1
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Zeng Q, Meng G, Zhao B, Lin H, Guan Y, Qin X, Yuan Y, Li Y, Wang Q. Peptide Drug Design Using Alchemical Free Energy Calculation: An Application and Validation on Agonists of Ghrelin Receptor. J Chem Inf Model 2024; 64:4863-4876. [PMID: 38836743 DOI: 10.1021/acs.jcim.4c00414] [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: 06/06/2024]
Abstract
With recent large-scale applications and validations, the relative binding free energy (RBFE) calculated using alchemical free energy methods has been proven to be an accurate measure to probe the binding of small-molecule drug candidates. On the other hand, given the flexibility of peptides, it is of great interest to find out whether sufficient sampling could be achieved within the typical time scale of such calculation, and a similar level of accuracy could be reached for peptide drugs. However, the systematic evaluation of such calculations on protein-peptide systems has been less reported. Most reported studies of peptides were restricted to a limited number of data points or lacking experimental support. To demonstrate the applicability of the alchemical free energy method for protein-peptide systems in a typical real-world drug discovery project, we report an application of the thermodynamic integration (TI) method to the RBFE calculation of ghrelin receptor and its peptide agonists. Along with the calculation, the synthesis and in vitro EC50 activity of relamorelin and 17 new peptide derivatives were also reported. A cost-effective criterion to determine the data collection time was proposed for peptides in the TI simulation. The average of three TI repeats yielded a mean absolute error of 0.98 kcal/mol and Pearson's correlation coefficient (R) of 0.77 against the experimental free energy derived from the in vitro EC50 activity, showing good repeatability of the proposed method and a slightly better agreement than the results obtained from the arbitrary time frames up to 20 ns. Although it is limited by having one target and a deduced binding pose, we hope that this study can add some insights into alchemical free energy calculation of protein-peptide systems, providing theoretical assistance to the development of peptide drugs.
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Affiliation(s)
- Qin Zeng
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Guangpeng Meng
- Chengdu Sintanovo Biotechnology Co., Ltd., Chengdu 610000, China
| | - Bingyu Zhao
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Haodian Lin
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Yuqing Guan
- Chengdu Sintanovo Biotechnology Co., Ltd., Chengdu 610000, China
| | - Xiaobin Qin
- Chengdu Sintanovo Biotechnology Co., Ltd., Chengdu 610000, China
| | - Yu Yuan
- Chengdu Sintanovo Biotechnology Co., Ltd., Chengdu 610000, China
| | - Yuanbo Li
- Chengdu Sintanovo Biotechnology Co., Ltd., Chengdu 610000, China
| | - Qiantao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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2
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Pandey V, Adhikrao PA, Motiram GM, Yadav N, Jagtap U, Kumar G, Paul A. Biaryl carboxamide-based peptidomimetics analogs as potential pancreatic lipase inhibitors for treating obesity. Arch Pharm (Weinheim) 2024; 357:e2300503. [PMID: 38251950 DOI: 10.1002/ardp.202300503] [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: 09/13/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
A series of 1,1'-biphenyl-3-carboxamide and furan-phenyl-carboxamide analogs were synthesized using an optimized scheme and confirmed by 1H and 13C nuclear magnetic resonance and high-resolution mass spectrometry techniques. The synthesized peptidomimetics analogs were screened in vitro to understand the inhibitory potential of pancreatic lipase (PL). Analogs were assessed for the PL inhibitory activity based on interactions, geometric complementarity, and docking score. Among the synthesized analogs, 9, 29, and 24 were found to have the most potent PL inhibitory activity with IC50 values of 3.87, 4.95, and 5.34 µM, respectively, compared to that of the standard drug, that is, orlistat, which inhibits PL with an IC50 value of 0.99 µM. The most potent analog, 9, exhibited a competitive-type inhibition with an inhibition constant (Ki) of 2.72 µM. In silico molecular docking of analog 9 with the PL (PDB ID:1LPB) showed a docking score of -11.00 kcal/mol. Analog 9 formed crucial hydrogen bond interaction with Ser152, His263, π-cation interaction with Asp79, Arg256, and π-π stacking with Phe77, Tyr114 at the protein's active site. The molecular dynamic simulation confirmed that analog 9 forms stable interactions with PL at the end of 200 ns with root mean square deviation values of 2.5 and 6 Å. No toxicity was observed for analog 9 (concentration range of 1-20 µM) when tested by MTT assay in RAW 264.7 cells.
