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Yan B, Chen N, Xu C, Wu Y, Li L, Lee C, He N. Covalently Bonded Heterostructures with Mixed-Dimensional Carbons for Suppressing Mechanochemical Wear of Diamond under Heavy Loads. ACS Appl Mater Interfaces 2024; 16:19751-19763. [PMID: 38581368 DOI: 10.1021/acsami.4c00032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2024]
Abstract
Diamond is widely acknowledged as the hardest naturally occurring material. Nevertheless, when exposed to friction against ferrous metals, it is prone to graphitization or amorphization, which limits the utilization of its extremely high hardness and wear resistance. These issues have persisted for decades without an effective solution. Here, we report that a covalently bonded heterostructure with mixed-dimensional carbons as a high-performance solid lubricant could effectively reduce diamond surface friction and mechanochemical wear with excellent load capacity and durability. When subjected to dry friction and heavy loads (20-150 N), the heterostructure exhibited a notable improvement over pristine diamond with reduced friction coefficients and relative wear rates by 22-45 and 67-91%, respectively. Especially under a 20 N load, the relative wear rate was an order of magnitude lower than that of pristine diamond. Additionally, experiments and molecular dynamics simulations revealed that the heterostructure integrated the outstanding properties of diamond (three-dimensional (3D)), nanographite (3D), and graphene (two-dimensional (2D)), resulting in improved lubrication and antiwear performance that could not be achieved by the individual carbon materials. The findings in this work will be beneficial to overcome the ferrous metal forbidden zone of diamond and are expected to expand the applications of engineered diamond surfaces and graphite/graphene in tribology, mechanics, and electronic fields.
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Affiliation(s)
- Bo Yan
- College of Mechanical and Electrical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Ni Chen
- College of Mechanical and Electrical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Chang Xu
- College of Mechanical and Electrical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Yang Wu
- College of Mechanical and Electrical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Liang Li
- College of Mechanical and Electrical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Changgu Lee
- SKKU Advanced Institute of Nanotechnology (SAINT), School of Mechanical Engineering, Sungkyunkwan University, Suwon 16419, Korea
| | - Ning He
- College of Mechanical and Electrical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
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Wang J, Cao J, Xu N, Meng T, Zhang G, Zhang Y. Ultrasound-enhanced covalent reaction of gliadin: the inhibition of antigenicity and its potential mechanisms. J Sci Food Agric 2024. [PMID: 38442023 DOI: 10.1002/jsfa.13436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/20/2024] [Accepted: 03/05/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Wheat proteins can be divided into water/salt-soluble protein (albumin/globulin) and water/salt-insoluble protein (gliadins and glutenins (Glu)) according to solubility. Gliadins (Glia) are one of the major allergens in wheat. The inhibition of Glia antigenicity by conventional processing techniques was not satisfactory. RESULTS In this study, free radical oxidation was used to induce covalent reactions. The effects of covalent reactions by high-intensity ultrasound (HIU) of different powers was compared. The enhancement of covalent grafting effectiveness between gliadin and (-)-epigallo-catechin 3-gallate (EGCG) was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry and Folin-Ciocalteu tests. HIU caused protein deconvolution and disrupted the intrastrand disulfide bonds that maintain the tertiary structure, causing a shift in the side chain structure, as proved by Fourier, fluorescence and Raman spectroscopic analysis. Comparatively, the antigenic response of the conjugates formed in the sonication environment was significantly weaker, while these conjugates were more readily hydrolyzed and less antigenic during simulated gastrointestinal fluid digestion. CONCLUSION HIU-enhanced free radical oxidation caused further transformation of the spatial structure of Glia, which hid or destroyed the antigenic epitope, effectively inhibiting protein antigenicity. This study widened the application of polyphenol modification in the inhibition of wheat allergens. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Junrong Wang
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China
| | - Jiaxing Cao
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China
| | - Ning Xu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Taihe Meng
- Cofco Flour Industry (Wuhan) Co. Ltd, Wuhan, China
| | - Guozhi Zhang
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, China
| | - Yu Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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Meyers M, Cismoski S, Panidapu A, Chie-Leon B, Nomura DK. Targeted Protein Degradation through Recruitment of the CUL4 Complex Adaptor Protein DDB1. ACS Chem Biol 2024; 19:58-68. [PMID: 38192078 PMCID: PMC11003717 DOI: 10.1021/acschembio.3c00487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Targeted protein degradation has arisen as a powerful therapeutic modality for eliminating proteins. Thus far, most heterobifunctional proteolysis targeting chimeras (PROTACs) have utilized recruiters against substrate receptors of Cullin RING E3 ubiquitin ligases, such as cereblon and VHL. However, previous studies have surprisingly uncovered molecular glue degraders that exploit a CUL4 adaptor protein DDB1 to degrade neosubstrate proteins. Here, we sought to investigate whether DDB1 recruiters can be discovered that can be exploited for PROTAC applications. We utilized activity-based protein profiling and cysteine chemoproteomic screening to identify a covalent recruiter that targets C173 on DDB1 and exploited this recruiter to develop PROTACs against BRD4 and androgen receptor (AR). We demonstrated that the BRD4 PROTAC results in selective degradation of the short BRD4 isoform over the long isoform in a proteasome, NEDDylation, and DDB1-dependent manner. We also demonstrated degradation of AR with the AR PROTAC in prostate cancer cells. Our study demonstrated that covalent chemoproteomic approaches can be used to discover recruiters against Cullin RING adapter proteins and that these recruiters can be used for PROTAC applications to degrade neo-substrates.
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Affiliation(s)
- Margot Meyers
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Sabine Cismoski
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Anoohya Panidapu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Barbara Chie-Leon
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608 USA
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
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Lahmy R, Hübner H, Lachmann D, Gmeiner P, König B. Development of Photoswitchable Tethered Ligands that Target the μ-Opioid Receptor. ChemMedChem 2023; 18:e202300228. [PMID: 37817331 DOI: 10.1002/cmdc.202300228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/12/2023]
Abstract
Converting known ligands into photoswitchable derivatives offers the opportunity to modulate compound structure with light and hence, biological activity. In doing so, these probes provide unique control when evaluating G-protein-coupled receptor (GPCR) mechanism and function. Further conversion of such compounds into covalent probes, known as photoswitchable tethered ligands (PTLs), offers additional advantages. These include localization of the PTLs to the receptor binding pocket. Covalent localization increases local ligand concentration, improves site selectivity and may improve the biological differences between the respective isomers. This work describes chemical, photophysical and biochemical characterizations of a variety of PTLs designed to target the μ-opioid receptor (μOR). These PTLs were modeled on fentanyl, with the lead disulfide-containing agonist found to covalently interact with a cysteine-enriched mutant of this medically-relevant receptor.
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Affiliation(s)
- Ranit Lahmy
- Department of Chemistry and Pharmacy, University of Regensburg, 93053, Regensburg, Germany
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Friedrich-Alexander University, 91058, Erlangen, Germany
| | - Daniel Lachmann
- Department of Chemistry and Pharmacy, University of Regensburg, 93053, Regensburg, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Friedrich-Alexander University, 91058, Erlangen, Germany
| | - Burkhard König
- Department of Chemistry and Pharmacy, University of Regensburg, 93053, Regensburg, Germany
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Jin B, Guan XL, Yan M, Wang YJ, Wu YB. Planar Hexacoordinate Beryllium: Covalent Bonding Between s-block Metals. Chemistry 2023; 29:e202302672. [PMID: 37695132 DOI: 10.1002/chem.202302672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/12/2023]
Abstract
Achieving a planar hypercoordinate arrangement of s-block metals through covalent bonding with ligands is challenging due to the strong ionicity involved. Herein, we report the first case of a neutral binary global minimum containing a planar hexacoordinate beryllium atom. The central Be atom is coordinated by six active Be atoms, the latter in turn are enclosed by an equal number of more electronegative chlorine atoms in the periphery, forming a star-like phBe cluster (Be©Be6 Cl6 ). Importantly, the cluster exhibits dynamically stabilized stemming geometrically from the appropriate matching of metal-ligand size and electronically from adherence to the octet rule as well as possessing a 6σ/2π double aromaticity. Remarkably, energy decomposition analysis-natural orbitals for chemical valence (EDA-NOCV) analysis reveals a significant covalent interaction between the ligand and the central metal beryllium atoms, a fact further supported by a large Wiberg bond index. This cluster is a promising synthetic as its excellent electronic, dynamic and thermodynamic stability.
