1
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Boonyarit B, Yamprasert N, Kaewnuratchadasorn P, Kinchagawat J, Prommin C, Rungrotmongkol T, Nutanong S. GraphEGFR: Multi-task and transfer learning based on molecular graph attention mechanism and fingerprints improving inhibitor bioactivity prediction for EGFR family proteins on data scarcity. J Comput Chem 2024; 45:2001-2023. [PMID: 38713612 DOI: 10.1002/jcc.27388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 05/09/2024]
Abstract
The proteins within the human epidermal growth factor receptor (EGFR) family, members of the tyrosine kinase receptor family, play a pivotal role in the molecular mechanisms driving the development of various tumors. Tyrosine kinase inhibitors, key compounds in targeted therapy, encounter challenges in cancer treatment due to emerging drug resistance mutations. Consequently, machine learning has undergone significant evolution to address the challenges of cancer drug discovery related to EGFR family proteins. However, the application of deep learning in this area is hindered by inherent difficulties associated with small-scale data, particularly the risk of overfitting. Moreover, the design of a model architecture that facilitates learning through multi-task and transfer learning, coupled with appropriate molecular representation, poses substantial challenges. In this study, we introduce GraphEGFR, a deep learning regression model designed to enhance molecular representation and model architecture for predicting the bioactivity of inhibitors against both wild-type and mutant EGFR family proteins. GraphEGFR integrates a graph attention mechanism for molecular graphs with deep and convolutional neural networks for molecular fingerprints. We observed that GraphEGFR models employing multi-task and transfer learning strategies generally achieve predictive performance comparable to existing competitive methods. The integration of molecular graphs and fingerprints adeptly captures relationships between atoms and enables both global and local pattern recognition. We further validated potential multi-targeted inhibitors for wild-type and mutant HER1 kinases, exploring key amino acid residues through molecular dynamics simulations to understand molecular interactions. This predictive model offers a robust strategy that could significantly contribute to overcoming the challenges of developing deep learning models for drug discovery with limited data and exploring new frontiers in multi-targeted kinase drug discovery for EGFR family proteins.
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Affiliation(s)
- Bundit Boonyarit
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
| | - Nattawin Yamprasert
- School of Information, Computer, and Communication Technology, Sirindhorn International Institute of Technology, Thammasat University, Pathum Thani, Thailand
| | | | - Jiramet Kinchagawat
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
| | - Chanatkran Prommin
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Sarana Nutanong
- School of Information Science and Technology, Vidyasirimedhi Institute of Science and Technology, Rayong, Thailand
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2
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Ma S, Patel H, Peeples CA, Shen J. QM/MM Simulations of Afatinib-EGFR Addition: The Role of β-Dimethylaminomethyl Substitution. J Chem Theory Comput 2024; 20:5528-5538. [PMID: 38877999 DOI: 10.1021/acs.jctc.4c00290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Acrylamides are the most commonly used warheads of targeted covalent inhibitors (TCIs) directed at cysteines; however, the reaction mechanisms of acrylamides in proteins remain controversial, particularly for those involving protonated or unreactive cysteines. Using the combined semiempirical quantum mechanics (QM)/molecular mechanics (MM) free energy simulations, we investigated the reaction between afatinib, the first TCI drug for cancer treatment, and Cys797 in the EGFR kinase. Afatinib contains a β-dimethylaminomethyl (β-DMAM) substitution which has been shown to enhance the intrinsic reactivity and potency against EGFR for related inhibitors. Two hypothesized reaction mechanisms were tested. Our data suggest that Cys797 becomes deprotonated in the presence of afatinib, and the reaction proceeds via a classical Michael addition mechanism, with Asp800 stabilizing the ion-pair reactant state β-DMAM+/C797- and the transition state of the nucleophilic attack. Our work elucidates an important structure-activity relationship of acrylamides in proteins.
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Affiliation(s)
- Shuhua Ma
- Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, Towson, Maryland 21252, United States
| | - Heeral Patel
- Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, Towson, Maryland 21252, United States
| | - Craig A Peeples
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
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3
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Ma S, Patel H, Peeples CA, Shen J. QM/MM simulations of EFGR with afatinib reveal the role of the β-dimethylaminomethyl substitution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.18.580887. [PMID: 38766221 PMCID: PMC11100610 DOI: 10.1101/2024.02.18.580887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Acrylamides are the most commonly used warheads of targeted covalent inhibitors (TCIs) directed at cysteines; however, the reaction mechanisms of acrylamides in proteins remain controversial, particularly for those involving protonated or unreactive cysteines. Using the combined semiempirical quantum mechanics (QM)/molecular mechanics (MM) free energy simulations, we investigated the reaction between afatinib, the first TCI drug for cancer treatment, and Cys797 in the EGFR kinase. Afatinib contains a β-dimethylaminomethyl (β-DMAM) substitution which has been shown to enhance the intrinsic reactivity and potency against EGFR for related inhibitors. Two hypothesized reaction mechanisms were tested. Our data suggest that Cys797 becomes deprotonated in the presence of afatinib and the reaction proceeds via a classical Michael addition mechanism, with Asp800 stabilizing the ion-pair reactant state β-DMAM+/C797- and the transition state of the nucleophilic attack. Our work elucidates an important structure-activity relationship of acrylamides in proteins.
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Affiliation(s)
- Shuhua Ma
- Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, Towson, MD 21252
| | - Heeral Patel
- Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, Towson, MD 21252
| | - Craig A Peeples
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201
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4
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Yoon HR, Park GJ, Balupuri A, Kang NS. TWN-FS method: A novel fragment screening method for drug discovery. Comput Struct Biotechnol J 2023; 21:4683-4696. [PMID: 37841326 PMCID: PMC10568351 DOI: 10.1016/j.csbj.2023.09.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023] Open
Abstract
Fragment-based drug discovery (FBDD) is a well-established and effective method for generating diverse and novel hits in drug design. Kinases are suitable targets for FBDD due to their well-defined structure. Water molecules contribute to structure and function of proteins and also influence the environment within the binding pocket. Water molecules form a variety of hydrogen-bonded cyclic water-ring networks, collectively known as topological water networks (TWNs). Analyzing the TWNs in protein binding sites can provide valuable insights into potential locations and shapes for fragments within the binding site. Here, we introduce TWN-based fragment screening (TWN-FS) method, a novel screening method that suggests fragments through grouped TWN analysis within the protein binding site. We used this method to screen known CDK2, CHK1, IGF1R and ERBB4 inhibitors. Our findings suggest that TWN-FS method has the potential to effectively screen fragments. The TWN-FS method package is available on GitHub at https://github.com/pkj0421/TWN-FS.
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Affiliation(s)
- Hye Ree Yoon
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
| | - Gyoung Jin Park
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
| | - Anand Balupuri
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
| | - Nam Sook Kang
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea
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5
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Liu R, Vázquez-Montelongo EA, Ma S, Shen J. Quantum Descriptors for Predicting and Understanding the Structure-Activity Relationships of Michael Acceptor Warheads. J Chem Inf Model 2023; 63:4912-4923. [PMID: 37463342 PMCID: PMC10837637 DOI: 10.1021/acs.jcim.3c00720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Predictive modeling and understanding of chemical warhead reactivities have the potential to accelerate targeted covalent drug discovery. Recently, the carbanion formation free energies as well as other ground-state electronic properties from density functional theory (DFT) calculations have been proposed as predictors of glutathione reactivities of Michael acceptors; however, no clear consensus exists. By profiling the thiol-Michael reactions of a diverse set of singly- and doubly-activated olefins, including several model warheads related to afatinib, here we reexamined the question of whether low-cost electronic properties can be used as predictors of reaction barriers. The electronic properties related to the carbanion intermediate were found to be strong predictors, e.g., the change in the Cβ charge accompanying carbanion formation. The least expensive reactant-only properties, the electrophilicity index, and the Cβ charge also show strong rank correlations, suggesting their utility as quantum descriptors. A second objective of the work is to clarify the effect of the β-dimethylaminomethyl (DMAM) substitution, which is incorporated in the warheads of several FDA-approved covalent drugs. Our data suggest that the β-DMAM substitution is cationic at neutral pH in solution and promotes acrylamide's intrinsic reactivity by enhancing the charge accumulation at Cα upon carbanion formation. In contrast, the inductive effect of the β-trimethylaminomethyl substitution is diminished due to steric hindrance. Together, these results reconcile the current views of the intrinsic reactivities of acrylamides and contribute to large-scale predictive modeling and an understanding of the structure-activity relationships of Michael acceptors for rational TCI design.
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Affiliation(s)
- Ruibin Liu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Erik A Vázquez-Montelongo
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Shuhua Ma
- Department of Chemistry, Jess and Mildred Fisher College of Science and Mathematics, Towson University, Towson, Maryland 21252, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
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6
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Köckenberger J, Klemt I, Sauer C, Arkhypov A, Reshetnikov V, Mokhir A, Heinrich MR. Cyanine- and Rhodamine-Derived Alkynes for the Selective Targeting of Cancerous Mitochondria through Radical Thiol-Yne Coupling in Live Cells. Chemistry 2023; 29:e202301340. [PMID: 37171462 DOI: 10.1002/chem.202301340] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/13/2023]
Abstract
Despite their long history and their synthetic potential underlined by various recent advances, radical thiol-yne coupling reactions have so far only rarely been exploited for the functionalization of biomolecules, and no examples yet exist for their application in live cells - although natural thiols show widespread occurrence therein. By taking advantage of the particular cellular conditions of mitochondria in cancer cells, we have demonstrated that radical thiol-yne coupling represents a powerful reaction principle for the selective targeting of these organelles. Within our studies, fluorescently labeled reactive alkyne probes were investigated, for which the fluorescent moiety was chosen to enable both mitochondria accumulation as well as highly sensitive detection. After preliminary studies under cell-free conditions, the most promising alkyne-dye conjugates were evaluated in various cellular experiments comprising analysis by flow cytometry and microscopy. All in all, these results pave the way for improved future therapeutic strategies relying on live-cell compatibility and selectivity among cellular compartments.
