1
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Gou W, Dai P, Wang M, Wang Y, Ma N, Zhou X, Xu Y, Zhang L, Li C. Synthesis of Diverse Ureas from Amines and CO 2 at Atmospheric Pressure and Room Temperature. J Org Chem 2024; 89:12498-12507. [PMID: 39180140 DOI: 10.1021/acs.joc.4c01474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
Abstract
A metal-free method is developed to perform the synthesis of urea derivatives utilizing CO2 as the C1 building block at atmospheric pressure and room temperature. In addition to diverse symmetric and dissymmetric ureas, benzimidazolones and quinazolinone can also be easily prepared using this protocol. Most importantly, the gram-scale preparation of fungicide pencycuron and antipsychotic drug pimavanserin proceeded smoothly under the mild conditions.
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Affiliation(s)
- Wenchang Gou
- School of Pharmaceutical Sciences, Guizhou Medical University, 550004 Guiyang, People's Republic of China
| | - Pinli Dai
- School of Pharmaceutical Sciences, Guizhou Medical University, 550004 Guiyang, People's Republic of China
| | - Mei Wang
- School of Pharmaceutical Sciences, Guizhou Medical University, 550004 Guiyang, People's Republic of China
| | - Yunhuan Wang
- School of Pharmaceutical Sciences, Guizhou Medical University, 550004 Guiyang, People's Republic of China
| | - Nana Ma
- School of Pharmaceutical Sciences, Guizhou Medical University, 550004 Guiyang, People's Republic of China
| | - Xuan Zhou
- School of Pharmaceutical Sciences, Guizhou Medical University, 550004 Guiyang, People's Republic of China
| | - Yingjian Xu
- GoldenKeys High-tech Materials Co., Ltd., Guian New Area, Guizhou 550025, People's Republic of China
| | - Lin Zhang
- School of Pharmaceutical Sciences, Guizhou Medical University, 550004 Guiyang, People's Republic of China
| | - Chun Li
- School of Pharmaceutical Sciences, Guizhou Medical University, 550004 Guiyang, People's Republic of China
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2
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Venkatraman V, Gaiser J, Demekas D, Roy A, Xiong R, Wheeler TJ. Do Molecular Fingerprints Identify Diverse Active Drugs in Large-Scale Virtual Screening? (No). Pharmaceuticals (Basel) 2024; 17:992. [PMID: 39204097 PMCID: PMC11356940 DOI: 10.3390/ph17080992] [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: 06/08/2024] [Revised: 07/18/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
Computational approaches for small-molecule drug discovery now regularly scale to the consideration of libraries containing billions of candidate small molecules. One promising approach to increased the speed of evaluating billion-molecule libraries is to develop succinct representations of each molecule that enable the rapid identification of molecules with similar properties. Molecular fingerprints are thought to provide a mechanism for producing such representations. Here, we explore the utility of commonly used fingerprints in the context of predicting similar molecular activity. We show that fingerprint similarity provides little discriminative power between active and inactive molecules for a target protein based on a known active-while they may sometimes provide some enrichment for active molecules in a drug screen, a screened data set will still be dominated by inactive molecules. We also demonstrate that high-similarity actives appear to share a scaffold with the query active, meaning that they could more easily be identified by structural enumeration. Furthermore, even when limited to only active molecules, fingerprint similarity values do not correlate with compound potency. In sum, these results highlight the need for a new wave of molecular representations that will improve the capacity to detect biologically active molecules based on their similarity to other such molecules.
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Affiliation(s)
- Vishwesh Venkatraman
- Department of Chemistry, Norwegian University of Science and Technology, 7034 Trondheim, Norway
| | - Jeremiah Gaiser
- School of Information, University of Arizona, Tucson, AZ 85721, USA
| | - Daphne Demekas
- R. Ken Coit College Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Amitava Roy
- Rocky Mountain Laboratories, Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA;
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MT 59812, USA
| | - Rui Xiong
- Department of Pharmacology & Toxicology, University of Arizona, Tucson, AZ 85721, USA
| | - Travis J. Wheeler
- R. Ken Coit College Pharmacy, University of Arizona, Tucson, AZ 85721, USA
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3
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Tan S, Dorokhov VS, White LV, Zard SZ. Synthesis of 4-Alkyl-2-chloro Imidazoles Using Intermolecular Radical Additions. Org Lett 2024; 26:5989-5994. [PMID: 38975858 DOI: 10.1021/acs.orglett.4c02071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Here, we report an intermolecular radical addition-based reaction sequence that permits preparation of functionalized imidazoles via a 5-step/3-pot procedure. In contrast to traditional, transition-metal mediated protocols, which generally provide access to 2-substituted imidazoles, the strategy described here allows incorporation of a structurally diverse range of complex alkyl side chains at the 4-position. This work demonstrates that intermolecular free-radical addition reactions are a powerful alternative to traditional methods used to synthesize medicinally important heterocyclic frameworks.
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Affiliation(s)
- Shen Tan
- Institute for Advanced and Applied Chemical Synthesis, College of Pharmacy, Jinan University, Guangzhou, Guangdong 510632, China
- Laboratoire de Synthèse Organique, CNRS, École Polytechnique, Palaiseau 91128, France
| | - Valentin S Dorokhov
- Laboratoire de Synthèse Organique, CNRS, École Polytechnique, Palaiseau 91128, France
| | - Lorenzo V White
- Institute for Advanced and Applied Chemical Synthesis, College of Pharmacy, Jinan University, Guangzhou, Guangdong 510632, China
- Laboratoire de Synthèse Organique, CNRS, École Polytechnique, Palaiseau 91128, France
| | - Samir Z Zard
- Laboratoire de Synthèse Organique, CNRS, École Polytechnique, Palaiseau 91128, France
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4
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Saylam M, Aydın Köse F, Pabuccuoglu A, Barut Celepci D, Aygün M, Pabuccuoglu V. Design, synthesis, and biological activity studies on benzimidazole derivatives targeting myeloperoxidase. Eur J Med Chem 2023; 248:115083. [PMID: 36634456 DOI: 10.1016/j.ejmech.2022.115083] [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: 09/23/2022] [Revised: 11/30/2022] [Accepted: 12/30/2022] [Indexed: 01/02/2023]
Abstract
Myeloperoxidase (MPO) plays a key role in human antimicrobial system by oxidizing vital molecules of microorganisms in phagolysosomes through produced hypochlorous acid (HOCl). However, MPO can be released outside the phagocyte and produces reactive intermediates leading to tissue damage. MPO, as a local mediator of tissue damage, has been associated with inflammatory diseases such as renal injury, multiple sclerosis, cardiovascular and neurodegenerative diseases. Therefore, the enzyme currently draws attention as a potential therapeutic target. In this study, isomeric 1,3-dihydro-2H-benzo[d]imidazole-2-thione derivatives having amide, hydrazide and hydroxamic acid groups either on nitrogen or on sulphur atom were designed and their inhibitory activity was determined on chlorination and peroxidation cycles of MPO. Among the compounds, 2-(2-thioxo-2,3-dihydro-1H-benzo[d]imidazole-1-yl)acetohydrazide(C19) was found as the most active inhibitor on both cycles.
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Affiliation(s)
- Merve Saylam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Izmir Katip Celebi University, Izmir, Turkey.
| | - Fadime Aydın Köse
- Department of Biochemistry, Faculty of Pharmacy, Izmir Katip Celebi University, Izmir, Turkey
| | - Aysun Pabuccuoglu
- Department of Biochemistry, Faculty of Pharmacy, Ege University, Izmir, Turkey
| | - Duygu Barut Celepci
- Department of Physics, Faculty of Science, Dokuz Eylul Univeristy, Izmir, Turkey
| | - Muhittin Aygün
- Department of Physics, Faculty of Science, Dokuz Eylul Univeristy, Izmir, Turkey
| | - Varol Pabuccuoglu
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ege University, Izmir, Turkey.
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5
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Nam K, Wolf-Watz M. Protein dynamics: The future is bright and complicated! STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2023; 10:014301. [PMID: 36865927 PMCID: PMC9974214 DOI: 10.1063/4.0000179] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Biological life depends on motion, and this manifests itself in proteins that display motion over a formidable range of time scales spanning from femtoseconds vibrations of atoms at enzymatic transition states, all the way to slow domain motions occurring on micro to milliseconds. An outstanding challenge in contemporary biophysics and structural biology is a quantitative understanding of the linkages among protein structure, dynamics, and function. These linkages are becoming increasingly explorable due to conceptual and methodological advances. In this Perspective article, we will point toward future directions of the field of protein dynamics with an emphasis on enzymes. Research questions in the field are becoming increasingly complex such as the mechanistic understanding of high-order interaction networks in allosteric signal propagation through a protein matrix, or the connection between local and collective motions. In analogy to the solution to the "protein folding problem," we argue that the way forward to understanding these and other important questions lies in the successful integration of experiment and computation, while utilizing the present rapid expansion of sequence and structure space. Looking forward, the future is bright, and we are in a period where we are on the doorstep to, at least in part, comprehend the importance of dynamics for biological function.
