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He R, Dai Z, Finel M, Zhang F, Tu D, Yang L, Ge G. Fluorescence-Based High-Throughput Assays for Investigating Cytochrome P450 Enzyme-Mediated Drug-Drug Interactions. Drug Metab Dispos 2023; 51:1254-1272. [PMID: 37349113 DOI: 10.1124/dmd.122.001068] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 05/05/2023] [Accepted: 05/25/2023] [Indexed: 06/24/2023] Open
Abstract
The cytochrome P450 enzymes (CYPs), a group of heme-containing enzymes, catalyze oxidative metabolism of a wide range of drugs and xenobiotics, as well as different endogenous molecules. Strong inhibition of human CYPs is the most common cause of clinically associated pharmacokinetic drug-drug/herb-drug interactions (DDIs/HDIs), which may result in serious adverse drug reactions, even toxicity. Accurate and rapid assessing of the inhibition potentials on CYP activities for therapeutic agents is crucial for the prediction of clinically relevant DDIs/HDIs. Over the past few decades, significant efforts have been invested into developing optical substrates for the human CYPs, generating a variety of powerful tools for high-throughput assays to detect CYP activities in biologic specimens and for screening of CYP inhibitors. This minireview focuses on recent advances in optical substrates developments for human CYPs, as well as their applications in screening CYP inhibitors and DDIs/HDIs studies. The examples for rational design and optimization of highly specific optical substrates for the target CYP enzyme, as well as applications in investigating CYP-mediated DDIs, are illustrated. Finally, the challenges and future perspectives in this field are proposed. Collectively, this review summarizes the reported optical-based biochemical assays for highly efficient CYP activities detection, which strongly facilitated the discovery of CYP inhibitors and the investigations on CYP-mediated DDIs. SIGNIFICANCE STATEMENT: Optical substrates for cytochrome P450 enzymes (CYPs) have emerged as powerful tools for the construction of high-throughput assays for screening of CYP inhibitors. This mini-review covers the advances and challenges in the development of highly specific optical substrates for sensing human CYP isoenzymes, as well as their applications in constructing fluorescence-based high-throughput assays for investigating CYP-mediated drug-drug interactions.
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Affiliation(s)
- Rongjing He
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China (R.H., F.Z., D.T., L.Y., G.G.); Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China (Z.D.); and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland (M.F.)
| | - Ziru Dai
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China (R.H., F.Z., D.T., L.Y., G.G.); Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China (Z.D.); and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland (M.F.)
| | - Moshe Finel
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China (R.H., F.Z., D.T., L.Y., G.G.); Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China (Z.D.); and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland (M.F.)
| | - Feng Zhang
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China (R.H., F.Z., D.T., L.Y., G.G.); Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China (Z.D.); and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland (M.F.)
| | - Dongzhu Tu
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China (R.H., F.Z., D.T., L.Y., G.G.); Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China (Z.D.); and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland (M.F.)
| | - Ling Yang
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China (R.H., F.Z., D.T., L.Y., G.G.); Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China (Z.D.); and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland (M.F.)
| | - Guangbo Ge
- Shanghai Frontiers Science Center for Chinese Medicine Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China (R.H., F.Z., D.T., L.Y., G.G.); Ministry of Education, Institute of Medicinal Plant Development, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China (Z.D.); and Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland (M.F.)
