1
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Xue L, van Kalken D, James EM, Giammo G, Labenski MT, Cantin S, Fahnoe K, Worm K, Wang Z, Corin AF. A Probe-Free Occupancy Assay to Assess a Targeted Covalent Inhibitor of Receptor Tyrosine-Protein Kinase erbB-2. ACS Pharmacol Transl Sci 2024; 7:2507-2515. [PMID: 39144565 PMCID: PMC11320722 DOI: 10.1021/acsptsci.4c00326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/16/2024]
Abstract
Establishing target engagement is fundamental to effective target-based drug development. It paves the way for efficient medicinal chemistry design and definitive answers about target validation in the clinic. For irreversible targeted covalent inhibitor (TCI) drugs, there is a unique opportunity to establish and quantify the target engagement or occupancy. This is typically accomplished by using a covalent molecular probe, often a TCI analogue, derivatized to allow unoccupied target sites to be tracked; the difference of total sites minus unoccupied sites yields the occupied sites. When such probes are not available or the target is not readily accessible to covalent probes, another approach is needed. Receptor tyrosine-protein kinase erbB-2 (HER2) occupancy by afatinib presents such a case. Available HER2 covalent probes were unable to consistently modify HER2 after sample preparation, resulting in inadequate data. We demonstrate an alternative quantitative probe-free occupancy (PFO) method. It employs the immunoprecipitation of HER2 and direct mass spectrometer analysis of the cysteine-containing peptide that is targeted and covalently occupied by afatinib. Nontarget HER2 peptides provide normalization to the total protein. We show that HER2 occupancy by afatinib correlates directly to the inhibition of the receptor tyrosine kinase activity in NCI-N87 cells in culture and in vivo using those cells in a mouse tumor xenograft mode.
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Affiliation(s)
| | | | | | | | | | | | | | - Karin Worm
- Leads Discovery & Optimization, Bristol Myers Squibb, 250 Water Street, Cambridge, Massachusetts 02141, United States
| | - Zhigang Wang
- Leads Discovery & Optimization, Bristol Myers Squibb, 250 Water Street, Cambridge, Massachusetts 02141, United States
| | - Alan F. Corin
- Leads Discovery & Optimization, Bristol Myers Squibb, 250 Water Street, Cambridge, Massachusetts 02141, United States
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2
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Emery-Corbin SJ, Yousef JM, Adhikari S, Sumardy F, Nhu D, van Delft MF, Lessene G, Dziekan J, Webb AI, Dagley LF. Improved drug target deconvolution with PISA-DIA using an extended, overlapping temperature gradient. Proteomics 2024; 24:e2300644. [PMID: 38766901 DOI: 10.1002/pmic.202300644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Thermal proteome profiling (TPP) is a powerful tool for drug target deconvolution. Recently, data-independent acquisition mass spectrometry (DIA-MS) approaches have demonstrated significant improvements to depth and missingness in proteome data, but traditional TPP (a.k.a. CEllular Thermal Shift Assay "CETSA") workflows typically employ multiplexing reagents reliant on data-dependent acquisition (DDA). Herein, we introduce a new experimental design for the Proteome Integral Solubility Alteration via label-free DIA approach (PISA-DIA). We highlight the proteome coverage and sensitivity achieved by using multiple overlapping thermal gradients alongside DIA-MS, which maximizes efficiencies in PISA sample concatenation and safeguards against missing protein targets that exist at high melting temperatures. We demonstrate our extended PISA-DIA design has superior proteome coverage as compared to using tandem-mass tags (TMT) necessitating DDA-MS analysis. Importantly, we demonstrate our PISA-DIA approach has the quantitative and statistical rigor using A-1331852, a specific inhibitor of BCL-xL. Due to the high melt temperature of this protein target, we utilized our extended multiple gradient PISA-DIA workflow to identify BCL-xL. We assert our novel overlapping gradient PISA-DIA-MS approach is ideal for unbiased drug target deconvolution, spanning a large temperature range whilst minimizing target dropout between gradients, increasing the likelihood of resolving the protein targets of novel compounds.
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Affiliation(s)
- Samantha J Emery-Corbin
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jumana M Yousef
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Subash Adhikari
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Fransisca Sumardy
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- ACRF Chemical Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Duong Nhu
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- ACRF Chemical Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Mark F van Delft
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Blood Cells and Blood Cancer Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Guillaume Lessene
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- ACRF Chemical Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Pharmacology and Therapeutics, University of Melbourne, Melbourne, Victoria, Australia
| | - Jerzy Dziekan
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Infection and Immunity Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Andrew I Webb
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Laura F Dagley
- Advanced Technology and Biology Division, the Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
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3
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Toy L, Huber ME, Lee M, Bartolomé AA, Ortiz Zacarías NV, Nasser S, Scholl S, Zlotos DP, Mandour YM, Heitman LH, Szpakowska M, Chevigné A, Schiedel M. Fluorophore-Labeled Pyrrolones Targeting the Intracellular Allosteric Binding Site of the Chemokine Receptor CCR1. ACS Pharmacol Transl Sci 2024; 7:2080-2092. [PMID: 39022357 PMCID: PMC11249626 DOI: 10.1021/acsptsci.4c00182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/18/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024]
Abstract
In this study, we describe the structure-based development of the first fluorescent ligands targeting the intracellular allosteric binding site (IABS) of the CC chemokine receptor type 1 (CCR1), a G protein-coupled receptor (GPCR) that has been pursued as a drug target in inflammation and immune diseases. Starting from previously reported intracellular allosteric modulators of CCR1, tetramethylrhodamine (TAMRA)-labeled ligands were designed, synthesized, and tested for their suitability as fluorescent tracers to probe binding to the IABS of CCR1. In the course of these studies, we developed LT166 (12) as a highly versatile fluorescent CCR1 ligand, enabling cell-free as well as cellular NanoBRET-based binding studies in a nonradioactive and high-throughput manner. Besides the detection of intracellular allosteric ligands by direct competition with 12, we were also able to monitor the binding of extracellular antagonists due to their positive cooperative binding with 12. Thereby, we provide a straightforward and nonradioactive method to easily distinguish between ligands binding to the IABS of CCR1 and extracellular negative modulators. Further, we applied 12 for the identification of novel chemotypes for intracellular CCR1 inhibition that feature high binding selectivity for CCR1 over CCR2. For one of the newly identified intracellular CCR1 ligands (i.e., 23), we were able to show CCR1 over CCR2 selectivity also on a functional level and demonstrated that this compound inhibits basal β-arrestin recruitment to CCR1, thereby acting as an inverse agonist. Thus, our fluorescent CCR1 ligand 12 represents a highly promising tool for future studies of CCR1-targeted pharmacology and drug discovery.