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Affiliation(s)
- Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, USA
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6
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Zaręba P, Drabczyk AK, Wnorowski A, Pindelska E, Latacz G, Jaśkowska J. Eco-friendly methods of synthesis and preliminary biological evaluation of sulfonamide derivatives of cyclic arylguanidines. ULTRASONICS SONOCHEMISTRY 2022; 90:106165. [PMID: 36183548 PMCID: PMC9529985 DOI: 10.1016/j.ultsonch.2022.106165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 09/09/2022] [Accepted: 09/10/2022] [Indexed: 06/16/2023]
Abstract
The chemotype of arylsulfonamide derivatives of cyclic arylguanidines is a source of molecules with valuable biological activities, including antimicrobial and antitumor properties. The methods of the synthesis presented in the literature are characterized with low selectivity and high environmental nuisance. In this publication, we present a developed alternative and earlier undescribed pathway C, for the synthesis of arylsulfonamide derivatives of cyclic arylguanidines (N-(1H-arylimidazol-2-yl)arylsulfonamides and N-(1,4-dihydroquinazolin-2-yl)arylsulfonamides), including reaction between 2-(methylsulfanyl)-benzimidazole or 2-(methylsulfanyl)-3,4-dihydroquinazoline with arylsulfonamides. We also optimized previously reported methods; A (reaction of 2-aminobenzimidazole or 2-amino-3,4-dihydroquinazoline with arylsulfonyl chlorides) and B (reaction of dimethyl-(arylsulfonyl)carbonodithioimidate with aryldiamines). The conducted research allowed achieving two independent ecological and quick methods of obtaining the desired products. We used ecological methods of ultrasound-assisted or microwave synthesis, solvent-free reactions and a"green" reaction environment. In both pathways, it has proven advantageous to use H2O as the solvent and K2CO3 (1 or 3 equivalent) as the basic agent. In the sonochemical variant, the efficiency reached B: 37-89 %, C: 90 % in 60 min (P = 80 W and f = 40 kHz), while in the microwave synthesis it was B: 38-74 %, C: 63-85 % in 0.5-4 min (P = 50 W). Path A led to a complementary substitution product (i.e. 1-(arylsulfonyl)-1H-benzimidazol-2-amine or 1-(arylsulfonyl)-1,4-dihydroquinazolin-2-amine). We obtained a small group of compounds that were tested for cytotoxicity. The 10f (N-(1,4-dihydroquinazolin-2-yl)naphthalene-1-sulfonamide) showed cytotoxic activity towards human astrocytoma cell line 1321 N1. The calculated IC50 value was 8.22 µM at 24 h timepoint (doxorubicin suppressed 1321 N1 cell viability with IC50 of 1.1 µM). The viability of the cells exposed to 10f for 24 h dropped to 48.0 % compared to vehicle control, while the cells treated with doxorubicin experienced decline to 47.5 %. We assessed its potential usefulness in pharmacotherapy in the ADMET study, confirming its ability to cross the blood-brain barrier (Pe = 5.0 ± 1.5 × 10-6 cm/s) and the safety of its potential use in terms of DDI and hepatotoxicity.
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Affiliation(s)
- Przemysław Zaręba
- Faculty of Chemical Engineering and Technology, Department of Chemical Technology and Environmental Analytics, Cracow University of Technology, 24 Warszawska Street, 31-155 Cracow, Poland.
| | - Anna K Drabczyk
- Faculty of Chemical Engineering and Technology, Department of Organic Chemistry and Technology, Cracow University of Technology, 24 Warszawska Street, 31-155 Cracow, Poland
| | - Artur Wnorowski
- Department of Biopharmacy, Faculty of Pharmacy, Medical University, Lublin, Poland
| | - Edyta Pindelska
- Department of Analytical Chemistry and Biomaterials, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha, 02-093 Warsaw, Poland
| | - Gniewomir Latacz
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, 9 Medyczna Street, 30-688 Cracow, Poland
| | - Jolanta Jaśkowska
- Faculty of Chemical Engineering and Technology, Department of Organic Chemistry and Technology, Cracow University of Technology, 24 Warszawska Street, 31-155 Cracow, Poland
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7
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Jiang T, Liu Z, Liu W, Chen J, Zheng Z, Duan M. The Conformational Transition Pathways and Hidden Intermediates in DFG-Flip Process of c-Met Kinase Revealed by Metadynamics Simulations. J Chem Inf Model 2022; 62:3651-3663. [PMID: 35848778 DOI: 10.1021/acs.jcim.2c00770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein kinases intrinsically translate their conformations between active and inactive states, which is key to their enzymatic activities. The conformational flipping of the three-residue conservative motif, Asp-Phe-Gly (DFG), is crucial for many kinases' biological functions. Obtaining a detailed demonstration of the DFG flipping process and its corresponding dynamical and thermodynamical features could broaden our understanding of kinases' conformation-activity relationship. In this study, we employed metadynamics simulation, a widely used enhanced sampling technique, to analyze the conformational transition pathways of the DFG flipping for the c-Met kinase. The corresponding free energy landscape suggested two distinct transition pathways between the "DFG-in" and "DFG-out" states of the DFG-flip from c-Met. On the basis of the orientation direction of the F1223 residue, we correspondingly named the two pathways the "DFG-up" path, featuring forming a commonly discovered "DFG-up" transition state, and the "DFG-down" path, a unique transition pathway with F1223 rotating along the opposite direction away from the hydrophobic cavity. The free energies along the two pathways were then calculated using the Path Collective Variable (PCV) metadynamics simulation. The simulation results showed that, though having similar free energy barriers, the free energy cuve for the DFG-down path suggested a two-step conformational transition mechanism, while that for the DFG-up path showed the one-step transition feature. The c-Met DFG flipping mechanism and the new intermediate state discovered in this work could provide a deeper understanding of the conformation-activity relationship for c-Met and, possibly, reveal a new conformational state as the drug target for c-Met and other similar kinases.
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Affiliation(s)
- Tao Jiang
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Zhenhao Liu
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Wenlang Liu
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Jiawen Chen
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, P. R. China
| | - Zheng Zheng
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Mojie Duan
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, P. R. China
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8
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Sharma S, Pablo JL, Tolentino KT, Gallegos W, Hinman J, Beninato M, Asche M, Greka A, Hopkins CR. Further exploration of the benzimidazole scaffold as TRPC5 inhibitors: identification of 1-alkyl-2-(pyrrolidin-1-yl)-1H-benzo[d]imidazoles as potent and selective inhibitors. ChemMedChem 2022; 17:e202200151. [PMID: 35557491 PMCID: PMC9308755 DOI: 10.1002/cmdc.202200151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/05/2022] [Indexed: 11/29/2022]
Abstract
The transient receptor potential cation channel 5 (TRPC5) plays an important role in numerous cellular processes. Due to this, it has gained considerable attention over the past few years as a potential therapeutic target. Recently, TRPC5 has been shown to be involved in the regulation of podocyte survival, indicating a potential treatment option for chronic kidney disease. In addition, a recent study has shown TRPC5 to be expressed in human sensory neurons and suggests that TRPC5 inhibition could be an effective treatment for spontaneous and tactile pain. To understand these processes more fully, potent and selective tool compounds are needed. Herein we report further exploration of the 2‐aminobenzimidazole scaffold as a potent TRPC5 inhibitor, culminating in the discovery of 16 f as a potent and selective TRPC5 inhibitor.
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Affiliation(s)
- Swagat Sharma
- University of Nebraska Medical Center College of Pharmacy, Pharmaceutical Sciences, UNITED STATES
| | | | - Kirsten T Tolentino
- University of Nebraska Medical Center College of Pharmacy, Pharmaceutical Sciences, UNITED STATES
| | - Wacey Gallegos
- University of Nebraska Medical Center College of Pharmacy, Pharmaceutical Sciences, UNITED STATES
| | - Jennifer Hinman
- University of Nebraska Medical Center College of Pharmacy, Pharmaceutical Sciences, UNITED STATES
| | - Madison Beninato
- University of Nebraska Medical Center College of Pharmacy, Pharmaceutical Sciences, UNITED STATES
| | - MacKenzie Asche
- University of Nebraska Medical Center College of Pharmacy, Pharmaceutical Sciences, UNITED STATES
| | - Anna Greka
- Broad Institute Harvard: Broad Institute, Pharmacology, UNITED STATES
| | - Corey R Hopkins
- University of Nebraska Medical Center College of Pharmacy, Pharmaceutical Sciences, 986125 Nebraska Medical Center, PDD 3015, 68198-6125, Omaha, UNITED STATES
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9
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Clauß O, Schäker-Hübner L, Wenzel B, Toussaint M, Deuther-Conrad W, Gündel D, Teodoro R, Dukić-Stefanović S, Ludwig FA, Kopka K, Brust P, Hansen FK, Scheunemann M. Development and Biological Evaluation of the First Highly Potent and Specific Benzamide-Based Radiotracer [ 18F]BA3 for Imaging of Histone Deacetylases 1 and 2 in Brain. Pharmaceuticals (Basel) 2022; 15:ph15030324. [PMID: 35337122 PMCID: PMC8950173 DOI: 10.3390/ph15030324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/25/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
The degree of acetylation of lysine residues on histones influences the accessibility of DNA and, furthermore, the gene expression. Histone deacetylases (HDACs) are overexpressed in various tumour diseases, resulting in the interest in HDAC inhibitors for cancer therapy. The aim of this work is the development of a novel 18F-labelled HDAC1/2-specific inhibitor with a benzamide-based zinc-binding group to visualize these enzymes in brain tumours by positron emission tomography (PET). BA3, exhibiting high inhibitory potency for HDAC1 (IC50 = 4.8 nM) and HDAC2 (IC50 = 39.9 nM), and specificity towards HDAC3 and HDAC6 (specificity ratios >230 and >2080, respectively), was selected for radiofluorination. The two-step one-pot radiosynthesis of [18F]BA3 was performed in a TRACERlab FX2 N radiosynthesizer by a nucleophilic aliphatic substitution reaction. The automated radiosynthesis of [18F]BA3 resulted in a radiochemical yield of 1%, a radiochemical purity of >96% and a molar activity between 21 and 51 GBq/µmol (n = 5, EOS). For the characterization of BA3, in vitro and in vivo experiments were carried out. The results of these pharmacological and pharmacokinetic studies indicate a suitable inhibitory potency of BA3, whereas the applicability for non-invasive imaging of HDAC1/2 by PET requires further optimization of the properties of this compound.
