Structure-Based Discovery of 1H-Indazole-3-carboxamides as a Novel Structural Class of Human GSK-3 Inhibitors.

Abstract:

:An in silico screening procedure was performed to select new inhibitors of glycogen synthase kinase 3β (GSK-3β), a serine/threonine protein kinase that in the last two decades has emerged as a key target in drug discovery, having been implicated in multiple cellular processes and linked with the pathogenesis of several diseases. GSK-3β inhibitors might prove useful as therapeutic compounds in the treatment of conditions associated with elevated levels of enzyme activity, such as type-2 diabetes and neurological disorders, for example, Alzheimer's disease, bipolar disorder, neuronal cell death, stroke, and depression. In this work, virtual screening studies were applied to proprietary compound libraries, and the functional activities of selected compounds were assayed on human GSK-3β. The in silico screening procedure enabled the identification of eight hit compounds showing pIC50 values ranging from 4.9 to 5.5. X-ray crystallographic studies resulted in a 2.50 Å three-dimensional structure of GSK-3β complexed with one of the selected compounds, confirming that the inhibitor interacts with the enzyme according to the docking hypothesis. Importantly, molecular docking was able to find a new chemical scaffold for GSK-3β inhibition, providing grounds for rational structure-based design aimed at further optimization of the initial hits.

journal_name

J Chem Inf Model

authors

Ombrato R,Cazzolla N,Mancini F,Mangano G

doi

10.1021/acs.jcim.5b00486

subject

Has Abstract

pub_date

2015-12-28 00:00:00

pages

2540-51

issue

12

eissn

1549-9596

issn

1549-960X

journal_volume

55

pub_type

杂志文章
  • T-Cell Receptor Binding Affects the Dynamics of the Peptide/MHC-I Complex.

    abstract::The recognition of peptide/MHC by T-cell receptors is one of the most important interactions in the adaptive immune system. A large number of computational studies have investigated the structural dynamics of this interaction. However, to date only limited attention has been paid to differences between the dynamics of...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00511

    authors: Knapp B,Deane CM

    更新日期:2016-01-25 00:00:00

  • Structural and Sequence Similarity Makes a Significant Impact on Machine-Learning-Based Scoring Functions for Protein-Ligand Interactions.

    abstract::The prediction of protein-ligand binding affinity has recently been improved remarkably by machine-learning-based scoring functions. For example, using a set of simple descriptors representing the atomic distance counts, the RF-Score improves the Pearson correlation coefficient to about 0.8 on the core set of the PDBb...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00049

    authors: Li Y,Yang J

    更新日期:2017-04-24 00:00:00

  • Symplectic molecular dynamics simulations on specially designed parallel computers.

    abstract::We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci050216q

    authors: Borstnik U,Janezic D

    更新日期:2005-11-01 00:00:00

  • Spatial sign preprocessing: a simple way to impart moderate robustness to multivariate estimators.

    abstract::The spatial sign is a multivariate extension of the concept of sign. Recently multivariate estimators of covariance structures based on spatial signs have been examined by various authors. These new estimators are found to be robust to outlying observations. From a computational point of view, estimators based on spat...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci050498u

    authors: Serneels S,De Nolf E,Van Espen PJ

    更新日期:2006-05-01 00:00:00

  • Direct Observation of β-Barrel Intermediates in the Self-Assembly of Toxic SOD128-38 and Absence in Nontoxic Glycine Mutants.

    abstract::Soluble low-molecular-weight oligomers formed during the early stage of amyloid aggregation are considered the major toxic species in amyloidosis. The structure-function relationship between oligomeric assemblies and the cytotoxicity in amyloid diseases are still elusive due to the heterogeneous and transient nature o...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c01319

    authors: Sun Y,Huang J,Duan X,Ding F

    更新日期:2021-01-14 00:00:00

  • A probabilistic approach to classifying metabolic stability.

    abstract::Metabolic stability is an important property of drug molecules that should-optimally-be taken into account early on in the drug design process. Along with numerous medium- or high-throughput assays being implemented in early drug discovery, a prediction tool for this property could be of high value. However, metabolic...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci700142c

    authors: Schwaighofer A,Schroeter T,Mika S,Hansen K,Ter Laak A,Lienau P,Reichel A,Heinrich N,Müller KR

