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Hamshaw I, Cominetti MMD, Nana‐Akyin P, Yee Ho EH, Searcey M, Mueller A. IS4-FAM, a fluorescent tool to study CXCR4 affinity and competitive antagonism in native cancer cells. Pharmacol Res Perspect 2024; 12:e70003. [PMID: 39207051 PMCID: PMC11359705 DOI: 10.1002/prp2.70003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 07/08/2024] [Accepted: 08/12/2024] [Indexed: 09/04/2024] Open
Abstract
The ability to accurately measure drug-target interaction is critical for the discovery of new therapeutics. Classical pharmacological bioassays such as radioligand or fluorescent ligand binding assays can define the affinity or Kd of a ligand for a receptor with the lower the Kd, the stronger the binding and the higher the affinity. However, in many drug discovery laboratories today, the target of interest if often artificially upregulated by means of transfection to modify the host cell's genetic makeup. This then potentially invalidates the assumptions of classical pharmacology affinity calculations as the receptor of interest is no longer at normal physiological densities. The CXCR4 receptor is expressed on many different cancer cell types and is associated with metastasis and poor prognosis. Therefore, the CXCR4 receptor is a desirable target for novel therapeutics. In this study, we explore the applicability of the newly developed fluorescently tagged CXCR4 antagonists, IS4-FAM as an investigative tool to study CXCR4 affinity and competitive antagonism in native, non-transfected cancer cells using confocal microscopy and flow cytometry. IS4-FAM directly labels CXCR4 in several cell lines including high CXCR4 expressing SK-MEL-28 (malignant melanoma) and PC3 (metastatic prostate cancer) and lower CXCR4 expressing THP-1 (acute monocytic leukemia) and was competitive with the established CXCR4 antagonist, AMD3100. This highlights the potential of IS4-FAM as a pharmacological tool for drug discovery in native cells lines and tissues.
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Affiliation(s)
| | | | | | | | - Mark Searcey
- School of PharmacyUniversity of East AngliaNorwichUK
| | - Anja Mueller
- School of PharmacyUniversity of East AngliaNorwichUK
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2
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Liu H, Fukuyama M, Ogura Y, Kasuya M, Onose S, Imai A, Shigemura K, Tokeshi M, Hibara A. Sensitivity-improved blocking agent-free fluorescence polarization assay through surface modification using polyethylene glycol. Analyst 2024. [PMID: 39247996 DOI: 10.1039/d4an00569d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024]
Abstract
Fluorescence polarization (FP) assays are widely used to quantify biomolecules, and their combination with microfluidic devices has the potential for application in onsite analysis. However, the hydrophobic surface of polydimethylsiloxane (PDMS)-based microfluidic devices and the amphiphilicity of the blocking agents can cause the nonspecific adsorption of biomolecules, which in turn reduces the sensitivity of the FP assay. To address this, we demonstrated an FP assay with improved sensitivity in microfluidic devices using a polyethylene glycol-based surface modification to avoid the use of blocking agents. We evaluated the effectiveness of the modification in inhibiting nonspecific protein adsorption and demonstrated the improved sensitivity of the FP immunoassay (FPIA). Our study addressed the lack of sensitivity of FP assays in microfluidic devices, particularly for the quantification of low-abundance analytes.
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Affiliation(s)
- Hao Liu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan.
- School of Science, Tohoku University, 6-3, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8578, Japan
| | - Mao Fukuyama
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan.
| | - Yu Ogura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan.
| | - Motohiro Kasuya
- Faculty of Production Systems Engineering and Sciences, Komatsu University, Nu 1-3 Shicho-machi, Komatsu, Ishikawa 923-8511, Japan
| | - Sho Onose
- Tianma Japan, Ltd., Shin-Kawasaki Mitsui Building West Tower 28F 1-1-2, Kashimada, Saiwai-ku, Kawasaki, Kanagawa 212-0058, Japan
| | - Ayuko Imai
- Tianma Japan, Ltd., Shin-Kawasaki Mitsui Building West Tower 28F 1-1-2, Kashimada, Saiwai-ku, Kawasaki, Kanagawa 212-0058, Japan
| | - Koji Shigemura
- Tianma Japan, Ltd., Shin-Kawasaki Mitsui Building West Tower 28F 1-1-2, Kashimada, Saiwai-ku, Kawasaki, Kanagawa 212-0058, Japan
| | - Manabu Tokeshi
- Division of Applied Chemistry, Hokkaido University, Kita 13 Nishi 8, Kita-ku, Sapporo 060-8628, Japan
| | - Akihide Hibara
- Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan.
