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Ham JM, Kim M, Kim T, Ryu SE, Park H. Structure-Based De Novo Design for the Discovery of Miniprotein Inhibitors Targeting Oncogenic Mutant BRAF. Int J Mol Sci 2024; 25:5535. [PMID: 38791574 PMCID: PMC11122373 DOI: 10.3390/ijms25105535] [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: 04/07/2024] [Revised: 05/10/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Being a component of the Ras/Raf/MEK/ERK signaling pathway crucial for cellular responses, the VRAF murine sarcoma viral oncogene homologue B1 (BRAF) kinase has emerged as a promising target for anticancer drug discovery due to oncogenic mutations that lead to pathway hyperactivation. Despite the discovery of several small-molecule BRAF kinase inhibitors targeting oncogenic mutants, their clinical utility has been limited by challenges such as off-target effects and suboptimal pharmacological properties. This study focuses on identifying miniprotein inhibitors for the oncogenic V600E mutant BRAF, leveraging their potential as versatile drug candidates. Using a structure-based de novo design approach based on binding affinity to V600E mutant BRAF and hydration energy, 39 candidate miniprotein inhibitors comprising three helices and 69 amino acids were generated from the substructure of the endogenous ligand protein (14-3-3). Through in vitro binding and kinase inhibition assays, two miniproteins (63 and 76) were discovered as novel inhibitors of V600E mutant BRAF with low-micromolar activity, with miniprotein 76 demonstrating a specific impediment to MEK1 phosphorylation in mammalian cells. These findings highlight miniprotein 76 as a potential lead compound for developing new cancer therapeutics, and the structural features contributing to its biochemical potency against V600E mutant BRAF are discussed in detail.
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Affiliation(s)
- Jae Min Ham
- Department of Bioengineering, College of Engineering, Hanyang University, 222 Wangsimri-ro, Seong-dong-gu, Seoul 04763, Republic of Korea; (J.M.H.); (M.K.)
| | - Myeongbin Kim
- Department of Bioengineering, College of Engineering, Hanyang University, 222 Wangsimri-ro, Seong-dong-gu, Seoul 04763, Republic of Korea; (J.M.H.); (M.K.)
| | - Taeho Kim
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Republic of Korea;
| | - Seong Eon Ryu
- Department of Bioengineering, College of Engineering, Hanyang University, 222 Wangsimri-ro, Seong-dong-gu, Seoul 04763, Republic of Korea; (J.M.H.); (M.K.)
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Republic of Korea;
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Niu P, Xu H, Fan M. Discovery and optimization of (2-naphthylthio)acetic acid derivative as selective Bfl-1 inhibitor. Bioorg Med Chem Lett 2024; 101:129658. [PMID: 38373466 DOI: 10.1016/j.bmcl.2024.129658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/10/2024] [Accepted: 02/14/2024] [Indexed: 02/21/2024]
Abstract
Bcl-2 anti-apoptotic protein family suppresses cell death by deploying a surface groove to capture the critical BH3 α-helix of pro-apoptotic members. Bfl-1 is a relatively understudied member of this family, though it has been implicated in the pathogenesis and chemoresistance of a variety of human cancers. Reported small molecular Bfl-1 inhibitors encountered the issue of either lack in potency or poor selectivity against its most homologous member Mcl-1. In order to tackle this issue, compound library was screened and a hit compound UMI-77 was identified. We modified its chemical structure to remove the characteristic of PAINS (pan-assay interference compounds), demonstrated the real binding affinity and achieved selectivity against Mcl-1 under the guidance of computational modeling. After optimization 15 was obtained as leading compound to block Bfl-1/BIM interaction in vitro with more than 10-fold selectivity over Mcl-1. We believe 15 is of great value for the exploration of Bfl-1 biological function and its potential as therapeutic target.
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Affiliation(s)
- Pengpeng Niu
- Academy of Medical Engineering and Translational Medicine (AMT), Tianjin University, Tianjin 300072, China; Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
| | - Huiqi Xu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Mengyang Fan
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China.
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Pandey M, Shah SK, Gromiha MM. Computational approaches for identifying disease-causing mutations in proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 139:141-171. [PMID: 38448134 DOI: 10.1016/bs.apcsb.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Advancements in genome sequencing have expanded the scope of investigating mutations in proteins across different diseases. Amino acid mutations in a protein alter its structure, stability and function and some of them lead to diseases. Identification of disease-causing mutations is a challenging task and it will be helpful for designing therapeutic strategies. Hence, mutation data available in the literature have been curated and stored in several databases, which have been effectively utilized for developing computational methods to identify deleterious mutations (drivers), using sequence and structure-based properties of proteins. In this chapter, we describe the contents of specific databases that have information on disease-causing and neutral mutations followed by sequence and structure-based properties. Further, characteristic features of disease-causing mutations will be discussed along with computational methods for identifying cancer hotspot residues and disease-causing mutations in proteins.
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Affiliation(s)
- Medha Pandey
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Suraj Kumar Shah
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India; International Research Frontiers Initiative, School of Computing, Tokyo Institute of Technology, Yokohama, Japan.
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Guay KP, Ibba R, Kiappes J, Vasiljević S, Bonì F, De Benedictis M, Zeni I, Le Cornu JD, Hensen M, Chandran AV, Kantsadi AL, Caputo AT, Blanco Capurro JI, Bayo Y, Hill JC, Hudson K, Lia A, Brun J, Withers SG, Martí M, Biasini E, Santino A, De Rosa M, Milani M, Modenutti CP, Hebert DN, Zitzmann N, Roversi P. A quinolin-8-ol sub-millimolar inhibitor of UGGT, the ER glycoprotein folding quality control checkpoint. iScience 2023; 26:107919. [PMID: 37822503 PMCID: PMC10562782 DOI: 10.1016/j.isci.2023.107919] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 07/05/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023] Open
Abstract
Misfolded glycoprotein recognition and endoplasmic reticulum (ER) retention are mediated by the ER glycoprotein folding quality control (ERQC) checkpoint enzyme, UDP-glucose glycoprotein glucosyltransferase (UGGT). UGGT modulation is a promising strategy for broad-spectrum antivirals, rescue-of-secretion therapy in rare disease caused by responsive mutations in glycoprotein genes, and many cancers, but to date no selective UGGT inhibitors are known. The small molecule 5-[(morpholin-4-yl)methyl]quinolin-8-ol (5M-8OH-Q) binds a CtUGGTGT24 "WY" conserved surface motif conserved across UGGTs but not present in other GT24 family glycosyltransferases. 5M-8OH-Q has a 47 μM binding affinity for CtUGGTGT24in vitro as measured by ligand-enhanced fluorescence. In cellula, 5M-8OH-Q inhibits both human UGGT isoforms at concentrations higher than 750 μM. 5M-8OH-Q binding to CtUGGTGT24 appears to be mutually exclusive to M5-9 glycan binding in an in vitro competition experiment. A medicinal program based on 5M-8OH-Q will yield the next generation of UGGT inhibitors.
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Affiliation(s)
- Kevin P. Guay
- Department of Biochemistry and Molecular Biology, and Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
| | - Roberta Ibba
- Oxford Glycobiology Institute, Department of Biochemistry and Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QU, UK
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Via Muroni 23A, 07100 Sassari, Italy
| | - J.L. Kiappes
- Oxford Glycobiology Institute, Department of Biochemistry and Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QU, UK
| | - Snežana Vasiljević
- Oxford Glycobiology Institute, Department of Biochemistry and Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QU, UK
| | - Francesco Bonì
- Institute of Biophysics, IBF-CNR Unit of Milano, via Celoria 26, 20133 Milano, Italy
| | - Maria De Benedictis
- Institute of Sciences of Food Production, C.N.R. Unit of Lecce, via Monteroni, 73100 Lecce, Italy
| | - Ilaria Zeni
- Department of Cellular, Computational and Integrative Biology, University of Trento, Povo, 38123 Trento, Italy
| | - James D. Le Cornu
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Mario Hensen
- Oxford Glycobiology Institute, Department of Biochemistry and Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QU, UK
| | - Anu V. Chandran
- Oxford Glycobiology Institute, Department of Biochemistry and Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QU, UK
| | - Anastassia L. Kantsadi
- Oxford Glycobiology Institute, Department of Biochemistry and Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QU, UK
| | - Alessandro T. Caputo
- Biomedical Manufacturing, Commonwealth Scientific and Industrial Research Organisation, 343 Royal Parade, Parkville, VIC 3052, Australia
| | - Juan I. Blanco Capurro
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina
| | - Yusupha Bayo
- Department of Biosciences, University of Milano, via Celoria 26, 20133 Milano, Italy
| | - Johan C. Hill
- Oxford Glycobiology Institute, Department of Biochemistry and Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QU, UK
| | - Kieran Hudson
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Andrea Lia
- Oxford Glycobiology Institute, Department of Biochemistry and Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QU, UK
- Institute of Biophysics, IBF-CNR Unit of Milano, via Celoria 26, 20133 Milano, Italy
| | - Juliane Brun
- Oxford Glycobiology Institute, Department of Biochemistry and Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QU, UK
| | - Stephen G. Withers
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada
| | - Marcelo Martí
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina
| | - Emiliano Biasini
- Department of Cellular, Computational and Integrative Biology, University of Trento, Povo, 38123 Trento, Italy
- Dulbecco Telethon Institute, University of Trento, Povo, 38123 Trento, Italy
| | - Angelo Santino
- Institute of Sciences of Food Production, C.N.R. Unit of Lecce, via Monteroni, 73100 Lecce, Italy
| | - Matteo De Rosa
- Institute of Biophysics, IBF-CNR Unit of Milano, via Celoria 26, 20133 Milano, Italy
| | - Mario Milani
- Institute of Biophysics, IBF-CNR Unit of Milano, via Celoria 26, 20133 Milano, Italy
| | - Carlos P. Modenutti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN) CONICET, Ciudad Universitaria, Pab. II (CE1428EHA), Buenos Aires, Argentina
| | - Daniel N. Hebert
- Department of Biochemistry and Molecular Biology, and Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA, USA
| | - Nicole Zitzmann
- Oxford Glycobiology Institute, Department of Biochemistry and Kavli Institute for Nanoscience Discovery, South Parks Road, Oxford OX1 3QU, UK
| | - Pietro Roversi
- Institute of Agricultural Biology and Biotechnology, IBBA-CNR Unit of Milano, via Bassini 15, 20133 Milano, Italy
- Leicester Institute of Chemical and Structural Biology and Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, Lancaster Road, LE1 7HR Leicester, UK
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Virtual screening, pharmacokinetic, and DFT studies of anticancer compounds as potential V600E-BRAF kinase inhibitors. J Taibah Univ Med Sci 2023; 18:933-946. [PMID: 36875340 PMCID: PMC9976450 DOI: 10.1016/j.jtumed.2023.01.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/12/2022] [Accepted: 01/24/2023] [Indexed: 02/07/2023] Open
Abstract
Objectives V600E-BRAF kinase is an essential therapeutic target in melanoma and other types of tumors. Because of its resistance to known inhibitors and the adverse effects of some identified inhibitors, investigation of new potent inhibitors is necessary. Methods In the present work, in silico strategies such as molecular docking simulation, pharmacokinetic evaluation, and density functional theory (DFT) computations were used to identify potential V600E-BRAF inhibitors from a set of 72 anticancer compounds in the PubChem database. Results Five top-ranked molecules (12, 15, 30, 31, and 35) with excellent docking scores (MolDock score ≥90 kcal mol-1, Rerank score ≥60 kcal mol-1) were selected. Several potential binding interactions were discovered between the molecules and V600E-BRAF. The formation of H-bonds and hydrophobic interactions with essential residues of V600E-BRAF suggested the high stability of these complexes. The selected compounds had excellent pharmacological properties according to the drug likeness rules (bioavailability) and pharmacokinetic properties. Similarly, the energy for the frontier molecular orbitals, such as the HOMO, LUMO, energy gap, and other reactivity parameters, was computed with DFT. The frontier molecular orbital surfaces and electrostatic potentials were investigated to demonstrate the charge-density distributions potentially associated with anticancer activity. Conclusion The identified compounds were found to be potent hit compounds for V600E-BRAF inhibition with superior pharmacokinetic properties; therefore, they may be promising cancer drug candidates.