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Affiliation(s)
- Bo Jin
- Department of Chemistry, Xinzhou Normal University, Xinzhou, Shanxi, 034000, P. R. China
- Institute of Molecular Science, Shanxi University, 92 Wucheng Road, Taiyuan, Shanxi, 030006, P. R. China
| | - Xiao-Ling Guan
- Institute of Molecular Science, Shanxi University, 92 Wucheng Road, Taiyuan, Shanxi, 030006, P. R. China
| | - Miao Yan
- Department of Chemistry, Xinzhou Normal University, Xinzhou, Shanxi, 034000, P. R. China
| | - Ying-Jin Wang
- Department of Chemistry, Xinzhou Normal University, Xinzhou, Shanxi, 034000, P. R. China
| | - Yan-Bo Wu
- Institute of Molecular Science, Shanxi University, 92 Wucheng Road, Taiyuan, Shanxi, 030006, P. R. China
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6
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Hong SH, Osa A, Huang OW, Wertz IE, Nomura DK. Exploiting the Cullin E3 Ligase Adaptor Protein SKP1 for Targeted Protein Degradation. bioRxiv 2023:2023.10.20.563371. [PMID: 37904950 PMCID: PMC10614948 DOI: 10.1101/2023.10.20.563371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Targeted protein degradation with Proteolysis Targeting Chimeras (PROTACs) is a powerful therapeutic modality for eliminating disease-causing proteins through targeted ubiquitination and proteasome-mediated degradation. Most PROTACs have exploited substrate receptors of Cullin-RING E3 ubiquitin ligases such as cereblon and VHL. Whether core, shared, and essential components of the Cullin-RING E3 ubiquitin ligase complex can be used for PROTAC applications remains less explored. Here, we discovered a cysteine-reactive covalent recruiter EN884 against the SKP1 adapter protein of the SKP1-CUL1-F-box containing SCF complex. We further showed that this recruiter can be used in PROTAC applications to degrade neo-substrate proteins such as BRD4 and the androgen receptor in a SKP1- and proteasome-dependent manner. Our studies demonstrate that core and essential adapter proteins within the Cullin-RING E3 ubiquitin ligase complex can be exploited for targeted protein degradation applications and that covalent chemoproteomic strategies can enable recruiter discovery against these targets.
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Affiliation(s)
- Seong Ho Hong
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Akane Osa
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | | | | | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
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7
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Guha AK. Can Dative Bond Between Two Anions Possible? Chemphyschem 2023; 24:e202300403. [PMID: 37450354 DOI: 10.1002/cphc.202300403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/18/2023]
Abstract
Formation of a genuine chemical bond between two similarly charged fragments is beyond expectation. Any such interaction generally lies in the realm of non-covalent interaction. Herein, formation of a strong dative covalent bond between two anionic fragments is reported for the first time. Calculation using ab initio coupled cluster theory reveals the formation of an unprecedented strong H3 Be- ←X- (X- =CH3 - , CN- , OH- , F- ) dative covalent bond. The calculated bond dissociation energies in polar solvents are significant, which indicates the possibility of their experimental realization.
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Affiliation(s)
- Ankur Kanti Guha
- Advanced Computational Chemistry Centre, Department of Chemistry, Cotton University Panbazar, Guwahati, Assam, 781001, India
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8
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Meyers M, Cismoski S, Panidapu A, Chie-Leon B, Nomura DK. Targeted Protein Degradation through Recruitment of the CUL4A Complex Adaptor Protein DDB1. bioRxiv 2023:2023.08.11.553046. [PMID: 37614621 PMCID: PMC10443223 DOI: 10.1101/2023.08.11.553046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Targeted protein degradation has arisen as a powerful therapeutic modality for eliminating proteins. Thus far, most heterobifunctional Proteolysis Targeting Chimeras (PROTACs) have utilized recruiters against substrate receptors of Cullin RING E3 ubiquitin ligases, such as cereblon and VHL. However, previous studies have surprisingly uncovered molecular glue degraders that exploit a CUL4A adaptor protein DDB1 to degrade neosubstrate proteins. Here, we sought to investigate whether DDB1 recruiters can be discovered that can be exploited for PROTAC applications. We utilized activity-based protein profiling and cysteine chemoproteomic screening to identify a covalent recruiter that targets C173 on DDB1 and exploited this recruiter to develop PROTACs against BRD4 and androgen receptor (AR). We demonstrated that the BRD4 PROTAC results in selective degradation of the short BRD4 isoform over the long isoform in a proteasome, NEDDylation, and DDB1-dependent manner. We also demonstrated degradation of AR with the AR PROTAC in prostate cancer cells. Our study demonstrated that covalent chemoproteomic approaches can be used to discover recruiters against Cullin RING adapter proteins and that these recruiters can be used for PROTAC applications to degrade neo-substrates.
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Affiliation(s)
- Margot Meyers
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Sabine Cismoski
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Anoohya Panidapu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Barbara Chie-Leon
- Novartis-Berkeley Translational Chemical Biology Institute
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608 USA
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
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9
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Lazear MR, Remsberg JR, Jaeger MG, Rothamel K, Her HL, DeMeester KE, Njomen E, Hogg SJ, Rahman J, Whitby LR, Won SJ, Schafroth MA, Ogasawara D, Yokoyama M, Lindsey GL, Li H, Germain J, Barbas S, Vaughan J, Hanigan TW, Vartabedian VF, Reinhardt CJ, Dix MM, Koo SJ, Heo I, Teijaro JR, Simon GM, Ghosh B, Abdel-Wahab O, Ahn K, Saghatelian A, Melillo B, Schreiber SL, Yeo GW, Cravatt BF. Proteomic discovery of chemical probes that perturb protein complexes in human cells. Mol Cell 2023; 83:1725-1742.e12. [PMID: 37084731 PMCID: PMC10198961 DOI: 10.1016/j.molcel.2023.03.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/09/2023] [Accepted: 03/28/2023] [Indexed: 04/23/2023]
Abstract
Most human proteins lack chemical probes, and several large-scale and generalizable small-molecule binding assays have been introduced to address this problem. How compounds discovered in such "binding-first" assays affect protein function, nonetheless, often remains unclear. Here, we describe a "function-first" proteomic strategy that uses size exclusion chromatography (SEC) to assess the global impact of electrophilic compounds on protein complexes in human cells. Integrating the SEC data with cysteine-directed activity-based protein profiling identifies changes in protein-protein interactions that are caused by site-specific liganding events, including the stereoselective engagement of cysteines in PSME1 and SF3B1 that disrupt the PA28 proteasome regulatory complex and stabilize a dynamic state of the spliceosome, respectively. Our findings thus show how multidimensional proteomic analysis of focused libraries of electrophilic compounds can expedite the discovery of chemical probes with site-specific functional effects on protein complexes in human cells.
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Affiliation(s)
- Michael R Lazear
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | | | - Martin G Jaeger
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Katherine Rothamel
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Hsuan-Lin Her
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Evert Njomen
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Simon J Hogg
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Jahan Rahman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Landon R Whitby
- Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA 92121, USA
| | - Sang Joon Won
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | | | | | - Minoru Yokoyama
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | | | - Haoxin Li
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Jason Germain
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Sabrina Barbas
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Joan Vaughan
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Thomas W Hanigan
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Vincent F Vartabedian
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | | | - Melissa M Dix
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| | - Seong Joo Koo
- Molecular and Cellular Pharmacology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Inha Heo
- Molecular and Cellular Pharmacology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - John R Teijaro
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Gabriel M Simon
- Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA 92121, USA
| | - Brahma Ghosh
- Discovery Chemistry, Janssen Research & Development, Spring House, PA 19477, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
| | - Kay Ahn
- Molecular and Cellular Pharmacology, Discovery Technologies and Molecular Pharmacology, Janssen Research and Development, Spring House, PA 19477, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Bruno Melillo
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA; Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
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Juste-Dolz A, Fernández E, Puchades R, Avella-Oliver M, Maquieira Á. Patterned Biolayers of Protein Antigens for Label-Free Biosensing in Cow Milk Allergy. Biosensors (Basel) 2023; 13:214. [PMID: 36831980 PMCID: PMC9953870 DOI: 10.3390/bios13020214] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
This paper focuses on creating one-dimensional diffractive grooved structures of antigen proteins on glass substrates for the label-free detection of antibodies to dairy allergens. In particular, the fabrication of protein structures is carried out by combining microcontact printing with physisorption, imines coupling, and thiol-ene click chemistry. The work first sets up these patterning methods and discusses and compares the main aspects involved in them (structure, biolayer thickness, functionality, stability). Homogeneous periodic submicron structures of proteins are created and characterized by diffractive measurements, AFM, FESEM, and fluorescence scanning. Then, this patterning method is applied to proteins involved in cow milk allergy, and the resulting structures are implemented as optical transducers to sense specific immunoglobulins G. In particular, gratings of bovine serum albumin, casein, and β-lactoglobulin are created and assessed, reaching limits of detection in the range of 30-45 ng·mL-1 of unlabeled antibodies by diffractive biosensing.
