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Ronzetti MH, Baljinnyam B, Itkin Z, Jain S, Rai G, Zakharov AV, Pal U, Simeonov A. Application of temperature-responsive HIS-tag fluorophores to differential scanning fluorimetry screening of small molecule libraries. Front Pharmacol 2022; 13:1040039. [PMID: 36506591 PMCID: PMC9729254 DOI: 10.3389/fphar.2022.1040039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/04/2022] [Indexed: 11/25/2022] Open
Abstract
Differential scanning fluorimetry is a rapid and economical biophysical technique used to monitor perturbations to protein structure during a thermal gradient, most often by detecting protein unfolding events through an environment-sensitive fluorophore. By employing an NTA-complexed fluorophore that is sensitive to nearby structural changes in histidine-tagged protein, a robust and sensitive differential scanning fluorimetry (DSF) assay is established with the specificity of an affinity tag-based system. We developed, optimized, and miniaturized this HIS-tag DSF assay (HIS-DSF) into a 1536-well high-throughput biophysical platform using the Borrelial high temperature requirement A protease (BbHtrA) as a proof of concept for the workflow. A production run of the BbHtrA HIS-DSF assay showed a tight negative control group distribution of Tm values with an average coefficient of variation of 0.51% and median coefficient of variation of compound Tm of 0.26%. The HIS-DSF platform will provide an additional assay platform for future drug discovery campaigns with applications in buffer screening and optimization, target engagement screening, and other biophysical assay efforts.
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Affiliation(s)
- Michael H. Ronzetti
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States,Department of Veterinary Medicine, College of Agriculture and Natural Resources, University of Maryland, College Park, MD, United States
| | - Bolormaa Baljinnyam
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States,*Correspondence: Bolormaa Baljinnyam, ; Anton Simeonov,
| | - Zina Itkin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Sankalp Jain
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Ganesha Rai
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Alexey V. Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Utpal Pal
- Department of Veterinary Medicine, College of Agriculture and Natural Resources, University of Maryland, College Park, MD, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States,*Correspondence: Bolormaa Baljinnyam, ; Anton Simeonov,
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Kirley TL, Norman AB. Critical evaluation of fluorescent dyes to evaluate the stability and ligand binding properties of an anti-cocaine mAb, h2E2. J Immunol Methods 2022; 508:113323. [PMID: 35843267 DOI: 10.1016/j.jim.2022.113323] [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: 06/03/2022] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022]
Abstract
Monoclonal antibodies have become a mainstay of modern drug development. However, unlike small molecule drugs, mAbs are large proteins that need to be characterized for their stability, heterogeneity, and tendency to aggregate. Many different extrinsic fluorescent dyes have been used to monitor the thermal stability, aggregation, and ligand binding characteristics of many different proteins. Some of these dyes change their fluorescence when bound to proteins due to changes in the hydrophobicity of their microenvironment (solvatochromic dyes such as Sypro Orange), while others respond to differences in rotational mobilities (rotor dyes such as DASPMI), and others have been used to detect fibrils and amyloid-like protein aggregation (amyloid dyes such as Thioflavin T). Previously, we used DASPMI dye and differential scanning fluorimetry to quantitate the binding of cocaine and cocaine metabolites to a humanized anti-cocaine h2E2 mAb under development for the treatment of cocaine use disorders. In the present study, we evaluated six dyes in these three classes for their ability to monitor domain denaturation and cocaine binding of the h2E2 mAb, both in its clinical formulation buffer and in PBS buffer. We noted that the Thioflavin T dye commonly used to assess amyloid formation was also capable of monitoring h2E2 mAb thermal denaturation and ligand binding using differential scanning calorimetry. However, unlike the DASPMI dye, the Thioflavin T dye caused a dose-dependent stabilization of the unliganded (apo) mAb, and when using the methodology developed with the DASPMI dye, decreased the apparent affinity of the mAb for cocaine as a function of dye concentration. Thus, although Thioflavin T differential fluorimetry data appears to be suitable for measuring cocaine affinity for this h2E2 mAb, the apparent mAb Kd values for cocaine are dependent on Thioflavin T dye concentration, reinforcing and extending the unique use of the DASPMI dye for this purpose.