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Ma Z, Li M. Engineered Bioluminescent Indicator Enables the Brain Imaging of Kinase Inhibitors. ACS CENTRAL SCIENCE 2023; 9:597-599. [PMID: 37122465 PMCID: PMC10141589 DOI: 10.1021/acscentsci.3c00367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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3
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Yue Y, Shu Y, Ye K, Sun J, Liu C, Dai S, Jin L, Ding C, Lu R. Molecular Twisting Affects the Solid-State Photochemical Reactions of Unsaturated Ketones and the Photomechanical Effects of Molecular Crystals. Chemistry 2023; 29:e202203178. [PMID: 36344439 DOI: 10.1002/chem.202203178] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022]
Abstract
Three groups of chalcone derivatives and their analogues involving halogen atoms (X=F, Cl, Br) have been synthesized. Firstly, the nearly planar acyclic chalcone derivatives were inclined to undergo photo-induced stereospecific [2+2] cycloaddition, which triggered the crystals to exhibit macroscopic motions of bending or cracking. In particular, the single-crystal-to-single-crystal transformation happened upon UV irradiation of the crystals, which was helpful for the understanding photomechanical effects. Cyclic 3,4-dihydronaphthalene-based chalcone analogues possess a more twisted conformation, and they tend to undergo trans-cis isomerization. No photomechanical effect was observed for the crystals of the cyclic chalcone analogues due to the lower isomerization rate. The twist degree of chroman-based molecules was in between of the first two, [2+2] cycloaddition and trans-cis isomerization simultaneously took place in crystals. Photo-induced bending and twisting were observed for the crystals of chroman-based chalcone analogues. Therefore, the differences in molecular dihedral angles in α,β-unsaturated ketones were responsible for their photochemical characters and in turn to tune the photomechanical effects. In this work, a bridge between the molecular structures and solid-state photochemical reactions triggered photomechanical crystals is built.
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Affiliation(s)
- Yuan Yue
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
| | - Yuanhong Shu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
| | - Kaiqi Ye
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
| | - Jingbo Sun
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
| | - Cheng Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
| | - Shuting Dai
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
| | - Liuyang Jin
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
| | - Chengde Ding
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
| | - Ran Lu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130021, P. R. China
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Liu YJ. Understanding the complete bioluminescence cycle from a multiscale computational perspective: A review. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2022. [DOI: 10.1016/j.jphotochemrev.2022.100537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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5
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Al-Handawi MB, Polavaram S, Kurlevskaya A, Commins P, Schramm S, Carrasco-López C, Lui NM, Solntsev KM, Laptenok SP, Navizet I, Naumov P. Spectrochemistry of Firefly Bioluminescence. Chem Rev 2022; 122:13207-13234. [PMID: 35926147 DOI: 10.1021/acs.chemrev.1c01047] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chemical reactions underlying the emission of light in fireflies and other bioluminescent beetles are some of the most thoroughly studied processes by scientists worldwide. Despite these remarkable efforts, fierce academic arguments continue around even some of the most fundamental aspects of the reaction mechanism behind the beetle bioluminescence. In an attempt to reach a consensus, we made an exhaustive search of the available literature and compiled the key discoveries on the fluorescence and chemiluminescence spectrochemistry of the emitting molecule, the firefly oxyluciferin, and its chemical analogues reported over the past 50+ years. The factors that affect the light emission, including intermolecular interactions, solvent polarity, and electronic effects, were analyzed in the context of both the reaction mechanism and the different colors of light emitted by different luciferases. The collective data points toward a combined emission of multiple coexistent forms of oxyluciferin as the most probable explanation for the variation in color of the emitted light. We also highlight realistic research directions to eventually address some of the remaining questions related to firefly bioluminescence. It is our hope that this extensive compilation of data and detailed analysis will not only consolidate the existing body of knowledge on this important phenomenon but will also aid in reaching a wider consensus on some of the mechanistic details of firefly bioluminescence.