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Affiliation(s)
- Oliver Clauß
- Department of Neuroradiopharmaceuticals, Institute of Radiopharmaceutical Cancer Research, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany; (B.W.); (M.T.); (W.D.-C.); (D.G.); (R.T.); (S.D.-S.); (F.-A.L.); (K.K.); (P.B.)
- Correspondence: (O.C.); (M.S.)
| | - Linda Schäker-Hübner
- Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany; (L.S.-H.); (F.K.H.)
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
| | - Barbara Wenzel
- Department of Neuroradiopharmaceuticals, Institute of Radiopharmaceutical Cancer Research, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany; (B.W.); (M.T.); (W.D.-C.); (D.G.); (R.T.); (S.D.-S.); (F.-A.L.); (K.K.); (P.B.)
| | - Magali Toussaint
- Department of Neuroradiopharmaceuticals, Institute of Radiopharmaceutical Cancer Research, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany; (B.W.); (M.T.); (W.D.-C.); (D.G.); (R.T.); (S.D.-S.); (F.-A.L.); (K.K.); (P.B.)
| | - Winnie Deuther-Conrad
- Department of Neuroradiopharmaceuticals, Institute of Radiopharmaceutical Cancer Research, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany; (B.W.); (M.T.); (W.D.-C.); (D.G.); (R.T.); (S.D.-S.); (F.-A.L.); (K.K.); (P.B.)
| | - Daniel Gündel
- Department of Neuroradiopharmaceuticals, Institute of Radiopharmaceutical Cancer Research, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany; (B.W.); (M.T.); (W.D.-C.); (D.G.); (R.T.); (S.D.-S.); (F.-A.L.); (K.K.); (P.B.)
| | - Rodrigo Teodoro
- Department of Neuroradiopharmaceuticals, Institute of Radiopharmaceutical Cancer Research, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany; (B.W.); (M.T.); (W.D.-C.); (D.G.); (R.T.); (S.D.-S.); (F.-A.L.); (K.K.); (P.B.)
| | - Sladjana Dukić-Stefanović
- Department of Neuroradiopharmaceuticals, Institute of Radiopharmaceutical Cancer Research, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany; (B.W.); (M.T.); (W.D.-C.); (D.G.); (R.T.); (S.D.-S.); (F.-A.L.); (K.K.); (P.B.)
| | - Friedrich-Alexander Ludwig
- Department of Neuroradiopharmaceuticals, Institute of Radiopharmaceutical Cancer Research, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany; (B.W.); (M.T.); (W.D.-C.); (D.G.); (R.T.); (S.D.-S.); (F.-A.L.); (K.K.); (P.B.)
| | - Klaus Kopka
- Department of Neuroradiopharmaceuticals, Institute of Radiopharmaceutical Cancer Research, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany; (B.W.); (M.T.); (W.D.-C.); (D.G.); (R.T.); (S.D.-S.); (F.-A.L.); (K.K.); (P.B.)
- Faculty of Chemistry and Food Chemistry, School of Science, Technical University Dresden, 01062 Dresden, Germany
| | - Peter Brust
- Department of Neuroradiopharmaceuticals, Institute of Radiopharmaceutical Cancer Research, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany; (B.W.); (M.T.); (W.D.-C.); (D.G.); (R.T.); (S.D.-S.); (F.-A.L.); (K.K.); (P.B.)
| | - Finn K. Hansen
- Pharmaceutical and Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany; (L.S.-H.); (F.K.H.)
| | - Matthias Scheunemann
- Department of Neuroradiopharmaceuticals, Institute of Radiopharmaceutical Cancer Research, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany; (B.W.); (M.T.); (W.D.-C.); (D.G.); (R.T.); (S.D.-S.); (F.-A.L.); (K.K.); (P.B.)
- Correspondence: (O.C.); (M.S.)
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10
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Shankaraiah N, Tokala R, Bora D. Contribution of Knoevenagel Condensation Products towards Development of Anticancer Agents: An Updated Review. ChemMedChem 2022; 17:e202100736. [PMID: 35226798 DOI: 10.1002/cmdc.202100736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/23/2022] [Indexed: 11/10/2022]
Abstract
Knoevenagel condensation is an entrenched, prevailing, prominent arsenal following greener principles in the generation of α, β-unsaturated ketones/carboxylic acids by involving carbonyl functionalities and active methylenes. This reaction has proved to be a major driving force in many multicomponent reactions indicating the prolific utility towards the development of biologically fascinating molecules. This eminent reaction was acclimatised on different pharmacophoric aldehydes (benzimidazole, β-carboline, phenanthrene, indole, imidazothiadiazole, pyrazole etc.) and active methylenes (oxindole, barbituric acid, Meldrum's acid, thiazolidinedione etc.) to generate the library of chemical compounds. Their potential was also explicit to understand the significance of functionalities involved, which thereby evoke further developments in drug discovery. Furthermore, most of these reaction products exhibited remarkable anticancer activity in nanomolar to micromolar ranges by targeting different cancer targets like DNA, microtubules, Topo-I/II, and kinases (PIM, PARP, NMP, p300/CBP) etc. This review underscores the efficiency of the Knoevenagel condensation explored in the past six-year to generate molecules of pharmacological interest, predominantly towards cancer. The present review also provides the aspects of structure-activity relationships, mode of action and docking study with possible interaction with the target protein.
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Affiliation(s)
- Nagula Shankaraiah
- National Institute of Pharmaceutical Education and Research NIPER, Department of Medicinal Chemistry, Balanagar, 500037, Hyderabad, INDIA
| | - Ramya Tokala
- NIPER Hyderabad: National Institute of Pharmaceutical Education and Research Hyderabad, Medicinal Chemistry, INDIA
| | - Darshana Bora
- NIPER Hyderabad: National Institute of Pharmaceutical Education and Research Hyderabad, Medicinal Chemistry, INDIA
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11
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Bellisario A, Maia FRNC, Ekeberg T. Noise reduction and mask removal neural network for X-ray single-particle imaging. J Appl Crystallogr 2022; 55:122-132. [PMID: 35145358 PMCID: PMC8805166 DOI: 10.1107/s1600576721012371] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/22/2021] [Indexed: 12/03/2022] Open
Abstract
Free-electron lasers could enable X-ray imaging of single biological macromolecules and the study of protein dynamics, paving the way for a powerful new imaging tool in structural biology, but a low signal-to-noise ratio and missing regions in the detectors, colloquially termed 'masks', affect data collection and hamper real-time evaluation of experimental data. In this article, the challenges posed by noise and masks are tackled by introducing a neural network pipeline that aims to restore diffraction intensities. For training and testing of the model, a data set of diffraction patterns was simulated from 10 900 different proteins with molecular weights within the range of 10-100 kDa and collected at a photon energy of 8 keV. The method is compared with a simple low-pass filtering algorithm based on autocorrelation constraints. The results show an improvement in the mean-squared error of roughly two orders of magnitude in the presence of masks compared with the noisy data. The algorithm was also tested at increasing mask width, leading to the conclusion that demasking can achieve good results when the mask is smaller than half of the central speckle of the pattern. The results highlight the competitiveness of this model for data processing and the feasibility of restoring diffraction intensities from unknown structures in real time using deep learning methods. Finally, an example is shown of this preprocessing making orientation recovery more reliable, especially for data sets containing very few patterns, using the expansion-maximization-compression algorithm.
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Affiliation(s)
- Alfredo Bellisario
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Filipe R. N. C. Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
| | - Tomas Ekeberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3 (Box 596), SE-751 24 Uppsala, Sweden
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12
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Gupta D, Kumar M, Singh M, Salman M, Das U, Kaur P. Identification of polypharmacological anticancerous molecules against Aurora kinase family of proteins. J Cell Biochem 2022; 123:719-735. [PMID: 35040172 DOI: 10.1002/jcb.30214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 12/28/2022]
Abstract
The Human Aurora Kinase (AURK) protein family is the key player of cell cycle events including spindle assembly, kinetochore formation, chromosomal segregation, centrosome separation, microtubule dynamics, and cytokinesis. Their aberrant expression has been extensively linked with chromosomal instability in addition to derangement of multiple tumor suppressors and oncoprotein regulated pathways. Therefore, the AURK family of kinases is a promising target for the treatment of various types of cancer. Over the past few decades, several potential inhibitors of AURK proteins have been identified and have reached various phases of clinical trials. But very few molecules have currently crossed the safety criteria due to their various toxic side effects. In the present study, we have adopted a computational polypharmacological strategy and identified four novel molecules that can target all three AURKs. These molecules were further investigated for their binding stabilities at the ATP binding pocket using molecular dynamics based simulation studies. The molecules selected adopting a multipronged computational approach can be considered as potential AURKs inhibitors for cancer therapeutics.
