Exploiting activity cliffs for building pharmacophore models and comparison with other pharmacophore generation methods: sphingosine kinase 1 as case study

Sphingosine-1-phosphate: From insipid lipid to a key regulator

(2020) Sarah Spiegel   JOURNAL OF BIOLOGICAL CHEMISTRY

Unbalanced Sphingolipid Metabolism and Its Implications for the Pathogenesis of Psoriasis

(2020) Katarzyna Bocheńska et al.   MOLECULES

Advances in exploring activity cliffs

(2020) Dagmar Stumpfe et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Antineoplastic Agents Targeting Sphingolipid Pathways

(2020) Alexander Kroll et al.   Frontiers in Oncology

Elaboration of Novel TTK1 Inhibitory Leads via QSAR-Guided Selection of Crystallographic Pharmacophores Followed By In vitro Assay

(2020) Mahmoud A. Al-Sha'er et al.   Current Computer-Aided Drug Design

Role of bioactive sphingolipids in physiology and pathology

(2020) Ana Gomez-Larrauri et al.   Essays in Biochemistry

Development of novel in silico prediction model for drug-induced ototoxicity by using naïve Bayes classifier approach

(2020) Hui Zhang et al.   TOXICOLOGY IN VITRO

Pharmacophore modeling of JAK1: A target infested with activity-cliffs

(2020) Safa Daoud et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Naive Bayes: applications, variations and vulnerabilities: a review of literature with code snippets for implementation

(2020) Indika Wickramasinghe et al.   Soft Computing

Structure-Based Discovery and Bioactivity Evaluation of Novel Aurora-A Kinase Inhibitors as Anticancer Agents via Docking-Based Comparative Intermolecular Contacts Analysis (dbCICA)

(2020) Majd S. Hijjawi et al.   MOLECULES

Predicting Activity Cliffs with Free-Energy Perturbation

(2019) Laura Pérez-Benito et al.   Journal of Chemical Theory and Computation

Broad-scale analysis of thermodynamic signatures in medicinal chemistry: are enthalpy-favored binders the better development option?

(2019) Gerhard Klebe   DRUG DISCOVERY TODAY

Discovery of novel Flt3 inhibitory chemotypes through extensive ligand-based and new structure-based pharmacophore modelling methods

(2019) Reem Fawaz Abutayeh et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Discovery of new JNK3 inhibitory chemotypes via QSAR-Guided selection of docking-based pharmacophores and comparison with other structure-based pharmacophore modeling methods

(2019) Ghada Omar Tuffaha et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Applications of machine learning in drug discovery and development

(2019) Jessica Vamathevan et al.   NATURE REVIEWS DRUG DISCOVERY

QSAR-guided pharmacophore modeling and subsequent virtual screening identify novel TYK2 inhibitor

(2019) Elham Y. Al-Barghouthy et al.   MEDICINAL CHEMISTRY RESEARCH

Discovery of new Gyrase β inhibitors via structure based modeling

(2018) Afaf H. Al-Nadaf et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Combining Stochastic Deformation/Relaxation and Intermolecular Contacts Analysis for Extracting Pharmacophores from Ligand–Receptor Complexes

(2018) Ma’mon M. Hatmal et al.   Journal of Chemical Information and Modeling

Ligand-based modeling of Akt3 lead to potent dual Akt1/Akt3 inhibitor

(2018) Mahmoud A. Al-Sha’er et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Virtual screening, Docking, ADMET and System Pharmacology studies on Garcinia caged Xanthone derivatives for Anticancer activity

(2018) Sarfaraz Alam et al.   Scientific Reports

Molecular mechanisms of regulation of sphingosine kinase 1

(2018) Michael J. Pulkoski-Gross et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Machine Learning-based Virtual Screening and Its Applications to Alzheimer’s Drug Discovery: A Review

(2018) Kristy A. Carpenter et al.   CURRENT PHARMACEUTICAL DESIGN

Automatic selection of molecular descriptors using random forest: Application to drug discovery

(2017) Gaspar Cano et al.   EXPERT SYSTEMS WITH APPLICATIONS

Development of novel prediction model for drug-induced mitochondrial toxicity by using naïve Bayes classifier method

(2017) Hui Zhang et al.   FOOD AND CHEMICAL TOXICOLOGY

Simulated annealing molecular dynamics and ligand–receptor contacts analysis for pharmacophore modeling