    更新日期:2008-04-01 00:00:00

  • Estimation of carcinogenicity using molecular fragments tree.

    abstract::Carcinogenicity is an important toxicological endpoint that poses high concern to drug discovery. In this study, we developed a method to extract structural alerts (SAs) and modulating factors of carcinogens on the basis of statistical analyses. First, the Gaston algorithm, a frequent subgraph mining method, was used ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci300266p

    authors: Wang Y,Lu J,Wang F,Shen Q,Zheng M,Luo X,Zhu W,Jiang H,Chen K

    更新日期:2012-08-27 00:00:00

  • Metabotropic glutamate receptor-mediated currents at the climbing fiber to Purkinje cell synapse.

    abstract::Different forms of synaptic plasticity in the cerebellum expressed at the synapses onto Purkinje cells (PCs) are mediated by membrane metabotropic glutamate receptors (mGluRs). There are three main mGluR groups with a total of 8 subtypes. Although mGluRs are also found at the climbing fiber (CF) to PC synapses, the di...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci050161s

    authors: Andjus PR,Bajić A,Zhu L,Strata P

    更新日期:2005-11-01 00:00:00

  • Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening.

    abstract::We demonstrate that using an all-atom molecular mechanics force field combined with an implicit solvent model for scoring protein-ligand complexes is a promising approach for improving inhibitor enrichment in the virtual screening of large compound databases. The rescoring method is evaluated by the extent to which kn...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci0502855

    authors: Huang N,Kalyanaraman C,Irwin JJ,Jacobson MP

    更新日期:2006-01-01 00:00:00

  • FlexAID: Revisiting Docking on Non-Native-Complex Structures.

    abstract::Small-molecule protein docking is an essential tool in drug design and to understand molecular recognition. In the present work we introduce FlexAID, a small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function, i.e. one that is not highly dependent on specifi...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00078

    authors: Gaudreault F,Najmanovich RJ

    更新日期:2015-07-27 00:00:00

  • Searching for coordinated activity cliffs using particle swarm optimization.

    abstract::Activity cliffs are formed by structurally similar compounds having large potency differences. Coordinated activity cliffs evolve when compounds within groups of structural neighbors form multiple cliffs with different partners, giving rise to local networks of cliffs in a data set. Using particle swarm optimization, ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci3000503

    authors: Namasivayam V,Bajorath J

    更新日期:2012-04-23 00:00:00

  • In silico drug screening approach for the design of magic bullets: a successful example with anti-HIV fullerene derivatized amino acids.

    abstract::A database has been derived from recently reported [60]fullerene derivatives, and their binding scores with HIV-1 PR have been computed using docking techniques. Computational methods have been used to predict which derivatives may have high binding affinities, and for these compounds biological tests have been perfor...

    journal_title:Journal of chemical information and modeling

    pub_type: 信件

    doi:10.1021/ci900047s

    authors: Durdagi S,Supuran CT,Strom TA,Doostdar N,Kumar MK,Barron AR,Mavromoustakos T,Papadopoulos MG

    更新日期:2009-05-01 00:00:00

  • Truncated variants of the GCN4 transcription activator protein bind DNA with dramatically different dynamical motifs.

    abstract::The yeast protein GCN4 is a transcriptional activator in the basic leucine zipper (bZip) family, whose distinguishing feature is the "chopstick-like" homodimer of alpha helices formed at the DNA-binding interface. While experiments have shown that truncated versions of the protein retain biologically relevant DNA-bind...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci500448e

    authors: McHarris DM,Barr DA

    更新日期:2014-10-27 00:00:00

  • LiCABEDS II. Modeling of ligand selectivity for G-protein-coupled cannabinoid receptors.

    abstract::The cannabinoid receptor subtype 2 (CB2) is a promising therapeutic target for blood cancer, pain relief, osteoporosis, and immune system disease. The recent withdrawal of Rimonabant, which targets another closely related cannabinoid receptor (CB1), accentuates the importance of selectivity for the development of CB2 ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci3003914

    authors: Ma C,Wang L,Yang P,Myint KZ,Xie XQ

    更新日期:2013-01-28 00:00:00

  • Conformator: A Novel Method for the Generation of Conformer Ensembles.