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Affiliation(s)
- Augusto Juste-Dolz
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, 46022 Valencia, Spain
| | - Estrella Fernández
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, 46022 Valencia, Spain
| | - Rosa Puchades
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, 46022 Valencia, Spain
- Departamento de Química, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Miquel Avella-Oliver
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, 46022 Valencia, Spain
- Departamento de Química, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Ángel Maquieira
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, 46022 Valencia, Spain
- Departamento de Química, Universitat Politècnica de València, 46022 Valencia, Spain
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11
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Algar‐Lizana S, Bonache MÁ, González‐Muñiz R. SARS-CoV-2 main protease inhibitors: What is moving in the field of peptides and peptidomimetics? J Pept Sci 2022; 29:e3467. [PMID: 36479966 PMCID: PMC9877768 DOI: 10.1002/psc.3467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is still affecting people worldwide. Despite the good degree of immunological protection achieved through vaccination, there are still severe cases that require effective antivirals. In this sense, two specific pharmaceutical preparations have been marketed already, the RdRp polymerase inhibitor molnupiravir and the main viral protease inhibitor nirmatrelvir (commercialized as Paxlovid, a combination with ritonavir). Nirmatrelvir is a peptidomimetic acting as orally available, covalent, and reversible inhibitor of SARS-CoV-2 main viral protease. The success of this compound has revitalized the search for new peptide and peptidomimetic protease inhibitors. This highlight collects some selected examples among those recently published in the field of SARS-CoV-2.
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12
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Jiang B, Zhong S, Yu H, Chen P, Li B, Li D, Liu C, Feng Z. Covalent and Noncovalent Complexation of Phosvitin and Gallic Acid: Effects on Protein Functionality and In Vitro Digestion Properties. J Agric Food Chem 2022; 70:11715-11726. [PMID: 36095172 DOI: 10.1021/acs.jafc.2c03990] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
To investigate the effects of different binding modes on the structure, function, and digestive properties of the phosvitin (Pv) and gallic acid (GA) complex, Pv was covalently and noncovalently combined with different concentrations of GA (0.5, 1.5, and 2.5 mM). The structural characterization of the two Pv-GA complexes was performed by Fourier transform infrared, circular dichroism, and LC-MS/MS to investigate the covalent and noncovalent binding of Pv and GA. In addition, the microstructure of the two Pv-GA complexes was investigated by super-resolution microscopy and transmission electron microscopy. The particle size and zeta potential results showed that the addition of GA increased the particle size and the absolute potential of Pv. The determination of protein digestibility, polyphenol content, SH and S-S group levels, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and antioxidant capacity of the digests indicated that noncovalent complexes had greater antioxidant and protective effects on polyphenols. Molecular docking revealed that GA was conjugated with Pv through hydrogen bond interactions.
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Affiliation(s)
- Bin Jiang
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Shaojing Zhong
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Hongliang Yu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Peifeng Chen
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Baoyun Li
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Dongmei Li
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Chunhong Liu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
| | - Zhibiao Feng
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, Heilongjiang 150030, People's Republic of China
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13
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Payne NC, Maksoud S, Tannous BA, Mazitschek R. A direct high-throughput protein quantification strategy facilitates discovery and characterization of a celastrol-derived BRD4 degrader. Cell Chem Biol 2022; 29:1333-1340.e5. [PMID: 35649410 PMCID: PMC9391279 DOI: 10.1016/j.chembiol.2022.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/03/2022] [Accepted: 05/10/2022] [Indexed: 12/31/2022]
Abstract
We describe a generalizable time-resolved Förster resonance energy transfer (TR-FRET)-based platform to profile the cellular action of heterobifunctional degraders (or proteolysis-targeting chimeras [PROTACs]) that is capable of both accurately quantifying protein levels in whole-cell lysates in less than 1 h and measuring small-molecule target engagement to endogenous proteins, here specifically for human bromodomain-containing protein 4 (BRD4). The detection mix consists of a single primary antibody targeting the protein of interest, a luminescent donor-labeled anti-species nanobody, and a fluorescent acceptor ligand. Importantly, our strategy can readily be applied to other targets of interest and will greatly facilitate the cell-based profiling of small-molecule inhibitors and PROTACs in a high-throughput format with unmodified cell lines. We furthermore validate our platform in the characterization of celastrol, a p-quinone methide-containing pentacyclic triterpenoid, as a broad cysteine-targeting E3 ubiquitin ligase warhead for potent and efficient targeted protein degradation.
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Affiliation(s)
- N Connor Payne
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Semer Maksoud
- Experimental Therapeutics and Molecular Imaging Unit, Department of Neurology, Neuro-Oncology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Bakhos A Tannous
- Experimental Therapeutics and Molecular Imaging Unit, Department of Neurology, Neuro-Oncology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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14
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Proj M, Knez D, Sosič I, Gobec S. Redox active or thiol reactive? Optimization of rapid screens to identify less evident nuisance compounds. Drug Discov Today 2022; 27:1733-1742. [PMID: 35301150 DOI: 10.1016/j.drudis.2022.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/03/2022] [Accepted: 03/11/2022] [Indexed: 01/01/2023]
Abstract
Compounds that exhibit assay interference or undesirable mechanisms of bioactivity are routinely encountered in assays at various stages of drug discovery. We observed that assays for the investigation of thiol-reactive and redox-active compounds have not been collected in a comprehensive review. Here, we review these assays and subject them to experimental optimization to improve their reliability. We demonstrate the usefulness of our assay cascade by assaying a library of bioactive compounds, chemical probes, and a set of approved drugs. These high-throughput assays should complement the array of wet-lab and in silico assays during the initial stages of hit discovery campaigns to pursue only hit compounds with tractable mechanisms of action. Teaser: We provide an overview of assays to detect redox active and thiol reactive compounds and the robust protocols for identification of nuisance compounds during early stages of drug discovery programs.
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Affiliation(s)
- Matic Proj
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Askerceva 7, SI-1000 Ljubljana, Slovenia
| | - Damijan Knez
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Askerceva 7, SI-1000 Ljubljana, Slovenia
| | - Izidor Sosič
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Askerceva 7, SI-1000 Ljubljana, Slovenia.
| | - Stanislav Gobec
- University of Ljubljana, Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Askerceva 7, SI-1000 Ljubljana, Slovenia.
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15
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Pinch BJ, Buckley DL, Gleim S, Brittain SM, Tandeske L, D'Alessandro PL, Hauseman ZJ, Lipps J, Xu L, Harvey EP, Schirle M, Sprague ER, Forrester WC, Dovala D, McGregor LM, Thoma CR. A strategy to assess the cellular activity of E3 ligase components against neo-substrates using electrophilic probes. Cell Chem Biol 2021; 29:57-66.e6. [PMID: 34499862 DOI: 10.1016/j.chembiol.2021.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 06/17/2021] [Accepted: 08/20/2021] [Indexed: 01/12/2023]
Abstract
While there are hundreds of predicted E3 ligases, characterizing their applications for targeted protein degradation has proved challenging. Here, we report a chemical biology approach to evaluate the ability of modified recombinant E3 ligase components to support neo-substrate degradation. Bypassing the need for specific E3 ligase binders, we use maleimide-thiol chemistry for covalent functionalization followed by E3 electroporation (COFFEE) in live cells. We demonstrate that electroporated recombinant von Hippel-Lindau (VHL) protein, covalently functionalized at its ligandable cysteine with JQ1 or dasatinib, induces degradation of BRD4 or tyrosine kinases, respectively. Furthermore, by applying COFFEE to SPSB2, a Cullin-RING ligase 5 receptor, as well as to SKP1, the adaptor protein for Cullin-RING ligase 1 F box (SCF) complexes, we validate this method as a powerful approach to define the activity of previously uncharacterized ubiquitin ligase components, and provide further evidence that not only E3 ligase receptors but also adaptors can be directly hijacked for neo-substrate degradation.
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Affiliation(s)
- Benika J Pinch
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
| | - Dennis L Buckley
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Scott Gleim
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Scott M Brittain
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Laura Tandeske
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | | | | | - Jennifer Lipps
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Lei Xu
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Edward P Harvey
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | | | - Dustin Dovala
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA.
| | - Lynn M McGregor
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
| | - Claudio R Thoma
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
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16
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Turner LD, Nielsen AL, Lin L, Pellett S, Sugane T, Olson ME, Janda KD. COVALENT INHIBITION OF BOTULINUM NEUROTOXIN A - EXPLORATION OF WARHEAD REACTIVITY AND FUNCTION USING A BIFUNCTIONAL APPROACH. Toxicon 2021; 190:S72-S73. [PMID: 34103769 PMCID: PMC8183569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
INTRODUCTION AND OBJECTIVES Botulinum neurotoxin A (BoNT/A) is extremely toxic possessing an estimated intravenous LD50 of 1-2 ng/kg and as such has been designated a category A bioterrorism agent.1, 2 BoNT/A also possesses an extremely long half-life and persists within muscle neurons for months to >1 year.3 Because of BoNT/A longevity, we have utilized covalent inhibition as a means to abrogate BoNT/A's toxicity. To this end, we describe an approach to designing inhibitors that possess both electrophilic warheads and metal-binding groups for the bifunctional inhibition of BoNT/A. METHODS Small molecule inhibitors that possessed electrophilic moieties were designed, using X-ray crystallography as guidance, to target both the zinc metal-binding region and Cys165 within the active site of BoNT/A. Synthesized compounds were evaluated for covalent inhibition using a continuous SNAPtide FRET assay4 and exhaustive dialysis. Compounds were also evaluated against a C165A variant. Compound reactivity, stability, MMP selectivity and cellular efficacy/toxicity was also evaluated. RESULTS Several electrophilic warhead types were confirmed to inhibit BoNT/A LC covalently with substantial differences in time-dependent inhibition between the WT and C165A variant. A trend in warhead reactivity was reflected in inhibitor stability and toxicity. Compounds exhibited moderate potency in a BoNT/A neuronal cellular assay but were not further explored due to undesirable therapeutic potential. CONCLUSIONS A fundamental framework for the bifunctional covalent inhibition of BoNT/A LC has been established. This approach has potential to be translated to other small molecule metal-binding inhibitors of BoNT/A LC with the vision that different pharmacophores, possessing improved physicochemical properties, will address BoNT/As toxicity and longevity within cells.