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Affiliation(s)
- Vikash Pandey
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Patil A Adhikrao
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Gudle M Motiram
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Nisha Yadav
- Laboratory of Natural Product Chemistry, Department of Pharmacy, Birla Institute of Technology and Science, Pilani (Pilani Campus), Pilani, Rajasthan, India
| | - Utkarsh Jagtap
- Laboratory of Natural Product Chemistry, Department of Pharmacy, Birla Institute of Technology and Science, Pilani (Pilani Campus), Pilani, Rajasthan, India
| | - Gautam Kumar
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Atish Paul
- Laboratory of Natural Product Chemistry, Department of Pharmacy, Birla Institute of Technology and Science, Pilani (Pilani Campus), Pilani, Rajasthan, India
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3
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Piserchio A, Isiorho EA, Dalby KN, Ghose R. Structure of the complex between calmodulin and a functional construct of eukaryotic elongation factor 2 kinase bound to an ATP-competitive inhibitor. J Biol Chem 2023:104813. [PMID: 37172726 DOI: 10.1016/j.jbc.2023.104813] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/15/2023] Open
Abstract
The calmodulin-activated α-kinase, eukaryotic elongation factor 2 kinase (eEF-2K) serves as a master regulator of translational elongation by specifically phosphorylating and reducing the ribosome-affinity of the guanosine triphosphatase, eukaryotic elongation factor 2 (eEF-2). Given its critical role in a fundamental cellular process, dysregulation of eEF-2K has been implicated in several human diseases, including those of the cardiovascular system, chronic neuropathies, and many cancers, making it a critical pharmacological target. In the absence of high-resolution structural information, high-throughput screening efforts have yielded small-molecule candidates that show promise as eEF-2K antagonists. Principal among these is the ATP-competitive pyrimido-pyrimidinedione inhibitor, A-484954, which shows high specificity towards eEF-2K relative to a panel of "typical" protein kinases. A-484954 has been shown to have some degree of efficacy in animal models of several disease states. It has also been widely deployed as a reagent in eEF-2K-specific biochemical and cell-biological studies. However, given the absence of structural information, the precise mechanism of the A-484954-mediated inhibition of eEF-2K has remained obscure. Leveraging our identification of the calmodulin-activatable catalytic core of eEF-2K and our recent determination of its long-elusive structure, here we present the structural basis for its specific inhibition by A-484954. This structure, which represents the first for an inhibitor-bound catalytic domain of a member of the α-kinase family, enables rationalization of the existing structure-activity relationship data for A-484954 variants and lays the groundwork for further optimization of this scaffold to attain enhanced specificity/potency against eEF-2K.
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Affiliation(s)
- Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031
| | - Eta A Isiorho
- Macromolecular Crystallization Facility, CUNY ASRC, New York, NY 10031
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, the University of Texas, Austin, TX 78712; Interdisciplinary Life Sciences Graduate Program, the University of Texas, Austin, TX 78712.
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031; PhD Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016; PhD Program in Chemistry, The Graduate Center of CUNY, New York, NY 10016; PhD Program in Physics, The Graduate Center of CUNY, New York, NY 10016.
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4
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Klupt KA, Jia Z. eEF2K Inhibitor Design: The Progression of Exemplary Structure-Based Drug Design. Molecules 2023; 28:molecules28031095. [PMID: 36770760 PMCID: PMC9921739 DOI: 10.3390/molecules28031095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/05/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
The α-kinase, eEF2K, phosphorylates the threonine 56 residue of eEF2 to inhibit global peptide elongation (protein translation). As a master regulator of protein synthesis, in combination with its unique atypical kinase active site, investigations into the targeting of eEF2K represents a case of intense structure-based drug design that includes the use of modern computational techniques. The role of eEF2K is incredibly diverse and has been scrutinized in several different diseases including cancer and neurological disorders-with numerous studies inhibiting eEF2K as a potential treatment option, as described in this paper. Using available crystal structures of related α-kinases, particularly MHCKA, we report how homology modeling has been used to improve inhibitor design and efficacy. This review presents an overview of eEF2K related drug discovery efforts predating from the 1990's, to more recent in vivo studies in rat models. We also provide the reader with a basic introduction to several approaches and software programs used to undertake such drug discovery campaigns. With the recent exciting publication of an eEF2K crystal structure, we present our view regarding the future of eEF2K drug discovery.
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Aranda J, Wieczór M, Terrazas M, Brun-Heath I, Orozco M. Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2. CHEM CATALYSIS 2022; 2:1084-1099. [PMID: 35465139 PMCID: PMC9016896 DOI: 10.1016/j.checat.2022.03.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/08/2022] [Accepted: 03/24/2022] [Indexed: 01/21/2023]
Abstract
We combine molecular dynamics, statistical mechanics, and hybrid quantum mechanics/molecular mechanics simulations to describe mechanistically the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp). Our study analyzes the binding mode of both natural triphosphate substrates as well as remdesivir triphosphate (the active form of drug), which is bound preferentially over ATP by RdRp while being poorly recognized by human RNA polymerase II (RNA Pol II). A comparison of incorporation rates between natural and antiviral nucleotides shows that remdesivir is incorporated more slowly into the nascent RNA compared with ATP, leading to an RNA duplex that is structurally very similar to an unmodified one, arguing against the hypothesis that remdesivir is a competitive inhibitor of ATP. We characterize the entire mechanism of reaction, finding that viral RdRp is highly processive and displays a higher catalytic rate of incorporation than human RNA Pol II. Overall, our study provides the first detailed explanation of the replication mechanism of RdRp.
