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Swinney DC. Why medicines work. Pharmacol Ther 2022; 238:108175. [DOI: 10.1016/j.pharmthera.2022.108175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 11/27/2022]
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Abstract
There is a great need for innovative new medicines to treat unmet medical needs. The discovery and development of innovative new medicines is extremely difficult, costly, and inefficient. In the last decade, phenotypic drug discovery (PDD) was reintroduced as a strategy to provide first-in-class medicines. PDD uses empirical, target-agnostic lead generation to identify pharmacologically active molecules and novel therapeutics which work through unprecedented drug mechanisms. The economic and scientific value of PDD is exemplified through game-changing medicines for hepatitis C virus, spinal muscular atrophy, and cystic fibrosis. In this short review, recent advances are noted for the implementation and de-risking of PDD (for compound library selection, biomarker development, mechanism identification, and safety studies) and the potential for artificial intelligence. A significant barrier in the decision to implement PDD is balancing the potential impact of a novel mechanism of drug action with an under-defined scientific path forward, with the desire to provide infrastructure and metrics to optimize return on investment, which a known mechanism provides. A means to address this knowledge gap in the future is to empower precompetitive research utilizing the empirical concepts of PDD to identify new mechanisms and pharmacologically active compounds.
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Haubrich BA, Ramesha C, Swinney DC. Development of a Bioluminescent High-Throughput Screening Assay for Nicotinamide Mononucleotide Adenylyltransferase (NMNAT). SLAS Discov 2019; 25:33-42. [PMID: 31583955 DOI: 10.1177/2472555219879644] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nicotinamide mononucleotide adenylyltransferase (NMNAT; EC 2.7.7.1) catalyzes the reversible production of NAD+ from NMN+ and ATP and is a potential drug target for cancer and neurodegenerative diseases. A sensitive bioluminescent assay format suitable to high-throughput screening (HTS) and mechanistic follow-up has not been reported and is of value to identify new modulators of NMNATs. To this end, we report the development of a bioluminescent assay using Photinus pyralis ATP-dependent luciferase and luciferin for NMNAT1 in a 384-well plate format. We also report a mechanistic follow-up paradigm using this format to determine time dependence and competition with substrates. The assay and follow-up paradigm were used to screen 912 compounds from the National Cancer Institute (NCI) Mechanistic Diversity Set II and the Approved Oncology Set VI against NMNAT1. Twenty inhibitors with greater than 35% inhibition at 20 µM were identified. The follow-up studies showed that seven actives were time-dependent inhibitors of NMNAT1. 2,3-Dibromo-1,4-naphthoquinone was the most potent, time-dependent inhibitor with IC50 values of 0.76 and 0.26 µM for inhibition of the forward and reverse reactions of the enzyme, respectively, and was shown to be NMN and ATP competitive. The bioluminescent NMNAT assay and mechanistic-follow-up will be of use to identify new modulators of NAD biosynthesis.
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Affiliation(s)
- Brad A Haubrich
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, CA, USA.,Department of Chemistry, University of Nevada, Reno, Reno, NV, USA
| | - Chakk Ramesha
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, CA, USA
| | - David C Swinney
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, CA, USA.,DCSwinney Consulting, Belmont, CA, USA
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Hekmatnejad M, Conwell S, Lok SM, Kutach A, Shaw D, Fang E, Swinney DC. Insights into kinetic mechanism of Janus kinase 3 and its inhibition by tofacitinib. Arch Biochem Biophys 2016; 612:22-34. [PMID: 27555492 DOI: 10.1016/j.abb.2016.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 08/13/2016] [Accepted: 08/16/2016] [Indexed: 12/17/2022]
Abstract
JAK3 kinase plays a critical role in several cytokine signaling pathways involved in immune cell development and function. The studies presented in this report were undertaken to elucidate the kinetic mechanism of the JAK3 kinase domain, investigate the role of activation loop phosphorylation in regulating its catalytic activity, and examine its inhibition by the anti-rheumatoid arthritis drug, tofacitinib. Phosphorylation of two Tyr residues in JAK3's activation loop has been reported to impact its kinase activity. The recombinant JAK3 kinase domain used in our studies was heterogeneous in its activation loop phosphorylation, with the non-phosphorylated protein being the dominant species. Kinetic analysis revealed similar kinetic parameters for the heterogeneously phosphorylated JAK3, JAK3 mono-phosphorylated on Tyr 980, and the activation loop mutant YY980/981FF. Bisubstrate and product inhibition kinetic results were consistent with both sequential random and sequential ordered kinetic mechanisms. Solvent viscosometric experiments showed perturbation of kcat, suggesting the phosphoryl transfer step is not likely rate limiting. This was supported by results from quench-flow experiments, where a rapid burst of product formation was observed. Kinetic analysis of JAK3 inhibition by tofacitinib indicated inhibition is time dependent, characterized by on- and off-rate constants of 1.4 ± 0.1 μM-1s-1 and 0.0016 ± 0.0005 s-1, respectively.
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Affiliation(s)
- Mohammad Hekmatnejad
- Department of Biochemical Pharmacology, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, USA.
| | - Sara Conwell
- Department of Biochemical Pharmacology, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, USA.
| | - Stephen M Lok
- Department of Molecular and Protein Sciences, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, USA.
| | - Alan Kutach
- Department of Molecular and Protein Sciences, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, USA.
| | - David Shaw
- Department of Molecular and Protein Sciences, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, USA.
| | - Eric Fang
- Protein Sciences, Novartis Institutes for Biomedical Research, 4560 Horton St., Emeryville, CA 94608, USA.
| | - David C Swinney
- Department of Biochemical Pharmacology, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, USA.
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Haubrich BA, Swinney DC. Enzyme Activity Assays for Protein Kinases: Strategies to Identify Active Substrates. Curr Drug Discov Technol 2016; 13:2-15. [PMID: 26768716 DOI: 10.2174/1570163813666160115125930] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 11/22/2022]
Abstract
Protein kinases are an important class of enzymes and drug targets. New opportunities to discover medicines for neglected diseases can be leveraged by the extensive kinase tools and knowledge created in targeting human kinases. A valuable tool for kinase drug discovery is an enzyme assay that measures catalytic function. The functional assay can be used to identify inhibitors, estimate affinity, characterize molecular mechanisms of action (MMOAs) and evaluate selectivity. However, establishing an enzyme assay for a new kinases requires identification of a suitable substrate. Identification of a new kinase's endogenous physiologic substrate and function can be extremely costly and time consuming. Fortunately, most kinases are promiscuous and will catalyze the phosphotransfer from ATP to alternative substrates with differing degrees of catalytic efficiency. In this manuscript we review strategies and successes in the identification of alternative substrates for kinases from organisms responsible for many of the neglected tropical diseases (NTDs) towards the goal of informing strategies to identify substrates for new kinases. Approaches for establishing a functional kinase assay include measuring auto-activation and use of generic substrates and peptides. The most commonly used generic substrates are casein, myelin basic protein, and histone. Sequence homology modeling can provide insights into the potential substrates and the requirement for activation. Empirical approaches that can identify substrates include screening of lysates (which may also help identify native substrates) and use of peptide arrays. All of these approaches have been used with a varying degree of success to identify alternative substrates.
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Affiliation(s)
- Brad A Haubrich
- Institute for Rare and Neglected Diseases Drug Discovery, 897 Independence Ave, Suite 2C, Mountain View, CA 94043, USA.
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Swinney DC. Challenges and Hurdles to Business as Usual in Drug Development for Treatment of Rare Diseases. Clin Pharmacol Ther 2016; 100:339-41. [PMID: 27393380 DOI: 10.1002/cpt.422] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 06/24/2016] [Accepted: 06/30/2016] [Indexed: 11/06/2022]
Abstract
Only 10-15 first-in-class new medicines are approved each year by the global pharmaceutical industry for all diseases, of which less than a third is for rare (orphan) diseases. The drug discovery processes to identify rare and common diseases are similar, suggesting it will be impossible to discover new drugs for even a small fraction of the rare diseases using the current paradigm. Different approaches are required to address this large unmet medical need.
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Affiliation(s)
- D C Swinney
- Institute for Rare and Neglected Diseases Drug Diseases, Mountain View, California, USA.