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Affiliation(s)
- Lewis D. Turner
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research, 10550 N Torrey Pines Road, La Jolla, CA 92037, United States
| | - Alexander L. Nielsen
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research, 10550 N Torrey Pines Road, La Jolla, CA 92037, United States
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Lucy Lin
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research, 10550 N Torrey Pines Road, La Jolla, CA 92037, United States
| | - Sabine Pellett
- Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, WI 53706, United States
| | - Takashi Sugane
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research, 10550 N Torrey Pines Road, La Jolla, CA 92037, United States
| | - Margaret E. Olson
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research, 10550 N Torrey Pines Road, La Jolla, CA 92037, United States
| | - Kim D. Janda
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), Scripps Research, 10550 N Torrey Pines Road, La Jolla, CA 92037, United States
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17
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Liu C, Reese R, Vu S, Rougé L, Shields SD, Kakiuchi-Kiyota S, Chen H, Johnson K, Shi YP, Chernov-Rogan T, Greiner DMZ, Kohli PB, Hackos D, Brillantes B, Tam C, Li T, Wang J, Safina B, Magnuson S, Volgraf M, Payandeh J, Zheng J, Rohou A, Chen J. A Non- covalent Ligand Reveals Biased Agonism of the TRPA1 Ion Channel. Neuron 2021; 109:273-284.e4. [PMID: 33152265 DOI: 10.1016/j.neuron.2020.10.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/31/2020] [Accepted: 10/09/2020] [Indexed: 12/19/2022]
Abstract
The TRPA1 ion channel is activated by electrophilic compounds through the covalent modification of intracellular cysteine residues. How non-covalent agonists activate the channel and whether covalent and non-covalent agonists elicit the same physiological responses are not understood. Here, we report the discovery of a non-covalent agonist, GNE551, and determine a cryo-EM structure of the TRPA1-GNE551 complex, revealing a distinct binding pocket and ligand-interaction mechanism. Unlike the covalent agonist allyl isothiocyanate, which elicits channel desensitization, tachyphylaxis, and transient pain, GNE551 activates TRPA1 into a distinct conducting state without desensitization and induces persistent pain. Furthermore, GNE551-evoked pain is relatively insensitive to antagonist treatment. Thus, we demonstrate the biased agonism of TRPA1, a finding that has important implications for the discovery of effective drugs tailored to different disease etiologies.
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18
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Beaupre BA, Moran GR. N5 Is the New C4a: Biochemical Functionalization of Reduced Flavins at the N5 Position. Front Mol Biosci 2020; 7:598912. [PMID: 33195440 PMCID: PMC7662398 DOI: 10.3389/fmolb.2020.598912] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 10/05/2020] [Indexed: 12/31/2022] Open
Abstract
For three decades the C4a-position of reduced flavins was the known site for covalency within flavoenzymes. The reactivity of this position of the reduced isoalloxazine ring with the dioxygen ground-state triplet established the C4a as a site capable of one-electron chemistry. Within the last two decades new types of reduced flavin reactivity have been documented. These studies reveal that the N5 position is also a protean site of reactivity, that is capable of nucleophilic attack to form covalent bonds with substrates. In addition, though the precise mechanism of dioxygen reactivity is yet to be definitively demonstrated, it is clear that the N5 position is directly involved in substrate oxygenation in some enzymes. In this review we document the lineage of discoveries that identified five unique modes of N5 reactivity that collectively illustrate the versatility of this position of the reduced isoalloxazine ring.
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Affiliation(s)
- Brett A Beaupre
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Graham R Moran
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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19
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Majdoub M, Anfar Z, Amedlous A. Emerging Chemical Functionalization of g-C 3N 4: Covalent/Noncovalent Modifications and Applications. ACS Nano 2020; 14:12390-12469. [PMID: 33052050 DOI: 10.1021/acsnano.0c06116] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Atomically 2D thin-layered structures, such as graphene nanosheets, graphitic carbon nitride nanosheets (g-C3N4), hexagonal boron nitride, and transition metal dichalcogenides are emerging as fascinating materials for a good array of domains owing to their rare physicochemical characteristics. In particular, graphitic carbon nitride has turned into a hot subject in the scientific community due to numerous qualities such as simple preparation, electrochemical properties, high adsorption capacity, good photochemical properties, thermal stability, and acid-alkali chemical resistance, etc. Basically, g-C3N4 is considered as a polymeric material consisting of N and C atoms forming a tri-s-triazine network connected by planar amino groups. In comparison with most C-based materials, g-C3N4 possesses electron-rich characteristics, basic moieties, and hydrogen-bonding groups owing to the presence of hydrogen and nitrogen atoms; therefore, it is taken into account as an interesting nominee to further complement carbon in applications of functional materials. Nevertheless, g-C3N4 has some intrinsic limitations and drawbacks mainly related to a relatively poor specific surface area, rapid charge recombination, a limited light absorption range, and a poor dispersibility in both aqueous and organic mediums. To overcome these shortcomings, numerous chemical modification approaches have been conducted with the aim of expanding the range of application of g-C3N4 and enhancing its properties. In the current review, the comprehensive survey is conducted on g-C3N4 chemical functionalization strategies including covalent and noncovalent approaches. Covalent approaches consist of establishing covalent linkage between the g-C3N4 structure and the chemical modifier such as oxidation/carboxylation, amidation, polymer grafting, etc., whereas the noncovalent approaches mainly consist of physical bonding and intermolecular interaction such as van der Waals interactions, electrostatic interactions, π-π interactions, and so on. Furthermore, the preparation, characterization, and diverse applications of functionalized g-C3N4 in various domains are described and recapped. We believe that this work will inspire scientists and readers to conduct research with the aim of exploring other functionalization strategies for this material in numerous applications.
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Affiliation(s)
- Mohammed Majdoub
- Laboratory of Materials, Catalysis & Valorization of Natural Resources, Hassan II University, Casablanca 20000, Morocco
| | - Zakaria Anfar
- Laboratory of Materials & Environment, Ibn Zohr University, Agadir 80000, Morocco
- Institute of Materials Science of Mulhouse, Haute Alsace University, Mulhouse 68100, France
- Strasbourg University, Strasbourg 67081, France
| | - Abdallah Amedlous
- Laboratory of Materials, Catalysis & Valorization of Natural Resources, Hassan II University, Casablanca 20000, Morocco
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20
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Takubo H, Taniguchi T, Iwanaga K, Nomura Y. Evaluation of the changes in exposure to thiol compounds in chronic kidney disease patients using the PBPK model. Xenobiotica 2020; 51:31-39. [PMID: 32744915 DOI: 10.1080/00498254.2020.1805816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Targeted covalent inhibitors designed to bind covalently to a specific molecular target have recently been a focus of drug development. Among these inhibitors, thiol compounds bind covalently to endogenous thiols in the body through a process involving disulfide bonds. We investigated the predictability of changes in the exposure to captopril, tiopronin, the active form of dalcetrapib and the active metabolite of prasugrel, R-138727, all of which have a sulfhydryl group, in moderate and severe chronic kidney disease (CKD) patients using a constructed PBPK model. The changes in the exposure to captopril, tiopronin and the active form of dalcetrapib under CKD conditions were well predicted. However, the change in exposure to R-138727, which is a secondary metabolite of prasugrel, was overpredicted. Although these thiol compounds covalently bind to endogenous thiols, our study concluded that changes in exposure to these compounds under CKD conditions can probably be predicted, except for compounds with a complicated mechanism whereby the thiol metabolite is generated.
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Affiliation(s)
- Hiroaki Takubo
- Drug Metabolism and Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, Japan
| | - Toshio Taniguchi
- Drug Metabolism and Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, Japan
| | - Kazunori Iwanaga
- Education and Research Center for Clinical Pharmacy, Osaka University of Pharmaceutical Sciences, Osaka, Japan
| | - Yukihiro Nomura
- Drug Metabolism and Pharmacokinetics Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., Osaka, Japan
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21
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Chen X, Xu J, Wong NK, Zhong S, Yang M, Liu Z, Lu Y, Li W, Zhou Y. Chemoproteomic Profiling of Cobalamin-Independent Methionine Synthases in Plants with a Covalent Probe. J Agric Food Chem 2020; 68:8050-8056. [PMID: 32618189 DOI: 10.1021/acs.jafc.0c03301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cobalamin-independent methionine synthases (MS) are zinc-binding methyltransferases that catalyze de novo methionine biosynthesis in higher plants, which are enzymes critically involved in seed germination and plant growth. Here, we report a highly selective sulfonyl fluoride-based probe for chemoproteomic profiling of MS enzymes in living systems of the model plant Arabidopsis thaliana, as implemented in in-gel-, mass spectrometry-, and imaging-based platforms. This probe holds promise for facilitating and accelerating fundamental research and industrial application of MS enzymes, particularly in the contexts of MS1/2-targeting herbicide screening and design.
