1
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Kelm JM, Ferrer M, Bittner MI, Lal-Nag M. Data standards in drug discovery: A long way to go. Drug Discov Today 2024; 29:103879. [PMID: 38216119 DOI: 10.1016/j.drudis.2024.103879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/31/2023] [Accepted: 01/08/2024] [Indexed: 01/14/2024]
Abstract
Each year, millions to trillions of data points are generated to evaluate the response of chemicals and biologicals to human cells in vitro and in vivo using various technologies and endpoints. Despite the vast amount of data available, the development process has not become significantly more efficient in recent years. Given the increasing use of more complex physiological models, which are time-consuming and significantly more expensive, it is crucial to maximize the value of these valuable data through improved standardization.
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Affiliation(s)
- Jens M Kelm
- Precomb Therapeutics AG, Hombrechtikon, Switzerland.
| | - Marc Ferrer
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health, Rockville, MD, USA
| | - Martin-Immanuel Bittner
- Arctoris Ltd, Oxford, UK; Young Academy of the German National Academy of Sciences, Berlin, Germany
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2
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Greenhough LA, Clarke G, Phillipou AN, Mazani F, Karamshi B, Rowe S, Rowland P, Messenger C, Haslam CP, Bingham RP, Craggs PD. Reducing False Positives through the Application of Fluorescence Lifetime Technology: A Comparative Study Using TYK2 Kinase as a Model System. SLAS Discov 2021; 26:663-675. [PMID: 33783261 DOI: 10.1177/24725552211002472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The predominant assay detection methodologies used for enzyme inhibitor identification during early-stage drug discovery are fluorescence-based. Each fluorophore has a characteristic fluorescence decay, known as the fluorescence lifetime, that occurs throughout a nanosecond-to-millisecond timescale. The measurement of fluorescence lifetime as a reporter for biological activity is less common than fluorescence intensity, even though the latter has numerous issues that can lead to false-positive readouts. The confirmation of hit compounds as true inhibitors requires additional assays, cost, and time to progress from hit identification to lead drug-candidate optimization. To explore whether the use of fluorescence lifetime technology (FLT) can offer comparable benefits to label-free-based approaches such as RapidFire mass spectroscopy (RF-MS) and a superior readout compared to time-resolved fluorescence resonance energy transfer (TR-FRET), three equivalent assays were developed against the clinically validated tyrosine kinase 2 (TYK2) and screened against annotated compound sets. FLT provided a marked decrease in the number of false-positive hits when compared to TR-FRET. Further cellular screening confirmed that a number of potential inhibitors directly interacted with TYK2 and inhibited the downstream phosphorylation of the signal transducer and activator of transcription 4 protein (STAT4).
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Affiliation(s)
- Luke A Greenhough
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Gabriella Clarke
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Alexander N Phillipou
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Faith Mazani
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Bhumika Karamshi
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Sam Rowe
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Paul Rowland
- Protein, Cellular and Structural Sciences, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Cassie Messenger
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Carl P Haslam
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Ryan P Bingham
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Peter D Craggs
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
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3
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Foley TL, Burchett W, Chen Q, Flanagan ME, Kapinos B, Li X, Montgomery JI, Ratnayake AS, Zhu H, Peakman MC. Selecting Approaches for Hit Identification and Increasing Options by Building the Efficient Discovery of Actionable Chemical Matter from DNA-Encoded Libraries. SLAS Discov 2021; 26:263-280. [PMID: 33412987 DOI: 10.1177/2472555220979589] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past 20 years, the toolbox for discovering small-molecule therapeutic starting points has expanded considerably. Pharmaceutical researchers can now choose from technologies that, in addition to traditional high-throughput knowledge-based and diversity screening, now include the screening of fragment and fragment-like libraries, affinity selection mass spectrometry, and selection against DNA-encoded libraries (DELs). Each of these techniques has its own unique combination of advantages and limitations that makes them more, or less, suitable for different target classes or discovery objectives, such as desired mechanism of action. Layered on top of this are the constraints of the drug-hunters themselves, including budgets, timelines, and available platform capacity; each of these can play a part in dictating the hit identification strategy for a discovery program. In this article, we discuss some of the factors that we use to govern our building of a hit identification roadmap for a program and describe the increasing role that DELs are playing in our discovery strategy. Furthermore, we share our learning during our initial exploration of DEL and highlight the approaches we have evolved to maximize the value returned from DEL selections. Topics addressed include the optimization of library design and production, reagent validation, data analysis, and hit confirmation. We describe how our thinking in these areas has led us to build a DEL platform that has begun to deliver tractable matter to our global discovery portfolio.
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Affiliation(s)
| | | | - Qiuxia Chen
- Lead Generation Unit, HitGen Inc., Chengdu, Shuangliu District, China
| | | | | | - Xianyang Li
- Lead Generation Unit, HitGen Inc., Chengdu, Shuangliu District, China
| | | | | | - Hongyao Zhu
- Simulation and Modelling Sciences, Pfizer Inc., Groton, CT, USA
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4
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Wang D, Hensman J, Kutkaite G, Toh TS, Galhoz A, Dry JR, Saez-Rodriguez J, Garnett MJ, Menden MP, Dondelinger F. A statistical framework for assessing pharmacological responses and biomarkers using uncertainty estimates. eLife 2020; 9:e60352. [PMID: 33274713 PMCID: PMC7746236 DOI: 10.7554/elife.60352] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/04/2020] [Indexed: 12/16/2022] Open
Abstract
High-throughput testing of drugs across molecular-characterised cell lines can identify candidate treatments and discover biomarkers. However, the cells' response to a drug is typically quantified by a summary statistic from a best-fit dose-response curve, whilst neglecting the uncertainty of the curve fit and the potential variability in the raw readouts. Here, we model the experimental variance using Gaussian Processes, and subsequently, leverage uncertainty estimates to identify associated biomarkers with a new Bayesian framework. Applied to in vitro screening data on 265 compounds across 1074 cancer cell lines, our models identified 24 clinically established drug-response biomarkers, and provided evidence for six novel biomarkers by accounting for association with low uncertainty. We validated our uncertainty estimates with an additional drug screen of 26 drugs, 10 cell lines with 8 to 9 replicates. Our method is applicable to any dose-response data without replicates, and improves biomarker discovery for precision medicine.