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Affiliation(s)
- Juan Aranda
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Milosz Wieczór
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Montserrat Terrazas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Inorganic and Organic Chemistry, Section of Organic Chemistry, IBUB, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Departament de Bioquímica i Biomedicine, Universitat de Barcelona, Universitat de Barcelona, Avinguda Diagonal 645, 08028 Barcelona, Spain
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6
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Onder FC, Durdagi S, Kahraman N, Uslu TN, Kandemir H, Atici EB, Ozpolat B, Ay M. Novel inhibitors of eukaryotic elongation factor 2 kinase: In silico, synthesis and in vitro studies. Bioorg Chem 2021; 116:105296. [PMID: 34488125 DOI: 10.1016/j.bioorg.2021.105296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Eukaryotic elongation factor 2 kinase (eEF2K) is an unusual alpha kinase whose expression is highly upregulated in various cancers and contributes to tumor growth, metastasis, and progression. More importantly, eEF2K expression is associated with poor clinical outcome and shorter patient survival in breast, lung and ovarian cancers. Therefore, eEF2K is an emerging molecular target for development of novel targeted therapeutics and precision medicine in solid cancers. Currently, there are not any available potent and specific eEF2K inhibitors for clinical translation. In this study, we designed and synthesized a series of novel compounds with coumarin scaffold with various substitutions and investigated their effects in inhibiting eEF2K activity using in silico approaches and in vitro studies in breast cancer cells. We utilized an amide substitution at position 3 on the coumarin ring with their pharmacologically active groups containing pyrrolidine, piperidine, morpholine and piperazine groups with (CH2)2 bridged for aliphatic amides. Due to their ability to form covalent binding to the target enzyme, we also investigated the effects of boron containing groups on functionalized coumarin ring (3 compounds) and designed novel aliphatic and aromatic derivatives of coumarin scaffolds (10 compounds) and phenyl ring with boron groups (4 compounds). The Glide/SP module of the Maestro molecular modeling package was used to perform in silico analysis and molecular docking studies. According to our combined results, structure activity relationship (SAR) was performed in detail. Among the newly designed, synthesized, and tested compounds, our in vitro findings revealed that several compounds displayed a highly effective eEF2K inhibition at submicromolar concentrations in in vitro breast cancer cells. In conclusion, we identified novel compounds that can be used as eEF2K inhibitors and that they should be further evaluated by in vivo preclinical tumor models studies for antitumor efficacy and clinical translation.
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Affiliation(s)
- Ferah Comert Onder
- Department of Medical Biology, Faculty of Medicine, Çanakkale Onsekiz Mart University, 17020 Çanakkale, Turkey; Natural Products and Drug Research Laboratory, Department of Chemistry, Faculty of Science and Arts, Çanakkale Onsekiz Mart University, 17020 Çanakkale, Turkey; Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, 34734 İstanbul, Turkey
| | - Nermin Kahraman
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States
| | - Tugce Nur Uslu
- Department of Chemistry, Tekirdağ Namık Kemal University, Tekirdağ, Turkey
| | - Hakan Kandemir
- Department of Chemistry, Tekirdağ Namık Kemal University, Tekirdağ, Turkey
| | | | - Bulent Ozpolat
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States; Department of Experimental Therapeutics and Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States.
| | - Mehmet Ay
- Natural Products and Drug Research Laboratory, Department of Chemistry, Faculty of Science and Arts, Çanakkale Onsekiz Mart University, 17020 Çanakkale, Turkey.
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7
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Piserchio A, Long K, Lee K, Kumar EA, Abzalimov R, Dalby KN, Ghose R. Structural dynamics of the complex of calmodulin with a minimal functional construct of eukaryotic elongation factor 2 kinase and the role of Thr348 autophosphorylation. Protein Sci 2021; 30:1221-1234. [PMID: 33890716 DOI: 10.1002/pro.4087] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 04/15/2021] [Indexed: 12/31/2022]
Abstract
The calmodulin (CaM) activated α-kinase, eukaryotic elongation factor 2 kinase (eEF-2K), plays a central role in regulating translational elongation by phosphorylating eukaryotic elongation factor 2 (eEF-2), thereby reducing its ability to associate with the ribosome and suppressing global protein synthesis. Using TR (for truncated), a minimal functional construct of eEF-2K, and utilizing hydrogen/deuterium exchange mass spectrometry (HXMS), solution-state nuclear magnetic resonance (NMR) and biochemical approaches, we investigate the conformational changes accompanying complex formation between Ca2+ -CaM and TR and the effects of autophosphorylation of the latter at Thr348, its primary regulatory site. Our results suggest that a CaM C-lobe surface, complementary to the one involved in recognizing the calmodulin-binding domain (CBD) of TR, provides a secondary TR-interaction platform. CaM helix F, which is part of this secondary surface, responds to both Thr348 phosphorylation and pH changes, indicating its integration into an allosteric network that encompasses both components of the Ca2+ -CaM•TR complex. Solution NMR data suggest that CaMH107K , which carries a helix F mutation, is compromised in its ability to drive the conformational changes in TR necessary to enable efficient Thr348 phosphorylation. Biochemical studies confirm the diminished capacity of CaMH107K to induce TR autophosphorylation compared to wild-type CaM.