(2017) Ma'mon M Hatmal et al.   Future Medicinal Chemistry

Transforming Sphingosine Kinase 1 Inhibitors into Dual and Sphingosine Kinase 2 Selective Inhibitors: Design, Synthesis, and in Vivo Activity

(2017) Elizabeth S. Childress et al.   JOURNAL OF MEDICINAL CHEMISTRY

Discovery of a Potent and Selective Sphingosine Kinase 1 Inhibitor through the Molecular Combination of Chemotype-Distinct Screening Hits

(2017) Mark E. Schnute et al.   JOURNAL OF MEDICINAL CHEMISTRY

Unsupervised pharmacophore modeling combined with QSAR analyses revealed novel low micromolar SIRT2 inhibitors

(2017) Mohammad A. Khanfar et al.   JOURNAL OF MOLECULAR RECOGNITION

Docking-based comparative intermolecular contacts analysis and in silico screening reveal new potent acetylcholinesterase inhibitors

(2017) Maha Habash et al.   MEDICINAL CHEMISTRY RESEARCH

Protein conformational flexibility modulates kinetics and thermodynamics of drug binding

(2017) M. Amaral et al.   Nature Communications

Soaking suggests “alternative facts”: Only co-crystallization discloses major ligand-induced interface rearrangements of a homodimeric tRNA-binding protein indicating a novel mode-of-inhibition

(2017) Frederik Rainer Ehrmann et al.   PLoS One

Development of hydroxy-based sphingosine kinase inhibitors and anti-inflammation in dextran sodium sulfate induced colitis in mice

(2016) Meiyang Xi et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Intrinsic Thermodynamics and Structures of 2,4- and 3,4-Substituted Fluorinated Benzenesulfonamides Binding to Carbonic Anhydrases

(2016) Asta Zubrienė et al.   ChemMedChem

Computer-aided discovery of new FGFR-1 inhibitors followed by in vitro validation

(2016) Shada J Alabed et al.   Future Medicinal Chemistry

Combining molecular dynamics simulation and ligand-receptor contacts analysis as a new approach for pharmacophore modeling: beta-secretase 1 and check point kinase 1 as case studies

(2016) Ma’mon M. Hatmal et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Discovery of new heat shock protein 90 inhibitors using virtual co-crystallized pharmacophore generation

(2016) Mahmoud A. Al-Sha'er et al.   JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY

From Sphingosine Kinase to Dihydroceramide Desaturase: A Structure–Activity Relationship (SAR) Study of the Enzyme Inhibitory and Anticancer Activity of 4-((4-(4-Chlorophenyl)thiazol-2-yl)amino)phenol (SKI-II)

(2016) Luigi Aurelio et al.   JOURNAL OF MEDICINAL CHEMISTRY

Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC

(2016) Aki Vehtari et al.   STATISTICS AND COMPUTING

Structural Requirements and Docking Analysis of Amidine-Based Sphingosine Kinase 1 Inhibitors Containing Oxadiazoles

(2016) Joseph D. Houck et al.   ACS Medicinal Chemistry Letters

Structure–Activity Relationship Studies and Molecular Modeling of Naphthalene-Based Sphingosine Kinase 2 Inhibitors

(2016) Molly D. Congdon et al.   ACS Medicinal Chemistry Letters

Machine-learning approaches in drug discovery: methods and applications

(2015) Antonio Lavecchia   DRUG DISCOVERY TODAY

Novel anthraquinone-based derivatives as potent inhibitors for receptor tyrosine kinases

(2015) M Stasevych et al.   INDIAN JOURNAL OF PHARMACEUTICAL SCIENCES

Fragment Binding Can Be Either More Enthalpy-Driven or Entropy-Driven: Crystal Structures and Residual Hydration Patterns Suggest Why

(2015) Eggert Rühmann et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structure−Activity Relationship Studies and in Vivo Activity of Guanidine-Based Sphingosine Kinase Inhibitors: Discovery of SphK1- and SphK2-Selective Inhibitors

(2015) Neeraj N. Patwardhan et al.   JOURNAL OF MEDICINAL CHEMISTRY

Ligand-based modeling followed by in vitro bioassay yielded new potent glucokinase activators

(2015) Mutasem O. Taha et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Evaluation of novel Akt1 inhibitors as anticancer agents using virtual co-crystallized pharmacophore generation

(2015) Mahmoud A. Al-Sha’er et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