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Affiliation(s)
- Marieh B Al-Handawi
- Smart Materials Lab (SML), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Srujana Polavaram
- Smart Materials Lab (SML), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Anastasiya Kurlevskaya
- Smart Materials Lab (SML), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Patrick Commins
- Smart Materials Lab (SML), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Stefan Schramm
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - César Carrasco-López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Nathan M Lui
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kyril M Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Sergey P Laptenok
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Isabelle Navizet
- Univ. Gustave Eiffel, Univ. Paris Est Creteil, CNRS, UMR 8208, MSME, F-77454 Marne-la-Vallée, France
| | - Panče Naumov
- Smart Materials Lab (SML), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Molecular Design Institute, Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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Li Y, Jin C, Xu H, Wu W, Wang Y, Wu J, Liu T, Wan G, Yue X, Bu X. Identification of 2-Benzylidene-tetralone Derivatives as Highly Potent and Reversible Firefly Luciferase Inhibitors. ACS Med Chem Lett 2022; 13:304-311. [PMID: 35178187 PMCID: PMC8842144 DOI: 10.1021/acsmedchemlett.1c00671] [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: 12/01/2021] [Accepted: 01/14/2022] [Indexed: 11/28/2022] Open
Abstract
The extensive applications of Firefly luciferase (Fluc) in numerous biological, biomedical, and clinical investigations rendered an urgent need for efficient and biocompatible Fluc inhibitors for the construction of novel assay platforms. Herein we describe the identification of 2-benzylidene-tetralone derivatives as highly potent and reversible Firefly luciferase inhibitors by competing with d-luciferin. The most active compound 48 was found to have >7000 fold higher potency (IC50 = 0.25 nM) than that of the well-known luciferase inhibitor resveratrol (IC50 = 1.9 μM) biochemically with sub- to low nanomolar IC50 values, and it can efficiently block the Fluc generated bioluminescence in vivo.
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Affiliation(s)
- Yunzhi Li
- School
of Pharmaceutical Sciences, Sun Yat-sen
University, Guangzhou 510006, China
| | - Chaoying Jin
- School
of Pharmaceutical Sciences, Sun Yat-sen
University, Guangzhou 510006, China
| | - Huiying Xu
- School
of Pharmaceutical Sciences, Sun Yat-sen
University, Guangzhou 510006, China
| | - Weijian Wu
- School
of Pharmaceutical Sciences, Sun Yat-sen
University, Guangzhou 510006, China
| | - Youqiao Wang
- School
of Pharmaceutical Sciences, Sun Yat-sen
University, Guangzhou 510006, China
| | - Jiaxin Wu
- School
of Pharmaceutical Sciences, Sun Yat-sen
University, Guangzhou 510006, China
| | - Tingyu Liu
- State
Key Laboratory of Oncology in South China, Collaborative Innovation
Center for Cancer Medicine, Sun Yat-sen
University Cancer Center, Guangzhou 510060, China
| | - Guohui Wan
- School
of Pharmaceutical Sciences, Sun Yat-sen
University, Guangzhou 510006, China
| | - Xin Yue
- Department
of Radiation Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- Institute
of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Xianzhang Bu
- School
of Pharmaceutical Sciences, Sun Yat-sen
University, Guangzhou 510006, China
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Hopkins MD, Ozmer GL, Witt RC, Brandeburg ZC, Rogers DA, Keating CE, Petcoff PL, Sheaff RJ, Lamar AA. PhI(OAc) 2 and iodine-mediated synthesis of N-alkyl sulfonamides derived from polycyclic aromatic hydrocarbon scaffolds and determination of their antibacterial and cytotoxic activities. Org Biomol Chem 2021; 19:1133-1144. [PMID: 33443507 DOI: 10.1039/d0ob02429e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The development of new approaches toward chemo- and regioselective functionalization of polycyclic aromatic hydrocarbon (PAH) scaffolds will provide opportunities for the synthesis of novel biologically active small molecules that exploit the high degree of lipophilicity imparted by the PAH unit. Herein, we report a new synthetic method for C-X bond substitution that is speculated to operate via a N-centered radical (NCR) mechanism according to experimental observations. A series of PAH sulfonamides have been synthesized and their biological activity has been evaluated against Gram-negative and Gram-positive bacterial strains (using a BacTiter-Glo assay) along with a series of mammalian cell lines (using CellTiter-Blue and CellTiter-Glo assays). The viability assays have resulted in the discovery of a number of bactericidal compounds that exhibit potency similar to other well-known antibacterials such as kanamycin and tetracycline, along with the discovery of a luciferase inhibitor. Additionally, the physicochemical and drug-likeness properties of the compounds were determined experimentally and using in silico approaches and the results are presented and discussed within.