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Affiliation(s)
- Lara Toy
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, Erlangen 91058, Germany
| | - Max E. Huber
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, Erlangen 91058, Germany
| | - Minhee Lee
- Institute
of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstraße 55, Braunschweig 38106, Germany
| | - Ana Alonso Bartolomé
- Immuno-Pharmacology
and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Rue Henri Koch 29, Esch-sur-Alzette L-4354, Luxembourg
- Faculty
of Science, Technology and Medicine, University
of Luxembourg, 2 Avenue
de l’Université, Esch-sur-Alzette L-4365, Luxembourg
| | - Natalia V. Ortiz Zacarías
- Leiden
Academic Centre for Drug Research (LACDR), Division of Chemistry, Leiden University, Leiden 2333 CC, Netherlands
| | - Sherif Nasser
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, the German University in Cairo, New Cairo City 11835, Cairo, Egypt
| | - Stephan Scholl
- Institute
for Chemical and Thermal Process Engineering (ICTV), Technische Universität Braunschweig, Langer Kamp 7, Braunschweig 38106, Germany
| | - Darius P. Zlotos
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, the German University in Cairo, New Cairo City 11835, Cairo, Egypt
| | - Yasmine M. Mandour
- School
of Life and Medical Sciences, University
of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo 11578, Egypt
| | - Laura H. Heitman
- Leiden
Academic Centre for Drug Research (LACDR), Division of Chemistry, Leiden University, Leiden 2333 CC, Netherlands
- Oncode
Institute, Leiden University, Leiden 2333 CC, Netherlands
| | - Martyna Szpakowska
- Immuno-Pharmacology
and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Rue Henri Koch 29, Esch-sur-Alzette L-4354, Luxembourg
| | - Andy Chevigné
- Immuno-Pharmacology
and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, Rue Henri Koch 29, Esch-sur-Alzette L-4354, Luxembourg
| | - Matthias Schiedel
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, Erlangen 91058, Germany
- Institute
of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstraße 55, Braunschweig 38106, Germany
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4
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Huber ME, Wurnig SL, Moumbock AFA, Toy L, Kostenis E, Alonso Bartolomé A, Szpakowska M, Chevigné A, Günther S, Hansen FK, Schiedel M. Development of a NanoBRET Assay Platform to Detect Intracellular Ligands for the Chemokine Receptors CCR6 and CXCR1. ChemMedChem 2024:e202400284. [PMID: 38932712 DOI: 10.1002/cmdc.202400284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/26/2024] [Accepted: 06/26/2024] [Indexed: 06/28/2024]
Abstract
A conserved intracellular allosteric binding site (IABS) was recently identified at several G protein-coupled receptors (GPCRs). This target site allows the binding of allosteric modulators and enables a new mode of GPCR inhibition. Herein, we report the development of a NanoBRET-based assay platform based on the fluorescent ligand LT221 (5), to detect intracellular binding to CCR6 and CXCR1, two chemokine receptors that have been pursued as promising drug targets in inflammation and immuno-oncology. Our assay platform enables cell-free as well as cellular NanoBRET-based binding studies in a nonisotopic and straightforward manner. By combining this screening platform with a previously reported CXCR2 assay, we investigated CXCR1/CXCR2/CCR6 selectivity profiles for both known and novel squaramide analogues derived from navarixin, a known intracellular CXCR1/CXCR2 antagonist and phase II clinical candidate for the treatment of pulmonary diseases. By means of these studies we identified compound 10, a previously reported tert-butyl analogue of navarixin, as a low nanomolar intracellular CCR6 antagonist. Further, our assay platform clearly indicated intracellular binding of the CCR6 antagonist PF-07054894, currently evaluated in phase I clinical trials for the treatment of ulcerative colitis, thereby providing profound evidence for the existence and the pharmacological relevance of a druggable IABS at CCR6.
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Affiliation(s)
- Max E Huber
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Silas L Wurnig
- Department of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Aurélien F A Moumbock
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, 79104, Freiburg, Germany
| | - Lara Toy
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Evi Kostenis
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115, Bonn, Germany
| | - Ana Alonso Bartolomé
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, rue Henri Koch 29, 4354, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Avenue de l'Université, L-4365, Esch-sur-Alzette, Luxembourg
| | - Martyna Szpakowska
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, rue Henri Koch 29, 4354, Esch-sur-Alzette, Luxembourg
| | - Andy Chevigné
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health, rue Henri Koch 29, 4354, Esch-sur-Alzette, Luxembourg
| | - Stefan Günther
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, 79104, Freiburg, Germany
| | - Finn K Hansen
- Department of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Matthias Schiedel
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstraße 55, 38106, Braunschweig, Germany
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5
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McMahon NP, Solanki A, Wang LG, Montaño AR, Jones JA, Samkoe KS, Tichauer KM, Gibbs SL. In situ single-cell therapeutic response imaging facilitated by the TRIPODD fluorescence imaging platform. Theranostics 2024; 14:2816-2834. [PMID: 38773974 PMCID: PMC11103495 DOI: 10.7150/thno.93256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/21/2024] [Indexed: 05/24/2024] Open
Abstract
Purpose: Small molecule drugs such as tyrosine kinase inhibitors (TKIs) targeting tumoral molecular dependencies have become standard of care for numerous cancer types. Notably, epidermal growth factor receptor (EGFR) TKIs (e.g., erlotinib, afatinib, osimertinib) are the current first-line treatment for non-small cell lung cancer (NSCLC) due to their improved therapeutic outcomes for EGFR mutated and overexpressing disease over traditional platinum-based chemotherapy. However, many NSCLC tumors develop resistance to EGFR TKI therapy causing disease progression. Currently, the relationship between in situ drug target availability (DTA), local protein expression and therapeutic response cannot be accurately assessed using existing analytical tools despite being crucial to understanding the mechanism of therapeutic efficacy. Procedure: We have previously reported development of our fluorescence imaging platform termed TRIPODD (Therapeutic Response Imaging through Proteomic and Optical Drug Distribution) that is capable of simultaneous quantification of single-cell DTA and protein expression with preserved spatial context within a tumor. TRIPODD combines two complementary fluorescence imaging techniques: intracellular paired agent imaging (iPAI) to measure DTA and cyclic immunofluorescence (cyCIF), which utilizes oligonucleotide conjugated antibodies (Ab-oligos) for spatial proteomic expression profiling on tissue samples. Herein, TRIPODD was modified and optimized to provide a downstream analysis of therapeutic response through single-cell DTA and proteomic response imaging. Results: We successfully performed sequential imaging of iPAI and cyCIF resulting in high dimensional imaging and biomarker assessment to quantify single-cell DTA and local protein expression on erlotinib treated NSCLC models. Pharmacodynamic and pharmacokinetic studies of the erlotinib iPAI probes revealed that administration of 2.5 mg/kg each of the targeted and untargeted probe 4 h prior to tumor collection enabled calculation of DTA values with high Pearson correlation to EGFR, the erlotinib molecular target, expression in the tumors. Analysis of single-cell biomarker expression revealed that a single erlotinib dose was insufficient to enact a measurable decrease in the EGFR signaling cascade protein expression, where only the DTA metric detected the presence of bound erlotinib. Conclusion: We demonstrated the capability of TRIPODD to evaluate therapeutic response imaging to erlotinib treatment as it relates to signaling inhibition, DTA, proliferation, and apoptosis with preserved spatial context.