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Affiliation(s)
- Dennis Wang
- Sheffield Institute for Translational Neuroscience, University of SheffieldSheffieldUnited Kingdom
- Department of Computer Science, University of SheffieldSheffieldUnited Kingdom
| | | | - Ginte Kutkaite
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental HealthNeuherbergGermany
- Department of Biology, Ludwig-Maximilians University MunichMartinsriedGermany
| | - Tzen S Toh
- The Medical School, University of SheffieldSheffieldUnited Kingdom
| | - Ana Galhoz
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental HealthNeuherbergGermany
- Department of Biology, Ludwig-Maximilians University MunichMartinsriedGermany
| | - Jonathan R Dry
- Research and Early Development, Oncology R&D, AstraZenecaBostonUnited States
| | - Julio Saez-Rodriguez
- Institute of Computational Biomedicine,Faculty of Medicine,Heidelberg Universityand Heidelberg University Hospital, BioquantHeidelbergGermany
| | | | - Michael P Menden
- Institute of Computational Biology, Helmholtz Zentrum München—German Research Center for Environmental HealthNeuherbergGermany
- Department of Biology, Ludwig-Maximilians University MunichMartinsriedGermany
- German Center for Diabetes Research (DZD e.V.)NeuherbergGermany
| | - Frank Dondelinger
- Centre for Health Informatics, Computation and Statistics, Lancaster Medical School, Lancaster UniversityLancasterUnited Kingdom
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5
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Yonchev D, Bajorath J. DeepCOMO: from structure-activity relationship diagnostics to generative molecular design using the compound optimization monitor methodology. J Comput Aided Mol Des 2020; 34:1207-1218. [PMID: 33015739 PMCID: PMC7595974 DOI: 10.1007/s10822-020-00349-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/29/2020] [Indexed: 11/26/2022]
Abstract
The compound optimization monitor (COMO) approach was originally developed as a diagnostic approach to aid in evaluating development stages of analog series and progress made during lead optimization. COMO uses virtual analog populations for the assessment of chemical saturation of analog series and has been further developed to bridge between optimization diagnostics and compound design. Herein, we discuss key methodological features of COMO in its scientific context and present a deep learning extension of COMO for generative molecular design, leading to the introduction of DeepCOMO. Applications on exemplary analog series are reported to illustrate the entire DeepCOMO repertoire, ranging from chemical saturation and structure-activity relationship progression diagnostics to the evaluation of different analog design strategies and prioritization of virtual candidates for optimization efforts, taking into account the development stage of individual analog series.
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Affiliation(s)
- Dimitar Yonchev
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, 53115, Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Endenicher Allee 19c, 53115, Bonn, Germany.
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6
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Abstract
While the COVID-19 pandemic has spurred intense research and collaborative discovery worldwide, the development of a safe, effective, and targeted antiviral from the ground up is time intensive. Therefore, most antiviral discovery efforts are focused on the re-purposing of clinical stage or approved drugs. While emerging data on drugs undergoing COVID-19 repurpose are intriguing, there is an undeniable need to develop broad-spectrum antivirals to prevent future viral pandemics of unknown origin. The ideal drug to curtail rapid viral spread would be a broad-acting agent with activity against a wide range of viruses. Such a drug would work by modulating host-proteins that are often shared by multiple virus families thereby enabling preemptive drug development and therefore rapid deployment at the onset of an outbreak. Targeting host-pathways and cellular proteins that are hijacked by viruses can potentially offer broad-spectrum targets for the development of future antiviral drugs. Such host-directed antivirals are also likely to offer a higher barrier to the development and selection of drug resistant mutations. Given that most approved antivirals do not target host-proteins, we reinforce the need for the development of such antivirals that can be used in pre- and post-exposure populations.
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Affiliation(s)
- Vipul C Chitalia
- Boston University Medical Center, 625 Albany Street, Boston, MA, USA
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ali H Munawar
- Bisect Therapeutics, Inc., 45 Dan Road, Canton, MA, USA.
