1
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Mudedla S, Lee H, Kim JJ, Jang SH, Doddareddy MR, Sanam SY, Gundabathula R, Park JJ, Wu S. Molecular Dynamics Simulation on the Suppression Mechanism of Phosphorylation to Ser222 by Allosteric Inhibitors Targeting MEK1/2 Kinase. ACS OMEGA 2024; 9:31946-31956. [PMID: 39072081 PMCID: PMC11270731 DOI: 10.1021/acsomega.4c03615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/30/2024]
Abstract
Allosteric inhibitors of mitogen-activated protein kinase 1 (MEK1) reveal distinct interactions with MEK1 activation loop residues. The structural analyses will determine whether, and how, distinct inhibitors suppress the phosphorylation of MEK1 and may guide future therapeutic development. In this study, we explored the suppression mechanism of the phosphorylation process in the presence of MEK allosteric inhibitors, such as selumetinib, trametinib, cobimetinib, and CH5126766, by employing molecular dynamics simulations accompanied by principal component analysis. The simulations of wildtype MEK1 show that Ser222 can come close to γ-phosphate but not Ser218. We have found the conformation where Ser222 is within 5 Å of distance, which makes Ser222 accessible for γ-phosphate. The conformation analysis from the simulations of MEK1 in the presence of allosteric inhibitors reveals that the inhibitor restricts the flexibility of Ser222 through strong interactions with the activation loop, Lys97, and water mediates interactions with amino acids in the vicinity. The results reveal that all the inhibitors act as screeners between the activation loop and Mg-ATP and restricting the flexibility of the activation loop through strong interaction causes the suppression of the phosphorylation process of MEK1. The results conclude that a strong interaction of allosteric inhibitors with the activation loop restricts the movement of Ser222 toward Mg-ATP, which could be the dominant factor for the suppression of phosphorylation in MEK1. This research will provide novel insights to design effective anticancer therapeutics for targeting MEK1 in the future.
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Affiliation(s)
- Sathish
K. Mudedla
- PharmCADD,
224, Engineering Building 7, Sinseon-Ro 365, Namgu, Busan 48548, Korea
| | - Hayoung Lee
- Drug
Discovery Division, ISU Abxis, Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Korea
| | - Jeom Ji Kim
- Drug
Discovery Division, ISU Abxis, Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Korea
| | - Seong Hun Jang
- PharmCADD,
224, Engineering Building 7, Sinseon-Ro 365, Namgu, Busan 48548, Korea
| | | | - Swetha Y. Sanam
- PharmCADD,
224, Engineering Building 7, Sinseon-Ro 365, Namgu, Busan 48548, Korea
| | - Rochish Gundabathula
- PharmCADD,
224, Engineering Building 7, Sinseon-Ro 365, Namgu, Busan 48548, Korea
| | - Jang-June Park
- Drug
Discovery Division, ISU Abxis, Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Korea
| | - Sangwook Wu
- PharmCADD,
224, Engineering Building 7, Sinseon-Ro 365, Namgu, Busan 48548, Korea
- Department
of Physics, Pukyong National University, Busan 48513, Korea
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2
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Milesi P, Baldelli Bombelli F, Lanfrancone L, Gomila RM, Frontera A, Metrangolo P, Terraneo G. Structural Insights on the Role of Halogen Bonding in Protein MEK Kinase-Inhibitor Complexes. Chem Asian J 2024; 19:e202301033. [PMID: 38501888 DOI: 10.1002/asia.202301033] [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: 11/22/2023] [Revised: 02/07/2024] [Indexed: 03/20/2024]
Abstract
Kinases are enzymes that play a critical role in governing essential biological processes. Due to their pivotal involvement in cancer cell signaling, they have become key targets in the development of anti-cancer drugs. Among these drugs, those containing the 2,4-dihalophenyl moiety demonstrated significant potential. Here we show how this moiety, particularly the 2-fluoro-4-iodophenyl one, is crucial for the structural stability of the formed drug-enzyme complexes. Crystallographic analysis of reported kinase-inhibitor complex structures highlights the role of the halogen bonding that this moiety forms with specific residues of the kinase binding site. This interaction is not limited to FDA-approved MEK inhibitors, but it is also relevant for other kinase inhibitors, indicating its broad relevance in the design of this class of drugs.
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Affiliation(s)
- Pietro Milesi
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
- Laboratory of Innovative approaches for tissue engineering and drug delivery, Joint Research Platform "ONCO-TECH LAB - Modeling and Applications for Human Health", Politecnico di Milano - IEO "European Institute of Oncology", IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Francesca Baldelli Bombelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
- Laboratory of Innovative approaches for tissue engineering and drug delivery, Joint Research Platform "ONCO-TECH LAB - Modeling and Applications for Human Health", Politecnico di Milano - IEO "European Institute of Oncology", IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Luisa Lanfrancone
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
- Laboratory of Innovative approaches for tissue engineering and drug delivery, Joint Research Platform "ONCO-TECH LAB - Modeling and Applications for Human Health", Politecnico di Milano - IEO "European Institute of Oncology", IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Rosa M Gomila
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), Spain
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), Spain
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
- Laboratory of Innovative approaches for tissue engineering and drug delivery, Joint Research Platform "ONCO-TECH LAB - Modeling and Applications for Human Health", Politecnico di Milano - IEO "European Institute of Oncology", IRCCS, Via Adamello 16, 20139, Milano, Italy
| | - Giancarlo Terraneo
- Laboratory of Supramolecular and Bio-Nanomaterials (SBNLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, 20131, Milano, Italy
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3
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Dedden D, Nitsche J, Schneider EV, Thomsen M, Schwarz D, Leuthner B, Grädler U. Cryo-EM Structures of CRAF 2/14-3-3 2 and CRAF 2/14-3-3 2/MEK1 2 Complexes. J Mol Biol 2024; 436:168483. [PMID: 38331211 DOI: 10.1016/j.jmb.2024.168483] [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: 09/15/2023] [Revised: 12/22/2023] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
RAF protein kinases are essential effectors in the MAPK pathway and are important cancer drug targets. Structural understanding of RAF activation is so far based on cryo-electron microscopy (cryo-EM) and X-ray structures of BRAF in different conformational states as inactive or active complexes with KRAS, 14-3-3 and MEK1. In this study, we have solved the first cryo-EM structures of CRAF2/14-3-32 at 3.4 Å resolution and CRAF2/14-3-32/MEK12 at 4.2 Å resolution using CRAF kinase domain expressed as constitutively active Y340D/Y341D mutant in insect cells. The overall architecture of our CRAF2/14-3-32 and CRAF2/14-3-32/MEK12 cryo-EM structures is highly similar to corresponding BRAF structures in complex with 14-3-3 or 14-3-3/MEK1 and represent the activated dimeric RAF conformation. Our CRAF cryo-EM structures provide additional insights into structural understanding of the activated CRAF2/14-3-32/MEK12 complex.