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Guyett PJ, Xia S, Swinney DC, Pollastri MP, Mensa-Wilmot K. Glycogen Synthase Kinase 3β Promotes the Endocytosis of Transferrin in the African Trypanosome. ACS Infect Dis 2016; 2:518-28. [PMID: 27626104 DOI: 10.1021/acsinfecdis.6b00077] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Human parasite Trypanosoma brucei proliferates in the blood of its host, where it takes up iron via receptor-mediated endocytosis of transferrin (Tf). Mechanisms of Tf endocytosis in the trypanosome are not fully understood. Small molecule lapatinib inhibits Tf endocytosis in T. brucei and associates with protein kinase GSK3β (TbGSK3β). Therefore, we hypothesized that Tf endocytosis may be regulated by TbGSK3β, and we used three approaches (both genetic and small molecule) to test this possibility. First, the RNAi knock-down of TbGSK3β reduced Tf endocytosis selectively, without affecting the uptake of haptaglobin-hemoglobin (Hp-Hb) or bovine serum albumin (BSA). Second, the overexpression of TbGSK3β increased the Tf uptake. Third, small-molecule inhibitors of TbGSK3β, TWS119 (IC50 = 600 nM), and GW8510 (IC50 = 8 nM) reduced Tf endocytosis. Furthermore, TWS119, but not GW8510, selectively blocked Tf uptake. Thus, TWS119 phenocopies the selective endocytosis effects of a TbGSK3β knockdown. Two new inhibitors of TbGSK3β, LY2784544 (IC50 = 0.6 μM) and sorafenib (IC50 = 1.7 μM), were discovered in a focused screen: at low micromolar concentrations, they prevented Tf endocytosis as well as trypanosome proliferation (GI50's were 1.0 and 3.1 μM, respectively). These studies show that (a) TbGSK3β regulates Tf endocytosis, (b) TWS119 is a small-molecule tool for investigating the endocytosis of Tf,
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Affiliation(s)
- Paul J. Guyett
- Department
of Cellular Biology, The Center for Tropical and Emerging Global Diseases, University of Georgia, 724 Biological Sciences Building, Athens, Georgia 30605, United States
| | - Shuangluo Xia
- Institute for Rare and Neglected Disease Drug Discovery (IRND3), 897 Independence Avenue #2C, Mountain View, California 94043, United States
| | - David C. Swinney
- Institute for Rare and Neglected Disease Drug Discovery (IRND3), 897 Independence Avenue #2C, Mountain View, California 94043, United States
| | - Michael P. Pollastri
- Department
of Chemistry and Chemical Biology, Northeastern University, 417 Egan
Building, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Kojo Mensa-Wilmot
- Department
of Cellular Biology, The Center for Tropical and Emerging Global Diseases, University of Georgia, 724 Biological Sciences Building, Athens, Georgia 30605, United States
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Fletcher SP, Chin DJ, Gruenbaum L, Bitter H, Rasmussen E, Ravindran P, Swinney DC, Birzele F, Schmucki R, Lorenz SH, Kopetzki E, Carter J, Triyatni M, Thampi LM, Yang J, AlDeghaither D, Murreddu MG, Cote P, Menne S. Correction: Intrahepatic Transcriptional Signature Associated with Response to Interferon-α Treatment in the Woodchuck Model of Chronic Hepatitis B. PLoS Pathog 2016; 12:e1005541. [PMID: 27022978 PMCID: PMC4811617 DOI: 10.1371/journal.ppat.1005541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Vauquelin G, Van Liefde I, Swinney DC. On the different experimental manifestations of two-state 'induced-fit' binding of drugs to their cellular targets. Br J Pharmacol 2016; 173:1268-85. [PMID: 26808227 DOI: 10.1111/bph.13445] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 09/03/2015] [Accepted: 01/12/2016] [Indexed: 01/17/2023] Open
Abstract
'Induced-fit' binding of drugs to a target may lead to high affinity, selectivity and a long residence time, and this mechanism has been proposed to apply to many drugs with high clinical efficacy. It is a multistep process that initially involves the binding of a drug to its target to form a loose RL complex and a subsequent isomerization/conformational change to yield a tighter binding R'L state. Equations with the same mathematical form may also describe the binding of bivalent antibodies and related synthetic drugs. Based on a selected range of 'microscopic' rate constants and variables such as the ligand concentration and incubation time, we have simulated the experimental manifestations that may go along with induced-fit binding. Overall, they validate different experimental procedures that have been used over the years to identify such binding mechanisms. However, they also reveal that each of these manifestations only becomes perceptible at particular combinations of rate constants. The simulations also show that the durable nature of R'L and the propensity of R'L to be formed repeatedly before the ligand dissociates will increase the residence time. This review may help pharmacologists and medicinal chemists obtain preliminary indications for identifying an induced-fit mechanism.
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Affiliation(s)
- Georges Vauquelin
- Department of Molecular and Biochemical Pharmacology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Isabelle Van Liefde
- Department of Molecular and Biochemical Pharmacology, Vrije Universiteit Brussel, Brussels, Belgium
| | - David C Swinney
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, CA, USA
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Swinney ZT, Haubrich BA, Xia S, Ramesha C, Gomez SR, Guyett P, Mensa-Wilmot K, Swinney DC. A Four-Point Screening Method for Assessing Molecular Mechanism of Action (MMOA) Identifies Tideglusib as a Time-Dependent Inhibitor of Trypanosoma brucei GSK3β. PLoS Negl Trop Dis 2016; 10:e0004506. [PMID: 26942720 PMCID: PMC4778863 DOI: 10.1371/journal.pntd.0004506] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 02/10/2016] [Indexed: 01/01/2023] Open
Abstract
Background New therapeutics are needed for neglected tropical diseases including Human African trypanosomiasis (HAT), a progressive and fatal disease caused by the protozoan parasites Trypanosoma brucei gambiense and T. b. rhodesiense. There is a need for simple, efficient, cost effective methods to identify new molecules with unique molecular mechanisms of action (MMOAs). The mechanistic features of a binding mode, such as competition with endogenous substrates and time-dependence can affect the observed inhibitory IC50, and differentiate molecules and their therapeutic usefulness. Simple screening methods to determine time-dependence and competition can be used to differentiate compounds with different MMOAs in order to identify new therapeutic opportunities. Methodology/Principal Findings In this work we report a four point screening methodology to evaluate the time-dependence and competition for inhibition of GSK3β protein kinase isolated from T. brucei. Using this method, we identified tideglusib as a time-dependent inhibitor whose mechanism of action is time-dependent, ATP competitive upon initial binding, which transitions to ATP non-competitive with time. The enzyme activity was not recovered following 100-fold dilution of the buffer consistent with an irreversible mechanism of action. This is in contrast to the T. brucei GSK3β inhibitor GW8510, whose inhibition was competitive with ATP, not time-dependent at all measured time points and reversible in dilution experiments. The activity of tideglusib against T. brucei parasites was confirmed by inhibition of parasite proliferation (GI50 of 2.3 μM). Conclusions/Significance Altogether this work demonstrates a straightforward method for determining molecular mechanisms of action and its application for mechanistic differentiation of two potent TbGSK3β inhibitors. The four point MMOA method identified tideglusib as a mechanistically differentiated TbGSK3β inhibitor. Tideglusib was shown to inhibit parasite growth in this work, and has been reported to be well tolerated in one year of dosing in human clinical studies. Consequently, further supportive studies on the potential therapeutic usefulness of tideglusib for HAT are justified. Drug discovery for neglected tropical diseases must use efficient methods due to limited resources. One preferred drug discovery strategy is target-based drug discovery. In this strategy it is assumed that drug action begins with binding of a drug to its target. However, while binding is required, it is not sufficient to describe all the molecular interactions that translate binding to a therapeutically useful response. The contribution of aspects of the molecular mechanism of action (MMOA) such as time-dependence and substrate competition can influence concentration response relationships. To address this, a four point MMOA methodology was developed to evaluate time-dependence and substrate competition. We used this method to evaluate the MMOA for T.brucei GSK3β inhibitors, and observed tideglusib to have a time-dependent, ATP-competitive mechanism that differentiated it from rapidly reversible inhibitors, such as GW8510. Adjusting the enzyme assays to account for these mechanisms showed that GW8510 and tideglusib had similar activities for TbGSK3β. However, this similarity did not translate to cellular activity, where GW-8510 was more active than tideglusib (0.12 μM to 2.3 μM, respectively). These data suggest that factors other than TbGSK3β MMOA differentiate the effect of these molecules against T. brucei.
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Affiliation(s)
- Zachary T. Swinney
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, California, United States of America
| | - Brad A. Haubrich
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, California, United States of America
| | - Shuangluo Xia
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, California, United States of America
| | - Chakk Ramesha
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, California, United States of America
| | - Stephen R. Gomez
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, California, United States of America
| | - Paul Guyett
- Department of Cellular Biology and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
| | - Kojo Mensa-Wilmot
- Department of Cellular Biology and Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, United States of America
| | - David C. Swinney
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, California, United States of America
- * E-mail:
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Vauquelin G, Van Liefde I, Swinney DC. Radioligand binding to intact cells as a tool for extended drug screening in a representative physiological context. Drug Discov Today Technol 2015; 17:28-34. [PMID: 26724334 DOI: 10.1016/j.ddtec.2015.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 09/04/2015] [Accepted: 09/09/2015] [Indexed: 06/05/2023]
Abstract
Radioligand binding assays on intact cells offer distinct advantages to those on membrane suspensions. Major pharmacological properties like drug affinity and binding kinetics are more physiologically relevant. Complex mechanisms can be studied with a wider choice of experimental approaches and so provide insights into induced-fit type binding, receptor internalisation and even into pharmacomicrokinetic phenomena like drug rebinding and partitioning into the membrane. Hence, intact cell binding constitutes a valuable addition to the pharmacologist's toolbox.