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6
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Guo M, Yu X, Zhu YZ, Yu Y. From Bench to Bedside: What Do We Know about Imidazothiazole Derivatives So Far? Molecules 2023; 28:5052. [PMID: 37446714 DOI: 10.3390/molecules28135052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Imidazothiazole derivatives are becoming increasingly important in therapeutic use due to their outstanding physiological activities. Recently, applying imidazothiazole as the core, researchers have synthesized a series of derivatives with biological effects such as antitumor, anti-infection, anti-inflammatory and antioxidant effects. In this review, we summarize the main pharmacological effects and pharmacological mechanisms of imidazothiazole derivates; the contents summarized herein are intended to advance the research and rational development of imidazothiazole-based drugs in the future.
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Affiliation(s)
- Mu Guo
- School of Pharmacy, Fujian Medical University, Fuzhou 350122, China
- Fujian Center for New Drug Safety Evaluation, Fuzhou 350122, China
| | - Xiangbin Yu
- School of Pharmacy, Fujian Medical University, Fuzhou 350122, China
- Fujian Center for New Drug Safety Evaluation, Fuzhou 350122, China
| | - Yi Zhun Zhu
- School of Pharmacy, Macau University of Science and Technology, Macau 999078, China
| | - Yue Yu
- School of Pharmacy, Fujian Medical University, Fuzhou 350122, China
- Fujian Center for New Drug Safety Evaluation, Fuzhou 350122, China
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KAHRİMAN N, PEKER K, SERDAROĞLU V, AYDIN A, TÜRKMENOĞLU B, USTA A, YAYLI N. New pyrimidine-N-β-D-glucosides: synthesis, biological evaluation, and molecular docking investigations. Turk J Chem 2023; 47:476-494. [PMID: 37528922 PMCID: PMC10387993 DOI: 10.55730/1300-0527.3553] [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: 11/10/2022] [Revised: 04/28/2023] [Accepted: 02/28/2023] [Indexed: 08/03/2023] Open
Abstract
In this study, syntheses of new pyrimidine-coupled N-β-glucosides and tetra-O-acetyl derivatives were carried out. All glycoconjugates were investigated in comparison with known chemotherapeutic agents in terms of their antimicrobial and anticancer functions and DNA/protein binding affinities. Spectral data showed that all glycoside derivatives were obtained by diastereoselectivity as β-anomers. Both tested groups exhibited strong antiproliferative activity (2.29-66.84 μg/mL), but some of them had sufficiently ideal % cytotoxicity values (10.01%-16.78%). And also all synthetic compounds exhibited remarkable antibacterial activity against human pathogenic bacteria. Binding of these compounds to CT-DNA resulted in significant changes in spectral properties, consistent with groove binding. Molecular docking studies of some compounds revealed that the docking score, complex energy, and MM-GBSA ΔGBind energy values were consistent with the experimental results, which showed that the new compounds were potent chemotherapeutic agents. Overall bioactivity results suggest that these compounds may be candidates as new chemotherapeutic agents and deserve further pharmacological evaluation.
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Affiliation(s)
- Nuran KAHRİMAN
- Department of Chemistry, Faculty of Science, Karadeniz Technical University, Trabzon,
Turkey
| | - Kıvanç PEKER
- Department of Chemistry, Faculty of Science, Karadeniz Technical University, Trabzon,
Turkey
| | - Vildan SERDAROĞLU
- Department of Chemistry, Faculty of Science, Karadeniz Technical University, Trabzon,
Turkey
| | - Ali AYDIN
- Department of Basic Medical Science, Faculty of Medicine Bozok University, Yozgat,
Turkey
| | - Burçin TÜRKMENOĞLU
- Department of Analytical Chemistry, Faculty of Pharmacy, Erzincan Binali Yıldırım University, Erzincan,
Turkey
| | - Asu USTA
- Department of Chemistry, Faculty of Arts and Sciences, Recep Tayyip Erdoğan University, Rize,
Turkey
| | - Nurettin YAYLI
- Faculty of Pharmacy, Karadeniz Technical University, Trabzon,
Turkey
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Pradhan V, Salahuddin, Kumar R, Mazumder A, Abdullah MM, Shahar Yar M, Ahsan MJ, Ullah Z. Molecular Target Interactions of Quinoline Derivatives as Anticancer Agents: A Review. Chem Biol Drug Des 2022; 101:977-997. [PMID: 36533867 DOI: 10.1111/cbdd.14196] [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: 10/17/2022] [Revised: 11/23/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
One of the leading causes of death worldwide is cancer, which poses substantial risks to both society and an individual's life. Cancer therapy is still challenging, despite developments in the field and continued research into cancer prevention. The search for novel anticancer active agents with a broader cytotoxicity range is therefore continuously ongoing. The benzene ring gets fused to a pyridine ring at two carbon atoms close to one another to form the double ring structure of the heterocyclic aromatic nitrogen molecule known as quinoline (1-azanaphthalene). Quinoline derivatives contain a wide range of pharmacological activities, including antitubercular, antifungal, antibacterial, and antimalarial properties. Quinoline derivatives have also been shown to have anticancer properties. There are many quinoline derivatives widely available as anticancer drugs that act via a variety of mechanisms on various molecular targets, such as inhibition of topoisomerase, inhibition of tyrosine kinases, inhibition of heat shock protein 90 (Hsp90), inhibition of histone deacetylases (HDACs), inhibition of cell cycle arrest and apoptosis, and inhibition of tubulin polymerization.
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Affiliation(s)
- Vikas Pradhan
- Department of Pharmaceutical Chemistry, Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida
| | - Salahuddin
- Department of Pharmaceutical Chemistry, Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida
| | - Rajnish Kumar
- Department of Pharmaceutical Chemistry, Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida
| | - Avijit Mazumder
- Department of Pharmaceutical Chemistry, Noida Institute of Engineering and Technology (Pharmacy Institute), Greater Noida
| | | | - Mohammad Shahar Yar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, New Delhi
| | - Mohamed Jawed Ahsan
- Department of Pharmaceutical Chemistry, Maharishi Arvind College of Pharmacy, Jaipur, Rajasthan, India
| | - Zabih Ullah
- Department of Pharmaceutical Sciences, College of Dentistry and Pharmacy, Buraydah Colleges, Al-Qassim, Saudi Arabia
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Kahriman N, Serdaroğlu V, Aydın A, Türkmenoğlu B, Usta A. Diastereoselective Synthesis, Characterization, Investigation of Anticancer, Antibacterial Activities, In Silico Approaches and DNA/BSA Binding Affinities of Novel Pyrimidine-Sugar Derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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10
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Aydın A, Korkmaz N, Kısa D, Türkmenoğlu B, Karadağ A. Dicyanoargentate(I)‐based complexes induced in vivo tumor inhibition by activating apoptosis‐related pathways. Appl Organomet Chem 2022. [DOI: 10.1002/aoc.6844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ali Aydın
- Department of Basic Medical Science, Faculty of Medicine Yozgat Bozok University Yozgat Türkiye
| | - Nesrin Korkmaz
- Department of Basic Sciences and Health Hemp Research Institute, Yozgat Bozok University Yozgat Türkiye
| | - Dursun Kısa
- Department of Molecular Biology and Genetics, Faculty of Science Bartin University Bartin Türkiye
| | - Burçin Türkmenoğlu
- Department of Analytical Chemistry, Faculty of Pharmacy Erzincan Binali Yıldırım University Türkiye
| | - Ahmet Karadağ
- Department of Chemistry, Science and Art Faculty Yozgat Bozok University Yozgat Türkiye
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Regulatory spine RS3 residue of protein kinases: a lipophilic bystander or a decisive element in the small-molecule kinase inhibitor binding? Biochem Soc Trans 2022; 50:633-648. [PMID: 35226061 PMCID: PMC9022976 DOI: 10.1042/bst20210837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 11/30/2022]
Abstract
In recent years, protein kinases have been one of the most pursued drug targets. These determined efforts have resulted in ever increasing numbers of small-molecule kinase inhibitors reaching to the market, offering novel treatment options for patients with distinct diseases. One essential component related to the activation and normal functionality of a protein kinase is the regulatory spine (R-spine). The R-spine is formed of four conserved residues named as RS1–RS4. One of these residues, RS3, located in the C-terminal part of αC-helix, is usually accessible for the inhibitors from the ATP-binding cavity as its side chain is lining the hydrophobic back pocket in many protein kinases. Although the role of RS3 has been well acknowledged in protein kinase function, this residue has not been actively considered in inhibitor design, even though many small-molecule kinase inhibitors display interactions to this residue. In this minireview, we will cover the current knowledge of RS3, its relationship with the gatekeeper, and the role of RS3 in kinase inhibitor interactions. Finally, we comment on the future perspectives how this residue could be utilized in the kinase inhibitor design.