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7
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Ferrero E, Brachat S, Jenkins JL, Marc P, Skewes-Cox P, Altshuler RC, Gubser Keller C, Kauffmann A, Sassaman EK, Laramie JM, Schoeberl B, Borowsky ML, Stiefl N. Ten simple rules to power drug discovery with data science. PLoS Comput Biol 2020; 16:e1008126. [PMID: 32853229 PMCID: PMC7451597 DOI: 10.1371/journal.pcbi.1008126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Enrico Ferrero
- Computational Sciences Council, Novartis Institutes for BioMedical Research, Basel, Switzerland
- * E-mail:
| | - Sophie Brachat
- Computational Sciences Council, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Jeremy L. Jenkins
- Computational Sciences Council, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Philippe Marc
- Computational Sciences Council, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Peter Skewes-Cox
- Computational Sciences Council, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Robert C. Altshuler
- Computational Sciences Council, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Caroline Gubser Keller
- Computational Sciences Council, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Audrey Kauffmann
- Computational Sciences Council, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Erik K. Sassaman
- Computational Sciences Council, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Jason M. Laramie
- Computational Sciences Council, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Birgit Schoeberl
- Computational Sciences Council, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Mark L. Borowsky
- Computational Sciences Council, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Nikolaus Stiefl
- Computational Sciences Council, Novartis Institutes for BioMedical Research, Basel, Switzerland
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8
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Jenkinson S, Schmidt F, Rosenbrier Ribeiro L, Delaunois A, Valentin JP. A practical guide to secondary pharmacology in drug discovery. J Pharmacol Toxicol Methods 2020; 105:106869. [PMID: 32302774 DOI: 10.1016/j.vascn.2020.106869] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/21/2020] [Accepted: 04/03/2020] [Indexed: 01/29/2023]
Abstract
Secondary pharmacological profiling is increasingly applied in pharmaceutical drug discovery to address unwanted pharmacological side effects of drug candidates before entering the clinic. Regulators, drug makers and patients share a demand for deep characterization of secondary pharmacology effects of novel drugs and their metabolites. The scope of such profiling has therefore expanded substantially in the past two decades, leading to the implementation of broad in silico profiling methods and focused in vitro off-target screening panels, to identify liabilities, but also opportunities, as early as possible. The pharmaceutical industry applies such panels at all stages of drug discovery routinely up to early development. Nevertheless, target composition, screening technologies, assay formats, interpretation and scheduling of panels can vary significantly between companies in the absence of dedicated guidelines. To contribute towards best practices in secondary pharmacology profiling, this review aims to summarize the state-of-the art in this field. Considerations are discussed with respect to panel design, screening strategy, implementation and interpretation of the data, including regulatory perspectives. The cascaded, or integrated, use of in silico and off-target profiling allows to exploit synergies for comprehensive safety assessment of drug candidates.
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Affiliation(s)
- Stephen Jenkinson
- Drug Safety Research and Development, Pfizer Inc., La Jolla, CA 92121, United States of America.
| | - Friedemann Schmidt
- Sanofi, R&D Preclinical Safety, Industriepark Höchst, 65926 Frankfurt/Main, Germany
| | - Lyn Rosenbrier Ribeiro
- Medicines Discovery Catapult, Block 35, Mereside, Alderley Park, Alderley Edge, SK10 4TG, United Kingdom
| | - Annie Delaunois
- UCB BioPharma SRL, Early Solutions, Development Science, Non-Clinical Safety, 1420 Braine L'Alleud, Walloon Region, Belgium
| | - Jean-Pierre Valentin
- UCB BioPharma SRL, Early Solutions, Development Science, Non-Clinical Safety, 1420 Braine L'Alleud, Walloon Region, Belgium
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9
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Gorgulla C, Boeszoermenyi A, Wang ZF, Fischer PD, Coote PW, Padmanabha Das KM, Malets YS, Radchenko DS, Moroz YS, Scott DA, Fackeldey K, Hoffmann M, Iavniuk I, Wagner G, Arthanari H. An open-source drug discovery platform enables ultra-large virtual screens. Nature 2020; 580:663-668. [PMID: 32152607 PMCID: PMC8352709 DOI: 10.1038/s41586-020-2117-z] [Citation(s) in RCA: 271] [Impact Index Per Article: 67.8] [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: 03/05/2019] [Accepted: 02/27/2020] [Indexed: 12/21/2022]
Abstract
On average, an approved drug currently costs US$2-3 billion and takes more than 10 years to develop1. In part, this is due to expensive and time-consuming wet-laboratory experiments, poor initial hit compounds and the high attrition rates in the (pre-)clinical phases. Structure-based virtual screening has the potential to mitigate these problems. With structure-based virtual screening, the quality of the hits improves with the number of compounds screened2. However, despite the fact that large databases of compounds exist, the ability to carry out large-scale structure-based virtual screening on computer clusters in an accessible, efficient and flexible manner has remained difficult. Here we describe VirtualFlow, a highly automated and versatile open-source platform with perfect scaling behaviour that is able to prepare and efficiently screen ultra-large libraries of compounds. VirtualFlow is able to use a variety of the most powerful docking programs. Using VirtualFlow, we prepared one of the largest and freely available ready-to-dock ligand libraries, with more than 1.4 billion commercially available molecules. To demonstrate the power of VirtualFlow, we screened more than 1 billion compounds and identified a set of structurally diverse molecules that bind to KEAP1 with submicromolar affinity. One of the lead inhibitors (iKeap1) engages KEAP1 with nanomolar affinity (dissociation constant (Kd) = 114 nM) and disrupts the interaction between KEAP1 and the transcription factor NRF2. This illustrates the potential of VirtualFlow to access vast regions of the chemical space and identify molecules that bind with high affinity to target proteins.
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Affiliation(s)
- Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA.
- Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Andras Boeszoermenyi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zi-Fu Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Patrick D Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Paul W Coote
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Krishna M Padmanabha Das
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yehor S Malets
- Enamine, Kyiv, Ukraine
- National Taras Shevchenko University of Kyiv, Kyiv, Ukraine
| | - Dmytro S Radchenko
- Enamine, Kyiv, Ukraine
- National Taras Shevchenko University of Kyiv, Kyiv, Ukraine
| | - Yurii S Moroz
- National Taras Shevchenko University of Kyiv, Kyiv, Ukraine
- Chemspace, Kyiv, Ukraine
| | - David A Scott
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Konstantin Fackeldey
- Zuse Institute Berlin, Berlin, Germany
- Institute of Mathematics, Technical University Berlin, Berlin, Germany
| | - Moritz Hoffmann
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | | | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA.
