1
|
Matada GSP, Dhiwar PS, Abbas N, Singh E, Ghara A, Patil R, Raghavendra NM. Pharmacophore modeling, virtual screening, molecular docking and dynamics studies for the discovery of HER2-tyrosine kinase inhibitors: An in-silico approach. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
2
|
EGFRisopred: a machine learning-based classification model for identifying isoform-specific inhibitors against EGFR and HER2. Mol Divers 2021; 26:1531-1543. [PMID: 34345964 DOI: 10.1007/s11030-021-10284-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
Abstract
The EGFR kinase pathway is one of the most frequently activated signaling pathways in human cancers. EGFR and HER2 are the two significant members of this pathway, which are attractive drug targets of clinical relevance in lung and breast cancer. Therefore, identifying EGFR- and HER2-specific inhibitors is one of the important challenges in cancer drug discovery. To address this issue, a dataset of 519 compounds having inhibitory activity against both the isoforms, i.e., EGFR and HER2, was collected from the literature and developed a knowledge-based computational classification model for predicting the specificity of a molecule for an isoform (EGFR/HER2) with precision. A total of seventy-two classification models using nine fingerprint types, four classifiers (IBK, NB, SMO and RF) and two different datasets (EGFR and HER2 isoform specific) were developed. It was observed that the models developed using random forest and IBK performed better for EGFR- and HER2-specific datasets, respectively. Scaffold and functional group analysis led to the identification of prevalent core and fragments in each of the datasets. The accuracy of the selected best performing models was also evaluated using the decoy dataset. We have also developed an application EGFRisopred, which integrates the best performing models and permits the user to predict the specificity of a compound as an EGFR-/HER2-specific anticancer agent. It is expected that the tool's availability as a free utility will allow researchers to identify new inhibitors against these targets important in cancer.
Collapse
|
3
|
Hrast M, Rožman K, Ogris I, Škedelj V, Patin D, Sova M, Barreteau H, Gobec S, Grdadolnik SG, Zega A. Evaluation of the published kinase inhibitor set to identify multiple inhibitors of bacterial ATP-dependent mur ligases. J Enzyme Inhib Med Chem 2019; 34:1010-1017. [PMID: 31072165 PMCID: PMC6522912 DOI: 10.1080/14756366.2019.1608981] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
The Mur ligases form a series of consecutive enzymes that participate in the intracellular steps of bacterial peptidoglycan biosynthesis. They therefore represent interesting targets for antibacterial drug discovery. MurC, D, E and F are all ATP-dependent ligases. Accordingly, with the aim being to find multiple inhibitors of these enzymes, we screened a collection of ATP-competitive kinase inhibitors, on Escherichia coli MurC, D and F, and identified five promising scaffolds that inhibited at least two of these ligases. Compounds 1, 2, 4 and 5 are multiple inhibitors of the whole MurC to MurF cascade that act in the micromolar range (IC50, 32-368 µM). NMR-assisted binding studies and steady-state kinetics studies performed on aza-stilbene derivative 1 showed, surprisingly, that it acts as a competitive inhibitor of MurD activity towards D-glutamic acid, and additionally, that its binding to the D-glutamic acid binding site is independent of the enzyme closure promoted by ATP.
Collapse
Affiliation(s)
- Martina Hrast
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
| | - Kaja Rožman
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia.,b Department of Medicinal Chemistry , University of Minnesota , Minneapolis , MN , USA
| | - Iza Ogris
- c Molecular Structural Dynamics, Theory Department , National Institute of Chemistry , Ljubljana , Slovenia
| | - Veronika Škedelj
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
| | - Delphine Patin
- d Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay , Gif-Sur-Yvette Cedex , France
| | - Matej Sova
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
| | - Hélène Barreteau
- d Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay , Gif-Sur-Yvette Cedex , France
| | - Stanislav Gobec
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
| | - Simona Golič Grdadolnik
- c Molecular Structural Dynamics, Theory Department , National Institute of Chemistry , Ljubljana , Slovenia
| | - Anamarija Zega
- a Faculty of Pharmacy , University of Ljubljana , Ljubljana , Slovenia
| |
Collapse
|
4
|
Foulkes DM, Byrne DP, Yeung W, Shrestha S, Bailey FP, Ferries S, Eyers CE, Keeshan K, Wells C, Drewry DH, Zuercher WJ, Kannan N, Eyers PA. Covalent inhibitors of EGFR family protein kinases induce degradation of human Tribbles 2 (TRIB2) pseudokinase in cancer cells. Sci Signal 2018; 11:11/549/eaat7951. [PMID: 30254057 DOI: 10.1126/scisignal.aat7951] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A major challenge associated with biochemical and cellular analysis of pseudokinases is a lack of target-validated small-molecule compounds with which to probe function. Tribbles 2 (TRIB2) is a cancer-associated pseudokinase with a diverse interactome, including the canonical AKT signaling module. There is substantial evidence that human TRIB2 promotes survival and drug resistance in solid tumors and blood cancers and therefore is of interest as a therapeutic target. The unusual TRIB2 pseudokinase domain contains a unique cysteine-rich C-helix and interacts with a conserved peptide motif in its own carboxyl-terminal tail, which also supports its interaction with E3 ubiquitin ligases. We found that TRIB2 is a target of previously described small-molecule protein kinase inhibitors, which were originally designed to inhibit the canonical kinase domains of epidermal growth factor receptor tyrosine kinase family members. Using a thermal shift assay, we discovered TRIB2-binding compounds within the Published Kinase Inhibitor Set (PKIS) and used a drug repurposing approach to classify compounds that either stabilized or destabilized TRIB2 in vitro. TRIB2 destabilizing agents, including the covalent drug afatinib, led to rapid TRIB2 degradation in human AML cancer cells, eliciting tractable effects on signaling and survival. Our data reveal new drug leads for the development of TRIB2-degrading compounds, which will also be invaluable for unraveling the cellular mechanisms of TRIB2-based signaling. Our study highlights that small molecule-induced protein down-regulation through drug "off-targets" might be relevant for other inhibitors that serendipitously target pseudokinases.