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Affiliation(s)
- Deepali Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Mandeep Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Mohd Salman
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Uddipan Das
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
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13
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Vangrunderbeeck S, Balcaen T, Veryser C, Steurs G, De Borggraeve WM. Carbonylation Chemistry Applied to the Synthesis of Benzimidazo[2,1‐
b
]quinazolin‐12‐ones. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sarah Vangrunderbeeck
- Molecular Design and Synthesis Department of Chemistry KU Leuven Celestijnenlaan 200F, Box 2404 3001 Leuven Belgium
| | - Tim Balcaen
- Molecular Design and Synthesis Department of Chemistry KU Leuven Celestijnenlaan 200F, Box 2404 3001 Leuven Belgium
| | - Cedrick Veryser
- Molecular Design and Synthesis Department of Chemistry KU Leuven Celestijnenlaan 200F, Box 2404 3001 Leuven Belgium
| | - Gert Steurs
- Molecular Design and Synthesis Department of Chemistry KU Leuven Celestijnenlaan 200F, Box 2404 3001 Leuven Belgium
| | - Wim M. De Borggraeve
- Molecular Design and Synthesis Department of Chemistry KU Leuven Celestijnenlaan 200F, Box 2404 3001 Leuven Belgium
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14
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Zhu D, Johannsen S, Masini T, Simonin C, Haupenthal J, Illarionov B, Andreas A, Awale M, Gierse RM, van der Laan T, van der Vlag R, Nasti R, Poizat M, Buhler E, Reiling N, Müller R, Fischer M, Reymond JL, Hirsch AKH. Discovery of novel drug-like antitubercular hits targeting the MEP pathway enzyme DXPS by strategic application of ligand-based virtual screening. Chem Sci 2022; 13:10686-10698. [PMID: 36320685 PMCID: PMC9491098 DOI: 10.1039/d2sc02371g] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/07/2022] [Indexed: 12/04/2022] Open
Abstract
In the present manuscript, we describe how we successfully used ligand-based virtual screening (LBVS) to identify two small-molecule, drug-like hit classes with excellent ADMET profiles against the difficult to address microbial enzyme 1-deoxy-d-xylulose-5-phosphate synthase (DXPS). In the fight against antimicrobial resistance (AMR), it has become increasingly important to address novel targets such as DXPS, the first enzyme of the 2-C-methyl-d-erythritol-4-phosphate (MEP) pathway, which affords the universal isoprenoid precursors. This pathway is absent in humans but essential for pathogens such as Mycobacterium tuberculosis, making it a rich source of drug targets for the development of novel anti-infectives. Standard computer-aided drug-design tools, frequently applied in other areas of drug development, often fail for targets with large, hydrophilic binding sites such as DXPS. Therefore, we introduce the concept of pseudo-inhibitors, combining the benefits of pseudo-ligands (defining a pharmacophore) and pseudo-receptors (defining anchor points in the binding site), for providing the basis to perform a LBVS against M. tuberculosis DXPS. Starting from a diverse set of reference ligands showing weak inhibition of the orthologue from Deinococcus radiodurans DXPS, we identified three structurally unrelated classes with promising in vitro (against M. tuberculosis DXPS) and whole-cell activity including extensively drug-resistant strains of M. tuberculosis. The hits were validated to be specific inhibitors of DXPS and to have a unique mechanism of inhibition. Furthermore, two of the hits have a balanced profile in terms of metabolic and plasma stability and display a low frequency of resistance development, making them ideal starting points for hit-to-lead optimization of antibiotics with an unprecedented mode of action. We identified two drug-like antitubercular hits with submicromolar inhibition constants against the target 1-deoxy-d-xylulose-5-phosphate synthase (DXPS) with a new mode of action and promising activity against drug-resistant tuberculosis.![]()
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Affiliation(s)
- Di Zhu
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Sandra Johannsen
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1 66123 Saarbrücken Germany
| | - Tiziana Masini
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Céline Simonin
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1 66123 Saarbrücken Germany
| | - Boris Illarionov
- Hamburg School of Food Science, Institute of Food Chemistry Grindelallee 117 20146 Hamburg Germany
| | - Anastasia Andreas
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1 66123 Saarbrücken Germany
| | - Mahendra Awale
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Robin M Gierse
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Tridia van der Laan
- Department of Mycobacteria, National Institute of Public Health and the Environment (RIVM), Diagnostics and Laboratory Surveillance (IDS) Infectious Diseases Research Antonie van Leeuwenhoeklaan 9 3721 MA Bilthoven The Netherlands
| | - Ramon van der Vlag
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Rita Nasti
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Mael Poizat
- Symeres Kadijk 3 9747 AT Groningen The Netherlands
| | - Eric Buhler
- Laboratoire Matière et Systèmes Complexes (MSC), UMR CNRS 7057, Université Paris Cité Bâtiment Condorcet 75205 Paris Cedex 13 France
| | - Norbert Reiling
- RG Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center Borstel Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems Borstel Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1 66123 Saarbrücken Germany
- Helmholtz International Lab for Anti-infectives Campus Building E8.1 66123 Saarbrücken Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry Grindelallee 117 20146 Hamburg Germany
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1 66123 Saarbrücken Germany
- Stratingh Institute for Chemistry, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
- Helmholtz International Lab for Anti-infectives Campus Building E8.1 66123 Saarbrücken Germany
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15
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Chakraborty A, Roy S, Chakraborty MP, Roy SS, Purkait K, Koley TS, Das R, Acharya M, Mukherjee A. Cytotoxic Ruthenium(II) Complexes of Pyrazolylbenzimidazole Ligands That Inhibit VEGFR2 Phosphorylation. Inorg Chem 2021; 60:18379-18394. [PMID: 34780170 DOI: 10.1021/acs.inorgchem.1c02979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Eight new ruthenium(II) complexes of N,N-chelating pyrazolylbenzimidazole ligands of the general formula [RuII(p-cym)(L)X]+ [where the ligand L is 2-(1H-pyrazol-1-yl)-1H-benzo[d]imidazole (L1) substituted at the 4 position of the pyrazole ring by Cl (L2), Br (L3), or I (L4) and X = Cl- and I-] were synthesized and characterized using various analytical techniques. Complexes 1 and 3 were also characterized by single-crystal X-ray crystallography, and they crystallized as a monoclinic crystal system in space groups P21/n and P21/c, respectively. The complexes display good solution stability at physiological pH 7.4. The iodido-coordinated pyrazolylbenzimidazole ruthenium(II) p-cymene complexes (2, 4, 6, and 8) are more resistant toward hydrolysis and have less tendency to form monoaquated complexes in comparison to their chlorido analogues (1, 3, 5, and 7). The halido-substituted 2-(1H-pyrazol-1-yl)-1H-benzo[d]imidazole ligands, designed as organic-directing molecules, inhibit vascular endothelial growth factor receptor 2 (VEGFR2) phosphorylation. In addition, the ruthenium(II) complexes display a potential to bind to DNA bases. The cytotoxicity profile of the complexes (IC50 ca. 9-12 μM for 4-8) against the triple-negative breast cancer cells (MDA-MB-231) show that most of the complexes are efficient. The lipophilicity and cellular accumulation data of the complexes show a good correlation with the cytotoxicity profile of 1-8. The representative complexes 3 and 7 demonstrate the capability of arresting the cell cycle in the G2/M phase and induce apoptosis. The inhibition of VEGFR2 phosphorylation with the representative ligands L2 and L4 and the corresponding metal complexes 3 and 7 in vitro shows that the organic-directing ligands and their complexes inhibit VEGFR2 phosphorylation. Besides, L2, L4, 3, and 7 inhibit the phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2) and proto-oncogene tyrosine-protein kinase (Src), capable of acting downstream of VEGFR2 as well as independently. Compounds L2, L4, 3, and 7 have a lesser effect on ERK1/2 and more prominently affect Src phosphorylation. We extended the study for L2 and 3 in the Tg(fli1:gfp) zebrafish model and found that L2 is more effective in vivo compared to 3 in inhibiting angiogenesis.
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16
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Tanaka I, Furukawa T, Morise M. The current issues and future perspective of artificial intelligence for developing new treatment strategy in non-small cell lung cancer: harmonization of molecular cancer biology and artificial intelligence. Cancer Cell Int 2021; 21:454. [PMID: 34446006 PMCID: PMC8393743 DOI: 10.1186/s12935-021-02165-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/19/2021] [Indexed: 12/12/2022] Open
Abstract
Comprehensive analysis of omics data, such as genome, transcriptome, proteome, metabolome, and interactome, is a crucial technique for elucidating the complex mechanism of cancer onset and progression. Recently, a variety of new findings have been reported based on multi-omics analysis in combination with various clinical information. However, integrated analysis of multi-omics data is extremely labor intensive, making the development of new analysis technology indispensable. Artificial intelligence (AI), which has been under development in recent years, is quickly becoming an effective approach to reduce the labor involved in analyzing large amounts of complex data and to obtain valuable information that is often overlooked in manual analysis and experiments. The use of AI, such as machine learning approaches and deep learning systems, allows for the efficient analysis of massive omics data combined with accurate clinical information and can lead to comprehensive predictive models that will be desirable for further developing individual treatment strategies of immunotherapy and molecular target therapy. Here, we aim to review the potential of AI in the integrated analysis of omics data and clinical information with a special focus on recent advances in the discovery of new biomarkers and the future direction of personalized medicine in non-small lung cancer.