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Affiliation(s)
- Terence L Kirley
- Department of Pharmacology and Systems Physiology, College of Medicine, University of Cincinnati, 231 Albert Sabin Way, Cincinnati, OH 45267-0575, United States of America.
| | - Andrew B Norman
- Department of Pharmacology and Systems Physiology, College of Medicine, University of Cincinnati, 231 Albert Sabin Way, Cincinnati, OH 45267-0575, United States of America
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Wang YT, Long XY, Ding X, Fan SR, Cai JY, Yang BJ, Zhang XF, Luo RH, Yang L, Ruan T, Ren J, Jing CX, Zheng YT, Hao XJ, Chen DZ. Novel nucleocapsid protein-targeting phenanthridine inhibitors of SARS-CoV-2. Eur J Med Chem 2022; 227:113966. [PMID: 34749200 PMCID: PMC8559303 DOI: 10.1016/j.ejmech.2021.113966] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is unprecedented in human history. As a major structural protein, nucleocapsid protein (NPro) is critical to the replication of SARS-CoV-2. In this work, 17 NPro-targeting phenanthridine derivatives were rationally designed and synthesized, based on the crystal structure of NPro. Most of these compounds can interact with SARS-CoV-2 NPro tightly and inhibit the replication of SARS-CoV-2 in vitro. Compounds 12 and 16 exhibited the most potent anti-viral activities with 50% effective concentration values of 3.69 and 2.18 μM, respectively. Furthermore, site-directed mutagenesis of NPro and Surface Plasmon Resonance (SPR) assays revealed that 12 and 16 target N-terminal domain (NTD) of NPro by binding to Tyr109. This work found two potent anti-SARS-CoV-2 bioactive compounds and also indicated that SARS-CoV-2 NPro-NTD can be a target for new anti-virus agents.
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Affiliation(s)
- Yi-Ting Wang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China
| | - Xin-Yan Long
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, PR China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, PR China
| | - Xiao Ding
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China
| | - Shi-Rui Fan
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China
| | - Jie-Yun Cai
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China
| | - Bi-Juan Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China
| | - Xin-Fang Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China; Department of Chemical Science and Engineering, Yunnan University, Kunming, Yunnan, 650091, PR China
| | - Rong-Hua Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, PR China
| | - Lian Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China
| | - Ting Ruan
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, PR China
| | - Juan Ren
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China; Department of Chemical Science and Engineering, Yunnan University, Kunming, Yunnan, 650091, PR China
| | - Chen-Xu Jing
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences/Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, PR China.
| | - Xiao-Jiang Hao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China.
| | - Duo-Zhi Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China.
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Markert C, Thoma G, Srinivas H, Bollbuck B, Lüönd RM, Miltz W, Wälchli R, Wolf R, Hinrichs J, Bergsdorf C, Azzaoui K, Penno CA, Klein K, Wack N, Jäger P, Hasler F, Beerli C, Loetscher P, Dawson J, Wieczorek G, Numao S, Littlewood-Evans A, Röhn TA. Discovery of LYS006, a Potent and Highly Selective Inhibitor of Leukotriene A 4 Hydrolase. J Med Chem 2021; 64:1889-1903. [PMID: 33592148 DOI: 10.1021/acs.jmedchem.0c01955] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The cytosolic metalloenzyme leukotriene A4 hydrolase (LTA4H) is the final and rate-limiting enzyme in the biosynthesis of pro-inflammatory leukotriene B4 (LTB4). Preclinical studies have validated this enzyme as an attractive drug target in chronic inflammatory diseases. Despite several attempts, no LTA4H inhibitor has reached the market, yet. Herein, we disclose the discovery and preclinical profile of LYS006, a highly potent and selective LTA4H inhibitor. A focused fragment screen identified hits that could be cocrystallized with LTA4H and inspired a fragment merging. Further optimization led to chiral amino acids and ultimately to LYS006, a picomolar LTA4H inhibitor with exquisite whole blood potency and long-lasting pharmacodynamic effects. Due to its high selectivity and its ability to fully suppress LTB4 generation at low exposures in vivo, LYS006 has the potential for a best-in-class LTA4H inhibitor and is currently investigated in phase II clinical trials in inflammatory acne, hidradenitis suppurativa, ulcerative colitis, and NASH.