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Affiliation(s)
- Johannes Köckenberger
- Department of Chemistry and Pharmacy Pharmaceutical Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Insa Klemt
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Caroline Sauer
- Department of Chemistry and Pharmacy Pharmaceutical Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Anton Arkhypov
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Viktor Reshetnikov
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Andriy Mokhir
- Department of Chemistry and Pharmacy, Organic Chemistry II, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Markus R Heinrich
- Department of Chemistry and Pharmacy Pharmaceutical Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
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7
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Li JW, Zheng G, Kaye FJ, Wu L. PROTAC therapy as a new targeted therapy for lung cancer. Mol Ther 2023; 31:647-656. [PMID: 36415148 PMCID: PMC10014230 DOI: 10.1016/j.ymthe.2022.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/01/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
Despite recent advances in molecular therapeutics, lung cancer is still a leading cause of cancer deaths. Currently, limited targeted therapy options and acquired drug resistance present significant barriers in the treatment of patients with lung cancer. New strategies in drug development, including those that take advantage of the intracellular ubiquitin-proteasome system to induce targeted protein degradation, have the potential to advance the field of personalized medicine for patients with lung cancer. Specifically, small molecule proteolysis targeting chimeras (PROTACs), consisting of two ligands connected by a linker that bind to a target protein and an E3 ubiquitin ligase, have been developed against many cancer targets, providing promising opportunities for advanced lung cancer. In this review, we focus on the rationale for PROTAC therapy as a new targeted therapy and the current status of PROTAC development in lung cancer.
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Affiliation(s)
- Jennifer W Li
- Department of Medicine, Brown University, Providence, RI 02912, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA
| | - Frederic J Kaye
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA; Department of Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, USA; UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Lizi Wu
- UF Health Cancer Center, University of Florida, Gainesville, FL 32610, USA; UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA; Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
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8
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Karges J, Cohen SM. Rhenium(V) Complexes as Cysteine-Targeting Coordinate Covalent Warheads. J Med Chem 2023; 66:3088-3105. [PMID: 36752718 PMCID: PMC9969397 DOI: 10.1021/acs.jmedchem.2c02074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Interest in covalent enzyme inhibitors as therapeutic agents has seen a recent resurgence. Covalent enzyme inhibitors typically possess an organic functional group that reacts with a key feature of the target enzyme, often a nucleophilic cysteine residue. Herein, the application of small, modular ReV complexes as inorganic cysteine-targeting warheads is described. These metal complexes were found to react with cysteine residues rapidly and selectively. To demonstrate the utility of these ReV complexes, their reactivity with SARS-CoV-2-associated cysteine proteases is presented, including the SARS-CoV-2 main protease and papain-like protease and human enzymes cathepsin B and L. As all of these proteins are cysteine proteases, these enzymes were found to be inhibited by the ReV complexes through the formation of adducts. These findings suggest that these ReV complexes could be used as a new class of warheads for targeting surface accessible cysteine residues in disease-relevant target proteins.
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9
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Yadav TT, Moin Shaikh G, Kumar MS, Chintamaneni M, YC M. A Review on Fused Pyrimidine Systems as EGFR Inhibitors and Their Structure–Activity Relationship. Front Chem 2022; 10:861288. [PMID: 35769445 PMCID: PMC9234326 DOI: 10.3389/fchem.2022.861288] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/28/2022] [Indexed: 01/05/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) belongs to the family of tyrosine kinase that is activated when a specific ligand binds to it. The EGFR plays a vital role in the cellular proliferation process, differentiation, and apoptosis. In the case of cancer, EGFR undergoes uncontrolled auto-phosphorylation that results in increased cellular proliferation and decreased apoptosis, causing cancer promotion. From the literature, it shows that pyrimidine is one of the most commonly studied heterocycles for its antiproliferative activity against EGFR inhibition. The authors have collated some interesting results in the heterocycle-fused pyrimidines that have been studied using different cell lines (sensitive and mutational) and in animal models to determine their activity and potency. It is quite clear that the fused systems are highly effective in inhibiting EGFR activity in cancer cells. Therefore, the structure–activity relationship (SAR) comes into play in determining the nature of the heterocycle and the substituents that are responsible for the increased activity and toxicity. Understanding the SAR of heterocycle-fused pyrimidines will help in getting a better overview of the molecules concerning their activity and potency profile as future EGFR inhibitors.
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Affiliation(s)
| | | | | | | | - Mayur YC
- *Correspondence: Mayur YC, mayur
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10
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Liu R, Verma N, Henderson JA, Zhan S, Shen J. Profiling MAP kinase cysteines for targeted covalent inhibitor design. RSC Med Chem 2022; 13:54-63. [PMID: 35224496 PMCID: PMC8792824 DOI: 10.1039/d1md00277e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/28/2021] [Indexed: 07/20/2023] Open
Abstract
Mitogen-activated protein kinases (MAPK) are important therapeutic targets, and yet no inhibitors have advanced to the market. Here we applied the GPU-accelerated continuous constant pH molecular dynamics (CpHMD) to calculate the pK a's and profile the cysteine reactivities of all 14 MAPKs for assisting the targeted covalent inhibitor design. The simulations not only recapitulated but also rationalized the reactive cysteines in the front pocket of JNK1/2/3 and the extended front pocket of p38α. Interestingly, the DFG - 1 cysteine in the DFG-in conformation of ERK1/ERK2 was found somewhat reactive or unreactive; however, simulations of MKK7 showed that switching to the DFG-out conformation makes the DFG - 1 cysteine reactive, suggesting the advantage of type II covalent inhibitors. Additionally, the simulations prospectively predicted several druggable cysteine and lysine sites, including the αH head cysteine in JNK1/3 and DFG + 6 cysteine in JNK2, corroborating the chemical proteomic screening data. Given the low cost and the ability to offer physics-based rationales, we envision CpHMD simulations to complement the chemo-proteomic platform for systematic profiling cysteine reactivities for targeted covalent drug discovery.
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Affiliation(s)
- Ruibin Liu
- University of Maryland School of Pharmacy Baltimore MD USA
| | - Neha Verma
- University of Maryland School of Pharmacy Baltimore MD USA
| | | | - Shaoqi Zhan
- University of Maryland School of Pharmacy Baltimore MD USA
| | - Jana Shen
- University of Maryland School of Pharmacy Baltimore MD USA
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11
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Liu R, Zhan S, Che Y, Shen J. Reactivities of the Front Pocket N-Terminal Cap Cysteines in Human Kinases. J Med Chem 2021; 65:1525-1535. [PMID: 34647463 DOI: 10.1021/acs.jmedchem.1c01186] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The front pocket (FP) N-terminal cap (Ncap) cysteine is the most popular site of covalent modification in kinases. A long-standing hypothesis associates the Ncap position with cysteine hyper-reactivity; however, traditional computational predictions suggest that the FP Ncap cysteines are predominantly unreactive. Here we applied the state-of-the-art continuous constant pH molecular dynamics (CpHMD) to test the Ncap hypothesis. Simulations found that the Ncap cysteines of BTK/BMX/TEC/ITK/TXK, JAK3, and MKK7 are reactive to varying degrees; however, those of BLK and EGFR/ERBB2/ERBB4 possessing a Ncap+3 aspartate are unreactive. Analysis suggested that hydrogen bonding and electrostatic interactions drive the reactivity, and their absence renders the Ncap cysteine unreactive. To further test the Ncap hypothesis, we examined the FP Ncap+2 cysteines in JNK1/JNK2/JNK3 and CASK. Our work offers a systematic understanding of the cysteine structure-reactivity relationship and illustrates the use of CpHMD to differentiate cysteines toward the design of targeted covalent inhibitors with reduced chemical reactivities.
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Affiliation(s)
- Ruibin Liu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Shaoqi Zhan
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - Ye Che
- Discovery Sciences, Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
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12
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Farghaly AM, AboulWafa OM, Baghdadi HH, Abd El Razik HA, Sedra SMY, Shamaa MM. New thieno[3,2-d]pyrimidine-based derivatives: Design, synthesis and biological evaluation as antiproliferative agents, EGFR and ARO inhibitors inducing apoptosis in breast cancer cells. Bioorg Chem 2021; 115:105208. [PMID: 34365057 DOI: 10.1016/j.bioorg.2021.105208] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/02/2021] [Accepted: 07/21/2021] [Indexed: 01/28/2023]
Abstract
An array of newly synthesized thieno[3,2-d]pyrimidine-based derivatives and thienotriazolopyrimidines hybridized with some pharmacophoric anticancer fragments were designed, synthesized and assessed for their in vitro antiproliferative activity against MCF-7 and MDA-MB-231 breast cancer cell lines using erlotinib and pictilisib as reference standards in the MTT assay. In general, many compounds were endowed with considerable antiproliferative activity (IC50 = 0.43-1.31 µM). Some of the tested compounds, namely 3c, 5b, 5c, 9d, 10, 11b and 13 displayed remarkable antiproliferative activity against both cell lines. Meanwhile, compounds 2c-e, 3b, 4a, 5a, 9c and 15b showed noticeable selectivity against MCF-7 cells while compounds 2b, 3a, 4b, 6a-c, 7, 8, 9b and 12 exhibited considerable selectivity against MDA-MB-231 cells. Further mechanistic evidences for their anticancer activities were provided by screening the most potent compounds against MCF-7 and/or MDA-MB-231 cells for EGFR and ARO inhibitory activities using erlotinib and letrozole as reference standards respectively. Results proved that, in general, tested compounds were better EGFRIs than ARIs. In addition, significant overexpression in caspase-9 level in treated MCF-7 breast cell line samples was observed for all tested compounds with the 4-fluorophenylhydrazone derivative 2d exhibiting the highest activation. In treated MDA-MB-231 breast cell line samples, 11b was found to highly induce caspase-9 level thereby inducing apoptosis. Cell cycle analysis and Annexin V-FITC/PI assay were also assessed for active compounds where results indicated that all tested compounds induced preG1 apoptosis and cell cycle arrest at G2/M phase. Compound 9d, as an inhibitor of ARO, was observed to downregulate the downstream signaling proteins HSP27 and p-ERK in MCF-7 cells. Furthermore, compound 11b downregulated EGFR expression as well as the downstream signaling protein p-AKT. Docking experiments on EGFR and ARO enzymes supported their in vitro results. Thus, the thienotriazolopyrimidines 11b and 12 showing good EGFR inhibition and the thieno[3,2-d]-pyrimidine derivatives 3b and 9d, eliciting the best ARO inhibition activity, can be considered as new candidates as anti-breast cancer agents that necessitate further development.