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Affiliation(s)
- Georges Vauquelin
- Dept. of Molecular and Biochemical Pharmacology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
| | - Isabelle Van Liefde
- Dept. of Molecular and Biochemical Pharmacology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - David C Swinney
- Institute for Rare and Neglected Diseases Drug Discovery, 897 Independence Ave, Suite 2C, Mountain View, CA 94043, United States
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Fletcher SP, Chin DJ, Gruenbaum L, Bitter H, Rasmussen E, Ravindran P, Swinney DC, Birzele F, Schmucki R, Lorenz SH, Kopetzki E, Carter J, Triyatni M, Thampi LM, Yang J, AlDeghaither D, Murredu MG, Cote P, Menne S. Intrahepatic Transcriptional Signature Associated with Response to Interferon-α Treatment in the Woodchuck Model of Chronic Hepatitis B. PLoS Pathog 2015; 11:e1005103. [PMID: 26352406 PMCID: PMC4564242 DOI: 10.1371/journal.ppat.1005103] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/21/2015] [Indexed: 02/06/2023] Open
Abstract
Recombinant interferon-alpha (IFN-α) is an approved therapy for chronic hepatitis B (CHB), but the molecular basis of treatment response remains to be determined. The woodchuck model of chronic hepatitis B virus (HBV) infection displays many characteristics of human disease and has been extensively used to evaluate antiviral therapeutics. In this study, woodchucks with chronic woodchuck hepatitis virus (WHV) infection were treated with recombinant woodchuck IFN-α (wIFN-α) or placebo (n = 12/group) for 15 weeks. Treatment with wIFN-α strongly reduced viral markers in the serum and liver in a subset of animals, with viral rebound typically being observed following cessation of treatment. To define the intrahepatic cellular and molecular characteristics of the antiviral response to wIFN-α, we characterized the transcriptional profiles of liver biopsies taken from animals (n = 8-12/group) at various times during the study. Unexpectedly, this revealed that the antiviral response to treatment did not correlate with intrahepatic induction of the majority of IFN-stimulated genes (ISGs) by wIFN-α. Instead, treatment response was associated with the induction of an NK/T cell signature in the liver, as well as an intrahepatic IFN-γ transcriptional response and elevation of liver injury biomarkers. Collectively, these data suggest that NK/T cell cytolytic and non-cytolytic mechanisms mediate the antiviral response to wIFN-α treatment. In summary, by studying recombinant IFN-α in a fully immunocompetent animal model of CHB, we determined that the immunomodulatory effects, but not the direct antiviral activity, of this pleiotropic cytokine are most closely correlated with treatment response. This has important implications for the rational design of new therapeutics for the treatment of CHB.
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MESH Headings
- Animals
- Antiviral Agents/administration & dosage
- Antiviral Agents/adverse effects
- Antiviral Agents/metabolism
- Antiviral Agents/therapeutic use
- Biomarkers/blood
- Biomarkers/metabolism
- Biopsy
- Dose-Response Relationship, Drug
- Gene Expression Profiling
- Hepatitis B Virus, Woodchuck/drug effects
- Hepatitis B Virus, Woodchuck/immunology
- Hepatitis B, Chronic/drug therapy
- Hepatitis B, Chronic/metabolism
- Hepatitis B, Chronic/veterinary
- Hepatitis B, Chronic/virology
- Immunity, Cellular/drug effects
- Immunologic Factors/administration & dosage
- Immunologic Factors/genetics
- Immunologic Factors/metabolism
- Immunologic Factors/therapeutic use
- Interferon-alpha/administration & dosage
- Interferon-alpha/genetics
- Interferon-alpha/metabolism
- Interferon-alpha/therapeutic use
- Killer Cells, Natural/drug effects
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Killer Cells, Natural/pathology
- Liver/immunology
- Liver/metabolism
- Liver/pathology
- Liver/virology
- Male
- Marmota
- Recombinant Proteins/administration & dosage
- Recombinant Proteins/adverse effects
- Recombinant Proteins/metabolism
- Recombinant Proteins/therapeutic use
- T-Lymphocytes/drug effects
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- T-Lymphocytes/pathology
- Transcription, Genetic
- Viral Load/drug effects
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Affiliation(s)
- Simon P. Fletcher
- Pharma Research & Early Development, Hoffmann-La Roche, Inc., Nutley, New Jersey, United States of America
| | - Daniel J. Chin
- Pharma Research & Early Development, Hoffmann-La Roche, Inc., Nutley, New Jersey, United States of America
| | - Lore Gruenbaum
- Pharma Research & Early Development, Hoffmann-La Roche, Inc., Nutley, New Jersey, United States of America
| | - Hans Bitter
- Pharma Research & Early Development, Hoffmann-La Roche, Inc., Nutley, New Jersey, United States of America
| | - Erik Rasmussen
- Pharma Research & Early Development, Hoffmann-La Roche, Inc., Nutley, New Jersey, United States of America
| | - Palanikumar Ravindran
- Pharma Research & Early Development, Hoffmann-La Roche, Inc., Nutley, New Jersey, United States of America
| | - David C. Swinney
- Pharma Research & Early Development, Hoffmann-La Roche, Inc., Nutley, New Jersey, United States of America
| | - Fabian Birzele
- Roche Pharma Research & Early Development, Roche Innovation Center Penzberg, Penzberg, Germany
| | - Roland Schmucki
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Stefan H. Lorenz
- Roche Pharma Research & Early Development, Roche Innovation Center Penzberg, Penzberg, Germany
| | - Erhard Kopetzki
- Roche Pharma Research & Early Development, Roche Innovation Center Penzberg, Penzberg, Germany
| | - Jade Carter
- Pharma Research & Early Development, Hoffmann-La Roche, Inc., Nutley, New Jersey, United States of America
| | - Miriam Triyatni
- Roche Pharma Research & Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Linta M. Thampi
- Department of Microbiology & Immunology, Georgetown University Medical Center, Washington, District of Columbia, United States of America
| | - Junming Yang
- Department of Microbiology & Immunology, Georgetown University Medical Center, Washington, District of Columbia, United States of America
| | - Dalal AlDeghaither
- Department of Microbiology & Immunology, Georgetown University Medical Center, Washington, District of Columbia, United States of America
| | - Marta G. Murredu
- Department of Microbiology & Immunology, Georgetown University Medical Center, Washington, District of Columbia, United States of America
| | - Paul Cote
- Department of Microbiology & Immunology, Georgetown University Medical Center, Washington, District of Columbia, United States of America
| | - Stephan Menne
- Department of Microbiology & Immunology, Georgetown University Medical Center, Washington, District of Columbia, United States of America
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Vauquelin G, Huber W, Swinney DC. Experimental Methods to Determine Binding Kinetics. Thermodynamics and Kinetics of Drug Binding 2015. [DOI: 10.1002/9783527673025.ch9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Swinney DC, Beavis P, Chuang KT, Zheng Y, Lee I, Gee P, Deval J, Rotstein DM, Dioszegi M, Ravendran P, Zhang J, Sankuratri S, Kondru R, Vauquelin G. A study of the molecular mechanism of binding kinetics and long residence times of human CCR5 receptor small molecule allosteric ligands. Br J Pharmacol 2015; 171:3364-75. [PMID: 24628038 DOI: 10.1111/bph.12683] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 02/04/2014] [Accepted: 02/26/2014] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND AND PURPOSE The human CCR5 receptor is a co-receptor for HIV-1 infection and a target for anti-viral therapy. A greater understanding of the binding kinetics of small molecule allosteric ligand interactions with CCR5 will lead to a better understanding of the binding process and may help discover new molecules that avoid resistance. EXPERIMENTAL APPROACH Using [(3) H] maraviroc as a radioligand, a number of different binding protocols were employed in conjunction with simulations to determine rate constants, kinetic mechanism and mutant kinetic fingerprints for wild-type and mutant human CCR5 with maraviroc, aplaviroc and vicriviroc. KEY RESULTS Kinetic characterization of maraviroc binding to the wild-type CCR5 was consistent with a two-step kinetic mechanism that involved an initial receptor-ligand complex (RA), which transitioned to a more stable complex, R'A, with at least a 13-fold increase in affinity. The dissociation rate from R'A, k-2 , was 1.2 × 10(-3) min(-1) . The maraviroc time-dependent transition was influenced by F85L, W86A, Y108A, I198A and Y251A mutations of CCR5. CONCLUSIONS AND IMPLICATIONS The interaction between maraviroc and CCR5 proceeded according to a multi-step kinetic mechanism, whereby initial mass action binding and later reorganizations of the initial maraviroc-receptor complex lead to a complex with longer residence time. Site-directed mutagenesis identified a kinetic fingerprint of residues that affected the binding kinetics, leading to the conclusion that allosteric ligand binding to CCR5 involved the rearrangement of the binding site in a manner specific to each allosteric ligand.