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Affiliation(s)
- Xin Chen
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jingyuan Xu
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
| | - Nai-Kei Wong
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen 518112, China
| | - Suyun Zhong
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
| | - Mengquan Yang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhen Liu
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
| | - Yan Lu
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
| | - Weichao Li
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yiqing Zhou
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu, Jiangsu 215500, China
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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22
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Vinogradova EV, Zhang X, Remillard D, Lazar DC, Suciu RM, Wang Y, Bianco G, Yamashita Y, Crowley VM, Schafroth MA, Yokoyama M, Konrad DB, Lum KM, Simon GM, Kemper EK, Lazear MR, Yin S, Blewett MM, Dix MM, Nguyen N, Shokhirev MN, Chin EN, Lairson LL, Melillo B, Schreiber SL, Forli S, Teijaro JR, Cravatt BF. An Activity-Guided Map of Electrophile-Cysteine Interactions in Primary Human T Cells. Cell 2020; 182:1009-1026.e29. [PMID: 32730809 DOI: 10.1016/j.cell.2020.07.001] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 05/14/2020] [Accepted: 06/30/2020] [Indexed: 12/19/2022]
Abstract
Electrophilic compounds originating from nature or chemical synthesis have profound effects on immune cells. These compounds are thought to act by cysteine modification to alter the functions of immune-relevant proteins; however, our understanding of electrophile-sensitive cysteines in the human immune proteome remains limited. Here, we present a global map of cysteines in primary human T cells that are susceptible to covalent modification by electrophilic small molecules. More than 3,000 covalently liganded cysteines were found on functionally and structurally diverse proteins, including many that play fundamental roles in immunology. We further show that electrophilic compounds can impair T cell activation by distinct mechanisms involving the direct functional perturbation and/or degradation of proteins. Our findings reveal a rich content of ligandable cysteines in human T cells and point to electrophilic small molecules as a fertile source for chemical probes and ultimately therapeutics that modulate immunological processes and their associated disorders.
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Affiliation(s)
| | - Xiaoyu Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David Remillard
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel C Lazar
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Radu M Suciu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yujia Wang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Giulia Bianco
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu Yamashita
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Medicinal Chemistry Research Laboratories, New Drug Research Division, Otsuka Pharmaceutical Co., Ltd., 463-10 Kawauchi-cho, Tokushima 771-0192, Japan
| | - Vincent M Crowley
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael A Schafroth
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Minoru Yokoyama
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David B Konrad
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kenneth M Lum
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel M Simon
- Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, CA 92121, USA
| | - Esther K Kemper
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael R Lazear
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sifei Yin
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Megan M Blewett
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Melissa M Dix
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nhan Nguyen
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Maxim N Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics Core, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Emily N Chin
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Luke L Lairson
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bruno Melillo
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02138, USA
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Teijaro
- Department of Immunology and Infectious Disease, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
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23
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Du Y, Xue J, Hong Z. Raman and Terahertz Spectroscopic Characterization of Solid-state Cocrystal Formation within Specific Active Pharmaceutical Ingredients. Curr Pharm Des 2020; 26:4829-4846. [PMID: 32445442 DOI: 10.2174/1381612826666200523173448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/23/2020] [Indexed: 11/22/2022]
Abstract
Cocrystallization of specific active pharmaceutical ingredients (APIs) in the solid-state phase is becoming a feasible way to improve their corresponding physicochemical properties and ultimate bioavailability without making and breaking any covalent bonds within them. Many recent reports deal with the characterization and analysis topics of pharmaceutical APIs-based cocrystals. In this mini-review, we will focus on the recent steady-state and time-dependent spectroscopic investigation into the cocrystallization of specific APIs based on both Raman and emerging terahertz spectroscopy in pharmaceutical fields. Distinctive spectral, structural and also kinetic information of pharmaceutical APIs-based cocrystals are obtained and discussed, which would highlight the potential of vibrational spectroscopy as an attractive technique for various drug research and development during cocrystallization of specific APIs.
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Affiliation(s)
- Yong Du
- Centre for THz Research, China Jiliang University, Hangzhou City, Zhejiang Province, China
| | - Jiadan Xue
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou City, Zhejiang Province, China
| | - Zhi Hong
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou City, Zhejiang Province, China
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24
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Dai J, Yang L, Addison G. Current Status in the Discovery of Covalent Janus Kinase 3 (JAK3) Inhibitors. Mini Rev Med Chem 2019; 19:1531-1543. [PMID: 31288716 DOI: 10.2174/1389557519666190617152011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 01/09/2023]
Abstract
The search for inhibitors of the Janus kinase family (JAK1, JAK2, JAK3 and TYK2) has been ongoing for several decades and has resulted in a number of JAK inhibitors being approved for use in patients, such as tofacitinib for the treatment of autoimmune diseases such as Rheumatoid Arthritis (RA). Although initially thought to be a JAK3 selective inhibitor, tofacitinib was subsequently found to possess significant activity to inhibit JAK1 and JAK2 which has contributed to some adverse side effects. A selective JAK3 inhibitor should only have an effect within the immune system since JAK3 is solely expressed in lymphoid tissue; this makes JAK3 a target of interest in the search for treatments of autoimmune diseases. A method to obtain selectivity for JAK3 over the other JAK family members, which has attracted more scientific attention recently, is the targeting of the active site cysteine residue, unique in JAK3 within the JAK family, with compounds containing electrophilic warheads which can form a covalent bond with the nucleophilic thiol of the cysteine residue. This review encompasses the historical search for a covalent JAK3 inhibitor and the most recently published research which hasn't been reviewed to date. The most important compounds from the publications reviewed the activity and selectivity of these compounds together with some of the more important biological results are condensed in to an easily digested form that should prove useful for those interested in the field.
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Affiliation(s)
- Jun Dai
- Changzhou Fangyuan Pharmaceutical Co. Ltd., Changzhou, Jiangsu, PC 213125, China
| | - LiXi Yang
- Changzhou Fangyuan Pharmaceutical Co. Ltd., Changzhou, Jiangsu, PC 213125, China
| | - Glynn Addison
- Changzhou Fangyuan Pharmaceutical Co. Ltd., Changzhou, Jiangsu, PC 213125, China
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25
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Nieves DJ, Hilzenrat G, Tran J, Yang Z, MacRae HH, Baker MAB, Gooding JJ, Gaus K. tagPAINT: covalent labelling of genetically encoded protein tags for DNA-PAINT imaging. R Soc Open Sci 2019; 6:191268. [PMID: 31903209 PMCID: PMC6936279 DOI: 10.1098/rsos.191268] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/12/2019] [Indexed: 05/17/2023]
Abstract
Recently, DNA-PAINT single-molecule localization microscopy (SMLM) has shown great promise for quantitative imaging; however, labelling strategies thus far have relied on multivalent and affinity-based approaches. Here, the covalent labelling of expressed protein tags (SNAP tag and Halo tag) with single DNA-docking strands and application of SMLM via DNA-PAINT is demonstrated. tagPAINT is then used for T-cell receptor signalling proteins at the immune synapse as a proof of principle.
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Affiliation(s)
- Daniel J. Nieves
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW 2052, Australia
- Authors for correspondence: Daniel J. Nieves e-mail:
| | - Geva Hilzenrat
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jason Tran
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW 2052, Australia
| | - Zhengmin Yang
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW 2052, Australia
| | - Hugh H. MacRae
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW 2052, Australia
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW 2052, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Synthetic Biology Future Science Platform, Brisbane, Australia
| | - J. Justin Gooding
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
- Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, NSW 2052, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW 2052, Australia
- Authors for correspondence: Katharina Gaus e-mail:
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Sasaki M, Miyahisa I, Itono S, Yashiro H, Hiyoshi H, Tsuchimori K, Hamagami K, Moritoh Y, Watanabe M, Tohyama K, Sasaki M, Sakamoto J, Kawamoto T. Discovery and characterization of a small-molecule enteropeptidase inhibitor, SCO-792. Pharmacol Res Perspect 2019; 7:e00517. [PMID: 31508234 PMCID: PMC6726858 DOI: 10.1002/prp2.517] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 07/19/2019] [Accepted: 07/26/2019] [Indexed: 12/11/2022] Open
Abstract
Enteropeptidase, localized into the duodenum brush border, is a key enzyme catalyzing the conversion of pancreatic trypsinogen proenzyme to active trypsin, thereby regulating protein digestion and energy homeostasis. We report the discovery and pharmacological profiles of SCO-792, a novel inhibitor of enteropeptidase. A screen employing fluorescence resonance energy transfer was performed to identify enteropeptidase inhibitors. Inhibitory profiles were determined by in vitro assays. To evaluate the in vivo inhibitory effect on protein digestion, an oral protein challenge test was performed in rats. Our screen identified a series of enteropeptidase inhibitors, and compound optimization resulted in identification of SCO-792, which inhibited enteropeptidase activity in vitro, with IC 50 values of 4.6 and 5.4 nmol/L in rats and humans, respectively. In vitro inhibition of enteropeptidase by SCO-792 was potentiated by increased incubation time, and the calculated Kinact/KI was 82 000/mol/L s. An in vitro dissociation assay showed that SCO-792 had a dissociation half-life of almost 14 hour, with a calculated koff rate of 0.047/hour, which suggested that SCO-792 is a reversible enteropeptidase inhibitor. In normal rats, a ≤4 hour prior oral dose of SCO-792 effectively inhibited plasma elevation of branched-chain amino acids in an oral protein challenge test, which indicated that SCO-792 effectively inhibited protein digestion in vivo. In conclusion, our new screen system identified SCO-792 as a potent and reversible inhibitor against enteropeptidase. SCO-792 slowly dissociated from enteropeptidase in vitro and inhibited protein digestion in vivo. Further study using SCO-792 could reveal the effects of inhibiting enteropeptidase on biological actions.