(2015) Lingle Wang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

(2015) Nuria Plattner et al.   Nature Communications

Molecular Dynamics, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review

(2015) Eric Paquet et al.   Biomed Research International

Methyl, Ethyl, Propyl, Butyl: Futile But Not for Water, as the Correlation of Structure and Thermodynamic Signature Shows in a Congeneric Series of Thermolysin Inhibitors

(2014) Stefan G. Krimmer et al.   ChemMedChem

Free Energy Calculations to Estimate Ligand-Binding Affinities in Structure-Based Drug Design

(2014) M. Reddy et al.   CURRENT PHARMACEUTICAL DESIGN

Discovery of nanomolar phosphoinositide 3-kinase gamma (PI3Kγ) inhibitors using ligand-based modeling and virtual screening followed by in vitro analysis

(2014) Mutasem O. Taha et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

The use of docking-based comparative intermolecular contacts analysis to identify optimal docking conditions within glucokinase and to discover of new GK activators

(2014) Mutasem O. Taha et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Importance of Sphingosine Kinase (SphK) as a Target in Developing Cancer Therapeutics and Recent Developments in the Synthesis of Novel SphK Inhibitors

(2014) Daniel Plano et al.   JOURNAL OF MEDICINAL CHEMISTRY

Elaborate ligand-based modeling reveals new human neutrophil elastase inhibitors

(2014) Maha Habash et al.   MEDICINAL CHEMISTRY RESEARCH

Intrinsic Thermodynamics and Structure Correlation of Benzenesulfonamides with a Pyrimidine Moiety Binding to Carbonic Anhydrases I, II, VII, XII, and XIII

(2014) Miglė Kišonaitė et al.   PLoS One

Chemical Feature-Based Molecular Modeling of Urotensin-II Receptor Antagonists: Generation of Predictive Pharmacophore Model for Early Drug Discovery

(2014) Anubhuti Pandey et al.   Journal of Chemistry

Structure guided design of a series of sphingosine kinase (SphK) inhibitors

(2013) Darin J. Gustin et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Prediction of Individual Compounds Forming Activity Cliffs Using Emerging Chemical Patterns

(2013) Vigneshwaran Namasivayam et al.   Journal of Chemical Information and Modeling

Accuracy Assessment and Automation of Free Energy Calculations for Drug Design

(2013) Clara D. Christ et al.   Journal of Chemical Information and Modeling

Elaborate ligand-based modeling coupled with QSAR analysis and in silico screening reveal new potent acetylcholinesterase inhibitors

(2013) Sawsan Abuhamdah et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Structure–Activity Relationships and Molecular Modeling of Sphingosine Kinase Inhibitors

(2013) Dong Jae Baek et al.   JOURNAL OF MEDICINAL CHEMISTRY

Pharmacophore modeling, homology modeling, and in silico screening reveal mammalian target of rapamycin inhibitory activities for sotalol, glyburide, metipranolol, sulfamethizole, glipizide, and pioglitazone

(2013) Mohammad A. Khanfar et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Novel sphingosine-containing analogues selectively inhibit sphingosine kinase (SK) isozymes, induce SK1 proteasomal degradation and reduce DNA synthesis in human pulmonary arterial smooth muscle cells

(2013) Hoe-Sup Byun et al.   MedChemComm

Anthraquinone Derivatives as Potent Inhibitors of c-Met Kinase and the Extracellular Signaling Pathway

(2013) Zhongjie Liang et al.   ACS Medicinal Chemistry Letters

Modulation of cellular S1P levels with a novel, potent and specific inhibitor of sphingosine kinase-1

(2012) Mark E. Schnute et al.   BIOCHEMICAL JOURNAL

Water Makes the Difference: Rearrangement of Water Solvation Layer Triggers Non-additivity of Functional Group Contributions in Protein-Ligand Binding

(2012) Adam Biela et al.   ChemMedChem

Collinearity: a review of methods to deal with it and a simulation study evaluating their performance

(2012) Carsten F. Dormann et al.   ECOGRAPHY

Modeling of activity landscapes for drug discovery

(2012) Jürgen Bajorath   Expert Opinion on Drug Discovery

Searching for Coordinated Activity Cliffs Using Particle Swarm Optimization

(2012) Vigneshwaran Namasivayam et al.   Journal of Chemical Information and Modeling

Prediction of Activity Cliffs Using Support Vector Machines

(2012) Kathrin Heikamp et al.   Journal of Chemical Information and Modeling

Exploring Uncharted Territories: Predicting Activity Cliffs in Structure–Activity Landscapes