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Coussens NP, Auld DS, Thielman JR, Wagner BK, Dahlin JL. Addressing Compound Reactivity and Aggregation Assay Interferences: Case Studies of Biochemical High-Throughput Screening Campaigns Benefiting from the National Institutes of Health Assay Guidance Manual Guidelines. SLAS DISCOVERY 2021; 26:1280-1290. [PMID: 34218710 DOI: 10.1177/24725552211026239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Compound-dependent assay interferences represent a continued burden in drug and chemical probe discovery. The open-source National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS) Assay Guidance Manual (AGM) established an "Assay Artifacts and Interferences" section to address different sources of artifacts and interferences in biological assays. In addition to the frequent introduction of new chapters in this important topic area, older chapters are periodically updated by experts from academia, industry, and government to include new technologies and practices. Section chapters describe many best practices for mitigating and identifying compound-dependent assay interferences. Using two previously reported biochemical high-throughput screening campaigns for small-molecule inhibitors of the epigenetic targets Rtt109 and NSD2, the authors review best practices and direct readers to high-yield resources in the AGM and elsewhere for the mitigation and identification of compound-dependent reactivity and aggregation assay interferences.
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Affiliation(s)
- Nathan P Coussens
- Molecular Pharmacology Laboratories, Division of Cancer Treatment and Diagnosis Laboratory Support, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Douglas S Auld
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jonathan R Thielman
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Bridget K Wagner
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA, USA
| | - Jayme L Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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13
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Spectroscopic (FT-IR, FT-Raman) investigations, quantum chemical calculations, ADMET and molecular docking studies of phloretin with B-RAF inhibitor. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01576-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Pandey M, Gromiha MM. Predicting potential residues associated with lung cancer using deep neural network. Mutat Res 2021; 822:111737. [PMID: 33508631 DOI: 10.1016/j.mrfmmm.2020.111737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/30/2020] [Accepted: 12/09/2020] [Indexed: 12/31/2022]
Abstract
Lung cancer is a prominent type of cancer, which leads to high mortality rate worldwide. The major lung cancers lung adenocarcinoma (LUAD) and lung squamous carcinoma (LUSC) occur mainly due to somatic driver mutations in proteins and screening of such mutations is often cost and time intensive. Hence, in the present study, we systematically analyzed the preferred residues, residues pairs and motifs of 4172 disease prone sites in 195 proteins and compared with 4137 neutral sites. We observed that the motifs LG, QF and TST are preferred in disease prone sites whereas GK, KA and ISL are predominant in neutral sites. In addition, Gly, Asp, Glu, Gln and Trp are preferred in disease prone sites whereas, Ile, Val, Lys, Asn and Phe are preferred in neutral sites. Further, utilizing deep neural networks, we have developed a method for predicting disease prone sites with amino acid sequence based features such as physicochemical properties, conservation scores, secondary structure and di and tri-peptide motifs. The model is able to predict the disease prone sites at an accuracy of 81 % with sensitivity, specificity and AUC of 82 %, 78 % and 0.91, respectively, on 10-fold cross-validation. When the model was tested with a set of 417 disease-causing and 413 neutral sites, we obtained an accuracy and AUC of 80 % and 0.89, respectively. We suggest that our method can serve as an effective method to identify the disease causing and neutral sites in lung cancer. We have developed a web server CanProSite for identifying the disease prone sites and it is freely available at-https://web.iitm.ac.in/bioinfo2/CanProSite/.
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Affiliation(s)
- Medha Pandey
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India; School of Computing, Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Kanagawa, 226-8503, Yokohama, Japan.
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15
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Nguyen D, Lin LY, Zhou JO, Kibby E, Sia TW, Tillis TD, Vapuryan N, Xu MR, Potluri R, Shin Y, Erler EA, Bronkema N, Boehlmer DJ, Chung CD, Burkhard C, Zeng SH, Grasso M, Acevedo LA, Marmorstein R, Fera D. Identification and Characterization of a B-Raf Kinase α-Helix Critical for the Activity of MEK Kinase in MAPK Signaling. Biochemistry 2020; 59:4755-4765. [PMID: 33272017 DOI: 10.1021/acs.biochem.0c00598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In the MAPK pathway, an oncogenic V600E mutation in B-Raf kinase causes the enzyme to be constitutively active, leading to aberrantly high phosphorylation levels of its downstream effectors, MEK and ERK kinases. The V600E mutation in B-Raf accounts for more than half of all melanomas and ∼3% of all cancers, and many drugs target the ATP binding site of the enzyme for its inhibition. Because B-Raf can develop resistance against these drugs and such drugs can induce paradoxical activation, drugs that target allosteric sites are needed. To identify other potential drug targets, we generated and kinetically characterized an active form of B-RafV600E expressed using a bacterial expression system. In doing so, we identified an α-helix on B-Raf, found at the B-Raf-MEK interface, that is critical for their interaction and the oncogenic activity of B-RafV600E. We assessed the binding between B-Raf mutants and MEK using pull downs and biolayer interferometry and assessed phosphorylation levels of MEK in vitro and in cells as well as its downstream target ERK to show that mutating certain residues on this α-helix is detrimental to binding and downstream activity. Our results suggest that this B-Raf α-helix binding site on MEK could be a site to target for drug development to treat B-RafV600E-induced melanomas.
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Affiliation(s)
- Diep Nguyen
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Linda Yingqi Lin
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Jeffrey O Zhou
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Emily Kibby
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Twan W Sia
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Tiara D Tillis
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Narine Vapuryan
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Ming-Ray Xu
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Rajiv Potluri
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - YongJoon Shin
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Elizabeth A Erler
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Naomi Bronkema
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Daniel J Boehlmer
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Christopher D Chung
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Caroline Burkhard
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Shirley H Zeng
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Michael Grasso
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Lucila A Acevedo
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Ronen Marmorstein
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States.,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
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16
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Ali EMH, Abdel-Maksoud MS, Ammar UM, Mersal KI, Ho Yoo K, Jooryeong P, Oh CH. Design, synthesis, and biological evaluation of novel imidazole derivatives possessing terminal sulphonamides as potential BRAF V600Einhibitors. Bioorg Chem 2020; 106:104508. [PMID: 33280830 DOI: 10.1016/j.bioorg.2020.104508] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023]
Abstract
BRAFV600E mutation has been detected in various malignant tumours. Developing of potent BRAFV600E inhibitors is considered a leading step in the way to cure different cancer types. In the current work, a series of 38 4-(1H-imidazol-5-yl)pyridin-2-amine derivatives was designed and synthesized using Dabrafenib as a lead compound for structural-guided optimization. The target compounds were evaluated as potential anticancer agents against NCI 60 human cancer cell lines. In 5-dose testing mode, two compounds 14h and 16e were tested to determine their IC50 values over each of the 60 cell lines. The selected candidates exhibited promising activity with mean IC50 values of 2.4 µM and 3.6 µM, respectively. Melanoma cancer cell lines exhibited the highest sensitivity after the treatment with the tested compounds 14h and 16e. The mean IC50 values of compounds 14h and 16e against Melanoma cancer cell lines are 1.8 µM and 1.88 µM, respectively. In addition, BRAFV600E kinase inhibitory activity was determined for each derivative. Compounds 15i, 15j, 16a, and 16d were the most potent inhibitors against BRAFV600E with IC50 76 nM, 32 nM, 35 nM, and 68 nM. The newly developed compounds represent a therapeutically promising approach for the treating various cancer types.
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Affiliation(s)
- Eslam M H Ali
- Center for Biomaterials, Korea Institute of Science & Technology (KIST School), Seongbuk-gu, Seoul 02792, Republic of Korea; University of Science & Technology (UST), Yuseong-gu, Daejeon 34113, Republic of Korea; Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University of Technology and Information (MTI), Cairo 12055, Egypt
| | - Mohammed S Abdel-Maksoud
- Medicinal & Pharmaceutical Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Centre NRC (ID: 60014618), Dokki, Giza 12622, Egypt
| | - Usama M Ammar
- Center for Biomaterials, Korea Institute of Science & Technology (KIST School), Seongbuk-gu, Seoul 02792, Republic of Korea; University of Science & Technology (UST), Yuseong-gu, Daejeon 34113, Republic of Korea; Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza 12566, Egypt
| | - Karim I Mersal
- Center for Biomaterials, Korea Institute of Science & Technology (KIST School), Seongbuk-gu, Seoul 02792, Republic of Korea; University of Science & Technology (UST), Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Kyung Ho Yoo
- Chemical Kinomics Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Park Jooryeong
- Department of Beauty Science, Hanseo University, Seosan 31962, Republic of Korea
| | - Chang-Hyun Oh
- Center for Biomaterials, Korea Institute of Science & Technology (KIST School), Seongbuk-gu, Seoul 02792, Republic of Korea; University of Science & Technology (UST), Yuseong-gu, Daejeon 34113, Republic of Korea.
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17
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Chavda J, Bhatt H. Systemic review on B-Raf V600E mutation as potential therapeutic target for the treatment of cancer. Eur J Med Chem 2020; 206:112675. [PMID: 32798788 DOI: 10.1016/j.ejmech.2020.112675] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/16/2020] [Accepted: 07/16/2020] [Indexed: 12/16/2022]
Abstract
Cancer is one of the major public catastrophes worldwide and as per WHO, cancer is the leading cause of death universally after CVS disorders accounting for 9.6 million deaths in 2018. WHO statistics revealed five dangerous types of cancer viz. lung, breast, colorectal, prostate and skin. In male, lung cancer causes highest death, while in female, breast cancer causes the most. Alteration in MAPK signalling pathway plays a significant role in majority of cancer cases. Raf protein is activated by phosphorylation via downstream regulation of the MAPK pathway. Raf composed of 3 subtypes, viz. A-Raf, B-Raf, and C-Raf. B-Raf kinase plays a significant role in healthy cell growth in the MAPK pathway and the problem associated with B-Raf mutation leads to the development of cancer and other diseases. The progression of mutant B-Raf (B-RafV600E) protein is higher in cancer as compare to other diseases. In 2002, B-RafV600E mutation was identified for the first time in the development of cancer. The frequency of B-RafV600E mutation is higher in melanoma, thyroid, colorectal and ovarian cancer. We have covered small molecule B-RafV600E inhibitors reported in various literatures; from 2002 to 2020 and also covered clinical trial data. To widen the scope of readers, we compiled details of small molecules, specifically inhibiting B-RafV600E mutant and showing anti-proliferative activity against various cancer cell lines along with in-vivo data. We believe that the information covered here will be important in signifying the potentials of B-RafV600E mutation and its inhibitors as potent anticancer agents.