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Affiliation(s)
- Ahmed M Farghaly
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, 21521 Alexandria, Egypt
| | - Omaima M AboulWafa
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, 21521 Alexandria, Egypt
| | - Hoda H Baghdadi
- Department of Environmental Studies, Institute of Graduate Studies and Research, Alexandria University, Alexandria, Egypt
| | - Heba A Abd El Razik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, 21521 Alexandria, Egypt.
| | - Samir M Y Sedra
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Pharos University in Alexandria, Alexandria, Egypt
| | - Marium M Shamaa
- Clinical and Biological Sciences (Biochemistry and Molecular Biology) Department, College of Pharmacy, Arab Academy for Science, Technology and Maritime Transport, Alexandria, Egypt
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13
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Dimov S, Mavrova AT, Yancheva D, Nikolova B, Tsoneva I. Thieno[2,3-d]pyrimidin-4(3H)-one Derivatives of Benzimidazole as Potential Anti- Breast Cancer (MDA-MB-231, MCF-7) Agents. Anticancer Agents Med Chem 2021; 21:1441-1450. [PMID: 32698751 DOI: 10.2174/1871520620666200721131431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/08/2020] [Accepted: 06/17/2020] [Indexed: 11/22/2022]
Abstract
AIMS The purpose of this study was the synthesis of some new thienopyrimidine derivatives of 1,3-disubstituted benzimidazoles and the evaluation of their cytotoxicity against MDA-MB-231, MCF-7, and 3T3 cells lines. BACKGROUND An overexpression or mutational activation of TK receptors EGFR and HER2/neu is characteristic of tumors. It has been found that some thieno[2,3-d]pyrimidines exhibited better inhibitory activity against Epidermal Growth Factor Receptor (EGFR/ErbB-2) tyrosine kinase in comparison to aminoquinazolines. Breast cancer activity towards MDA-MB-231 and MCF-7 cell lines by inhibiting EGFR was revealed by a novel 2-arylbenzimidazole. This motivated the synthesis of new thienopyrimidines possessing benzimidazole fragments in order to evaluate their cytotoxicity to the above-mentioned cell lines. OBJECTIVE The objectives of the study were to design and synthesize a novel series of thieno[2,3-d]pyrimidines bearing biologically active moieties, such as 1,3-disubstituted-benzimidazole heterocycle, structurally similar to diaryl ureas in order to evaluate their cytotoxicity against MDA-MB-231, and MCF-7 breast cancer cell lines. METHODS N,N-disubstituted benzimidazole-2-one carbonitriles were synthesized by Aza-Michael addition and used as precursors to generate some of the new thieno[2,3-d]pyrimidines in acidic medium The interaction of chloroethyl-2-thienopyrimidines, 2-amino-benzimidazole and benzimidazol-2-one nitriles under solid-liquid transfer catalysis conditions led to new thienopyrimidines. MTT assay for cell survival was performed in order to evaluate the cytotoxicity of the tested compounds. A fluorescence study was conducted to elucidate some aspects of the mechanism of action. RESULTS The effects of nine synthesized compounds were investigated towards MDA-MB-231, MCF-7 and 3T3 cell lines. Thieno[2,3-d]pyirimidine-4-one 16 (IC50 - 0.058μM) and 21 (IC50 - 0.029μM) possess high cytotoxicity against MDA-MB-231 cells after 24h. The most cytotoxic compounds against breast cancer MCF-7 cells was compound 21 (IC50 - 0.074μM), revealing lower cytotoxicity against mouse fibroblast 3T3 cells with IC50 - 0.20μM. SAR analysis was performed. Fluorescence study of the treatment of MDA-MB cells with compound 21 was carried out in order to clarify some aspects of the mechanism of action. CONCLUSION The relationship between cytotoxicity of compounds 14 and 20 against MCF-7 and 3T3 cells can suggest a similar mechanism of action. The antitumor potential of the tested compounds proves the necessity for further investigation to estimate the exact inhibition pathway in the cellular processes. The fluorescence study of the treatment of MDA-MB cells with compound 21 showed a rapid process of apoptosis.
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Affiliation(s)
- Stefan Dimov
- Department of Organic Synthesis, University of Chemical Technology and Metallurgy, 8 Kliment Ohridski Blvd., 1756 Sofia, Bulgaria
| | - Anelia Ts Mavrova
- Department of Organic Synthesis, University of Chemical Technology and Metallurgy, 8 Kliment Ohridski Blvd., 1756 Sofia, Bulgaria
| | - Denitsa Yancheva
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Build. 9, 1113 Sofia, Bulgaria
| | - Biliana Nikolova
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Street, Build. 21, 1113 Sofia, Bulgaria
| | - Iana Tsoneva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Acad. G. Bonchev Street, Build. 21, 1113 Sofia, Bulgaria
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14
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Mons E, Kim RQ, van Doodewaerd BR, van Veelen PA, Mulder MPC, Ovaa H. Exploring the Versatility of the Covalent Thiol-Alkyne Reaction with Substituted Propargyl Warheads: A Deciding Role for the Cysteine Protease. J Am Chem Soc 2021; 143:6423-6433. [PMID: 33885283 PMCID: PMC8154518 DOI: 10.1021/jacs.0c10513] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Indexed: 12/17/2022]
Abstract
Terminal unactivated alkynes are nowadays considered the golden standard for cysteine-reactive warheads in activity-based probes (ABPs) targeting cysteine deubiquitinating enzymes (DUBs). In this work, we study the versatility of the thiol-alkyne addition reaction in more depth. Contrary to previous findings with UCHL3, we now show that covalent adduct formation can progress with substituents on the terminal or internal alkyne position. Strikingly, acceptance of alkyne substituents is strictly DUB-specific as this is not conserved among members of the same subfamily. Covalent adduct formation with the catalytic cysteine residue was validated by gel analysis and mass spectrometry of intact ABP-treated USP16CDWT and catalytically inactive mutant USP16CDC205A. Bottom-up mass spectrometric analysis of the covalent adduct with a deuterated propargyl ABP provides mechanistic understanding of the in situ thiol-alkyne reaction, identifying the alkyne rather than an allenic intermediate as the reactive species. Furthermore, kinetic analysis revealed that introduction of (bulky/electron-donating) methyl substituents on the propargyl moiety decreases the rate of covalent adduct formation, thus providing a rational explanation for the commonly lower level of observed covalent adduct compared to unmodified alkynes. Altogether, our work extends the scope of possible propargyl derivatives in cysteine targeting ABPs from unmodified terminal alkynes to internal and substituted alkynes, which we anticipate will have great value in the development of ABPs with improved selectivity profiles.
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Affiliation(s)
- Elma Mons
- Department
of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Robbert Q. Kim
- Department
of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Bjorn R. van Doodewaerd
- Department
of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Peter A. van Veelen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Monique P. C. Mulder
- Department
of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Huib Ovaa
- Department
of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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15
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Guan I, Williams K, Pan J, Liu X. New Cysteine Covalent Modification Strategies Enable Advancement of Proteome‐wide Selectivity of Kinase Modulators. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202100036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ivy Guan
- School of Chemistry The Heart Research Institute The University of Sydney Sydney New South Wales 2006 Australia
| | - Kayla Williams
- School of Chemistry The University of Sydney Sydney New South Wales 2006 Australia
| | - Jolyn Pan
- Faculty of Science & Engineering The University of Waikato 124 Hillcrest Road, Hillcrest Hamilton 3216 New Zealand
| | - Xuyu Liu
- School of Chemistry The Heart Research Institute The University of Sydney Sydney New South Wales 2006 Australia
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16
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Veale CGL. Into the Fray! A Beginner's Guide to Medicinal Chemistry. ChemMedChem 2021; 16:1199-1225. [PMID: 33591595 DOI: 10.1002/cmdc.202000929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Indexed: 12/31/2022]
Abstract
Modern medicinal chemistry is a complex, multidimensional discipline that operates at the interface of the chemical and biological sciences. The medicinal chemistry contribution to drug discovery is typically described in the context of the well-recited linear progression of the drug discovery pipeline. However, compound optimization is idiosyncratic to each project, and clear definitions of hit and lead molecules and the subsequent progress along the pipeline becomes easily blurred. In addition, this description lacks insight into the entangled relationship between chemical and pharmacological properties, and thus provides limited guidance on how innovative medicinal chemistry strategies can be applied to solve optimization problems, regardless of the stage in the pipeline. Through discussion and illustrative examples, this article seeks to provide insights into the finesse of medicinal chemistry and the subtlety of balancing chemical properties pharmacology. In so doing, it aims to serve as an accessible and simple-to-digest guide for anyone who wishes to learn about the underlying principles of medicinal chemistry, in a context that has been decoupled from the pipeline description.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg, Scottsville, 3209, South Africa
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17
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Saber AF, Sayed M, Tolba MS, Kamal El-Dean AM, Hassanien R, Ahmed M. A facile method for preparation and evaluation of the antimicrobial efficiency of various heterocycles containing thieno[2,3-d]pyrimidine. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1829645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ahmed F. Saber
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
| | - Mostafa Sayed
- Chemistry Department, Faculty of Science, New Valley University, El-Kharja, Egypt
| | - Mahmoud S. Tolba
- Chemistry Department, Faculty of Science, New Valley University, El-Kharja, Egypt
| | | | - Reda Hassanien
- Chemistry Department, Faculty of Science, New Valley University, El-Kharja, Egypt
| | - Mostafa Ahmed
- Chemistry Department, Faculty of Science, New Valley University, El-Kharja, Egypt
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18
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Canonical ErbB-2 isoform and ErbB-2 variant c located in the nucleus drive triple negative breast cancer growth. Oncogene 2020; 39:6245-6262. [PMID: 32843720 DOI: 10.1038/s41388-020-01430-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023]
Abstract
Triple negative breast cancer (TNBC) refers to tumors that do not express clinically significant levels of estrogen and progesterone receptors, and lack membrane overexpression or gene amplification of ErbB-2/HER2, a receptor tyrosine kinase. Transcriptome and proteome heterogeneity of TNBC poses a major challenge to precision medicine. Clinical biomarkers and targeted therapies for this disease remain elusive, so chemotherapy has been the standard of care for early and metastatic TNBC. Our present findings placed ErbB-2 in an unanticipated scenario: the nucleus of TNBC (NErbB-2). Our study on ErbB-2 alternative splicing events, using a PCR-sequencing approach combined with an RNA interference strategy, revealed that TNBC cells express either the canonical (wild-type) ErbB-2, encoded by transcript variant 1, or the non-canonical ErbB-2 isoform c, encoded by alternative variant 3 (RefSeq), or both. These ErbB-2 isoforms function in the nucleus as transcription factors. Evicting both from the nucleus or silencing isoform c only, blocks TN cell and tumor growth. This reveals not only NErbB-2 canonical and alternative isoforms role as targets of therapy in TNBC, but also isoform c dominant oncogenic potential. Furthermore, we validated our findings in the clinic and observed that NErbB-2 correlates with poor prognosis in primary TN tumors, disclosing NErbB-2 as a novel biomarker for TNBC. Our discoveries challenge the present scenario of drug development for personalized BC medicine that focuses on wild-type RefSeq proteins, which conserve the canonical domains and are located in their classical cellular compartments.