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Affiliation(s)
- Dirk Dedden
- Proteros biostructures GmbH, Bunsenstraße 7a, D-82152 Planegg-Martinsried, Germany
| | - Julius Nitsche
- Proteros biostructures GmbH, Bunsenstraße 7a, D-82152 Planegg-Martinsried, Germany
| | | | - Maren Thomsen
- Proteros biostructures GmbH, Bunsenstraße 7a, D-82152 Planegg-Martinsried, Germany
| | - Daniel Schwarz
- The Healthcare Business of Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Birgitta Leuthner
- The Healthcare Business of Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany
| | - Ulrich Grädler
- The Healthcare Business of Merck KGaA, Frankfurter Str. 250, 64293 Darmstadt, Germany.
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4
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Maddeboina K, Yada B, Kumari S, McHale C, Pal D, Durden DL. Recent advances in multitarget-directed ligands via in silico drug discovery. Drug Discov Today 2024; 29:103904. [PMID: 38280625 DOI: 10.1016/j.drudis.2024.103904] [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: 09/21/2023] [Revised: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 01/29/2024]
Abstract
To combat multifactorial refractory diseases, such as cancer, cardiovascular, and neurodegenerative diseases, multitarget drugs have become an emerging area of research aimed at 'synthetic lethality' (SL) relationships associated with drug-resistance mechanisms. In this review, we discuss the in silico design of dual and triple-targeted ligands, strategies by which specific 'warhead' groups are incorporated into a parent compound or scaffold with primary inhibitory activity against one target to develop one small molecule that inhibits two or three molecular targets in an effort to increase potency against multifactorial diseases. We also discuss the analytical exploration of structure-activity relationships (SARs), physicochemical properties, polypharmacology, scaffold feature extraction of US Food and Drug Administration (FDA)-approved multikinase inhibitors (MKIs), and updates regarding the clinical status of dual-targeted chemotypes.
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Affiliation(s)
- Krishnaiah Maddeboina
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute/Atrium Health, Charlotte, NC 28204, USA; Department of Biochemistry, Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston Salem, NC 27157, USA.
| | - Bharath Yada
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute/Atrium Health, Charlotte, NC 28204, USA
| | - Shikha Kumari
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA
| | - Cody McHale
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute/Atrium Health, Charlotte, NC 28204, USA
| | - Dhananjaya Pal
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute/Atrium Health, Charlotte, NC 28204, USA
| | - Donald L Durden
- Molecular Targeted Therapeutics Laboratory, Levine Cancer Institute/Atrium Health, Charlotte, NC 28204, USA; Department of Biochemistry, Atrium Health Wake Forest Baptist Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston Salem, NC 27157, USA.
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5
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Ram T, Singh AK, Kumar A, Singh H, Pathak P, Grishina M, Khalilullah H, Jaremko M, Emwas AH, Verma A, Kumar P. MEK inhibitors in cancer treatment: structural insights, regulation, recent advances and future perspectives. RSC Med Chem 2023; 14:1837-1857. [PMID: 37859720 PMCID: PMC10583825 DOI: 10.1039/d3md00145h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/12/2023] [Indexed: 10/21/2023] Open
Abstract
MEK1/2 are critical components of the RAS-RAF-MEK-ERK or MAPK signalling pathway that regulates a variety of cellular functions including proliferation, survival, and differentiation. In 1997, a lung cancer cell line was first found to have a MEK mutation (encoding MEK2P298L). MEK is involved in various human cancers such as non-small cell lung cancer (NSCLC), spurious melanoma, and pancreatic, colorectal, basal, breast, and liver cancer. To date, 4 MEK inhibitors i.e., trametinib, cobimetinib, selumetinib, and binimetinib have been approved by the FDA and several are under clinical trials. In this review, we have highlighted structural insights into the MEK1/2 proteins, such as the αC-helix, catalytic loop, P-loop, F-helix, hydrophobic pocket, and DFG motif. We have also discussed current issues with all FDA-approved MEK inhibitors or drugs under clinical trials and combination therapies to improve the efficacy of clinical drugs. Finally, this study addressed recent developments on synthetic MEK inhibitors (from their discovery in 1997 to 2022), their unique properties, and their relevance to MEK mutant inhibition.
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Affiliation(s)
- Teja Ram
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab Ghudda Bathinda 151401 India
| | - Ankit Kumar Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab Ghudda Bathinda 151401 India
| | - Adarsh Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab Ghudda Bathinda 151401 India
| | - Harshwardhan Singh
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab Ghudda Bathinda 151401 India
| | - Prateek Pathak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University Chelyabinsk 454008 Russia
- Pharmaceutical Analysis and Quality Assurance and Pharmaceutical Chemistry, GITAM School of Pharmacy at "Hyderabad Campus", GITAM (Deemed to be University) India
| | - Maria Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University Chelyabinsk 454008 Russia
| | - Habibullah Khalilullah
- Department of Pharmaceutical Chemistry and Pharmacognosy, Unaizah College of Pharmacy, Qassim University Unayzah 51911 Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia
| | - Amita Verma
- Bioorganic and Med. Chem. Res., Laboratory, Department of Pharmaceutical Sciences, Sam Higginbottom University of Agriculture, Technology and Sciences Prayagraj 211007 India
| | - Pradeep Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab Ghudda Bathinda 151401 India
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6
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Ayala-Aguilera CC, Valero T, Lorente-Macías Á, Baillache DJ, Croke S, Unciti-Broceta A. Small Molecule Kinase Inhibitor Drugs (1995-2021): Medical Indication, Pharmacology, and Synthesis. J Med Chem 2021; 65:1047-1131. [PMID: 34624192 DOI: 10.1021/acs.jmedchem.1c00963] [Citation(s) in RCA: 114] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The central role of dysregulated kinase activity in the etiology of progressive disorders, including cancer, has fostered incremental efforts on drug discovery programs over the past 40 years. As a result, kinase inhibitors are today one of the most important classes of drugs. The FDA approved 73 small molecule kinase inhibitor drugs until September 2021, and additional inhibitors were approved by other regulatory agencies during that time. To complement the published literature on clinical kinase inhibitors, we have prepared a review that recaps this large data set into an accessible format for the medicinal chemistry community. Along with the therapeutic and pharmacological properties of each kinase inhibitor approved across the world until 2020, we provide the synthesis routes originally used during the discovery phase, many of which were only available in patent applications. In the last section, we also provide an update on kinase inhibitor drugs approved in 2021.
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Affiliation(s)
- Cecilia C Ayala-Aguilera
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, United Kingdom
| | - Teresa Valero
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, United Kingdom
| | - Álvaro Lorente-Macías
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, United Kingdom
| | - Daniel J Baillache
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, United Kingdom
| | - Stephen Croke
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, United Kingdom
| | - Asier Unciti-Broceta
- Cancer Research UK Edinburgh Centre, Institute of Genetics & Cancer, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, United Kingdom
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7
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Gonzalez-Del Pino GL, Li K, Park E, Schmoker AM, Ha BH, Eck MJ. Allosteric MEK inhibitors act on BRAF/MEK complexes to block MEK activation. Proc Natl Acad Sci U S A 2021; 118:e2107207118. [PMID: 34470822 PMCID: PMC8433572 DOI: 10.1073/pnas.2107207118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The RAF/MEK/ERK pathway is central to the control of cell physiology, and its dysregulation is associated with many cancers. Accordingly, the proteins constituting this pathway, including MEK1/2 (MEK), have been subject to intense drug discovery and development efforts. Allosteric MEK inhibitors (MEKi) exert complex effects on RAF/MEK/ERK pathway signaling and are employed clinically in combination with BRAF inhibitors in malignant melanoma. Although mechanisms and structures of MEKi bound to MEK have been described for many of these compounds, recent studies suggest that RAF/MEK complexes, rather than free MEK, should be evaluated as the target of MEKi. Here, we describe structural and biochemical studies of eight structurally diverse, clinical-stage MEKi to better understand their mechanism of action on BRAF/MEK complexes. We find that all of these agents bind in the MEK allosteric site in BRAF/MEK complexes, in which they stabilize the MEK activation loop in a conformation that is resistant to BRAF-mediated dual phosphorylation required for full activation of MEK. We also show that allosteric MEK inhibitors act most potently on BRAF/MEK complexes rather than on free active MEK, further supporting the notion that a BRAF/MEK complex is the physiologically relevant pharmacologic target for this class of compounds. Our findings provide a conceptual and structural framework for rational development of RAF-selective MEK inhibitors as an avenue to more effective and better-tolerated agents targeting this pathway.
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Affiliation(s)
- Gonzalo L Gonzalez-Del Pino
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Kunhua Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Eunyoung Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Anna M Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Byung Hak Ha
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Michael J Eck
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215;
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
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8
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Kalpana K, Syed R, Saranya J, Rafi M, Kiran BR. Synthesis and Theoretical Study of Novel Imidazo[4,5-b]pyrazine-Conjugated Benzamides as Potential Anticancer Agents. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1070428021090153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Mennie KM, Reutershan MH, White C, Adams B, Becker B, Deng J, Katz JD, LaBlue E, Margrey K, Saurí J. Divergent and Regioselective Synthesis of Pyrazolo[1,5- a]pyridines and Imidazo[1,5- a]pyridines. Org Lett 2021; 23:4694-4698. [PMID: 34037404 DOI: 10.1021/acs.orglett.1c01431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nitrogenous heterocycles are ubiquitous in pharmaceuticals and drug-like compounds; however, regioselective synthesis has proved challenging. Herein we report our efforts to develop a regioselective method for the synthesis of pyrazolo[1,5-a]pyridines and the serendipitous discovery of a protocol for the regioselective formation of imidazo[1,5-a]pyridines. Together, these transformations allow for the rapid and selective formation of two important heterocyclic motifs from a common intermediate.
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Affiliation(s)
| | | | - Catherine White
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Bruce Adams
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Bridget Becker
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - James Deng
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Jason D Katz
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | | | - Kaila Margrey
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Josep Saurí
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
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10
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Properties of FDA-approved small molecule protein kinase inhibitors: A 2021 update. Pharmacol Res 2021; 165:105463. [DOI: 10.1016/j.phrs.2021.105463] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 02/06/2023]
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11
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Barbosa R, Acevedo LA, Marmorstein R. The MEK/ERK Network as a Therapeutic Target in Human Cancer. Mol Cancer Res 2021; 19:361-374. [PMID: 33139506 PMCID: PMC7925338 DOI: 10.1158/1541-7786.mcr-20-0687] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/01/2020] [Accepted: 10/27/2020] [Indexed: 11/16/2022]
Abstract
The RAS-RAF-MEK-ERK pathway is the most well-studied of the MAPK cascades and is critical for cell proliferation, differentiation, and survival. Abnormalities in regulation resulting from mutations in components of this pathway, particularly in upstream proteins, RAS and RAF, are responsible for a significant fraction of human cancers and nearly all cutaneous melanomas. Activation of receptor tyrosine kinases by growth factors and various extracellular signals leads to the sequential activation of RAS, RAF, MEK, and finally ERK, which activates numerous transcription factors and facilitates oncogenesis in the case of aberrant pathway activation. While extensive studies have worked to elucidate the activation mechanisms and structural components of upstream MAPK components, comparatively less attention has been directed toward the kinases, MEK and ERK, due to the infrequency of oncogenic-activating mutations in these kinases. However, acquired drug resistance has become a major issue in the treatment of RAS- and RAF-mutated cancers. Targeting the terminal kinases in the MAPK cascade has shown promise for overcoming many of these resistance mechanisms and improving treatment options for patients with MAPK-aberrant cancers. Here, we will describe the role of MEK and ERK in MAPK signaling and summarize the current understanding of their interaction and activation mechanisms. We will also discuss existing approaches for targeting MEK and ERK, and the benefits of alternative strategies. Areas requiring further exploration will be highlighted to guide future research endeavors and aid in the development of alternative therapeutic strategies to combat surmounting drug resistance in treating MAPK-mediated cancers. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/molcanres/19/3/361/F1.large.jpg.
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Affiliation(s)
- Renee Barbosa
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lucila A Acevedo
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ronen Marmorstein
- Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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12
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A machine learning-based chemoproteomic approach to identify drug targets and binding sites in complex proteomes. Nat Commun 2020; 11:4200. [PMID: 32826910 PMCID: PMC7442650 DOI: 10.1038/s41467-020-18071-x] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/27/2020] [Indexed: 01/20/2023] Open
Abstract
Chemoproteomics is a key technology to characterize the mode of action of drugs, as it directly identifies the protein targets of bioactive compounds and aids in the development of optimized small-molecule compounds. Current approaches cannot identify the protein targets of a compound and also detect the interaction surfaces between ligands and protein targets without prior labeling or modification. To address this limitation, we here develop LiP-Quant, a drug target deconvolution pipeline based on limited proteolysis coupled with mass spectrometry that works across species, including in human cells. We use machine learning to discern features indicative of drug binding and integrate them into a single score to identify protein targets of small molecules and approximate their binding sites. We demonstrate drug target identification across compound classes, including drugs targeting kinases, phosphatases and membrane proteins. LiP-Quant estimates the half maximal effective concentration of compound binding sites in whole cell lysates, correctly discriminating drug binding to homologous proteins and identifying the so far unknown targets of a fungicide research compound. Proteomics is often used to map protein-drug interactions but identifying a drug’s protein targets along with the binding interfaces has not been achieved yet. Here, the authors integrate limited proteolysis and machine learning for the proteome-wide mapping of drug protein targets and binding sites.
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13
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Balasubramaniam S, Vijayan S, Goldman LV, May XA, Dodson K, Adhikari S, Rivas F, Watkins DL, Stoddard SV. Design and synthesis of diazine-based panobinostat analogues for HDAC8 inhibition. Beilstein J Org Chem 2020; 16:628-637. [PMID: 32318119 PMCID: PMC7155894 DOI: 10.3762/bjoc.16.59] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
Guided by computational analysis, herein we report the design, synthesis and evaluation of four novel diazine-based histone deacetylase inhibitors (HDACis). The targets of interest (TOI) are analogues of panobinostat, one of the most potent and versatile HDACi reported. By simply replacing the phenyl core of panobinostat with that of a diazine derivative, docking studies against HDAC2 and HDAC8 revealed that the four analogues exhibit inhibition activities comparable to that of panobinostat. Multistep syntheses afforded the visualized targets TOI1, TOI2, TOI3-rev and TOI4 whose biological evaluation confirmed the strength of HDAC8 inhibition with TOI4 displaying the greatest efficacy at varying concentrations. The results of this study lay the foundation for future design strategies toward more potent HDACis for HDAC8 isozymes and further therapeutic applications for neuroblastoma.
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Affiliation(s)
| | - Sajith Vijayan
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677-1848, USA
| | - Liam V Goldman
- Department of Chemistry, Rhodes College, Memphis, TN 38112, USA
| | - Xavier A May
- Department of Chemistry, Rhodes College, Memphis, TN 38112, USA
| | - Kyra Dodson
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677-1848, USA
| | - Sweta Adhikari
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677-1848, USA
| | - Fatima Rivas
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN 38105-3678, USA
| | - Davita L Watkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677-1848, USA
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14
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Zhu J, Li C, Yang H, Guo X, Huang T, Han W. Computational Study on the Effect of Inactivating/Activating Mutations on the Inhibition of MEK1 by Trametinib. Int J Mol Sci 2020; 21:ijms21062167. [PMID: 32245216 PMCID: PMC7139317 DOI: 10.3390/ijms21062167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 12/13/2022] Open
Abstract
Activation of the mitogen-activated protein kinase (MAPK) signaling pathway regulated by human MAP kinase 1 (MEK1) is associated with the carcinogenesis and progression of numerous cancers. In addition, two active mutations (P124S and E203K) have been reported to enhance the activity of MEK1, thereby eventually leading to the tumorigenesis of cancer. Trametinib is an MEK1 inhibitor for treating EML4-ALK-positive, EGFR-activated, and KRAS-mutant lung cancers. Therefore, in this study, molecular docking and molecular dynamic (MD) simulations were performed to explore the effects of inactive/active mutations (A52V/P124S and E203K) on the conformational changes of MEK1 and the changes in the interaction of MEK1 with trametinib. Moreover, steered molecular dynamic (SMD) simulations were further utilized to compare the dissociation processes of trametinib from the wild-type (WT) MEK1 and two active mutants (P124S and E203K). As a result, trametinib had stronger interactions with the non-active MEK1 (WT and A52V mutant) than the two active mutants (P124S and E203K). Moreover, two active mutants may make the allosteric channel of MEK1 wider and shorter than that of the non-active types (WT and A52V mutant). Hence, trametinib could dissociate from the active mutants (P124S and E203K) more easily compared with the WT MEK1. In summary, our theoretical results demonstrated that the active mutations may attenuate the inhibitory effects of MEK inhibitor (trametinib) on MEK1, which could be crucial clues for future anti-cancer treatment.
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15
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Lazzara PR, Moore TW. Scaffold-hopping as a strategy to address metabolic liabilities of aromatic compounds. RSC Med Chem 2019; 11:18-29. [PMID: 33479602 DOI: 10.1039/c9md00396g] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 10/09/2019] [Indexed: 12/31/2022] Open
Abstract
Understanding and minimizing oxidative metabolism of aromatic compounds is a key hurdle in lead optimization. Metabolic processes not only clear compounds from the body, but they can also transform parent compounds into reactive metabolites. One particularly useful strategy when addressing metabolically labile or oxidation-prone structures is scaffold-hopping. Replacement of an aromatic system with a more electron-deficient ring system can often increase robustness towards cytochrome P450-mediated oxidation while conserving the structural requirements of the pharmacophore. The most common example of this substitution strategy, replacement of a phenyl ring with a pyridyl substituent, is prevalent throughout the literature; however scaffold-hopping encompasses a much wider scope of heterocycle replacement. This review will showcase recent examples where different scaffold-hopping approaches were used to reduce metabolic clearance or block the formation of reactive metabolites. Additionally, we will highlight considerations that should be made to garner the most benefit from a scaffold-hopping strategy for lead optimization.
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Affiliation(s)
- Phillip R Lazzara
- Department of Pharmaceutical Sciences , College of Pharmacy , University of Illinois at Chicago , 833 S. Wood Street , Chicago , IL 60612 , USA .
| | - Terry W Moore
- Department of Pharmaceutical Sciences , College of Pharmacy , University of Illinois at Chicago , 833 S. Wood Street , Chicago , IL 60612 , USA . .,University of Illinois Cancer Center , University of Illinois at Chicago , 1801 W. Taylor Street , Chicago , IL 60612 , USA
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16
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Ahmad S, Hussain A, Hussain A, Abdullah I, Ali MS, Froeyen M, Mirza MU. Quantification of Berberine in Berberis vulgaris L. Root Extract and Its Curative and Prophylactic Role in Cisplatin-Induced In Vivo Toxicity and In Vitro Cytotoxicity. Antioxidants (Basel) 2019; 8:E185. [PMID: 31248160 PMCID: PMC6616455 DOI: 10.3390/antiox8060185] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/10/2019] [Accepted: 06/12/2019] [Indexed: 01/16/2023] Open
Abstract
Cisplatin is amongst the most potent chemotherapeutic drugs with applications in more than 50% of cancer treatments, but dose-dependent side effects limit its usefulness. Berberis vulgaris L. (B. vulgaris) has a proven role in several therapeutic applications in the traditional medicinal system. High-performance liquid chromatography was used to quantify berberine, a potent alkaloid in the methanolic root extract of B. vulgaris (BvRE). Berberine chloride in BvRE was found to be 10.29% w/w. To assess the prophylactic and curative protective effects of BvRE on cisplatin-induced nephrotoxicity, hepatotoxicity, and hyperlipidemia, in vivo toxicity trials were carried out on 25 healthy male albino Wistar rats (130-180 g). Both prophylactic and curative trials included a single dose of cisplatin (4 mg/kg, i.p.) and nine doses of BvRE (500 mg/kg/day, orally). An array of marked toxicity effects appeared in response to cisplatin dosage evident by morphological condition, biochemical analysis of serum (urea, creatinine, total protein, alanine transaminase, aspartate transaminase, total cholesterol, and triglyceride), and organ tissue homogenates (malondialdehyde and catalase). Statistically-significant (p < 0.05) variations were observed in various parameters. Moreover, histological studies of liver and kidney tissues revealed that the protective effect of BvRE effectively minimized and reversed nephrotoxic, hepatotoxic, and hyperlipidemic effects caused by cisplatin in both prophylactic and curative groups with relatively promising ameliorative effects in the prophylactic regimen. The in vitro cell viability effect of cisplatin, BvRE, and their combination was determined on HeLa cells using the tetrazolium (MTT) assay. MTT clearly corroborated that HeLa cells appeared to be less sensitive to cisplatin and berberine individually, while the combination of both at the same concentrations resulted in growth inhibition of HeLa cells in a remarkable synergistic way. The present study validated the use of BvRE as a protective agent in combination therapy with cisplatin.
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Affiliation(s)
- Sarfraz Ahmad
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Amina Hussain
- Department of Biochemistry, Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore, Lahore 54000, Pakistan.
| | - Aroosha Hussain
- Department of Biochemistry, Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore, Lahore 54000, Pakistan.
| | - Iskandar Abdullah
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
| | - Muhammad Sajjad Ali
- Department of Biochemistry, Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore, Lahore 54000, Pakistan.
| | - Matheus Froeyen
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium.
| | - Muhammad Usman Mirza
- Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, University of Leuven, B-3000 Leuven, Belgium.
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17
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Cheng Y, Wang X, Xia X, Zhang W, Tian H. A benzoxazole compound as a novel MEK inhibitor for the treatment of RAS/RAF mutant cancer. Int J Cancer 2019; 145:586-596. [PMID: 30628057 DOI: 10.1002/ijc.32119] [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: 09/18/2018] [Accepted: 12/20/2018] [Indexed: 11/07/2022]
Abstract
Mutations in RAS/RAF occur in large portion of malignancies and are associated with aggressive clinical behaviors and poor prognosis. Therefore, we developed a novel benzoxazole compound (KZ-001) as a highly potent and selective MEK 1/2 inhibitor. Our efforts were focused on enhancing the activity of the known MEK inhibitor AZD6244 and overcoming the shortcomings existing in current MEK inhibitors. Here we show that compound KZ-001 exhibits approximately 30-fold greater inhibition against BRAF- and KRAS-mutant tumor cells than that of AZD6244. These results were also demonstrated using in vivo xenograft models. Furthermore, pharmacokinetics (PK) analysis was performed for KZ-001, and this compound showed good orally bioavailability (28%) and exposure (AUC0-∞ = 337 ± 169 ng h/mL). To determine its potential clinical application, the synergistic effect of KZ-001 with other agents was investigated both in vitro and in vivo (xenograft models). KZ-001 exhibited synergistic anti-cancer effect in combination with BRAF inhibitor vemurafenib and a microtubule-stabilizing chemotherapeutic agent docetaxel. In addition, KZ-001 inhibited the MAPK pathway like known MEK inhibitors. In summary, KZ-001, a structurally novel benzoxazole compound, was developed as a MEK inhibitor that has potential for cancer treatment.
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Affiliation(s)
- Ying Cheng
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Center for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | | | | | - Wei Zhang
- Center for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Hongqi Tian
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
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18
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Shaw J, Dale I, Hemsley P, Leach L, Dekki N, Orme JP, Talbot V, Narvaez AJ, Bista M, Martinez Molina D, Dabrowski M, Main MJ, Gianni D. Positioning High-Throughput CETSA in Early Drug Discovery through Screening against B-Raf and PARP1. SLAS DISCOVERY 2018; 24:121-132. [PMID: 30543471 PMCID: PMC6484527 DOI: 10.1177/2472555218813332] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Methods to measure cellular target engagement are increasingly being used in early drug discovery. The Cellular Thermal Shift Assay (CETSA) is one such method. CETSA can investigate target engagement by measuring changes in protein thermal stability upon compound binding within the intracellular environment. It can be performed in high-throughput, microplate-based formats to enable broader application to early drug discovery campaigns, though high-throughput forms of CETSA have only been reported for a limited number of targets. CETSA offers the advantage of investigating the target of interest in its physiological environment and native state, but it is not clear yet how well this technology correlates to more established and conventional cellular and biochemical approaches widely used in drug discovery. We report two novel high-throughput CETSA (CETSA HT) assays for B-Raf and PARP1, demonstrating the application of this technology to additional targets. By performing comparative analyses with other assays, we show that CETSA HT correlates well with other screening technologies and can be applied throughout various stages of hit identification and lead optimization. Our results support the use of CETSA HT as a broadly applicable and valuable methodology to help drive drug discovery campaigns to molecules that engage the intended target in cells.
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Affiliation(s)
- Joseph Shaw
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Ian Dale
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Paul Hemsley
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Lindsey Leach
- 2 Hit Discovery, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Alderley Park, UK
| | | | - Jonathan P Orme
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Verity Talbot
- 4 Mechanistic Biology & Profiling, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Ana J Narvaez
- 4 Mechanistic Biology & Profiling, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Michal Bista
- 5 Structure, Biophysics & Fragment Based Lead Generation, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | | | | | - Martin J Main
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK.,6 Medicines Discovery Catapult, Mereside, Alderley Park, UK
| | - Davide Gianni
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
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19
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Study of Molecular Mechanism of the Interaction Between MEK1/2 and Trametinib with Docking and Molecular Dynamic Simulation. Interdiscip Sci 2018; 11:115-124. [PMID: 30465279 DOI: 10.1007/s12539-018-0305-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/16/2018] [Accepted: 08/31/2018] [Indexed: 10/27/2022]
Abstract
Trametinib was endorsed by the FDA in 2013 as a single agent for adult melanoma patients. Trametinib inhibits cell growth and proliferation in multiple tumor xenografts by preventing RAF phosphorylation of MEK and thus restricting accumulation of activated MEK. In this study, the focus of investigation was the mechanism of the interaction between trametinib and MEK1/2 via computational simulation. To specify the best interaction site of inhibitor with MEK1/2 based on the interaction energy ranking, first we performed a docking and then we studied the interactions of the ATP-bound MEK with trametinib, with RAF and the complex of the ATP-bound MEK-trametinib with RAF via molecular dynamic simulations. The results showed that trametinib inactivates the enzyme by bonding to a group of amino acids including Lys97/101, SER218/216, Asp208/212, and Met143/147 in MEK1/2. By bonding to the essential amino acids, trametinib inhibits the activity of the enzyme. All in all, the acquired results can be of great use in designing new inhibitors.
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20
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Mioc M, Avram S, Bercean V, Kurunczi L, Ghiulai RM, Oprean C, Coricovac DE, Dehelean C, Mioc A, Balan-Porcarasu M, Tatu C, Soica C. Design, Synthesis and Biological Activity Evaluation of S-Substituted 1 H-5-Mercapto-1,2,4-Triazole Derivatives as Antiproliferative Agents in Colorectal Cancer. Front Chem 2018; 6:373. [PMID: 30234098 PMCID: PMC6134806 DOI: 10.3389/fchem.2018.00373] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/02/2018] [Indexed: 12/11/2022] Open
Abstract
Colon cancer is a widespread pathology with complex biochemical etiology based on a significant number of intracellular signaling pathways that play important roles in carcinogenesis, tumor proliferation and metastasis. These pathways function due to the action of key enzymes that can be used as targets for new anticancer drug development. Herein we report the synthesis and biological antiproliferative evaluation of a series of novel S-substituted 1H-3-R-5-mercapto-1,2,4-triazoles, on a colorectal cancer cell line, HT-29. Synthesized compounds were designed by docking based virtual screening (DBVS) of a previous constructed compound library against protein targets, known for their important role in colorectal cancer signaling: MEK1, ERK2, PDK1, VEGFR2. Among all synthesized structures, TZ55.7, which was retained as a possible PDK1 (phospholipid-dependent kinase 1) inhibitor, exhibited the most significant cytotoxic activity against HT-29 tumor cell line. The same compound alongside other two, TZ53.7 and TZ3a.7, led to a significant cell cycle arrest in both sub G0/G1 and G0/G1 phase. This study provides future perspectives for the development of new agents containing the 1,2,4-mercapto triazole scaffold with antiproliferative activities in colorectal cancer.
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Affiliation(s)
- Marius Mioc
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy, Timisoara, Romania
| | - Sorin Avram
- Department of Computational Chemistry, Institute of Chemistry Timisoara of the Romanian Academy, Timisoara, Romania
| | | | - Ludovic Kurunczi
- Department of Computational Chemistry, Institute of Chemistry Timisoara of the Romanian Academy, Timisoara, Romania
| | - Roxana M Ghiulai
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy, Timisoara, Romania
| | - Camelia Oprean
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy, Timisoara, Romania.,"Pius Brinzeu" Timisoara County Emergency Clinical Hospital, Oncogen Institute, Timisoara, Romania
| | - Dorina E Coricovac
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy, Timisoara, Romania
| | - Cristina Dehelean
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy, Timisoara, Romania
| | - Alexandra Mioc
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy, Timisoara, Romania
| | | | - Calin Tatu
- "Pius Brinzeu" Timisoara County Emergency Clinical Hospital, Oncogen Institute, Timisoara, Romania
| | - Codruta Soica
- Faculty of Pharmacy, 'Victor Babes' University of Medicine and Pharmacy, Timisoara, Romania
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21
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Meanwell NA. Fluorine and Fluorinated Motifs in the Design and Application of Bioisosteres for Drug Design. J Med Chem 2018; 61:5822-5880. [PMID: 29400967 DOI: 10.1021/acs.jmedchem.7b01788] [Citation(s) in RCA: 1340] [Impact Index Per Article: 223.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The electronic properties and relatively small size of fluorine endow it with considerable versatility as a bioisostere and it has found application as a substitute for lone pairs of electrons, the hydrogen atom, and the methyl group while also acting as a functional mimetic of the carbonyl, carbinol, and nitrile moieties. In this context, fluorine substitution can influence the potency, conformation, metabolism, membrane permeability, and P-gp recognition of a molecule and temper inhibition of the hERG channel by basic amines. However, as a consequence of the unique properties of fluorine, it features prominently in the design of higher order structural metaphors that are more esoteric in their conception and which reflect a more sophisticated molecular construction that broadens biological mimesis. In this Perspective, applications of fluorine in the construction of bioisosteric elements designed to enhance the in vitro and in vivo properties of a molecule are summarized.
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Affiliation(s)
- Nicholas A Meanwell
- Discovery Chemistry and Molecular Technologies Bristol-Myers Squibb Research and Development P.O. Box 4000, Princeton , New Jersey 08543-4000 , United States
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22
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Vandyshev DY, Shikhaliev KS, Potapov AY, Krysin MY, Zubkov FI, Sapronova LV. A novel synthetic approach to hydroimidazo[1,5- b]pyridazines by the recyclization of itaconimides and HPLC-HRMS monitoring of the reaction pathway. Beilstein J Org Chem 2017; 13:2561-2568. [PMID: 29259665 PMCID: PMC5727784 DOI: 10.3762/bjoc.13.252] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/14/2017] [Indexed: 11/23/2022] Open
Abstract
The novel cascade two-stage reaction between itaconimides and 1,2-diamino-4-phenylimidazole proceeds regio- and chemoselectively to form tetrahydroimidazo[1,5-b]pyridazines and includes nucleophilic C-addition by the activated C=C double bond and subsequent intramolecular recyclization of the intermediate with the amino group involved.