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Affiliation(s)
- Jaydeepsinh Chavda
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, 382 481, India
| | - Hardik Bhatt
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, 382 481, India.
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18
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Systematic profiling of staralog response to acquired drug resistant kinase gatekeeper mutations in targeted cancer therapy. Amino Acids 2020; 52:511-521. [PMID: 32206932 DOI: 10.1007/s00726-020-02832-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/19/2020] [Indexed: 12/14/2022]
Abstract
Kinase-targeted therapy has been widely used as a lifesaving strategy for cancer patients. However, many patients treated with targeted cancer drugs are clinically observed to rapidly develop acquired resistance. Kinase gatekeeper mutation is one of the most chief factors contributing to the resistance, which modulates the accessibility of kinase's ATP-binding pocket. Previously, the pan-kinase inhibitor Staurosporine and its analogs (termed as Staralogs) have been reported to exhibit wild-type sparing selectivity for some kinase gatekeeper mutants, such as EGFR T790M, Her2 T798M and cSrc T338M. Here, we describe an integrative approach to systematically profile the molecular response of 15 representative Staralogs to 17 kinase gatekeeper mutations in targeted cancer therapy. With the profile we are able to divide gatekeeper mutations into three classes (i.e. classes I, II and III) and to divide Staralogs into two groups (i.e. groups 1 and 2) using heuristic clustering. The class I and II mutations confer consistent sensitivity and resistance for all Staralogs, respectively, while the class III mutations address divergent effects on different Staralogs. The mutations to Ile residue can generally reduce Staralog affinity by inducing unfavorable steric hindrance, whereas the mutations to Met and Leu residues would improve Staralog affinity by establishing favorable S···π interaction, van der Waals packing and/or hydrophobic contact. The group 1 and 2 Staralogs are primarily determined by carbonyl or hydroxyl substitution state at the position 7 of Staralog core, where points to kinase gatekeeper residue and can thus be directly influenced by gatekeeper mutation.
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19
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Cope NJ, Novak B, Liu Z, Cavallo M, Gunderwala AY, Connolly M, Wang Z. Analyses of the oncogenic BRAF D594G variant reveal a kinase-independent function of BRAF in activating MAPK signaling. J Biol Chem 2020; 295:2407-2420. [PMID: 31929109 DOI: 10.1074/jbc.ra119.011536] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 01/07/2020] [Indexed: 12/19/2022] Open
Abstract
Class 3 mutations in B-Raf proto-oncogene, Ser/Thr kinase (BRAF), that result in kinase-impaired or kinase-dead BRAF have the highest mutation frequency in BRAF gene in lung adenocarcinoma. Several studies have reported that kinase-dead BRAF variants amplify mitogen-activated protein kinase (MAPK) signaling by dimerizing with and activating WT C-Raf proto-oncogene, Ser/Thr kinase (CRAF). However, the structural and functional principles underlying their activation remain elusive. Herein, using cell biology and various biochemical approaches, we established that variant BRAFD594G, a kinase-dead representative of class 3 mutation-derived BRAF variants, has a higher dimerization potential as compared with WT BRAF. Molecular dynamics simulations uncovered that the D594G substitution orients the αC-helix toward the IN position and extends the activation loop within the kinase domain, shifting the equilibrium toward the active, dimeric conformation, thus priming BRAFD594G as an effective allosteric activator of CRAF. We found that B/CRAF heterodimers are the most thermodynamically stable RAF dimers, suggesting that RAF heterodimers, and not homodimers, are the major players in determining the amplitude of MAPK signaling in cells. Additionally, we show that BRAFD594G:CRAF heterodimers bypass autoinhibitory P-loop phosphorylation, which might contribute to longer duration of MAPK pathway signaling in cancer cells. Last, we propose that the dimer interface of the BRAFD594G:CRAF heterodimer may represent a promising target in the design of novel anticancer therapeutics.
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Affiliation(s)
- Nicholas J Cope
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104
| | - Borna Novak
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104
| | - Zhiwei Liu
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104
| | - Maria Cavallo
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104
| | - Amber Y Gunderwala
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104
| | - Matthew Connolly
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104
| | - Zhihong Wang
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104.
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20
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Abstract
Aim: The druggability of epigenetic targets has prompted researchers to develop small-molecule therapeutics. However, no systematic assessment has ever been done to investigate the chemical space of epigenetic modulators. Herein, we report a comprehensive chemoinformatic analysis of epigenetic ligands from EpiDBase, HEMD, ChEMBL and PubChem databases. Results: Nearly, 0.45 × 106 ligands were analyzed for assay interference compounds, target profiling, drug-like properties and hit prioritization. After eliminating approximately 96,000 problematic compounds, the remaining 0.36 × 106 compounds were studied for their physicochemical distributions, principal component analysis and hit prioritization. More than 30% of assay interference compounds were determined for many proteins. Conclusion: This systematic assessment of epigenetic ligands will help in the enrichment of screening libraries with high-quality compounds and thus, the generation of efficacious drug candidates.
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21
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Cope N, Novak B, Candelora C, Wong K, Cavallo M, Gunderwala A, Liu Z, Li Y, Wang Z. Biochemical Characterization of Full-Length Oncogenic BRAF V600E together with Molecular Dynamics Simulations Provide Insight into the Activation and Inhibition Mechanisms of RAF Kinases. Chembiochem 2019; 20:2850-2861. [PMID: 31152574 DOI: 10.1002/cbic.201900266] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Indexed: 12/12/2022]
Abstract
The most prevalent BRAF mutation, V600E, occurs frequently in melanoma and other cancers. Although extensive progress has been made toward understanding the biology of RAF kinases, little in vitro characterization of full-length BRAFV600E is available. Herein, we show the successful purification of active, full-length BRAFV600E from mammalian cells for in vitro experiments. Our biochemical characterization of intact BRAFV600E together with molecular dynamics (MD) simulations of the BRAF kinase domain and cell-based assays demonstrate that BRAFV600E has several unique features that contribute to its tumorigenesis. Firstly, steady-state kinetic analyses reveal that purified BRAFV600E is more active than fully activated wild-type BRAF; this is consistent with the notion that elevated signaling output is necessary for transformation. Secondly, BRAFV600E has a higher potential to form oligomers, despite the fact that the V600E substitution confers constitutive kinase activation independent of an intact side-to-side dimer interface. Thirdly, BRAFV600E bypasses inhibitory P-loop phosphorylation to enforce the necessary elevated signaling output for tumorigenesis. Together, these results provide new insight into the biochemical properties of BRAFV600E , complementing the understanding of BRAF regulation under normal and disease conditions.
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Affiliation(s)
- Nicholas Cope
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Borna Novak
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Christine Candelora
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Kenneth Wong
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Maria Cavallo
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Amber Gunderwala
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Zhiwei Liu
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
| | - Yana Li
- Eukaryotic Tissue Culture Facility, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Zhihong Wang
- Department of Chemistry and Biochemistry, University of the Sciences, Philadelphia, PA, 19104, USA
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22
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Gunderwala AY, Nimbvikar AA, Cope NJ, Li Z, Wang Z. Development of Allosteric BRAF Peptide Inhibitors Targeting the Dimer Interface of BRAF. ACS Chem Biol 2019; 14:1471-1480. [PMID: 31243962 DOI: 10.1021/acschembio.9b00191] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BRAF is the most frequently mutated kinase in human cancers and is one of the major effectors of oncogenic RAS, making BRAF a target of considerable interest for anticancer drug development. Wild-type BRAF and a variety of oncogenic BRAF mutants are dependent on dimerization of the kinase domain, which also emerges as a culprit of drug resistance and side effects of current BRAF therapies. Thus, allosteric BRAF inhibitors capable of disrupting BRAF dimers could abrogate hyperactivated MAPK (mitogen-activated protein kinase) signaling driven by oncogenic BRAF or RAS and overcome the major limitations of current BRAF inhibitors. To establish this, we applied an in silico approach to design a series of peptide inhibitors targeting the dimer interface of BRAF. One resulting inhibitor was found to potently inhibit the kinase activity of BRAF homo- and heterodimers, including oncogenic BRAFG469A mutant. Moreover, this inhibitor synergizes with FDA-approved, ATP-competitive BRAF inhibitors against dimeric BRAF, suggesting that allosteric BRAF inhibitors have great potential to extend the application of current BRAF therapies. Additionally, targeting the dimer interface of BRAF kinase leads to protein degradation of both RAF and MEK, uncovering a novel scaffolding function of RAF in protecting large MAPK complexes from protein degradation. In conclusion, we have developed a potent lead peptide inhibitor for targeting the dimer interface of BRAF in cancer cells. The dual function of this peptide inhibitor validates the strategy for developing allosteric BRAF inhibitors that specifically dissociate RAF dimers and destabilize the MAPK signaling complex.
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Affiliation(s)
- Amber Y. Gunderwala
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, United States
| | - Anushri A. Nimbvikar
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, United States
| | - Nicholas J. Cope
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, United States
| | - Zhijun Li
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, United States
| | - Zhihong Wang
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, Pennsylvania 19104, United States
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23
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Couto GK, Segatto NV, Oliveira TL, Seixas FK, Schachtschneider KM, Collares T. The Melding of Drug Screening Platforms for Melanoma. Front Oncol 2019; 9:512. [PMID: 31293965 PMCID: PMC6601395 DOI: 10.3389/fonc.2019.00512] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/28/2019] [Indexed: 12/30/2022] Open
Abstract
The global incidence of cancer is rising rapidly and continues to be one of the leading causes of death in the world. Melanoma deserves special attention since it represents one of the fastest growing types of cancer, with advanced metastatic forms presenting high mortality rates due to the development of drug resistance. The aim of this review is to evaluate how the screening of drugs and compounds for melanoma has been performed over the last seven decades. Thus, we performed literature searches to identify melanoma drug screening methods commonly used by research groups during this timeframe. In vitro and in vivo tests are essential for the development of new drugs; however, incorporation of in silico analyses increases the possibility of finding more suitable candidates for subsequent tests. In silico techniques, such as molecular docking, represent an important and necessary first step in the screening process. However, these techniques have not been widely used by research groups to date. Our research has shown that the vast majority of research groups still perform in vitro and in vivo tests, with emphasis on the use of in vitro enzymatic tests on melanoma cell lines such as SKMEL and in vivo tests using the B16 mouse model. We believe that the union of these three approaches (in silico, in vitro, and in vivo) is essential for improving the discovery and development of new molecules with potential antimelanoma action. This workflow would provide greater confidence and safety for preclinical trials, which will translate to more successful clinical trials and improve the translatability of new melanoma treatments into clinical practice while minimizing the unnecessary use of laboratory animals under the principles of the 3R's.