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19
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Prakash P. A regulatory role of membrane by direct modulation of the catalytic kinase domain. Small GTPases 2020; 12:246-256. [PMID: 32663062 DOI: 10.1080/21541248.2020.1788886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cell membrane modulates the function and activity of specific proteins and acts more than just a non-specific scaffolding machinery. In this review, I focus on studies that highlight a direct membrane-mediated modulation of the catalytic kinase domain of a variety of kinases thereby regulating the kinase activity. It emerges that membrane provides a second level of regulation once kinase domain is relieved of its inactive auto-inhibitory state. For the first time a generalized regulatory role of membrane is proposed that governs the kinase activity by modulating the catalytic kinase domain. Striking similarities among a variety of multi-domain kinases as well as single-domain lipidated enzymes such as RAS proteins are presented.
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Affiliation(s)
- Priyanka Prakash
- Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX, USA
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20
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Abstract
The use of an acetylene (ethynyl) group in medicinal chemistry coincides with the launch of the Journal of Medicinal Chemistry in 1959. Since then, the acetylene group has been broadly exploited in drug discovery and development. As a result, it has become recognized as a privileged structural feature for targeting a wide range of therapeutic target proteins, including MAO, tyrosine kinases, BACE1, steroid receptors, mGlu5 receptors, FFA1/GPR40, and HIV-1 RT. Furthermore, a terminal alkyne functionality is frequently introduced in chemical biology probes as a click handle to identify molecular targets and to assess target engagement. This Perspective is divided into three parts encompassing: (1) the physicochemical properties of the ethynyl group, (2) the advantages and disadvantages of the ethynyl group in medicinal chemistry, and (3) the impact of the ethynyl group on chemical biology approaches.
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Affiliation(s)
- Tanaji T Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York 11439, United States
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21
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Abdeldayem A, Raouf YS, Constantinescu SN, Moriggl R, Gunning PT. Advances in covalent kinase inhibitors. Chem Soc Rev 2020; 49:2617-2687. [DOI: 10.1039/c9cs00720b] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This comprehensive review details recent advances, challenges and innovations in covalent kinase inhibition within a 10 year period (2007–2018).
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Affiliation(s)
- Ayah Abdeldayem
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | - Yasir S. Raouf
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
| | | | - Richard Moriggl
- Institute of Animal Breeding and Genetics
- University of Veterinary Medicine
- 1210 Vienna
- Austria
| | - Patrick T. Gunning
- Department of Chemical & Physical Sciences
- University of Toronto
- Mississauga
- Canada
- Department of Chemistry
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22
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Ahammad I, Sarker MRI, Khan AM, Islam S, Hossain M. Virtual Screening to Identify Novel Inhibitors of Pan ERBB Family of Proteins from Natural Products with Known Anti-tumorigenic Properties. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09992-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Awoonor-Williams E, Isley WC, Dale SG, Johnson ER, Yu H, Becke AD, Roux B, Rowley CN. Quantum Chemical Methods for Modeling Covalent Modification of Biological Thiols. J Comput Chem 2019; 41:427-438. [PMID: 31512279 DOI: 10.1002/jcc.26064] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/24/2019] [Accepted: 08/16/2019] [Indexed: 02/06/2023]
Abstract
Targeted covalent inhibitor drugs require computational methods that go beyond simple molecular-mechanical force fields in order to model the chemical reactions that occur when they bind to their targets. Here, several semiempirical and density-functional theory (DFT) methods are assessed for their ability to describe the potential energy surface and reaction energies of the covalent modification of a thiol by an electrophile. Functionals such as PBE and B3LYP fail to predict a stable enolate intermediate. This is largely due to delocalization error, which spuriously stabilizes the prereaction complex, in which excess electron density is transferred from the thiolate to the electrophile. Functionals with a high-exact exchange component, range-separated DFT functionals, and variationally optimized exact exchange (i.e., the LC-B05minV functional) correct this issue to various degrees. The large gradient behavior of the exchange enhancement factor is also found to significantly affect the results, leading to the improved performance of PBE0. While ωB97X-D and M06-2X were reasonably accurate, no method provided quantitative accuracy for all three electrophiles, making this a very strenuous test of functional performance. Additionally, one drawback of M06-2X was that molecular dynamics (MD) simulations using this functional were only stable if a fine integration grid was used. The low-cost semiempirical methods, PM3, AM1, and PM7, provide a qualitatively correct description of the reaction mechanism, although the energetics is not quantitatively reliable. As a proof of concept, the potential of mean force for the addition of methylthiolate to methylvinyl ketone was calculated using quantum mechanical/molecular mechanical MD in an explicit polarizable aqueous solvent. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - William C Isley
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Stephen G Dale
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Axel D Becke
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois
| | - Christopher N Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
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24
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Xie Q, Wang J, Liu M, Wang X, Jiao D, Ma Q, Jin Z, Meng Q, Hu C. Discovery of 7-bromo-1,4-dihydrothieno[3’,2’:5,6]thiopyrano[4,3-c]pyrazole-3-carboxamide derivatives as the potential epidermal growth factor receptors for tyrosine kinase inhibitors. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02354-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Martin-Fernandez ML, Clarke DT, Roberts SK, Zanetti-Domingues LC, Gervasio FL. Structure and Dynamics of the EGF Receptor as Revealed by Experiments and Simulations and Its Relevance to Non-Small Cell Lung Cancer. Cells 2019; 8:E316. [PMID: 30959819 PMCID: PMC6523254 DOI: 10.3390/cells8040316] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/29/2019] [Accepted: 03/30/2019] [Indexed: 12/25/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is historically the prototypical receptor tyrosine kinase, being the first cloned and the first where the importance of ligand-induced dimer activation was ascertained. However, many years of structure determination has shown that EGFR is not completely understood. One challenge is that the many structure fragments stored at the PDB only provide a partial view because full-length proteins are flexible entities and dynamics play a key role in their functionality. Another challenge is the shortage of high-resolution data on functionally important higher-order complexes. Still, the interest in the structure/function relationships of EGFR remains unabated because of the crucial role played by oncogenic EGFR mutants in driving non-small cell lung cancer (NSCLC). Despite targeted therapies against EGFR setting a milestone in the treatment of this disease, ubiquitous drug resistance inevitably emerges after one year or so of treatment. The magnitude of the challenge has inspired novel strategies. Among these, the combination of multi-disciplinary experiments and molecular dynamic (MD) simulations have been pivotal in revealing the basic nature of EGFR monomers, dimers and multimers, and the structure-function relationships that underpin the mechanisms by which EGFR dysregulation contributes to the onset of NSCLC and resistance to treatment.
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Affiliation(s)
- Marisa L Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
| | - David T Clarke
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
| | - Selene K Roberts
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
| | - Laura C Zanetti-Domingues
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxford OX11 0QX, UK.
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26
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Gehringer M, Laufer SA. Emerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology. J Med Chem 2019; 62:5673-5724. [PMID: 30565923 DOI: 10.1021/acs.jmedchem.8b01153] [Citation(s) in RCA: 374] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Targeted covalent inhibitors (TCIs) are designed to bind poorly conserved amino acids by means of reactive groups, the so-called warheads. Currently, targeting noncatalytic cysteine residues with acrylamides and other α,β-unsaturated carbonyl compounds is the predominant strategy in TCI development. The recent ascent of covalent drugs has stimulated considerable efforts to characterize alternative warheads for the covalent-reversible and irreversible engagement of noncatalytic cysteine residues as well as other amino acids. This Perspective article provides an overview of warheads-beyond α,β-unsaturated amides-recently used in the design of targeted covalent ligands. Promising reactive groups that have not yet demonstrated their utility in TCI development are also highlighted. Special emphasis is placed on the discussion of reactivity and of case studies illustrating applications in medicinal chemistry and chemical biology.