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Affiliation(s)
- Nathan P. McMahon
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Allison Solanki
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Lei G. Wang
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
| | - Antonio R. Montaño
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Jocelyn A. Jones
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
| | - Kimberley S. Samkoe
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, USA
- Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
| | - Kenneth M. Tichauer
- Department of Biomedical Engineering, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Summer L. Gibbs
- Biomedical Engineering Department, Oregon Health & Science University, Portland, OR 97201, USA
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
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6
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Luchinat E, Barbieri L, Davis B, Brough PA, Pennestri M, Banci L. Ligand-Based Competition Binding by Real-Time 19F NMR in Human Cells. J Med Chem 2024; 67:1115-1126. [PMID: 38215028 PMCID: PMC10823471 DOI: 10.1021/acs.jmedchem.3c01600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/17/2023] [Accepted: 12/26/2023] [Indexed: 01/14/2024]
Abstract
The development of more effective drugs requires knowledge of their bioavailability and binding efficacy directly in the native cellular environment. In-cell nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for investigating ligand-target interactions directly in living cells. However, the target molecule may be NMR-invisible due to interactions with cellular components, while observing the ligand by 1H NMR is impractical due to the cellular background. Such limitations can be overcome by observing fluorinated ligands by 19F in-cell NMR as they bind to the intracellular target. Here we report a novel approach based on real-time in-cell 19F NMR that allows measuring ligand binding affinities in human cells by competition binding, using a fluorinated compound as a reference. The binding of a set of compounds toward Hsp90α was investigated. In principle, this approach could be applied to other pharmacologically relevant targets, thus aiding the design of more effective compounds in the early stages of drug development.
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Affiliation(s)
- Enrico Luchinat
- Dipartimento
di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum—Università di Bologna, Piazza Goidanich 60, Cesena 47521, Italy
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Letizia Barbieri
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
| | - Ben Davis
- Vernalis
Research, Granta Park, Great Abington, Cambridge CB21 6GB, U.K.
| | - Paul A. Brough
- Vernalis
Research, Granta Park, Great Abington, Cambridge CB21 6GB, U.K.
| | - Matteo Pennestri
- Pharmaceutical
Business Unit, Bruker UK Limited, Banner Lane, Coventry CV4 9GH, U.K.
| | - Lucia Banci
- Consorzio
Interuniversitario Risonanze Magnetiche di Metallo Proteine—CIRMMP, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
- Centro
di Risonanze Magnetiche—CERM, Università
degli Studi di Firenze, Via Luigi Sacconi 6, Sesto Fiorentino 50019, Italy
- Dipartimento
di Chimica, Università degli Studi
di Firenze, Via della
Lastruccia 3, Sesto Fiorentino 50019, Italy
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7
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Yin Y, Zhao SL, Rane D, Lin Z, Wu M, Peterson BR. Quantification of Binding of Small Molecules to Native Proteins Overexpressed in Living Cells. J Am Chem Soc 2024; 146:187-200. [PMID: 38118119 PMCID: PMC10910633 DOI: 10.1021/jacs.3c07488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
The affinity and selectivity of small molecules for proteins drive drug discovery and development. We report a fluorescent probe cellular binding assay (FPCBA) for determination of these values for native (untagged) proteins overexpressed in living cells. This method uses fluorophores such as Pacific Blue (PB) linked to cell-permeable protein ligands to generate probes that rapidly and reversibly equilibrate with intracellular targets, as established by kinetic assays of cellular uptake and efflux. To analyze binding to untagged proteins, an internal ribosomal entry site (IRES) vector was employed that allows a single mRNA to encode both the protein target and a separate orthogonal fluorescent protein (mVenus). This enabled cellular uptake of the probe to be correlated with protein expression by flow cytometry, allowing measurement of cellular dissociation constants (Kd) of the probe. This approach was validated by studies of the binding of allosteric activators to eight different Protein Kinase C (PKC) isozymes. Full-length PKCs expressed in transiently transfected HEK293T cells were used to measure cellular Kd values of a probe comprising PB linked to the natural product phorbol via a carbamate. These values were further used to determine competitive binding constants (cellular Ki values) of the nonfluorescent phorbol ester PDBu and the anticancer agent bryostatin 1 for each isozyme. For some PKC-small molecule pairs, these cellular Ki values matched known biochemical Ki values, but for others, altered selectivity was observed in cells. This approach can facilitate quantification of interactions of small molecules with physiologically relevant native proteins.
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Affiliation(s)
- Yuwen Yin
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, College of Pharmacy, 500 W. 12 Ave., Columbus, OH 43210, USA
| | - Serena Li Zhao
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, College of Pharmacy, 500 W. 12 Ave., Columbus, OH 43210, USA
| | - Digamber Rane
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, College of Pharmacy, 500 W. 12 Ave., Columbus, OH 43210, USA
| | - Zhihong Lin
- The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, 460 W. 10 Ave., Columbus, OH 43210, USA
| | - Meng Wu
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, College of Pharmacy, 500 W. 12 Ave., Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, 460 W. 10 Ave., Columbus, OH 43210, USA
| | - Blake R. Peterson
- Division of Medicinal Chemistry and Pharmacognosy, The Ohio State University, College of Pharmacy, 500 W. 12 Ave., Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, 460 W. 10 Ave., Columbus, OH 43210, USA
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8
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Zhang Y, Zhou Y, Zhou Y, Yu X, Shen X, Hong Y, Zhang Y, Wang S, Mou M, Zhang J, Tao L, Gao J, Qiu Y, Chen Y, Zhu F. TheMarker: a comprehensive database of therapeutic biomarkers. Nucleic Acids Res 2024; 52:D1450-D1464. [PMID: 37850638 PMCID: PMC10767989 DOI: 10.1093/nar/gkad862] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/21/2023] [Accepted: 09/29/2023] [Indexed: 10/19/2023] Open
Abstract
Distinct from the traditional diagnostic/prognostic biomarker (adopted as the indicator of disease state/process), the therapeutic biomarker (ThMAR) has emerged to be very crucial in the clinical development and clinical practice of all therapies. There are five types of ThMAR that have been found to play indispensable roles in various stages of drug discovery, such as: Pharmacodynamic Biomarker essential for guaranteeing the pharmacological effects of a therapy, Safety Biomarker critical for assessing the extent or likelihood of therapy-induced toxicity, Monitoring Biomarker indispensable for guiding clinical management by serially measuring patients' status, Predictive Biomarker crucial for maximizing the clinical outcome of a therapy for specific individuals, and Surrogate Endpoint fundamental for accelerating the approval of a therapy. However, these data of ThMARs has not been comprehensively described by any of the existing databases. Herein, a database, named 'TheMarker', was therefore constructed to (a) systematically offer all five types of ThMAR used at different stages of drug development, (b) comprehensively describe ThMAR information for the largest number of drugs among available databases, (c) extensively cover the widest disease classes by not just focusing on anticancer therapies. These data in TheMarker are expected to have great implication and significant impact on drug discovery and clinical practice, and it is freely accessible without any login requirement at: https://idrblab.org/themarker.