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
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10
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Robinson MC, Glen RC, Lee AA. Validating the validation: reanalyzing a large-scale comparison of deep learning and machine learning models for bioactivity prediction. J Comput Aided Mol Des 2020; 34:717-730. [PMID: 31960253 PMCID: PMC7292817 DOI: 10.1007/s10822-019-00274-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 12/22/2019] [Indexed: 11/26/2022]
Abstract
Machine learning methods may have the potential to significantly accelerate drug discovery. However, the increasing rate of new methodological approaches being published in the literature raises the fundamental question of how models should be benchmarked and validated. We reanalyze the data generated by a recently published large-scale comparison of machine learning models for bioactivity prediction and arrive at a somewhat different conclusion. We show that the performance of support vector machines is competitive with that of deep learning methods. Additionally, using a series of numerical experiments, we question the relevance of area under the receiver operating characteristic curve as a metric in virtual screening. We further suggest that area under the precision–recall curve should be used in conjunction with the receiver operating characteristic curve. Our numerical experiments also highlight challenges in estimating the uncertainty in model performance via scaffold-split nested cross validation.
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Affiliation(s)
| | - Robert C Glen
- The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, CB21EW, UK
- Computational and Systems Medicine, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College, South Kensington, London, SW72AZ, UK
| | - Alpha A Lee
- Department of Physics, J J Thomson Avenue, Cambridge, CB3 0HE, UK.
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11
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Wilson JL, Racz R, Liu T, Adeniyi O, Sun J, Ramamoorthy A, Pacanowski M, Altman R. PathFX provides mechanistic insights into drug efficacy and safety for regulatory review and therapeutic development. PLoS Comput Biol 2018; 14:e1006614. [PMID: 30532240 PMCID: PMC6285459 DOI: 10.1371/journal.pcbi.1006614] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 06/06/2018] [Accepted: 10/31/2018] [Indexed: 12/14/2022] Open
Abstract
Failure to demonstrate efficacy and safety issues are important reasons that drugs do not reach the market. An incomplete understanding of how drugs exert their effects hinders regulatory and pharmaceutical industry projections of a drug's benefits and risks. Signaling pathways mediate drug response and while many signaling molecules have been characterized for their contribution to disease or their role in drug side effects, our knowledge of these pathways is incomplete. To better understand all signaling molecules involved in drug response and the phenotype associations of these molecules, we created a novel method, PathFX, a non-commercial entity, to identify these pathways and drug-related phenotypes. We benchmarked PathFX by identifying drugs' marketed disease indications and reported a sensitivity of 41%, a 2.7-fold improvement over similar approaches. We then used PathFX to strengthen signals for drug-adverse event pairs occurring in the FDA Adverse Event Reporting System (FAERS) and also identified opportunities for drug repurposing for new diseases based on interaction paths that associated a marketed drug to that disease. By discovering molecular interaction pathways, PathFX improved our understanding of drug associations to safety and efficacy phenotypes. The algorithm may provide a new means to improve regulatory and therapeutic development decisions.
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Affiliation(s)
- Jennifer L. Wilson
- Department of Bioengineering, Stanford University, Palo Alto California, United States of America
| | - Rebecca Racz
- Division of Applied Regulatory Science, US Food and Drug Administration, Silver Spring Maryland, United States of America
| | - Tianyun Liu
- Department of Bioengineering, Stanford University, Palo Alto California, United States of America
| | - Oluseyi Adeniyi
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring Maryland, United States of America
| | - Jielin Sun
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring Maryland, United States of America
| | - Anuradha Ramamoorthy
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring Maryland, United States of America
| | - Michael Pacanowski
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring Maryland, United States of America
| | - Russ Altman
- Department of Bioengineering, Stanford University, Palo Alto California, United States of America
- Department of Genetics, Stanford University, Palo Alto California, United States of America
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12
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Hodges TR, Abbott JR, Little AJ, Sarkar D, Salovich JM, Howes JE, Akan DT, Sai J, Arnold AL, Browning C, Burns MC, Sobolik T, Sun Q, Beesetty Y, Coker JA, Scharn D, Stadtmueller H, Rossanese OW, Phan J, Waterson AG, McConnell DB, Fesik SW. Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on RAS. J Med Chem 2018; 61:8875-8894. [PMID: 30205005 PMCID: PMC8314423 DOI: 10.1021/acs.jmedchem.8b01108] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Son of sevenless homologue 1 (SOS1) is a guanine nucleotide exchange factor that catalyzes the exchange of GDP for GTP on RAS. In its active form, GTP-bound RAS is responsible for numerous critical cellular processes. Aberrant RAS activity is involved in ∼30% of all human cancers; hence, SOS1 is an attractive therapeutic target for its role in modulating RAS activation. Here, we describe a new series of benzimidazole-derived SOS1 agonists. Using structure-guided design, we discovered small molecules that increase nucleotide exchange on RAS in vitro at submicromolar concentrations, bind to SOS1 with low double-digit nanomolar affinity, rapidly enhance cellular RAS-GTP levels, and invoke biphasic signaling changes in phosphorylation of ERK 1/2. These compounds represent the most potent series of SOS1 agonists reported to date.