Collapse
Affiliation(s)
- Daniel M Foulkes
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Dominic P Byrne
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Wayland Yeung
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Safal Shrestha
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Fiona P Bailey
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Samantha Ferries
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.,Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Claire E Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.,Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Karen Keeshan
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, University of Glasgow, Scotland, UK
| | - Carrow Wells
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William J Zuercher
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natarajan Kannan
- Institute of Bioinformatics and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Patrick A Eyers
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| |
Collapse
|
5
|
Qu D, Yan A, Zhang JS. SAR and QSAR study on the bioactivities of human epidermal growth factor receptor-2 (HER2) inhibitors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:111-132. [PMID: 28235391 DOI: 10.1080/1062936x.2017.1284898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/16/2017] [Indexed: 06/06/2023]
Abstract
In this paper, structure-activity relationship (SAR, classification) and quantitative structure-activity relationship (QSAR) models have been established to predict the bioactivity of human epidermal growth factor receptor-2 (HER2) inhibitors. For the SAR study, we established six SAR (or classification) models to distinguish highly and weakly active HER2 inhibitors. The dataset contained 868 HER2 inhibitors, which was split into a training set including 580 inhibitors and a test set including 288 inhibitors by a Kohonen's self-organizing map (SOM), or a random method. The SAR models were performed using support vector machine (SVM), random forest (RF) and multilayer perceptron (MLP) methods. Among the six models, SVM models obtained superior results compared with other models. The prediction accuracy of the best model (model 1A) was 90.27% and the Matthews correlation coefficient (MCC) was 0.80 on the test set. For the QSAR study, we chose 286 HER2 inhibitors to establish six quantitative prediction models using MLR, SVM and MLP methods. The correlation coefficient (r) of the best model (model 4B) was 0.92 on the test set. The descriptors analysis showed that HAccN, lone pair electronegativity and π electronegativity were closely related to the bioactivity of HER2 inhibitors.
Collapse
Affiliation(s)
- D Qu
- a State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing , P.R. China
| | - A Yan
- a State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology , Beijing , P.R. China
| | - J S Zhang
- b The High School Affiliated to Renmin University of China , Beijing , P.R. China
| |
Collapse
|
6
|
|
7
|
Design, synthesis and biological evaluation of novel pyrimidine, 3-cyanopyridine and m-amino-N-phenylbenzamide based monocyclic EGFR tyrosine kinase inhibitors. Bioorg Med Chem 2013; 21:3090-104. [DOI: 10.1016/j.bmc.2013.03.053] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/09/2013] [Accepted: 03/19/2013] [Indexed: 02/05/2023]
|
8
|
Abstract
Protein kinases are now considered highly druggable due to the fact that there are kinase inhibitors on the market as effective drugs (e.g. Gleevec, Tarceva, and Nexavar). The class of drugs remains plagued by questions about how the inhibition profile affects the efficacy, and whether truly selective kinase inhibitors actually exist. Lapatinib remains one of the most selective kinase inhibitors in use for cancer therapy. This chapter will focus on our strategies to discover this novel, dual EGFR and ERBB-2 tyrosine kinase inhibitor using a carefully designed biological evaluation cascade coupled with a multidimensional data analysis. The primary topics discussed will cover the optimization of potency for two kinase targets, yet selective among over 500 kinases within the highly homologous ATP binding site, cellular selectivity and efficacy, and subsequent studies to understand the mechanism of action.