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Affiliation(s)
- Yintao Zhang
- College of Pharmaceutical Sciences, The First Affiliated Hospital, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Ying Zhou
- College of Pharmaceutical Sciences, The First Affiliated Hospital, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- National Key Laboratory of Diagnosis and Treatment of Severe Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Yuan Zhou
- College of Pharmaceutical Sciences, The First Affiliated Hospital, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xinyuan Yu
- College of Pharmaceutical Sciences, The First Affiliated Hospital, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Xinyi Shen
- Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven 06510, USA
| | - Yanfeng Hong
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuxin Zhang
- College of Pharmaceutical Sciences, The First Affiliated Hospital, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shanshan Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, The First Affiliated Hospital, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Jinsong Zhang
- College of Pharmaceutical Sciences, The First Affiliated Hospital, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China
| | - Jianqing Gao
- College of Pharmaceutical Sciences, The First Affiliated Hospital, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yunqing Qiu
- College of Pharmaceutical Sciences, The First Affiliated Hospital, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- National Key Laboratory of Diagnosis and Treatment of Severe Infectious Disease, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310000, China
| | - Yuzong Chen
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, The Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, The First Affiliated Hospital, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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9
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Tsukidate T, Hespen CW, Hang HC. Small molecule modulators of immune pattern recognition receptors. RSC Chem Biol 2023; 4:1014-1036. [PMID: 38033733 PMCID: PMC10685800 DOI: 10.1039/d3cb00096f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/03/2023] [Indexed: 12/02/2023] Open
Abstract
Pattern recognition receptors (PRRs) represent a re-emerging class of therapeutic targets for vaccine adjuvants, inflammatory diseases and cancer. In this review article, we summarize exciting developments in discovery and characterization of small molecule PRR modulators, focusing on Toll-like receptors (TLRs), NOD-like receptors (NLRs) and the cGAS-STING pathway. We also highlight PRRs that are currently lacking small molecule modulators and opportunities for chemical biology and therapeutic discovery.
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Affiliation(s)
- Taku Tsukidate
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York New York 10065 USA
| | - Charles W Hespen
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York New York 10065 USA
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York New York 10065 USA
- Department of Immunology and Microbiology and Department of Chemistry, Scripps Research, La Jolla California 92037 USA
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10
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Liu J, Zhu T, Liu J, Cui Y, Yang S, Zhao R. Synergistic antitumor effects of circularly permuted TRAIL with doxorubicin in triple-negative breast cancer. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1247-1256. [PMID: 37559457 PMCID: PMC10449636 DOI: 10.3724/abbs.2023160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/03/2023] [Indexed: 08/11/2023] Open
Abstract
Circularly permuted TRAIL (CPT), a novel recombinant TRAIL mutant, is a potent antitumor agent. However, its efficacy in triple-negative breast cancer (TNBC) remains unclear. Treatment with CPT alone and in combination with doxorubicin (Dox) is explored for its effects on the proliferation and apoptosis of MDA-MB-231 (MB231) and MDA-MB-436 (MB436) breast cancer cells in vitro and in vivo. Here, we show that CPT combined with Dox exhibits time- and dose-dependent synergy to inhibit cell viability and enhance apoptosis of MB231 and MB436 cells. Combined treatment substantially increases caspase-8, caspase-3, and PARP cleavage in both cell lines and significantly suppresses tumor growth in nude mice bearing MB231 xenografts. Collectively, our findings demonstrate that treatment with CPT in combination with Dox exerts synergistic antitumor effects through activation of the caspase cascade pathway, a mechanism that is partly dependent on the Dox-induced upregulation of death receptor 4 and death receptor 5. Therefore, CPT combined with Dox may be a feasible therapeutic strategy for the management of TNBC.
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Affiliation(s)
- Jia Liu
- Department of OncologyHebei Medical UniversityShijiazhuang050017China
- Department of HematologyAffiliated Hospital of Hebei UniversityBaoding071000China
| | - Tienian Zhu
- Department of OncologyHebei Medical UniversityShijiazhuang050017China
- Department of Medical OncologyBethune International Peace HospitalShijiazhuang050082China
| | - Jiankun Liu
- Department of OncologyHebei Medical UniversityShijiazhuang050017China
| | - Yujie Cui
- of OncologyHebei General HospitalShijiazhuang050057China
| | - Shifang Yang
- Beijing Sunbio Biotech Co.Ltd.Beijing100000China
| | - Ruijing Zhao
- of ImmunologyHebei Medical UniversityKey Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei ProvinceShijiazhuang050017China
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11
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Huber ME, Wurnig S, Toy L, Weiler C, Merten N, Kostenis E, Hansen FK, Schiedel M. Fluorescent Ligands Enable Target Engagement Studies for the Intracellular Allosteric Binding Site of the Chemokine Receptor CXCR2. J Med Chem 2023. [PMID: 37463496 PMCID: PMC10388362 DOI: 10.1021/acs.jmedchem.3c00769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Herein, we report the structure-based development of fluorescent ligands targeting the intracellular allosteric binding site (IABS) of CXC chemokine receptor 2 (CXCR2), a G protein-coupled receptor (GPCR) that has been pursued as a drug target in oncology and inflammation. Starting from the cocrystallized intracellular CXCR2 antagonist 00767013 (1), tetramethylrhodamine (TAMRA)-labeled CXCR2 ligands were designed, synthesized, and tested for their suitability as fluorescent reporters to probe binding to the IABS of CXCR2. By means of these studies, we developed Mz438 (9a) as a high-affinity and selective fluorescent CXCR2 ligand, enabling cell-free as well as cellular NanoBRET-based binding studies in a nonisotopic and high-throughput manner. Further, we show that 9a can be used as a tool to visualize intracellular target engagement for CXCR2 via fluorescence microscopy. Thus, our small-molecule-based fluorescent CXCR2 ligand 9a represents a promising tool for future studies of CXCR2 pharmacology.
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Affiliation(s)
- Max E Huber
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Silas Wurnig
- Department of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Lara Toy
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Corinna Weiler
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Nicole Merten
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Evi Kostenis
- Molecular, Cellular and Pharmacobiology Section, Institute for Pharmaceutical Biology, University of Bonn, Nussallee 6, 53115 Bonn, Germany
| | - Finn K Hansen
- Department of Pharmaceutical & Cell Biological Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Matthias Schiedel
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstraße 55, 38106 Braunschweig, Germany
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12
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Peyear TA, Andersen OS. Screening for bilayer-active and likely cytotoxic molecules reveals bilayer-mediated regulation of cell function. J Gen Physiol 2023; 155:e202213247. [PMID: 36763053 PMCID: PMC9948646 DOI: 10.1085/jgp.202213247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/06/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023] Open
Abstract
A perennial problem encountered when using small molecules (drugs) to manipulate cell or protein function is to assess whether observed changes in function result from specific interactions with a desired target or from less specific off-target mechanisms. This is important in laboratory research as well as in drug development, where the goal is to identify molecules that are unlikely to be successful therapeutics early in the process, thereby avoiding costly mistakes. We pursued this challenge from the perspective that many bioactive molecules (drugs) are amphiphiles that alter lipid bilayer elastic properties, which may cause indiscriminate changes in membrane protein (and cell) function and, in turn, cytotoxicity. Such drug-induced changes in bilayer properties can be quantified as changes in the monomer↔dimer equilibrium for bilayer-spanning gramicidin channels. Using this approach, we tested whether molecules in the Pathogen Box (a library of 400 drugs and drug-like molecules with confirmed activity against tropical diseases released by Medicines for Malaria Venture to encourage the development of therapies for neglected tropical diseases) are bilayer modifiers. 32% of the molecules in the Pathogen Box were bilayer modifiers, defined as molecules that at 10 µM shifted the monomer↔dimer equilibrium toward the conducting dimers by at least 50%. Correlation analysis of the molecules' reported HepG2 cell cytotoxicity to bilayer-modifying potency, quantified as the shift in the gramicidin monomer↔dimer equilibrium, revealed that molecules producing <25% change in the equilibrium had significantly lower probability of being cytotoxic than molecules producing >50% change. Neither cytotoxicity nor bilayer-modifying potency (quantified as the shift in the gramicidin monomer↔dimer equilibrium) was well predicted by conventional physico-chemical descriptors (hydrophobicity, polar surface area, etc.). We conclude that drug-induced changes in lipid bilayer properties are robust predictors of the likelihood of membrane-mediated off-target effects, including cytotoxicity.