    abstract::Computer-aided drug design methods such as docking, pharmacophore searching, 3D database searching, and the creation of 3D-QSAR models need conformational ensembles to handle the flexibility of small molecules. Here, we present Conformator, an accurate and effective knowledge-based algorithm for generating conformer e...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00704

    authors: Friedrich NO,Flachsenberg F,Meyder A,Sommer K,Kirchmair J,Rarey M

    更新日期:2019-02-25 00:00:00

  • Virtual drug screen schema based on multiview similarity integration and ranking aggregation.

    abstract::The current drug virtual screen (VS) methods mainly include two categories. i.e., ligand/target structure-based virtual screen and that, utilizing protein-ligand interaction fingerprint information based on the large number of complex structures. Since the former one focuses on the one-side information while the later...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci200481c

    authors: Kang H,Sheng Z,Zhu R,Huang Q,Liu Q,Cao Z

    更新日期:2012-03-26 00:00:00

  • Knowledge-based scoring functions in drug design: 2. Can the knowledge base be enriched?

    abstract::Fast and accurate predicting of the binding affinities of large sets of diverse protein−ligand complexes is an important, yet extremely challenging, task in drug discovery. The development of knowledge-based scoring functions exploiting structural information of known protein−ligand complexes represents a valuable con...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci100343j

    authors: Shen Q,Xiong B,Zheng M,Luo X,Luo C,Liu X,Du Y,Li J,Zhu W,Shen J,Jiang H

    更新日期:2011-02-28 00:00:00

  • Potent Human Telomerase Inhibitors: Molecular Dynamic Simulations, Multiple Pharmacophore-Based Virtual Screening, and Biochemical Assays.

    abstract::Telomere maintenance is a universal cancer hallmark, and small molecules that disrupt telomere maintenance generally have anticancer properties. Since the vast majority of cancer cells utilize telomerase activity for telomere maintenance, the enzyme has been considered as an anticancer drug target. Recently, rational ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.5b00336

    authors: Shirgahi Talari F,Bagherzadeh K,Golestanian S,Jarstfer M,Amanlou M

    更新日期:2015-12-28 00:00:00

  • Gas-phase and solution conformations of selected dimeric structural units of heparin.

    abstract::The molecular structure of four dimeric units (D-E, E-F, F-G, and G-H) of the DEFGH structural unit of heparin, their anionic forms, and their sodium salts have been studied using the B3LYP/6-31+G(d) method. The optimized geometries indicate that the most stable structure of these dimeric units in neutral state is sta...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci060060+

    authors: Remko M,von der Lieth CW

    更新日期:2006-07-01 00:00:00

  • Molecular simulations of aromatase reveal new insights into the mechanism of ligand binding.

    abstract::CYP19A1, also known as aromatase or estrogen synthetase, is the rate-limiting enzyme in the biosynthesis of estrogens from their corresponding androgens. Several clinically used breast cancer therapies target aromatase. In this work, explicitly solvated all-atom molecular dynamics simulations of aromatase with a model...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci400225w

    authors: Park J,Czapla L,Amaro RE

    更新日期:2013-08-26 00:00:00

  • Expanding the Range of Force Fields Available for ONIOM Calculations: The SICTWO Interface.

    abstract::The ONIOM scheme is one of the most popular QM/MM approaches, but its extended application has been so far hindered by the limited availability of force fields in most practical implementations. This paper describes a simple software code to overcome this limitation, and its application to three representative chemica...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00332

    authors: Sameera WMC,Maseras F

    更新日期:2018-09-24 00:00:00

  • TAMkin: a versatile package for vibrational analysis and chemical kinetics.

    abstract::TAMkin is a program for the calculation and analysis of normal modes, thermochemical properties and chemical reaction rates. At present, the output from the frequently applied software programs ADF, CHARMM, CPMD, CP2K, Gaussian, Q-Chem, and VASP can be analyzed. The normal-mode analysis can be performed using a broad ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci100099g

    authors: Ghysels A,Verstraelen T,Hemelsoet K,Waroquier M,Van Speybroeck V

    更新日期:2010-09-27 00:00:00

  • Flux (1): a virtual synthesis scheme for fragment-based de novo design.