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Affiliation(s)
- David C Swinney
- Roche Palo Alto, Palo Alto, CA, USA; Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, CA, USA
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15
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Selen A, Dickinson PA, Müllertz A, Crison JR, Mistry HB, Cruañes MT, Martinez MN, Lennernäs H, Wigal TL, Swinney DC, Polli JE, Serajuddin AT, Cook JA, Dressman JB. The Biopharmaceutics Risk Assessment Roadmap for Optimizing Clinical Drug Product Performance. J Pharm Sci 2014; 103:3377-3397. [DOI: 10.1002/jps.24162] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 08/20/2014] [Accepted: 08/22/2014] [Indexed: 02/06/2023]
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Abstract
Rare disease research has reached a tipping point, with the confluence of scientific and technologic developments that if appropriately harnessed, could lead to key breakthroughs and treatments for this set of devastating disorders. Industry-wide trends have revealed that the traditional drug discovery research and development (R&D) model is no longer viable, and drug companies are evolving their approach. Rather than only pursue blockbuster therapeutics for heterogeneous, common diseases, drug companies have increasingly begun to shift their focus to rare diseases. In academia, advances in genetics analyses and disease mechanisms have allowed scientific understanding to mature, but the lack of funding and translational capability severely limits the rare disease research that leads to clinical trials. Simultaneously, there is a movement towards increased research collaboration, more data sharing, and heightened engagement and active involvement by patients, advocates, and foundations. The growth in networks and social networking tools presents an opportunity to help reach other patients but also find researchers and build collaborations. The growth of collaborative software that can enable researchers to share their data could also enable rare disease patients and foundations to manage their portfolio of funded projects for developing new therapeutics and suggest drug repurposing opportunities. Still there are many thousands of diseases without treatments and with only fragmented research efforts. We will describe some recent progress in several rare diseases used as examples and propose how collaborations could be facilitated. We propose that the development of a center of excellence that integrates and shares informatics resources for rare diseases sponsored by all of the stakeholders would help foster these initiatives.
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Affiliation(s)
| | - Michele Rhee
- National Brain Tumor Society, Newton, MA, 02458, USA
| | - David C Swinney
- Institute for Rare and Neglected Diseases Drug Discovery (iRND3), Mountain View, CA, 94043, USA
| | - Sean Ekins
- Collaborative Drug Discovery, Inc., Burlingame, CA, 94010, USA ; Collaborations in Chemistry, Fuquay Varina, NC, 27526, USA ; Phoenix Nest Inc., Brooklyn, NY, 11215, USA ; Hereditary Neuropathy Foundation, New York, NY, 10016, USA ; Hannah's Hope Fund, Rexford, NY, NY 12148, USA
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17
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Abstract
Phenotypic assays are tools essential for drug discovery. Phenotypic assays have different types of endpoints depending on the goals; (1) empirical endpoints for basic research to understand the underlying biology that will lead to identification of translation biomarkers, (2) empirical endpoints to identify undesired effects related to toxicity of drug candidates, and (3) knowledge-based endpoints (biomarkers) for drug discovery which ideally are translational biomarkers that will be used to identify new drug candidates and their corresponding molecular mechanisms of action. The value of phenotypic assays is increased through effective alignment of phenotypic assay endpoints with the objectives of the relevant stage in the drug discovery and development cycle.
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Affiliation(s)
- David C. Swinney
- Institute for Rare and Neglected Diseases Drug Discovery, Mountain ViewCA, USA
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18
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Abstract
The level of mechanistic understanding required for drug discovery is a central feature of most strategies. However, an understanding of mechanism is not required for regulatory approval. This paradox is particularly relevant to the role of phenotypic assays in drug discovery. A recent analysis revealed that phenotypic drug discovery strategies were more successful for first-in-class medicines, whereas target-based molecular strategies were more successful for followers (Nat. Rev. Drug Discov. 2011, 10, 507-519). The rationale for the success of phenotypic screening was the unbiased identification of the molecular mechanism of action. In this follow-up analysis, the format and mechanistic information used to establish the phenotypic assays that led to the first-in-class small-molecule new molecular entities approved by the U.S. Food and Drug Administration between 1999 and 2008 were analyzed and compared with those approved in 2012. Not surprisingly, some level of mechanistic understanding was used to select the assay formats and chemicals screened. It is concluded that mechanism takes on different connotations depending on context and perspective and that a target need not always be the exclusive definition of mechanism.
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Affiliation(s)
- David C Swinney
- 1Institute for Rare and Neglected Diseases Drug Discovery, Mountain View, CA, USA
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Kim S, Ishida H, Yamane D, Yi M, Swinney DC, Foung S, Lemon SM. Contrasting roles of mitogen-activated protein kinases in cellular entry and replication of hepatitis C virus: MKNK1 facilitates cell entry. J Virol 2013; 87:4214-24. [PMID: 23365451 PMCID: PMC3624358 DOI: 10.1128/jvi.00954-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 01/24/2013] [Indexed: 12/12/2022] Open
Abstract
The human kinome comprises over 800 individual kinases. These contribute in multiple ways to regulation of cellular metabolism and may have direct and indirect effects on virus replication. Kinases are tempting therapeutic targets for drug development, but achieving sufficient specificity is often a challenge for chemical inhibitors. While using inhibitors to assess whether c-Jun N-terminal (JNK) kinases regulate hepatitis C virus (HCV) replication, we encountered unexpected off-target effects that led us to discover a role for a mitogen-activated protein kinase (MAPK)-related kinase, MAPK interacting serine/threonine kinase 1 (MKNK1), in viral entry. Two JNK inhibitors, AS601245 and SP600125, as well as RNA interference (RNAi)-mediated knockdown of JNK1 and JNK2, enhanced replication of HCV replicon RNAs as well as infectious genome-length RNA transfected into Huh-7 cells. JNK knockdown also enhanced replication following infection with cell-free virus, suggesting that JNK actively restricts HCV replication. Despite this, AS601245 and SP600125 both inhibited viral entry. Screening of a panel of inhibitors targeting kinases that may be modulated by off-target effects of AS601245 and SP600125 led us to identify MKNK1 as a host factor involved in HCV entry. Chemical inhibition or siRNA knockdown of MKNK1 significantly impaired entry of genotype 1a HCV and HCV-pseudotyped lentiviral particles (HCVpp) in Huh-7 cells but had only minimal impact on viral RNA replication or cell proliferation and viability. We propose a model by which MKNK1 acts to facilitate viral entry downstream of the epidermal growth factor receptor (EGFR) and extracellular signal-regulated kinase (ERK), both of which have been implicated in the entry process.
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Affiliation(s)
- Seungtaek Kim
- Division of Infectious Diseases, Department of Medicine, and the Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Hisashi Ishida
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Daisuke Yamane
- Division of Infectious Diseases, Department of Medicine, and the Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - MinKyung Yi
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - David C. Swinney
- Biochemical Pharmacology, Virology DBA, Roche Palo Alto, Palo Alto, California, USA
| | - Steven Foung
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Stanley M. Lemon
- Division of Infectious Diseases, Department of Medicine, and the Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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20
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Fletcher SP, Chin DJ, Ji Y, Iniguez AL, Taillon B, Swinney DC, Ravindran P, Cheng DT, Bitter H, Lopatin U, Ma H, Klumpp K, Menne S. Transcriptomic analysis of the woodchuck model of chronic hepatitis B. Hepatology 2012; 56:820-30. [PMID: 22431061 PMCID: PMC3401284 DOI: 10.1002/hep.25730] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 03/06/2012] [Indexed: 01/03/2023]
Abstract
UNLABELLED The Eastern woodchuck (Marmota monax) is naturally infected with woodchuck hepatitis virus (WHV), a hepadnavirus closely related to the human hepatitis B virus (HBV). The woodchuck is used as an animal model for studying chronic hepatitis B (CHB) and HBV-associated hepatocellular carcinoma (HCC) in humans, but the lack of sequence information has hitherto precluded functional genomics analysis. To address this major limitation of the model, we report here the sequencing, assembly, and annotation of the woodchuck transcriptome, together with the generation of custom woodchuck microarrays. Using this new platform, we characterized the transcriptional response to persistent WHV infection and WHV-induced HCC. This revealed that chronic WHV infection, like HBV, is associated with (1) a limited intrahepatic type I interferon response; (2) intrahepatic induction of markers associated with T cell exhaustion; (3) elevated levels of suppressor of cytokine signaling 3 (SOCS3) in the liver; and (4) intrahepatic accumulation of neutrophils. Underscoring the translational value of the woodchuck model, this study also determined that WHV-induced HCC shares molecular characteristics with a subtype of human HCC with poor prognosis. CONCLUSION Our data establish the translational value of the woodchuck model and provide new insight into immune pathways which may play a role either in the persistence of HBV infection or the sequelae of CHB.
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Affiliation(s)
- Simon P. Fletcher
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | - Daniel J. Chin
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | - Yongmei Ji
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | | | - Bruce Taillon
- 454 Life Sciences, A Roche Company, 1 Commercial Street, Branford, CT 06457, USA
| | - David C. Swinney
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | | | - Donavan T. Cheng
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | - Hans Bitter
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | - Uri Lopatin
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | - Han Ma
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | - Klaus Klumpp
- Hoffmann-La Roche, Inc., 340 Kingsland Street, Nutley, NJ 07006, USA
| | - Stephan Menne
- Georgetown University Medical Center, Department of Microbiology & Immunology, Medical-Dental Building, Room C 301, 3900 Reservoir Road, Washington, DC 20057, USA
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21
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Soth M, Abbot S, Abubakari A, Arora N, Arzeno H, Billedeau R, Dewdney N, Durkin K, Frauchiger S, Ghate M, Goldstein DM, Hill RJ, Kuglstatter A, Li F, Loe B, McCaleb K, McIntosh J, Papp E, Park J, Stahl M, Sung ML, Suttman R, Swinney DC, Weller P, Wong B, Zecic H, Gabriel T. 3-Amino-pyrazolo[3,4-d]pyrimidines as p38α kinase inhibitors: design and development to a highly selective lead. Bioorg Med Chem Lett 2011; 21:3452-6. [PMID: 21515047 DOI: 10.1016/j.bmcl.2011.03.098] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 03/23/2011] [Accepted: 03/24/2011] [Indexed: 11/26/2022]
Abstract
Learnings from previous Roche p38-selective inhibitors were applied to a new fragment hit, which was optimized to a potent, exquisitely selective preclinical lead with a good pharmacokinetic profile.