Collapse
Affiliation(s)
- Karen E. Lackey
- Hoffmann-La Roche Discovery Chemistry 340 Kingsland Street, Nutley NJ 07110, USA
| |
Collapse
|
9
|
Suzuki N, Shiota T, Watanabe F, Haga N, Murashi T, Ohara T, Matsuo K, Oomori N, Yari H, Dohi K, Inoue M, Iguchi M, Sentou J, Wada T. Synthesis and evaluation of novel pyrimidine-based dual EGFR/Her-2 inhibitors. Bioorg Med Chem Lett 2011; 21:1601-6. [DOI: 10.1016/j.bmcl.2011.01.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 01/25/2011] [Accepted: 01/26/2011] [Indexed: 11/26/2022]
|
10
|
La Motta C, Sartini S, Tuccinardi T, Nerini E, Da Settimo F, Martinelli A. Computational studies of epidermal growth factor receptor: docking reliability, three-dimensional quantitative structure-activity relationship analysis, and virtual screening studies. J Med Chem 2009; 52:964-75. [PMID: 19170633 DOI: 10.1021/jm800829v] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
An aberrant activity of the epidermal growth factor receptor (EGFR) has been shown to be related to many human cancers, such as breast and liver cancers, thus making EGFR an attractive target for antitumor drug discovery. In this study we evaluated the reliability of various kinds of docking software and procedures to predict the binding disposition of EGFR inhibitors. By application of the best procedure and use of more than 200 compounds, a receptor-based 3D-QSAR model for EGFR inhibition was developed. On the basis of the results obtained, the possibility of developing virtual screening studies was also evaluated. The VS procedure that proved to be the most reliable from a computational point of view was then used to filter the Maybridge database in order to identify new EGFR inhibitors. Enzymatic assays revealed that among the eight top-scoring compounds, seven proved to inhibit EGFR activity at a concentration of 100 microM, two of them exhibiting IC(50) values in the low micromolar range and one in the nanomolar range. These results demonstrate the validity of the methodologies followed. Furthermore, the two low micromolar compounds may be considered as very interesting leads for the development of new EGFR inhibitors.
Collapse
Affiliation(s)
- Concettina La Motta
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | | | | | | | | | | |
Collapse
|
11
|
Sasada T, Kobayashi F, Sakai N, Konakahara T. An Unprecedented Approach to 4,5-Disubstituted Pyrimidine Derivatives by a ZnCl2-Catalyzed Three-Component Coupling Reaction. Org Lett 2009; 11:2161-4. [DOI: 10.1021/ol900382j] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toshiaki Sasada
- Department of Pure and Applied Chemistry, Faculty of Science and Technology, Tokyo University of Science (RIKADAI), Noda, Chiba 278-8510, Japan
| | - Fuminori Kobayashi
- Department of Pure and Applied Chemistry, Faculty of Science and Technology, Tokyo University of Science (RIKADAI), Noda, Chiba 278-8510, Japan
| | - Norio Sakai
- Department of Pure and Applied Chemistry, Faculty of Science and Technology, Tokyo University of Science (RIKADAI), Noda, Chiba 278-8510, Japan
| | - Takeo Konakahara
- Department of Pure and Applied Chemistry, Faculty of Science and Technology, Tokyo University of Science (RIKADAI), Noda, Chiba 278-8510, Japan
| |
Collapse
|
12
|
El‐Ziaty AK, Shiba SA. Antibacterial Activities of New (E) 2‐Cyano‐3‐(3′,4′‐dimethoxyphenyl)‐2‐propenoylamide Derivatives. SYNTHETIC COMMUN 2007. [DOI: 10.1080/00397910701575491] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
13
|
Liu LT, Yuan TT, Liu HH, Chen SF, Wu YT. Synthesis and biological evaluation of substituted 6-alkynyl-4-anilinoquinazoline derivatives as potent EGFR inhibitors. Bioorg Med Chem Lett 2007; 17:6373-7. [PMID: 17889528 DOI: 10.1016/j.bmcl.2007.08.061] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2007] [Revised: 08/15/2007] [Accepted: 08/24/2007] [Indexed: 11/24/2022]
Abstract
A series of C-6 or C-3' alkynyl-substituted 4-anilinoquinazoline derivatives was prepared straightforwardly by a Sonogashira reaction of the corresponding bromo-substituted 4-anilinoquinazolines. Bioactive assay of these compounds for in vitro EGFR kinase inhibition demonstrated that the novel 6-hydroxypropynyl-4-anilinoquinazoline 5e was a very potent EGFR kinase inhibitor with an IC(50) of 14 nM.
Collapse
Affiliation(s)
- Lee Tai Liu
- Development Center for Biotechnology, 102 Lane 169 Kang Ning Street, Xi Zhi, Taipei, Taiwan, ROC.
| | | | | | | | | |
Collapse
|