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Affiliation(s)
- Thasin A. Peyear
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences. New York, NY, USA
| | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
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13
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Quancard J, Vulpetti A, Bach A, Cox B, Guéret SM, Hartung IV, Koolman HF, Laufer S, Messinger J, Sbardella G, Craft R. The European Federation for Medicinal Chemistry and Chemical Biology (EFMC) Best Practice Initiative: Hit Generation. ChemMedChem 2023; 18:e202300002. [PMID: 36892096 DOI: 10.1002/cmdc.202300002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/14/2023] [Indexed: 03/10/2023]
Abstract
Hit generation is a crucial step in drug discovery that will determine the speed and chance of success of identifying drug candidates. Many strategies are now available to identify chemical starting points, or hits, and each biological target warrants a tailored approach. In this set of best practices, we detail the essential approaches for target centric hit generation and the opportunities and challenges they come with. We then provide guidance on how to validate hits to ensure medicinal chemistry is only performed on compounds and scaffolds that engage the target of interest and have the desired mode of action. Finally, we discuss the design of integrated hit generation strategies that combine several approaches to maximize the chance of identifying high quality starting points to ensure a successful drug discovery campaign.
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Affiliation(s)
- Jean Quancard
- Global Discovery Chemistry, Novartis Institute for Biomedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Anna Vulpetti
- Global Discovery Chemistry, Novartis Institute for Biomedical Research, Novartis Pharma AG, Novartis Campus, 4056, Basel, Switzerland
| | - Anders Bach
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Brian Cox
- School of Life Sciences, University of Sussex, Brighton, BN1 9RH, UK
| | - Stéphanie M Guéret
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, 43183, Gothenburg, Sweden
| | - Ingo V Hartung
- Medicinal Chemistry, Global R&D, Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | - Hannes F Koolman
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397, Biberach an der Riss, Germany
| | - Stefan Laufer
- Pharmaceutical & Medicinal Chemistry, Institute of Pharmacy & Biochemistry, Tübingen Center for Academic Drug Discovery, Auf der Morgenstelle 8, 72070, Tübingen, Germany
| | - Josef Messinger
- Medicine Design, Orionpharma, Orionintie 1, 02101, Espoo, Finland
| | - Gianluca Sbardella
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano (SA), Italy
| | - Russell Craft
- Medicinal chemistry, Symeres, Kadijk 3, 9747 AT, Groningen, The Netherlands
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14
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Abstract
Measurement of target engagement in cells is critical to understand the molecular pharmacology of drugs and chemical probes. Many targeted protein degraders engage the E3 ligase CRL4CRBN and induce proximity with target neosubstrates resulting in their polyubiquitination and subsequent proteasomal degradation. Here we describe the development of a sensitive and robust cellular NanoBRET-based assay that measures occupancy of the CRBN ligand binding site. The assay is based on a bioluminescence resonance energy transfer (BRET) between NanoLuc luciferase tagged CRBN and a BODIPY-lenalidomide tracer which can be competed out by CRBN ligands, including PROTACs and molecular glues. The assay is compatible with a 384-well plate setup, does not require transfections and can be performed in a single day with only 3-4h of laboratory time. The protocols can be used to design other NanoLuc fusion engagement assays based on BODIPY tracers.
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15
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Daghlas I, Gill D. Mendelian randomization as a tool to inform drug development using human genetics. CAMBRIDGE PRISMS. PRECISION MEDICINE 2023; 1:e16. [PMID: 38550933 PMCID: PMC10953771 DOI: 10.1017/pcm.2023.5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/14/2023] [Accepted: 01/30/2023] [Indexed: 04/11/2024]
Abstract
Drug development is essential to the advancement of human health, however, the process is slow, costly, and at high risk of failure at all stages. A promising strategy for expediting and improving the probability of success in the drug development process is the use of naturally randomized human genetic variation for drug target identification and validation. These data can be harnessed using the Mendelian randomization (MR) analytic paradigm to proxy the lifelong consequences of genetic perturbations of drug targets. In this review, we discuss the myriad applications of the MR paradigm for human drug target identification and validation. We review the methodology and applications of MR, key limitations of MR, and potential future opportunities for research. Throughout the review, we refer to illustrative examples of MR analyses investigating the consequences of genetic inhibition of interleukin 6 signaling which, in some cases, have anticipated results from randomized controlled trials. As human genetic data become more widely available, we predict that MR will serve as a key pillar of support for drug development efforts.
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Affiliation(s)
- Iyas Daghlas
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Dipender Gill
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Chief Scientific Advisor Office, Research and Early Development, Novo Nordisk, Copenhagen, Denmark
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16
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Lipidomics analysis in drug discovery and development. Curr Opin Chem Biol 2023; 72:102256. [PMID: 36586190 DOI: 10.1016/j.cbpa.2022.102256] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/08/2022] [Accepted: 11/28/2022] [Indexed: 12/30/2022]
Abstract
Despite being a relatively new addition to the Omics' landscape, lipidomics is increasingly being recognized as an important tool for the identification of druggable targets and biochemical markers. In this review we present recent advances of lipid analysis in drug discovery and development. We cover current state of the art technologies which are constantly evolving to meet demands in terms of sensitivity and selectivity. A careful selection of important examples is then provided, illustrating the versatility of lipidomics analysis in the drug discovery and development process. Integration of lipidomics with other omics', stem-cell technologies, and metabolic flux analysis will open new avenues for deciphering pathophysiological mechanisms and the discovery of novel targets and biomarkers.
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17
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Rothweiler EM, Huber KVM. Global Assessment of Drug Target Engagement and Selectivity of Covalent Cysteine-Reactive Inhibitors Using Alkyne-Functionalized Probes. Methods Mol Biol 2023; 2706:191-200. [PMID: 37558950 DOI: 10.1007/978-1-0716-3397-7_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Covalent inhibitors are emerging as a promising therapeutic means for efficient and sustained targeting of key disease-driving proteins. As for classic non-covalent inhibitors, understanding target engagement and selectivity is essential for determining optimal dosing and limiting potential on- or off-target toxicity. Here, we present a complementary activity-based protein profiling (ABPP) strategy for unbiased proteome-wide profiling of cysteine-reactive inhibitors based on two orthogonal approaches. We illustrate the use of clickable alkyne probes for in-gel fluorescence and mass spectrometry studies using a series of therapeutic XPO1 inhibitors as an example.