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Affiliation(s)
- Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry , Eberhard Karls University Tübingen , Auf der Morgenstelle 8 , 72076 Tübingen , Germany
| | - Stefan A Laufer
- Department of Pharmaceutical/Medicinal Chemistry , Eberhard Karls University Tübingen , Auf der Morgenstelle 8 , 72076 Tübingen , Germany
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27
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Woodring J, Behera R, Sharma A, Wiedeman J, Patel G, Singh B, Guyett P, Amata E, Erath J, Roncal N, Penn E, Leed SE, Rodriguez A, Sciotti RJ, Mensa-Wilmot K, Pollastri MP. Series of Alkynyl-Substituted Thienopyrimidines as Inhibitors of Protozoan Parasite Proliferation. ACS Med Chem Lett 2018; 9:996-1001. [PMID: 30344906 PMCID: PMC6187419 DOI: 10.1021/acsmedchemlett.8b00245] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/04/2018] [Indexed: 12/23/2022] Open
Abstract
Discovery of new chemotherapeutic lead agents can be accelerated by optimizing chemotypes proven to be effective in other diseases to act against parasites. One such medicinal chemistry campaign has focused on optimizing the anilinoquinazoline drug lapatinib (1) and the alkynyl thieno[3,2-d]pyrimidine hit GW837016X (NEU-391, 3) into leads for antitrypanosome drugs. We now report the structure-activity relationship studies of 3 and its analogs against Trypanosoma brucei, which causes human African trypanosomiasis (HAT). The series was also tested against Trypanosoma cruzi, Leishmania major, and Plasmodium falciparum. In each case, potent antiparasitic hits with acceptable toxicity margins over mammalian HepG2 and NIH3T3 cell lines were identified. In a mouse model of HAT, 3 extended life of treated mice by 50%, compared to untreated controls. At the cellular level, 3 inhibited mitosis and cytokinesis in T. brucei. Thus, the alkynylthieno[3,2-d]pyrimidine chemotype is an advanced hit worthy of further optimization as a potential chemotherapeutic agent for HAT.
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Affiliation(s)
- Jennifer
L. Woodring
- Department
of Chemistry & Chemical Biology, Northeastern
University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Ranjan Behera
- Department
of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, United States
| | - Amrita Sharma
- Department
of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, United States
| | - Justin Wiedeman
- Department
of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, United States
| | - Gautam Patel
- Department
of Chemistry & Chemical Biology, Northeastern
University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Baljinder Singh
- Department
of Chemistry & Chemical Biology, Northeastern
University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Paul Guyett
- Department
of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, United States
| | - Emanuele Amata
- Department
of Chemistry & Chemical Biology, Northeastern
University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Jessey Erath
- Department
of Microbiology, New York University School
of Medicine, 430 E. 29th Street New York, New York 10010, United
States
- Anti-Infectives
Screening Core, New York University School
of Medicine, New York, New York 10010, United
States
| | - Norma Roncal
- Experimental
Therapeutics, Walter Reed Army Institute
of Research, 2460 Linden Lane, Silver Spring, Maryland 20910, United
States
| | - Erica Penn
- Experimental
Therapeutics, Walter Reed Army Institute
of Research, 2460 Linden Lane, Silver Spring, Maryland 20910, United
States
| | - Susan E. Leed
- Experimental
Therapeutics, Walter Reed Army Institute
of Research, 2460 Linden Lane, Silver Spring, Maryland 20910, United
States
| | - Ana Rodriguez
- Department
of Microbiology, New York University School
of Medicine, 430 E. 29th Street New York, New York 10010, United
States
- Anti-Infectives
Screening Core, New York University School
of Medicine, New York, New York 10010, United
States
| | - Richard J. Sciotti
- Experimental
Therapeutics, Walter Reed Army Institute
of Research, 2460 Linden Lane, Silver Spring, Maryland 20910, United
States
| | - Kojo Mensa-Wilmot
- Department
of Cellular Biology, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, United States
| | - Michael P. Pollastri
- Department
of Chemistry & Chemical Biology, Northeastern
University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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28
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Awoonor-Williams E, Rowley CN. How Reactive are Druggable Cysteines in Protein Kinases? J Chem Inf Model 2018; 58:1935-1946. [DOI: 10.1021/acs.jcim.8b00454] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ernest Awoonor-Williams
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, NL A1B 3X9, Canada
| | - Christopher N. Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, NL A1B 3X9, Canada
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29
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Giordano A, Forte G, Massimo L, Riccio R, Bifulco G, Di Micco S. Discovery of new erbB4 inhibitors: Repositioning an orphan chemical library by inverse virtual screening. Eur J Med Chem 2018; 152:253-263. [PMID: 29730188 DOI: 10.1016/j.ejmech.2018.04.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/05/2018] [Accepted: 04/09/2018] [Indexed: 01/20/2023]
Abstract
Inverse Virtual Screening (IVS) is a docking based approach aimed to the evaluation of the virtual ability of a single compound to interact with a library of proteins. For the first time, we applied this methodology to a library of synthetic compounds, which proved to be inactive towards the target they were initially designed for. Trifluoromethyl-benzenesulfonamides 3-21 were repositioned by means of IVS identifying new lead compounds (14-16, 19 and 20) for the inhibition of erbB4 in the low micromolar range. Among these, compound 20 exhibited an interesting value of IC50 on MCF7 cell lines, thus validating IVS in lead repurposing.
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Affiliation(s)
- Assunta Giordano
- Institute of Biomolecular Chemistry (ICB), Consiglio Nazionale delle Ricerche (CNR), Via Campi Flegrei 34, I-80078, Pozzuoli, Napoli, Italy; Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Giovanni Forte
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Luigia Massimo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, I-84084, Fisciano, SA, Italy
| | - Raffaele Riccio
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
| | - Simone Di Micco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, 132, 84084, Fisciano, SA, Italy.
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30
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Liu L, Thaker TM, Freed DM, Frazier N, Malhotra K, Lemmon MA, Jura N. Regulation of Kinase Activity in the Caenorhabditis elegans EGF Receptor, LET-23. Structure 2018; 26:270-281.e4. [PMID: 29358026 DOI: 10.1016/j.str.2017.12.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 11/07/2017] [Accepted: 12/20/2017] [Indexed: 12/11/2022]
Abstract
In the active HER receptor dimers, kinases play distinct roles; one is the catalytically active kinase and the other is its allosteric activator. This specialization enables signaling by the catalytically inactive HER3, which functions exclusively as an allosteric activator upon heterodimerization with other HER receptors. It is unclear whether the allosteric activation mechanism evolved before HER receptors functionally specialized. We determined the crystal structure of the kinase domain of the only EGF receptor in Caenorhabditis elegans, LET-23. Our structure of a non-human EGFR kinase reveals autoinhibitory features conserved in the human counterpart. Strikingly, mutations within the putative allosteric dimer interface abrogate activity of the isolated LET-23 kinase and of the full-length receptor despite these regions being only partially conserved with human EGFR. Our results indicate that ancestral EGFRs have built-in features that poise them for allosteric activation that could facilitate emergence of the catalytically dead, yet functional, orthologs.
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Affiliation(s)
- Lijun Liu
- Cardiovascular Research Institute, University of California - San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California - San Francisco, San Francisco, CA 94158, USA
| | - Tarjani M Thaker
- Cardiovascular Research Institute, University of California - San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California - San Francisco, San Francisco, CA 94158, USA
| | - Daniel M Freed
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Nicole Frazier
- Cardiovascular Research Institute, University of California - San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California - San Francisco, San Francisco, CA 94158, USA
| | - Ketan Malhotra
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Mark A Lemmon
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA; Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California - San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California - San Francisco, San Francisco, CA 94158, USA.
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Milik SN, Lasheen DS, Serya RA, Abouzid KA. How to train your inhibitor: Design strategies to overcome resistance to Epidermal Growth Factor Receptor inhibitors. Eur J Med Chem 2017; 142:131-151. [DOI: 10.1016/j.ejmech.2017.07.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/11/2017] [Accepted: 07/14/2017] [Indexed: 01/05/2023]
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Ghith A, Ismail NS, Youssef K, Abouzid KA. Medicinal Attributes of Thienopyrimidine Based Scaffold Targeting Tyrosine Kinases and Their Potential Anticancer Activities. Arch Pharm (Weinheim) 2017; 350. [DOI: 10.1002/ardp.201700242] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/14/2017] [Accepted: 09/05/2017] [Indexed: 01/02/2023]
Affiliation(s)
- Amna Ghith
- Faculty of Pharmaceutical Sciences and Pharmaceutical Industries; Department of Pharmaceutical Chemistry; Future University in Egypt; Cairo Egypt
| | - Nasser S.M. Ismail
- Faculty of Pharmaceutical Sciences and Pharmaceutical Industries; Department of Pharmaceutical Chemistry; Future University in Egypt; Cairo Egypt
| | - Khairia Youssef
- Faculty of Pharmaceutical Sciences and Pharmaceutical Industries; Department of Pharmaceutical Chemistry; Future University in Egypt; Cairo Egypt
| | - Khaled A.M. Abouzid
- Faculty of Pharmacy; Department of Pharmaceutical Chemistry; Ain Shams University; Abbassia, Cairo Egypt
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Knittle AM, Helkkula M, Johnson MS, Sundvall M, Elenius K. SUMOylation regulates nuclear accumulation and signaling activity of the soluble intracellular domain of the ErbB4 receptor tyrosine kinase. J Biol Chem 2017; 292:19890-19904. [PMID: 28974580 DOI: 10.1074/jbc.m117.794271] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/22/2017] [Indexed: 01/24/2023] Open
Abstract
Erb-B2 receptor tyrosine kinase 4 (ErbB4) is a kinase that can signal via a proteolytically released intracellular domain (ICD) in addition to classical receptor tyrosine kinase-activated signaling cascades. Previously, we have demonstrated that ErbB4 ICD is posttranslationally modified by the small ubiquitin-like modifier (SUMO) and functionally interacts with the PIAS3 SUMO E3 ligase. However, direct evidence of SUMO modification in ErbB4 signaling has remained elusive. Here, we report that the conserved lysine residue 714 in the ErbB4 ICD undergoes SUMO modification, which was reversed by sentrin-specific proteases (SENPs) 1, 2, and 5. Although ErbB4 kinase activity was not necessary for the SUMOylation, the SUMOylated ErbB4 ICD was tyrosine phosphorylated to a higher extent than unmodified ErbB4 ICD. Mutation of the SUMOylation site compromised neither ErbB4-induced phosphorylation of the canonical signaling pathway effectors Erk1/2, Akt, or STAT5 nor ErbB4 stability. In contrast, SUMOylation was required for nuclear accumulation of the ErbB4 ICD. We also found that Lys-714 was located within a leucine-rich stretch, which resembles a nuclear export signal, and could be inactivated by site-directed mutagenesis. Furthermore, SUMOylation modulated the interaction of ErbB4 with chromosomal region maintenance 1 (CRM1), the major nuclear export receptor for proteins. Finally, the SUMO acceptor lysine was functionally required for ErbB4 ICD-mediated inhibition of mammary epithelial cell differentiation in a three-dimensional cell culture model. Our findings indicate that a SUMOylation-mediated mechanism regulates nuclear localization and function of the ICD of ErbB4 receptor tyrosine kinase.