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Affiliation(s)
- Timothy R. Hodges
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Jason R. Abbott
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Andrew J. Little
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Dhruba Sarkar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - James M. Salovich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Jennifer E. Howes
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Denis T. Akan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Jiqing Sai
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Allison L. Arnold
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Carrie Browning
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Michael C. Burns
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Tammy Sobolik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Qi Sun
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Yugandhar Beesetty
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Jesse A. Coker
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Dirk Scharn
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Heinz Stadtmueller
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Olivia W. Rossanese
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Jason Phan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
| | - Alex G. Waterson
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232-0146, USA
| | - Darryl B. McConnell
- Boehringer Ingelheim RCV GmbH & Co KG, Doktor-Boehringer-Gasse 5-11, 1120 Vienna, Austria
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232-0146, USA
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Leveridge M, Chung CW, Gross JW, Phelps CB, Green D. Integration of Lead Discovery Tactics and the Evolution of the Lead Discovery Toolbox. SLAS Discov 2018; 23:881-897. [PMID: 29874524 DOI: 10.1177/2472555218778503] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
There has been much debate around the success rates of various screening strategies to identify starting points for drug discovery. Although high-throughput target-based and phenotypic screening has been the focus of this debate, techniques such as fragment screening, virtual screening, and DNA-encoded library screening are also increasingly reported as a source of new chemical equity. Here, we provide examples in which integration of more than one screening approach has improved the campaign outcome and discuss how strengths and weaknesses of various methods can be used to build a complementary toolbox of approaches, giving researchers the greatest probability of successfully identifying leads. Among others, we highlight case studies for receptor-interacting serine/threonine-protein kinase 1 and the bromo- and extra-terminal domain family of bromodomains. In each example, the unique insight or chemistries individual approaches provided are described, emphasizing the synergy of information obtained from the various tactics employed and the particular question each tactic was employed to answer. We conclude with a short prospective discussing how screening strategies are evolving, what this screening toolbox might look like in the future, how to maximize success through integration of multiple tactics, and scenarios that drive selection of one combination of tactics over another.
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Affiliation(s)
- Melanie Leveridge
- 1 GlaxoSmithKline Drug Design and Selection, Platform Technology and Science, Stevenage, Hertfordshire, UK
| | - Chun-Wa Chung
- 1 GlaxoSmithKline Drug Design and Selection, Platform Technology and Science, Stevenage, Hertfordshire, UK
| | - Jeffrey W Gross
- 2 GlaxoSmithKline Drug Design and Selection, Platform Technology and Science, Collegeville, PA, USA
| | - Christopher B Phelps
- 3 GlaxoSmithKline Drug Design and Selection, Platform Technology and Science, Cambridge, MA, USA
| | - Darren Green
- 1 GlaxoSmithKline Drug Design and Selection, Platform Technology and Science, Stevenage, Hertfordshire, UK
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Nijsen MJ, Wu F, Bansal L, Bradshaw‐Pierce E, Chan JR, Liederer BM, Mettetal JT, Schroeder P, Schuck E, Tsai A, Xu C, Chimalakonda A, Le K, Penney M, Topp B, Yamada A, Spilker ME. Preclinical QSP Modeling in the Pharmaceutical Industry: An IQ Consortium Survey Examining the Current Landscape. CPT Pharmacometrics Syst Pharmacol 2018; 7:135-146. [PMID: 29349875 PMCID: PMC5869550 DOI: 10.1002/psp4.12282] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/15/2018] [Accepted: 01/16/2018] [Indexed: 01/01/2023] Open
Abstract
A cross-industry survey was conducted to assess the landscape of preclinical quantitative systems pharmacology (QSP) modeling within pharmaceutical companies. This article presents the survey results, which provide insights on the current state of preclinical QSP modeling in addition to future opportunities. Our results call attention to the need for an aligned definition and consistent terminology around QSP, yet highlight the broad applicability and benefits preclinical QSP modeling is currently delivering.
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Affiliation(s)
| | - Fan Wu
- Novartis Institutes for Biomedical ResearchEast HanoverNew JerseyUSA
| | | | | | | | | | - Jerome T. Mettetal
- AstraZeneca, Drug Safety and Metabolism, IMED Biotech Unit, AstraZenecaBostonMassachusettsUSA
| | | | | | - Alice Tsai
- Vertex Pharmaceuticals IncorporatedBostonMassachusettsUSA
| | | | | | - Kha Le
- AgiosBostonMassachusettsUSA
| | | | | | | | - Mary E. Spilker
- Pfizer Worldwide Research and DevelopmentSan DiegoCaliforniaUSA
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Abstract
In this month's editorial, the PLOS Medicine Editors discuss the challenges of addressing a growing population with Alzheimer disease and dementia amidst disappointing news from the pharmaceutical industry.
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Affiliation(s)
- Björn Jobke
- Public Library of Science, San Francisco, California, United States of America, and Cambridge, United Kingdom
| | - Thomas McBride
- Public Library of Science, San Francisco, California, United States of America, and Cambridge, United Kingdom
| | - Linda Nevin
- Public Library of Science, San Francisco, California, United States of America, and Cambridge, United Kingdom
| | - Larry Peiperl
- Public Library of Science, San Francisco, California, United States of America, and Cambridge, United Kingdom
| | - Amy Ross
- Public Library of Science, San Francisco, California, United States of America, and Cambridge, United Kingdom
| | - Clare Stone
- Public Library of Science, San Francisco, California, United States of America, and Cambridge, United Kingdom
| | - Richard Turner
- Public Library of Science, San Francisco, California, United States of America, and Cambridge, United Kingdom
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Abstract
Chemists at The Scripps Research Institute in La Jolla, CA, and Pfizer's La Jolla Laboratories have devised a new way to rapidly synthesize strained-ring structures, which are increasingly favored to optimize potential drugs. With this method, strain-release amination, Pfizer researchers were able to produce sufficient quantities of a particular structure they needed to evaluate a promising cancer drug candidate.