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Affiliation(s)
- Gabriela Klein Couto
- Research Group in Molecular and Cellular Oncology, Postgraduate Program in Biochemistry and Bioprospecting, Cancer Biotechnology Laboratory, Center for Technological Development, Federal University of Pelotas, Pelotas, Brazil
| | - Natália Vieira Segatto
- Biotechnology Graduate Program, Molecular and Cellular Oncology Research Group, Laboratory of Cancer Biotechnology, Technology Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Thaís Larré Oliveira
- Biotechnology Graduate Program, Molecular and Cellular Oncology Research Group, Laboratory of Cancer Biotechnology, Technology Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Fabiana Kömmling Seixas
- Biotechnology Graduate Program, Molecular and Cellular Oncology Research Group, Laboratory of Cancer Biotechnology, Technology Development Center, Federal University of Pelotas, Pelotas, Brazil
| | - Kyle M Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, United States.,Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, IL, United States.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Tiago Collares
- Biotechnology Graduate Program, Molecular and Cellular Oncology Research Group, Laboratory of Cancer Biotechnology, Technology Development Center, Federal University of Pelotas, Pelotas, Brazil
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24
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Zhu LX, Liu Q, Hua YF, Yang N, Zhang XG, Ding X. Systematic Profiling and Evaluation of Structure-based Kinase–Inhibitor Interactome in Cervical Cancer by Integrating In Silico Analyses and In Vitro Assays at Molecular and Cellular Levels. Comput Biol Chem 2019; 80:324-332. [DOI: 10.1016/j.compbiolchem.2019.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/08/2019] [Accepted: 04/30/2019] [Indexed: 12/16/2022]
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25
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El-Naggar M, Amr AEGE, Fayed AA, Elsayed EA, Al-Omar MA, Abdalla MM. Potent Anti-Ovarian Cancer with Inhibitor Activities on both Topoisomerase II and V600EBRAF of Synthesized Substituted Estrone Candidates. Molecules 2019; 24:molecules24112054. [PMID: 31146483 PMCID: PMC6600292 DOI: 10.3390/molecules24112054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/23/2019] [Accepted: 05/28/2019] [Indexed: 01/05/2023] Open
Abstract
A series of 16-(α-alkoxyalkane)-17-hydrazino-estra-1(10),2,4-trien[17,16-c]-3-ol (3a–l) and estra-1(10),2,4-trien-[17,16-c]pyrazoline-3-ol derivatives (4a–d) were synthesized from corresponding arylidines 2a,b which was prepared from estrone 1 as starting material. Condensation of 1 with aldehydes gave the corresponding arylidine derivatives 2a,b which were treated with hydrazine derivatives in alcohols to give the corresponding derivatives 3a–l, respectively. Additionally, treatment of 2a,b with methyl- or phenylhydrazine in ethanolic potassium hydroxide afforded the corresponding N-substituted pyrazoline derivatives 4a–d, respectively. All these derivatives showed potent anti-ovarian cancer both in vitro and in vivo. The mechanism of anti-ovarian cancer was suggested to process via topoisomerase II and V600EBRAF inhibition.
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Affiliation(s)
- Mohamed El-Naggar
- Chemistry Department, Faculty of Sciences, University of Sharjah, Sharjah 27272, UAE.
| | - Abd El-Galil E Amr
- Drug Exploration & Development Chair (DEDC), Pharmaceutical Chemistry Department, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.
- Applied Organic Chemistry Department, National Research Center, Cairo 12622, Egypt.
| | - Ahmed A Fayed
- Applied Organic Chemistry Department, National Research Center, Cairo 12622, Egypt.
- Respiratory Therapy Department, College of Medical Rehabilitation Sciences, Taibah University, Madinah Munawara 22624, Saudi Arabia.
| | - Elsayed A Elsayed
- Zoology Department, Bioproducts Research Chair, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.
- Chemistry of Natural and Microbial Products Department, National Research Centre, Cairo 12622, Egypt.
| | - Mohamed A Al-Omar
- Drug Exploration & Development Chair (DEDC), Pharmaceutical Chemistry Department, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.
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26
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Beneker CM, Rovoli M, Kontopidis G, Röring M, Galda S, Braun S, Brummer T, McInnes C. Design and Synthesis of Type-IV Inhibitors of BRAF Kinase That Block Dimerization and Overcome Paradoxical MEK/ERK Activation. J Med Chem 2019; 62:3886-3897. [PMID: 30977659 DOI: 10.1021/acs.jmedchem.8b01288] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Despite the clinical success of BRAF inhibitors like vemurafenib in treating metastatic melanoma, resistance has emerged through "paradoxical MEK/ERK signaling" where transactivation of one protomer occurs as a result of drug inhibition of the other partner in the activated dimer. The importance of the dimerization interface in the signaling potential of wild-type BRAF in cells expressing oncogenic Ras has recently been demonstrated and proposed as a site of therapeutic intervention in targeting cancers resistant to adenosine triphosphate competitive drugs. The proof of concept for a structure-guided approach targeting the dimerization interface is described through the design and synthesis of macrocyclic peptides that bind with high affinity to BRAF and that block paradoxical signaling in malignant melanoma cells occurring through this drug target. The lead compounds identified are type-IV kinase inhibitors and represent an ideal framework for conversion into next-generation BRAF inhibitors through macrocyclic drug discovery.
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Affiliation(s)
- Chad M Beneker
- Drug Discovery and Biomedical Sciences , College of Pharmacy , Columbia , South Carolina 29208 , United States
| | - Magdalini Rovoli
- Laboratory of Biochemistry, Department of Veterinary Medicine , University of Thessaly , Karditsa 43131 , Greece
| | - George Kontopidis
- Laboratory of Biochemistry, Department of Veterinary Medicine , University of Thessaly , Karditsa 43131 , Greece
| | - Michael Röring
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine , University of Freiburg , Freiburg 79085 , Germany
| | - Simeon Galda
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine , University of Freiburg , Freiburg 79085 , Germany
| | - Sandra Braun
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine , University of Freiburg , Freiburg 79085 , Germany
| | - Tilman Brummer
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine , University of Freiburg , Freiburg 79085 , Germany.,Centre for Biological Signalling Studies, BIOSS , University of Freiburg , Schänzlestrasse 18 , Freiburg 79104 , Germany.,German Consortium for Translational Cancer Research DKTK, Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg 69120 , Germany
| | - Campbell McInnes
- Drug Discovery and Biomedical Sciences , College of Pharmacy , Columbia , South Carolina 29208 , United States
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27
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Abdel-Maksoud MS, Ammar UM, Oh CH. Anticancer profile of newly synthesized BRAF inhibitors possess 5-(pyrimidin-4-yl)imidazo[2,1-b]thiazole scaffold. Bioorg Med Chem 2019; 27:2041-2051. [PMID: 30955995 DOI: 10.1016/j.bmc.2019.03.062] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 03/18/2019] [Accepted: 03/31/2019] [Indexed: 12/11/2022]
Abstract
In this work, a new series of imidazo[2,1-b]thiazole was designed and synthesized. The new compounds are having 3-fluorophenyl at position 6 of imidazo[2,1-b]thiazole and pyrimidine ring at position 5. The pyrimidine ring containing either amide or sulphonamide moiety attached to a linker (ethyl or propyl) at position 2 of the pyrimidine ring. The final compounds were selected by NCI for in vitro cytotoxicity screening. Most derivatives showed cytotoxic activity against colon cancer and melanoma cell lines. In addition, IC50s of the target compounds were determined over A375 and SK-MEL-28 cell lines using sorafenib as positive control. Compounds12b, 12c, 12e, 12f, 15a, 15d, 15f, 14g and 15h exhibited superior activity when compared to sorafenib. The most potent compounds were tested against wild type BRAF, v600e BRAF, and CRAF. Compound 15h exhibited a potential inhibitory effect againstV600EBRAF (IC50 = 9.3 nM).
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Affiliation(s)
- Mohammed S Abdel-Maksoud
- Medicinal & Pharmaceutical Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Centre (NRC), Dokki, Giza 12622, Egypt
| | - Usama M Ammar
- Center for Biomaterials, Korea Institute of Science & Technology (KIST School), Seoul, Seongbuk-gu 02792, Republic of Korea; University of Science & Technology (UST), Daejeon, Yuseong-gu 34113, Republic of Korea; Department of Biomolecular Science, University of Science & Technology (UST), Daejeon, Yuseong-gu 34113, Republic of Korea; Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, Giza 12566, Egypt
| | - Chang-Hyun Oh
- Center for Biomaterials, Korea Institute of Science & Technology (KIST School), Seoul, Seongbuk-gu 02792, Republic of Korea; University of Science & Technology (UST), Daejeon, Yuseong-gu 34113, Republic of Korea; Department of Biomolecular Science, University of Science & Technology (UST), Daejeon, Yuseong-gu 34113, Republic of Korea.