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Affiliation(s)
- Megan D Hopkins
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, Oklahoma 74104, USA.
| | - Garett L Ozmer
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, Oklahoma 74104, USA.
| | - Ryan C Witt
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, Oklahoma 74104, USA.
| | - Zachary C Brandeburg
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, Oklahoma 74104, USA.
| | - David A Rogers
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, Oklahoma 74104, USA.
| | - Claire E Keating
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, Oklahoma 74104, USA.
| | - Presley L Petcoff
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, Oklahoma 74104, USA.
| | - Robert J Sheaff
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, Oklahoma 74104, USA.
| | - Angus A Lamar
- Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa, Oklahoma 74104, USA.
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8
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Carrasco-López C, Lui NM, Schramm S, Naumov P. The elusive relationship between structure and colour emission in beetle luciferases. Nat Rev Chem 2020; 5:4-20. [PMID: 37118106 DOI: 10.1038/s41570-020-00238-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2020] [Indexed: 12/23/2022]
Abstract
In beetles, luciferase enzymes catalyse the conversion of chemical energy into light through bioluminescence. The principles of this process have become a fundamental biotechnological tool that revolutionized biological research. Different beetle species can emit different colours of light, despite using the same substrate and highly homologous luciferases. The chemical reasons for these different colours are hotly debated yet remain unresolved. This Review summarizes the structural, biochemical and spectrochemical data on beetle bioluminescence reported over the past three decades. We identify the factors that govern what colour is emitted by wild-type and mutant luciferases. This topic is controversial, but, in general, we note that green emission requires cationic residues in a specific position near the benzothiazole fragment of the emitting molecule, oxyluciferin. The commonly emitted green-yellow light can be readily changed to red by introducing a variety of individual and multiple mutations. However, complete switching of the emitted light from red to green has not been accomplished and the synergistic effects of combined mutations remain unexplored. The minor colour shifts produced by most known mutations could be important in establishing a 'mutational catalogue' to fine-tune emission of beetle luciferases, thereby expanding the scope of their applications.
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9
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Carboxylated Chalcone and Benzaldehyde Derivatives of Triosmium Carbonyl Clusters: Synthesis, Characterization and Biological Activity Towards MCF-7 Cells. J CLUST SCI 2020. [DOI: 10.1007/s10876-019-01684-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Xue Y, Liu Y, Wang G, An L, Teng Y, Chen M, Xie Y, Zhang L. TDDFT study on the photophysical properties of coumarinyl chalcones and sensing mechanism of a derived fluorescent probe for hydrogen sulfide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 234:118263. [PMID: 32203689 DOI: 10.1016/j.saa.2020.118263] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/23/2020] [Accepted: 03/15/2020] [Indexed: 06/10/2023]
Abstract
Coumarin-chalcone hybrids have attracted much attention in recent years due to their important optical properties. Herein, the photophysical properties of a series of coumarinyl chalcones and the sensing mechanism for H2S of a related fluorescent probe CC-DNP were investigated using density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods. The predicted spectral properties agree well with the experimental results, which allowed an assignment of the spectra. Our calculations successfully clarified the experimental observed fluorescence "off-on" effect and the fluorescent quenching mechanism of the probe. The results revealed that the first excited state (S1) of the probe CC-DNP is a dark state with obvious charge transfer from coumarin unit to 2,4-dinitrophenyl (DNP) moiety, which results in the fluorescence quenching via the nonradiative photoinduced electron transfer (PET) process. On the other hand, the excited state S1 in the thiolysis product CC-OH decayed directly to S0, and thus the fluorescence is recovered.
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Affiliation(s)
- Yunsheng Xue
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China.
| | - Yunping Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China
| | - Guirong Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China
| | - Lin An
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China
| | - Yangxin Teng
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China
| | - Mohan Chen
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China
| | - Yuxin Xie
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China
| | - Ling Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, No. 209, Tongshan Road, Xuzhou, Jiangsu 221004, China.