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Affiliation(s)
- Michael Soth
- Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, CA 94304, USA.
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22
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23
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Jin Z, Deval J, Johnson KA, Swinney DC. Characterization of the elongation complex of dengue virus RNA polymerase: assembly, kinetics of nucleotide incorporation, and fidelity. J Biol Chem 2010; 286:2067-77. [PMID: 21078673 PMCID: PMC3023504 DOI: 10.1074/jbc.m110.162685] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dengue virus (DENV) infects 50–100 million people worldwide per year, causing severe public health problems. DENV RNA-dependent RNA polymerase, an attractive target for drug development, catalyzes de novo replication of the viral genome in three phases: initiation, transition, and elongation. The aim of this work was to characterize the mechanism of nucleotide addition catalyzed by the polymerase domain of DENV serotype 2 during elongation using transient kinetic methods. We measured the kinetics of formation of the elongation complex containing the polymerase and a double-stranded RNA by preincubation experiments. The elongation complex assembly is slow, following a one-step binding mechanism with an association rate of 0.0016 ± 0.0001 μm−1s−1 and a dissociation rate of 0.00020 ± 0.00005 s−1 at 37 °C. The elongation complex assembly is 6 times slower at 30 °C and requires Mg2+ during preincubation. The assembled elongation complex incorporates a correct nucleotide, GTP, to the primer with a Kd of 275 ± 52 μm and kpol of 18 ± 1 s−1. The fidelity of the polymerase is 1/34,000, 1/59,000, 1/135,000 for misincorporation of UTP, ATP, and CTP opposite CMP in the template, respectively. The fidelity of DENV polymerase is comparable with HIV reverse transcriptase and the poliovirus polymerase. This work reports the first description of presteady-state kinetics and fidelity for an RNA-dependent RNA polymerase from the Flaviviridae family.
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Affiliation(s)
- Zhinan Jin
- Virology DTA, Roche Palo Alto LLC, Palo Alto, California 94034, USA
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24
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Latour DR, Jekle A, Javanbakht H, Henningsen R, Gee P, Lee I, Tran P, Ren S, Kutach AK, Harris SF, Wang SM, Lok SJ, Shaw D, Li J, Heilek G, Klumpp K, Swinney DC, Deval J. Biochemical characterization of the inhibition of the dengue virus RNA polymerase by beta-d-2'-ethynyl-7-deaza-adenosine triphosphate. Antiviral Res 2010; 87:213-22. [PMID: 20470829 DOI: 10.1016/j.antiviral.2010.05.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 04/30/2010] [Accepted: 05/05/2010] [Indexed: 11/17/2022]
Abstract
Dengue virus (DENV), an emerging pathogen from the Flaviviridae family with neither vaccine nor antiviral treatment available, causes a serious worldwide public health threat. In theory, there are several ways by which small molecules could inhibit the replication cycle of DENV. Here, we show that the nucleoside analogue beta-d-2'-ethynyl-7-deaza-adenosine inhibits representative strains of all four serotypes of DENV with an EC(50) around or below 1microM. Using membrane-associated native replicase complex as well as recombinant RNA polymerase from each DENV serotype in enzymatic assays, we provide evidence that beta-d-2'-ethynyl-7-deaza-adenosine triphosphate (2'E-7D-ATP) targets viral replication at the polymerase active site by competing with the natural nucleotide substrate with an apparent K(i) of 0.060+/-0.016microM. In single-nucleotide incorporation experiments, the catalytic efficiency of 2'E-7D-ATP is 10-fold lower than for natural ATP, and the incorporated nucleotide analogue causes immediate chain termination. A combination of bioinformatics and site-directed mutagenesis demonstrates that 2'E-7D-ATP is equipotent across all serotypes because the nucleotide binding site residues are conserved in dengue virus. Overall, beta-d-2'-ethynyl-7-deaza-adenosine provides a promising scaffold for the development of inhibitors of dengue virus polymerase.
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Affiliation(s)
- Derek R Latour
- Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, CA, United States
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25
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Hekmat-Nejad M, Cai T, Swinney DC. Steady-state kinetic characterization of kinase activity and requirements for Mg2+ of interleukin-1 receptor-associated kinase-4. Biochemistry 2010; 49:1495-506. [PMID: 20104875 DOI: 10.1021/bi901609m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Interleukin-1 receptor-associated kinase-4 (IRAK-4) is a Ser/Thr-specific protein kinase that plays a critical role in intracellular signaling cascades mediated by Toll-like and interleukin-1 (IL-1) receptors. Despite a growing body of information on the physiological functions of IRAK-4, its kinase activity remains poorly studied. The present study entails characterization of the steady-state kinetic properties and Mg(2+) requirements of full-length, recombinant human IRAK-4 preactivated by incubation with MgATP. In the presence of 20 mM Mg(2+), activated IRAK-4 herein is demonstrated to phosphorylate a peptide substrate (IRAK-1 peptide), derived from the activation loop of IRAK-1, with a k(cat) of 30 +/- 2.9 s(-1) and K(m) values of 668 +/- 120 and 852 +/- 273 microM for ATP and the peptide, respectively. Two-substrate, dead-end and product inhibition data, using analogues of ATP, are consistent with both a sequential ordered kinetic mechanism with ATP binding to the enzyme prior to the peptide and a sequential random mechanism. Investigation of the Mg(2+) requirements for phosphoryl transfer activity of IRAK-4 revealed that more than one Mg(2+) ion interacts with the enzyme and that the enzyme is maximally active in the presence of 5-10 mM free Mg(2+). While one divalent metal, as part of a chelate complex with ATP, is essential for catalysis, kinetic evidence is provided to show that uncomplexed Mg(2+) further enhances the catalytic activity of IRAK-4 by bringing about an approximately 3-fold increase in k(cat) and an approximately 6-fold reduction in the K(m) for ATP and by rendering the interaction between the nucleotide and peptide substrate binding sites less antagonistic.
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Affiliation(s)
- Mohammad Hekmat-Nejad
- Department of Virology, Roche Palo Alto, LLC, 3431 Hillview Avenue, Palo Alto, California 94304, USA.
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26
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Swinney DC, Anthony J. Mechanisms of Successful Drug Action. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.527.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Jin Z, Deval J, Johnson KA, Swinney DC. Transient kinetic analysis of the elongation mode of Dengue Virus RNA polymerase domain. FASEB J 2010. [DOI: 10.1096/fasebj.24.1_supplement.lb75] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Zhinan Jin
- Virology Biology AreaRoche Palo Alto LLCPalo AltoCA
| | - Jerome Deval
- Virology Biology AreaRoche Palo Alto LLCPalo AltoCA
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28
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Swinney DC. The role of binding kinetics in therapeutically useful drug action. Curr Opin Drug Discov Devel 2009; 12:31-39. [PMID: 19152211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Binding kinetics help define how a medicine will communicate with physiology to produce a desired therapeutic response. Clinical efficacy, duration of action, clinical differentiation and safety may all be influenced by binding kinetics. The optimization of binding kinetics can be used to maximize a drug's therapeutic index and thereby decrease drug attrition. The gap between basic scientific principles and the potential medical value of a drug is currently bridged by the use of empirical assays. The value of binding kinetics to drug discovery will be increased through an improved ability to identify optimal kinetic mechanisms and define kinetic structure activity relationships.
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29
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Gee P, Chua PK, Gevorkyan J, Klumpp K, Najera I, Swinney DC, Deval J. Essential role of the N-terminal domain in the regulation of RIG-I ATPase activity. J Biol Chem 2008; 283:9488-96. [PMID: 18268020 DOI: 10.1074/jbc.m706777200] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Retinoic acid-inducible gene I (RIG-I) is a cytosolic receptor that recognizes viral RNA and activates the interferon-mediated innate antiviral response. To understand the mechanism of signal activation at the receptor level, we cloned, expressed, and purified human RIG-I containing the two caspase activation and recruitment domains (CARDs) followed by the C-terminal helicase domain. We found that recombinant RIG-I is a functional protein that interacts with double-stranded RNA with substantially higher affinity as compared with single-stranded RNA structures unless they contain a 5'-triphosphate group. Viral RNA binding to RIG-I stimulates the velocity of ATP hydrolysis by 33-fold, which at the cellular level translates into a 43-fold increase of interferon-beta expression. In contrast, the isolated ATPase/helicase domain is constitutively activated while also retaining its RNA ligand binding properties. These results support the recent model by which RIG-I signaling is autoinhibited in the absence of RNA by intra-molecular interactions between the CARDs and the C terminus. Based on pH profile and metal ion dependence experiments, we propose that the active site of RIG-I cannot efficiently accommodate divalent cations under the RNA-free repressed conformation. Overall, these results show a direct correlation between RNA binding and ATPase enzymatic function leading to signal transduction and suggest that a tight control of ATPase activity by the CARDs prevents RIG-I signaling in the absence of viral RNA.
