIOPHYSICAL CHEMISTRY

Markov state models of biomolecular conformational dynamics

(2014) John D Chodera et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Targeting Chemokine Receptor CXCR4 for Treatment of HIV-1 Infection, Tumor Progression, and Metastasis

(2014) Won-Tak Choi et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Focused chemical libraries – design and enrichment: an example of protein–protein interaction chemical space

(2014) Xu Zhang et al.   Future Medicinal Chemistry

The novel Parkinson's disease linked mutation G51D attenuates in vitro aggregation and membrane binding of  -synuclein, and enhances its secretion and nuclear localization in cells

(2014) M.-B. Fares et al.   HUMAN MOLECULAR GENETICS

Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR–Ligand Recognition Pathway in a Nanosecond Time Scale

(2014) Davide Sabbadin et al.   Journal of Chemical Information and Modeling

Hydrocarbon-Stapled Peptides: Principles, Practice, and Progress

(2014) Loren D. Walensky et al.   JOURNAL OF MEDICINAL CHEMISTRY

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

The Crystal Structure of Giardia duodenalis 14-3-3 in the Apo Form: When Protein Post-Translational Modifications Make the Difference

(2014) Annarita Fiorillo et al.   PLoS One

Disruption of the Na+ion binding site as a mechanism for positive allosteric modulation of the mu-opioid receptor

(2014) Kathryn E. Livingston et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hot spots in protein–protein interfaces: Towards drug discovery

(2014) Engin Cukuroglu et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Binding Site Detection and Druggability Prediction of Protein Targets for Structure- Based Drug Design

(2013) Yaxia Yuan et al.   CURRENT PHARMACEUTICAL DESIGN

Identification of a second Nutlin-3 responsive interaction site in the N-terminal domain of MDM2 using hydrogen/deuterium exchange mass spectrometry

(2013) Lenka Hernychova et al.   PROTEOMICS

Extra-intestinal and long term consequences of Giardia duodenalis infections

(2013) Marie CM Halliez   WORLD JOURNAL OF GASTROENTEROLOGY

Using Steered Molecular Dynamics to Predict and Assess Hsp70 Substrate-Binding Domain Mutants that Alter Prion Propagation

(2013) Linan Xu et al.   PLoS Computational Biology

Computational drug discovery

(2012) Si-sheng Ou-Yang et al.   ACTA PHARMACOLOGICA SINICA

Modulating Protein-Protein Interactions: From Structural Determinants of Binding to Druggability Prediction to Application

(2012) Alexander Metz et al.   CURRENT PHARMACEUTICAL DESIGN

Steered molecular dynamics simulations on the binding of the appendant structure and helix-β2 in domain-swapped human cystatin C dimer

(2012) Manli Shen et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules

(2012) Ahmet Bakan et al.   Journal of Chemical Theory and Computation

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions

(2012) W. Liu et al.   SCIENCE

Structure of the Acid-sensing ion channel 1 in complex with the gating modifier Psalmotoxin 1

(2012) Roger J.P. Dawson et al.   Nature Communications

Fragment screening to predict druggability (ligandability) and lead discovery success

(2011) Fredrik N.B. Edfeldt et al.   DRUG DISCOVERY TODAY

Heteromeric Acid-Sensing Ion Channels (ASICs) Composed of ASIC2b and ASIC1a Display Novel Channel Properties and Contribute to Acidosis-Induced Neuronal Death

(2011) T. W. Sherwood et al.   JOURNAL OF NEUROSCIENCE

Molecular Basis of Ligand Dissociation in β-Adrenergic Receptors

(2011) Angel González et al.   PLoS One

Steered molecular dynamics simulations of ligand–receptor interaction in lipocalins

(2010) Janne Kalikka et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Drug-like Density: A Method of Quantifying the “Bindability” of a Protein Target Based on a Very Large Set of Pockets and Drug-like Ligands from the Protein Data Bank

(2010) Robert P. Sheridan et al.   Journal of Chemical Information and Modeling

Full Protein Flexibility Is Essential for Proper Hot-Spot Mapping

(2010) Katrina W. Lexa et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Acid-Sensing Ion Channels (ASICs): Pharmacology and implication in pain

(2010) Emmanuel Deval et al.   PHARMACOLOGY & THERAPEUTICS

Calculation of the free energy of association for protein complexes

(2010) Nancy Horton et al.   PROTEIN SCIENCE

Long-timescale molecular dynamics simulations of protein structure and function

(2009) John L Klepeis et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Rationalizing the chemical space of protein–protein interaction inhibitors

(2009) Olivier Sperandio et al.   DRUG DISCOVERY TODAY

Rational drug design

(2009) Soma Mandal et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

Involvement of 14-3-3 protein post-translational modifications in Giardia duodenalis encystation

(2009) Marco Lalle et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Binding Site Detection and Druggability Index from First Principles

(2009) Jesus Seco et al.   JOURNAL OF MEDICINAL CHEMISTRY

Using generalized ensemble simulations and Markov state models to identify conformational states

(2009) Gregory R. Bowman et al.   METHODS

X-ray vs. NMR structures as templates for computational protein design

(2009) Michael Schneider et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

c-Abl Phosphorylates Hdmx and Regulates Its Interaction with p53

(2008) Valentina Zuckerman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Estimating the size of the human interactome

(2008) M. P. H. Stumpf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computer-aided drug discovery and development (CADDD): In silico-chemico-biological approach

(2006) I.M. Kapetanovic   CHEMICO-BIOLOGICAL INTERACTIONS

Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations

(2002) Buyong Ma et al.   PROTEIN SCIENCE