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11
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Yang ZY, Dong J, Yang ZJ, Lu AP, Hou TJ, Cao DS. Structural Analysis and Identification of False Positive Hits in Luciferase-Based Assays. J Chem Inf Model 2020; 60:2031-2043. [PMID: 32202787 DOI: 10.1021/acs.jcim.9b01188] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Luciferase-based bioluminescence detection techniques are highly favored in high-throughput screening (HTS), in which the firefly luciferase (FLuc) is the most commonly used variant. However, FLuc inhibitors can interfere with the activity of luciferase, which may result in false positive signals in HTS assays. In order to reduce the unnecessary cost of time and money, an in silico prediction model for FLuc inhibitors is highly desirable. In this study, we built an extensive data set consisting of 20 888 FLuc inhibitors and 198 608 noninhibitors, and then developed a group of classification models based on the combination of three machine learning (ML) algorithms and four types of molecular representations. The best prediction model based on XGBoost and ECFP4 and MOE2d descriptors yielded a balanced accuracy (BA) of 0.878 and an area under the receiver operating characteristic curve (AUC) value of 0.958 for the validation set, and a BA of 0.886 and an AUC of 0.947 for the test set. Three external validation sets, including set 1 (3231 FLuc inhibitors and 69 783 noninhibitors), set 2 (695 FLuc inhibitors and 75 913 noninhibitors), and set 3 (1138 FLuc inhibitors and 8155 noninhibitors), were used to verify the predictive ability of our models. The BA values for the three external validation sets given by the best model are 0.864, 0.845, and 0.791, respectively. In addition, the important features or structural fragments related to FLuc inhibitors were recognized by the Shapley additive explanations (SHAP) method along with their influences on predictions, which may provide valuable clues to detecting undesirable luciferase inhibitors. Based on the important and explanatory features, 16 rules were proposed for detecting FLuc inhibitors, which can achieve a correction rate of 70% for FLuc inhibitors. Furthermore, a comparison with existing prediction rules and models for FLuc inhibitors used in virtual screening verified the high reliability of the models and rules proposed in this study. We also used the model to screen three curated chemical databases, and almost 10% of the molecules in the evaluated databases were predicted as inhibitors, highlighting the potential risk of false positives in luciferase-based assays. Finally, a public web server called ChemFLuc was developed (http://admet.scbdd.com/chemfluc/index/), and it offers a free available service to predict potential FLuc inhibitors.
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Affiliation(s)
- Zi-Yi Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410003, P.R. China
| | - Jie Dong
- Central South University of Forestry and Technology, Changsha, 410004, P.R. China
| | - Zhi-Jiang Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410003, P.R. China
| | - Ai-Ping Lu
- Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, P.R. China
| | - Ting-Jun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P.R. China
| | - Dong-Sheng Cao
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410003, P.R. China.,Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, P.R. China
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12
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Wilkinson IVL, Reynolds JK, Galan SRG, Vuorinen A, Sills AJ, Pires E, Wynne GM, Wilson FX, Russell AJ. Characterisation of utrophin modulator SMT C1100 as a non-competitive inhibitor of firefly luciferase. Bioorg Chem 2019; 94:103395. [PMID: 31733898 DOI: 10.1016/j.bioorg.2019.103395] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022]
Abstract
Firefly luciferase (FLuc) is a powerful tool for molecular and cellular biology, and popular in high-throughput screening and drug discovery. However, FLuc assays have been plagued with positive and negative artefacts due to stabilisation and inhibition by small molecules from a range of chemical classes. Here we disclose Phase II clinical compound SMT C1100 for the treatment of Duchenne muscular dystrophy as an FLuc inhibitor (KD of 0.40 ± 0.15 µM). Enzyme kinetic studies using SMT C1100 and other non-competitive inhibitors including resveratrol and NFκBAI4 identified previously undescribed modes of inhibition with respect to FLuc's luciferyl adenylate intermediate. Employing a photoaffinity strategy to identify SMT C1100's binding site, a photolabelled SMT C1100 probe instead underwent FLuc-dependent photooxidation. Our findings support novel binding sites on FLuc for non-competitive inhibitors.