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Affiliation(s)
- Ichidai Tanaka
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan.
| | - Taiki Furukawa
- Center for Healthcare Information Technology (C-HiT), Nagoya University, Nagoya, Japan
| | - Masahiro Morise
- Department of Respiratory Medicine, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
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17
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Winiewska-Szajewska M, Maciejewska AM, Speina E, Poznański J, Paprocki D. Synthesis of Novel Halogenated Heterocycles Based on o-Phenylenediamine and Their Interactions with the Catalytic Subunit of Protein Kinase CK2. Molecules 2021; 26:molecules26113163. [PMID: 34070615 PMCID: PMC8198750 DOI: 10.3390/molecules26113163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/18/2021] [Accepted: 05/22/2021] [Indexed: 01/07/2023] Open
Abstract
Protein kinase CK2 is a highly pleiotropic protein kinase capable of phosphorylating hundreds of protein substrates. It is involved in numerous cellular functions, including cell viability, apoptosis, cell proliferation and survival, angiogenesis, or ER-stress response. As CK2 activity is found perturbed in many pathological states, including cancers, it becomes an attractive target for the pharma. A large number of low-mass ATP-competitive inhibitors have already been developed, the majority of them halogenated. We tested the binding of six series of halogenated heterocyclic ligands derived from the commercially available 4,5-dihalo-benzene-1,2-diamines. These ligand series were selected to enable the separation of the scaffold effect from the hydrophobic interactions attributed directly to the presence of halogen atoms. In silico molecular docking was initially applied to test the capability of each ligand for binding at the ATP-binding site of CK2. HPLC-derived ligand hydrophobicity data are compared with the binding affinity assessed by low-volume differential scanning fluorimetry (nanoDSF). We identified three promising ligand scaffolds, two of which have not yet been described as CK2 inhibitors but may lead to potent CK2 kinase inhibitors. The inhibitory activity against CK2α and toxicity against four reference cell lines have been determined for eight compounds identified as the most promising in nanoDSF assay.
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18
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Meng H, Sun K, Xu Z, Tian L, Wang Y. P(III)‐Assisted Electrochemical Access to Ureas via in situ Generation of Isocyanates from Hydroxamic Acids. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Haiwen Meng
- Technical Institute of Fluorochemistry (TIF) Institute of Advanced Synthesis School of Chemistry and Molecular Engineering Nanjing Tech University 211816 Nanjing China
| | - Kunhui Sun
- Technical Institute of Fluorochemistry (TIF) Institute of Advanced Synthesis School of Chemistry and Molecular Engineering Nanjing Tech University 211816 Nanjing China
| | - Zhimin Xu
- Technical Institute of Fluorochemistry (TIF) Institute of Advanced Synthesis School of Chemistry and Molecular Engineering Nanjing Tech University 211816 Nanjing China
| | - Lifang Tian
- Technical Institute of Fluorochemistry (TIF) Institute of Advanced Synthesis School of Chemistry and Molecular Engineering Nanjing Tech University 211816 Nanjing China
| | - Yahui Wang
- Technical Institute of Fluorochemistry (TIF) Institute of Advanced Synthesis School of Chemistry and Molecular Engineering Nanjing Tech University 211816 Nanjing China
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19
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Antiparasitic Effects of Selected Isoflavones on Flatworms. Helminthologia 2021; 58:1-16. [PMID: 33664614 PMCID: PMC7912234 DOI: 10.2478/helm-2021-0004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 12/07/2020] [Indexed: 01/13/2023] Open
Abstract
Medicinal plants have been successfully used in the ethno medicine for a wide range of diseases since ancient times. The research on natural products has allowed the discovery of biologically relevant compounds inspired by plant secondary metabolites, what contributed to the development of many chemotherapeutic drugs. Flavonoids represent a group of therapeutically very effective plant secondary metabolites and selected molecules were shown to exert also antiparasitic activity. This work summarizes the recent knowledge generated within past three decades about potential parasitocidal activities of several flavonoids with different chemical structures, particularly on medically important flatworms such as Schistosoma spp., Fasciola spp., Echinococcus spp., Raillietina spp., and model cestode Mesocestoides vogae. Here we focus on curcumin, genistein, quercetin and silymarin complex of flavonolignans. All of them possess a whole spectrum of biological activities on eukaryotic cells which have multi-therapeutic effects in various diseases. In vitro they can induce profound alterations in the tegumental architecture and its functions as well as their activity can significantly modulate or damage worm´s metabolism directly by interaction with enzymes or signaling molecules in dose-dependent manner. Moreover, they seem to differentially regulate the RNA activity in numbers of worm´s genes. This review suggests that examined flavonoids and their derivates are promising molecules for antiparasitic drug research. Due to lack of toxicity, isoflavons could be used directly for therapy, or as adjuvant therapy for diseases caused by medically important cestodes and trematodes.
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20
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Synthesis, characterization and in-silico assessment of novel thiazolidinone derivatives for cyclin-dependent kinases-2 inhibitors. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129311] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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21
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Pattarawarapan M, Yamano D, Wiriya N, Yimklan S, Phakhodee W. Simultaneous Formation and Functionalization of Aryliminophosphoranes Using 1,3-Dihydro-1 H-benzimidazol-2-ones as Precursors. J Org Chem 2020; 85:13330-13338. [PMID: 33006471 DOI: 10.1021/acs.joc.0c01979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An atom- and step-economic synthesis of aryliminophosphoranes bearing ortho urea was achieved via unprecedented Ph3P-I2 mediated ring-opening of 1,3-dihydro-1H-benzimidazol-2-ones with secondary amines. Tandem aza-Wittig/heterocyclization of the functionalized aryliminophosphoranes upon treatment with isothiocyanates enables a facile access to a single regioisomer of N1-substituted 2-aminobenzimidazoles as well as fused tetracyclic quinazolinone derivatives in one-pot. 31P{1H} NMR studies suggested that the urea C-N bond of benzimidazolone is weakened by N-phosphorylation, leading to aminolysis rather than the expected deoxygenative amination.
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Affiliation(s)
- Mookda Pattarawarapan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Research Center on Chemistry for Development of Health Promoting Products from Northern Resources, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Dolnapa Yamano
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nittaya Wiriya
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Saranphong Yimklan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wong Phakhodee
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.,Research Center on Chemistry for Development of Health Promoting Products from Northern Resources, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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22
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Gray JL, von Delft F, Brennan PE. Targeting the Small GTPase Superfamily through Their Regulatory Proteins. Angew Chem Int Ed Engl 2020; 59:6342-6366. [PMID: 30869179 PMCID: PMC7204875 DOI: 10.1002/anie.201900585] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/11/2019] [Indexed: 12/11/2022]
Abstract
The Ras superfamily of small GTPases are guanine-nucleotide-dependent switches essential for numerous cellular processes. Mutations or dysregulation of these proteins are associated with many diseases, but unsuccessful attempts to target the small GTPases directly have resulted in them being classed as "undruggable". The GTP-dependent signaling of these proteins is controlled by their regulators; guanine nucleotide exchange factors (GEFs), GTPase activating proteins (GAPs), and in the Rho and Rab subfamilies, guanine nucleotide dissociation inhibitors (GDIs). This review covers the recent small molecule and biologics strategies to target the small GTPases through their regulators. It seeks to critically re-evaluate recent chemical biology practice, such as the presence of PAINs motifs and the cell-based readout using compounds that are weakly potent or of unknown specificity. It highlights the vast scope of potential approaches for targeting the small GTPases in the future through their regulatory proteins.
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Affiliation(s)
- Janine L. Gray
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOld Road CampusOxfordOX3 7FZUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0QXUK
| | - Frank von Delft
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0QXUK
- Department of BiochemistryUniversity of JohannesburgAuckland Park2006South Africa
| | - Paul E. Brennan
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOld Road CampusOxfordOX3 7FZUK
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of OxfordOxfordOX3 7FZUK
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23
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Lin Y, Li E, Wu X, Wang L, Wang H, Li X, Kang H, Zhou L, Shen G, Lv X. One-pot synthesis of 2-azolylimidazole derivatives through a domino addition/A 3 coupling/cyclization process under copper catalysis. Org Biomol Chem 2020; 18:1476-1486. [PMID: 32026913 DOI: 10.1039/c9ob02532d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel one-pot approach for the synthesis of multi-substituted 2-imidazolylimidazoles, 2-pyrazolylimidazoles and 2-indazolylimidazoles was developed through a domino addition/A3 coupling/cyclization process under copper catalysis. A variety of aminoethyl- or hydroxylethyl-tethered 2-azolylimidazole derivatives were conveniently and efficiently assembled in one pot using N-propargylcarbodiimides, azoles, paraformaldehyde and secondary amines as starting materials. The products containing an o-iodoaryl group could be further converted to imidazo[1,2-c]imidazo[1,2-a]quinazoline derivatives through a copper-catalyzed intramolecular C-H arylation.
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Affiliation(s)
- Yifan Lin
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China.
| | - Erfei Li
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China.
| | - Xin Wu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China.
| | - Luyu Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China.
| | - Haofeng Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China.
| | - Xiaoyu Li
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China.
| | - Honglan Kang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China.
| | - Liejin Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China.
| | - Guodong Shen
- School of Chemistry and Chemical Engineering, Shandong Provincial Key Laboratory of Chemical Energy Storage and Novel Cell Technology, Liaocheng University, Liaocheng 252059, Shandong, People's Republic of China
| | - Xin Lv
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People's Republic of China.