(2012) Rajarshi Guha   Journal of Chemical Information and Modeling

Extending the Activity Cliff Concept: Structural Categorization of Activity Cliffs and Systematic Identification of Different Types of Cliffs in the ChEMBL Database

(2012) Ye Hu et al.   Journal of Chemical Information and Modeling

Free Energy Calculations Reveal the Origin of Binding Preference for Aminoadamantane Blockers of Influenza A/M2TM Pore

(2012) Paraskevi Gkeka et al.   Journal of Chemical Theory and Computation

Exploring Activity Cliffs in Medicinal Chemistry

(2012) Dagmar Stumpfe et al.   JOURNAL OF MEDICINAL CHEMISTRY

Ligand-induced fit affects binding modes and provokes changes in crystal packing of aldose reductase

(2011) Cornelia Koch et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Elaborate ligand-based modeling and subsequent synthetic exploration unveil new nanomolar Ca2+/calmodulin-dependent protein kinase II inhibitory leads

(2011) Rand Shahin et al.   BIOORGANIC & MEDICINAL CHEMISTRY

From Activity Cliffs to Target-Specific Scoring Models and Pharmacophore Hypotheses

(2011) Birte Seebeck et al.   ChemMedChem

From Activity Cliffs to Activity Ridges: Informative Data Structures for SAR Analysis

(2011) Martin Vogt et al.   Journal of Chemical Information and Modeling

Elaborate ligand-based modeling reveal new submicromolar Rho kinase inhibitors

(2011) Rand Shahin et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Development of Amidine-Based Sphingosine Kinase 1 Nanomolar Inhibitors and Reduction of Sphingosine 1-Phosphate in Human Leukemia Cells

(2011) Andrew J. Kennedy et al.   JOURNAL OF MEDICINAL CHEMISTRY

Sphingosine-1-phosphate signaling and its role in disease

(2011) Michael Maceyka et al.   TRENDS IN CELL BIOLOGY

Discovery of novel sphingosine kinase-1 inhibitors. Part 2

(2010) Yibin Xiang et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Development of a sphingosine kinase 1 specific small-molecule inhibitor

(2010) Jeremy A. Hengst et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Discovery of new cholesteryl ester transfer protein inhibitors via ligand-based pharmacophore modeling and QSAR analysis followed by synthetic exploration

(2010) Reema Abu Khalaf et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Computationally Efficient Algorithm to Identify Matched Molecular Pairs (MMPs) in Large Data Sets

(2010) Jameed Hussain et al.   Journal of Chemical Information and Modeling

Iodophenyl tagged sphingosine derivatives: Synthesis and preliminary biological evaluation

(2009) Wenchao Qu et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Discovery of novel sphingosine kinase 1 inhibitors

(2009) Yibin Xiang et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Tumor classification by combining PNN classifier ensemble with neighborhood rough set based gene reduction

(2009) Shu-Lin Wang et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Pharmacophore Modeling, Quantitative Structure−Activity Relationship Analysis, and Shape-Complementedin SilicoScreening Allow Access to Novel Influenza Neuraminidase Inhibitors

(2009) Areej M. Abu Hammad et al.   Journal of Chemical Information and Modeling

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Three-Dimensional Pharmacophore Methods in Drug Discovery

(2009) Andrew R. Leach et al.   JOURNAL OF MEDICINAL CHEMISTRY

Calculation of Proteins’ Total Side-Chain Torsional Entropy and Its Influence on Protein–Ligand Interactions

(2009) Kateri H. DuBay et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure−Activity Landscape Index:  Identifying and Quantifying Activity Cliffs

(2008) Rajarshi Guha et al.   Journal of Chemical Information and Modeling

Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?

(2008) Johannes Kirchmair et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Combining Ligand-Based Pharmacophore Modeling, Quantitative Structure−Activity Relationship Analysis and in Silico Screening for the Discovery of New Potent Hormone Sensitive Lipase Inhibitors

(2008) Mutasem O. Taha et al.   JOURNAL OF MEDICINAL CHEMISTRY

Evaluation of Random Forest and Adaboost tree-based ensemble classification and spectral band selection for ecotope mapping using airborne hyperspectral imagery

(2008) Jonathan Cheung-Wai Chan et al.   REMOTE SENSING OF ENVIRONMENT