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Affiliation(s)
- Isabel V L Wilkinson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Jessica K Reynolds
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Sébastien R G Galan
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Aini Vuorinen
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Adam J Sills
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Elisabete Pires
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Graham M Wynne
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK
| | - Francis X Wilson
- Summit Therapeutics plc, 136a Eastern Avenue, Milton Park, Abingdon, Oxfordshire OX14 4SB, UK
| | - Angela J Russell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, UK; Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3PQ, UK.
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Yang Y, Fei C, Wang K, Liu B, Jiang D, Yin B. Access to Densely Functionalized Chalcone Derivatives with a 2-Pyridone Subunit via Pd/Cu-Catalyzed Oxidative Furan–Yne Cyclization of N-(2-Furanylmethyl) Alkynamides under Air. Org Lett 2018; 20:2273-2277. [DOI: 10.1021/acs.orglett.8b00618] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yongjie Yang
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
| | - ChengCheng Fei
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, Laboratory of Insect Toxicology, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Kai Wang
- Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou 510006, P. R. China
| | - Bo Liu
- Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou 510006, P. R. China
| | - Dingxin Jiang
- Key Laboratory of Natural Pesticide and Chemical Biology, Ministry of Education, Laboratory of Insect Toxicology, South China Agricultural University, Guangzhou 510642, P. R. China
| | - Biaolin Yin
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou 510640, P. R. China
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Soccio M, Laus MN, Alfarano M, Pastore D. Measuring Activity of Native Plant Sirtuins - The Wheat Mitochondrial Model. FRONTIERS IN PLANT SCIENCE 2018; 9:961. [PMID: 30026749 PMCID: PMC6041729 DOI: 10.3389/fpls.2018.00961] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/14/2018] [Indexed: 05/04/2023]
Abstract
Sirtuins are NAD+-dependent deacetylase enzymes that have gained considerable interest in mammals for their recognized importance in gene silencing and expression and in cell metabolism. Conversely, knowledge about plant sirtuins remains limited, although a sirtuin-mediated regulation of mitochondrial energy metabolism has been recently reported in Arabidopsis. However, so far, no information is available about direct measurement of intracellular plant sirtuin activity, i.e., in cell extracts and/or subcellular organelles. In this study, a novel approach was proposed for reliable evaluation of native sirtuin activity in plant samples, based on (i) an adequate combinatory application of enzymatic assays very different for chemical basis and rationale and (ii) a comparative measurement of activity of a recombinant sirtuin isoform. In particular, two sirtuin assays were applied, based on bioluminescence emission and Homogeneous Time-Resolved Fluorescence (HTRF®) technology, and the human SIRT1 isoform (hSIRT1) was used for comparison. For the first time in plants, this new approach allowed measuring directly a high and nicotinamide-sensitive sirtuin activity in highly purified mitochondrial fraction obtained from durum wheat (WM). WM-sirtuin activity was 268 ± 10 mU⋅mg-1 protein, as measured by HTRF® assay, and 166 ± 12 ng hSIRT1 eq.⋅mg-1 protein, as evaluated by the bioluminescent assay and calculated on the basis of the hSIRT1 calibration curve. Moreover, effects of resveratrol and quercetin, reported as potent hSIRT1 activators, but whose activation mechanism is still debated, were also studied. No effect of resveratrol was found on both WM-sirtuin and hSIRT1 activities, while only a slight increase, up to about 20%, of hSIRT1 activity by quercetin was observed. In the whole, results of this study indicate that WM may represent a good system for studying native plant sirtuins. In fact, the high yield of purified WM and their high sirtuin activity, together with use of microplate readers, allow performing a large number of measurements from the same preparation, so qualifying the approach for application to large-scale high-throughput screening. Moreover, WM may also represent an excellent tool to investigate physiological role and modulation of plant sirtuins under experimental conditions more physiologically relevant with respect to recombinant purified enzymes.
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