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Affiliation(s)
- Masako Sasaki
- ResearchTakeda Pharmaceutical Company LimitedFujisawaKanagawaJapan
| | - Ikuo Miyahisa
- ResearchTakeda Pharmaceutical Company LimitedFujisawaKanagawaJapan
| | - Sachiko Itono
- ResearchTakeda Pharmaceutical Company LimitedFujisawaKanagawaJapan
- Present address:
Axcelead Drug Discovery Partners, Inc.FujisawaKanagawaJapan
| | - Hiroaki Yashiro
- ResearchTakeda Pharmaceutical Company LimitedFujisawaKanagawaJapan
| | - Hideyuki Hiyoshi
- ResearchTakeda Pharmaceutical Company LimitedFujisawaKanagawaJapan
| | - Kazue Tsuchimori
- ResearchTakeda Pharmaceutical Company LimitedFujisawaKanagawaJapan
| | | | | | | | - Kimio Tohyama
- ResearchTakeda Pharmaceutical Company LimitedFujisawaKanagawaJapan
| | - Minoru Sasaki
- ResearchTakeda Pharmaceutical Company LimitedFujisawaKanagawaJapan
| | - Jun‐ichi Sakamoto
- ResearchTakeda Pharmaceutical Company LimitedFujisawaKanagawaJapan
- Present address:
Axcelead Drug Discovery Partners, Inc.FujisawaKanagawaJapan
| | - Tomohiro Kawamoto
- ResearchTakeda Pharmaceutical Company LimitedFujisawaKanagawaJapan
- Present address:
Axcelead Drug Discovery Partners, Inc.FujisawaKanagawaJapan
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27
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Adeniji EA, Olotu FA, Soliman MES. Exploring the Lapse in Druggability: Sequence Analysis, Structural Dynamics and Binding Site Characterization of K-RasG12C Variant, a Feasible Oncotherapeutics Target. Anticancer Agents Med Chem 2019; 18:1540-1550. [PMID: 30019652 DOI: 10.2174/1871520618666180718110231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/28/2018] [Accepted: 07/04/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND The difficulty in druggability of K-Ras variant has presented a challenge in the treatment of cancer diseases associated with its dysfunctionality. Despite the identification of different binding sites, limited information exists in the literature about their characteristics. Therefore, identification, crossvalidation and characterization of its druggable sites would aid the design of chemical compounds that will arrest its dysfunctionality related oncogenesis. OBJECTIVE This study entails the identification, cross-validation and characterization of K-Ras G12C variant's binding sites for potential druggability, coupled with the elucidation of alterations in 3D conformations and dynamics. METHOD Molecular dynamics simulation was carried out on the inactive, the active and the hyperactive K-RasG12Cvariant using the amber software package. The SiteMap software was employed in identifying and characterizing the druggable binding sites while the validation of the binding sites was carried out with the SiteHound and MetaPocket servers. RESULTS Four druggable binding sites were identified, validated and characterized based on physicochemical attributes such as size, volume, degree of enclosure or exposure, degree of contact, hydrophobic/hydrophilic character, hydrophobic/hydrophilic balance and hydrogen-bonding features. Conformational studies also revealed that the K-Ras variant exhibited notable structural instability, increased flexibility and a strongly anticorrelated movement compared to the inactive and active wildtype forms. CONCLUSION The attributes of the characterized druggable sites will be useful in designing site-specific K-Ras inhibitors for the treatment of K-Ras variant associated cancer diseases.
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Affiliation(s)
- Emmanuel A Adeniji
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Fisayo A Olotu
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4001, South Africa
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28
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Rokic MB, Castro P, Leiva-Salcedo E, Tomic M, Stojilkovic SS, Coddou C. Opposing Roles of Calcium and Intracellular ATP on Gating of the Purinergic P2X2 Receptor Channel. Int J Mol Sci 2018; 19:ijms19041161. [PMID: 29641486 PMCID: PMC5979340 DOI: 10.3390/ijms19041161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 03/30/2018] [Accepted: 04/03/2018] [Indexed: 11/16/2022] Open
Abstract
P2X2 receptors (P2X2R) exhibit a slow desensitization during the initial ATP application and a progressive, calcium-dependent increase in rates of desensitization during repetitive stimulation. This pattern is observed in whole-cell recordings from cells expressing recombinant and native P2X2R. However, desensitization is not observed in perforated-patched cells and in two-electrode voltage clamped oocytes. Addition of ATP, but not ATPγS or GTP, in the pipette solution also abolishes progressive desensitization, whereas intracellular injection of apyrase facilitates receptor desensitization. Experiments with injection of alkaline phosphatase or addition of staurosporine and ATP in the intracellular solution suggest a role for a phosphorylation-dephosphorylation in receptor desensitization. Mutation of residues that are potential phosphorylation sites identified a critical role of the S363 residue in the intracellular ATP action. These findings indicate that intracellular calcium and ATP have opposing effects on P2X2R gating: calcium allosterically facilitates receptor desensitization and ATP covalently prevents the action of calcium. Single cell measurements further revealed that intracellular calcium stays elevated after washout in P2X2R-expressing cells and the blockade of mitochondrial sodium/calcium exchanger lowers calcium concentrations during washout periods to basal levels, suggesting a role of mitochondria in this process. Therefore, the metabolic state of the cell can influence P2X2R gating.
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Affiliation(s)
- Milos B Rokic
- Section on Cellular Signaling, National Institutes of Child Health and Human Development, NIH, Bethesda, MD 20892, USA.
| | - Patricio Castro
- Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad Católica del Norte, Coquimbo 1781421, Chile.
- Laboratory of Developmental Physiology, Department of Physiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción 4030000, Chile.
| | - Elias Leiva-Salcedo
- Section on Cellular Signaling, National Institutes of Child Health and Human Development, NIH, Bethesda, MD 20892, USA.
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 9170022, Chile.
- Centro para el Desarrollo de Nanociencias y Nanotecnología (CEDENNA), Santiago 9170022, Chile.
| | - Melanija Tomic
- Section on Cellular Signaling, National Institutes of Child Health and Human Development, NIH, Bethesda, MD 20892, USA.
| | - Stanko S Stojilkovic
- Section on Cellular Signaling, National Institutes of Child Health and Human Development, NIH, Bethesda, MD 20892, USA.
| | - Claudio Coddou
- Section on Cellular Signaling, National Institutes of Child Health and Human Development, NIH, Bethesda, MD 20892, USA.
- Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad Católica del Norte, Coquimbo 1781421, Chile.
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29
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Pels K, Dickson P, An H, Kodadek T. DNA-Compatible Solid-Phase Combinatorial Synthesis of β-Cyanoacrylamides and Related Electrophiles. ACS Comb Sci 2018; 20:61-69. [PMID: 29298042 DOI: 10.1021/acscombsci.7b00169] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We demonstrate that the Knoevenagel condensation can be exploited in combinatorial synthesis on the solid phase. Condensation products from such reactions were structurally characterized, and their Michael reactivity with thiol and phosphine nucleophiles is described. Cyanoacrylamides were previously reported to react reversibly with thiols, and notably, we show that dilution into low pH buffer can trap covalent adducts, which are isolable via chromatography. Finally, we synthesized both traditional and DNA-encoded one-bead, one-compound libraries containing cyanoacrylamides as a source of cysteine-reactive reversibly covalent protein ligands.