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Affiliation(s)
- Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York, USA
| | - Kimberly Long
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas, USA
| | - Kwangwoon Lee
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York, USA.,Graduate Programs in Biochemistry, The Graduate Center of CUNY, New York, New York, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Eric A Kumar
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas, USA
| | - Rinat Abzalimov
- Biomolecular Mass Spectrometry Facility, CUNY ASRC, New York, New York, USA
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas, USA.,Graduate Program in Cell and Molecular Biology, University of Texas, Austin, Texas, USA
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York, USA.,Graduate Programs in Biochemistry, The Graduate Center of CUNY, New York, New York, USA.,Graduate Programs in Chemistry, The Graduate Center of CUNY, New York, New York, USA.,Graduate Programs in Physics, The Graduate Center of CUNY, New York, New York, USA
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8
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Comert Onder F, Kahraman N, Bellur Atici E, Cagir A, Kandemir H, Tatar G, Taskin Tok T, Kara G, Karliga B, Durdagi S, Ay M, Ozpolat B. Target-Driven Design of a Coumarinyl Chalcone Scaffold Based Novel EF2 Kinase Inhibitor Suppresses Breast Cancer Growth In Vivo. ACS Pharmacol Transl Sci 2021; 4:926-940. [PMID: 33860211 DOI: 10.1021/acsptsci.1c00030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Indexed: 11/28/2022]
Abstract
Eukaryotic elongation factor 2 kinase (eEF-2K) is an unusual alpha kinase involved in protein synthesis through phosphorylation of elongation factor 2 (EF2). eEF-2K is highly overexpressed in breast cancer, and its activity is associated with significantly shortened patient survival and proven to be a potential molecular target in breast cancer. The crystal structure of eEF-2K remains unknown, and there is no potent, safe, and effective inhibitor available for clinical applications. We designed and synthesized several generations of potential inhibitors. The effect of the inhibitors at the binding pocket of eEF-2K was analyzed after developing a 3D target model by using a domain of another α-kinase called myosin heavy-chain kinase A (MHCKA) that closely resembles eEF-2K. In silico studies showed that compounds with a coumarin-chalcone core have high predicted binding affinities for eEF-2K. Using in vitro studies in highly aggressive and invasive (MDA-MB-436, MDA-MB-231, and BT20) and noninvazive (MCF-7) breast cancer cells, we identified a lead compound that was highly effective in inhibiting eEF-2K activity at submicromolar concentrations and at inhibiting cell proliferation by induction of apoptosis with no toxicity in normal breast epithelial cells. In vivo systemic administration of the lead compound encapsulated in single lipid-based liposomal nanoparticles twice a week significantly suppressed growth of MDA-MB-231 tumors in orthotopic breast cancer models in nude mice with no observed toxicity. In conclusion, our study provides a highly potent and in vivo effective novel small-molecule eEF-2K inhibitor that may be used as a molecularly targeted therapy breast cancer or other eEF-2K-dependent tumors.