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3
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Eberle SA, Gustavsson M. Bilayer lipids modulate ligand binding to atypical chemokine receptor 3. Structure 2024; 32:1174-1183.e5. [PMID: 38776922 DOI: 10.1016/j.str.2024.04.018] [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: 10/18/2023] [Revised: 02/28/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Chemokine receptors belong to the large class of G protein-coupled receptors (GPCRs) and are involved in a number of (patho)physiological processes. Previous studies highlighted the importance of membrane lipids for modulating GPCR structure and function. However, the underlying mechanisms of how lipids regulate GPCRs are often poorly understood. Here, we report that anionic lipid bilayers increase the binding affinity of the chemokine CXCL12 for the atypical chemokine receptor 3 (ACKR3) by modulating the CXCL12 binding kinetics. Notably, the anionic bilayer favors CXCL12 over the more positively charged chemokine CXCL11, which we explained by bilayer interactions orienting CXCL12 but not CXCL11 for productive ACKR3 binding. Furthermore, our data suggest a stabilization of active ACKR3 conformations in anionic bilayers. Taken together, the described regulation of chemokine selectivity of ACKR3 by the lipid bilayer proposes an extended version of the classical model of chemokine binding including the lipid environment of the receptor.
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Affiliation(s)
- Stefanie Alexandra Eberle
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Martin Gustavsson
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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4
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Kenakin T. Know your molecule: pharmacological characterization of drug candidates to enhance efficacy and reduce late-stage attrition. Nat Rev Drug Discov 2024; 23:626-644. [PMID: 38890494 DOI: 10.1038/s41573-024-00958-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2024] [Indexed: 06/20/2024]
Abstract
Despite advances in chemical, computational and biological sciences, the rate of attrition of drug candidates in clinical development is still high. A key point in the small-molecule discovery process that could provide opportunities to help address this challenge is the pharmacological characterization of hit and lead compounds, culminating in the selection of a drug candidate. Deeper characterization is increasingly important, because the 'quality' of drug efficacy, at least for G protein-coupled receptors (GPCRs), is now understood to be much more than activation of commonly evaluated pathways such as cAMP signalling, with many more 'efficacies' of ligands that could be harnessed therapeutically. Such characterization is being enabled by novel assays to characterize the complex behaviour of GPCRs, such as biased signalling and allosteric modulation, as well as advances in structural biology, such as cryo-electron microscopy. This article discusses key factors in the assessments of the pharmacology of hit and lead compounds in the context of GPCRs as a target class, highlighting opportunities to identify drug candidates with the potential to address limitations of current therapies and to improve the probability of them succeeding in clinical development.
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Affiliation(s)
- Terry Kenakin
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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5
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Popović L, Wintgens JP, Wu Y, Brankatschk B, Menninger S, Degenhart C, Jensen N, Wichert SP, Klebl B, Rossner MJ, Wehr MC. Profiling of ERBB receptors and downstream pathways reveals selectivity and hidden properties of ERBB4 antagonists. iScience 2024; 27:108839. [PMID: 38303712 PMCID: PMC10831936 DOI: 10.1016/j.isci.2024.108839] [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: 10/11/2023] [Revised: 11/20/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024] Open
Abstract
ERBB receptor tyrosine kinases are involved in development and diseases like cancer, cardiovascular, neurodevelopmental, and mental disorders. Although existing drugs target ERBB receptors, the next generation of drugs requires enhanced selectivity and understanding of physiological pathway responses to improve efficiency and reduce side effects. To address this, we developed a multilevel barcoded reporter profiling assay, termed 'ERBBprofiler', in living cells to monitor the activity of all ERBB targets and key physiological pathways simultaneously. This assay helps differentiate on-target therapeutic effects from off-target and off-pathway side effects of ERBB antagonists. To challenge the assay, eight established ERBB antagonists were profiled. Known effects were confirmed, and previously uncharacterized properties were discovered, such as pyrotinib's preference for ERBB4 over EGFR. Additionally, two lead compounds selectively targeting ERBB4 were profiled, showing promise for clinical trials. Taken together, this multiparametric profiling approach can guide early-stage drug development and lead to improved future therapeutic interventions.