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Affiliation(s)
- Anna M Knittle
- From the Department of Medical Biochemistry and Genetics, and MediCity Research Laboratory, University of Turku, FI-20520 Turku, Finland.,Turku Doctoral Programmes of Biomedical Sciences and Molecular Medicine, University of Turku, FI-20014 Turku, Finland
| | - Maria Helkkula
- From the Department of Medical Biochemistry and Genetics, and MediCity Research Laboratory, University of Turku, FI-20520 Turku, Finland
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, FI-20500 Turku, Finland, and
| | - Maria Sundvall
- From the Department of Medical Biochemistry and Genetics, and MediCity Research Laboratory, University of Turku, FI-20520 Turku, Finland, .,Department of Oncology and Radiotherapy, University of Turku and Turku University Hospital, FI-20014 Turku, Finland
| | - Klaus Elenius
- From the Department of Medical Biochemistry and Genetics, and MediCity Research Laboratory, University of Turku, FI-20520 Turku, Finland, .,Department of Oncology and Radiotherapy, University of Turku and Turku University Hospital, FI-20014 Turku, Finland
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Natural Products as Chemopreventive Agents by Potential Inhibition of the Kinase Domain in ErbB Receptors. Molecules 2017; 22:molecules22020308. [PMID: 28218686 PMCID: PMC6155853 DOI: 10.3390/molecules22020308] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 02/04/2017] [Accepted: 02/06/2017] [Indexed: 01/24/2023] Open
Abstract
Small molecules found in natural products provide therapeutic benefits due to their pharmacological or biological activity, which may increase or decrease the expression of human epidermal growth factor receptor (HER), a promising target in the modification of signaling cascades involved in excessive cellular growth. In this study, in silico molecular protein-ligand docking protocols were performed with AutoDock Vina in order to evaluate the interaction of 800 natural compounds (NPs) from the NatProd Collection (http://www.msdiscovery.com/natprod.html), with four human HER family members: HER1 (PDB: 2ITW), HER2 (PDB: 3PP0), HER3 (PDB: 3LMG) and HER4 (PDB: 2R4B). The best binding affinity values (kcal/mol) for docking pairs were obtained for HER1-podototarin (−10.7), HER2-hecogenin acetate (−11.2), HER3-hesperidin (−11.5) and HER4-theaflavin (−10.7). The reliability of the theoretical calculations was evaluated employing published data on HER inhibition correlated with in silico binding calculations. IC50 values followed a significant linear relationship with the theoretical binding Affinity data for HER1 (R = 0.656, p < 0.0001) and HER2 (R = 0.543, p < 0.0001), but not for HER4 (R = 0.364, p > 0.05). In short, this methodology allowed the identification of several NPs as HER inhibitors, being useful in the discovery and design of more potent and selective anticancer drugs.
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35
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Abd El Hadi SR, Lasheen DS, Hassan MA, Abouzid KAM. Design and Synthesis of 4-Anilinothieno[2,3-d
]pyrimidine-Based Compounds as Dual EGFR/HER-2 Inhibitors. Arch Pharm (Weinheim) 2016; 349:827-847. [DOI: 10.1002/ardp.201600197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/11/2016] [Accepted: 09/14/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Soha R. Abd El Hadi
- Faculty of Pharmacy, Department of Pharmaceutical Organic Chemistry; Egyptian Russian University; Badr City, Cairo Egypt
| | - Deena S. Lasheen
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry; Ain Shams University; Cairo Egypt
| | - Mahmoud A. Hassan
- Faculty of Pharmacy, Department of Pharmaceutical Organic Chemistry; Egyptian Russian University; Badr City, Cairo Egypt
| | - Khaled A. M. Abouzid
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry; Ain Shams University; Cairo Egypt
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Smaill JB, Gonzales AJ, Spicer JA, Lee H, Reed JE, Sexton K, Althaus IW, Zhu T, Black SL, Blaser A, Denny WA, Ellis PA, Fakhoury S, Harvey PJ, Hook K, McCarthy FOJ, Palmer BD, Rivault F, Schlosser K, Ellis T, Thompson AM, Trachet E, Winters RT, Tecle H, Bridges A. Tyrosine Kinase Inhibitors. 20. Optimization of Substituted Quinazoline and Pyrido[3,4-d]pyrimidine Derivatives as Orally Active, Irreversible Inhibitors of the Epidermal Growth Factor Receptor Family. J Med Chem 2016; 59:8103-24. [DOI: 10.1021/acs.jmedchem.6b00883] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jeff B. Smaill
- Auckland
Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Andrea J. Gonzales
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
| | - Julie A. Spicer
- Auckland
Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Helen Lee
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
| | - Jessica E. Reed
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
| | - Karen Sexton
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
| | - Irene W. Althaus
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
| | - Tong Zhu
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
| | - Shannon L. Black
- Auckland
Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Adrian Blaser
- Auckland
Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - William A. Denny
- Auckland
Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Paul A. Ellis
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
| | - Stephen Fakhoury
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
| | - Patricia J. Harvey
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
| | - Ken Hook
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
| | - Florence O. J. McCarthy
- Auckland
Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Brian D. Palmer
- Auckland
Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Maurice
Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Freddy Rivault
- Auckland
Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Kevin Schlosser
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
| | - Teresa Ellis
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
| | - Andrew M. Thompson
- Auckland
Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Erin Trachet
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
| | - R. Thomas Winters
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
| | - Haile Tecle
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
| | - Alexander Bridges
- Pfizer
Global Research and Development, Michigan Laboratories, 2800 Plymouth
Road, Ann Arbor, Michigan 48105-1047, United States
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37
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Kinases inhibitors in lung cancer: From benchside to bedside. Biochim Biophys Acta Rev Cancer 2016; 1866:128-40. [DOI: 10.1016/j.bbcan.2016.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 07/01/2016] [Accepted: 07/02/2016] [Indexed: 12/31/2022]
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Hu P, Han DX, Ruan RS, Zheng LM, Chou SH, Tzeng CM. Transtinib, a potent tyrosine kinase inhibitor inhibits L858R/T790M mutant NSCLC cell lines and xenografts. Oncotarget 2016; 7:35741-35752. [PMID: 26848869 PMCID: PMC5094958 DOI: 10.18632/oncotarget.7140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/23/2016] [Indexed: 11/25/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) patients with activating epidermal growth factor receptor (EGFR) mutations initially respond well to the EGFR tyrosine kinase inhibitors (TKIs) erlotinib and gefitinib. However, clinical efficacy is limited by the development of resistance. In most cases, this resistance is in the form of the T790M mutation. Here, we report the design, synthesis and biochemical evaluation of a novel series of irreversible EGFR tyrosine kinase inhibitors (EGFR-TKIs) that are derived from the anilinoquinazoline scaffold. Guided by molecular modeling, this series of analogs was evolved to target a cysteine residue in the ATP binding site via covalent bond formation and to achieve high levels of anti-tumor activity in cell cultures and in xenografts. The most promising compound 13c ((E) –N - (4 - (4 - (3-fluorobenzyloxy) -3- chlorophenylamino) -7-ethoxyquinazolin-6-yl) -3- ((S) -pyrrolidin-2-yl)acrylamide, which we named Transtinib) displayed strong anti-proliferative activity against the H1975 and A431 cell lines with IC50 values of 34 nM and 62 nM, respectively. In xenograft models, Transtinib significantly decreases tumor size for a prolonged period of time. These results suggest that Transtinib is a potential cancer therapeutic drug lead for the inhibition of mutant EGFR to overcome the development of resistance.