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28
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Integrated Chemoinformatics Approaches Toward Epigenetic Drug Discovery. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2019. [DOI: 10.1007/978-3-030-05282-9_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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29
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Liu T, Wang Z, Guo P, Ding N. Electrostatic mechanism of V600E mutation-induced B-Raf constitutive activation in colorectal cancer: molecular implications for the selectivity difference between type-I and type-II inhibitors. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2018; 48:73-82. [DOI: 10.1007/s00249-018-1334-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/10/2018] [Accepted: 09/06/2018] [Indexed: 02/04/2023]
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30
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Cope N, Candelora C, Wong K, Kumar S, Nan H, Grasso M, Novak B, Li Y, Marmorstein R, Wang Z. Mechanism of BRAF Activation through Biochemical Characterization of the Recombinant Full-Length Protein. Chembiochem 2018; 19:1988-1997. [PMID: 29992710 DOI: 10.1002/cbic.201800359] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Indexed: 12/17/2022]
Abstract
BRAF kinase plays an important role in mitogen-activated protein kinase (MAPK) signaling and harbors activating mutations in about half of melanomas and in a smaller percentage in many other cancers. Despite its importance, few in vitro studies have been performed to characterize the biochemical properties of full-length BRAF. Herein, a strategy to generate an active, intact form of BRAF protein suitable for in vitro enzyme kinetics is described. It is shown that purified, intact BRAF protein autophosphorylates the kinase activation loop and this can be enhanced by binding the MEK protein substrate through an allosteric mechanism. These studies provide in vitro evidence that BRAF selectively binds to active RAS and that the BRAF/CRAF heterodimer is the most active form, relative to their respective homodimers. Full-length BRAF analysis with small-molecule BRAF inhibitors shows that two drugs, dabrafenib and vemurafenib, can modestly enhance kinase activity of BRAF at low concentration. Taken together, this characterization of intact BRAF contributes to a framework for understanding its role in cell signaling.
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Affiliation(s)
- Nicholas Cope
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Christine Candelora
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Kenneth Wong
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Sujeet Kumar
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Haihan Nan
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Michael Grasso
- Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Borna Novak
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
| | - Yana Li
- Eukaryotic Tissue Culture Facility, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zhihong Wang
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA, 19004, USA
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31
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Wang CR, Wang ZF, Shi L, Wang ZC, Zhu HL. Design, synthesis, and biological evaluation of pyrazole derivatives containing acetamide bond as potential BRAF V600E inhibitors. Bioorg Med Chem Lett 2018; 28:2382-2390. [DOI: 10.1016/j.bmcl.2018.06.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/04/2018] [Accepted: 06/14/2018] [Indexed: 12/24/2022]
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32
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Chu M, Chen X, Wang J, Guo L, Wang Q, Gao Z, Kang J, Zhang M, Feng J, Guo Q, Li B, Zhang C, Guo X, Chu Z, Wang Y. Polypharmacology of Berberine Based on Multi-Target Binding Motifs. Front Pharmacol 2018; 9:801. [PMID: 30087614 PMCID: PMC6066535 DOI: 10.3389/fphar.2018.00801] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 07/03/2018] [Indexed: 12/13/2022] Open
Abstract
Background: Polypharmacology is emerging as the next paradigm in drug discovery. However, considerable challenges still exist for polypharmacology modeling. In this study, we developed a rational design to identify highly potential targets (HPTs) for polypharmacological drugs, such as berberine. Methods and Results: All the proven co-crystal structures locate berberine in the active cavities of a redundancy of aromatic, aliphatic, and acidic residues. The side chains from residues provide hydrophobic and electronic interactions to aid in neutralization for the positive charge of berberine. Accordingly, we generated multi-target binding motifs (MBM) for berberine, and established a new mathematical model to identify HPTs based on MBM. Remarkably, the berberine MBM was embodied in 13 HPTs, including beta-secretase 1 (BACE1) and amyloid-β1-42 (Aβ1-42). Further study indicated that berberine acted as a high-affinity BACE1 inhibitor and prevented Aβ1-42 aggregation to delay the pathological process of Alzheimer's disease. Conclusion: Here, we proposed a MBM-based drug-target space model to analyze the underlying mechanism of multi-target drugs against polypharmacological profiles, and demonstrated the role of berberine in Alzheimer's disease. This approach can be useful in derivation of rules, which will illuminate our understanding of drug action in diseases.
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Affiliation(s)
- Ming Chu
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory of Medical Immunology, Ministry of Health, Peking University, Beijing, China
| | - Xi Chen
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Likai Guo
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory of Medical Immunology, Ministry of Health, Peking University, Beijing, China
| | - Qianqian Wang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory of Medical Immunology, Ministry of Health, Peking University, Beijing, China
| | - Zirui Gao
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jiarui Kang
- Department of Pathology, First Affiliated Hospital of Chinese PLA General Hospital, Beijing, China
| | - Mingbo Zhang
- Pharmacy Departments, Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Jinqiu Feng
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory of Medical Immunology, Ministry of Health, Peking University, Beijing, China
| | - Qi Guo
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Binghua Li
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory of Medical Immunology, Ministry of Health, Peking University, Beijing, China
| | - Chengrui Zhang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory of Medical Immunology, Ministry of Health, Peking University, Beijing, China
| | - Xueyuan Guo
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory of Medical Immunology, Ministry of Health, Peking University, Beijing, China
| | - Zhengyun Chu
- Pharmacy Departments, Liaoning University of Traditional Chinese Medicine, Shenyang, China
| | - Yuedan Wang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Key Laboratory of Medical Immunology, Ministry of Health, Peking University, Beijing, China
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33
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Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling. Cell Syst 2018; 7:161-179.e14. [PMID: 30007540 DOI: 10.1016/j.cels.2018.06.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 03/09/2018] [Accepted: 06/04/2018] [Indexed: 12/19/2022]
Abstract
Clinically used RAF inhibitors are ineffective in RAS mutant tumors because they enhance homo- and heterodimerization of RAF kinases, leading to paradoxical activation of ERK signaling. Overcoming enhanced RAF dimerization and the resulting resistance is a challenge for drug design. Combining multiple inhibitors could be more effective, but it is unclear how the best combinations can be chosen. We built a next-generation mechanistic dynamic model to analyze combinations of structurally different RAF inhibitors, which can efficiently suppress MEK/ERK signaling. This rule-based model of the RAS/ERK pathway integrates thermodynamics and kinetics of drug-protein interactions, structural elements, posttranslational modifications, and cell mutational status as model rules to predict RAF inhibitor combinations for inhibiting ERK activity in oncogenic RAS and/or BRAFV600E backgrounds. Predicted synergistic inhibition of ERK signaling was corroborated by experiments in mutant NRAS, HRAS, and BRAFV600E cells, and inhibition of oncogenic RAS signaling was associated with reduced cell proliferation and colony formation.
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34
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Roman G. 2-Naphthol-pyrazole conjugates as substrates in the Mannich reaction. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2018. [DOI: 10.1515/znb-2017-0209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Several novel 2-naphthol-pyrazole conjugates have been synthesized through the O-alkylation of 1-[(3,5-dimethyl-1H-pyrazol-1-yl)methyl]naphthalen-2-ol with methyl iodide, benzyl chloride, methyl bromoacetate and N-benzyl-2-bromoacetamide. The aminomethylation of these 2-naphthol-pyrazole conjugates has been examined employing the classical conditions for the Mannich reaction, and also by using N,N-dimethylmethyleneiminium chloride as preformed aminomethylating reagent. In both situations, aminomethylation of these substrates occurred at C-4 of the pyrazole ring. The bifunctional substrate 1-[(3,5-dimethyl-1H-pyrazol-1-yl)methyl]naphthalen-2-ol has been chemoselectively aminomethylated in the pyrazole ring using the same preformed aminomethylating reagent.
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Affiliation(s)
- Gheorghe Roman
- Department of Inorganic Polymers , Petru Poni Institute of Macromolecular Chemistry , 700487 Iaşi , Romania
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35
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Ramírez D, Caballero J. Is It Reliable to Take the Molecular Docking Top Scoring Position as the Best Solution without Considering Available Structural Data? Molecules 2018; 23:molecules23051038. [PMID: 29710787 PMCID: PMC6102569 DOI: 10.3390/molecules23051038] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 04/21/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022] Open
Abstract
Molecular docking is the most frequently used computational method for studying the interactions between organic molecules and biological macromolecules. In this context, docking allows predicting the preferred pose of a ligand inside a receptor binding site. However, the selection of the “best” solution is not a trivial task, despite the widely accepted selection criterion that the best pose corresponds to the best energy score. Here, several rigid-target docking methods were evaluated on the same dataset with respect to their ability to reproduce crystallographic binding orientations, to test if the best energy score is a reliable criterion for selecting the best solution. For this, two experiments were performed: (A) to reconstruct the ligand-receptor complex by performing docking of the ligand in its own crystal structure receptor (defined as self-docking), and (B) to reconstruct the ligand-receptor complex by performing docking of the ligand in a crystal structure receptor that contains other ligand (defined as cross-docking). Root-mean square deviation (RMSD) was used to evaluate how different the obtained docking orientation is from the corresponding co-crystallized pose of the same ligand molecule. We found that docking score function is capable of predicting crystallographic binding orientations, but the best ranked solution according to the docking energy is not always the pose that reproduces the experimental binding orientation. This happened when self-docking was achieved, but it was critical in cross-docking. Taking into account that docking is typically used with predictive purposes, during cross-docking experiments, our results indicate that the best energy score is not a reliable criterion to select the best solution in common docking applications. It is strongly recommended to choose the best docking solution according to the scoring function along with additional structural criteria described for analogue ligands to assure the selection of a correct docking solution.
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Affiliation(s)
- David Ramírez
- Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, 5 Poniente No. 1670, 3460000 Talca, Chile.
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca. 1 Poniente No. 1141, 3460000 Talca, Chile.
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36
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Meng N, Tang H, Zhang H, Jiang C, Su L, Min X, Zhang W, Zhang H, Miao Z, Zhang W, Zhuang C. Fragment-growing guided design of Keap1-Nrf2 protein-protein interaction inhibitors for targeting myocarditis. Free Radic Biol Med 2018; 117:228-237. [PMID: 29428410 DOI: 10.1016/j.freeradbiomed.2018.02.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/01/2018] [Accepted: 02/05/2018] [Indexed: 12/30/2022]
Abstract
Small-molecule inhibitors that block the Keap1-Nrf2 protein-protein interactions are being intensely pursued as a new therapeutic strategy for oxidative stress-related diseases, such as cancer, diabetes, Alzheimer's disease, arteriosclerosis, inflammation and myocarditis. However, there are not enough studies on antioxidant treatments using small molecules in myocarditis. We herein provided a series of novel hydronaphthoquinones as the Keap1-Nrf2 interaction inhibitors targeting LPS-induced myocarditis both in vitro and in vivo. These compounds were designed through an in-silico fragment growing approach based on our previous reported compound, S47 (1). The new compounds were predicted to form additional hydrogen bonds with the S363 residue, leading to higher inhibitory activity. Among these new derivatives, compounds S01 and S05 emerged as inhibitors with significant biochemical potency, as determined by fluorescent anisotropy assay and confirmed by surface plasmon resonance (SPR) and differential scanning fluorimetry (DSF) assays. These inhibitors can dose-dependently protect the H9c2 cardiac cells against LPS-induced injury (100% at 2 μM and 4 μM) and effectively prolong survival or save the life of LPS-injured mice. Mechanistic studies showed that these inhibitors could release Nrf2 in H9c2 cells and LPS-inflammatory mouse models and translocate into the nucleus in a dose-response manner, which significantly increased the downstream genes (HO-1, NQO-1) and the pro-inflammatory cytokines (TNF-α, IL-1β, IL-6), while ROS production dramatically decreased. Their protective effects and the mechanism of action were further confirmed by siNrf2 transfected experiment. Collectively, the novel hydronaphthoquinones can be used as promising lead compounds for the study of Keap1-Nrf2 protein-protein interactions and further anti-myocarditis drug development.