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Wang W. Integration of Regulatory Guidelines into Protein Drug Product Development. PDA J Pharm Sci Technol 2016; 70:2-11. [PMID: 26889052 DOI: 10.5731/pdajpst.2015.005553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
UNLABELLED The drug product development process for proteins went through its infancy in the early eighties of last century and is in its maturity today. This has been driven largely by the rapid growth of the biotechnology industry, which led to the development and issuance of many regulatory guidelines/directories, especially those through the International Conference of Harmonization (ICH). These guidelines have certainly guided different aspects of a drug product development process. On the other hand, they were issued separately on different topics and in different time periods. An integration of all relevant guidelines into the corresponding areas in drug product development would greatly facilitate the development process. The purpose of this short review is to integrate the relevant (mainly ICH) regulatory guidelines into protein drug product development and to discuss remaining issues, which may lead to further revision of existing guidelines or development of new ones. Drug product development scientists need to collect adequate and relevant development data for a successful product registration. The key is the ability to justify the final drug product in terms of choice of the drug product formulation, container closure system, and manufacturing process. LAY ABSTRACT The drug product development process for proteins has matured today, largely due to the rapid growth of the biotechnology industry. In this process, many regulatory guidelines/directories were developed and issued, especially through the International Conference of Harmonization (ICH). However, they were issued separately on different topics and in different time periods. An integration of all relevant guidelines into the corresponding areas in drug product development would greatly facilitate the development process. The purpose of this short review is to integrate the relevant (mainly ICH) regulatory guidelines into protein drug product development and to discuss remaining issues, which may lead to further revision of existing guidelines or development of new ones. Drug product development scientists need to collect adequate and relevant development data for a successful product registration. The key is the ability to justify the final drug product in terms of choice of the product formulation, container closure system, and manufacturing process.
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Affiliation(s)
- Wei Wang
- Wang Biologics, LLC, Chesterfield, MO 36017, USA; 636-795-0285;
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Tiefer L, Laan E, Basson R. Missed Opportunities in the Patient-Focused Drug Development Public Meeting and Scientific Workshop on Female Sexual Dysfunction Held at the FDA, October 2014. J Sex Res 2015; 52:601-603. [PMID: 26010838 DOI: 10.1080/00224499.2014.1003362] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
There were numerous missed opportunities at the October 2014 U.S. Food and Drug Administration (FDA) meeting on female sexual dysfunction (FSD). They included opportunities to hear from a diverse range of patients and to engage in evidence-based discussions of unmet medical needs, diagnostic instruments, trial end points, and inclusion criteria for clinical trials. Contributions of the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) nomenclature, based on extensive research, were dismissed in favor of language favoring a seemingly clear but scientifically unsupportable distinction between women's sexual desire and arousal. Numerous participants, including patients recruited by their physicians, acknowledged travel expenses paid for by interested pharmaceutical companies. Conflicts of interest were manifold. The meeting did not advance the FDA's understanding of women's sexual distress and represents a setback for our field.
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Drici MD, Baldin B. [Is the clinical development of drugs appropriate in the elderly population?]. Rev Prat 2015; 65:602-604. [PMID: 26165088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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Abstract
The number of academic drug discovery centres has grown considerably in recent years, providing new opportunities to couple the curiosity-driven research culture in academia with rigorous preclinical drug discovery practices used in industry. To fully realize the potential of these opportunities, it is important that academic researchers understand the risks inherent in preclinical drug discovery, and that translational research programmes are effectively organized and supported at an institutional level. In this article, we discuss strategies to mitigate risks in several key aspects of preclinical drug discovery at academic drug discovery centres, including organization, target selection, assay design, medicinal chemistry and preclinical pharmacology.
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Affiliation(s)
- Jayme L Dahlin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
| | - James Inglese
- 1] National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, Maryland 20850, USA. [2] National Human Genome Research Institute, Bethesda, Maryland, 20892, USA
| | - Michael A Walters
- Institute for Therapeutics Discovery and Development, University of Minnesota Twin Cities, 717 Delaware St SE, Room 609, Minneapolis, Minnesota 55414, USA
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Abstract
Over the past 30 years, China has significantly improved the drug development environment by establishing a series of policies for the regulation of new drug approval. The regulatory system for new drug evaluation and registration in China was gradually developed in accordance with international standards. The approval and registration of TCM in China became as strict as those of chemical drugs and biological products. In this review, TCM-based new drug discovery and development are introduced according to the TCM classification of nine categories.
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Affiliation(s)
- Wan-Ying Wu
- Shanghai Research Center for Modernization of Traditional Chinese Medicine and National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jin-Jun Hou
- Shanghai Research Center for Modernization of Traditional Chinese Medicine and National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hua-Li Long
- Shanghai Research Center for Modernization of Traditional Chinese Medicine and National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wen-Zhi Yang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine and National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jian Liang
- Shanghai Research Center for Modernization of Traditional Chinese Medicine and National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine and National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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Manrique A, Adams E, Barouch DH, Fast P, Graham BS, Kim JH, Kublin JG, McCluskey M, Pantaleo G, Robinson HL, Russell N, Snow W, Johnston MI. The immune space: a concept and template for rationalizing vaccine development. AIDS Res Hum Retroviruses 2014; 30:1017-22. [PMID: 24857015 PMCID: PMC4208609 DOI: 10.1089/aid.2014.0040] [Citation(s) in RCA: 11] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Empirical testing of candidate vaccines has led to the successful development of a number of lifesaving vaccines. The advent of new tools to manipulate antigens and new methods and vectors for vaccine delivery has led to a veritable explosion of potential vaccine designs. As a result, selection of candidate vaccines suitable for large-scale efficacy testing has become more challenging. This is especially true for diseases such as dengue, HIV, and tuberculosis where there is no validated animal model or correlate of immune protection. Establishing guidelines for the selection of vaccine candidates for advanced testing has become a necessity. A number of factors could be considered in making these decisions, including, for example, safety in animal and human studies, immune profile, protection in animal studies, production processes with product quality and stability, availability of resources, and estimated cost of goods. The "immune space template" proposed here provides a standardized approach by which the quality, level, and durability of immune responses elicited in early human trials by a candidate vaccine can be described. The immune response profile will demonstrate if and how the candidate is unique relative to other candidates, especially those that have preceded it into efficacy testing and, thus, what new information concerning potential immune correlates could be learned from an efficacy trial. A thorough characterization of immune responses should also provide insight into a developer's rationale for the vaccine's proposed mechanism of action. HIV vaccine researchers plan to include this general approach in up-selecting candidates for the next large efficacy trial. This "immune space" approach may also be applicable to other vaccine development endeavors where correlates of vaccine-induced immune protection remain unknown.
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Affiliation(s)
| | - Elizabeth Adams
- Division of AIDS, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Dan H. Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Pat Fast
- International AIDS Vaccine Initiative, New York, New York
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Jerome H. Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - James G. Kublin
- HIV Vaccine Trials Network and the Vaccine and Infectious Disease Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Giuseppe Pantaleo
- Division of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | | | - Nina Russell
- The Bill & Melinda Gates Foundation, Seattle, Washington
| | - William Snow
- Global HIV Vaccine Enterprise, New York, New York
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Affiliation(s)
- Steven Joffe
- Department of Medical Ethics and Health Policy, Perelman School of Medicine, University of Pennsylvania, Philadelphia
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Kleiman RB, Shah RR, Morganroth J. Replacing the thorough QT study: reflections of a baby in the bath water. Br J Clin Pharmacol 2014; 78:195-201. [PMID: 24286381 PMCID: PMC4137815 DOI: 10.1111/bcp.12296] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 11/21/2013] [Indexed: 01/03/2023] Open
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Affiliation(s)
- Laurent Verkoczy
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Pathology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
- * E-mail:
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FDA AD Drug Development Guidance. J Nucl Med 2013; 54:16N. [PMID: 23546928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
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Cai DJ, Shu Q, Xu BQ, Peng LM, He Y. Orthogonal test design for optimization of the extraction of flavonid from the Fructus Gardeniae. Biomed Environ Sci 2011; 24:688-693. [PMID: 22365407 DOI: 10.3967/0895-3988.2011.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 04/25/2011] [Indexed: 05/31/2023]
Abstract
OBJECTIVE It is imperative to provide some consistent experimental results for the extraction of flavonid from Fructus Gardeniae. METHODS The key extraction parameters that influenced the yield of flavonid from Fructus Gardeniae were optimized by employing an orthogonal experiment [L(9)(3)(4)], including the ratio of buffer solution (Na(2)B(4)O(7)·10H(2)O) to raw material, concentration of Fructus Gardeniae in extracting solution, extraction time and pH of buffer solution. An UV/Vis detector was used to perform the qualitative and quantitative analyses of the extracted flavonid with the using of the standard sample. RESULTS The maximum extraction yield of the crude extract was 5.0533 (mg/g) after 20 min when the mass ratio of Na(2)B(4)O(7)·10H(2)O to raw material was 0.4%, the concentration of Fructus Gardeniae in the extraction solution was 1/12 (g/mL), and pH of buffer solution was 4.5. The positive reactions to the Molish and HCl-Mg tests suggested that the extracted compound was flavonoid, and FTIR measurements also identified the presence of flavonoid in the extracts. CONCLUSION This work is expected to provide a basis for further research, development, and utilization of Fructus gardenia in flavonid extraction.