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Structural Characterization of Diazabicyclooctane β-Lactam "Enhancers" in Complex with Penicillin-Binding Proteins PBP2 and PBP3 of Pseudomonas aeruginosa. mBio 2021; 12:mBio.03058-20. [PMID: 33593978 PMCID: PMC8545096 DOI: 10.1128/mbio.03058-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidrug-resistant (MDR) pathogens pose a significant public health threat. A major mechanism of resistance expressed by MDR pathogens is β-lactamase-mediated degradation of β-lactam antibiotics. The diazabicyclooctane (DBO) compounds zidebactam and WCK 5153, recognized as β-lactam “enhancers” due to inhibition of Pseudomonas aeruginosa penicillin-binding protein 2 (PBP2), are also class A and C β-lactamase inhibitors. To structurally probe their mode of PBP2 inhibition as well as investigate why P. aeruginosa PBP2 is less susceptible to inhibition by β-lactam antibiotics compared to the Escherichia coli PBP2, we determined the crystal structure of P. aeruginosa PBP2 in complex with WCK 5153. WCK 5153 forms an inhibitory covalent bond with the catalytic S327 of PBP2. The structure suggests a significant role for the diacylhydrazide moiety of WCK 5153 in interacting with the aspartate in the S-X-N/D PBP motif. Modeling of zidebactam in the active site of PBP2 reveals a similar binding mode. Both DBOs increase the melting temperature of PBP2, affirming their stabilizing interactions. To aid in the design of DBOs that can inhibit multiple PBPs, the ability of three DBOs to interact with P. aeruginosa PBP3 was explored crystallographically. Even though the DBOs show covalent binding to PBP3, they destabilized PBP3. Overall, the studies provide insights into zidebactam and WCK 5153 inhibition of PBP2 compared to their inhibition of PBP3 and the evolutionarily related KPC-2 β-lactamase. These molecular insights into the dual-target DBOs advance our knowledge regarding further DBO optimization efforts to develop novel potent β-lactamase-resistant, non-β-lactam PBP inhibitors.
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Zhu ZL, Qiu XD, Wu S, Liu YT, Zhao T, Sun ZH, Li ZR, Shan GZ. Blocking Effect of Demethylzeylasteral on the Interaction between Human ACE2 Protein and SARS-CoV-2 RBD Protein Discovered Using SPR Technology. Molecules 2020; 26:molecules26010057. [PMID: 33374387 PMCID: PMC7794844 DOI: 10.3390/molecules26010057] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 12/13/2022] Open
Abstract
The novel coronavirus disease (2019-nCoV) has been affecting global health since the end of 2019, and there is no sign that the epidemic is abating. Targeting the interaction between the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptor is a promising therapeutic strategy. In this study, surface plasmon resonance (SPR) was used as the primary method to screen a library of 960 compounds. A compound 02B05 (demethylzeylasteral, CAS number: 107316-88-1) that had high affinities for S-RBD and ACE2 was discovered, and binding affinities (KD, μM) of 02B05-ACE2 and 02B05-S-RBD were 1.736 and 1.039 μM, respectively. The results of a competition experiment showed that 02B05 could effectively block the binding of S-RBD to ACE2 protein. Furthermore, pseudovirus infection assay revealed that 02B05 could inhibit entry of SARS-CoV-2 pseudovirus into 293T cells to a certain extent at nontoxic concentration. The compoundobtained in this study serve as references for the design of drugs which have potential in the treatment of COVID-19 and can thus accelerate the process of developing effective drugs to treat SARS-CoV-2 infections.
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Coyle J, Walser R. Applied Biophysical Methods in Fragment-Based Drug Discovery. SLAS DISCOVERY 2020; 25:471-490. [PMID: 32345095 DOI: 10.1177/2472555220916168] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Fragment-based drug discovery (FBDD) has come of age in the last decade with the FDA approval of four fragment-derived drugs. Biophysical methods are at the heart of hit discovery and validation in FBDD campaigns. The three most commonly used methods, thermal shift, surface plasmon resonance, and nuclear magnetic resonance, can be daunting for the novice user. We aim here to provide the nonexpert user of these methods with a summary of problems and challenges that might be faced, but also highlight the potential gains that each method can contribute to an FBDD project. While our view on FBDD is slightly biased toward enabling structure-guided drug discovery, most of the points we address in this review are also valid for non-structure-focused FBDD.