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Affiliation(s)
- Ning Meng
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Hua Tang
- Research Center for Marine Drugs, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Hao Zhang
- Research Center for Marine Drugs, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China; School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Chengshi Jiang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China
| | - Li Su
- Research Center for Marine Drugs, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Xiao Min
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Wannian Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China; School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
| | - Hua Zhang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China.
| | - Zhenyuan Miao
- Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China.
| | - Wen Zhang
- Research Center for Marine Drugs, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China.
| | - Chunlin Zhuang
- Research Center for Marine Drugs, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China; Department of Medicinal Chemistry, School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China.
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37
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Wang GM, Wang X, Zhu JM, Guo BB, Yang Z, Xu ZJ, Li B, Wang HY, Meng LH, Zhu WL, Ding J. Docking-based structural splicing and reassembly strategy to develop novel deazapurine derivatives as potent B-Raf V600E inhibitors. Acta Pharmacol Sin 2017; 38:1059-1068. [PMID: 28414204 DOI: 10.1038/aps.2016.173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/24/2016] [Indexed: 12/11/2022] Open
Abstract
The mutation of B-RafV600E is widespread in a variety of human cancers. Its inhibitors vemurafenib and dabrafenib have been launched as drugs for treating unresectable melanoma, demonstrating that B-RafV600E is an ideal drug target. This study focused on developing novel B-RafV600E inhibitors as drug leads against various cancers with B-RafV600E mutation. Using molecular modeling approaches, 200 blockbuster drugs were spliced to generate 283 fragments followed by molecular docking to identify potent fragments. Molecular structures of potential inhibitors of B-RafV600E were then obtained by fragment reassembly followed by docking to predict the bioactivity of the reassembled molecules. The structures with high predicted bioactivity were synthesized, followed by in vitro study to identify potent B-RafV600E inhibitors. A highly potent fragment binding to the hinge area of B-RafV600E was identified via a docking-based structural splicing approach. Using the fragment, 14 novel structures were designed by structural reassembly, two of which were predicted to be as strong as marketed B-RafV600E inhibitors. Biological evaluation revealed that compound 1m is a potent B-RafV600E inhibitor with an IC50 value of 0.05 μmol/L, which was lower than that of vemurafenib (0.13 μmol/L). Moreover, the selectivity of 1m against B-RafWT was enhanced compared with vemurafenib. In addition, 1m exhibits desirable solubility, bioavailability and metabolic stability in in vitro assays. Thus, a highly potent and selective B-RafV600E inhibitor was designed via a docking-based structural splicing and reassembly strategy and was validated by medicinal synthesis and biological evaluation.
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38
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Grasso M, Estrada MA, Ventocilla C, Samanta M, Maksimoska J, Villanueva J, Winkler JD, Marmorstein R. Chemically Linked Vemurafenib Inhibitors Promote an Inactive BRAF V600E Conformation. ACS Chem Biol 2016; 11:2876-2888. [PMID: 27571413 PMCID: PMC5108658 DOI: 10.1021/acschembio.6b00529] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The BRAF kinase, within the mitogen activated protein kinase (MAPK) signaling pathway, harbors activating mutations in about half of melanomas and to a significant extent in many other cancers. A single valine to glutamic acid substitution at residue 600 (BRAFV600E) accounts for about 90% of these activating mutations. While BRAFV600E-selective small molecule inhibitors, such as debrafenib and vemurafenib, have shown therapeutic benefit, almost all patients develop resistance. Resistance often arises through reactivation of the MAPK pathway, typically through mutation of upstream RAS, downstream MEK, or splicing variants. RAF kinases signal as homo- and heterodimers, and another complication associated with small molecule BRAFV600E inhibition is drug-induced allosteric activation of a wild-type RAF subunit (BRAF or CRAF) of the kinase dimer, a process called "transactivation" or "paradoxical activation." Here, we used BRAFV600E and vemurafenib as a model system to develop chemically linked kinase inhibitors to lock RAF dimers in an inactive conformation that cannot undergo transactivation. This structure-based design effort resulted in the development of Vem-BisAmide-2, a compound containing two vemurafenib molecules connected by a bis amide linker. We show that Vem-BisAmide-2 has comparable inhibitory potency as vemurafenib to BRAFV600E both in vitro and in cells but promotes an inactive dimeric BRAFV600E conformation unable to undergo transactivation. The crystal structure of a BRAFV600E/Vem-BisAmide-2 complex and associated biochemical studies reveal the molecular basis for how Vem-BisAmide-2 mediates selectivity for an inactive over an active dimeric BRAFV600E conformation. These studies have implications for targeting BRAFV600E/RAF heterodimers and other kinase dimers for therapy.
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Affiliation(s)
- Michael Grasso
- Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, 421 Curie Blvd., Philadelphia, PA 19104, USA,Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA 19104, USA
| | - Michelle A. Estrada
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA 19104, USA
| | - Christian Ventocilla
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA 19104, USA
| | - Minu Samanta
- Wistar Institute, Philadelphia, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Jasna Maksimoska
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA 19104, USA
| | - Jessie Villanueva
- Wistar Institute, Philadelphia, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Jeffrey D. Winkler
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, 421 Curie Blvd., Philadelphia, PA 19104, USA,Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, PA 19104, USA
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Yao H, Sun Q, Zhu J. Identification and Characterization of Small-Molecule Inhibitors to Selectively Target the DFG-in over the DFG-out Conformation of the B-Raf Kinase V600E Mutant in Colorectal Cancer. Arch Pharm (Weinheim) 2016; 349:808-815. [PMID: 27624806 DOI: 10.1002/ardp.201600184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/01/2016] [Accepted: 09/01/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Huixiang Yao
- Department of Gastroenterology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai P. R. China
| | - Qun Sun
- Department of Gastroenterology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai P. R. China
| | - Jinshui Zhu
- Department of Gastroenterology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai P. R. China
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40
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Design, synthesis and biological evaluation of novel benzo-α-pyrone containing piperazine derivatives as potential BRAF V600E inhibitors. Bioorg Med Chem Lett 2016; 26:4983-4991. [PMID: 27634195 DOI: 10.1016/j.bmcl.2016.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/13/2016] [Accepted: 09/02/2016] [Indexed: 12/25/2022]
Abstract
The increasingly acquired resistance to vemurafenib and side effects of known inhibitors motivate the search for new and more effective anti-melanoma drugs. In this Letter, virtual screening and scaffold growth were combined together to achieve new molecules as BRAFV600E inhibitors. Along with docking simulation, a primary screen in vitro was performed to filter the modifications for the lead compound, which was then substituted, synthesized and evaluated for their inhibitory activity against BRAFV600E and several melanoma cell lines. Out of the obtained compounds, derivative 3l was identified as a potent BRAFV600E inhibitor and exerted an anticancer effect through BRAFV600E inhibition. The following biological evaluation assays confirmed that 3l could induce cell apoptosis and marked DNA fragmentation. Furthermore, 3l could arrest the cell cycle at the G0/G1 phase in melanoma cells. The docking simulation displayed that 3l could tightly bind with the crystal structure of BRAFV600E at the active site. Overall, the biological profile of 3l suggests that this compound may be developed as a potential anticancer agent.
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41
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Sun D, Han Y, Wang W, Wang Z, Ma X, Hou Y, Bai G. Screening and identification of Caulis Sinomenii bioactive ingredients with dual-target NF-κB inhibition and β 2- AR agonizing activities. Biomed Chromatogr 2016; 30:1843-1853. [PMID: 27187693 DOI: 10.1002/bmc.3761] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 05/02/2016] [Accepted: 05/06/2016] [Indexed: 11/07/2022]
Abstract
Caulis Sinomenii (CS) is a valuable traditional medicine in China. Its extract can act as an anti-inflammatory agent and a vascular smooth muscle relaxant. However, the underlying mechanisms remain unknown. In this study, we developed a simple dual-target method based on ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry combined with a dual-target bioactive screening assay for anti-inflammatory and antispasmodic activities to characterize the chemical structure of various bioactive compounds of CS rapidly. Seven potential NF-κB inhibitors were identified, including laudanosoline-1-O-xylopyranose, 6-O-methyl-laudanosoline-1-O-glucopyranoside, menisperine, sinomenine, laurifoline, magnoflorine and norsinoacutin. Furthermore, IL-6 and IL-8 assays confirmed the anti-inflammatory effects of these potential NF-κB inhibitors, in which laudanosoline-1-O-d-xylopyranose and menisperine were revealed as novel NF-κB inhibitors. Among the seven identified alkaloids, three potential β2 -adrenergic receptor agonists, including sinomenine, magnoflorine and laurifoline, were characterized using a luciferase reporter system to measure for the activity of β2 -adrenergic receptor agonists. Finally, sinomenine, magnoflorine and laurifoline were identified not only as potential NF-κB inhibitors but also as potential β2 -adrenegic receptor agonists, which is the first time this has been reported. Molecular dynamic simulation and docking results suggest that the three dual-bioactive constituents could not only inhibit Pseudomonas aeruginosa PAK strain-induced inflammatory responses via a negative regulation of the Braf protein that participates in MAPK signaling pathway but also activate the β2 -adrenegic receptor. These results suggest that CS extract has dual signaling activities with potential clinical application as a novel drug for asthma.
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Affiliation(s)
- Dan Sun
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, People's Republic of China
| | - Yanqi Han
- Department of Traditional Chinese Medicine, Tianjin Institute of Pharmaceutical Research Co. Ltd, Tianjin, People's Republic of China
| | - Weiya Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, People's Republic of China
| | - Zengyong Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, People's Republic of China
| | - Xiaoyao Ma
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, People's Republic of China
| | - Yuanyuan Hou
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China.
- Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, People's Republic of China.
| | - Gang Bai
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
- Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, People's Republic of China
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42
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Amin KM, El-Badry OM, Rahman DEA, Ammar UM, Abdalla MM. Design, synthesis, anticancer evaluation and molecular docking of new V600EBRAF inhibitors derived from pyridopyrazinone. ACTA ACUST UNITED AC 2016. [DOI: 10.5155/eurjchem.7.1.19-29.1346] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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43
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Jambrina PG, Rauch N, Pilkington R, Rybakova K, Nguyen LK, Kholodenko BN, Buchete NV, Kolch W, Rosta E. Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Nora Rauch
- Systems Biology Ireland and Conway Institute; University College Dublin, Belfield; Dublin 4 Ireland
| | - Ruth Pilkington
- Systems Biology Ireland and Conway Institute; University College Dublin, Belfield; Dublin 4 Ireland
| | - Katja Rybakova
- Systems Biology Ireland and Conway Institute; University College Dublin, Belfield; Dublin 4 Ireland
| | - Lan K. Nguyen
- Systems Biology Ireland; University College Dublin, Belfield; Dublin 4 Ireland
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute; Monash University; Melbourne Victoria 3800 Australia
| | - Boris N. Kholodenko
- Systems Biology Ireland and Conway Institute; University College Dublin, Belfield; Dublin 4 Ireland
| | - Nicolae-Viorel Buchete
- School of Physics and Complex and Adaptative Systems Laboratory; University College Dublin, Belfield; Dublin 4 Ireland
| | - Walter Kolch
- Systems Biology Ireland and Conway Institute; University College Dublin, Belfield; Dublin 4 Ireland
- School of Medicine & Medical Sciences; University College Dublin, Belfield; Dublin 4 Ireland
| | - Edina Rosta
- Department of Chemistry; King's College London; London SE1 1DB UK
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44
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Verkhivker GM. Molecular dynamics simulations and modelling of the residue interaction networks in the BRAF kinase complexes with small molecule inhibitors: probing the allosteric effects of ligand-induced kinase dimerization and paradoxical activation. MOLECULAR BIOSYSTEMS 2016; 12:3146-65. [DOI: 10.1039/c6mb00298f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The computational analysis of residue interaction networks dissects the allosteric effects of inhibitor-induced BRAF kinase dimerization and paradoxical activation.
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Affiliation(s)
- G. M. Verkhivker
- Graduate Program in Computational and Data Sciences
- Department of Computational Sciences
- Schmid College of Science and Technology
- Chapman University
- Orange
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45
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Jambrina PG, Rauch N, Pilkington R, Rybakova K, Nguyen LK, Kholodenko BN, Buchete NV, Kolch W, Rosta E. Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation. Angew Chem Int Ed Engl 2015; 55:983-6. [PMID: 26644280 PMCID: PMC4736688 DOI: 10.1002/anie.201509272] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Indexed: 12/19/2022]
Abstract
RAF kinases are key players in the MAPK signaling pathway and are important targets for personalized cancer therapy. RAF dimerization is part of the physiological activation mechanism, together with phosphorylation, and is known to convey resistance to RAF inhibitors. Herein, molecular dynamics simulations are used to show that phosphorylation of a key N-terminal acidic (NtA) motif facilitates RAF dimerization by introducing several interprotomer salt bridges between the αC-helix and charged residues upstream of the NtA motif. Additionally, we show that the R-spine of RAF interacts with a conserved Trp residue in the vicinity of the NtA motif, connecting the active sites of two protomers and thereby modulating the cooperative interactions in the RAF dimer. Our findings provide a first structure-based mechanism for the auto-transactivation of RAF and could be generally applicable to other kinases, opening new pathways for overcoming dimerization-related drug resistance.
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Affiliation(s)
- Pablo G Jambrina
- Department of Chemistry, King's College London, London, SE1 1DB, UK
| | - Nora Rauch
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Ruth Pilkington
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Katja Rybakova
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Lan K Nguyen
- Systems Biology Ireland, University College Dublin, Belfield, Dublin, 4, Ireland.,Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, 3800, Australia
| | - Boris N Kholodenko
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Nicolae-Viorel Buchete
- School of Physics and Complex and Adaptative Systems Laboratory, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Walter Kolch
- Systems Biology Ireland and Conway Institute, University College Dublin, Belfield, Dublin, 4, Ireland. .,School of Medicine & Medical Sciences, University College Dublin, Belfield, Dublin, 4, Ireland.
| | - Edina Rosta
- Department of Chemistry, King's College London, London, SE1 1DB, UK.
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46
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Marino KA, Sutto L, Gervasio FL. The effect of a widespread cancer-causing mutation on the inactive to active dynamics of the B-Raf kinase. J Am Chem Soc 2015; 137:5280-3. [PMID: 25868080 DOI: 10.1021/jacs.5b01421] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein kinases play a key role in regulating cellular processes. Kinase dysfunction can lead to disease, making them an attractive target for drug design. The B-Raf kinase is a key target for the treatment of melanoma since a single mutation (V600E) is found in more than 50% of all malignant melanomas. Despite the importance of B-Raf in melanoma treatment, the molecular mechanism by which the mutation increases kinase activity remains elusive. Since kinases are tightly regulated by a conformational transition between an active and inactive state, which is difficult to capture experimentally, large-scale enhanced-sampling simulations are performed to examine the mechanism by which the V600E mutation enhances the activity of the B-Raf monomer. The results reveal that the mutation has a twofold effect. First, the mutation increases the barrier of the active to inactive transition trapping B-Raf in the active state. The mutation also increases the flexibility of the activation loop which might speed-up the rate-limiting step of phosphorylation. Both effects can be explained by the formation of salt-bridges with the Glu600 residue.
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Affiliation(s)
| | - Ludovico Sutto
- Department of Chemistry, University College London, London, U.K
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47
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Dahlin JL, Inglese J, Walters MA. Mitigating risk in academic preclinical drug discovery. Nat Rev Drug Discov 2015; 14:279-94. [PMID: 25829283 PMCID: PMC6002840 DOI: 10.1038/nrd4578] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The number of academic drug discovery centres has grown considerably in recent years, providing new opportunities to couple the curiosity-driven research culture in academia with rigorous preclinical drug discovery practices used in industry. To fully realize the potential of these opportunities, it is important that academic researchers understand the risks inherent in preclinical drug discovery, and that translational research programmes are effectively organized and supported at an institutional level. In this article, we discuss strategies to mitigate risks in several key aspects of preclinical drug discovery at academic drug discovery centres, including organization, target selection, assay design, medicinal chemistry and preclinical pharmacology.
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Affiliation(s)
- Jayme L Dahlin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
| | - James Inglese
- 1] National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, USA. [2] National Human Genome Research Institute, Bethesda, Maryland, 20892, USA
| | - Michael A Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota Twin Cities, 717 Delaware St SE, Room 609, Minneapolis, Minnesota 55414, USA
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Abstract
Protein phosphorylation lies at the heart of cell signalling, and somatic mutation(s) in kinases drives and sustains a multitude of human diseases, including cancer. The human protein kinase superfamily (the kinome) encodes approximately 50 'pseudokinases', which were initially predicted to be incapable of dynamic cell signalling when compared with canonical enzymatically active kinases. This assumption was supported by bioinformatics, which showed that amino acid changes at one or more key loci, making up the nucleotide-binding site or phosphotransferase machinery, were conserved in multiple vertebrate and non-vertebrate pseudokinase homologues. Protein kinases are highly attractive targets for drug discovery, as evidenced by the approval of almost 30 kinase inhibitors in oncology, and the successful development of the dual JAK1/2 (Janus kinase 1/2) inhibitor ruxolitinib for inflammatory indications. However, for such a large (>550) protein family, a remarkable number have still not been analysed at the molecular level, and only a surprisingly small percentage of kinases have been successfully targeted clinically. This is despite evidence that many are potential candidates for the development of new therapeutics. Indeed, several recent reports confirm that disease-associated pseudokinases can bind to nucleotide co-factors at concentrations achievable in the cell. Together, these findings suggest that drug targeting using either ATP-site or unbiased ligand-discovery approaches should now be attempted using the validation technology currently employed to evaluate their classic protein kinase counterparts. In the present review, we discuss members of the human pseudokinome repertoire, and catalogue somatic amino acid pseudokinase mutations that are emerging as the depth and clinical coverage of the human cancer pseudokinome expand.
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49
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Snape TJ, Warr T. Approaches toward improving the prognosis of pediatric patients with glioma: pursuing mutant drug targets with emerging small molecules. Semin Pediatr Neurol 2015; 22:28-34. [PMID: 25976258 DOI: 10.1016/j.spen.2014.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gliomas represent approximately 70% of all pediatric brain tumors, and most of these are of astrocytic lineage; furthermore, malignant or high-grade astrocytomas account for approximately 20% of pediatric astrocytoma. Treatment options for pediatric patients with glioma are limited. Although low-grade astrocytomas are relatively slow-growing tumors that can often be cured through surgical resection, a significant proportion of cases recur, as such, new treatments are desperately needed. This review covers the various approaches that are currently being made toward improving the prognosis of pediatric patients with glioma by pursuing pediatric-selective mutant drug targets with emerging small molecules.
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Affiliation(s)
- Timothy J Snape
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Lancashire, UK.
| | - Tracy Warr
- Brain Tumour Research Centre, University of Wolverhampton, Wolverhampton, UK
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50
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Abstract
A new model of kinase regulation based on the assembly of hydrophobic spines has been proposed. Changes in their positions can explain the mechanism of kinase activation. Here, we examined mutations in human cancer for clues about the regulation of the hydrophobic spines by focusing initially on mutations to Phe. We identified a selected number of Phe mutations in a small group of kinases that included BRAF, ABL1, and the epidermal growth factor receptor. Testing some of these mutations in BRAF, we found that one of the mutations impaired ATP binding and catalytic activity but promoted noncatalytic allosteric functions. Other Phe mutations functioned to promote constitutive catalytic activity. One of these mutations revealed a previously underappreciated hydrophobic surface that functions to position the dynamic regulatory αC-helix. This supports the key role of the C-helix as a signal integration motif for coordinating multiple elements of the kinase to create an active conformation. The importance of the hydrophobic space around the αC-helix was further tested by studying a V600F mutant, which was constitutively active in the absence of the negative charge that is associated with the common V600E mutation. Many hydrophobic mutations strategically localized along the C-helix can thus drive kinase activation.
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