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Affiliation(s)
- Elisabeth M Rothweiler
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kilian V M Huber
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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18
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Leng Y, Hu X, Li L, Nkwocha J, Satta T, Sharma K, Kmeiciak M, Zhou H, Zhang Z, Zhou L, Chen W, Grant S. Mechanisms underlying synergism between circularized tumor necrosis factor-related apoptosis inducing ligand and bortezomib in bortezomib-sensitive or -resistant myeloma cells. Hematol Oncol 2022; 40:999-1008. [PMID: 35789025 PMCID: PMC10084357 DOI: 10.1002/hon.3045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022]
Abstract
Mechanisms underlying interactions between a novel, clinically relevant circularized tumor necrosis factor-related apoptosis inducing ligand (TRAIL) agonist, circularly permuted TRAIL (CPT) have been examined in multiple myeloma (MM) cells sensitive or resistant to bortezomib (BTZ). Various MM cell lines for example, U266, including those resistant to bortezomib-resistant U266 cells were exposed to low nanomolar concentrations of bortezomib ± CPT and apoptosis monitored. Circularly permuted TRAIL and bortezomib synergistically induced apoptosis in both BTZ-naïve and -resistant cells. The regimen up-regulated DR4 receptor internalization in MM cells, known to modulate both NF-κB and extrinsic apoptotic pathways. CPT/BTZ disrupted the non-canonical NF-κB pathway, reflected by tumor necrosis factor (TNF) receptor associated factors 3 (TRAF3) up-regulation, NF-κB inducing kinase down-regulation, diminished p52 and p50 processing, and B-cell lymphoma-extra large (BCL-XL) down-regulation, but failed to inactivate the canonical NF-κB pathway, reflected by unchanged or increased expression of phospho-p65. The regimen also sharply increased extrinsic apoptotic pathway activation. Cells exhibiting TRAF3 knock-down, dominant-negative Fas-associated protein with death domain, knock-down of caspase-8, BCL-2/BCL-XL, or exposure to a caspase-9 inhibitor displayed markedly reduced CPT/BTZ sensitivity. Concordant results were observed in bortezomib-resistant cells. The regimen was also active in the presence of stromal cells and was relatively sparing toward normal CD34+ hematopoietic cells. Finally, ex vivo results revealed synergism in primary MM primary cells, including those BTZ, and the CPT/BTZ regimen significantly decreased tumor growth in a patient-derived MM xenograft model. These results indicate that the CPT/BTZ regimen acts via the non-canonical NF-κB as well as intrinsic/extrinsic apoptotic pathways to induce cell death in MM cells, and may represent an effective strategy in the setting of bortezomib resistance.
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Affiliation(s)
- Yun Leng
- Department of HematologyBeijing Chao‐Yang HospitalCapital Medical UniversityBeijingChina
| | - Xiaoyan Hu
- Division of Hematology/OncologyDepartment of MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Lin Li
- Division of Hematology/OncologyDepartment of MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Jewel Nkwocha
- Division of Hematology/OncologyDepartment of MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Toshihisa Satta
- Division of Hematology/OncologyDepartment of MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Kanika Sharma
- Division of Hematology/OncologyDepartment of MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Maciej Kmeiciak
- Division of Hematology/OncologyDepartment of MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Huixing Zhou
- Department of HematologyBeijing Chao‐Yang HospitalCapital Medical UniversityBeijingChina
| | - Zhiyao Zhang
- Department of HematologyBeijing Chao‐Yang HospitalCapital Medical UniversityBeijingChina
| | - Liang Zhou
- Division of Hematology/OncologyDepartment of MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Wenming Chen
- Department of HematologyBeijing Chao‐Yang HospitalCapital Medical UniversityBeijingChina
| | - Steven Grant
- Division of Hematology/OncologyDepartment of MedicineVirginia Commonwealth UniversityRichmondVirginiaUSA
- Massey Cancer CenterVirginia Commonwealth UniversityRichmondVirginiaUSA
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19
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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20
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Kantae V, Polanski R, Lewis HJ, Haider A, Barratt D, Srinivasan B. Accelerating the Validation of Endogenous On-Target Engagement and In Cellulo Kinetic Assessment for Covalent Inhibitors of KRAS G12C in Early Drug Discovery. ACS Chem Biol 2022; 17:2366-2376. [PMID: 35881961 DOI: 10.1021/acschembio.2c00483] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Covalent inhibition is a valuable modality in drug discovery because of its potential ability in decoupling pharmacokinetics from pharmacodynamics by prolonging the residence time of the drug on the target of interest. This increase in target occupancy is limited only by the rate of target turnover. However, a limitation in such studies is to translate the in vitro inhibition assessment to the appropriate in cellulo target engagement parameter by covalent probes. Estimation of such parameters is often impeded by the low-throughput nature of current probe-free approaches. In this study, an ultra-performance liquid chromatography-multiple reaction monitoring mass spectrometry platform was utilized to develop a targeted proteomics workflow that can evaluate cellular on-target engagement of covalent molecules in an increased throughput manner. This workflow enabled a throughput increase of 5-10 fold when compared to traditional nanoLC-based proteomics studies. To demonstrate the applicability of the method, KRASG12C was used as a model system to investigate the interaction of an irreversible covalent small molecule, compound 25, both in vitro and in cellulo. Initial biochemical studies confirmed that the small molecule forms an adduct with the targeted cysteine on the protein, as assessed at the level of both intact protein and on the target peptide. In cellulo studies were carried out to quantify target engagement and allele selectivity assessment for the small molecule in the heterozygous NCI-H358 cell line for KRASG12C with respect to the WT type protein. The workflow enabled evaluation of in vitro and in cellulo target engagement kinetics, providing mechanistic insights into the irreversible mode of inhibition. In summary, the method has the potential for target agnostic application in the assessment of on-target engagement of covalent probes compatible with the high-throughput requirements of early drug discovery.
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Affiliation(s)
- Vasudev Kantae
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Radoslaw Polanski
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | - Afreen Haider
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Derek Barratt
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Bharath Srinivasan
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, U.K
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21
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Rezende Miranda R, Zhang C. Reactivity-based chemical-genetic study of protein kinases. RSC Med Chem 2022; 13:783-797. [PMID: 35923719 PMCID: PMC9298188 DOI: 10.1039/d1md00389e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/28/2022] [Indexed: 11/21/2022] Open
Abstract
The human protein kinase superfamily comprises over 500 members that operate in nearly every signal transduction pathway and regulate essential cellular processes. Deciphering the functional roles of protein kinases with small-molecule inhibitors is essential to enhance our understanding of cell signaling and to facilitate the development of new therapies. However, it is rather challenging to identify selective kinase inhibitors because of the conserved nature of the ATP binding site. A number of chemical-genetic approaches have been developed during the past two decades to enable selective chemical perturbation of the activity of individual kinases. Herein, we review the development and application of chemical-genetic strategies that feature the use of covalent inhibitors targeting cysteine residues to dissect the cellular functions of protein kinases.