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Affiliation(s)
- Lukša Popović
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstrasse 7, 80336 Munich, Germany
- Systasy Bioscience GmbH, Balanstrasse 6, 81669 Munich, Germany
| | - Jan P. Wintgens
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstrasse 7, 80336 Munich, Germany
- Systasy Bioscience GmbH, Balanstrasse 6, 81669 Munich, Germany
| | - Yuxin Wu
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstrasse 7, 80336 Munich, Germany
| | - Ben Brankatschk
- Systasy Bioscience GmbH, Balanstrasse 6, 81669 Munich, Germany
| | - Sascha Menninger
- Lead Discovery Center GmbH, Otto-Hahn-Strasse 15, 44227 Dortmund, Germany
| | - Carsten Degenhart
- Lead Discovery Center GmbH, Otto-Hahn-Strasse 15, 44227 Dortmund, Germany
| | - Niels Jensen
- Section of Molecular Neurobiology, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstrasse 7, 80336 Munich, Germany
| | - Sven P. Wichert
- Systasy Bioscience GmbH, Balanstrasse 6, 81669 Munich, Germany
- Section of Molecular Neurobiology, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstrasse 7, 80336 Munich, Germany
| | - Bert Klebl
- Lead Discovery Center GmbH, Otto-Hahn-Strasse 15, 44227 Dortmund, Germany
| | - Moritz J. Rossner
- Systasy Bioscience GmbH, Balanstrasse 6, 81669 Munich, Germany
- Section of Molecular Neurobiology, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstrasse 7, 80336 Munich, Germany
| | - Michael C. Wehr
- Research Group Cell Signalling, Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, Nussbaumstrasse 7, 80336 Munich, Germany
- Systasy Bioscience GmbH, Balanstrasse 6, 81669 Munich, Germany
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6
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Wang Y, Xu Y, Tan J, Ye J, Cui W, Hou J, Liu P, Li J, Wang S, Zhao Q. Anti-inflammation is an important way that Qingre-Huazhuo-Jiangsuan recipe treats acute gouty arthritis. Front Pharmacol 2023; 14:1268641. [PMID: 37881185 PMCID: PMC10597652 DOI: 10.3389/fphar.2023.1268641] [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: 07/28/2023] [Accepted: 09/21/2023] [Indexed: 10/27/2023] Open
Abstract
Background: Acute gouty arthritis (AGA) significantly impairs patients' quality of life. Currently, existing therapeutic agents exhibit definite efficacy but also lead to serious adverse reactions. Therefore, it is essential to develop highly efficient therapeutic agents with minimal adverse reactions, especially within traditional Chinese medicine (TCM). Additionally, food polyphenols have shown potential in treating various inflammatory diseases. The Qingre-Huazhuo-Jiangsuan-Recipe (QHJR), a modification of Si-Miao-San (SMS), has emerged as a TCM remedy for AGA with no reported side effects. Recent research has also highlighted a strong genetic link to gout. Methods: The TCM System Pharmacology (TCMSP) database was used to collect the main chemical components of QHJR and AGA-related targets for predicting the metabolites in QHJR. HPLC-Q-Orbitrap-MS was employed to identify the ingredients of QHJR. The collected metabolites were then used to construct a Drugs-Targets Network in Cytoscape software, ranked based on their "Degree" of significance. Differentially expressed genes (DEGs) were screened in the Gene Expression Omnibus (GEO) database using GEO2R online analysis. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed. The DEGs were utilized to construct a Protein-Protein Interaction (PPI) Network via the STRING database. In vivo experimental validation was conducted using colchicine, QHJR, rapamycin (RAPA), and 3-methyladenine (3-MA) as controls to observe QHJR's efficacy in AGA. Synovial tissues from rats were collected, and qRT-PCR and Western blot assays were employed to investigate Ampk-related factors (Ampk, mTOR, ULK1), autophagy-related factors (Atg5, Atg7, LC3, p62), and inflammatory-related factors (NLRP3). ELISA assays were performed to measure inflammatory-related factor levels (IL-6, IL-1β, TNF-α), and H&E staining was used to examine tissue histology. Results: Network analysis screened out a total of 94 metabolites in QHJR for AGA. HPLC-Q-Orbitrap-MS analysis identified 27 of these metabolites. Notably, five metabolites (Neochlorogenic acid, Caffeic acid, Berberine, Isoliquiritigenin, Formononetin) were not associated with any individual herbal component of QHJR in TCMSP database, while six metabolites (quercetin, luteolin, formononetin, naringenin, taxifolin, diosgenin) overlapped with the predicted results from the previous network analysis. Further network analysis highlighted key components, such as Caffeic acid, cis-resveratrol, Apigenin, and Isoliquiritigenin. Other studies have found that their treatment of AGA is achieved through reducing inflammation, consistent with this study, laying the foundation for the mechanism study of QHJR against AGA. PPI analysis identified TNF, IL-6, and IL-1β as hub genes. GO and KEGG analyses indicated that anti-inflammation was a key mechanism in AGA treatment. All methods demonstrated that inflammatory expression increased in the Model group but was reversed by