Virtual screening of small molecules databases for discovery of novel PARP-1 inhibitors: combination of in silico and in vitro studies

Mutated form (G52E) of inactive diphtheria toxin CRM197: molecular simulations clearly display effect of the mutation to NAD binding

(2016) Ramin Ekhteiari Salmas et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Atomistic molecular dynamics simulations of typical and atypical antipsychotic drugs at the dopamine D2 receptor (D2R) elucidates their inhibition mechanism

(2016) Ramin Ekhteiari Salmas et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Virtual screening of eighteen million compounds against dengue virus: Combined molecular docking and molecular dynamics simulations study

(2016) Shaher Bano Mirza et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Binding Interactions of Dopamine and Apomorphine in D2High and D2Low States of Human Dopamine D2 Receptor Using Computational and Experimental Techniques

(2015) Serdar Durdagi et al.   ACS Chemical Neuroscience

Identification of novel PARP-1 inhibitors: Drug design, synthesis and biological evaluation

(2015) Zhouling Xie et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Molecular Simulations of Solved Co-crystallized X-Ray Structures Identify Action Mechanisms of PDEδ Inhibitors

(2015) Ramin Ekhteiari Salmas et al.   BIOPHYSICAL JOURNAL

Discovering novel carbonic anhydrase type IX (CA IX) inhibitors from seven million compounds using virtual screening andin vitroanalysis

(2015) Ramin Ekhteiari Salmas et al.   JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY

Kinetic andin silicostudies of hydroxy-based inhibitors of carbonic anhydrase isoforms I and II

(2015) Ramin Ekhteiari Salmas et al.   JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY

In silicoinvestigation of PARP-1 catalytic domains inholoandapostates for the design of high-affinity PARP-1 inhibitors

(2015) Ramin Ekhteiari Salmas et al.   JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY

Niraparib: A Poly(ADP-ribose) Polymerase (PARP) Inhibitor for the Treatment of Tumors with Defective Homologous Recombination

(2015) Philip Jones et al.   JOURNAL OF MEDICINAL CHEMISTRY

Investigation of Inhibition Mechanism of Chemokine Receptor CCR5 by Micro-second Molecular Dynamics Simulations

(2015) Ramin Ekhteiari Salmas et al.   Scientific Reports

Stepwise development of structure–activity relationship of diverse PARP-1 inhibitors through comparative and validatedin silico modeling techniques and molecular dynamics simulation

(2014) Amit K. Halder et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Elucidation of Conformational States, Dynamics, and Mechanism of Binding in Human κ-Opioid Receptor Complexes

(2014) Georgios Leonis et al.   Journal of Chemical Information and Modeling

Nitric Oxide (NO) Releasing Poly ADP-ribose Polymerase 1 (PARP-1) Inhibitors Targeted to Glutathione S-Transferase P1-Overexpressing Cancer Cells

(2014) Anna E. Maciag et al.   JOURNAL OF MEDICINAL CHEMISTRY

Rehabilitating drug-induced long-QT promoters: In-silico design of hERG-neutral cisapride analogues with retained pharmacological activity

(2014) Serdar Durdagi et al.   BMC Pharmacology & Toxicology

Identification of novel PARP-1 inhibitors by structure-based virtual screening

(2013) Kevin Hannigan et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

(2013) G. Madhavi Sastry et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Design, Synthesis, and Biological Evaluation of a Series of Benzo[de][1,7]naphthyridin-7(8H)-ones Bearing a Functionalized Longer Chain Appendage as Novel PARP1 Inhibitors

(2013) Na Ye et al.   JOURNAL OF MEDICINAL CHEMISTRY

Exploring the effect of PARP-1 flexibility in docking studies

(2013) Albert A. Antolin et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Targeting Poly (ADP-Ribose) Polymerase Partially Contributes to Bufalin-Induced Cell Death in Multiple Myeloma Cells

(2013) He Huang et al.   PLoS One

Structural Implications for Selective Targeting of PARPs

(2013) Jamin D. Steffen et al.   Frontiers in Oncology

Synthesis and SAR optimization of quinazolin-4(3H)-ones as poly(ADP-ribose)polymerase-1 inhibitors

(2012) Shridhar S. Kulkarni et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

ZINC: A Free Tool to Discover Chemistry for Biology

(2012) John J. Irwin et al.   Journal of Chemical Information and Modeling

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

(2012) Bill R. Miller et al.   Journal of Chemical Theory and Computation

BRCAness: Finding the Achilles Heel in Ovarian Cancer

(2012) G. Rigakos et al.   ONCOLOGIST

Optimization of Phenyl-Substituted Benzimidazole Carboxamide Poly(ADP-Ribose) Polymerase Inhibitors: Identification of (S)-2-(2-Fluoro-4-(pyrrolidin-2-yl)phenyl)-1H-benzimidazole-4-carboxamide (A-966492), a Highly Potent and Efficacious Inhibitor

(2010) Thomas D. Penning et al.   JOURNAL OF MEDICINAL CHEMISTRY

Evolution of Poly(ADP-ribose) Polymerase-1 (PARP-1) Inhibitors. From Concept to Clinic

(2010) Dana V. Ferraris   JOURNAL OF MEDICINAL CHEMISTRY

Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations

(2010) Julia Subbotina et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Discovery of 2-{4-[(3S)-Piperidin-3-yl]phenyl}-2H-indazole-7-carboxamide (MK-4827): A Novel Oral Poly(ADP-ribose)polymerase (PARP) Inhibitor Efficacious in BRCA-1 and -2 Mutant Tumors

(2009) Philip Jones et al.   JOURNAL OF MEDICINAL CHEMISTRY

Potentiation of Temozolomide Cytotoxicity by Poly(ADP)Ribose Polymerase Inhibitor ABT-888 Requires a Conversion of Single-Stranded DNA Damages to Double-Stranded DNA Breaks

(2008) X. Liu et al.   MOLECULAR CANCER RESEARCH

Very fast prediction and rationalization of pKa values for protein-ligand complexes

(2008) Delphine C. Bas et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS