1
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Klett T, Schwer M, Ernst LN, Engelhardt MU, Jaag SJ, Masberg B, Knappe C, Lämmerhofer M, Gehringer M, Boeckler FM. Evaluation of a Covalent Library of Diverse Warheads (CovLib) Binding to JNK3, USP7, or p53. Drug Des Devel Ther 2024; 18:2653-2679. [PMID: 38974119 PMCID: PMC11226190 DOI: 10.2147/dddt.s466829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/12/2024] [Indexed: 07/09/2024] Open
Abstract
Purpose Over the last few years, covalent fragment-based drug discovery has gained significant importance. Thus, striving for more warhead diversity, we conceived a library consisting of 20 covalently reacting compounds. Our covalent fragment library (CovLib) contains four different warhead classes, including five α-cyanoacacrylamides/acrylates (CA), three epoxides (EO), four vinyl sulfones (VS), and eight electron-deficient heteroarenes with a leaving group (SNAr/SN). Methods After predicting the theoretical solubility of the fragments by LogP and LogS during the selection process, we determined their experimental solubility using a turbidimetric solubility assay. The reactivities of the different compounds were measured in a high-throughput 5,5'-dithiobis-(2-nitrobenzoic acid) DTNB assay, followed by a (glutathione) GSH stability assay. We employed the CovLib in a (differential scanning fluorimetry) DSF-based screening against different targets: c-Jun N-terminal kinase 3 (JNK3), ubiquitin-specific protease 7 (USP7), and the tumor suppressor p53. Finally, the covalent binding was confirmed by intact protein mass spectrometry (MS). Results In general, the purchased fragments turned out to be sufficiently soluble. Additionally, they covered a broad spectrum of reactivity. All investigated α-cyanoacrylamides/acrylates and all structurally confirmed epoxides turned out to be less reactive compounds, possibly due to steric hindrance and reversibility (for α-cyanoacrylamides/acrylates). The SNAr and vinyl sulfone fragments are either highly reactive or stable. DSF measurements with the different targets JNK3, USP7, and p53 identified reactive fragment hits causing a shift in the melting temperatures of the proteins. MS confirmed the covalent binding mode of all these fragments to USP7 and p53, while additionally identifying the SNAr-type electrophile SN002 as a mildly reactive covalent hit for p53. Conclusion The screening and target evaluation of the CovLib revealed first interesting hits. The highly cysteine-reactive fragments VS004, SN001, SN006, and SN007 covalently modify several target proteins and showed distinct shifts in the melting temperatures up to +5.1 °C and -9.1 °C.
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Affiliation(s)
- Theresa Klett
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Martin Schwer
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Larissa N Ernst
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Marc U Engelhardt
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Simon J Jaag
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Benedikt Masberg
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Cornelius Knappe
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Michael Lämmerhofer
- Pharmaceutical (Bio-) Analysis, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Matthias Gehringer
- Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Medicinal Chemistry, Institute for Biomedical Engineering, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
| | - Frank M Boeckler
- Laboratory for Molecular Design & Pharmaceutical Biophysics, Institute of Pharmaceutical Sciences, Department of Pharmacy and Biochemistry, Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
- Interfaculty Institute for Biomedical Informatics (IBMI), Eberhard Karls Universität Tübingen, Tübingen, 72076, Germany
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2
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Zhang S, Zhang X, Li L, Shi Z, Wang Y. Synthesis of Pyridazino[4,5-b]indoles by [3+3] Annulation of 2-Alkenylindoles and Hydrazonyl Chlorides. Chemistry 2024; 30:e202400278. [PMID: 38406889 DOI: 10.1002/chem.202400278] [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: 01/22/2024] [Revised: 02/25/2024] [Accepted: 02/26/2024] [Indexed: 02/27/2024]
Abstract
A novel [3+3] annulation reaction of 2-alkenylindoles with hydrazonyl chlorides in the presence of base for the formation of pyridazino[4,5-b]indoles was developed. This approach provided a convenient and efficient way to synthesize a series of functionalized pyridazino[4,5-b]indoles derivatives. The method exhibited a broad substrate scope and provided the corresponding pyridazino[4,5-b]indoles products with excellent yields.
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Affiliation(s)
- Shuting Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Xinyu Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Lesong Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Zhenyu Shi
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
| | - Yang Wang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao, 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology (QNLM), Qingdao, 266237, China
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3
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Zhang T, Jiang S, Li T, Liu Y, Zhang Y. Identified Isosteric Replacements of Ligands' Glycosyl Domain by Data Mining. ACS OMEGA 2023; 8:25165-25184. [PMID: 37483233 PMCID: PMC10357434 DOI: 10.1021/acsomega.3c02243] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023]
Abstract
Biologically equivalent replacements of key moieties in molecules rationalize scaffold hopping, patent busting, or R-group enumeration. Yet, this information may depend upon the expert-defined space, and might be subjective and biased toward the chemistries they get used to. Most importantly, these practices are often informatively incomplete since they are often compromised by a try-and-error cycle, and although they depict what kind of substructures are suitable for the replacement occurrence, they fail to explain the driving forces to support such interchanges. The protein data bank (PDB) encodes a receptor-ligand interaction pattern and could be an optional source to mine structural surrogates. However, manual decoding of PDB has become almost impossible and redundant to excavate the bioisosteric know-how. Therefore, a text parsing workflow has been developed to automatically extract the local structural replacement of a specific structure from PDB by finding spatial and steric interaction overlaps between the fragments in endogenous ligands and particular ligand fragments. Taking the glycosyl domain for instance, a total of 49 520 replacements that overlap on nucleotide ribose were identified and categorized based on their SMILE codes. A predominately ring system, such as aliphatic and aromatic rings, was observed; yet, amide and sulfonamide replacements also occur. We believe these findings may enlighten medicinal chemists on the structure design and optimization of ligands using the bioisosteric replacement strategy.
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Affiliation(s)
- Tinghao Zhang
- Xi’an
Institute of Flexible Electronics (IFE) and Xi’an Institute
of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical
University, 127 West Youyi Road, Xi’an 710072, China
| | - Shenghao Jiang
- School of
Computer Science, Northwestern Polytechnical
University, 127 West
Youyi Road, Xi’an 710072, China
| | - Ting Li
- Xi’an
Institute of Flexible Electronics (IFE) and Xi’an Institute
of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical
University, 127 West Youyi Road, Xi’an 710072, China
| | - Yan Liu
- Xi’an
Institute of Flexible Electronics (IFE) and Xi’an Institute
of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical
University, 127 West Youyi Road, Xi’an 710072, China
| | - Yuezhou Zhang
- Xi’an
Institute of Flexible Electronics (IFE) and Xi’an Institute
of Biomedical Materials & Engineering (IBME), Northwestern Polytechnical
University, 127 West Youyi Road, Xi’an 710072, China
- Ningbo
Institute of Northwestern Polytechnical University, Frontiers Science
Center for Flexible Electronics (FSCFE), Key laboratory of Flexible
Electronics of Zhejiang Province, Ningbo Institute of Northwestern
Polytechnical University, 218 Qingyi Road, Ningbo 315103, China
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4
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Lindberg MF, Deau E, Arfwedson J, George N, George P, Alfonso P, Corrionero A, Meijer L. Comparative Efficacy and Selectivity of Pharmacological Inhibitors of DYRK and CLK Protein Kinases. J Med Chem 2023; 66:4106-4130. [PMID: 36876904 DOI: 10.1021/acs.jmedchem.2c02068] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Dual-specificity, tyrosine phosphorylation-regulated kinases (DYRKs) and cdc2-like kinases (CLKs) play a large variety of cellular functions and are involved in several diseases (cognitive disorders, diabetes, cancers, etc.). There is, thus, growing interest in pharmacological inhibitors as chemical probes and potential drug candidates. This study presents an unbiased evaluation of the kinase inhibitory activity of a library of 56 reported DYRK/CLK inhibitors on the basis of comparative, side-by-side, catalytic activity assays on a panel of 12 recombinant human kinases, enzyme kinetics (residence time and Kd), in-cell inhibition of Thr-212-Tau phosphorylation, and cytotoxicity. The 26 most active inhibitors were modeled in the crystal structure of DYRK1A. The results show a rather large diversity of potencies and selectivities among the reported inhibitors and emphasize the difficulties to avoid "off-targets" in this area of the kinome. The use of a panel of DYRKs/CLKs inhibitors is suggested to analyze the functions of these kinases in cellular processes.
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Affiliation(s)
| | - Emmanuel Deau
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
| | - Jonas Arfwedson
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
| | - Nicolas George
- Oncodesign, 25-27 avenue du Québec, 91140 Villebon-sur-Yvette, France
| | - Pascal George
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
| | - Patricia Alfonso
- Enzymlogic, Qube Technology Park, C/Santiago Grisolía, 2, 28760 Madrid, Spain
| | - Ana Corrionero
- Enzymlogic, Qube Technology Park, C/Santiago Grisolía, 2, 28760 Madrid, Spain
| | - Laurent Meijer
- Perha Pharmaceuticals, Perharidy Peninsula, 29680 Roscoff, France
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5
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Patel V, Bambharoliya T, Shah D, Patel Y, Savaliya N, Patel Y, Patel R, Bhavsar V, Patel H, Patel M, Patel A. Recent Progress for the Synthesis of β-Carboline Derivatives – an Update. Polycycl Aromat Compd 2023. [DOI: 10.1080/10406638.2023.2180525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Affiliation(s)
- Vidhi Patel
- Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, CHARUSAT Campus, Changa, India
| | | | - Drashti Shah
- Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, CHARUSAT Campus, Changa, India
| | - Yug Patel
- Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, CHARUSAT Campus, Changa, India
| | - Neel Savaliya
- Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, CHARUSAT Campus, Changa, India
| | - Yash Patel
- Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, CHARUSAT Campus, Changa, India
| | - Riddhisiddhi Patel
- Department of Pharmaceutical Sciences, Saurashtra University, Rajkot, India
| | | | - Harnisha Patel
- Department of Pharmaceutical Chemistry, Parul Institute of Pharmacy, Parul University, Vadodara, India
| | - Mehul Patel
- Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, CHARUSAT Campus, Changa, India
| | - Ashish Patel
- Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, CHARUSAT Campus, Changa, India
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6
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Soni JP, Nikitha Reddy G, Rahman Z, Sharma A, Spandana A, Phanindranath R, Dandekar MP, Nagesh N, Shankaraiah N. Synthesis and cytotoxicity evaluation of DNA-interactive β-carboline indolyl-3-glyoxamide derivatives: Topo-II inhibition and in silico modelling studies. Bioorg Chem 2023; 131:106313. [PMID: 36516521 DOI: 10.1016/j.bioorg.2022.106313] [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: 10/19/2022] [Revised: 11/18/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
In a quest for effective cancer targeted drug therapy, a series of new β-carboline tethered indole-3-glyoxylamide derivatives, conjoining salient pharmacophoric properties with prominent cytotoxicity, were synthesized. The in vitro cytotoxic ability of the compounds was established, and many of the compounds exhibited remarkable cytotoxicity (IC50 < 10 μM) on human cancer cell lines like HCT116, A549, SK-MEL-28, and MCF7. Precisely, compound 12x expressed the best cytotoxic potential against melanoma cancer cell line (SK-MEL-28) with an IC50 value of 4.37 μM. In addition, cytotoxicity evaluation against normal kidney cell line (NRK52E) entrenched the cytospecificity and selectivity index of 12x. The traditional apoptosis assays advised morphological and nuclear alterations such as apoptotic body formation, condensed/horseshoe-shaped/fragmented nuclei, and generation of ROS. The flow cytometric analysis revealed significant early and slight late-stage induction of apoptosis. The target-based physiochemical assays indicated the ability of compound 12x to bind with DNA and inhibition of Topoisomerase II. Moreover, molecular modeling studies affirm the excellent DNA intercalation potential and stabilized interactions of 12x with DNA base pairs. In silico prediction of physicochemical parameters revealed the promising drug-like properties of the synthesized derivatives.
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Affiliation(s)
- Jay Prakash Soni
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - G Nikitha Reddy
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Ziaur Rahman
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Anamika Sharma
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Akella Spandana
- CSIR-Centre for Cellular and Molecular Biology, Medical Biotechnology Complex, ANNEXE II, Uppal Road, Hyderabad 500007, India
| | - Regur Phanindranath
- CSIR-Centre for Cellular and Molecular Biology, Medical Biotechnology Complex, ANNEXE II, Uppal Road, Hyderabad 500007, India
| | - Manoj P Dandekar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India.
| | - Narayana Nagesh
- CSIR-Centre for Cellular and Molecular Biology, Medical Biotechnology Complex, ANNEXE II, Uppal Road, Hyderabad 500007, India.
| | - Nagula Shankaraiah
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India.
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7
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Al-Sha'er MA, Basheer HA, Taha MO. Discovery of new PKN2 inhibitory chemotypes via QSAR-guided selection of docking-based pharmacophores. Mol Divers 2023; 27:443-462. [PMID: 35507210 DOI: 10.1007/s11030-022-10434-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/05/2022] [Indexed: 12/13/2022]
Abstract
Serine/threonine-protein kinase N2 (PKN2) plays an important role in cell cycle progression, cell migration, cell adhesion and transcription activation signaling processes. In cancer, however, it plays important roles in tumor cell migration, invasion and apoptosis. PKN2 inhibitors have been shown to be promising in treating cancer. This prompted us to model this interesting target using our QSAR-guided selection of docking-based pharmacophores approach where numerous pharmacophores are extracted from docked ligand poses and allowed to compete within the context of QSAR. The optimal pharmacophore was sterically-refined, validated by receiver operating characteristic (ROC) curve analysis and used as virtual search query to screen the National Cancer Institute (NCI) database for new promising anti-PKN2 leads of novel chemotypes. Three low micromolar hits were identified with IC50 values ranging between 9.9 and 18.6 µM. Pharmacological assays showed promising cytotoxic properties for active hits in MTT and wound healing assays against MCF-7 and PANC-1 cancer cells.
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Affiliation(s)
- Mahmoud A Al-Sha'er
- Faculty of Pharmacy, Zarqa University, P.O. Box 132222, Zarqa, 13132, Jordan.
| | - Haneen A Basheer
- Faculty of Pharmacy, Zarqa University, P.O. Box 132222, Zarqa, 13132, Jordan
| | - Mutasem O Taha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Amman, Jordan.
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8
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Segretti ND, Takarada JE, Ferreira MA, da Silva Santiago A, Teodoro BVM, Damião MCFCB, Godoi PH, Cunha MR, Fala AM, Ramos PZ, Ishikawa EE, Mascarello A, Serafim RAM, Azevedo H, Guimarães CRW, Couñago RM. Discovery of novel benzothiophene derivatives as potent and narrow spectrum inhibitors of DYRK1A and DYRK1B. Bioorg Med Chem Lett 2022; 68:128764. [PMID: 35504513 DOI: 10.1016/j.bmcl.2022.128764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/18/2022]
Abstract
The discovery of potent and selective inhibitors for understudied kinases can provide relevant pharmacological tools to illuminate their biological functions. DYRK1A and DYRK1B are protein kinases linked to chronic human diseases. Current DYRK1A/DYRK1B inhibitors also antagonize the function of related protein kinases, such as CDC2-like kinases (CLK1, CLK2, CLK4) and DYRK2. Here, we reveal narrow spectrum dual inhibitors of DYRK1A and DYRK1B based on a benzothiophene scaffold. Compound optimization exploited structural differences in the ATP-binding sites of the DYRK1 kinases and resulted in the discovery of 3n, a potent and cell-permeable DYRK1A/DYRK1B inhibitor. This compound has a different scaffold and a narrower off-target profile compared to current DYRK1A/DYRK1B inhibitors. We expect the benzothiophene derivatives described here to aid establishing DYRK1A/DYRK1B cellular functions and their role in human pathologies.
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Affiliation(s)
| | - Jéssica E Takarada
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil
| | - Marcos A Ferreira
- Aché Laboratórios Farmacêuticos S.A., Guarulhos, SP 07034-904, Brazil
| | - André da Silva Santiago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil
| | - Bruno V M Teodoro
- Aché Laboratórios Farmacêuticos S.A., Guarulhos, SP 07034-904, Brazil
| | | | - Paulo H Godoi
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil
| | - Micael R Cunha
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil
| | - Angela M Fala
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil
| | - Priscila Z Ramos
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil
| | - Eloisa E Ishikawa
- Aché Laboratórios Farmacêuticos S.A., Guarulhos, SP 07034-904, Brazil
| | | | - Ricardo A M Serafim
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil
| | - Hatylas Azevedo
- Aché Laboratórios Farmacêuticos S.A., Guarulhos, SP 07034-904, Brazil.
| | | | - Rafael M Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-875, Brazil.
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9
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Chen HM, MacDonald JA. Death-associated protein kinases and intestinal epithelial homeostasis. Anat Rec (Hoboken) 2022; 306:1062-1087. [PMID: 35735750 DOI: 10.1002/ar.25022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/12/2022] [Accepted: 06/06/2022] [Indexed: 12/15/2022]
Abstract
The family of death-associated protein kinases (DAPKs) and DAPK-related apoptosis-inducing protein kinases (DRAKs) act as molecular switches for a multitude of cellular processes, including apoptotic and autophagic cell death events. This review summarizes the mechanisms for kinase activity regulation and discusses recent molecular investigations of DAPK and DRAK family members in the intestinal epithelium. In general, recent literature convincingly supports the importance of this family of protein kinases in the homeostatic processes that govern the proper function of the intestinal epithelium. Each of the DAPK family of proteins possesses distinct biochemical properties, and we compare similarities in the information available as well as those cases where functional distinctions are apparent. As the prototypical member of the family, DAPK1 is noteworthy for its tumor suppressor function and association with colorectal cancer. In the intestinal epithelium, DAPK2 is associated with programmed cell death, potential tumor-suppressive functions, and a unique influence on granulocyte biology. The impact of the DRAKs in the epithelium is understudied, but recent studies support a role for DRAK1 in inflammation-mediated tumor growth and metastasis. A commentary is provided on the potential importance of DAPK3 in facilitating epithelial restitution and wound healing during the resolution of colitis. An update on efforts to develop selective pharmacologic effectors of individual DAPK members is also supplied.
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Affiliation(s)
- Huey-Miin Chen
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Justin A MacDonald
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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10
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Pavić K, Beus M, Poje G, Uzelac L, Kralj M, Rajić Z. Synthesis and Biological Evaluation of Harmirins, Novel Harmine-Coumarin Hybrids as Potential Anticancer Agents. Molecules 2021; 26:molecules26216490. [PMID: 34770906 PMCID: PMC8587047 DOI: 10.3390/molecules26216490] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
As cancer remains one of the major health burdens worldwide, novel agents, due to the development of resistance, are needed. In this work, we designed and synthesized harmirins, which are hybrid compounds comprising harmine and coumarin scaffolds, evaluated their antiproliferative activity, and conducted cell localization and cell cycle analysis experiments. Harmirins were prepared from the corresponding alkynes and azides under mild reaction conditions using Cu(I) catalyzed azide–alkyne cycloaddition, leading to the formation of the 1H-1,2,3-triazole ring. Antiproliferative activity of harmirins was evaluated in vitro against four human cancer cell lines (MCF-7, HCT116, SW620, and HepG2) and one human non-cancer cell line (HEK293T). The most pronounced activities were exerted against MCF-7 and HCT116 cell lines (IC50 in the single-digit micromolar range), while the most selective harmirins were 5b and 12b, substituted at C-3 and O-7 of the β-carboline core and bearing methyl substituent at position 6 of the coumarin ring (SIs > 7.2). Further experiments demonstrated that harmirin 12b is localized exclusively in the cytoplasm. In addition, it induced a strong G1 arrest and reduced the percentage of cells in the S phase, suggesting that it might exert its antiproliferative activity through inhibition of DNA synthesis, rather than DNA damage. In conclusion, harmirin 12b is a novel harmine and coumarin hybrid with significant antiproliferative activity and warrants further evaluation as a potential anticancer agent.
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Affiliation(s)
- Kristina Pavić
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10 000 Zagreb, Croatia; (K.P.); (M.B.); (G.P.)
| | - Maja Beus
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10 000 Zagreb, Croatia; (K.P.); (M.B.); (G.P.)
| | - Goran Poje
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10 000 Zagreb, Croatia; (K.P.); (M.B.); (G.P.)
| | - Lidija Uzelac
- Laboratory of Experimental Therapy, Division of Molecular Medicine, Ruđer Bošković Institute, 10 000 Zagreb, Croatia; (L.U.); (M.K.)
| | - Marijeta Kralj
- Laboratory of Experimental Therapy, Division of Molecular Medicine, Ruđer Bošković Institute, 10 000 Zagreb, Croatia; (L.U.); (M.K.)
| | - Zrinka Rajić
- Faculty of Pharmacy and Biochemistry, University of Zagreb, 10 000 Zagreb, Croatia; (K.P.); (M.B.); (G.P.)
- Correspondence:
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11
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Huang B, Chen Y, Zhang X, Yan M. Cross‐Dehydrogenative Coupling of Tetrahydroisoquinolines and 2‐Fluoro‐1,3‐benzodithiole‐1,1,3,3‐tetraoxide: A New Synthetic Approach to α‐Monofluoromethyl Tertiary Amines. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Bao‐qin Huang
- Guangdong Provincial Key Laboratory of Chiral Molecules and Drug Discovery School of Pharmaceutical Sciences Sun Yat-sen University Guangzhou 510006 China
| | - Yuan Chen
- State Key Laboratory of Medicinal Chemical Biology College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research Nankai University Tianjin 300353 China
| | - Xue‐jing Zhang
- Guangdong Provincial Key Laboratory of Chiral Molecules and Drug Discovery School of Pharmaceutical Sciences Sun Yat-sen University Guangzhou 510006 China
| | - Ming Yan
- Guangdong Provincial Key Laboratory of Chiral Molecules and Drug Discovery School of Pharmaceutical Sciences Sun Yat-sen University Guangzhou 510006 China
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12
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Weber C, Sipos M, Paczal A, Balint B, Kun V, Foloppe N, Dokurno P, Massey AJ, Walmsley DL, Hubbard RE, Murray J, Benwell K, Edmonds T, Demarles D, Bruno A, Burbridge M, Cruzalegui F, Kotschy A. Structure-Guided Discovery of Potent and Selective DYRK1A Inhibitors. J Med Chem 2021; 64:6745-6764. [PMID: 33975430 DOI: 10.1021/acs.jmedchem.1c00023] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The kinase DYRK1A is an attractive target for drug discovery programs due to its implication in multiple diseases. Through a fragment screen, we identified a simple biaryl compound that is bound to the DYRK1A ATP site with very high efficiency, although with limited selectivity. Structure-guided optimization cycles enabled us to convert this fragment hit into potent and selective DYRK1A inhibitors. Exploiting the structural differences in DYRK1A and its close homologue DYRK2, we were able to fine-tune the selectivity of our inhibitors. Our best compounds potently inhibited DYRK1A in the cell culture and in vivo and demonstrated drug-like properties. The inhibition of DYRK1A in vivo translated into dose-dependent tumor growth inhibition in a model of ovarian carcinoma.
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Affiliation(s)
- Csaba Weber
- Servier Research Institute of Medicinal Chemistry, Záhony u. 7., H-1031 Budapest, Hungary
| | - Melinda Sipos
- Servier Research Institute of Medicinal Chemistry, Záhony u. 7., H-1031 Budapest, Hungary
| | - Attila Paczal
- Servier Research Institute of Medicinal Chemistry, Záhony u. 7., H-1031 Budapest, Hungary
| | - Balazs Balint
- Servier Research Institute of Medicinal Chemistry, Záhony u. 7., H-1031 Budapest, Hungary
| | - Vilibald Kun
- Servier Research Institute of Medicinal Chemistry, Záhony u. 7., H-1031 Budapest, Hungary
| | | | - Pawel Dokurno
- Vernalis (R&D) Ltd., Granta Park, CB21 6GB Cambridge, U.K
| | | | | | | | - James Murray
- Vernalis (R&D) Ltd., Granta Park, CB21 6GB Cambridge, U.K
| | - Karen Benwell
- Vernalis (R&D) Ltd., Granta Park, CB21 6GB Cambridge, U.K
| | - Thomas Edmonds
- Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Didier Demarles
- Technologie Servier, 27 Rue Eugène Vignat, 45000 Orleans, France
| | - Alain Bruno
- Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Mike Burbridge
- Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Francisco Cruzalegui
- Institut de Recherches Servier, 125 Chemin de Ronde, 78290 Croissy-sur-Seine, France
| | - Andras Kotschy
- Servier Research Institute of Medicinal Chemistry, Záhony u. 7., H-1031 Budapest, Hungary
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13
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β-Carbolines as potential anticancer agents. Eur J Med Chem 2021; 216:113321. [PMID: 33684825 DOI: 10.1016/j.ejmech.2021.113321] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 01/18/2023]
Abstract
β-Carbolines are indole alkaloids having a tricyclic pyrido[3,4-b]indole ring in their structure. Since the isolation of first β-carboline from Peganum harmala in 1841, the isolation and synthesis of various β-carboline derivatives surged in the following centuries. β-Carboline derivatives due to their widespread availability from natural sources, structural flexibility, quick reactivity and interaction with varied anticancer targets such as DNA (intercalation, groove binding, etc.), enzymes (GPX4, topoisomerases, kinases, etc.) and proteins (tubulin, ABCG2/BRCP1, etc.) have established themselves as promising lead compounds for the synthesis of various anticancer active agents. The current review covers the synthesis and isolation, anticancer activity, mechanism of action and SAR of various β-carboline containing molecules, its derivatives and congeners.
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14
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Wurzlbauer A, Rüben K, Gürdal E, Chaikuad A, Knapp S, Sippl W, Becker W, Bracher F. How to Separate Kinase Inhibition from Undesired Monoamine Oxidase A Inhibition-The Development of the DYRK1A Inhibitor AnnH75 from the Alkaloid Harmine. Molecules 2020; 25:E5962. [PMID: 33339338 PMCID: PMC7765920 DOI: 10.3390/molecules25245962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/15/2023] Open
Abstract
The β-carboline alkaloid harmine is a potent DYRK1A inhibitor, but suffers from undesired potent inhibition of MAO-A, which strongly limits its application. We synthesized more than 60 analogues of harmine, either by direct modification of the alkaloid or by de novo synthesis of β-carboline and related scaffolds aimed at learning about structure-activity relationships for inhibition of both DYRK1A and MAO-A, with the ultimate goal of separating desired DYRK1A inhibition from undesired MAO-A inhibition. Based on evidence from published crystal structures of harmine bound to each of these enzymes, we performed systematic structure modifications of harmine yielding DYRK1A-selective inhibitors characterized by small polar substituents at N-9 (which preserve DYRK1A inhibition and eliminate MAO-A inhibition) and beneficial residues at C-1 (methyl or chlorine). The top compound AnnH75 remains a potent DYRK1A inhibitor, and it is devoid of MAO-A inhibition. Its binding mode to DYRK1A was elucidated by crystal structure analysis, and docking experiments provided additional insights for this attractive series of DYRK1A and MAO-A inhibitors.
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Affiliation(s)
- Anne Wurzlbauer
- Department of Pharmacy—Center for Drug Research, Ludwig-Maximilians University, 81377 Munich, Germany;
| | - Katharina Rüben
- Institute of Pharmacology and Toxicology, RWTH Aachen University, 52074 Aachen, Germany; (K.R.); (W.B.)
| | - Ece Gürdal
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (E.G.); (W.S.)
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry and Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, 60438 Frankfurt, Germany; (A.C.); (S.K.)
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry and Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, 60438 Frankfurt, Germany; (A.C.); (S.K.)
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany; (E.G.); (W.S.)
| | - Walter Becker
- Institute of Pharmacology and Toxicology, RWTH Aachen University, 52074 Aachen, Germany; (K.R.); (W.B.)
| | - Franz Bracher
- Department of Pharmacy—Center for Drug Research, Ludwig-Maximilians University, 81377 Munich, Germany;
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15
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Tokala R, Sana S, Lakshmi UJ, Sankarana P, Sigalapalli DK, Gadewal N, Kode J, Shankaraiah N. Design and synthesis of thiadiazolo-carboxamide bridged β-carboline-indole hybrids: DNA intercalative topo-IIα inhibition with promising antiproliferative activity. Bioorg Chem 2020; 105:104357. [PMID: 33091673 PMCID: PMC7543778 DOI: 10.1016/j.bioorg.2020.104357] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/03/2020] [Accepted: 10/05/2020] [Indexed: 02/05/2023]
Abstract
The conjoining of salient pharmacophoric properties directing the development of prominent cytotoxic agents was executed by constructing thiadiazolo-carboxamide bridged β-carboline-indole hybrids. On the evaluation of in vitro cytotoxic potential, 12c exhibited prodigious cytotoxicity among the synthesized new molecules 12a-k, with an IC50 < 5 μM in all the tested cancer cell lines (A549, MDA-MB-231, BT-474, HCT-116, THP-1) and the best cytotoxic potential was expressed in lung cancer cell line (A549) with an IC50 value of 2.82 ± 0.10 μM. Besides, another compound 12a also displayed impressive cytotoxicity against A549 cell line (IC50: 3.00 ± 1.40 μM). Further target-based assay of these two compounds 12c and 12a revealed their potential as DNA intercalative topoisomerase-IIα inhibitors. Additionally, the antiproliferative activity of compound 12c was measured in A549 cells by traditional apoptosis assays revealing the nuclear, morphological alterations, and depolarization of membrane potential in mitochondria and externalization of phosphatidylserine in a concentration-dependent manner. Cell cycle analysis unveiled the G0/G1 phase inhibition and wound healing assay inferred the inhibition of in vitro cell migration by compound 12c in lung cancer cells. Remarkably, the safety profile of compound 12c was disclosed by screening against normal human lung epithelial cell line (BEAS-2B: IC50: 71.2 ± 7.95 μM) with a selectivity index range of 14.9-25.26. Moreover, Molecular modeling studies affirm the intercalative binding of compound 12c and 12a in the active pocket of topo-IIα. Furthermore, in silico prediction of physico-chemical parameters divulged the propitious drug-like properties of the synthesized derivatives.
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Affiliation(s)
- Ramya Tokala
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Sravani Sana
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Uppu Jaya Lakshmi
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Prasanthi Sankarana
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Dilep Kumar Sigalapalli
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Nikhil Gadewal
- Bioinformatics Centre, Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India
| | - Jyoti Kode
- Tumor Immunology & Immunotherapy Group, Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, India; Homi-Bhabha National Institute (HBNI), Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Nagula Shankaraiah
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India.
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16
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Schröder M, Bullock AN, Fedorov O, Bracher F, Chaikuad A, Knapp S. DFG-1 Residue Controls Inhibitor Binding Mode and Affinity, Providing a Basis for Rational Design of Kinase Inhibitor Selectivity. J Med Chem 2020; 63:10224-10234. [PMID: 32787076 DOI: 10.1021/acs.jmedchem.0c00898] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Selectivity remains a challenge for ATP-mimetic kinase inhibitors, an issue that may be overcome by targeting unique residues or binding pockets. However, to date only few strategies have been developed. Here we identify that bulky residues located N-terminal to the DFG motif (DFG-1) represent an opportunity for designing highly selective inhibitors with unexpected binding modes. We demonstrate that several diverse inhibitors exerted selective, noncanonical binding modes that exclusively target large hydrophobic DFG-1 residues present in many kinases including PIM, CK1, DAPK, and CLK. By use of the CLK family as a model, structural and biochemical data revealed that the DFG-1 valine controlled a noncanonical binding mode in CLK1, providing a rationale for selectivity over the closely related CLK3 which harbors a smaller DFG-1 alanine. Our data suggest that targeting the restricted back pocket in the small fraction of kinases that harbor bulky DFG-1 residues offers a versatile selectivity filter for inhibitor design.
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Affiliation(s)
- Martin Schröder
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestraße 9, 60438 Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, Max von Lauestraße 15, 60438 Frankfurt, Germany
| | - Alex N Bullock
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, U.K
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, U.K
| | - Franz Bracher
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestraße 9, 60438 Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, Max von Lauestraße 15, 60438 Frankfurt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestraße 9, 60438 Frankfurt, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-University Frankfurt, Max von Lauestraße 15, 60438 Frankfurt, Germany.,German Translational Cancer Network (DKTK), Frankfurt/Mainz Site, 60438 Frankfurt, Germany
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17
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Kamlah A, Bracher F. A Novel Approach to Highly Substituted β‐Carbolines via Reductive Ring Transformation of 2‐Acyl‐3‐isoxazolylindoles. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Alexandra Kamlah
- Department of Pharmacy Center for Drug Research Ludwig‐Maximilians University Butenandtstr. 5‐13 81377 Munich Germany
| | - Franz Bracher
- Department of Pharmacy Center for Drug Research Ludwig‐Maximilians University Butenandtstr. 5‐13 81377 Munich Germany
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18
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Untergehrer M, Bracher F. A short divergent approach to highly substituted carbazoles and β-carbolines via in situ-generated diketoindoles. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Fillery SM, Gregson CL, Guérot CM. Expeditious Access to Functionalized Tricyclic Pyrrolo-Pyridones via Tandem or Sequential C–N/C–C Bond Formations. Org Lett 2019; 21:9128-9132. [PMID: 31696715 DOI: 10.1021/acs.orglett.9b03514] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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20
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Guryev AA, Hahn F, Marschall M, Tsogoeva SB. Visible‐Light‐Driven C−H Oxidation of Cyclic Tertiary Amines: Access to Synthetic
Strychnos
Alkaloids with Antiviral Activity. Chemistry 2019; 25:4062-4066. [DOI: 10.1002/chem.201900078] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Anton A. Guryev
- Organic Chemistry Chair I and Interdisciplinary Center for, Molecular Materials (ICMM)Friedrich-Alexander University of Erlangen-Nürnberg Nikolaus-Fiebiger-Strasse 10 91058 Erlangen Germany
| | - Friedrich Hahn
- Institute for Clinical and Molecular VirologyFriedrich-Alexander University of Erlangen-Nürnberg Schlossgarten 4 91054 Erlangen Germany
| | - Manfred Marschall
- Institute for Clinical and Molecular VirologyFriedrich-Alexander University of Erlangen-Nürnberg Schlossgarten 4 91054 Erlangen Germany
| | - Svetlana B. Tsogoeva
- Organic Chemistry Chair I and Interdisciplinary Center for, Molecular Materials (ICMM)Friedrich-Alexander University of Erlangen-Nürnberg Nikolaus-Fiebiger-Strasse 10 91058 Erlangen Germany
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21
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Sahoo CR, Paidesetty SK, Padhy RN. Norharmane as a potential chemical entity for development of anticancer drugs. Eur J Med Chem 2018; 162:752-764. [PMID: 30496990 DOI: 10.1016/j.ejmech.2018.11.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 10/30/2018] [Accepted: 11/08/2018] [Indexed: 11/24/2022]
Abstract
Cancer is a leading cause of death generally, and to overcome this problem the introduction of a new drug developing is a continuous endeavour. An alkaloid, norharmane and its derivatives, which have anticancer activities, widely distributed in several living and synthetic chemical sources. Herewith, the suggested mechanisms of organic reactions and synthetic approaches of norharmane available so far were considered. Active sites of norharmane nucleus positions, C-1, C-3, and N-9, were used for developing new molecules and based on structure activity relationship (SAR), those have been seen with anticancer activities. This review summarizes on chemistry of synthetic strategies of norharmane derivatives, which may provide a framework to design a novel anticancer drug, in future.
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Affiliation(s)
- Chita Ranjan Sahoo
- Central Research Laboratory, Institute of Medical Sciences & Sum Hospital, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751003, Odisha, India
| | - Sudhir Kumar Paidesetty
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751003, Odisha, India.
| | - Rabindra Nath Padhy
- Central Research Laboratory, Institute of Medical Sciences & Sum Hospital, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, 751003, Odisha, India.
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22
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Al-Ghabkari A, Moffat LD, Walsh MP, MacDonald JA. Validation of chemical genetics for the study of zipper-interacting protein kinase signaling. Proteins 2018; 86:1211-1217. [PMID: 30381843 DOI: 10.1002/prot.25607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/05/2018] [Accepted: 09/14/2018] [Indexed: 01/23/2023]
Abstract
Zipper-interacting protein kinase (ZIPK) is a Ser/Thr kinase that mediates a variety of cellular functions. Analogue-sensitive kinase technology was applied to the study of ZIPK signaling in coronary artery smooth muscle cells. ZIPK was engineered in the ATP-binding pocket by substitution of a bulky gatekeeper amino acid (Leu93) with glycine. Cell-permeable derivatives of pyrazolo[3,4-d]pyrimidine provided effective inhibition of L93G-ZIPK (1NM-PP1, IC50 , 1.0 μM; 3MB-PP1, IC50 , 2.0 μM; and 1NA-PP1, IC50 , 8.6 μM) but only 3MB-PP1 had inhibitory potential (IC50 > 10 μM) toward wild-type ZIPK. Each of the compounds also attenuated Rho-associated coiled-coil containing protein kinase (ROCK) activity under experimental conditions found to be optimal for inhibition of L93G-ZIPK. In silico molecular simulations showed effective docking of 1NM-PP1 into ZIPK following mutational enlargement of the ATP-binding pocket. Molecular simulation of 1NM-PP1 docking in the ATP-binding pocket of ROCK was also completed. The 1NM-PP1 inhibitor was selected as the optimal compound for selective chemical genetics in smooth muscle cells since it displayed the highest potency for L93G-ZIPK relative to WT-ZIPK and the weakest off-target effects against other relevant kinases. Finally, the 1NM-PP1 and L93G-ZIPK pairing was effectively applied in vascular smooth muscle cells to manipulate the phosphorylation level of LC20, a previously defined target of ZIPK.
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Affiliation(s)
- Abdulhameed Al-Ghabkari
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Lori D Moffat
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Michael P Walsh
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Justin A MacDonald
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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23
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Carlson DA, Singer MR, Sutherland C, Redondo C, Alexander LT, Hughes PF, Knapp S, Gurley SB, Sparks MA, MacDonald JA, Haystead TAJ. Targeting Pim Kinases and DAPK3 to Control Hypertension. Cell Chem Biol 2018; 25:1195-1207.e32. [PMID: 30033129 PMCID: PMC6863095 DOI: 10.1016/j.chembiol.2018.06.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 03/16/2018] [Accepted: 06/20/2018] [Indexed: 01/19/2023]
Abstract
Sustained vascular smooth muscle hypercontractility promotes hypertension and cardiovascular disease. The etiology of hypercontractility is not completely understood. New therapeutic targets remain vitally important for drug discovery. Here we report that Pim kinases, in combination with DAPK3, regulate contractility and control hypertension. Using a co-crystal structure of lead molecule (HS38) in complex with DAPK3, a dual Pim/DAPK3 inhibitor (HS56) and selective DAPK3 inhibitors (HS94 and HS148) were developed to provide mechanistic insight into the polypharmacology of hypertension. In vitro and ex vivo studies indicated that Pim kinases directly phosphorylate smooth muscle targets and that Pim/DAPK3 inhibition, unlike selective DAPK3 inhibition, significantly reduces contractility. In vivo, HS56 decreased blood pressure in spontaneously hypertensive mice in a dose-dependent manner without affecting heart rate. These findings suggest including Pim kinase inhibition within a multi-target engagement strategy for hypertension management. HS56 represents a significant step in the development of molecularly targeted antihypertensive medications.
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Affiliation(s)
- David A Carlson
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Miriam R Singer
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Cindy Sutherland
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada
| | - Clara Redondo
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Leila T Alexander
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Philip F Hughes
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Stefan Knapp
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK; Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Susan B Gurley
- Division of Nephrology, Department of Medicine, Duke University and Durham VA Medical Centers, Durham, NC 27710, USA
| | - Matthew A Sparks
- Division of Nephrology, Department of Medicine, Duke University and Durham VA Medical Centers, Durham, NC 27710, USA
| | - Justin A MacDonald
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada
| | - Timothy A J Haystead
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA.
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24
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Madhavachary R, Naveen N, Wang Y, Wang Q, Konstantinidou M, Dömling A. β-Carbolinone Analogues from the Ugi Silver Mine. European J Org Chem 2018; 2018:3139-3143. [PMID: 31440115 DOI: 10.1002/ejoc.201800557] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Here we describe a facile, tandem synthetic route for β-carbolinones, a class of natural products of high biological significance. Commercially available building blocks yield highly diverse analogues in just two simple steps.
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Affiliation(s)
- Rudrakshula Madhavachary
- Drug Design, University of Groningen, Deusinglaan 1, 9713 AV Groningen, The Netherlands, , http://www.drugdesign.nl/
| | - Naganaboina Naveen
- Drug Design, University of Groningen, Deusinglaan 1, 9713 AV Groningen, The Netherlands, , http://www.drugdesign.nl/
| | - Yuanze Wang
- Drug Design, University of Groningen, Deusinglaan 1, 9713 AV Groningen, The Netherlands, , http://www.drugdesign.nl/
| | - Qian Wang
- Drug Design, University of Groningen, Deusinglaan 1, 9713 AV Groningen, The Netherlands, , http://www.drugdesign.nl/
| | - Markella Konstantinidou
- Drug Design, University of Groningen, Deusinglaan 1, 9713 AV Groningen, The Netherlands, , http://www.drugdesign.nl/
| | - Alexander Dömling
- Drug Design, University of Groningen, Deusinglaan 1, 9713 AV Groningen, The Netherlands, , http://www.drugdesign.nl/
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25
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Farag AK, Roh EJ. Death-associated protein kinase (DAPK) family modulators: Current and future therapeutic outcomes. Med Res Rev 2018; 39:349-385. [DOI: 10.1002/med.21518] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/06/2018] [Accepted: 06/03/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Ahmed Karam Farag
- Chemical Kinomics Research Center; Korea Institute of Science and Technology (KIST); Seoul Republic of Korea
- Division of Bio-Medical Science &Technology, Korea Institute of Science and Technology (KIST) School; University of Science and Technology; Seoul Republic of Korea
| | - Eun Joo Roh
- Chemical Kinomics Research Center; Korea Institute of Science and Technology (KIST); Seoul Republic of Korea
- Division of Bio-Medical Science &Technology, Korea Institute of Science and Technology (KIST) School; University of Science and Technology; Seoul Republic of Korea
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26
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Ramakrishnan C, Mary Thangakani A, Velmurugan D, Anantha Krishnan D, Sekijima M, Akiyama Y, Gromiha MM. Identification of type I and type II inhibitors of c-Yes kinase using in silico and experimental techniques. J Biomol Struct Dyn 2017; 36:1566-1576. [DOI: 10.1080/07391102.2017.1329098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Chandrasekaran Ramakrishnan
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600036, Tamilnadu, India
| | - Anthony Mary Thangakani
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, Tamilnadu, India
| | - Devadasan Velmurugan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, Tamilnadu, India
| | - Dhanabalan Anantha Krishnan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600025, Tamilnadu, India
| | - Masakazu Sekijima
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama 226-8501, Japan
- Advanced Computational Drug Discovery Unit (ACDD), Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama 226-8501, Japan
- Department of Computer Science, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Yutaka Akiyama
- Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama 226-8501, Japan
- Advanced Computational Drug Discovery Unit (ACDD), Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsutacho, Midori-ku, Yokohama 226-8501, Japan
- Department of Computer Science, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - M. Michael Gromiha
- Department of Biotechnology, Bhupat Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai 600036, Tamilnadu, India
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27
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Bataille CJR, Brennan MB, Byrne S, Davies SG, Durbin M, Fedorov O, Huber KVM, Jones AM, Knapp S, Liu G, Nadali A, Quevedo CE, Russell AJ, Walker RG, Westwood R, Wynne GM. Thiazolidine derivatives as potent and selective inhibitors of the PIM kinase family. Bioorg Med Chem 2017; 25:2657-2665. [PMID: 28341403 DOI: 10.1016/j.bmc.2017.02.056] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/23/2017] [Accepted: 02/25/2017] [Indexed: 12/31/2022]
Abstract
The PIM family of serine/threonine kinases have become an attractive target for anti-cancer drug development, particularly for certain hematological malignancies. Here, we describe the discovery of a series of inhibitors of the PIM kinase family using a high throughput screening strategy. Through a combination of molecular modeling and optimization studies, the intrinsic potencies and molecular properties of this series of compounds was significantly improved. An excellent pan-PIM isoform inhibition profile was observed across the series, while optimized examples show good selectivity over other kinases. Two PIM-expressing leukemic cancer cell lines, MV4-11 and K562, were employed to evaluate the in vitro anti-proliferative effects of selected inhibitors. Encouraging activities were observed for many examples, with the best example (44) giving an IC50 of 0.75μM against the K562 cell line. These data provide a promising starting point for further development of this series as a new cancer therapy through PIM kinase inhibition.
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Affiliation(s)
- Carole J R Bataille
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Méabh B Brennan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Simon Byrne
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Stephen G Davies
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK.
| | - Matthew Durbin
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Oleg Fedorov
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Kilian V M Huber
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Alan M Jones
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Stefan Knapp
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, UK
| | - Gu Liu
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Anna Nadali
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Camilo E Quevedo
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Angela J Russell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK; Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK.
| | - Roderick G Walker
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Robert Westwood
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Graham M Wynne
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
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28
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Al-Ghabkari A, Deng JT, McDonald PC, Dedhar S, Alshehri M, Walsh MP, MacDonald JA. A novel inhibitory effect of oxazol-5-one compounds on ROCKII signaling in human coronary artery vascular smooth muscle cells. Sci Rep 2016; 6:32118. [PMID: 27573465 PMCID: PMC5004178 DOI: 10.1038/srep32118] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/02/2016] [Indexed: 12/27/2022] Open
Abstract
The selectivity of (4Z)-2-(4-chloro-3-nitrophenyl)-4-(pyridin-3-ylmethylidene)-1,3-oxazol-5-one (DI) for zipper-interacting protein kinase (ZIPK) was previously described by in silico computational modeling, screening a large panel of kinases, and determining the inhibition efficacy. Our assessment of DI revealed another target, the Rho-associated coiled-coil-containing protein kinase 2 (ROCKII). In vitro studies showed DI to be a competitive inhibitor of ROCKII (Ki, 132 nM with respect to ATP). This finding was supported by in silico molecular surface docking of DI with the ROCKII ATP-binding pocket. Time course analysis of myosin regulatory light chain (LC20) phosphorylation catalyzed by ROCKII in vitro revealed a significant decrease upon treatment with DI. ROCKII signaling was investigated in situ in human coronary artery vascular smooth muscle cells (CASMCs). ROCKII down-regulation using siRNA revealed several potential substrates involved in smooth muscle contraction (e.g., LC20, Par-4, MYPT1) and actin cytoskeletal dynamics (cofilin). The application of DI to CASMCs attenuated LC20, Par-4, LIMK, and cofilin phosphorylations. Notably, cofilin phosphorylation was not significantly decreased with a novel ZIPK selective inhibitor (HS-38). In addition, CASMCs treated with DI underwent cytoskeletal changes that were associated with diminution of cofilin phosphorylation. We conclude that DI is not selective for ZIPK and is a potent inhibitor of ROCKII.
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Affiliation(s)
- Abdulhameed Al-Ghabkari
- Department of Biochemistry &Molecular Biology, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Jing-Ti Deng
- Department of Biochemistry &Molecular Biology, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Paul C McDonald
- Department of Integrative Oncology, BC Cancer Research Centre, 675 West 10th Ave, Vancouver, BC, V5Z 1L3, Canada
| | - Shoukat Dedhar
- Department of Integrative Oncology, BC Cancer Research Centre, 675 West 10th Ave, Vancouver, BC, V5Z 1L3, Canada
| | - Mana Alshehri
- Department of Biochemistry &Molecular Biology, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Michael P Walsh
- Department of Biochemistry &Molecular Biology, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Justin A MacDonald
- Department of Biochemistry &Molecular Biology, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
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29
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Rasse-Suriani FAO, Paula Denofrio M, Yañuk JG, Micaela Gonzalez M, Wolcan E, Seifermann M, Erra-Balsells R, Cabrerizo FM. Chemical and photochemical properties of chloroharmine derivatives in aqueous solutions. Phys Chem Chem Phys 2016; 18:886-900. [DOI: 10.1039/c5cp05866j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In water, chloroharmines follow very distinctive thermal and photochemical pH- and O2-dependent-reaction pathways.
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Affiliation(s)
- Federico A. O. Rasse-Suriani
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomús (IIB-INTECH)
- Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
- Chascomús
- Argentina
| | - M. Paula Denofrio
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomús (IIB-INTECH)
- Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
- Chascomús
- Argentina
| | - Juan G. Yañuk
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomús (IIB-INTECH)
- Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
- Chascomús
- Argentina
| | - M. Micaela Gonzalez
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomús (IIB-INTECH)
- Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
- Chascomús
- Argentina
| | - Ezequiel Wolcan
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA, UNLP, CCT La Plata-CONICET)
- (B1906ZAA) La Plata
- Argentina
| | - Marco Seifermann
- Institute of Pharmacy and Biochemistry
- University of Mainz
- Mainz
- Germany
| | - Rosa Erra-Balsells
- CIHIDECAR – CONICET
- Departamento de Química Orgánica
- Facultad de Ciencias Exactas y Naturales
- Universidad de Buenos Aires
- (1428) Buenos Aires
| | - Franco M. Cabrerizo
- Instituto de Investigaciones Biotecnológicas – Instituto Tecnológico de Chascomús (IIB-INTECH)
- Universidad Nacional de San Martín (UNSAM) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)
- Chascomús
- Argentina
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30
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Agarwal T, Annamalai N, Maiti TK, Arsad H. Biophysical changes of ATP binding pocket may explain loss of kinase activity in mutant DAPK3 in cancer: A molecular dynamic simulation analysis. Gene 2015; 580:17-25. [PMID: 26748242 DOI: 10.1016/j.gene.2015.12.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 12/29/2015] [Accepted: 12/30/2015] [Indexed: 12/31/2022]
Abstract
DAPK3 belongs to family of DAPK (death-associated protein kinases) and is involved in the regulation of progression of the cell cycle, cell proliferation, apoptosis and autophagy. It is considered as a tumor suppressor kinase, suggesting the loss of its function in case of certain specific mutations. The T112M, D161N and P216S mutations in DAPK3 have been observed in cancer patients. These DAPK3 mutants have been associated with very low kinase activity, which results in the cellular progression towards cancer. However, a clear understanding of the structural and biophysical variations that occur in DAPK3 with these mutations, resulting in the decreased kinase activity has yet not been deciphered. We performed a molecular dynamic simulation study to investigate such structural variations. Our results revealed that mutations caused a significant structural variation in DAPK3, majorly concentrated in the flexible loops that form part of the ATP binding pocket. Interestingly, D161N and P216S mutations collapsed the ATP binding pocket through flexible loops invasion, hindering ATP binding which resulted in very low kinase activity. On the contrary, T112M mutant DAPK3 reduces ATP binding potential through outward distortion of flexible loops. In addition, the mutant lacked characteristic features of the active protein kinase including proper interaction between HR/FD and DFG motifs, well structured hydrophobic spine and Lys42-Glu64 salt bridge interaction. These observations could possibly explain the underlying mechanism associated with the loss of kinase activity with T112M, D161N and P216S mutation in DAPK3.
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Affiliation(s)
- Tarun Agarwal
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, West Bengal, Pin: 721302, India.
| | - Nithyanan Annamalai
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Bertam, Pulau Pinang, Malaysia.
| | - Tapas Kumar Maiti
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, West Bengal, Pin: 721302, India.
| | - Hasni Arsad
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Bertam, Pulau Pinang, Malaysia.
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31
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Lunagariya NA, Gohil VM, Kushwah V, Neelagiri S, Jain S, Singh S, Bhutani KK. Design, synthesis and biological evaluation of 1,3,6-trisubstituted β-carboline derivatives for cytotoxic and anti-leishmanial potential. Bioorg Med Chem Lett 2015; 26:789-794. [PMID: 26791014 DOI: 10.1016/j.bmcl.2015.12.095] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 11/19/2015] [Accepted: 12/29/2015] [Indexed: 11/28/2022]
Abstract
In the present study, 23 derivatives of 1,3,6-trisubstituted β-carboline were synthesized and evaluated for cytotoxic potential against four human cancer cells, namely A-549, HeLa, Hep G2 and MCF-7 as well as anti-leishmanial activity against Leishmania donovani (MHOM/80/IN/Dd8) promastigotes. Among the studied compounds, compounds 13c and 13q showed potent cytotoxic activity better than the parent compound 10. For instance, compound 13c was found to be the most cytotoxic with IC50 of 4.72, 3.59, 3.65 and 4.17 μM against A-549, HeLa, Hep G2 and MCF-7 respectively, while for compound 13q, IC50 were 15.47, 5.30, 6.15 and 13.39 μM against the same cancer cells respectively. Further, these two compounds were found to be apoptotic in A-549 and MCF-7 cells when observed using Annexin V/propidium iodide staining under confocal microscope. All the compounds were also tested for anti-leishmanial potential. In which, compounds 13u and 13c were found to show moderate inhibition with IC50 of 23.5±9.0 and 68.0±0.0 μM respectively, while compound 10 was the most active with IC50 of 9.0±2.8 μM, suggesting the modification at C-6 detrimental for anti-leishmanial activity. Interestingly, amongst all, compound 13c was found to be the most active for cytotoxic and moderately active for anti-leishmanial activity which can be further developed as a lead for these disease areas.
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Affiliation(s)
- Nitin A Lunagariya
- Department of Natural Products, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160062, India
| | - Vikrantsinh M Gohil
- Department of Natural Products, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160062, India
| | - Varun Kushwah
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160062, India
| | - Soumya Neelagiri
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160062, India
| | - Sanyog Jain
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160062, India
| | - Sushma Singh
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160062, India
| | - Kamlesh K Bhutani
- Department of Natural Products, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160062, India.
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32
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Xu Q, Malecka KL, Fink L, Jordan EJ, Duffy E, Kolander S, Peterson JR, Dunbrack RL. Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases. Sci Signal 2015; 8:rs13. [PMID: 26628682 DOI: 10.1126/scisignal.aaa6711] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Crystal structures of several homomeric protein kinase complexes have a serine, threonine, or tyrosine autophosphorylation site of one kinase monomer located in the active site of another monomer, a structural complex that we call an "autophosphorylation complex." We developed and applied a structural bioinformatics method to identify all such autophosphorylation complexes in x-ray crystallographic structures in the Protein Data Bank (PDB). We identified 15 autophosphorylation complexes in the PDB, of which five complexes had not previously been described in the publications describing the crystal structures. These five complexes consist of tyrosine residues in the N-terminal juxtamembrane regions of colony-stimulating factor 1 receptor (CSF1R, Tyr(561)) and ephrin receptor A2 (EPHA2, Tyr(594)), tyrosine residues in the activation loops of the SRC kinase family member LCK (Tyr(394)) and insulin-like growth factor 1 receptor (IGF1R, Tyr(1166)), and a serine in a nuclear localization signal region of CDC-like kinase 2 (CLK2, Ser(142)). Mutations in the complex interface may alter autophosphorylation activity and contribute to disease; therefore, we mutated residues in the autophosphorylation complex interface of LCK and found that two mutations impaired autophosphorylation (T445V and N446A) and mutation of Pro(447) to Ala, Gly, or Leu increased autophosphorylation. The identified autophosphorylation sites are conserved in many kinases, suggesting that, by homology, these complexes may provide insight into autophosphorylation complex interfaces of kinases that are relevant drug targets.
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Affiliation(s)
- Qifang Xu
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Kimberly L Malecka
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Lauren Fink
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - E Joseph Jordan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erin Duffy
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Samuel Kolander
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Jeffrey R Peterson
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Roland L Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.
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33
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Rodrigues T, Reker D, Welin M, Caldera M, Brunner C, Gabernet G, Schneider P, Walse B, Schneider G. De Novo Fragment Design for Drug Discovery and Chemical Biology. Angew Chem Int Ed Engl 2015; 54:15079-83. [DOI: 10.1002/anie.201508055] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Indexed: 01/08/2023]
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34
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Rodrigues T, Reker D, Welin M, Caldera M, Brunner C, Gabernet G, Schneider P, Walse B, Schneider G. De-novo-Fragmententwurf für die Wirkstoffforschung und chemische Biologie. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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35
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MacDonald JA, Sutherland C, Carlson DA, Bhaidani S, Al-Ghabkari A, Swärd K, Haystead TAJ, Walsh MP. A Small Molecule Pyrazolo[3,4-d]Pyrimidinone Inhibitor of Zipper-Interacting Protein Kinase Suppresses Calcium Sensitization of Vascular Smooth Muscle. Mol Pharmacol 2015; 89:105-17. [DOI: 10.1124/mol.115.100529] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/09/2015] [Indexed: 11/22/2022] Open
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36
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Strödke B, Gehring AP, Bracher F. Synthesis of desaza analogues of annomontine and canthin-4-one alkaloids. Arch Pharm (Weinheim) 2015; 348:125-31. [PMID: 25664630 DOI: 10.1002/ardp.201400328] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/17/2014] [Accepted: 12/01/2014] [Indexed: 11/11/2022]
Abstract
1-Acetylcarbazoles are readily converted to 3-desazacanthin-4-ones upon treatment with Bredereck's reagent, but in contrast to canthin-4-ones, these do not undergo ring transformation reactions with guanidine. Only after N-protection (methyl or 2-(trimethylsilyl)ethoxymethyl group), 2-desaza analogues of the alkaloid annomontine are accessible via the enaminoketones obtained by condensation with Bredereck's reagent. One of the annomontine analogues is an inhibitor of the Plasmodium falciparum CDC-like kinases (CLK) and shows antimalarial activity.
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Affiliation(s)
- Benjamin Strödke
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-University of Munich, Munich, Germany
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37
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Gilday LC, Robinson SW, Barendt TA, Langton MJ, Mullaney BR, Beer PD. Halogen Bonding in Supramolecular Chemistry. Chem Rev 2015; 115:7118-95. [DOI: 10.1021/cr500674c] [Citation(s) in RCA: 913] [Impact Index Per Article: 101.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lydia C. Gilday
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sean W. Robinson
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Timothy A. Barendt
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Matthew J. Langton
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Benjamin R. Mullaney
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Paul D. Beer
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
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38
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Falke H, Chaikuad A, Becker A, Loaëc N, Lozach O, Abu Jhaisha S, Becker W, Jones P, Preu L, Baumann K, Knapp S, Meijer L, Kunick C. 10-iodo-11H-indolo[3,2-c]quinoline-6-carboxylic acids are selective inhibitors of DYRK1A. J Med Chem 2015; 58:3131-43. [PMID: 25730262 PMCID: PMC4506206 DOI: 10.1021/jm501994d] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Indexed: 01/18/2023]
Abstract
The protein kinase DYRK1A has been suggested to act as one of the intracellular regulators contributing to neurological alterations found in individuals with Down syndrome. For an assessment of the role of DYRK1A, selective synthetic inhibitors are valuable pharmacological tools. However, the DYRK1A inhibitors described in the literature so far either are not sufficiently selective or have not been tested against closely related kinases from the DYRK and the CLK protein kinase families. The aim of this study was the identification of DYRK1A inhibitors exhibiting selectivity versus the structurally and functionally closely related DYRK and CLK isoforms. Structure modification of the screening hit 11H-indolo[3,2-c]quinoline-6-carboxylic acid revealed structure-activity relationships for kinase inhibition and enabled the design of 10-iodo-substituted derivatives as very potent DYRK1A inhibitors with considerable selectivity against CLKs. X-ray structure determination of three 11H-indolo[3,2-c]quinoline-6-carboxylic acids cocrystallized with DYRK1A confirmed the predicted binding mode within the ATP binding site.