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Gray JL, Delft F, Brennan PE. Targeting der kleinen GTPasen über ihre regulatorischen Proteine. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201900585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Janine L. Gray
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Old Road Campus Oxford OX3 7FZ Großbritannien
- Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0QX Großbritannien
| | - Frank Delft
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0QX Großbritannien
- Department of BiochemistryUniversity of Johannesburg Auckland Park 2006 Südafrika
| | - Paul E. Brennan
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Old Road Campus Oxford OX3 7FZ Großbritannien
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of Oxford Oxford OX3 7FZ Großbritannien
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Shawky AM, Abourehab MA, Abdalla AN, Gouda AM. Optimization of pyrrolizine-based Schiff bases with 4-thiazolidinone motif: Design, synthesis and investigation of cytotoxicity and anti-inflammatory potency. Eur J Med Chem 2020; 185:111780. [DOI: 10.1016/j.ejmech.2019.111780] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 10/04/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022]
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Liu B, He H, Luo H, Zhang T, Jiang J. Artificial intelligence and big data facilitated targeted drug discovery. Stroke Vasc Neurol 2019; 4:206-213. [PMID: 32030204 PMCID: PMC6979871 DOI: 10.1136/svn-2019-000290] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 10/28/2019] [Indexed: 12/20/2022] Open
Abstract
Different kinds of biological databases publicly available nowadays provide us a goldmine of multidiscipline big data. The Cancer Genome Atlas is a cancer database including detailed information of many patients with cancer. DrugBank is a database including detailed information of approved, investigational and withdrawn drugs, as well as other nutraceutical and metabolite structures. PubChem is a chemical compound database including all commercially available compounds as well as other synthesisable compounds. Protein Data Bank is a crystal structure database including X-ray, cryo-EM and nuclear magnetic resonance protein three-dimensional structures as well as their ligands. On the other hand, artificial intelligence (AI) is playing an important role in the drug discovery progress. The integration of such big data and AI is making a great difference in the discovery of novel targeted drug. In this review, we focus on the currently available advanced methods for the discovery of highly effective lead compounds with great absorption, distribution, metabolism, excretion and toxicity properties.
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Affiliation(s)
- Benquan Liu
- Jiangsu Key Lab of Drug Screening, China Pharmaceutical University, Nanjing, China
| | - Huiqin He
- Jiangsu Key Lab of Drug Screening, China Pharmaceutical University, Nanjing, China
| | - Hongyi Luo
- Jiangsu Key Lab of Drug Screening, China Pharmaceutical University, Nanjing, China
| | - Tingting Zhang
- Jiangsu Key Lab of Drug Screening, China Pharmaceutical University, Nanjing, China
| | - Jingwei Jiang
- Jiangsu Key Lab of Drug Screening, China Pharmaceutical University, Nanjing, China
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Qi B, Zhong L, He J, Zhang H, Li F, Wang T, Zou J, Lin YX, Zhang C, Guo X, Li R, Shi J. Discovery of Inhibitors of Aurora/PLK Targets as Anticancer Agents. J Med Chem 2019; 62:7697-7707. [PMID: 31381325 DOI: 10.1021/acs.jmedchem.9b00353] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Aurora and polo-like kinases control the G2/M phase in cell mitosis, which are both considered as crucial targets for cancer cell proliferations. Here, naphthalene-based Aurora/PLK coinhibitors as leading compounds were designed through in silico approach, and a total of 36 derivatives were synthesized. One candidate (AAPK-25) was selected under in vitro cell based high throughput screening with an IC50 value = 0.4 μM to human colon cancer cell HCT-116. A kinome scan assay showed that AAPK-25 was remarkably selective to both Aurora and PLK families. The relevant genome pathways were also depicted by microarray based gene expression analysis. Furthermore, validated from a set of in vitro and in vivo studies, AAPK-25 significantly inhibited the development of the colon cancer growth and prolonged the median survival time at the end of the administration (p < 0.05). To sum up, AAPK-25 has a great potential to be developed for a chemotherapeutic agent in clinical use.
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Affiliation(s)
- Baowen Qi
- College of Pharmacy and Biological Engineering , Chengdu University , Chengdu 610106 , China
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Ling Zhong
- Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Individualized Medication Key Laboratory of Sichuan Province, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, School of Medicine, Center for Information in Medicine , University of Electronic Science and Technology of China , Chengdu 610072 , China
- Chengdu Institute of Biology , Chinese Academy of Sciences , Chengdu 610041 , China
| | - Jun He
- Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Sichuan 610041 , China
| | - Hongjia Zhang
- Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Individualized Medication Key Laboratory of Sichuan Province, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, School of Medicine, Center for Information in Medicine , University of Electronic Science and Technology of China , Chengdu 610072 , China
| | - Fengqiong Li
- Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Individualized Medication Key Laboratory of Sichuan Province, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, School of Medicine, Center for Information in Medicine , University of Electronic Science and Technology of China , Chengdu 610072 , China
| | - Ting Wang
- Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Individualized Medication Key Laboratory of Sichuan Province, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, School of Medicine, Center for Information in Medicine , University of Electronic Science and Technology of China , Chengdu 610072 , China
| | - Jing Zou
- Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Individualized Medication Key Laboratory of Sichuan Province, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, School of Medicine, Center for Information in Medicine , University of Electronic Science and Technology of China , Chengdu 610072 , China
| | - Yao-Xin Lin
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Chengchen Zhang
- Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Individualized Medication Key Laboratory of Sichuan Province, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, School of Medicine, Center for Information in Medicine , University of Electronic Science and Technology of China , Chengdu 610072 , China
| | - Xiaoqiang Guo
- College of Pharmacy and Biological Engineering , Chengdu University , Chengdu 610106 , China
| | - Rui Li
- Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Sichuan 610041 , China
| | - Jianyou Shi
- Sichuan Academy of Medical Science & Sichuan Provincial People's Hospital, Individualized Medication Key Laboratory of Sichuan Province, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, School of Medicine, Center for Information in Medicine , University of Electronic Science and Technology of China , Chengdu 610072 , China
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Lamb R, Revil-Baudard VL, Zard SZ. A Direct Approach to Orthogonally Protected α-Amino Aldehydes. Org Lett 2019; 21:6352-6356. [PMID: 31343880 DOI: 10.1021/acs.orglett.9b02237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
O-Neopentyl-xanthate 19 bearing a masked α-amino aldehyde, with the two functional groups orthogonally protected, reacts cleanly with many functional alkenes. The radical addition-transfer furnishes densely functionalized adducts that can be further transformed into an array of amino-substituted carbocycles and heteroaromatics. They are also easily converted into imidazolones.
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Affiliation(s)
- Richard Lamb
- Laboratoire de Synthèse Organique, CNRS UMR 7652 , Ecole Polytechnique , 91128 Palaiseau Cedex, France
| | - Vincent L Revil-Baudard
- Laboratoire de Synthèse Organique, CNRS UMR 7652 , Ecole Polytechnique , 91128 Palaiseau Cedex, France
| | - Samir Z Zard
- Laboratoire de Synthèse Organique, CNRS UMR 7652 , Ecole Polytechnique , 91128 Palaiseau Cedex, France
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Dou X, Huang H, Li Y, Jiang L, Wang Y, Jin H, Jiao N, Zhang L, Zhang L, Liu Z. Multistage Screening Reveals 3-Substituted Indolin-2-one Derivatives as Novel and Isoform-Selective c-Jun N-terminal Kinase 3 (JNK3) Inhibitors: Implications to Drug Discovery for Potential Treatment of Neurodegenerative Diseases. J Med Chem 2019; 62:6645-6664. [DOI: 10.1021/acs.jmedchem.9b00537] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Xiaodong Dou
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Huixia Huang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yibo Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Lan Jiang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yanxing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ning Jiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Liangren Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Zhenming Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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Duarte Y, Márquez-Miranda V, Miossec MJ, González-Nilo F. Integration of target discovery, drug discovery and drug delivery: A review on computational strategies. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2019; 11:e1554. [PMID: 30932351 DOI: 10.1002/wnan.1554] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 12/14/2018] [Accepted: 01/23/2019] [Indexed: 12/22/2022]
Abstract
Most of the computational tools involved in drug discovery developed during the 1980s were largely based on computational chemistry, quantitative structure-activity relationship (QSAR) and cheminformatics. Subsequently, the advent of genomics in the 2000s gave rise to a huge number of databases and computational tools developed to analyze large quantities of data, through bioinformatics, to obtain valuable information about the genomic regulation of different organisms. Target identification and validation is a long process during which evidence for and against a target is accumulated in the pursuit of developing new drugs. Finally, the drug delivery system appears as a novel approach to improve drug targeting and releasing into the cells, leading to new opportunities to improve drug efficiency and avoid potential secondary effects. In each area: target discovery, drug discovery and drug delivery, different computational strategies are being developed to accelerate the process of selection and discovery of new tools to be applied to different scientific fields. Research on these three topics is growing rapidly, but still requires a global view of this landscape to detect the most challenging bottleneck and how computational tools could be integrated in each topic. This review describes the current state of the art in computational strategies for target discovery, drug discovery and drug delivery and how these fields could be integrated. Finally, we will discuss about the current needs in these fields and how the continuous development of databases and computational tools will impact on the improvement of those areas. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.
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Affiliation(s)
- Yorley Duarte
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Valeria Márquez-Miranda
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Matthieu J Miossec
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Fernando González-Nilo
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Centro Interdisciplinario de Neurociencias de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
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Delalande C, Awale M, Rubin M, Probst D, Ozhathil LC, Gertsch J, Abriel H, Reymond JL. Optimizing TRPM4 inhibitors in the MHFP6 chemical space. Eur J Med Chem 2019; 166:167-177. [DOI: 10.1016/j.ejmech.2019.01.048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/18/2018] [Accepted: 01/19/2019] [Indexed: 12/12/2022]
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Bana P, Szigetvári Á, Kóti J, Éles J, Greiner I. Flow-oriented synthetic design in the continuous preparation of the aryl piperazine drug flibanserin. REACT CHEM ENG 2019. [DOI: 10.1039/c8re00266e] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The first integrated continuous-flow synthesis of the drug substance flibanserin was developed, using an uninterrupted four-step sequence, via an unprecedented route.