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Affiliation(s)
- Peng Hu
- Translational Medicine Research Center, School of Pharmaceutical Science, Xiamen University, Xiamen, P.R. China.,Key Laboratory for Cancer T-Cell Theranostics and Clinical Translation (CTCTCT), Xiamen, P.R. China
| | - Da-Xiong Han
- Translational Medicine Research Center, School of Pharmaceutical Science, Xiamen University, Xiamen, P.R. China
| | - Run-Sheng Ruan
- Translational Medicine Research Center, School of Pharmaceutical Science, Xiamen University, Xiamen, P.R. China.,Key Laboratory for Cancer T-Cell Theranostics and Clinical Translation (CTCTCT), Xiamen, P.R. China
| | - Li-Mou Zheng
- Translational Medicine Research Center, School of Pharmaceutical Science, Xiamen University, Xiamen, P.R. China
| | - Shiu-Huey Chou
- Department of Life Science, Fu-Jen Catholic University, Xinzhuang District, New Taipei City, Taiwan
| | - Chi-Meng Tzeng
- Translational Medicine Research Center, School of Pharmaceutical Science, Xiamen University, Xiamen, P.R. China.,Key Laboratory for Cancer T-Cell Theranostics and Clinical Translation (CTCTCT), Xiamen, P.R. China
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Bugge S, Buene AF, Jurisch-Yaksi N, Moen IU, Skjønsfjell EM, Sundby E, Hoff BH. Extended structure–activity study of thienopyrimidine-based EGFR inhibitors with evaluation of drug-like properties. Eur J Med Chem 2016; 107:255-74. [DOI: 10.1016/j.ejmech.2015.11.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/04/2015] [Accepted: 11/05/2015] [Indexed: 01/08/2023]
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40
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Liu W, Ning JF, Meng QW, Hu J, Zhao YB, Liu C, Cai L. Navigating into the binding pockets of the HER family protein kinases: discovery of novel EGFR inhibitor as antitumor agent. DRUG DESIGN DEVELOPMENT AND THERAPY 2015; 9:3837-51. [PMID: 26229444 PMCID: PMC4517520 DOI: 10.2147/dddt.s85357] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The epidermal growth factor receptor (EGFR) family has been validated as a successful antitumor drug target for decades. Known EGFR inhibitors were exposed to distinct drug resistance against the various EGFR mutants within non-small-cell lung cancer (NSCLC), particularly the T790M mutation. Although so far a number of studies have been reported on the development of third-generation EGFR inhibitors for overcoming the resistance issue, the design procedure largely depends on the intuition of medicinal chemists. Here we retrospectively make a detailed analysis of the 42 EGFR family protein crystal complexes deposited in the Protein Data Bank (PDB). Based on the analysis of inhibitor binding modes in the kinase catalytic cleft, we identified a potent EGFR inhibitor (compound A-10) against drug-resistant EGFR through fragment-based drug design. This compound showed at least 30-fold more potency against EGFR T790M than the two control molecules erlotinib and gefitinib in vitro. Moreover, it could exhibit potent HER2 inhibitory activities as well as tumor growth inhibitory activity. Molecular docking studies revealed a structural basis for the increased potency and mutant selectivity of this compound. Compound A-10 may be selected as a promising candidate in further preclinical studies. In addition, our findings could provide a powerful strategy to identify novel selective kinase inhibitors on the basis of detailed kinase–ligand interaction space in the PDB.
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Affiliation(s)
- Wei Liu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
| | - Jin-Feng Ning
- The Thoracic Surgery Department, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
| | - Qing-Wei Meng
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
| | - Jing Hu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
| | - Yan-Bin Zhao
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
| | - Chao Liu
- General Surgery Department, Mudanjiang Guanliju Central Hospital, Mishan, Heilongjiang Province, People's Republic of China
| | - Li Cai
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, People's Republic of China
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41
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Devine W, Woodring JL, Swaminathan U, Amata E, Patel G, Erath J, Roncal NE, Lee PJ, Leed SE, Rodriguez A, Mensa-Wilmot K, Sciotti RJ, Pollastri MP. Protozoan Parasite Growth Inhibitors Discovered by Cross-Screening Yield Potent Scaffolds for Lead Discovery. J Med Chem 2015; 58:5522-37. [PMID: 26087257 PMCID: PMC4515785 DOI: 10.1021/acs.jmedchem.5b00515] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
Tropical protozoal infections are
a significant cause of morbidity
and mortality worldwide; four in particular (human African trypanosomiasis
(HAT), Chagas disease, cutaneous leishmaniasis, and malaria) have
an estimated combined burden of over 87 million disability-adjusted
life years. New drugs are needed for each of these diseases. Building
on the previous identification of NEU-617 (1) as a potent
and nontoxic inhibitor of proliferation for the HAT pathogen (Trypanosoma brucei), we have now tested this class of analogs
against other protozoal species: T. cruzi (Chagas
disease), Leishmania major (cutaneous leishmaniasis),
and Plasmodium falciparum (malaria). Based on hits
identified in this screening campaign, we describe the preparation
of several replacements for the quinazoline scaffold and report these
inhibitors’ biological activities against these parasites.
In doing this, we have identified several potent proliferation inhibitors
for each pathogen, such as 4-((3-chloro-4-((3-fluorobenzyl)oxy)phenyl)amino)-6-(4-((4-methyl-1,4-diazepan-1-yl)sulfonyl)phenyl)quinoline-3-carbonitrile
(NEU-924, 83) for T. cruzi and N-(3-chloro-4-((3-fluorobenzyl)oxy)phenyl)-7-(4-((4-methyl-1,4-diazepan-1-yl)sulfonyl)phenyl)cinnolin-4-amine
(NEU-1017, 68) for L. major and P. falciparum.
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Affiliation(s)
| | | | | | | | | | - Jessey Erath
- ‡Division of Parasitology, Department of Microbiology, New York University School of Medicine, 341 E. 25th St., New York, New York 10010, United States
| | - Norma E Roncal
- §Experimental Therapeutics, Walter Reed Army Institute for Research, 2460 Linden Lane, Silver Spring, Maryland 20910, United States
| | - Patricia J Lee
- §Experimental Therapeutics, Walter Reed Army Institute for Research, 2460 Linden Lane, Silver Spring, Maryland 20910, United States
| | - Susan E Leed
- §Experimental Therapeutics, Walter Reed Army Institute for Research, 2460 Linden Lane, Silver Spring, Maryland 20910, United States
| | - Ana Rodriguez
- ‡Division of Parasitology, Department of Microbiology, New York University School of Medicine, 341 E. 25th St., New York, New York 10010, United States.,⊥Anti-Infectives Screening Core, New York University School of Medicine, New York, New York 10010, United States
| | - Kojo Mensa-Wilmot
- ∥Department of Cellular Biology, University of Georgia, Athens, Georgia 30602, United States
| | - Richard J Sciotti
- §Experimental Therapeutics, Walter Reed Army Institute for Research, 2460 Linden Lane, Silver Spring, Maryland 20910, United States
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Molecular dynamics of the asymmetric dimers of EGFR: Simulations on the active and inactive conformations of the kinase domain. J Mol Graph Model 2015; 58:16-29. [DOI: 10.1016/j.jmgm.2015.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 01/10/2023]
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Truncated structures used in search for new lead compounds and in a retrospective analysis of thienopyrimidine-based EGFR inhibitors. Eur J Med Chem 2015; 94:175-94. [DOI: 10.1016/j.ejmech.2015.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 02/28/2015] [Accepted: 03/02/2015] [Indexed: 12/15/2022]
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Singh H, Singh S, Singla D, Agarwal SM, Raghava GPS. QSAR based model for discriminating EGFR inhibitors and non-inhibitors using Random forest. Biol Direct 2015; 10:10. [PMID: 25880749 PMCID: PMC4372225 DOI: 10.1186/s13062-015-0046-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 03/06/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Epidermal Growth Factor Receptor (EGFR) is a well-characterized cancer drug target. In the past, several QSAR models have been developed for predicting inhibition activity of molecules against EGFR. These models are useful to a limited set of molecules for a particular class like quinazoline-derivatives. In this study, an attempt has been made to develop prediction models on a large set of molecules (~3500 molecules) that include diverse scaffolds like quinazoline, pyrimidine, quinoline and indole. RESULTS We train, test and validate our classification models on a dataset called EGFR10 that contains 508 inhibitors (having inhibition activity IC50 less than 10 nM) and 2997 non-inhibitors. Our Random forest based model achieved maximum MCC 0.49 with accuracy 83.7% on a validation set using 881 PubChem fingerprints. In this study, frequency-based feature selection technique has been used to identify best fingerprints. It was observed that PubChem fingerprints FP380 (C(~O) (~O)), FP579 (O = C-C-C-C), FP388 (C(:C) (:N) (:N)) and FP 816 (ClC1CC(Br)CCC1) are more frequent in the inhibitors in comparison to non-inhibitors. In addition, we created different datasets namely EGFR100 containing inhibitors having IC50 < 100 nM and EGFR1000 containing inhibitors having IC50 < 1000 nM. We trained, test and validate our models on datasets EGFR100 and EGFR1000 datasets and achieved and maximum MCC 0.58 and 0.71 respectively. In addition, models were developed for predicting quinazoline and pyrimidine based EGFR inhibitors. CONCLUSIONS In summary, models have been developed on a large set of molecules of various classes for discriminating EGFR inhibitors and non-inhibitors. These highly accurate prediction models can be used to design and discover novel EGFR inhibitors. In order to provide service to the scientific community, a web server/standalone EGFRpred also has been developed ( http://crdd.osdd.net/oscadd/egfrpred/ ).
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Affiliation(s)
- Harinder Singh
- Bioinformatics Center, Institute of Microbial Technology, Sector 39-A, Chandigarh, India.
| | - Sandeep Singh
- Bioinformatics Center, Institute of Microbial Technology, Sector 39-A, Chandigarh, India.
| | - Deepak Singla
- Bioinformatics Center, Institute of Microbial Technology, Sector 39-A, Chandigarh, India.
| | - Subhash M Agarwal
- Institute of Cytology and Preventive Oncology, Sector 39, Noida, 201301, Uttar Pradesh, India.
| | - Gajendra P S Raghava
- Bioinformatics Center, Institute of Microbial Technology, Sector 39-A, Chandigarh, India.
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Kim Y, Kim M, Park M, Tae J, Baek DJ, Park KD, Choo H. Synthesis of novel dihydropyridothienopyrimidin-4,9-dione derivatives. Molecules 2015; 20:5074-84. [PMID: 25808151 PMCID: PMC6272423 DOI: 10.3390/molecules20035074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/12/2015] [Accepted: 03/13/2015] [Indexed: 11/26/2022] Open
Abstract
A novel molecular scaffold, dihydropyridothienopyrimidin-4,9-dione, was synthesized from benzylamine or p-methoxybenzylamine in six steps involving successive ring closure to form a fused ring system composed of dihydropyridone, thiophene and pyrimidone. The pharmacological versatility of the dihydropyridothenopyrimidin-4,9-dione scaffold was demonstrated by inhibitory activity against metabotropic glutamate receptor subtype 1 (mGluR1), which shows that the title compounds can serve as an interesting scaffold for the discovery of potential bioactive molecules for the treatment of human diseases.