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Affiliation(s)
- Renata Rezende Miranda
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of Southern California Los Angeles California 90089 USA
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology Rochester New York 14623 USA
| | - Chao Zhang
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of Southern California Los Angeles California 90089 USA
- USC Norris Comprehensive Cancer Center, University of Southern California Los Angeles California 90089 USA
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22
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Toy L, Huber ME, Schmidt MF, Weikert D, Schiedel M. Fluorescent Ligands Targeting the Intracellular Allosteric Binding Site of the Chemokine Receptor CCR2. ACS Chem Biol 2022; 17:2142-2152. [PMID: 35838163 DOI: 10.1021/acschembio.2c00263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Fluorescently labeled ligands are versatile molecular tools to study G protein-coupled receptors (GPCRs) and can be used for a range of different applications, including bioluminescence resonance energy transfer (BRET) assays. Here, we report the structure-based development of fluorescent ligands targeting the intracellular allosteric binding site (IABS) of the CC chemokine receptor 2 (CCR2), a class A GPCR that has been pursued as a drug target in oncology and inflammation. Starting from previously reported intracellular CCR2 antagonists, several tetramethylrhodamine (TAMRA)-labeled CCR2 ligands were designed, synthesized, and tested for their suitability as fluorescent reporters to probe binding to the IABS of CCR2. By means of these studies, we developed 14 as a fluorescent CCR2 ligand, enabling cell-free as well as cellular NanoBRET-based binding studies in a non-isotopic and high-throughput manner. Further, we show that 14 can be used as a tool for fragment-based screening approaches. Thus, our small-molecule-based fluorescent CCR2 ligand 14 represents a promising tool for future studies of CCR2 pharmacology.
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Affiliation(s)
- Lara Toy
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Max E Huber
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Maximilian F Schmidt
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Dorothee Weikert
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Matthias Schiedel
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
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23
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Brunst S, Schönfeld J, Breunig P, Burgers LD, DeMeglio M, Ehrler JHM, Lillich FF, Weizel L, Hefendehl JK, Fürst R, Proschak E, Hiesinger K. Designing a Small Fluorescent Inhibitor to Investigate Soluble Epoxide Hydrolase Engagement in Living Cells. ACS Med Chem Lett 2022; 13:1062-1067. [DOI: 10.1021/acsmedchemlett.2c00073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Affiliation(s)
- Steffen Brunst
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Julia Schönfeld
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Peter Breunig
- Buchmann Institute for Molecular Life Sciences and Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt, Germany
| | - Luisa D. Burgers
- Institute of Pharmaceutical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Murphy DeMeglio
- Buchmann Institute for Molecular Life Sciences and Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt, Germany
| | - Johanna H. M. Ehrler
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Felix F. Lillich
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Lilia Weizel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Jasmin K. Hefendehl
- Buchmann Institute for Molecular Life Sciences and Institute for Cell Biology and Neuroscience, Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438 Frankfurt, Germany
| | - Robert Fürst
- Institute of Pharmaceutical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Kerstin Hiesinger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
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24
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Hauser S, Sommerfeld P, Wodtke J, Hauser C, Schlitterlau P, Pietzsch J, Löser R, Pietsch M, Wodtke R. Application of a Fluorescence Anisotropy-Based Assay to Quantify Transglutaminase 2 Activity in Cell Lysates. Int J Mol Sci 2022; 23:4475. [PMID: 35562866 PMCID: PMC9104438 DOI: 10.3390/ijms23094475] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 02/05/2023] Open
Abstract
Transglutaminase 2 (TGase 2) is a multifunctional protein which is involved in various physiological and pathophysiological processes. The latter also include its participation in the development and progression of malignant neoplasms, which are often accompanied by increased protein synthesis. In addition to the elucidation of the molecular functions of TGase 2 in tumor cells, knowledge of its concentration that is available for targeting by theranostic agents is a valuable information. Herein, we describe the application of a recently developed fluorescence anisotropy (FA)-based assay for the quantitative expression profiling of TGase 2 by means of transamidase-active enzyme in cell lysates. This assay is based on the incorporation of rhodamine B-isonipecotyl-cadaverine (R-I-Cad) into N,N-dimethylated casein (DMC), which results in an increase in the FA signal over time. It was shown that this reaction is not only catalyzed by TGase 2 but also by TGases 1, 3, and 6 and factor XIIIa using recombinant proteins. Therefore, control measurements in the presence of a selective irreversible TGase 2 inhibitor were mandatory to ascertain the specific contribution of TGase 2 to the overall FA rate. To validate the assay regarding the quality of quantification, spike/recovery and linearity of dilution experiments were performed. A total of 25 cancer and 5 noncancer cell lines were characterized with this assay method in terms of their activatable TGase 2 concentration (fmol/µg protein lysate) and the results were compared to protein synthesis data obtained by Western blotting. Moreover, complementary protein quantification methods using a biotinylated irreversible TGase 2 inhibitor as an activity-based probe and a commercially available ELISA were applied to selected cell lines to further validate the results obtained by the FA-based assay. Overall, the present study demonstrates that the FA-based assay using the substrate pair R-I-Cad and DMC represents a facile, homogenous and continuous method for quantifying TGase 2 activity in cell lysates.
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Affiliation(s)
- Sandra Hauser
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany; (S.H.); (J.W.); (P.S.); (J.P.); (R.L.)
| | - Paul Sommerfeld
- Institute II of Pharmacology, Center of Pharmacology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Gleueler Straße 24, 50931 Cologne, Germany; (P.S.); (C.H.)
| | - Johanna Wodtke
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany; (S.H.); (J.W.); (P.S.); (J.P.); (R.L.)
| | - Christoph Hauser
- Institute II of Pharmacology, Center of Pharmacology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Gleueler Straße 24, 50931 Cologne, Germany; (P.S.); (C.H.)
| | - Paul Schlitterlau
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany; (S.H.); (J.W.); (P.S.); (J.P.); (R.L.)
| | - Jens Pietzsch
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany; (S.H.); (J.W.); (P.S.); (J.P.); (R.L.)
- Faculty of Chemistry and Food Chemistry, School of Science, Technische University Dresden, Mommsenstraße 4, 01069 Dresden, Germany
| | - Reik Löser
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany; (S.H.); (J.W.); (P.S.); (J.P.); (R.L.)
- Faculty of Chemistry and Food Chemistry, School of Science, Technische University Dresden, Mommsenstraße 4, 01069 Dresden, Germany
| | - Markus Pietsch
- Institute II of Pharmacology, Center of Pharmacology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Gleueler Straße 24, 50931 Cologne, Germany; (P.S.); (C.H.)
| | - Robert Wodtke
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Bautzner Landstraße 400, 01328 Dresden, Germany; (S.H.); (J.W.); (P.S.); (J.P.); (R.L.)