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Kimuda MP, Laming D, Hoppe HC, Tastan Bishop Ö. Identification of Novel Potential Inhibitors of Pteridine Reductase 1 in Trypanosoma brucei via Computational Structure-Based Approaches and in Vitro Inhibition Assays. Molecules 2019; 24:molecules24010142. [PMID: 30609681 PMCID: PMC6337619 DOI: 10.3390/molecules24010142] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 11/16/2022] Open
Abstract
Pteridine reductase 1 (PTR1) is a trypanosomatid multifunctional enzyme that provides a mechanism for escape of dihydrofolate reductase (DHFR) inhibition. This is because PTR1 can reduce pterins and folates. Trypanosomes require folates and pterins for survival and are unable to synthesize them de novo. Currently there are no anti-folate based Human African Trypanosomiasis (HAT) chemotherapeutics in use. Thus, successful dual inhibition of Trypanosoma brucei dihydrofolate reductase (TbDHFR) and Trypanosoma brucei pteridine reductase 1 (TbPTR1) has implications in the exploitation of anti-folates. We carried out molecular docking of a ligand library of 5742 compounds against TbPTR1 and identified 18 compounds showing promising binding modes. The protein-ligand complexes were subjected to molecular dynamics to characterize their molecular interactions and energetics, followed by in vitro testing. In this study, we identified five compounds which showed low micromolar Trypanosome growth inhibition in in vitro experiments that might be acting by inhibition of TbPTR1. Compounds RUBi004, RUBi007, RUBi014, and RUBi018 displayed moderate to strong antagonism (mutual reduction in potency) when used in combination with the known TbDHFR inhibitor, WR99210. This gave an indication that the compounds might inhibit both TbPTR1 and TbDHFR. RUBi016 showed an additive effect in the isobologram assay. Overall, our results provide a basis for scaffold optimization for further studies in the development of HAT anti-folates.
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Affiliation(s)
- Magambo Phillip Kimuda
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Grahamstown 6140, South Africa.
- College of Veterinary Medicine, Animal Resources and Biosecurity (COVAB), Makerere University, P.O. Box 7062, Kampala 00256, Uganda.
| | - Dustin Laming
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa.
- Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown 6140, South Africa.
| | - Heinrich C Hoppe
- Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa.
- Centre for Chemico- and Biomedicinal Research, Rhodes University, Grahamstown 6140, South Africa.
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, P.O. Box 94, Grahamstown 6140, South Africa.
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Qiu XL, Gou SH, Wei W, Zou P, Hu L, Yan XM, Li XY. Practical Synthesis of Pimobendan. HETEROCYCLES 2019. [DOI: 10.3987/com-19-14059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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35
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Poirier M, Awale M, Roelli MA, Giuffredi GT, Ruddigkeit L, Evensen L, Stooss A, Calarco S, Lorens JB, Charles RP, Reymond JL. Identifying Lysophosphatidic Acid Acyltransferase β (LPAAT-β) as the Target of a Nanomolar Angiogenesis Inhibitor from a Phenotypic Screen Using the Polypharmacology Browser PPB2. ChemMedChem 2018; 14:224-236. [PMID: 30520265 DOI: 10.1002/cmdc.201800554] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Indexed: 12/11/2022]
Abstract
By screening a focused library of kinase inhibitor analogues in a phenotypic co-culture assay for angiogenesis inhibition, we identified an aminotriazine that acts as a cytostatic nanomolar inhibitor. However, this aminotriazine was found to be completely inactive in a whole-kinome profiling assay. To decipher its mechanism of action, we used the online target prediction tool PPB2 (http://ppb2.gdb.tools), which suggested lysophosphatidic acid acyltransferase β (LPAAT-β) as a possible target for this aminotriazine as well as several analogues identified by structure-activity relationship profiling. LPAAT-β inhibition (IC50 ≈15 nm) was confirmed in a biochemical assay and by its effects on cell proliferation in comparison with a known LPAAT-β inhibitor. These experiments illustrate the value of target-prediction tools to guide target identification for phenotypic screening hits and significantly expand the rather limited pharmacology of LPAAT-β inhibitors.
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Affiliation(s)
- Marion Poirier
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Matthias A Roelli
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3000, Bern 9, Switzerland
| | - Guy T Giuffredi
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Lars Ruddigkeit
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Lasse Evensen
- Department of Biomedicine, Centre for Cancer Biomarkers (CCBIO), University of Bergen, Jonas Lies vei 91, 5009, Bergen, Norway
| | - Amandine Stooss
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3000, Bern 9, Switzerland
| | - Serafina Calarco
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3000, Bern 9, Switzerland
| | - James B Lorens
- Department of Biomedicine, Centre for Cancer Biomarkers (CCBIO), University of Bergen, Jonas Lies vei 91, 5009, Bergen, Norway
| | - Roch-Philippe Charles
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCure, University of Bern, Bühlstrasse 28, 3000, Bern 9, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
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Wang W, Feng X, Liu HX, Chen SW, Hui L. Synthesis and biological evaluation of 2,4-disubstituted phthalazinones as Aurora kinase inhibitors. Bioorg Med Chem 2018; 26:3217-3226. [DOI: 10.1016/j.bmc.2018.04.048] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 04/20/2018] [Accepted: 04/21/2018] [Indexed: 02/06/2023]
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Pitsawong W, Buosi V, Otten R, Agafonov RV, Zorba A, Kern N, Kutter S, Kern G, Pádua RA, Meniche X, Kern D. Dynamics of human protein kinase Aurora A linked to drug selectivity. eLife 2018; 7:36656. [PMID: 29901437 PMCID: PMC6054532 DOI: 10.7554/elife.36656] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/12/2018] [Indexed: 12/24/2022] Open
Abstract
Protein kinases are major drug targets, but the development of highly-selective inhibitors has been challenging due to the similarity of their active sites. The observation of distinct structural states of the fully-conserved Asp-Phe-Gly (DFG) loop has put the concept of conformational selection for the DFG-state at the center of kinase drug discovery. Recently, it was shown that Gleevec selectivity for the Tyr-kinase Abl was instead rooted in conformational changes after drug binding. Here, we investigate whether protein dynamics after binding is a more general paradigm for drug selectivity by characterizing the binding of several approved drugs to the Ser/Thr-kinase Aurora A. Using a combination of biophysical techniques, we propose a universal drug-binding mechanism, that rationalizes selectivity, affinity and long on-target residence time for kinase inhibitors. These new concepts, where protein dynamics in the drug-bound state plays the crucial role, can be applied to inhibitor design of targets outside the kinome. Protein kinases are a family of enzymes found in all living organisms. These enzymes help to control many biological processes, including cell division. When particular protein kinases do not work correctly, cells may start to divide uncontrollably, which can lead to cancer. One example is the kinase Aurora A, which is over-active in many common human cancers. As a result, researchers are currently trying to design drugs that reduce the activity of Aurora A in the hope that these could form new anticancer treatments. In general, drugs are designed to be as specific in their action as possible to reduce the risk of harmful side effects to the patient. Designing a drug that affects a single protein kinase, however, is difficult because there are hundreds of different kinases in the body, all with similar structures. Because drugs often work by binding to specific structural features, a drug that targets one protein kinase can often alter the activity of a large number of others too. Gleevec is a successful anti-leukemia drug that specifically works on one target kinase, producing minimal side effects. It was recently discovered that the drug works through a phenomenon called ‘induced fit’. This means that after the drug binds it causes a change in the enzyme’s overall shape that alters the activity of the enzyme. The shape change is complex, and so even small structural differences can change the effect of a particular drug. Do other drugs that target other protein kinases also produce induced fit effects? To find out, Pitsawong, Buosi, Otten, Agafonov et al. studied how three anti-cancer drugs interact with Aurora A: two drugs specifically designed to switch off Aurora A, and Gleevec (which does not target Aurora A). The two drugs that specifically target Aurora A were thought to work by targeting one structural feature of the enzyme. However, the biochemical and biophysical experiments performed by Pitsawong et al. revealed that these drugs instead work through an induced fit effect. By contrast, Gleevec did not trigger an induced fit on Aurora A and so bound less tightly to it. In light of these results, Pitsawong et al. suggest that future efforts to design drugs that target protein kinases should focus on exploiting the induced fit process. This will require more research into the structure of particular kinases.