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Affiliation(s)
- Kevin Pels
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Paige Dickson
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Hongchan An
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
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30
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Bar-Peled L, Kemper EK, Suciu RM, Vinogradova EV, Backus KM, Horning BD, Paul TA, Ichu TA, Svensson RU, Olucha J, Chang MW, Kok BP, Zhu Z, Ihle NT, Dix MM, Jiang P, Hayward MM, Saez E, Shaw RJ, Cravatt BF. Chemical Proteomics Identifies Druggable Vulnerabilities in a Genetically Defined Cancer. Cell 2017; 171:696-709.e23. [PMID: 28965760 DOI: 10.1016/j.cell.2017.08.051] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 07/07/2017] [Accepted: 08/30/2017] [Indexed: 01/11/2023]
Abstract
The transcription factor NRF2 is a master regulator of the cellular antioxidant response, and it is often genetically activated in non-small-cell lung cancers (NSCLCs) by, for instance, mutations in the negative regulator KEAP1. While direct pharmacological inhibition of NRF2 has proven challenging, its aberrant activation rewires biochemical networks in cancer cells that may create special vulnerabilities. Here, we use chemical proteomics to map druggable proteins that are selectively expressed in KEAP1-mutant NSCLC cells. Principal among these is NR0B1, an atypical orphan nuclear receptor that we show engages in a multimeric protein complex to regulate the transcriptional output of KEAP1-mutant NSCLC cells. We further identify small molecules that covalently target a conserved cysteine within the NR0B1 protein interaction domain, and we demonstrate that these compounds disrupt NR0B1 complexes and impair the anchorage-independent growth of KEAP1-mutant cancer cells. Our findings designate NR0B1 as a druggable transcriptional regulator that supports NRF2-dependent lung cancers.
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31
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Abstract
Rapid and covalent layer-by-layer (LbL) assembly is of significance for practical applications because of superior chemical and mechanical stability. The electrochemical LbL assembly via an accelerating trigger can be automated and programmable in response to electrical signals to in situ fabricate covalently layered thin films with chemical and mechanical stability. In this paper, electroreductive coupling layer-by-layer assembly is introduced as both covalent and rapid methodology for preparing layered thin films. This assembly is triggered by C-C coupling of peripheral alkynyls, which have own absorption below 300 nm and can transform to optical and electrical inert double/single or triple/single alternative bonding formations significantly without optical or electric alternations of desirable photoelectric building blocks, superior to other linkers among covalent LbL assemblies. Not limited to fabrication of optical thin films, this assembly is readily available for oxygen sensitive substrates or materials and also a powerful addition to electrooxidative coupling LbL assembly for developing the economically dynamoelectric LbL machines without moving or changing experimental gears.
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Affiliation(s)
- Shusen Kang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, China
- University of the Chinese Academy of Science , Beijing 100864, China
| | - Lei Wang
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University , Changchun 130012, China
| | - Jian Zhang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, China
- University of the Chinese Academy of Science , Beijing 100864, China
| | - Jia Du
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, China
- University of the Chinese Academy of Science , Beijing 100864, China
| | - Mao Li
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun 130022, China
| | - Qidai Chen
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University , Changchun 130012, China
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Abstract
The clinical and commercial success of covalent drugs has prompted a renewed and more deliberate pursuit of covalent and irreversible mechanisms within drug discovery. A covalent mechanism can produce potent inhibition in a biochemical, cellular, or in vivo setting. In many cases, teams choose to focus on the consequences of the covalent event, defined by an IC50 value. In a biochemical assay, the IC50 may simply reflect the target protein concentration in the assay. What has received less attention is the importance of the rate of covalent modification, defined by kinact/KI. The kinact/KI is a rate constant describing the efficiency of covalent bond formation resulting from the potency (KI) of the first reversible binding event and the maximum potential rate (kinact) of inactivation. In this perspective, it is proposed that the kinact/KI should be employed as a critical parameter to identify covalent inhibitors, interpret structure-activity relationships (SARs), translate activity from biochemical assays to the cell, and more accurately define selectivity. It is also proposed that a physiologically relevant kinact/KI and an (unbound) AUC generated from a pharmacokinetic profile reflecting direct exposure of the inhibitor to the target protein are two critical determinants of in vivo covalent occupancy. A simple equation is presented to define this relationship and improve the interpretation of covalent and irreversible kinetics.
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Affiliation(s)
- John M Strelow
- 1 Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, USA
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33
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Peyrot D, Silly F. On-Surface Synthesis of Two-Dimensional Covalent Organic Structures versus Halogen-Bonded Self-Assembly: Competing Formation of Organic Nanoarchitectures. ACS Nano 2016; 10:5490-5498. [PMID: 27158901 DOI: 10.1021/acsnano.6b01938] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The competition between the on-surface synthesis of covalent nanoarchitectures and the self-assembly of star-shaped 1,3,5-Tris(4-iodophenyl)benzene molecules on Au(111) in vacuum is investigated using scanning tunneling microscopy above room temperature. The molecules form covalent polygonal nanoachitectures at the gold surface step edges and at the elbows of the gold reconstruction at low coverage. With coverage increasing two-dimensional halogen-bonded structures appear and grow on the surface terraces. Two different halogen-bonded nanoarchitectures are coexisting on the surface and hybrid covalent-halogen bonded structures are locally observed. At high coverage covalent nanoarchitectures are squeezed at the domain boundary of the halogen-bonded structures. The competitive growth between the covalent and halogen-bonded nanoarchitectures leads to formation of a two-layer film above one monolayer deposition. For this coverage, the covalent nanoarchitectures are propelled on top of the halogen-bonded first layer. These observations open up new opportunities for decoupling covalent nanoarchitectures from catalytically active and metal surfaces in vacuum.
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Affiliation(s)
- David Peyrot
- TITANS, CEA, IRAMIS, SPEC, CNRS, Université Paris Saclay , CEA Saclay, F-91191 Gif sur Yvette, France
| | - Fabien Silly
- TITANS, CEA, IRAMIS, SPEC, CNRS, Université Paris Saclay , CEA Saclay, F-91191 Gif sur Yvette, France
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34
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Ryder CR, Wood JD, Wells SA, Hersam MC. Chemically Tailoring Semiconducting Two-Dimensional Transition Metal Dichalcogenides and Black Phosphorus. ACS Nano 2016; 10:3900-17. [PMID: 27018800 DOI: 10.1021/acsnano.6b01091] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Two-dimensional (2D) semiconducting transition metal dichalcogenides (TMDCs) and black phosphorus (BP) have beneficial electronic, optical, and physical properties at the few-layer limit. As atomically thin materials, 2D TMDCs and BP are highly sensitive to their environment and chemical modification, resulting in a strong dependence of their properties on substrate effects, intrinsic defects, and extrinsic adsorbates. Furthermore, the integration of 2D semiconductors into electronic and optoelectronic devices introduces unique challenges at metal-semiconductor and dielectric-semiconductor interfaces. Here, we review emerging efforts to understand and exploit chemical effects to influence the properties of 2D TMDCs and BP. In some cases, surface chemistry leads to significant degradation, thus necessitating the development of robust passivation schemes. On the other hand, appropriately designed chemical modification can be used to beneficially tailor electronic properties, such as controlling doping levels and charge carrier concentrations. Overall, chemical methods allow substantial tunability of the properties of 2D TMDCs and BP, thereby enabling significant future opportunities to optimize performance for device applications.
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Affiliation(s)
- Christopher R Ryder
- Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | - Joshua D Wood
- Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | - Spencer A Wells
- Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
| | - Mark C Hersam
- Department of Materials Science and Engineering, Northwestern University , Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
- Department of Medicine, Northwestern University , Evanston, Illinois 60208, United States
- Department of Electrical Engineering and Computer Science, Northwestern University , Evanston, Illinois 60208, United States
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Keith JM, Jones WM, Tichenor M, Liu J, Seierstad M, Palmer JA, Webb M, Karbarz M, Scott BP, Wilson S, Luo L, Wennerholm ML, Chang L, Rizzolio M, Rynberg R, Chaplan SR, Breitenbucher JG. Preclinical Characterization of the FAAH Inhibitor JNJ-42165279. ACS Med Chem Lett 2015; 6:1204-8. [PMID: 26713105 PMCID: PMC4677372 DOI: 10.1021/acsmedchemlett.5b00353] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/02/2015] [Indexed: 01/20/2023] Open
Abstract
The pre-clinical characterization of the aryl piperazinyl urea inhibitor of fatty acid amide hydrolase (FAAH) JNJ-42165279 is described. JNJ-42165279 covalently inactivates the FAAH enzyme, but is highly selective with regard to other enzymes, ion channels, transporters, and receptors. JNJ-42165279 exhibited excellent ADME and pharmacodynamic properties as evidenced by its ability to block FAAH in the brain and periphery of rats and thereby cause an elevation of the concentrations of anandamide (AEA), oleoyl ethanolamide (OEA), and palmitoyl ethanolamide (PEA). The compound was also efficacious in the spinal nerve ligation (SNL) model of neuropathic pain. The combination of good physical, ADME, and PD properties of JNJ-42165279 supported it entering the clinical portfolio.