QHJR. Additionally, autophagy-related expression increased following QHJR treatment. The study suggested that AMPKα and p-AMPKα1 proteins were insensitive to 3 MA and RAPA, implying that AMPK may not activate autophagy directly but through ULK1 and mTOR. Conclusion: In conclusion, this study confirms the effectiveness of QHJR, a modified formulation of SMS (a classic traditional Chinese medicine prescription for treating gout), against AGA. QHJR, as a TCM formula, offers advantages such as minimal safety concerns and potential long-term use. The study suggests that the mechanism by which QHJR treats AGA may involve the activation of the AMPK/mTOR/ULK1 pathway, thereby regulating autophagy levels, reducing inflammation, and alleviating AGA. These findings provide new therapeutic approaches and ideas for the clinical treatment of AGA.
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Affiliation(s)
- Yazhuo Wang
- Institute of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yang Xu
- Institute of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jingrui Tan
- Institute of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jiaxue Ye
- Institute of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Weizhen Cui
- Institute of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jie Hou
- Institute of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Peiyu Liu
- Institute of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jianwei Li
- Institute of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Shiyuan Wang
- Institute of Nursing, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Qingyang Zhao
- Institute of Nursing, Shandong University of Traditional Chinese Medicine, Jinan, China
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7
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Srinivasan B. Non-equilibrium modalities of inhibition: Characterizing irreversible inhibition for the ErbB receptor family members. Methods Enzymol 2023; 690:85-108. [PMID: 37858541 DOI: 10.1016/bs.mie.2023.08.004] [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: 10/21/2023]
Abstract
Most drug target interactions for clinically approved small-molecules are non-equilibrium slow-onset, tight-binding or irreversible in nature, with pronounced element of time-dependence of inhibition. Analysis of such modality of inhibition requires a continuous enzyme kinetic measurement that can yield complete progress curves and an automated high-throughput analysis pipeline. Given the increasing emphasis on designing non-equilibrium modes of inhibiting an enzyme target (especially irreversible), the above specified pipeline for data generation and analysis is essential for extracting parameters to guide decisions in early drug discovery. In this manuscript, the methodology and data analysis protocol from our irreversible inhibitor characterization campaigns for the ErbB receptor family members is presented. Guidance is provided on the appropriate design of assay to generate quality data, setting up the analysis and estimation of inactivation rate (kinact) and the pseudo-equilibrium binding affinity (KI) constant (or their ratio kinact/KI) in a high-throughput manner for the inhibitor interacting with the protein target of interest.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom.
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8
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Weber J, Djurberg K, Lundsten Salomonsson S, Kamprath M, Hoehne A, Westin H, Vergara F, Bondza S. Modelling ligand depletion for simultaneous affinity and binding site quantification on cells and tissue. Sci Rep 2023; 13:10031. [PMID: 37340068 DOI: 10.1038/s41598-023-37015-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/14/2023] [Indexed: 06/22/2023] Open
Abstract
The quantification of the number of targets in biological systems is an important parameter to assess the suitability of surface markers as targets for drugs, drug delivery and medical imaging. Likewise, quantifying the interaction with the target in terms of affinity and binding kinetics is essential during drug development. Commonly used approaches to quantify membrane antigens on live cells are based on manual saturation techniques that are labour-intensive, require careful calibration of the generated signal and do not quantify the binding rates. Here, we present how measuring interactions in real-time on live cells and tissue under ligand depletion conditions can be used to simultaneously quantify the kinetic binding parameters as well as the number of available binding sites in a biological system. Suitable assay design was explored with simulated data and feasibility of the method verified with experimental data for exemplary low molecular weight peptide and antibody radiotracers as well as fluorescent antibodies. In addition to revealing the number of accessible target sites and improving the accuracy of binding kinetics and affinities, the presented method does not require knowledge about the absolute signal generated per ligand molecule. This enables a simplified workflow for use with both radioligands and fluorescent binders.