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Affiliation(s)
- Peter Gee
- Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, CA 94304, USA
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30
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Papp E, Tse JKY, Ho H, Wang S, Shaw D, Lee S, Barnett J, Swinney DC, Bradshaw JM. Steady state kinetics of spleen tyrosine kinase investigated by a real time fluorescence assay. Biochemistry 2007; 46:15103-14. [PMID: 18052078 DOI: 10.1021/bi701596u] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spleen tyrosine kinase (Syk) is a cytoplasmic tyrosine kinase that plays an important signaling role in several types of immune cells. To improve our understanding of the enzymology and activation mechanism of Syk, we characterized the steady state kinetics of Syk substrate phosphorylation. A new real time fluorescence kinase assay was employed that utilizes a nonnatural amino acid in the peptide substrate which undergoes an enhancement in fluorescence following phosphorylation. Characterizing the steady state kinetics using a Syk kinase domain construct [Syk(360-635)] revealed that Syk employs a ternary complex kinetic mechanism involving little cooperativity between substrate binding sites and a Km(ATP) of 36 +/- 5 microM and a Km(peptide substrate) of 4.4 +/- 0.9 microM. The order of substrate binding was determined to be either random or ordered with ATP binding first, as determined in substrate analogue inhibitor studies. Utilizing the real time capabilities of the fluorescence assay, we established that Syk demonstrates no lag phase in product formation. Furthermore, a Syk mutant lacking tyrosine in the activation loop (Syk Y525F,Y526F) exhibited activity identical to that of wild-type Syk. These two findings indicate that autophosphorylation of the activation loop of Syk does not regulate Syk(360-635) activity. We also compared the activity of Syk(360-635) to that of full-length Syk and revealed that Syk(360-635) is 10-fold more active, suggesting that residues outside the catalytic domain of Syk suppress kinase activity. The findings presented here provide the first kinetic description of the Syk enzyme mechanism.
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Affiliation(s)
- Eva Papp
- Department of Biochemical Pharmacology, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304, USA
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Abstract
Little is known about the kinetic mechanism of E3 ubiquitin ligases. This work describes basic methodology to investigate the kinetic mechanism of E3 ubiquitin ligases. The method used steady state, bi-substrate kinetic analysis of an E3 ligase-catalyzed monoubiquitylation reaction using ubiquitin-conjugated E2 (E2ub) and a mutant IkappaBalpha as substrates to evaluate whether the E3-catalyzed ubiquitin transfer from E2ub to protein substrate was sequential, meaning both substrates bound before products leaving, or ping pong, meaning that ubiquitin-conjugated E2 would bind, transfer ubiquitin to the E3, and debind before binding of protein substrate. The method requires the E3 reaction to be rate limiting and at steady state. This was accomplished through optimization of the conditions to ensure that the E3-dependent transfer of ubiquitin from E2ub to substrate was rate limiting. We observed a sequential bi-substrate E3-dependent ubiquitylation reaction on using E2UBCH7 and IkappaBalphaSS32/36EE (IkappaBalphaee as substrates and a partially purified Jurkat cell lysate as a source for the E3 ligase activity). The sequential bi-substrate kinetic mechanism is consistent with the formation of a ternary complex among E2UBCH7, IkappaBalphaSS32/36EE, and E3 before the transfer of ubiquitin from E2UBCH7 to IkappaBalphaSS32/36EE. The described method should be of use to characterize the kinetic mechanism of other E3 ligase-catalyzed ubiquitylation reactions.
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Affiliation(s)
- David C Swinney
- Biochemical Pharmacology, Roche Bioscience, Palo Alto, California, USA
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Niu L, Chang KC, Wilson S, Tran P, Zuo F, Swinney DC. Kinetic Characterization of Human JNK2α2 Reaction Mechanism Using Substrate Competitive Inhibitors. Biochemistry 2007; 46:4775-84. [PMID: 17397142 DOI: 10.1021/bi602423e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Jun N-terminal kinase (JNK) is a stress activated serine/threonine protein kinase that phosphorylates numerous cellular protein substrates including the transcription factors c-Jun and ATF2. In this study, we defined the kinetic mechanism for the active form of JNK2alpha2. Double reciprocal plots of initial rates versus concentrations of substrate revealed the sequential nature of the JNK2alpha2 catalyzed ATF2 phosphorylation. Dead-end JNK inhibitors were then used to differentiate ordered and random kinetic mechanisms for the reaction. A peptide inhibitor containing the homology JNK docking sequence for substrate recognition, derived from amino acid residues 153-163 of JNK-interacting protein 1 (JIP-1), inhibited JNK activity via competition with ATF2. This peptide functioned as a noncompetitive inhibitor against ATP. In contrast, the anthrapyrazolone compound, SP600125, exhibited competitive inhibition for ATP and noncompetitive inhibition against ATF2. Furthermore, binding of one substrate had no significant effect on the affinity for the other substrate. The data in this study are consistent with a kinetic mechanism for activated JNK2alpha2 in which (1) substrate binding is primarily due to the distal contacts in the JNK2alpha2 docking groove that allow the delivery of the substrate phosphorylation sequence into the catalytic center, (2) there is minimal allosteric communication between the protein-substrate docking site and the ATP binding site in the catalytic center for activated JNK2alpha2, and (3) the reaction proceeds via a random sequential mechanism.
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Affiliation(s)
- Linghao Niu
- Department of Biochemical Pharmacology, Roche Palo Alto LLC, 3431 Hillview Avenue, Palo Alto, California 94304, USA
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Dinh M, Grunberger D, Ho H, Tsing SY, Shaw D, Lee S, Barnett J, Hill RJ, Swinney DC, Bradshaw JM. Activation mechanism and steady state kinetics of Bruton's tyrosine kinase. J Biol Chem 2007; 282:8768-76. [PMID: 17264076 DOI: 10.1074/jbc.m609920200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bruton's tyrosine kinase (BTK) is a member of the Tec non-receptor tyrosine kinase family that is involved in regulating B cell proliferation. To better understand the enzymatic mechanism of the Tec family of kinases, the kinetics of BTK substrate phosphorylation were characterized using a radioactive enzyme assay. We first examined whether autophosphorylation regulates BTK activity. Western blotting with a phosphospecific antibody revealed that BTK rapidly autophosphorylates at Tyr(551) within its activation loop in vitro. Examination of a Y551F BTK mutant indicated that phosphorylation of Tyr(551) causes a 10-fold increase in BTK activity. We then proceeded to characterize the steady state kinetic mechanism of BTK. Varying the concentrations of ATP and S1 peptide (biotin-Aca-AAAEEIY-GEI-NH2) revealed that BTK employs a ternary complex mechanism with KmATP = 84 +/- 20 microM and KmS1 = 37 +/- 8 microM. Inhibition studies were also performed to examine the order of substrate binding. The inhibitors ADP and staurosporine were both found to be competitive with ATP and non-competitive with S1, indicating binding of ATP and S1 to BTK is either random or ordered with ATP binding first. Negative cooperativity was also found between the S1 and ATP binding sites. Unlike ATP site inhibitors, substrate analog inhibitors did not inhibit BTK at concentrations less than 1 mm, suggesting that BTK may employ a "substrate clamping" type of kinetic mechanism whereby the substrate Kd is weaker than Km. This investigation of BTK provides the first detailed kinetic characterization of a Tec family kinase.
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Affiliation(s)
- Marie Dinh
- Department of Biochemical Pharmacology, Roche Palo Alto LLC, CA 94304, USA
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34
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Baginski TK, Dabbagh K, Satjawatcharaphong C, Swinney DC. Cigarette smoke synergistically enhances respiratory mucin induction by proinflammatory stimuli. Am J Respir Cell Mol Biol 2006; 35:165-74. [PMID: 16543607 DOI: 10.1165/rcmb.2005-0259oc] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Pathogenic factors associated with chronic obstructive pulmonary disease (COPD), such as cigarette smoke, proinflammatory cytokines, and bacterial infections, can individually induce respiratory mucins in vitro and in vivo. Since co-presence of these factors is common in lungs of patients with COPD, we hypothesized that cigarette smoke can amplify mucin induction by bacterial exoproducts and proinflammatory cytokines, resulting in mucin hyperproduction. We demonstrated that cigarette smoke extract (CSE) synergistically increased gene expression and protein production of MUC5AC mucin induced by LPS or TNF-alpha in human airway epithelial NCI-H292 cells. CSE also enhanced expression and production of MUC5AC mucin induced by epidermal growth factor receptor (EGFR) ligands TGF-alpha and amphiregulin, as well as LPS- and TNF-alpha- induced expression and/or release of TGF-alpha and amphiregulin. Furthermore, (4-[(3-bromophenyl)amino]-6,7-diaminoquinazoline), a potent inhibitor of EGFR, blocked synergistic induction of MUC5AC mucin. H(2)O(2) mimicked the synergistic effects of CSE, while antioxidant N-acetyl-L-cysteine prevented synergistic induction of MUC5AC mucin by CSE. In a rat model of LPS-induced airway inflammation, concurrent cigarette smoke inhalation enhanced mucin content of the bronchoalveolar lavage fluid, muc5AC gene expression, and mucous cell metaplasia in the airways. These results suggest that cigarette smoke has the potential to synergistically amplify induction of respiratory mucins by proinflammatory stimuli relevant to COPD pathogenesis and contribute to mucin hyperproduction observed in patients with COPD.