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Affiliation(s)
- Ferah Comert Onder
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 422, Houston, Texas 77030, United States.,Department of Medical Biology, Çanakkale Onsekiz Mart University, Faculty of Medicine, 17020 Canakkale, Turkey.,Department of Chemistry, Natural Products and Drug Research Laboratory, Faculty of Science and Arts, Çanakkale Onsekiz Mart University, 17020 Canakkale, Turkey
| | - Nermin Kahraman
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 422, Houston, Texas 77030, United States
| | | | - Ali Cagir
- Izmir Institute of Technology, Department of Chemistry, Bioorganic and Medicinal Chemistry Laboratory, 35430 Urla, Turkey
| | - Hakan Kandemir
- Tekirdag Namik Kemal University, Department of Chemistry, 59030 Tekirdag, Turkey
| | - Gizem Tatar
- Gaziantep University, Institute of Health Sciences, Department of Bioinformatics and Computational Biology, 27310 Gaziantep, Turkey
| | - Tugba Taskin Tok
- Gaziantep University, Institute of Health Sciences, Department of Bioinformatics and Computational Biology, 27310 Gaziantep, Turkey.,Gaziantep University, Faculty of Arts and Sciences, Department of Chemistry, 27310 Gaziantep, Turkey
| | - Goknur Kara
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 422, Houston, Texas 77030, United States
| | | | - Serdar Durdagi
- Department of Biophysics, School of Medicine, Computational Biology and Molecular Simulations Laboratory, Bahcesehir University, 34734 Istanbul, Turkey
| | - Mehmet Ay
- Department of Chemistry, Natural Products and Drug Research Laboratory, Faculty of Science and Arts, Çanakkale Onsekiz Mart University, 17020 Canakkale, Turkey
| | - Bulent Ozpolat
- Department of Experimental Therapeutics, The University of Texas, MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 422, Houston, Texas 77030, United States.,Center for RNA Interference and Non-Coding RNAs, The University of Texas, MD Anderson Cancer Center, Houston, Texas 77030, United States
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9
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The promise and current status of CDK12/13 inhibition for the treatment of cancer. Future Med Chem 2020; 13:117-141. [PMID: 33295810 DOI: 10.4155/fmc-2020-0240] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
CDK12 and CDK13 are Ser/Thr protein kinases that regulate transcription and co-transcriptional processes. Genetic silencing of CDK12 is associated with genomic instability in a variety of cancers, including difficult-to-treat breast, ovarian, colorectal, brain and pancreatic cancers, and is synthetic lethal with PARP, MYC or EWS/FLI inhibition. CDK13 is amplified in hepatocellular carcinoma. Consequently, selective CDK12/13 inhibitors constitute powerful research tools as well as promising anti-cancer therapeutics, either alone or in combination therapy. Herein the authors discuss the role of CDK12 and CDK13 in normal and cancer cells, describe their utility as a biomarker and therapeutic target, review the medicinal chemistry optimization of existing CDK12/13 inhibitors and outline strategies for the rational design of CDK12/13 selective inhibitors.
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10
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Lee K, Kumar EA, Dalby KN, Ghose R. The role of calcium in the interaction between calmodulin and a minimal functional construct of eukaryotic elongation factor 2 kinase. Protein Sci 2020; 28:2089-2098. [PMID: 31626716 DOI: 10.1002/pro.3753] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/13/2019] [Accepted: 10/15/2019] [Indexed: 12/13/2022]
Abstract
Eukaryotic elongation factor 2 kinase (eEF-2K) regulates protein synthesis by phosphorylating eukaryotic elongation factor 2 (eEF-2), thereby reducing its affinity for the ribosome and suppressing global translational elongation rates. eEF-2K is regulated by calmodulin (CaM) through a mechanism that is distinct from that of other CaM-regulated kinases. We had previously identified a minimal construct of eEF-2K (TR) that is activated similarly to the wild-type enzyme by CaM in vitro and retains its ability to phosphorylate eEF-2 efficiently in cells. Here, we employ solution nuclear magnetic resonance techniques relying on Ile δ1-methyls of TR and Ile δ1- and Met ε-methyls of CaM, as probes of their mutual interaction and the influence of Ca2+ thereon. We find that in the absence of Ca2+ , CaM exclusively utilizes its C-terminal lobe (CaMC ) to engage the N-terminal CaM-binding domain (CBD) of TR in a high-affinity interaction. Avidity resulting from additional weak interactions of TR with the Ca2+ -loaded N-terminal lobe of CaM (CaMN ) at increased Ca2+ levels serves to enhance the affinity further. These latter interactions under Ca2+ saturation result in minimal perturbations in the spectra of TR in the context of its complex with CaM, suggesting that the latter is capable of driving TR to its final, presumably active conformation, in the Ca2+ -free state. Our data are consistent with a scenario in which Ca2+ enhances the affinity of the TR/CaM interactions, resulting in the increased effective concentration of the CaM-bound species without significantly modifying the conformation of TR within the final, active complex.
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Affiliation(s)
- Kwangwoon Lee
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York.,Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, New York
| | - Eric A Kumar
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas.,Graduate Program in Cell and Molecular Biology, University of Texas, Austin, Texas
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York.,Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, New York.,Graduate Program in Chemistry, The Graduate Center of CUNY, New York, New York.,Graduate Program in Physics, The Graduate Center of CUNY, New York, New York
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11
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Comert Onder F, Durdagi S, Sahin K, Ozpolat B, Ay M. Design, Synthesis, and Molecular Modeling Studies of Novel Coumarin Carboxamide Derivatives as eEF-2K Inhibitors. J Chem Inf Model 2020; 60:1766-1778. [PMID: 32027127 DOI: 10.1021/acs.jcim.9b01083] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Eukaryotic elongation factor-2 kinase (eEF-2K) is an unusual alpha kinase commonly upregulated in various human cancers, including breast, pancreatic, lung, and brain tumors. We have demonstrated that eEF-2K is relevant to poor prognosis and shorter patient survival in breast and lung cancers and validated it as a molecular target using genetic methods in related in vivo tumor models. Although several eEF-2K inhibitors have been published, none of them have shown to be potent and specific enough for translation into clinical trials. Therefore, development of highly effective novel inhibitors targeting eEF-2K is needed for clinical applications. However, currently, the crystal structure of eEF-2K is not known, limiting the efforts for designing novel inhibitor compounds. Therefore, using homology modeling of eEF-2K, we designed and synthesized novel coumarin-3-carboxamides including compounds A1, A2, and B1-B4 and evaluated their activity by performing in silico analysis and in vitro biological assays in breast cancer cells. The Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) area results showed that A1 and A2 have interaction energies with eEF-2K better than those of B1-B4 compounds. Our in vitro results indicated that compounds A1 and A2 were highly effective in inhibiting eEF-2K at 1.0 and 2.5 μM concentrations compared to compounds B1-B4, supporting the in silico findings. In conclusion, the results of this study suggest that our homology modeling along with in silico analysis may be effectively used to design inhibitors for eEF-2K. Our newly synthesized compounds A1 and A2 may be used as novel eEF-2K inhibitors with potential therapeutic applications.