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Affiliation(s)
- Hannes Falke
- Institut
für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany
| | - Apirat Chaikuad
- Nuffield
Department
of Clinical Medicine, Structural Genomics Consortium, University of
Oxford, Old Road Campus Research Building,
Roosevelt Drive, Headington, Oxford OX3 7DQ, U.K.
| | - Anja Becker
- Institut
für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany
| | - Nadège Loaëc
- ManRos
Therapeutics, Perharidy Research Center, 29680 Roscoff, Bretagne, France
- “Protein
Phosphorylation and Human Disease” Group, Station Biologique
de Roscoff, CNRS, 29680 Roscoff, France
| | - Olivier Lozach
- “Protein
Phosphorylation and Human Disease” Group, Station Biologique
de Roscoff, CNRS, 29680 Roscoff, France
| | - Samira Abu Jhaisha
- Institute
of Pharmacology and Toxicology, RWTH Aachen
University, Wendlingweg
2, 52074 Aachen, Germany
| | - Walter Becker
- Institute
of Pharmacology and Toxicology, RWTH Aachen
University, Wendlingweg
2, 52074 Aachen, Germany
| | - Peter
G. Jones
- Institut
für Anorganische und Analytische Chemie, Technische Universität Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Lutz Preu
- Institut
für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany
| | - Knut Baumann
- Institut
für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany
| | - Stefan Knapp
- Nuffield
Department
of Clinical Medicine, Structural Genomics Consortium, University of
Oxford, Old Road Campus Research Building,
Roosevelt Drive, Headington, Oxford OX3 7DQ, U.K.
| | - Laurent Meijer
- ManRos
Therapeutics, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Conrad Kunick
- Institut
für Medizinische und Pharmazeutische Chemie, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany
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39
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Bovonsombat P, Sophanpanichkul P, Pandey A, Tungsirisurp S, Limthavornlit P, Chobtumskul K, Kuhataparuk P, Sathityatiwat S, Teecomegaet P. Novel regioselective aromatic chlorination via catalytic thiourea activation of N-chlorosuccinimide. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.03.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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40
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Wang KB, Yuan CM, Xue CM, Li DH, Jing YK, He HP, Hao XJ, Di YT, Li ZL, Hua HM. Pegaharmalines A and B, two novel β-carboline alkaloids with unprecedented carbon skeletons from Peganum harmala. RSC Adv 2014. [DOI: 10.1039/c4ra07985j] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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41
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Kern S, Agarwal S, Huber K, Gehring AP, Strödke B, Wirth CC, Brügl T, Abodo LO, Dandekar T, Doerig C, Fischer R, Tobin AB, Alam MM, Bracher F, Pradel G. Inhibition of the SR protein-phosphorylating CLK kinases of Plasmodium falciparum impairs blood stage replication and malaria transmission. PLoS One 2014; 9:e105732. [PMID: 25188378 PMCID: PMC4154858 DOI: 10.1371/journal.pone.0105732] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 07/28/2014] [Indexed: 01/01/2023] Open
Abstract
Cyclin-dependent kinase-like kinases (CLKs) are dual specificity protein kinases that phosphorylate Serine/Arginine-rich (SR) proteins involved in pre-mRNA processing. Four CLKs, termed PfCLK-1-4, can be identified in the human malaria parasite Plasmodium falciparum, which show homology with the yeast SR protein kinase Sky1p. The four PfCLKs are present in the nucleus and cytoplasm of the asexual blood stages and of gametocytes, sexual precursor cells crucial for malaria parasite transmission from humans to mosquitoes. We identified three plasmodial SR proteins, PfSRSF12, PfSFRS4 and PfSF-1, which are predominantly present in the nucleus of blood stage trophozoites, PfSRSF12 and PfSF-1 are further detectable in the nucleus of gametocytes. We found that recombinantly expressed SR proteins comprising the Arginine/Serine (RS)-rich domains were phosphorylated by the four PfCLKs in in vitro kinase assays, while a recombinant PfSF-1 peptide lacking the RS-rich domain was not phosphorylated. Since it was hitherto not possible to knock-out the pfclk genes by conventional gene disruption, we aimed at chemical knock-outs for phenotype analysis. We identified five human CLK inhibitors, belonging to the oxo-β-carbolines and aminopyrimidines, as well as the antiseptic chlorhexidine as PfCLK-targeting compounds. The six inhibitors block P. falciparum blood stage replication in the low micromolar to nanomolar range by preventing the trophozoite-to-schizont transformation. In addition, the inhibitors impair gametocyte maturation and gametogenesis in in vitro assays. The combined data show that the four PfCLKs are involved in phosphorylation of SR proteins with essential functions for the blood and sexual stages of the malaria parasite, thus pointing to the kinases as promising targets for antimalarial and transmission blocking drugs.
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Affiliation(s)
- Selina Kern
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
- Institute of Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Shruti Agarwal
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
| | - Kilian Huber
- Department of Pharmacy – Center for Drug Research, Ludwig-Maximillians University, Munich, Germany
| | - André P. Gehring
- Department of Pharmacy – Center for Drug Research, Ludwig-Maximillians University, Munich, Germany
| | - Benjamin Strödke
- Department of Pharmacy – Center for Drug Research, Ludwig-Maximillians University, Munich, Germany
| | - Christine C. Wirth
- Institute of Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Thomas Brügl
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
| | | | - Thomas Dandekar
- Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Christian Doerig
- INSERM U609, Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Rainer Fischer
- Institute of Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Andrew B. Tobin
- Department of Cell Physiology and Pharmacology, MRC Toxicology Unit, University of Leicester, Leicester, United Kingdom
| | - Mahmood M. Alam
- Department of Cell Physiology and Pharmacology, MRC Toxicology Unit, University of Leicester, Leicester, United Kingdom
| | - Franz Bracher
- Department of Pharmacy – Center for Drug Research, Ludwig-Maximillians University, Munich, Germany
| | - Gabriele Pradel
- Institute of Molecular Biotechnology, RWTH Aachen University, Aachen, Germany
- * E-mail:
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42
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Gehringer M, Forster M, Pfaffenrot E, Bauer SM, Laufer SA. Novel hinge-binding motifs for Janus kinase 3 inhibitors: a comprehensive structure-activity relationship study on tofacitinib bioisosteres. ChemMedChem 2014; 9:2516-27. [PMID: 25139757 DOI: 10.1002/cmdc.201402252] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Indexed: 11/09/2022]
Abstract
The Janus kinases (JAKs) are a family of cytosolic tyrosine kinases crucially involved in cytokine signaling. JAKs have been demonstrated to be valid targets in the treatment of inflammatory and myeloproliferative disorders, and two inhibitors, tofacitinib and ruxolitinib, recently received their marketing authorization. Despite this success, selectivity within the JAK family remains a major issue. Both approved compounds share a common 7H-pyrrolo[2,3-d]pyrimidine hinge binding motif, and little is known about modifications tolerated at this heterocyclic core. In the current study, a library of tofacitinib bioisosteres was prepared and tested against JAK3. The compounds possessed the tofacitinib piperidinyl side chain, whereas the hinge binding motif was replaced by a variety of heterocycles mimicking its pharmacophore. In view of the promising expectations obtained from molecular modeling, most of the compounds proved to be poorly active. However, strategies for restoring activity within this series of novel chemotypes were discovered and crucial structure-activity relationships were deduced. The compounds presented may serve as starting point for developing novel JAK inhibitors and as a valuable training set for in silico models.
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Affiliation(s)
- Matthias Gehringer
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical and Medicinal Chemistry, Eberhard Karls University of Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen (Germany), Fax: (+49) 7071-29-5037
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43
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Wang KB, Di YT, Bao Y, Yuan CM, Chen G, Li DH, Bai J, He HP, Hao XJ, Pei YH, Jing YK, Li ZL, Hua HM. Peganumine A, a β-carboline dimer with a new octacyclic scaffold from Peganum harmala. Org Lett 2014; 16:4028-31. [PMID: 25054213 DOI: 10.1021/ol501856v] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Peganumine A (1), a new dimeric β-carboline alkaloid characterized by a unique 3,9-diazatetracyclo[6.5.2.0(1,9).0(3,8)]pentadec-2-one scaffold, was isolated from the seeds of Peganum harmala. The structure including the absolute configuration was determined by spectroscopic data, X-ray crystallography, ECD calculation, and CD exciton chirality approaches. Compound 1 showed moderate cytotoxic activity against MCF-7, PC-3, and HepG2 cells and selective effects on HL-60 cells with an IC50 value of 5.8 μM.
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Affiliation(s)
- Kai-Bo Wang
- Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University , Shenyang 110016, Liaoning, P. R. China
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44
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Halogen-enriched fragment libraries as chemical probes for harnessing halogen bonding in fragment-based lead discovery. Future Med Chem 2014; 6:617-39. [DOI: 10.4155/fmc.14.20] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Halogen bonding has recently experienced a renaissance, gaining increased recognition as a useful molecular interaction in the life sciences. Halogen bonds are favorable, fairly directional interactions between an electropositive region on the halogen (the σ-hole) and a number of different nucleophilic interaction partners. Some aspects of halogen bonding are not yet understood well enough to take full advantage of its potential in drug discovery. We describe and present the concept of halogen-enriched fragment libraries. These libraries consist of unique chemical probes, facilitating the identification of favorable halogen bonds by sharing the advantages of classical fragment-based screening. Besides providing insights into the nature and applicability of halogen bonding, halogen-enriched fragment libraries provide smart starting points for hit-to-lead evolution.