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Affiliation(s)
| | | | - Sara Lundsten Salomonsson
- Ridgeview Instruments AB, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | | | | | | | - Sina Bondza
- Ridgeview Instruments AB, Uppsala, Sweden.
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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9
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Pharmacodynamic model of slow reversible binding and its applications in pharmacokinetic/pharmacodynamic modeling: review and tutorial. J Pharmacokinet Pharmacodyn 2022; 49:493-510. [PMID: 36040645 PMCID: PMC9578295 DOI: 10.1007/s10928-022-09822-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 08/12/2022] [Indexed: 10/14/2022]
Abstract
Therapeutic responses of most drugs are initiated by the rate and degree of binding to their receptors or targets. The law of mass action describes the rate of drug-receptor complex association (kon) and dissociation (koff) where the ratio koff/kon is the equilibrium dissociation constant (Kd). Drugs with slow reversible binding (SRB) often demonstrate delayed onset and prolonged pharmacodynamic effects. This report reviews evidence for drugs with SRB features, describes previous pharmacokinetic/pharmacodynamic (PK/PD) modeling efforts of several such drugs, provides a tutorial on the mathematics and properties of SRB models, demonstrates applications of SRB models to additional compounds, and compares PK/PD fittings of SRB with other mechanistic models. We identified and summarized 52 drugs with in vitro-confirmed SRB from a PubMed literature search. Simulations with a SRB model and observed PK/PD profiles showed delayed and prolonged responses and that increasing doses/kon or decreasing koff led to greater expected maximum effects and a longer duration of effects. Recession slopes for return of responses to baseline after single doses were nearly linear with an inflection point that approaches a limiting value at larger doses. The SRB model newly captured literature data for the antihypertensive effects of candesartan and antiallergic effects of noberastine. Their PD profiles could also be fitted with indirect response and biophase models with minimal differences. The applicability of SRB models is probably commonplace, but underappreciated, owing to the need for in vitro confirmation of binding kinetics and the similarity of PK/PD profiles to models with other mechanistic determinants.
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10
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Shave S, Pham NT, Auer M. CLAffinity: A Software Tool for Identification of Optimum Ligand Affinity for Competition-Based Primary Screens. J Chem Inf Model 2022; 62:2264-2268. [PMID: 35442032 PMCID: PMC9131445 DOI: 10.1021/acs.jcim.2c00285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Indexed: 12/02/2022]
Abstract
A simplistic assumption in setting up a competition assay is that a low affinity labeled ligand can be more easily displaced from a target protein than a high affinity ligand, which in turn produces a more sensitive assay. An often-cited paper correctly rallies against this assumption and recommends the use of the highest affinity ligand available for experiments aiming to determine competitive inhibitor affinities. However, we have noted this advice being applied incorrectly to competition-based primary screens where the goal is optimum assay sensitivity, enabling a clear yes/no binding determination for even low affinity interactions. The published advice only applies to secondary, confirmatory assays intended for accurate affinity determination of primary screening hits. We demonstrate that using very high affinity ligands in competition-based primary screening can lead to reduced assay sensitivity and, ultimately, the discarding of potentially valuable active compounds. We build on techniques developed in our PyBindingCurve software for a mechanistic understanding of complex biological interaction systems, developing the "CLAffinity tool" for simulating competition experiments using protein, ligand, and inhibitor concentrations common to drug screening campaigns. CLAffinity reveals optimum labeled ligand affinity ranges based on assay parameters, rather than general rules to optimize assay sensitivity. We provide the open source CLAffinity software toolset to carry out assay simulations and a video summarizing key findings to aid in understanding, along with a simple lookup table allowing identification of optimal dynamic ranges for competition-based primary screens. The application of our freely available software and lookup tables will lead to the consistent creation of more performant competition-based primary screens identifying valuable hit compounds, particularly for difficult targets.