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Affiliation(s)
- John M. Keith
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - William M. Jones
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Mark Tichenor
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Jing Liu
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Mark Seierstad
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - James A. Palmer
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Michael Webb
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Mark Karbarz
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Brian P. Scott
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Sandy
J. Wilson
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Lin Luo
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Michelle L. Wennerholm
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Leon Chang
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Michele Rizzolio
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Raymond Rynberg
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - Sandra R. Chaplan
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
| | - J. Guy Breitenbucher
- Janssen Pharmaceutical Companies
of Johnson & Johnson, L.L.C., 3210 Merryfield Row, San Diego, California 92121, United States
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Hajimiri M, Shahverdi S, Kamalinia G, Dinarvand R. Growth factor conjugation: strategies and applications. J Biomed Mater Res A 2014; 103:819-38. [PMID: 24733811 DOI: 10.1002/jbm.a.35193] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/17/2014] [Accepted: 04/03/2014] [Indexed: 12/17/2022]
Abstract
Growth factors, first known for their essential role in the initiation of mitosis, are required for a variety of cellular processes and their localized delivery is considered as a rational approach in their therapeutic application to assure a safe and effective treatment while avoiding unwanted adverse effects. Noncovalent immobilization of growth factors as well as their covalent conjugation is amongst the most common strategies for localized delivery of growth factors. Today, immobilized and covalently conjugated growth factors are considered as a promising drug design and are widely used for protein reformulation and material design to cover the unwanted characteristics of growth factors as well as improving their functions. Selection of a suitable conjugation technique depends on the substrate chemistry and the availability of functional reactive groups in the structure of growth factor, the position of reactive groups in growth factor molecules and its relation with the receptor binding area, and the intention of creating either patterned or unpatterned conjugation. Various approaches for growth factor reformulation have been reported. This review provides an overview on chemical conjugation of growth factors and covers the relevant studies accomplished for bioconjugation of growth factors and their related application.
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Affiliation(s)
- Mirhamed Hajimiri
- Nanomedicine and Biomaterial Lab, Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, 1417614411, Iran; Nano Alvand Co., Avicenna Tech Park, Tehran University of Medical Sciences, Tehran, 1439955991, Iran
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Marquez BV, Ikotun OF, Parry JJ, Rogers BE, Meares CF, Lapi SE. Development of a Radiolabeled Irreversible Peptide Ligand for PET Imaging of Vascular Endothelial Growth Factor. J Nucl Med 2014; 55:1029-34. [PMID: 24732153 DOI: 10.2967/jnumed.113.130898] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 01/24/2014] [Indexed: 01/30/2023] Open
Abstract
UNLABELLED Imaging agents based on peptide probes have desirable pharmacokinetic properties provided that they have high affinities for their target in vivo. An approach to improve a peptide ligand's affinity for its target is to make this interaction covalent and irreversible. For this purpose, we evaluated a (64)Cu-labeled affinity peptide tag, (64)Cu-L19K-(5-fluoro-2,4-dinitrobenzene) ((64)Cu-L19K-FDNB), which binds covalently and irreversibly to vascular endothelial growth factor (VEGF) as a PET imaging agent. We compared the in vivo properties of (64)Cu-L19K-FDNB in VEGF-expressing tumor xenografts with its noncovalent binding analogs, (64)Cu-L19K-(2,4-dinitrophenyl) ((64)Cu-L19K-DNP) and (64)Cu-L19K. METHODS The L19K peptide (GGNECDIARMWEWECFERK-CONH2) was constructed with 1,4,7-triazacyclononane-1,4,7-triacetic acid at the N terminus for radiolabeling with (64)Cu with a polyethylene glycol spacer between peptide and chelate. 1,5-difluoro-2,4-dinitrobenzene was conjugated at the C-terminal lysine for cross-linking to VEGF, resulting in L19K-FDNB. (64)Cu-L19K-FDNB was assayed for covalent binding to VEGF in vitro. As a control, L19K was conjugated to 1-fluoro-2,4-dinitrobenzene, resulting in L19K-DNP. PET imaging and biodistribution studies of (64)Cu-L19K-FDNB, (64)Cu-L19K-DNP, and the native (64)Cu-L19K were compared in HCT-116 xenografts. Blocking studies of (64)Cu-L19K-FDNB was performed with a coinjection of excess unlabeled L19K-FDNB. RESULTS In vitro binding studies confirmed the covalent and irreversible binding of (64)Cu-L19K-FDNB to VEGF, whereas (64)Cu-L19K-DNP and (64)Cu-L19K did not bind covalently. PET imaging showed higher tumor uptake with (64)Cu-L19K-FDNB than with (64)Cu-L19K-DNP and (64)Cu-L19K, with mean standardized uptake values of 0.62 ± 0.05, 0.18 ± 0.06, and 0.34 ± 0.14, respectively, at 24 h after injection (P < 0.05), and 0.53 ± 0.05, 0.32 ± 0.14, and 0.30 ± 0.09, respectively, at 48 h after injection (P < 0.05). Blocking studies with (64)Cu-L19K-FDNB in the presence of excess unlabeled peptide showed a 53% reduction in tumor uptake at 48 h after injection. CONCLUSION In this proof-of-concept study, the use of a covalent binding peptide ligand against VEGF improves tracer accumulation at the tumor site in vivo, compared with its noncovalent binding peptide analogs. This technique is a promising tool to enhance the potency of peptide probes as imaging agents.
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Affiliation(s)
- Bernadette V Marquez
- Department of Radiology, Washington University School of Medicine, Saint Louis, Missouri
| | - Oluwatayo F Ikotun
- Department of Radiology, Washington University School of Medicine, Saint Louis, Missouri
| | - Jesse J Parry
- Department of Radiation Oncology, Washington University School of Medicine, Saint Louis, Missouri; and
| | - Buck E Rogers
- Department of Radiation Oncology, Washington University School of Medicine, Saint Louis, Missouri; and
| | - Claude F Meares
- Department of Chemistry, University of California, Davis, California
| | - Suzanne E Lapi
- Department of Radiology, Washington University School of Medicine, Saint Louis, Missouri
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Nien PC, Chen PY, Ho KC. Fabricating an Amperometric Cholesterol Biosensor by a Covalent Linkage between Poly(3-thiopheneacetic acid) and Cholesterol Oxidase. Sensors (Basel) 2009; 9:1794-806. [PMID: 22573987 DOI: 10.3390/s90301794] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 03/02/2009] [Accepted: 03/13/2009] [Indexed: 11/17/2022]
Abstract
In this study, use of the covalent enzyme immobilization method was proposed to attach cholesterol oxidase (ChO) on a conducting polymer, poly(3-thiopheneacetic acid), [poly(3-TPAA)]. Three red-orange poly(3-TPAA) films, named electrodes A, B and C, were electropolymerized on a platinum electrode by applying a constant current of 1.5 mA, for 5, 20 and 100 s, respectively. Further, 1-ethyl-3-(3-dimethylamiopropyl)carbodiimide hydrochloride (EDC · HCl) and N-hydroxysuccinimide (NHS) were used to activate the free carboxylic groups of the conducting polymer. Afterwards, the amino groups of the cholesterol oxidase were linked on the activated groups to form peptide bonds. The best sensitivity obtained for electrode B is 4.49 mA M(-1) cm(-2), with a linear concentration ranging from 0 to 8 mM, which is suitable for the analysis of cholesterol in humans. The response time (t(95)) is between 70 and 90 s and the limit of detection is 0.42 mM, based on the signal to noise ratio equal to 3. The interference of species such as ascorbic acid and uric acid increased to 5.2 and 10.3% of the original current response, respectively, based on the current response of cholesterol (100%). With respect to the long-term stability, the sensing response retains 88% of the original current after 13 days.
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Eghtedari M, Liopo AV, Copland JA, Oraevsky AA, Motamedi M. Engineering of hetero-functional gold nanorods for the in vivo molecular targeting of breast cancer cells. Nano Lett 2009; 9:287-91. [PMID: 19072129 PMCID: PMC4153361 DOI: 10.1021/nl802915q] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A novel technique is described to functionalize gold nanorods (GNRs) allowing for in vivo targeting of breast cancer tumors grown in athymic nude mice. GNRs were functionalized by covalent attachment of Herceptin (HER), a monoclonal antibody that enables molecular recognition of breast cancer cells expressing highly specific tumor associated antigens, and poly(ethylene glycol) (PEG) which obscures particles against the reticuloendothelial system in the body. The stability and functionality of fabricated particles (Her-PEG GNRs) were demonstrated in vitro in the presence of blood and then in vivo in nude mice model for breast cancer. The results demonstrate successful tumor accumulation of functionalized gold nanorods within HER2/neu overexpressing breast tumors in tumor-bearing nude mice and support the notions that GNRs can be used for molecular imaging of tumor.
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Affiliation(s)
- Mohammad Eghtedari
- Center for Biomedical Engineering, The University of Texas Medical Branch in Galveston, 301 University Blvd., UTMB Route 0456, Galveston, Texas 77555, U.S.A
| | - Anton V. Liopo
- Center for Biomedical Engineering, The University of Texas Medical Branch in Galveston, 301 University Blvd., UTMB Route 0456, Galveston, Texas 77555, U.S.A
| | - John A. Copland
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, 4500 San Pablo Road, Mayo Clinic, Jacksonville, Florida, 32224
| | | | - Massoud Motamedi
- Center for Biomedical Engineering, The University of Texas Medical Branch in Galveston, 301 University Blvd., UTMB Route 0456, Galveston, Texas 77555, U.S.A
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