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Affiliation(s)
- Ferah Comert Onder
- Department of Chemistry, Faculty of Science and Arts, Natural Products and Drug Research Laboratory, Canakkale Onsekiz Mart University, 17020 Canakkale, Turkey.,Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 422, Houston, Texas 77030, United States
| | - Serdar Durdagi
- Department of Biophysics, School of Medicine, Computational Biology and Molecular Simulations Laboratory, Bahcesehir University, Kadikoy, 34734 Istanbul, Turkey
| | - Kader Sahin
- Department of Biophysics, School of Medicine, Computational Biology and Molecular Simulations Laboratory, Bahcesehir University, Kadikoy, 34734 Istanbul, Turkey
| | - Bulent Ozpolat
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 422, Houston, Texas 77030, United States.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - Mehmet Ay
- Department of Chemistry, Faculty of Science and Arts, Natural Products and Drug Research Laboratory, Canakkale Onsekiz Mart University, 17020 Canakkale, Turkey
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12
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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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13
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What is the impact of eukaryotic elongation factor 2 kinase on cancer: A systematic review. Eur J Pharmacol 2019; 857:172470. [DOI: 10.1016/j.ejphar.2019.172470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 06/08/2019] [Accepted: 06/17/2019] [Indexed: 11/19/2022]
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14
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Piserchio A, Will N, Giles DH, Hajredini F, Dalby KN, Ghose R. Solution Structure of the Carboxy-Terminal Tandem Repeat Domain of Eukaryotic Elongation Factor 2 Kinase and Its Role in Substrate Recognition. J Mol Biol 2019; 431:2700-2717. [PMID: 31108082 PMCID: PMC6599559 DOI: 10.1016/j.jmb.2019.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/15/2019] [Accepted: 05/12/2019] [Indexed: 12/31/2022]
Abstract
Eukaryotic elongation factor 2 kinase (eEF-2K), an atypical calmodulin-activated protein kinase, regulates translational elongation by phosphorylating its substrate, eukaryotic elongation factor 2 (eEF-2), thereby reducing its affinity for the ribosome. The activation and activity of eEF-2K are critical for survival under energy-deprived conditions and is implicated in a variety of essential physiological processes. Previous biochemical experiments have indicated that the binding site for the substrate eEF-2 is located in the C-terminal domain of eEF-2K, a region predicted to harbor several α-helical repeats. Here, using NMR methodology, we have determined the solution structure of a C-terminal fragment of eEF-2K, eEF-2K562-725 that encodes two α-helical repeats. The structure of eEF-2K562-725 shows signatures characteristic of TPR domains and of their SEL1-like sub-family. Furthermore, using the analyses of NMR spectral perturbations and ITC measurements, we have localized the eEF-2 binding site on eEF-2K562-725. We find that eEF-2K562-725 engages eEF-2 with an affinity comparable to that of the full-length enzyme. Furthermore, eEF-2K562-725 is able to inhibit the phosphorylation of eEF-2 by full-length eEF-2K in trans. Our present studies establish that eEF-2K562-725 encodes the major elements necessary to enable the eEF-2K/eEF-2 interactions.
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Affiliation(s)
- Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, NewYork, NY 10031, USA
| | - Nathan Will
- Department of Chemistry and Biochemistry, The City College of New York, NewYork, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
| | - David H Giles
- Graduate Program in Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA
| | - Fatlum Hajredini
- Department of Chemistry and Biochemistry, The City College of New York, NewYork, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
| | - Kevin N Dalby
- Graduate Program in Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA; Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, TX 78712, USA
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, NewYork, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA; Graduate Program in Chemistry, The Graduate Center of CUNY, New York, NY 10016, USA; Graduate Program in Physics, The Graduate Center of CUNY, New York, NY 10016, USA.