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Affiliation(s)
- Dmitry Yu Vandyshev
- Faculty of Chemistry, Voronezh State University, Universitetskaya sq., 1, Voronezh 394018, Russian Federation
| | - Khidmet S Shikhaliev
- Faculty of Chemistry, Voronezh State University, Universitetskaya sq., 1, Voronezh 394018, Russian Federation
| | - Andrey Yu Potapov
- Faculty of Chemistry, Voronezh State University, Universitetskaya sq., 1, Voronezh 394018, Russian Federation
| | - Michael Yu Krysin
- Faculty of Chemistry, Voronezh State University, Universitetskaya sq., 1, Voronezh 394018, Russian Federation
| | - Fedor I Zubkov
- Faculty of Physics and Mathematics and Natural Sciences, RUDN University, Miklukho-Maklaya St., 6, Moscow 117198, Russian Federation
| | - Lyudmila V Sapronova
- Faculty of Physics and Mathematics and Natural Sciences, RUDN University, Miklukho-Maklaya St., 6, Moscow 117198, Russian Federation
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23
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Basken J, Stuart SA, Kavran AJ, Lee T, Ebmeier CC, Old WM, Ahn NG. Specificity of Phosphorylation Responses to Mitogen Activated Protein (MAP) Kinase Pathway Inhibitors in Melanoma Cells. Mol Cell Proteomics 2017; 17:550-564. [PMID: 29255136 DOI: 10.1074/mcp.ra117.000335] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 11/08/2017] [Indexed: 01/01/2023] Open
Abstract
The BRAF-MKK1/2-ERK1/2 pathway is constitutively activated in response to oncogenic mutations of BRAF in many cancer types, including melanoma. Although small molecules that inhibit oncogenic BRAF and MAP kinase kinase (MKK)1/2 have been successful in clinical settings, resistance invariably develops. High affinity inhibitors of ERK1/2 have been shown in preclinical studies to bypass the resistance of melanoma and colon cancer cells to BRAF and MKK1/2 inhibitors, and are thus promising additions to current treatment protocols. But still unknown is how molecular responses to ERK1/2 inhibitors compare with inhibitors currently in clinical use. Here, we employ quantitative phosphoproteomics to evaluate changes in phosphorylation in response to the ERK inhibitors, SCH772984 and GDC0994, and compare these to the clinically used MKK1/2 inhibitor, trametinib. Combined with previous studies measuring phosphoproteomic responses to the MKK1/2 inhibitor, selumetinib, and the BRAF inhibitor, vemurafenib, the outcomes reveal key insights into pathway organization, phosphorylation specificity and off-target effects of these inhibitors. The results demonstrate linearity in signaling from BRAF to MKK1/2 and from MKK1/2 to ERK1/2. They identify likely targets of direct phosphorylation by ERK1/2, as well as inhibitor off-targets, including an off-target regulation of the p38α mitogen activated protein kinase (MAPK) pathway by the MKK1/2 inhibitor, trametinib, at concentrations used in the literature but higher than in vivo drug concentrations. In addition, several known phosphorylation targets of ERK1/2 are insensitive to MKK or ERK inhibitors, revealing variability in canonical pathway responses between different cell systems. By comparing multiple inhibitors targeted to multiple tiers of protein kinases in the MAPK pathway, we gain insight into regulation and new targets of the oncogenic BRAF driver pathway in cancer cells, and a useful approach for evaluating the specificity of drugs and drug candidates.
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Affiliation(s)
- Joel Basken
- From the ‡Department of Chemistry and Biochemistry
| | | | - Andrew J Kavran
- From the ‡Department of Chemistry and Biochemistry.,§BioFrontiers Institute
| | - Thomas Lee
- From the ‡Department of Chemistry and Biochemistry
| | - Christopher C Ebmeier
- ¶Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO 80303
| | - William M Old
- ¶Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO 80303
| | - Natalie G Ahn
- From the ‡Department of Chemistry and Biochemistry, .,§BioFrontiers Institute
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24
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Zou F, Yang Y, Ma T, Xi J, Zhou J, Zha X. Identification of novel MEK1 inhibitors by pharmacophore and docking based virtual screening. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1788-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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25
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Herbrink M, Schellens JHM, Beijnen JH, Nuijen B. Inherent formulation issues of kinase inhibitors. J Control Release 2016; 239:118-27. [PMID: 27578098 DOI: 10.1016/j.jconrel.2016.08.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 08/24/2016] [Accepted: 08/26/2016] [Indexed: 12/18/2022]
Abstract
The small molecular Kinase Inhibitor (smKI) drug class is very promising and rapidly expanding. All of these drugs are administered orally. The clear relationship between structure and function has led to drugs with a general low intrinsic solubility. The majority of the commercial pharmaceutical formulations of the smKIs are physical mixtures that are limited by the low drug solubility of a salt form. This class of drugs is therefore characterized by an impaired and variable bioavailability rendering them costly and their therapies suboptimal. New formulations are sparingly being reported in literature and patents. The presented data suggests that continued research into formulation design can help to develop more efficient and cost-effective smKI formulation. Moreover, it may also be of help in the future design of the formulations of new smKIs.
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Affiliation(s)
- M Herbrink
- Department of Pharmacy and Pharmacology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Louwesweg 6, 1006 BK Amsterdam, The Netherlands.
| | - J H M Schellens
- Department of Pharmacy and Pharmacology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Louwesweg 6, 1006 BK Amsterdam, The Netherlands
| | - J H Beijnen
- Department of Pharmacy and Pharmacology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Louwesweg 6, 1006 BK Amsterdam, The Netherlands
| | - B Nuijen
- Department of Pharmacy and Pharmacology, Netherlands Cancer Institute-Antoni van Leeuwenhoek, Louwesweg 6, 1006 BK Amsterdam, The Netherlands
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26
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Takahashi RH, Ma S, Robinson SJ, Yue Q, Choo EF, Khojasteh SC. Elucidating the Mechanisms of Formation for Two Unusual Cytochrome P450–Mediated Fused Ring Metabolites of GDC-0623, a MAPK/ERK Kinase Inhibitor. Drug Metab Dispos 2015; 43:1929-33. [DOI: 10.1124/dmd.115.067181] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/02/2015] [Indexed: 11/22/2022] Open
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27
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The nuclear translocation of ERK1/2 as an anticancer target. Nat Commun 2015; 6:6685. [PMID: 25819065 DOI: 10.1038/ncomms7685] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 02/18/2015] [Indexed: 12/22/2022] Open
Abstract
A hallmark of the ERK1/2 functioning is their nuclear translocation, which is mainly required for the induction of proliferation. Activated ERK1/2 molecules that remain in the cytoplasm initiate other activities, including immediate feedback loops. Prevention of the nuclear translocation should therefore inhibit proliferation, without affecting cytoplasm-induced cellular processes. Here we present an NTS-derived myristoylated phosphomimetic peptide, which blocks the interaction of importin7 and ERK1/2, and consequently the nuclear translocation of the latter. In culture, the peptide induces apoptosis of melanoma cells inhibits the viability of other cancer cells, but has no effect on non-transformed, immortalized cells. It even inhibits the viability of PLX4032- and U0126-resistant melanoma cells. In xenograft models, the peptide inhibits several cancers, and acts much better than PLX4032 in preventing melanoma recurrence. This study provides a proof of concept for using the nuclear translocation of ERK1/2 as a drug target for the combat of various ERK1/2-related cancers.
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