    abstract::It is demonstrated that the fragmentation of druglike molecules by applying simplistic pseudo-retrosynthesis results in a stock of chemically meaningful building blocks for de novo molecule generation. A stochastic search algorithm in conjunction with ligand-based similarity scoring (Flux: fragment-based ligand builde...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci0503560

    authors: Fechner U,Schneider G

    更新日期:2006-03-01 00:00:00

  • Reaction site mapping of xenobiotic biotransformations.

    abstract::Predictive metabolism methods can be used in drug discovery projects to enhance the understanding of structure-metabolism relationships. The present study uses data mining methods to exploit biotransformation data that have been recorded in the MDL Metabolite database. Reacting center fingerprints were derived from a ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci600376q

    authors: Boyer S,Arnby CH,Carlsson L,Smith J,Stein V,Glen RC

    更新日期:2007-03-01 00:00:00

  • Tuning Interaction Parameters of Thermoplastic Polyurethanes in a Binary Solvent To Achieve Precise Control over Microphase Separation.

    abstract::Thermoplastic polyurethanes (TPUs) are designed using a large variety of basic building blocks but are only synthesized in a limited number of solvent systems. Understanding the behavior of the copolymers in a selected solvent system is of particular interest to tune the intricate balance of microphase separation/mixi...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00781

    authors: Avaz Seven S,Oguz O,Menceloglu YZ,Atilgan C

    更新日期:2019-05-28 00:00:00

  • Develop and test a solvent accessible surface area-based model in conformational entropy calculations.

    abstract::It is of great interest in modern drug design to accurately calculate the free energies of protein-ligand or nucleic acid-ligand binding. MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) and MM-GBSA (molecular mechanics generalized Born surface area) have gained popularity in this field. For both methods, ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci300064d

    authors: Wang J,Hou T

    更新日期:2012-05-25 00:00:00

  • Getting Docking into Shape Using Negative Image-Based Rescoring.

    abstract::The failure of default scoring functions to ensure virtual screening enrichment is a persistent problem for the molecular docking algorithms used in structure-based drug discovery. To remedy this problem, elaborate rescoring and postprocessing schemes have been developed with a varying degree of success, specificity, ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00383

    authors: Kurkinen ST,Lätti S,Pentikäinen OT,Postila PA

    更新日期:2019-08-26 00:00:00

  • Bridging molecular docking to membrane molecular dynamics to investigate GPCR-ligand recognition: the human A₂A adenosine receptor as a key study.

    abstract::G protein-coupled receptors (GPCRs) represent the largest family of cell-surface receptors and about one-third of the actual targets of clinically used drugs. Following the progress made in the field of GPCRs structural determination, docking-based screening for novel potent and selective ligands is becoming an increa...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci400532b

    authors: Sabbadin D,Ciancetta A,Moro S

    更新日期:2014-01-27 00:00:00

  • Target-independent prediction of drug synergies using only drug lipophilicity.

    abstract::Physicochemical properties of compounds have been instrumental in selecting lead compounds with increased drug-likeness. However, the relationship between physicochemical properties of constituent drugs and the tendency to exhibit drug interaction has not been systematically studied. We assembled physicochemical descr...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci500276x

    authors: Yilancioglu K,Weinstein ZB,Meydan C,Akhmetov A,Toprak I,Durmaz A,Iossifov I,Kazan H,Roth FP,Cokol M

    更新日期:2014-08-25 00:00:00

  • Molecular Self-Assembly Strategy for Encapsulation of an Amphipathic α-Helical Antimicrobial Peptide into the Different Polymeric and Copolymeric Nanoparticles.

    abstract::Encapsulation of peptide and protein-based drugs in polymeric nanoparticles is one of the fundamental fields in controlled-release drug delivery systems. The molecular mechanisms of absorption of peptides to the polymeric nanoparticles are still unknown, and there is no precise molecular data on the encapsulation proc...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00641

    authors: Jafari M,Doustdar F,Mehrnejad F

    更新日期:2019-01-28 00:00:00