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Affiliation(s)
- Warintra Pitsawong
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Vanessa Buosi
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Renee Otten
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Roman V Agafonov
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Adelajda Zorba
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Nadja Kern
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Steffen Kutter
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Gunther Kern
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Ricardo Ap Pádua
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
| | - Xavier Meniche
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Dorothee Kern
- Department of Biochemistry, Howard Hughes Medical Institute, Brandeis University, Waltham, United States
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Ozhathil LC, Delalande C, Bianchi B, Nemeth G, Kappel S, Thomet U, Ross‐Kaschitza D, Simonin C, Rubin M, Gertsch J, Lochner M, Peinelt C, Reymond J, Abriel H. Identification of potent and selective small molecule inhibitors of the cation channel TRPM4. Br J Pharmacol 2018; 175:2504-2519. [PMID: 29579323 PMCID: PMC6002741 DOI: 10.1111/bph.14220] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/08/2018] [Accepted: 03/16/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND AND PURPOSE TRPM4 is a calcium-activated non-selective cation channel expressed in many tissues and implicated in several diseases, and has not yet been validated as a therapeutic target due to the lack of potent and selective inhibitors. We sought to discover a novel series of small-molecule inhibitors by combining in silico methods and cell-based screening assay, with sub-micromolar potency and improved selectivity from previously reported TRPM4 inhibitors. EXPERIMENTAL APPROACH Here, we developed a high throughput screening compatible assay to record TRPM4-mediated Na+ influx in cells using a Na+ -sensitive dye and used this assay to screen a small set of compounds selected by ligand-based virtual screening using previously known weakly active and non-selective TRPM4 inhibitors as seed molecules. Conventional electrophysiological methods were used to validate the potency and selectivity of the hit compounds in HEK293 cells overexpressing TRPM4 and in endogenously expressing prostate cancer cell line LNCaP. Chemical chaperone property of compound 5 was studied using Western blots and electrophysiology experiments. KEY RESULTS A series of halogenated anthranilic amides were identified with TRPM4 inhibitory properties with sub-micromolar potency and adequate selectivity. We also showed for the first time that a naturally occurring variant of TRPM4, which displays loss-of-expression and function, is rescued by the most promising compound 5 identified in this study. CONCLUSIONS AND IMPLICATIONS The discovery of compound 5, a potent and selective inhibitor of TRPM4 with an additional chemical chaperone feature, revealed new opportunities for studying the role of TRPM4 in human diseases and developing clinical drug candidates.
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Affiliation(s)
- Lijo Cherian Ozhathil
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCureUniversity of BernBernSwitzerland
| | - Clémence Delalande
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCureUniversity of BernBernSwitzerland
| | - Beatrice Bianchi
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCureUniversity of BernBernSwitzerland
| | - Gabor Nemeth
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCureUniversity of BernBernSwitzerland
| | - Sven Kappel
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCureUniversity of BernBernSwitzerland
| | - Urs Thomet
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCureUniversity of BernBernSwitzerland
| | - Daniela Ross‐Kaschitza
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCureUniversity of BernBernSwitzerland
| | - Céline Simonin
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCureUniversity of BernBernSwitzerland
| | - Matthias Rubin
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCureUniversity of BernBernSwitzerland
| | - Jürg Gertsch
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCureUniversity of BernBernSwitzerland
| | - Martin Lochner
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCureUniversity of BernBernSwitzerland
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCureUniversity of BernBernSwitzerland
| | - Christine Peinelt
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCureUniversity of BernBernSwitzerland
| | - Jean‐Louis Reymond
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCureUniversity of BernBernSwitzerland
| | - Hugues Abriel
- Institute of Biochemistry and Molecular Medicine, National Center of Competence in Research NCCR TransCureUniversity of BernBernSwitzerland
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Wang G, Wang Q, Li Z, Liu C, He X. Clinical value of Xenopus kinesin-like protein 2 as a prognostic marker in patients with digestive system cancers: a systematic review and meta-analysis. Onco Targets Ther 2018; 11:1229-1243. [PMID: 29551902 PMCID: PMC5843138 DOI: 10.2147/ott.s150829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Xenopus kinesin-like protein 2 (TPX2) is a microtubule-associated protein that plays an important role in spindle assembly and dynamics. However, the clinical and prognostic value of TPX2 in the digestive system cancers remains unclear. The objective of this review was to evaluate the association of TPX2 expression with disease-free survival (DFS), overall survival (OS), and clinicopathological features of digestive system cancers. The software Stata 12.0 was used to analyze the outcomes, including OS, disease-free survival (DFS), and clinicopathological characteristics. A total of 10 eligible studies with 906 patients were included. Elevated TPX2 expression was significantly associated with poor DFS (pooled hazard ratio [HR] =2.48, 95% confidence interval [CI]: 1.96–3.13) and OS (pooled HR =2.66, 95% CI: 2.04–3.48) of digestive system malignancies. Subgroup analyses showed that cancer type, sample size, study quality, and laboratory detection methods did not alter the significant prognostic value of TPX2. Additionally, TPX2 expression was found to be an independent predictive factor for DFS (HR =2.31, 95% CI: 1.78–3.01). TPX2 expression might be associated with TNM stage and pathological grade in digestive system cancer. In conclusion, TPX2 is an independent prognostic factor for survival of patients with digestive system cancer. Furthermore, its overexpression is associated with TNM stage and pathological grade in digestive system cancer.
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Affiliation(s)
- Gang Wang
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Qian Wang
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Zhengyan Li
- Department of Surgery, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Chaoxu Liu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Xianli He
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
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Kong Y, Bender A, Yan A. Identification of Novel Aurora Kinase A (AURKA) Inhibitors via Hierarchical Ligand-Based Virtual Screening. J Chem Inf Model 2017; 58:36-47. [DOI: 10.1021/acs.jcim.7b00300] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yue Kong
- State
Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical
Engineering, Beijing University of Chemical Technology, P.O. Box 53, 15 BeiSanHuan East Road, Beijing 100029, P. R. China
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Andreas Bender
- Centre
for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Aixia Yan
- State
Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical
Engineering, Beijing University of Chemical Technology, P.O. Box 53, 15 BeiSanHuan East Road, Beijing 100029, P. R. China
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41
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Rekunge DS, Khatri CK, Chaturbhuj GU. Sulfated polyborate-catalyzed efficient and expeditious synthesis of (un)symmetrical ureas and benzimidazolones. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.10.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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42
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Damodaran AP, Vaufrey L, Gavard O, Prigent C. Aurora A Kinase Is a Priority Pharmaceutical Target for the Treatment of Cancers. Trends Pharmacol Sci 2017; 38:687-700. [DOI: 10.1016/j.tips.2017.05.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 05/09/2017] [Accepted: 05/15/2017] [Indexed: 01/23/2023]
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Jasial S, Hu Y, Bajorath J. How Frequently Are Pan-Assay Interference Compounds Active? Large-Scale Analysis of Screening Data Reveals Diverse Activity Profiles, Low Global Hit Frequency, and Many Consistently Inactive Compounds. J Med Chem 2017; 60:3879-3886. [PMID: 28421750 DOI: 10.1021/acs.jmedchem.7b00154] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Undetected pan-assay interference compounds (PAINS) with false-positive activities in assays often propagate through medicinal chemistry programs and compromise their outcomes. Although a large number of PAINS have been classified, often on the basis of individual studies or chemical experience, little has been done so far to systematically assess their activity profiles. Herein we report a large-scale analysis of the behavior of PAINS in biological screening assays. More than 23 000 extensively tested compounds containing PAINS substructures were detected, and their hit rates were determined. Many consistently inactive compounds were identified. The hit frequency was low overall, with median values of two to five hits for PAINS tested in hundreds of assays. Only confined subsets of PAINS produced abundant hits. The same PAINS substructure was often found in consistently inactive and frequently active compounds, indicating that the structural context in which PAINS occur modulates their effects.
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Affiliation(s)
- Swarit Jasial
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität , Dahlmannstr. 2, D-53113 Bonn, Germany
| | - Ye Hu
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität , Dahlmannstr. 2, D-53113 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität , Dahlmannstr. 2, D-53113 Bonn, Germany
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. ACS Infect Dis 2017; 3:259-262. [PMID: 28244723 DOI: 10.1021/acsinfecdis.7b00023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. ACS Med Chem Lett 2017; 8:379-382. [PMID: 28435522 DOI: 10.1021/acsmedchemlett.7b00056] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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46
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Awale M, Probst D, Reymond JL. WebMolCS: A Web-Based Interface for Visualizing Molecules in Three-Dimensional Chemical Spaces. J Chem Inf Model 2017; 57:643-649. [PMID: 28316236 DOI: 10.1021/acs.jcim.6b00690] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The concept of chemical space provides a convenient framework to analyze large collections of molecules by placing them in property spaces where distances represent similarities. Here we report webMolCS, a new type of web-based interface visualizing up to 5000 user-defined molecules in six different three-dimensional (3D) chemical spaces obtained by principal component analysis or similarity mapping of multidimensional property spaces describing composition (MQN: 42D molecular quantum numbers, SMIfp: 34D SMILES fingerprint), shapes and pharmacophores (APfp: 20D atom pair fingerprint, Xfp: 55D category extended atom pair fingerprint), and substructures (Sfp: 1024D binary substructure fingerprint, ECfp4:1024D extended connectivity fingerprint). Each molecule is shown as a sphere, and its structure appears on mouse over. The sphere is color-coded by similarity to the first compound in the list, by the list rank, or by a user-defined value, which reveals the relationship between any property encoded by these values and structural similarities. WebMolCS is freely available at www.gdb.unibe.ch .
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Affiliation(s)
- Mahendra Awale
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Daniel Probst
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, National Center of Competence in Research NCCR TransCure, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. ACS CENTRAL SCIENCE 2017; 3:143-147. [PMID: 28386587 PMCID: PMC5364449 DOI: 10.1021/acscentsci.7b00069] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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48
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. ACS Chem Biol 2017; 12:575-578. [PMID: 28244728 DOI: 10.1021/acschembio.7b00119] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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49
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. ACS Chem Neurosci 2017; 8:420-423. [PMID: 28244737 DOI: 10.1021/acschemneuro.7b00064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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50
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Aldrich C, Bertozzi C, Georg GI, Kiessling L, Lindsley C, Liotta D, Merz KM, Schepartz A, Wang S. The Ecstasy and Agony of Assay Interference Compounds. J Chem Inf Model 2017; 57:387-390. [PMID: 28244743 DOI: 10.1021/acs.jcim.7b00105] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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