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Swinney DC. Biochemical mechanisms of New Molecular Entities (NMEs) approved by United States FDA during 2001-2004: mechanisms leading to optimal efficacy and safety. Curr Top Med Chem 2006; 6:461-78. [PMID: 16719803 DOI: 10.2174/156802606776743093] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The United States FDA approved 85 New Molecular Entities (NMEs) during the period from January 2001 to November 2004 of which 60 were pharmaceuticals with known molecular targets. The majority targeted enzymes (48%) or G-protein coupled receptors (GPCRs) (33%). Eighty percent of the NMEs interacted at the same site as endogenous effector; either as competitive inhibitor/antagonist (67%) or agonist (13%). Three biochemical operations defined the modes of action of the NMEs: 1) mass action competition (equilibrium), 2) a drug stabilized conformational change in the target that is important to the response (conformational) and/or 3) drug action is less-responsive to mass action competition with effectors due to non-equilibrium kinetics (non-equilibrium kinetic). Approximately 80% of the NMEs elicit a response utilizing conformational and/or non-equilibrium kinetic mechanisms. The remaining 20% of NMEs find mass action competition with the endogenous substrate or ligand sufficient for therapeutic utility. These observations indicate that for the majority of drug targets, mass action driven equilibrium binding alone may not be sufficient for maximal therapeutic utility. A key determinant of the biochemical mode of action for these NMEs was to minimize the potential for toxicity, either by providing a maximal response at a low dose to minimize off-target toxicities, or by providing a mechanism to minimize the incidence of mechanism-based toxicity while retaining a sufficiently efficacious response. This principle appears to be independent of target class and provides insight as to intrinsic biochemical features and approaches required for a maximal therapeutic index.
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Affiliation(s)
- David C Swinney
- Biochemical Pharmacology, Roche Palo Alto, 3431 Hillview Ave. Palo Alto, CA 94304, USA.
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37
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Papp E, Mackenzie R, Swinney DC. Assay to evaluate factors that contribute to the correlation between enzyme and cellular potency for ATP competitive inhibitors of p38 kinase. FASEB J 2006. [DOI: 10.1096/fasebj.20.4.a42-d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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39
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Swinney DC. Biochemical Mechanisms of New Molecular Entities (NMEs) approved by United States FDA during 2001‐2004: Mechanisms leading to optimal efficacy and safety. FASEB J 2006. [DOI: 10.1096/fasebj.20.4.a267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- David C Swinney
- Biochemical PharmacologyRoche Palo Alto3431 Hillview AvePalo AltoCA94304
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40
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Swinney DC, Beavis P, Kondru RK, Dioszegi ME, Gee P, Zhang J, Sankuratri S, Mirzadegan T. CCR5 antagonists have different conformational requirements for the transition to the most thermodynamically stable CCR5 receptor:antagonist complex. FASEB J 2006. [DOI: 10.1096/fasebj.20.5.a918-b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Paul Beavis
- Roche Palo Alto3431 Hillview AvePalo AltoCA94304
| | | | | | - Peter Gee
- Roche Palo Alto3431 Hillview AvePalo AltoCA94304
| | - Jun Zhang
- Roche Palo Alto3431 Hillview AvePalo AltoCA94304
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41
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Niu L, Chang A, Wilson S, Tran P, Zuo F, Swinney DC. Kinetic characterization of JNK reaction mechanism using substrate competitive inhibitors. FASEB J 2006. [DOI: 10.1096/fasebj.20.4.a479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Alice Chang
- InflammationAutoimmunity and TransplantationRoche Palo Alto3431 Hillview Ave.Palo AltoCalifornia94304
| | - Stacy Wilson
- InflammationAutoimmunity and TransplantationRoche Palo Alto3431 Hillview Ave.Palo AltoCalifornia94304
| | | | - Fengrong Zuo
- InflammationAutoimmunity and TransplantationRoche Palo Alto3431 Hillview Ave.Palo AltoCalifornia94304
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42
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Ravindran P, Lee I, Swinney DC. A competitive method to obtain kinetic dissociation rates for unlabeled ligands binding to membrane bound receptors. FASEB J 2006. [DOI: 10.1096/fasebj.20.5.a919-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Ina Lee
- Biochemical PharmacologyRoche Palo alto LLC3431 Hillview AvenuePalo AltoCA94304‐1397
| | - David C Swinney
- Biochemical PharmacologyRoche Palo alto LLC3431 Hillview AvenuePalo AltoCA94304‐1397
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Abstract
Drug discovery is extremely difficult. There are many unanticipated scientific, medical and business challenges to every drug discovery programme. It is important to increase our understanding of the fundamental properties of effective drugs so that we can anticipate potential problems in developing new agents. This article addresses potential drug discovery and development risks associated with the biochemical mechanism of drug action, and proposes simple rules to minimize these risks.
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Affiliation(s)
- David C Swinney
- Roche Palo Alto, 3431 Hillview Avenue, Palo Alto, California 94304, USA.
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44
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Swinney DC, Xu YZ, Scarafia LE, Lee I, Mak AY, Gan QF, Ramesha CS, Mulkins MA, Dunn J, So OY, Biegel T, Dinh M, Volkel P, Barnett J, Dalrymple SA, Lee S, Huber M. A small molecule ubiquitination inhibitor blocks NF-kappa B-dependent cytokine expression in cells and rats. J Biol Chem 2002; 277:23573-81. [PMID: 11950839 DOI: 10.1074/jbc.m200842200] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A small molecule inhibitor of NF-kappaB-dependent cytokine expression was discovered that blocked tumor necrosis factor (TNF) alpha-induced IkappaB(alpha) degradation in MM6 cells but not the degradation of beta-catenin in Jurkat cells. Ro106-9920 blocked lipopolysaccharide (LPS)-dependent expression of TNFalpha, interleukin-1beta, and interleukin-6 in fresh human peripheral blood mononuclear cells with IC(50) values below 1 microm. Ro106-9920 also blocked TNFalpha production in a dose-dependent manner following oral administration in two acute models of inflammation (air pouch and LPS challenge). Ro106-9920 was observed to inhibit an ubiquitination activity that does not require betaTRCP but associates with IkappaB(alpha) and will ubiquitinate IkappaB(alpha) S32E,S36E (IkappaB(alpha)(ee)) specifically at lysine 21 or 22. Ro106-9920 was identified in a cell-free system as a time-dependent inhibitor of IkappaB(alpha)(ee) ubiquitination with an IC(50) value of 2.3 +/- 0.09 microm. The ubiquitin E3 ligase activity is inhibited by cysteine-alkylating reagents, supported by E2UBCH7, and requires cIAP2 or a cIAP2-associated protein for activity. These activities are inconsistent with what has been reported for SCF(betaTRCP), the putative E3 for IkappaB(alpha) ubiquitination. Ro106-9920 was observed to be selective for IkappaB(alpha)(ee) ubiquitination over the ubiquitin-activating enzyme (E1), E2UBCH7, nonspecific ubiquitination of cellular proteins, and 97 other molecular targets. We propose that Ro106-9920 selectively inhibits an uncharacterized but essential ubiquitination activity associated with LPS- and TNFalpha-induced IkappaB(alpha) degradation and NF-kappaB activation.
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Affiliation(s)
- David C Swinney
- Inflammatory and Viral Diseases Unit, Roche Bioscience, Palo Alto, California 94304, USA.
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45
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Mak AY, Swinney DC. 17-O-Acetyltestosterone formation from progesterone in microsomes from pig testes: evidence for the Baeyer-Villiger rearrangement in androgen formation catalyzed by CYP17. J Am Chem Soc 2002. [DOI: 10.1021/ja00047a063] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Abstract
We evaluated the expression of 28 gene sequences with homology to the carboxy terminal of HECT E3 ubiquitin ligases in nine human cell lines using RT-PCR, to determine whether gene expression could be associated with cell-specific functions (HECT is "homologous to E6AP C-terminus"). In general, HECT-domain E3 ligases are constitutively expressed at low levels with a broad range between cell types. hecth3, 21, and 23 had higher levels in three leukocytic lines (Jurkat, MM6, THP1); hecth11 was more abundant in HepG2 and A495; and hecth15 and hecth12 were differentially expressed in lung fibroblasts derived from normal and severe emphysema patients (CCD16 and CCD29, respectively). Absolute quantitation showed that most HECT E3s have about 20-100 copies of mRNA per Jurkat cell. By comparison, UBCH7 (an ubiquitin-conjugating E2) is 10-fold more abundant in Jurkat cells and 30-fold more abundant than E2 UBCH5A. We interpret the broad range of transcript levels to be consistent with the hypothesis that the concentrations of E3 are important for ubiquitination selectivity, leading us to conclude that substrate activation is necessary but not sufficient for selectivity.