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15
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Will N, Lee K, Hajredini F, Giles DH, Abzalimov RR, Clarkson M, Dalby KN, Ghose R. Structural Dynamics of the Activation of Elongation Factor 2 Kinase by Ca 2+-Calmodulin. J Mol Biol 2018; 430:2802-2821. [PMID: 29800565 DOI: 10.1016/j.jmb.2018.05.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/16/2018] [Accepted: 05/16/2018] [Indexed: 11/18/2022]
Abstract
Eukaryotic elongation factor 2 kinase (eEF-2K), the only known calmodulin (CaM)-activated α-kinase, phosphorylates eukaryotic elongation factor 2 (eEF-2) on a specific threonine (Thr-56) diminishing its affinity for the ribosome and reducing the rate of nascent chain elongation during translation. Despite its critical cellular role, the precise mechanisms underlying the CaM-mediated activation of eEF-2K remain poorly defined. Here, employing a minimal eEF-2K construct (TR) that exhibits activity comparable to the wild-type enzyme and is fully activated by CaM in vitro and in cells, and using a variety of complimentary biophysical techniques in combination with computational modeling, we provide a structural mechanism by which CaM activates eEF-2K. Native mass analysis reveals that CaM, with two bound Ca2+ ions, forms a stoichiometric 1:1 complex with TR. Chemical crosslinking mass spectrometry and small-angle X-ray scattering measurements localize CaM near the N-lobe of the TR kinase domain and the spatially proximal C-terminal helical repeat. Hydrogen/deuterium exchange mass spectrometry and methyl NMR indicate that the conformational changes induced on TR by the engagement of CaM are not localized but are transmitted to remote regions that include the catalytic site and the functionally important phosphate binding pocket. The structural insights obtained from the present analyses, together with our previously published kinetics data, suggest that TR, and by inference, wild-type eEF-2K, upon engaging CaM undergoes a conformational transition resulting in a state that is primed to efficiently auto-phosphorylate on the primary activating T348 en route to full activation.
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Affiliation(s)
- Nathan Will
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
| | - Kwangwoon Lee
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
| | - Fatlum Hajredini
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA
| | - David H Giles
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, TX 78712, USA
| | - Rinat R Abzalimov
- Biomolecular Mass Spectrometry Facility, CUNY ASRC, New York, NY 10031, USA
| | - Michael Clarkson
- Molecular Structures Core, University of Arizona, Tucson, AZ 85721, USA
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, TX 78712, USA; Graduate Program in Cell and Molecular Biology, University of Texas, Austin, TX 78712, USA.
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of CUNY, New York, NY 10016, USA; Graduate Program in Chemistry, The Graduate Center of CUNY, New York, NY 10016, USA; Graduate Program in Physics, The Graduate Center of CUNY, New York, NY 10016, USA.
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16
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Progress with covalent small-molecule kinase inhibitors. Drug Discov Today 2018; 23:727-735. [PMID: 29337202 DOI: 10.1016/j.drudis.2018.01.035] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/23/2017] [Accepted: 01/09/2018] [Indexed: 01/07/2023]
Abstract
With reduced risk of toxicity and high selectivity, covalent small-molecule kinase inhibitors (CSKIs) have emerged rapidly. Through the lens of structural system pharmacology, here we review this rapid progress by considering design strategies and the challenges and opportunities offered by current CSKIs.
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17
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Abstract
In the history of therapeutics, covalent drugs occupy a very distinct category. While representing a significant fraction of the drugs on the market, very few have been deliberately designed to interact covalently with their biological target. In this review, the prevalence of covalent drugs will first be briefly covered, followed by an introduction to their mechanisms of action and more detailed discussions of their discovery and the development of safe and efficient covalent enzyme inhibitors. All stages of a drug discovery program will be covered, from target considerations to lead optimization, strategies to tune reactivity and computational methods. The goal of this article is to provide an overview of the field and to outline good practices that are needed for the proper assessment and development of covalent inhibitors as well as a good understanding of the potential and limitations of current computational methods for the design of covalent drugs.
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Affiliation(s)
- Stephane De Cesco
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montréal, Québec H3A 0B8, Canada
| | - Jerry Kurian
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montréal, Québec H3A 0B8, Canada
| | - Caroline Dufresne
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montréal, Québec H3A 0B8, Canada
| | - Anthony K Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montréal, Québec H3A 0B8, Canada
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montréal, Québec H3A 0B8, Canada.