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Affiliation(s)
- Steven Shave
- School of Biological Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, Scotland EH9
3BF, United Kingdom
| | - Nhan T. Pham
- School of Biological Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, Scotland EH9
3BF, United Kingdom
| | - Manfred Auer
- School of Biological Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, Scotland EH9
3BF, United Kingdom
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11
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Eberle SA, Gustavsson M. A Scintillation Proximity Assay for Real-Time Kinetic Analysis of Chemokine-Chemokine Receptor Interactions. Cells 2022; 11:1317. [PMID: 35455996 PMCID: PMC9024993 DOI: 10.3390/cells11081317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/05/2022] [Accepted: 04/11/2022] [Indexed: 11/23/2022] Open
Abstract
Chemokine receptors are extensively involved in a broad range of physiological and pathological processes, making them attractive drug targets. However, despite considerable efforts, there are very few approved drugs targeting this class of seven transmembrane domain receptors to date. In recent years, the importance of including binding kinetics in drug discovery campaigns was emphasized. Therefore, kinetic insight into chemokine-chemokine receptor interactions could help to address this issue. Moreover, it could additionally deepen our understanding of the selectivity and promiscuity of the chemokine-chemokine receptor network. Here, we describe the application, optimization and validation of a homogenous Scintillation Proximity Assay (SPA) for real-time kinetic profiling of chemokine-chemokine receptor interactions on the example of ACKR3 and CXCL12. The principle of the SPA is the detection of radioligand binding to receptors reconstituted into nanodiscs by scintillation light. No receptor modifications are required. The nanodiscs provide a native-like environment for receptors and allow for full control over bilayer composition and size. The continuous assay format enables the monitoring of binding reactions in real-time, and directly accounts for non-specific binding and potential artefacts. Minor adaptations additionally facilitate the determination of equilibrium binding metrics, making the assay a versatile tool for the study of receptor-ligand interactions.
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Affiliation(s)
| | - Martin Gustavsson
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark;
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12
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Upchurch WJ, Iaizzo PA. In vitro contractile studies within isolated tissue baths: Translational research from Visible Heart ® Laboratories. Exp Biol Med (Maywood) 2022; 247:584-597. [PMID: 35068214 PMCID: PMC9014520 DOI: 10.1177/15353702211070535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023] Open
Abstract
The isolated tissue bath research methodology was first developed in 1904. Since then, it has been recognized as an important tool in pharmacology and physiology research, including investigations into neuromuscular disorders. The tissue bath is still used routinely as the instrument for performing the "gold standard" test for clinical diagnosis of malignant hyperthermia susceptibility - the caffeine-halothane contracture test. Our research group has utilized this tool for several decades for a range of research studies, and we are currently one of four North American diagnostic centers for determining susceptibility for malignant hyperthermia. This review provides a brief summary of some of the historical uses of the tissue bath. Important experimental considerations for the operation of the tissue bath are further described. Finally, we discuss the different studies our group has performed using isolated tissue baths to highlight the broad potential applications.
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Affiliation(s)
- Weston J Upchurch
- Department of Surgery, University of
Minnesota, Minneapolis, MN 55455, USA
- Bioinformatics and Computational
Biology Program, University of Minnesota, Minneapolis, MN 55455, USA
| | - Paul A Iaizzo
- Department of Surgery, University of
Minnesota, Minneapolis, MN 55455, USA
- Bioinformatics and Computational
Biology Program, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Engineering in Medicine,
University of Minnesota, Minneapolis, MN 55455, USA
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13
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Srinivasan B. A guide to enzyme kinetics in early drug discovery. FEBS J 2022; 290:2292-2305. [PMID: 35175693 DOI: 10.1111/febs.16404] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 12/28/2022]
Abstract