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Affiliation(s)
- L E Scarafia
- Inflammatory Diseases Unit, Roche Bioscience, Palo Alto, California 94304, USA
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47
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So OY, Scarafia LE, Mak AY, Callan OH, Swinney DC. The dynamics of prostaglandin H synthases. Studies with prostaglandin h synthase 2 Y355F unmask mechanisms of time-dependent inhibition and allosteric activation. J Biol Chem 1998; 273:5801-7. [PMID: 9488715 DOI: 10.1074/jbc.273.10.5801] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Prostaglandin H synthases (PGHSs) catalyze the conversion of arachidonic acid to prostaglandins. In this report, we describe the effect of a PGHS2 Y355F mutation on the dynamics of PGHS2 catalysis and inhibition. Tyr355 is part of a hydrogen-bonding network located at the entrance to the cyclooxygenase active site. The Y355F mutant exhibited allosteric activation kinetics in the presence of arachidonic acid that was defined by a curved Eadie-Scatchard plot and a Hill coefficient of 1.36 +/- 0.05. Arachidonic acid-induced allosteric activation has not been directly observed with wild type PGHS2. The mutation also decreased the observed time-dependent inhibition by indomethacin, flurbiprofen, RS-57067, and SC-57666. Detailed kinetic analysis showed that the Y355F mutation decreased the transition state energy associated with slow-binding inhibition (EIdouble dagger) relative to the energy associated with catalysis (ESdouble dagger) by 1.33, 0.67, and 1.06 kcal/mol, respectively, for indomethacin, flurbiprofen, and RS-57067. These observations show Tyr355 to be involved in the molecular mechanism of time-dependent inhibition. We interpret these results to indicate that slow binding inhibitors and the Y355F mutant slow the rate and unmask intrinsic, dynamic events associated with product formation. We hypothesize that the dynamic events are the equilibrium between relaxed and tightened organizations of the hydrogen-bonding network at the entrance to the cyclooxygenase active site. It is these rearrangements that control the rate of substrate binding and ultimately the rate of prostaglandin formation.
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Affiliation(s)
- O Y So
- Inflammatory Diseases Unit, Roche Bioscience, Palo Alto, California 94304, USA
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48
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Tsai AL, Palmer G, Xiao G, Swinney DC, Kulmacz RJ. Structural characterization of arachidonyl radicals formed by prostaglandin H synthase-2 and prostaglandin H synthase-1 reconstituted with mangano protoporphyrin IX. J Biol Chem 1998; 273:3888-94. [PMID: 9461572 DOI: 10.1074/jbc.273.7.3888] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A tyrosyl radical generated in the peroxidase cycle of prostaglandin H synthase-1 (PGHS-1) can serve as the initial oxidant for arachidonic acid (AA) in the cyclooxygenase reaction. Peroxides also induce radical formation in prostaglandin H synthase-2 (PGHS-2) and in PGHS-1 reconstituted with mangano protoporphyrin IX (MnPGHS-1), but the EPR spectra of these radicals are distinct from the initial tyrosyl radical in PGHS-1. We have examined the ability of the radicals in PGHS-2 and MnPGHS-1 to oxidize AA, using single-turnover EPR studies. One wide singlet tyrosyl radical with an overall EPR line width of 29-31 gauss (G) was generated by reaction of PGHS-2 with ethyl hydroperoxide. Anaerobic addition of AA to PGHS-2 immediately after formation of this radical led to its disappearance and emergence of an AA radical (AA.) with a 7-line EPR, substantiated by experiments using octadeuterated AA. Subsequent addition of oxygen resulted in regeneration of the tyrosyl radical. In contrast, the peroxide-generated radical (a 21G narrow singlet) in a Y371F PGHS-2 mutant lacking cyclooxygenase activity failed to react with AA. The peroxide-generated radical in MnPGHS-1 exhibited a line width of 36-38G, but was also able to convert AA to an AA. with an EPR spectrum similar to that found with PGHS-2. These results indicate that the peroxide-generated radicals in PGHS-2 and MnPGHS-1 can each serve as immediate oxidants of AA to form the same carbon-centered fatty acid radical that subsequently reacts with oxygen to form a hydroperoxide. The EPR data for the AA-derived radical formed by PGHS-2 and MnPGHS-1 could be accounted for by a planar pentadienyl radical with two strongly interacting beta-protons at C10 of AA. These results support a functional role for peroxide-generated radicals in cyclooxygenase catalysis by both PGHS isoforms and provide important structural characterization of the carbon-centered AA..
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Affiliation(s)
- A l Tsai
- Department of Internal Medicine, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA.
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49
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Abstract
Prostaglandins are synthesized by prostaglandin H synthase (PGHS) 1 and 2. PGHS2 is regulated through inducible expression. We report here the regulation of PGHS1 activity by substrate-dependent cooperative activation. The cooperativity is characterized by a Hill coefficient of 1.29 +/- 0.06, a curved Eadie-Scatchard plot, and activation by low concentrations of competitive inhibitors. The activation also appears to induce a conformational change in the cyclooxygenase site. The cooperativity produces a 2-4-fold greater rate of PGHS2-dependent prostaglandin formation compared with PGHS1-dependent prostaglandin formation at arachidonic acid concentrations below 0.5 microM. A consequence of the PGHS1 cooperativity is that the affinity of many cyclooxygenase inhibitors for PGHS1 decreases in parallel to the activation by arachidonic acid. In contrast, the affinity of these inhibitors for PGHS2 is unaffected by the changes in arachidonic acid concentration. This results in a dramatic difference in PGHS2/PGHS1 selectivity at different arachidonic acid concentrations.
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Affiliation(s)
- D C Swinney
- Inflammatory Diseases Unit, Roche Bioscience, Palo Alto, California 94304, USA.
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50
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Callan OH, So OY, Swinney DC. The kinetic factors that determine the affinity and selectivity for slow binding inhibition of human prostaglandin H synthase 1 and 2 by indomethacin and flurbiprofen. J Biol Chem 1996; 271:3548-54. [PMID: 8631960 DOI: 10.1074/jbc.271.7.3548] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We present here for the first time a method for determining the rate constants associated with slow binding inhibition of prostaglandin H synthase (PGHS). The rate constants were determined by a method using initial steady-state conditions, which minimize the impact of catalytic autoinactivation of the enzyme. The currently available methods for determining the kinetic constants associated with slow binding enzyme inhibition do not distinguish between rate decreases due to enzyme inhibition or due to autoinactivation of the enzyme. A mathematical model was derived assuming a rapid reversible formation of an initial enzyme-inhibitor complex (EI) followed by a slow reversible formation of a second enzyme-inhibitor complex (EI*). The two enzyme inhibitor complexes are assumed to be in slow equilibrium. This method was used to evaluate the kinetic parameters associated with the binding and selectivity of the nonsteroidal antinflammatory drugs (NSAIDs), flurbiprofen and indomethacin. The KI values associated with the formation of the first reversible complex (EI) for flurbiprofen with PGHS1 and PGHS2 were 0.53 +/- 0. 06 and 0.61 +/- 0.08 microM, respectively; the rate constants for the forward isomerization, k2, into the second reversible complex (EI*) were 0.97 +/- 0.99 and 0.11 +/- 0.01 s-1, respectively, and rates of the reverse isomerization from EI*, k-2, were 0.031 +/- 0.004 and 0.0082 +/- 0.0008 s-1, respectively. Indomethacin was estimated to form the EI complex with the same affinity for both PGHS1 and PGHS2, 10.0 +/- 2.8 microM and 11.2 +/- 2.0 microM, respectively, and dissociate from EI* at approximately the same rate 0.0011 +/- 0.0002 s-1 and 0.0031 +/- 0.0003 s-1, respectively. However, the rate of isomerization into EI* from EI was much greater for PGHS1 than PGHS2, 0.33 +/- 0.08 s-1 as compared with 0.034 +/- 0.004 s-1. These results show that the overall affinity for the inhibition of PGHS1 versus PGHS2 was 30-fold greater for indomethacin (KI* = 0.032 +/- 0.005 and 1.02 +/- 0.08 microM, respectively) and 3-fold greater for flurbiprofen (KI* = 0.017 +/- 0.002 and 0.045 +/- 0.004 microM, respectively). The results also show that for both PGHS1 and PGHS2, flurbiprofen was bound tighter to the initial EI complex than indomethacin; however, the rate of dissociation from EI* was slower for indomethacin than flurbiprofen. The rate of the forward isomerization to EI* is primarily responsible for the selectivity of both NSAIDs for PGHS1. This analysis shows the quantitative importance of the different kinetic parameters upon the overall binding affinity of these NSAIDs and should greatly assist in our understanding of the structural interactions that promote enzyme-inhibitor binding.
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Affiliation(s)
- O H Callan
- Department of Enzymology, Roche Bioscience, Palo Alto, California 94304, USA
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