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18
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Will N, Piserchio A, Snyder I, Ferguson SB, Giles DH, Dalby KN, Ghose R. Structure of the C-Terminal Helical Repeat Domain of Eukaryotic Elongation Factor 2 Kinase. Biochemistry 2016; 55:5377-86. [PMID: 27571275 DOI: 10.1021/acs.biochem.6b00711] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Eukaryotic elongation factor 2 kinase (eEF-2K) phosphorylates its only known physiological substrate, elongation factor 2 (eEF-2), which reduces the affinity of eEF-2 for the ribosome and results in an overall reduction in protein translation rates. The C-terminal region of eEF-2K, which is predicted to contain several SEL-1-like helical repeats (SLRs), is required for the phosphorylation of eEF-2. Using solution nuclear magnetic resonance methodology, we have determined the structure of a 99-residue fragment from the extreme C-terminus of eEF-2K (eEF-2K627-725) that encompasses a region previously suggested to be essential for eEF-2 phosphorylation. eEF-2K627-725 contains four helices, of which the first (αI) is flexible, and does not pack stably against the ordered helical core formed by the last three helices (αII-αIV). The helical core is structurally similar to members of the tetratricopeptide repeat (TPR) family that includes SLRs. The two penultimate helices, αII and αIII, comprise the TPR, and the last helix, αIV, appears to have a capping function. The eEF-2K627-725 structure illustrates that the C-terminal deletion that was shown to abolish eEF-2 phosphorylation does so by destabilizing αIV and, therefore, the helical core. Indeed, mutation of two conserved C-terminal tyrosines (Y712A/Y713A) in eEF-2K previously shown to abolish eEF-2 phosphorylation leads to the unfolding of eEF-2K627-725. Preliminary functional analyses indicate that neither a peptide encoding a region deemed crucial for eEF-2 binding nor isolated eEF-2K627-725 inhibits eEF-2 phosphorylation by full-length eEF-2K. Taken together, our data suggest that the extreme C-terminal region of eEF-2K, in isolation, does not provide a primary docking site for eEF-2.
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Affiliation(s)
- Nathan Will
- Department of Chemistry and Biochemistry, The City College of New York , New York, New York 10031, United States
| | - Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York , New York, New York 10031, United States
| | - Isaac Snyder
- Department of Chemistry and Biochemistry, The City College of New York , New York, New York 10031, United States
| | - Scarlet B Ferguson
- Division of Chemical Biology and Medicinal Chemistry, University of Texas , Austin, Texas 78712, United States
| | - David H Giles
- Division of Chemical Biology and Medicinal Chemistry, University of Texas , Austin, Texas 78712, United States
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, University of Texas , Austin, Texas 78712, United States.,Graduate Program in Cell and Molecular Biology, University of Texas , Austin, Texas 78712, United States
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York , New York, New York 10031, United States
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19
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Baillie TA. Targeted Covalent Inhibitors for Drug Design. Angew Chem Int Ed Engl 2016; 55:13408-13421. [DOI: 10.1002/anie.201601091] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Thomas A. Baillie
- Department of Medicinal Chemistry, School of Pharmacy; University of Washington; Box 357610 Seattle WA 98195-7610 USA
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20
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Affiliation(s)
- Thomas A. Baillie
- Department of Medicinal Chemistry, School of Pharmacy; University of Washington; Box 357610 Seattle WA 98195-7610 USA
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21
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Wang Q, Edupuganti R, Tavares CDJ, Dalby KN, Ren P. Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis. Front Mol Biosci 2015; 2:9. [PMID: 25988177 PMCID: PMC4429643 DOI: 10.3389/fmolb.2015.00009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/03/2015] [Indexed: 01/09/2023] Open
Abstract
A-484954 is a known eEF2K inhibitor with submicromolar IC50 potency. However, the binding mechanism and the crystal structure of the kinase remains unknown. Here, we employ a homology eEF2K model, docking and alchemical free energy simulations to probe the binding mechanism of eEF2K, and in turn, guide the optimization of potential lead compounds. The inhibitor was docked into the ATP-binding site of a homology model first. Three different binding poses, hypothesis 1, 2, and 3, were obtained and subsequently applied to molecular dynamics (MD) based alchemical free energy simulations. The calculated relative binding free energy of the analogs of A-484954 using the binding pose of hypothesis 1 show a good correlation with the experimental IC50 values, yielding an r2 coefficient of 0.96 after removing an outlier (compound 5). Calculations using another two poses show little correlation with experimental data, (r2 of less than 0.5 with or without removing any outliers). Based on hypothesis 1, the calculated relative free energy suggests that bigger cyclic groups, at R1 e.g., cyclobutyl and cyclopentyl promote more favorable binding than smaller groups, such as cyclopropyl and hydrogen. Moreover, this study also demonstrates the ability of the alchemical free energy approach in combination with docking and homology modeling to prioritize compound synthesis. This can be an effective means of facilitating structure-based drug design when crystal structures are not available.
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Affiliation(s)
- Qiantao Wang
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin Austin, TX, USA ; Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin Austin, TX, USA
| | - Ramakrishna Edupuganti
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin Austin, TX, USA
| | - Clint D J Tavares
- Graduate Program in Cell and Molecular Biology, The University of Texas at Austin Austin, TX, USA
| | - Kevin N Dalby
- Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin Austin, TX, USA ; Graduate Program in Cell and Molecular Biology, The University of Texas at Austin Austin, TX, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin Austin, TX, USA
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