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25
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Baumel WT, Lu L, Huang X, Drysdale AT, Sweeny JA, Gong Q, Sylvester CM, Strawn JR. Neurocircuitry of Treatment in Anxiety Disorders. Biomark Neuropsychiatry 2022; 6. [PMID: 35756886 PMCID: PMC9222661 DOI: 10.1016/j.bionps.2022.100052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background: Methods: Results: Conclusions:
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Affiliation(s)
- W. Tommy Baumel
- Department of Psychiatry & Behavioral Neuroscience, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
- Correspondence to: University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH 45267, USA. (W.T. Baumel)
| | - Lu Lu
- Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
- Psychoradiology Research Unit of Chinese Academy of Medical Sciences, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Xiaoqi Huang
- Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
- Psychoradiology Research Unit of Chinese Academy of Medical Sciences, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Andrew T. Drysdale
- Department of Psychiatry, School of Medicine, Washington University in St. Louis, St Louis, MO, USA
| | - John A. Sweeny
- Department of Psychiatry & Behavioral Neuroscience, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
- Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
| | - Qiyong Gong
- Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu, China
- Psychoradiology Research Unit of Chinese Academy of Medical Sciences, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Chad M. Sylvester
- Department of Psychiatry, School of Medicine, Washington University in St. Louis, St Louis, MO, USA
| | - Jeffrey R. Strawn
- Department of Psychiatry & Behavioral Neuroscience, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
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26
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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27
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Owens AE, Iannotti MJ, Sanchez TW, Voss T, Kapoor A, Hall MD, Marugan JJ, Michael S, Southall N, Henderson MJ. High-Throughput Cellular Thermal Shift Assay Using Acoustic Transfer of Protein Lysates. ACS Chem Biol 2022; 17:322-330. [PMID: 35119255 PMCID: PMC10026039 DOI: 10.1021/acschembio.1c00760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cellular thermal shift assay (CETSA) is a valuable method to confirm target engagement within a complex cellular environment, by detecting changes in a protein's thermal stability upon ligand binding. The classical CETSA method measures changes in the thermal stability of endogenous proteins using immunoblotting, which is low-throughput and laborious. Reverse-phase protein arrays (RPPAs) have been demonstrated as a detection modality for CETSA; however, the reported procedure requires manual processing steps that limit throughput and preclude screening applications. We developed a high-throughput CETSA using an acoustic RPPA (HT-CETSA-aRPPA) protocol that is compatible with 96- and 384-well microplates from start-to-finish, using low speed centrifugation to remove thermally destabilized proteins. The utility of HT-CETSA-aRPPA for guiding structure-activity relationship studies was demonstrated for inhibitors of lactate dehydrogenase A. Additionally, a collection of kinase inhibitors was screened to identify compounds that engage MEK1, a clinically relevant kinase target.
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Affiliation(s)
- Ashley E. Owens
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Michael J. Iannotti
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Tino W. Sanchez
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Ty Voss
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Abhijeet Kapoor
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Juan J. Marugan
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Mark J. Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
- Corresponding Author: Mark Henderson;
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28
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Vogelmann A, Jung M, Hansen FK, Schiedel M. Comparison of Cellular Target Engagement Methods for the Tubulin Deacetylases Sirt2 and HDAC6: NanoBRET, CETSA, Tubulin Acetylation, and PROTACs. ACS Pharmacol Transl Sci 2022; 5:138-140. [PMID: 35187421 PMCID: PMC8844959 DOI: 10.1021/acsptsci.2c00004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Indexed: 01/29/2023]
Abstract
The tubulin deacetylases Sirt2 and HDAC6 have been associated with the development of various diseases. Herein, we discuss recent approaches that enable cellular target engagement studies for these deacetylases and thus play a critical role in the evaluation of small molecule inhibitors of Sirt2 or HDAC6 as potential therapeutic agents.
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Affiliation(s)
- Anja Vogelmann
- Institute
of Pharmaceutical Sciences, Albert-Ludwigs-University
Freiburg, Albertstraße 25, 79104 Freiburg im Breisgau, Germany
| | - Manfred Jung
- Institute
of Pharmaceutical Sciences, Albert-Ludwigs-University
Freiburg, Albertstraße 25, 79104 Freiburg im Breisgau, Germany
| | - Finn K. Hansen
- Department
of Pharmaceutical & Medicinal Chemistry, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Matthias Schiedel
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
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29
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Mortison JD, Cornella-Taracido I, Venkatchalam G, Partridge AW, Siriwardana N, Bushell SM. Rapid Evaluation of Small Molecule Cellular Target Engagement with a Luminescent Thermal Shift Assay. ACS Med Chem Lett 2021; 12:1288-1294. [PMID: 34413958 DOI: 10.1021/acsmedchemlett.1c00276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/07/2021] [Indexed: 12/13/2022] Open
Abstract
Determination of target engagement for candidate drug molecules in the native cellular environment is a significant challenge for drug discovery programs. The cellular thermal shift assay (CETSA) has emerged as a powerful tool for determining compound target engagement through measurement of changes to a protein's thermal stability upon ligand binding. Here, we present a HiBiT thermal shift assay (BiTSA) that deploys a quantitative peptide tag for determination of compound target engagement in the native cellular environment using a high throughput, plate-based luminescence readout. We demonstrate that BiTSA can rapidly assess cellular target engagement of small molecule ligands against their cognate targets and highlight two applications of BiTSA for differentiating small molecules targeting mutant KRAS and TP53.
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Affiliation(s)
| | | | | | | | | | - Simon M. Bushell
- Chemical Biology, Merck & Co., Inc., Boston, Massachusetts 02115, United States
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30
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Quantification of Trastuzumab-HER2 Engagement In Vitro and In Vivo. Molecules 2020; 25:molecules25245976. [PMID: 33348564 PMCID: PMC7767145 DOI: 10.3390/molecules25245976] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/22/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
Human EGF Receptor 2 (HER2) is an important oncogene driving aggressive metastatic growth in up to 20% of breast cancer tumors. At the same time, it presents a target for passive immunotherapy such as trastuzumab (TZM). Although TZM has been widely used clinically since 1998, not all eligible patients benefit from this therapy due to primary and acquired drug resistance as well as potentially lack of drug exposure. Hence, it is critical to directly quantify TZM–HER2 binding dynamics, also known as cellular target engagement, in undisturbed tumor environments in live, intact tumor xenograft models. Herein, we report the direct measurement of TZM–HER2 binding in HER2-positive human breast cancer cells and tumor xenografts using fluorescence lifetime Forster Resonance Energy Transfer (FLI-FRET) via near-infrared (NIR) microscopy (FLIM-FRET) as well as macroscopy (MFLI-FRET) approaches. By sensing the reduction of fluorescence lifetime of donor-labeled TZM in the presence of acceptor-labeled TZM, we successfully quantified the fraction of HER2-bound and internalized TZM immunoconjugate both in cell culture and tumor xenografts in live animals. Ex vivo immunohistological analysis of tumors confirmed the binding and internalization of TZM–HER2 complex in breast cancer cells. Thus, FLI-FRET imaging presents a powerful analytical tool to monitor and quantify cellular target engagement and subsequent intracellular drug delivery in live HER2-positive tumor xenografts.
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31
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Tsukidate T, Li Q, Hang HC. Nuclear Receptor Chemical Reporter Enables Domain-Specific Analysis of Ligands in Mammalian Cells. ACS Chem Biol 2020; 15:2324-2330. [PMID: 32909738 DOI: 10.1021/acschembio.0c00432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The characterization of specific metabolite-protein interactions is important in chemical biology and drug discovery. For example, nuclear receptors (NRs) are a family of ligand-activated transcription factors that regulate diverse physiological processes in animals and are key targets for therapeutic development. However, the identification and characterization of physiological ligands for many NRs remains challenging, because of limitations in domain-specific analysis of ligand binding in cells. To address these limitations, we developed a domain-specific covalent chemical reporter for peroxisome proliferator-activated receptors (PPARs) and demonstrated its utility to screen and characterize the potency of candidate NR ligands in live cells. These studies demonstrate targeted and domain-specific chemical reporters provide excellent tools to evaluate endogenous and exogenous (diet, microbiota, therapeutics) ligands of PPARs in mammalian cells, as well as additional protein targets for further investigation.
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Affiliation(s)
- Taku Tsukidate
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Qiang Li
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Howard C. Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
- Departments of Immunology and Microbiology, Chemistry, Scripps Research, La Jolla, California 92037, United States
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