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Affiliation(s)
- Youngjae Kim
- Center for Neuro-Medicine, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 136-791, Korea.
- Department of Chemistry, Yonsei University, Seodaemun-gu, Seoul 120-749, Korea.
| | - Minjoo Kim
- Center for Neuro-Medicine, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 136-791, Korea.
- Department of Chemistry, College of Natural Sciences, Sangmyung University, Seoul 110-743, Korea.
| | - Mooseong Park
- Center for Neuro-Medicine, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 136-791, Korea.
- Department of Biological Chemistry, University of Science and Technology, Youseong-gu, Daejeon 305-350, Korea.
| | - Jinsung Tae
- Department of Biological Chemistry, University of Science and Technology, Youseong-gu, Daejeon 305-350, Korea.
| | - Du-Jong Baek
- Department of Chemistry, College of Natural Sciences, Sangmyung University, Seoul 110-743, Korea.
| | - Ki Duk Park
- Center for Neuro-Medicine, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 136-791, Korea.
- Department of Biological Chemistry, University of Science and Technology, Youseong-gu, Daejeon 305-350, Korea.
| | - Hyunah Choo
- Center for Neuro-Medicine, Korea Institute of Science and Technology, Seongbuk-gu, Seoul 136-791, Korea.
- Department of Biological Chemistry, University of Science and Technology, Youseong-gu, Daejeon 305-350, Korea.
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Kovacs E, Zorn JA, Huang Y, Barros T, Kuriyan J. A structural perspective on the regulation of the epidermal growth factor receptor. Annu Rev Biochem 2015; 84:739-64. [PMID: 25621509 DOI: 10.1146/annurev-biochem-060614-034402] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase that plays a critical role in the pathogenesis of many cancers. The structure of intact forms of this receptor has yet to be determined, but intense investigations of fragments of the receptor have provided a detailed view of its activation mechanism, which we review here. Ligand binding converts the receptor to a dimeric form, in which contacts are restricted to the receptor itself, allowing heterodimerization of the four EGFR family members without direct ligand involvement. Activation of the receptor depends on the formation of an asymmetric dimer of kinase domains, in which one kinase domain allosterically activates the other. Coupling between the extracellular and intracellular domains may involve a switch between alternative crossings of the transmembrane helices, which form dimeric structures. We also discuss how receptor regulation is compromised by oncogenic mutations and the structural basis for negative cooperativity in ligand binding.
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Woodring JL, Patel G, Erath J, Behera R, Lee PJ, Leed SE, Rodriguez A, Sciotti RJ, Mensa-Wilmot K, Pollastri MP. EVALUATION OF AROMATIC 6-SUBSTITUTED THIENOPYRIMIDINES AS SCAFFOLDS AGAINST PARASITES THAT CAUSE TRYPANOSOMIASIS, LEISHMANIASIS, AND MALARIA. MEDCHEMCOMM 2015; 6:339-346. [PMID: 25685309 DOI: 10.1039/c4md00441h] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Target repurposing is a proven method for finding new lead compounds that target Trypanosoma brucei, the causative agent of human African trypanosomiasis. Due to the recent discovery of a lapatinib-derived analog 2 with excellent potency against T. brucei (EC50 = 42 nM) and selectivity over human host cells, we have explored other classes of human tyrosine kinase inhibitor scaffolds in order to expand the range of chemotypes for pursuit. Following library expansion, we found compound 11e to have an EC50 of 84 nM against T. brucei cells while maintaining selectivity over human hepatocytes. In addition, the library was tested against causative agents of Chagas' disease, leishmaniasis, and malaria. Two analogs with sub-micromolar potencies for T. cruzi (4j) and Plasmodium falciparum (11j) were discovered, along with an analog with considerable potency against Leishmania major amastigotes (4e). Besides identifying new and potent protozoan growth inhibitors, these data highlight the value of concurrent screening of a chemical library against different protozoan parasites.
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Affiliation(s)
- Jennifer L Woodring
- Northeastern University Department of Chemistry & Chemical Biology, 360 Huntington Avenue, Boston, MA 02115 USA. Tel: 617-373-2703
| | - Gautam Patel
- Northeastern University Department of Chemistry & Chemical Biology, 360 Huntington Avenue, Boston, MA 02115 USA. Tel: 617-373-2703
| | - Jessey Erath
- New York University School of Medicine, Department of Microbiology, Division of Parasitology, 341 E. 25 St. New York, NY 10010 USA
| | - Ranjan Behera
- University of Georgia, Department of Cellular Biology, Athens, GA 30602 USA
| | - Patricia J Lee
- Experimental Therapeutics, Walter Reed Army Institute for Research,2460 Linden Lane, Silver Spring, MD 20910 USA
| | - Susan E Leed
- Experimental Therapeutics, Walter Reed Army Institute for Research,2460 Linden Lane, Silver Spring, MD 20910 USA
| | - Ana Rodriguez
- New York University School of Medicine, Department of Microbiology, Division of Parasitology, 341 E. 25 St. New York, NY 10010 USA ; Anti-Infectives Screening Core, New York University School of Medicine, New York, NY 10010 USA
| | - Richard J Sciotti
- Experimental Therapeutics, Walter Reed Army Institute for Research,2460 Linden Lane, Silver Spring, MD 20910 USA
| | - Kojo Mensa-Wilmot
- University of Georgia, Department of Cellular Biology, Athens, GA 30602 USA
| | - Michael P Pollastri
- Northeastern University Department of Chemistry & Chemical Biology, 360 Huntington Avenue, Boston, MA 02115 USA. Tel: 617-373-2703
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Littlefield P, Liu L, Mysore V, Shan Y, Shaw DE, Jura N. Structural analysis of the EGFR/HER3 heterodimer reveals the molecular basis for activating HER3 mutations. Sci Signal 2014; 7:ra114. [PMID: 25468994 PMCID: PMC4492339 DOI: 10.1126/scisignal.2005786] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The human epidermal growth factor receptor (HER) tyrosine kinases homo- and heterodimerize to activate downstream signaling pathways. HER3 is a catalytically impaired member of the HER family that contributes to the development of several human malignancies and is mutated in a subset of cancers. HER3 signaling depends on heterodimerization with a catalytically active partner, in particular epidermal growth factor receptor (EGFR) (the founding family member, also known as HER1) or HER2. The activity of homodimeric complexes of catalytically active HER family members depends on allosteric activation between the two kinase domains. To determine the structural basis for HER3 signaling through heterodimerization with a catalytically active HER family member, we solved the crystal structure of the heterodimeric complex formed by the isolated kinase domains of EGFR and HER3. The structure showed HER3 as an allosteric activator of EGFR and revealed a conserved role of the allosteric mechanism in activation of HER family members through heterodimerization. To understand the effects of cancer-associated HER3 mutations at the molecular level, we solved the structures of two kinase domains of HER3 mutants, each in a heterodimeric complex with the kinase domain of EGFR. These structures, combined with biochemical analysis and molecular dynamics simulations, indicated that the cancer-associated HER3 mutations enhanced the allosteric activator function of HER3 by redesigning local interactions at the dimerization interface.
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Affiliation(s)
- Peter Littlefield
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Lijun Liu
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | | | - Yibing Shan
- D. E. Shaw Research, New York, NY 10036, USA
| | - David E Shaw
- D. E. Shaw Research, New York, NY 10036, USA. Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA. Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA.
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James KA, Verkhivker GM. Structure-based network analysis of activation mechanisms in the ErbB family of receptor tyrosine kinases: the regulatory spine residues are global mediators of structural stability and allosteric interactions. PLoS One 2014; 9:e113488. [PMID: 25427151 PMCID: PMC4245119 DOI: 10.1371/journal.pone.0113488] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 10/27/2014] [Indexed: 12/27/2022] Open
Abstract
The ErbB protein tyrosine kinases are among the most important cell signaling families and mutation-induced modulation of their activity is associated with diverse functions in biological networks and human disease. We have combined molecular dynamics simulations of the ErbB kinases with the protein structure network modeling to characterize the reorganization of the residue interaction networks during conformational equilibrium changes in the normal and oncogenic forms. Structural stability and network analyses have identified local communities integrated around high centrality sites that correspond to the regulatory spine residues. This analysis has provided a quantitative insight to the mechanism of mutation-induced “superacceptor” activity in oncogenic EGFR dimers. We have found that kinase activation may be determined by allosteric interactions between modules of structurally stable residues that synchronize the dynamics in the nucleotide binding site and the αC-helix with the collective motions of the integrating αF-helix and the substrate binding site. The results of this study have pointed to a central role of the conserved His-Arg-Asp (HRD) motif in the catalytic loop and the Asp-Phe-Gly (DFG) motif as key mediators of structural stability and allosteric communications in the ErbB kinases. We have determined that residues that are indispensable for kinase regulation and catalysis often corresponded to the high centrality nodes within the protein structure network and could be distinguished by their unique network signatures. The optimal communication pathways are also controlled by these nodes and may ensure efficient allosteric signaling in the functional kinase state. Structure-based network analysis has quantified subtle effects of ATP binding on conformational dynamics and stability of the EGFR structures. Consistent with the NMR studies, we have found that nucleotide-induced modulation of the residue interaction networks is not limited to the ATP site, and may enhance allosteric cooperativity with the substrate binding region by increasing communication capabilities of mediating residues.
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Affiliation(s)
- Kevin A. James
- School of Computational Sciences and Crean School of Health and Life Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Gennady M. Verkhivker
- School of Computational Sciences and Crean School of Health and Life Sciences, Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
- Department of Pharmacology, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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Improved and Scalable Preparation of 6-Bromo-4-Chlorothieno[2,3-d]Pyrimidine. Chem Heterocycl Compd (N Y) 2014. [DOI: 10.1007/s10593-014-1579-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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