Drugs interact with their target of interest to bring about the desired phenotypic outcome that results in disease alleviation. Traditionally, most lead optimization exercises were driven by affinity measures (like IC50 ) to inform structure-activity relationship (SAR)-guided medicinal chemistry. However, an IC50 value is a thermodynamic estimate measured under equilibrium conditions that can vary as a function of substrate concentration and/or time (the latter especially for nonequilibrium modalities). Further, like other thermodynamic estimates, it is a state-function that is indifferent to the path traversed from the initial state to the final state. This can be a cause for concern in drug discovery given the predominance of nonequilibrium interactions and the open thermodynamic nature of the human system. Under such situations, employing rates along with equilibrium constants (or IC50 values) would be far more relevant to capture the time evolution of the small molecule's interaction with the target of interest. These rates are generally typified by the rate of association, rate of dissociation and the residence time of the small molecule on the target (target occupancy). These parameters, when combined with the concept of target vulnerability, therapeutic window, pharmacokinetic profile of the small molecule, estimates of endogenous ligand and target turnover, will shed critical insights into the kinetics and dynamics of a small molecule's interaction with the protein, and allow realistic modelling of the system to enable optimizations and dosing decisions. With that aim, this guide will attempt to introduce the traditional role of mechanistic enzymology within drug discovery and emphasize the importance of kinetics in guiding SAR-based optimizations. It will also present initial ideas on how kinetic investigation should be positioned relative to the temporal span of a drug-discovery pipeline to leverage maximal utility from the investment in time and effort.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic and Structural Biology Discovery Sciences R&D AstraZeneca Cambridge UK
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14
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Kotulova J, Lonova K, Kubickova A, Vrbkova J, Kourilova P, Hajduch M, Dzubak P. 2‑Cl‑IB‑MECA regulates the proliferative and drug resistance pathways, and facilitates chemosensitivity in pancreatic and liver cancer cell lines. Int J Mol Med 2022; 49:31. [PMID: 35039871 PMCID: PMC8788926 DOI: 10.3892/ijmm.2022.5086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/14/2021] [Indexed: 12/24/2022] Open
Abstract
Specific A3 adenosine receptor (A3AR) agonist, 2-chloro-N6-(3-iodobenzyl)-5′-N-methylcarboxamidoadenosine (2-Cl-IB-MECA), demonstrates anti-proliferative effects on various types of tumor. In the present study, the cytotoxicity of 2-Cl-IB-MECA was analyzed in a panel of tumor and non-tumor cell lines and its anticancer mechanisms in JoPaca-1 pancreatic and Hep-3B hepatocellular carcinoma cell lines were also investigated. Initially, decreased tumor cell proliferation, cell accumulation in the G1 phase and inhibition of DNA and RNA synthesis was found. Furthermore, western blot analysis showed decreased protein expression level of β-catenin, patched1 (Ptch1) and glioma-associated oncogene homolog zinc finger protein 1 (Gli1), which are components of the Wnt/β-catenin and Sonic hedgehog/Ptch/Gli transduction pathways. In concordance with these findings, the protein expression levels of cyclin D1 and c-Myc were reduced. Using a luciferase assay, it was revealed for the first time a decrease in β-catenin transcriptional activity, as an early event following 2-Cl-IB-MECA treatment. In addition, the protein expression levels of multidrug resistance-associated protein 1 and P-glycoprotein (P-gp) were reduced and the P-gp xenobiotic efflux function was also reduced. Next, the enhancing effects of 2-Cl-IB-MECA on the cytotoxicity of conventional chemotherapy was investigated. It was found that 2-Cl-IB-MECA enhanced carboplatin and doxorubicin cytotoxic effects in the JoPaca-1 and Hep-3B cell lines, and a greater synergy was found in the highly tumorigenic JoPaca-1 cell line. This provides a novel in vitro rationale for the utiliza- tion of 2-Cl-IB-MECA in combination with chemotherapeutic agents, not only for hepatocellular carcinoma, but also for pancreatic cancer. Other currently used conventional chemo- therapeutics, fluorouracil and gemcitabine, showed synergy only when combined with high doses of 2-Cl-IB-MECA. Notably, experiments with A3AR-specific antagonist, N-[9-Chloro-2-(2-furanyl)(1,2,4)-triazolo(1,5-c)quinazolin-5-yl] benzene acetamide, revealed that 2-Cl-IB-MECA had antitumor effects via both A3AR-dependent and -independent pathways. In conclusion, the present study identified novel antitumor mechanisms of 2-Cl-IB-MECA in pancreatic and hepatocellular carcinoma in vitro that further underscores the importance of A3AR agonists in cancer therapy.
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Affiliation(s)
- Jana Kotulova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, 77900 Olomouc, Czech Republic
| | - Katerina Lonova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, 77900 Olomouc, Czech Republic
| | - Agata Kubickova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, 77900 Olomouc, Czech Republic
| | - Jana Vrbkova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, 77900 Olomouc, Czech Republic
| | - Pavla Kourilova
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, 77900 Olomouc, Czech Republic
| | - Marian Hajduch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, 77900 Olomouc, Czech Republic
| | - Petr Dzubak
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, 77900 Olomouc, Czech Republic
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15
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Dahlin JL. Approaches for Prioritizing High-Quality Chemical Matter in Chemical Probe and Drug Discovery. SLAS DISCOVERY 2021; 26:833-834. [PMID: 34283653 DOI: 10.1177/24725552211027215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Jayme L Dahlin
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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