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45
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Functional role and therapeutic potential of the pim-1 kinase in colon carcinoma. Neoplasia 2014; 15:783-94. [PMID: 23814490 DOI: 10.1593/neo.13172] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 04/16/2013] [Accepted: 04/22/2013] [Indexed: 12/16/2022] Open
Abstract
PURPOSE The provirus integration site for Moloney murine leukemia virus 1 (Pim-1) kinase is overexpressed in various tumors and has been linked to poor prognosis. Its role as proto-oncogene is based on several Pim-1 target proteins involved in pivotal cellular processes. Here, we explore the functional relevance of Pim-1 in colon carcinoma. EXPERIMENTAL DESIGN RNAi-based knockdown approaches, as well as a specific small molecule inhibitor, were used to inhibit Pim-1 in colon carcinoma cells. The effects were analyzed regarding proliferation, apoptosis, sensitization toward cytostatic treatment, and overall antitumor effect in vitro and in mouse tumor models in vivo. RESULTS We demonstrate antiproliferative, proapoptotic, and overall antitumor effects of Pim-1 inhibition. The sensitization to 5-fluorouracil (5-FU) treatment upon Pim-1 knockdown offers new possibilities for combinatorial treatment approaches. Importantly, this also antagonizes a 5-FU-triggered Pim-1 up-regulation, which is mediated by decreased levels of miR-15b, a microRNA we newly identify to regulate Pim-1. The analysis of the molecular effects of Pim-1 inhibition reveals a complex regulatory network, with therapeutic Pim-1 repression leading to major changes in oncogenic signal transduction with regard to p21(Cip1/WAF1), STAT3, c-jun-N-terminal kinase (JNK), c-Myc, and survivin and in the levels of apoptosis-related proteins Puma, Bax, and Bcl-xL. CONCLUSIONS We demonstrate that Pim-1 plays a pivotal role in several tumor-relevant signaling pathways and establish the functional relevance of Pim-1 in colon carcinoma. Our results also substantiate the RNAi-mediated Pim-1 knockdown based on polymeric polyethylenimine/small interfering RNA nanoparticles as a promising therapeutic approach.
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46
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Carlson DA, Franke AS, Weitzel DH, Speer BL, Hughes PF, Hagerty L, Fortner CN, Veal JM, Barta TE, Zieba BJ, Somlyo AV, Sutherland C, Deng JT, Walsh MP, MacDonald JA, Haystead TAJ. Fluorescence linked enzyme chemoproteomic strategy for discovery of a potent and selective DAPK1 and ZIPK inhibitor. ACS Chem Biol 2013; 8:2715-23. [PMID: 24070067 DOI: 10.1021/cb400407c] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
DAPK1 and ZIPK (also called DAPK3) are closely related serine/threonine protein kinases that regulate programmed cell death and phosphorylation of non-muscle and smooth muscle myosin. We have developed a fluorescence linked enzyme chemoproteomic strategy (FLECS) for the rapid identification of inhibitors for any element of the purinome and identified a selective pyrazolo[3,4-d]pyrimidinone (HS38) that inhibits DAPK1 and ZIPK in an ATP-competitive manner at nanomolar concentrations. In cellular studies, HS38 decreased RLC20 phosphorylation. In ex vivo studies, HS38 decreased contractile force generated in mouse aorta, rabbit ileum, and calyculin A stimulated arterial muscle by decreasing RLC20 and MYPT1 phosphorylation. The inhibitor also promoted relaxation in Ca(2+)-sensitized vessels. A close structural analogue (HS43) with 5-fold lower affinity for ZIPK produced no effect on cells or tissues. These findings are consistent with a mechanism of action wherein HS38 specifically targets ZIPK in smooth muscle. The discovery of HS38 provides a lead scaffold for the development of therapeutic agents for smooth muscle related disorders and a chemical means to probe the function of DAPK1 and ZIPK across species.
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Affiliation(s)
- David A. Carlson
- Department
of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Aaron S. Franke
- Department
of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Douglas H. Weitzel
- Department
of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Brittany L. Speer
- Department
of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Philip F. Hughes
- Department
of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Laura Hagerty
- Department
of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Christopher N. Fortner
- Department
of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - James M. Veal
- Quanticel
Pharmaceuticals, San Francisco, California 94158, United States
| | - Thomas E. Barta
- Department
of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Bartosz J. Zieba
- Department
of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Avril V. Somlyo
- Department
of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Cindy Sutherland
- Smooth Muscle Research Group at the Libin Cardiovascular Institute of Alberta. Department of Biochemistry & Molecular Biology, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada
| | - Jing Ti Deng
- Smooth Muscle Research Group at the Libin Cardiovascular Institute of Alberta. Department of Biochemistry & Molecular Biology, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada
| | - Michael P. Walsh
- Smooth Muscle Research Group at the Libin Cardiovascular Institute of Alberta. Department of Biochemistry & Molecular Biology, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada
| | - Justin A. MacDonald
- Smooth Muscle Research Group at the Libin Cardiovascular Institute of Alberta. Department of Biochemistry & Molecular Biology, University of Calgary, 3280 Hospital Drive NW, Calgary, AB T2N 4Z6, Canada
| | - Timothy A. J. Haystead
- Department
of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, United States
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47
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Lange A, Zimmermann MO, Wilcken R, Zahn S, Boeckler FM. Targeting Histidine Side Chains in Molecular Design through Nitrogen–Halogen Bonds. J Chem Inf Model 2013; 53:3178-89. [DOI: 10.1021/ci4004305] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Andreas Lange
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Markus O. Zimmermann
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Rainer Wilcken
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Stefan Zahn
- Wilhelm-Ostwald-Institut
für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstraβe 2, 04103 Leipzig, Germany
| | - Frank M. Boeckler
- Laboratory
for Molecular Design and Pharmaceutical Biophysics, Department of
Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard-Karls-University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
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48
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Lee SJ, Han BG, Cho JW, Choi JS, Lee J, Song HJ, Koh JS, Lee BI. Crystal structure of pim1 kinase in complex with a pyrido[4,3-d]pyrimidine derivative suggests a unique binding mode. PLoS One 2013; 8:e70358. [PMID: 23936194 PMCID: PMC3729456 DOI: 10.1371/journal.pone.0070358] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 06/18/2013] [Indexed: 02/07/2023] Open
Abstract
Human Pim1 kinase is a serine/threonine protein kinase that plays important biological roles in cell survival, apoptosis, proliferation, and differentiation. Moreover, Pim1 is up-regulated in various hematopoietic malignancies and solid tumors. Thus, Pim1 is an attractive target for cancer therapeutics, and there has been growing interest in developing small molecule inhibitors for Pim1. Here, we describe the crystal structure of Pim1 in complex with a newly developed pyrido[4,3-d]pyrimidine-derivative inhibitor (SKI-O-068). Our inhibitor exhibits a half maximum inhibitory concentration (IC50) of 123 (±14) nM and has an unusual binding mode in complex with Pim1 kinase. The interactions between SKI-O-068 and the Pim1 active site pocket residue are different from those of other scaffold inhibitor-bound structures. The binding mode analysis suggests that the SKI-O-068 inhibitor can be improved by introducing functional groups that facilitate direct interaction with Lys67, which aid in the design of an optimized inhibitor.
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Affiliation(s)
- Sang Jae Lee
- Biomolecular Function Research Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi, Republic of Korea
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Byeong-Gu Han
- Biomolecular Function Research Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Jea-Won Cho
- Biomolecular Function Research Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | | | - Jaekyoo Lee
- Genosco, Cambridge, Massachusetts, United States of America
| | - Ho-Juhn Song
- Genosco, Cambridge, Massachusetts, United States of America
| | - Jong Sung Koh
- Oscotec Inc., Seongnam, Gyeonggi, Republic of Korea
- Genosco, Cambridge, Massachusetts, United States of America
- * E-mail: (JSK); (BIL)
| | - Byung Il Lee
- Biomolecular Function Research Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi, Republic of Korea
- * E-mail: (JSK); (BIL)
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Lori C, Lantella A, Pasquo A, Alexander LT, Knapp S, Chiaraluce R, Consalvi V. Effect of single amino acid substitution observed in cancer on Pim-1 kinase thermodynamic stability and structure. PLoS One 2013; 8:e64824. [PMID: 23755147 PMCID: PMC3673989 DOI: 10.1371/journal.pone.0064824] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 04/18/2013] [Indexed: 11/19/2022] Open
Abstract
Pim-1 kinase, a serine/threonine protein kinase encoded by the pim proto-oncogene, is involved in several signalling pathways such as the regulation of cell cycle progression and apoptosis. Many cancer types show high expression levels of Pim kinases and particularly Pim-1 has been linked to the initiation and progression of the malignant phenotype. In several cancer tissues somatic Pim-1 mutants have been identified. These natural variants are nonsynonymous single nucleotide polymorphisms, variations of a single nucleotide occurring in the coding region and leading to amino acid substitutions. In this study we investigated the effect of amino acid substitution on the structural stability and on the activity of Pim-1 kinase. We expressed and purified some of the mutants of Pim-1 kinase that are expressed in cancer tissues and reported in the single nucleotide polymorphisms database. The point mutations in the variants significantly affect the conformation of the native state of Pim-1. All the mutants, expressed as soluble recombinant proteins, show a decreased thermal and thermodynamic stability and a lower activation energy values for kinase activity. The decreased stability accompanied by an increased flexibility suggests that Pim-1 variants may be involved in a wider network of protein interactions. All mutants bound ATP and ATP mimetic inhibitors with comparable IC50 values suggesting that the studied Pim-1 kinase mutants can be efficiently targeted with inhibitors developed for the wild type protein.
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Affiliation(s)
- Clorinda Lori
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome, Italy
| | - Antonella Lantella
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome, Italy
| | | | - Leila T. Alexander
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Roberta Chiaraluce
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome, Italy
- * E-mail:
| | - Valerio Consalvi
- Department of Biochemical Sciences “A. Rossi Fanelli”, Sapienza University of Rome, Rome, Italy
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50
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Wilcken R, Zimmermann MO, Lange A, Joerger AC, Boeckler FM. Principles and Applications of Halogen Bonding in Medicinal Chemistry and Chemical Biology. J Med Chem 2013; 56:1363-88. [DOI: 10.1021/jm3012068] [Citation(s) in RCA: 839] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rainer Wilcken
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard Karls University, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Markus O. Zimmermann
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard Karls University, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
| | - Andreas Lange
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard Karls University, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
| | - Andreas C. Joerger
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH,
United Kingdom
| | - Frank M. Boeckler
- Laboratory for Molecular Design
and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal
Chemistry, Institute of Pharmacy, Eberhard Karls University, Tuebingen, Auf der Morgenstelle 8, 72076 Tuebingen,
Germany
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