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Affiliation(s)
- Joe Coyle
- Astex Pharmaceuticals, Cambridge, UK
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Structural Insights into Ceftobiprole Inhibition of Pseudomonas aeruginosa Penicillin-Binding Protein 3. Antimicrob Agents Chemother 2020; 64:AAC.00106-20. [PMID: 32152075 DOI: 10.1128/aac.00106-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/28/2020] [Indexed: 02/08/2023] Open
Abstract
Ceftobiprole is an advanced-generation broad-spectrum cephalosporin antibiotic with potent and rapid bactericidal activity against Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus, as well as susceptible Gram-negative pathogens, including Pseudomonas sp. pathogens. In the case of Pseudomonas aeruginosa, ceftobiprole acts by inhibiting P. aeruginosa penicillin-binding protein 3 (PBP3). Structural studies were pursued to elucidate the molecular details of this PBP inhibition. The crystal structure of the His-tagged PBP3-ceftobiprole complex revealed a covalent bond between the ligand and the catalytic residue S294. Ceftobiprole binding leads to large active site changes near binding sites for the pyrrolidinone and pyrrolidine rings. The S528 to L536 region adopts a conformation previously not observed in PBP3, including partial unwinding of the α11 helix. These molecular insights can lead to a deeper understanding of β-lactam-PBP interactions that result in major changes in protein structure, as well as suggesting how to fine-tune current inhibitors and to develop novel inhibitors of this PBP.
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Kirley TL, Norman AB, Wetzel HN. A novel differential scanning fluorimetry analysis of a humanized anti-cocaine mAb and its ligand binding characteristics. J Immunol Methods 2019; 476:112676. [PMID: 31634480 DOI: 10.1016/j.jim.2019.112676] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 02/02/2023]
Abstract
An anti-cocaine monoclonal antibody (mAb) designated h2E2 will soon enter clinical trials for the treatment of cocaine abuse disorders. Importantly, this antibody selectively binds cocaine and its active metabolite, cocaethylene, with high affinity, while binding inactive metabolites with substantially lower affinities. Here, we used differential scanning fluorimetry (DSF) to characterize the stability and ligand binding properties of this antibody and its cocaine-binding Fab fragment. The Sypro orange dye commonly used for DSF revealed multiple overlapping thermal protein denaturation transitions for both the mAb and the Fab fragment, making quantitative analysis of ligand binding by thermal stabilization problematic. However, by using the "rotor" dye, DASPMI (4-(4-(dimethylamino)styryl)-N-methylpyridinium iodide), which measures the rotational restriction of the fluorescent dye (as opposed to the Sypro orange dye which measures the hydrophobicity of the dye microenvironment), a simple two state thermal denaturation transition that is stabilized by ligand binding was observed for the h2E2 mAb, enabling Boltzmann fitting and quantitative thermodynamic analysis of the DASPMI DSF mAb cocaine and metabolite binding data. The computed affinities were consistent with ligand binding affinities determined using other techniques. Thus, this novel DASPMI DSF method can simply, inexpensively, and very rapidly generate ligand binding constants for the h2E2 mAb, despite the presence of multiple, overlapping, thermally unfolding protein domains characteristic of all mAbs. This approach is likely applicable to other mAbs currently in use for many research and therapeutic applications.
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Affiliation(s)
- Terence L Kirley
- From the Department of Pharmacology and Systems Physiology, College of Medicine, University of Cincinnati, 231 Albert Sabin Way, Cincinnati, OH 45267-0575, United States of America.
| | - Andrew B Norman
- From the Department of Pharmacology and Systems Physiology, College of Medicine, University of Cincinnati, 231 Albert Sabin Way, Cincinnati, OH 45267-0575, United States of America
| | - Hanna N Wetzel
- From the Department of Pharmacology and Systems Physiology, College of Medicine, University of Cincinnati, 231 Albert Sabin Way, Cincinnati, OH 45267-0575, United States of America
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Ralph EC, Hall J. An SPR-based analysis of cGAS substrate K D and steady-state K M values. Methods Enzymol 2019; 625:61-76. [PMID: 31455537 DOI: 10.1016/bs.mie.2019.04.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Surface plasmon resonance (SPR) is a standard method for evaluating direct protein-small molecule binding. While studying the catalytic mechanism of cyclic GMP-AMP synthase (cGAS), we developed an SPR-based method to measure steady-state KM values that complements traditional SPR affinity measurements. The method relies on refractive changes to detect protein interaction with substrates and products, and takes advantage of stimulator of type 1 interferon genes (STING) binding to the cGAS product, 2',3'-cGAMP. The specific method described here uses co-immobilization of cGAS and double-stranded DNA through a biotin tag; it should be generally applicable to other proteins and protein complexes.
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Affiliation(s)
- Erik C Ralph
- Worldwide Medicinal Chemistry, Pfizer, Groton, CT, United States.
| | - Justin Hall
- Worldwide Medicinal Chemistry, Pfizer, Groton, CT, United States
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