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Affiliation(s)
- Ding Jian Cai
- School of Metallurgy and Chemical Engineering, Jiangxi University of Science and Technology, Ganzhou 341000, Jiangxi, China
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31
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Ramanathan R, Jemal M, Ramagiri S, Xia YQ, Humpreys WG, Olah T, Korfmacher WA. It is time for a paradigm shift in drug discovery bioanalysis: from SRM to HRMS. J Mass Spectrom 2011; 46:595-601. [PMID: 21630388 DOI: 10.1002/jms.1921] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
It can be argued that the last true paradigm shift in the bioanalytical (BA) arena was the shift from high-performance liquid chromatography (HPLC) with ultraviolet (UV) detection to HPLC with tandem mass spectrometry (MS/MS) detection after the commercialization of the triple quadrupole mass spectrometer in the 1990s. HPLC-MS/MS analysis based on selected reaction monitoring (SRM) has become the gold standard for BA assays and is used by all the major pharmaceutical companies for the quantitative analysis of new drug entities (NCEs) as part of the new drug discovery and development process. While LC-MS/MS continues to be the best tool for drug discovery bioanalysis, a new paradigm involving high-resolution mass spectrometry (HRMS) and ultrahigh-pressure liquid chromatography (uHPLC) is starting to make inroads into the pharmaceutical industry. The ability to collect full scan spectra, with excellent mass accuracy, mass resolution, 10-250 ms scan speeds and no NCE-related MS parameter optimization, makes the uHPLC-HRMS techniques suitable for quantitative analysis of NCEs while preserving maximum qualitative information about other drug-related and endogenous components such as metabolites, degradants, biomarkers and formulation materials. In this perspective article, we provide some insight into the evolution of the hybrid quadrupole-time-of-flight (Qq-TOF) mass spectrometer and propose some of the desirable specifications that such HRMS systems should have to be integrated into the drug discovery bioanalytical workflow for performing integrated qualitative and quantitative bioanalysis of drugs and related components.
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Affiliation(s)
- Ragu Ramanathan
- Bristol-Myers Squibb Co., Pharmaceutical Candidate Optimization, Princeton, NJ 08540, USA.
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Wagner AD, Kolb JM, Ozbal CC, Herbst JJ, Olah TV, Weller HN, Zvyaga TA, Shou WZ. Ultrafast mass spectrometry based bioanalytical method for digoxin supporting an in vitro P-glycoprotein (P-gp) inhibition screen. Rapid Commun Mass Spectrom 2011; 25:1231-1240. [PMID: 21488121 DOI: 10.1002/rcm.4984] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The evaluation of interactions between drug candidates and transporters such as P-glycoprotein (P-gp) has gained considerable interest in drug discovery and development. Inhibition of P-gp can be assessed by performing bi-directional permeability studies with in vitro P-gp-expressing cellular model systems such as Caco-2 (human colon carcinoma) cells, using digoxin as a substrate probe. Existing methodologies include either assaying (3)H-digoxin with liquid scintillation counting (LSC) detection or assaying non-labeled digoxin with liquid chromatography-tandem mass spectrometric (LC-MS/MS) analysis at a speed of several minutes per sample. However, it is not feasible to achieve a throughput high enough using these approaches to sustain an early liability screen that generates more than a thousand samples on a daily basis. To address this challenge, we developed an ultrafast (9 s per sample) bioanalytical method for digoxin analysis using RapidFire™, an on-line solid-phase extraction (SPE) system, with MS/MS detection. A stable isotope labeled analog, d3-digoxin, was used as internal standard to minimize potential ionization matrix effect during the RF-MS/MS analysis. The RF-MS/MS method was more than 16 times faster than the LC-MS/MS method but demonstrated similar sensitivity, selectivity, reproducibility, linearity and robustness. P-gp inhibition results of multiple validation compounds obtained with this RF-MS/MS method were in agreement with those generated by both the LC-MS/MS method and the (3)H-radiolabel assay. This method has been successfully deployed to assess P-gp inhibition potential as an important early liability screen for drug-transporter interaction.
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Affiliation(s)
- Andrew D Wagner
- Applied Biotechnology, Bristol-Myers Squibb, Wallingford, CT 06492, USA
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Wang N, Lipworth WL, Ritchie JE, Williams KM, Day RO. Eliciting views of Australian pharmaceutical industry employees on collaboration and the concept of Quality Use of Medicines. Intern Med J 2011; 41:314-20. [PMID: 20403068 DOI: 10.1111/j.1445-5994.2010.02239.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- N Wang
- Faculty of Medicine and 2 School of Public Health and Community Medicine, University of New South Wales, Australia
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Abstract
A common view within the pharmaceutical industry is that there is a problem with drug discovery and we should do something about it. There is much sympathy for this from academics, regulators and politicians. In this article I propose that lessons learnt from evolution help identify those factors that favour successful drug discovery. This personal view is influenced by a decade spent reviewing drug development programmes submitted for European regulatory approval. During the prolonged gestation of a new medicine few candidate molecules survive. This process of elimination of many variants and the survival of so few has much in common with evolution, an analogy that encourages discussion of the forces that favour, and those that hinder, successful drug discovery. Imagining a world without vaccines, anaesthetics, contraception and anti-infectives reveals how medicines revolutionized humanity. How to manipulate conditions that favour such discoveries is worth consideration.
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Affiliation(s)
- Wolfgang Löscher
- Department of Pharmacology, Toxicology, and Pharmacy, University of Veterinary Medicine, Hannover, Germany.
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Naeger LK, Struble KA, Murray JS, Birnkrant DB. Running a tightrope: regulatory challenges in the development of antiretrovirals. Antiviral Res 2009; 85:232-40. [PMID: 19665489 DOI: 10.1016/j.antiviral.2009.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 07/22/2009] [Accepted: 07/30/2009] [Indexed: 11/18/2022]
Abstract
Since the approval of Retrovir, (zidovudine, AZT) in 1987 by the Food and Drug Administration, a number of regulatory initiatives were codified into regulation which contributed to the rapid development of new treatments for HIV-1 infection. These initiatives are a testament to the efforts of AIDS activists and regulators to improve access to drugs for serious and life-threatening diseases. Currently, 28 antiretroviral drugs and combinations of antiretrovirals are available to treat HIV-1 infection. The broadening armamentarium of approved antiretroviral drugs provides new options and more choices for physicians and HIV patients. Importantly, the introduction of these newly approved HIV drugs has shown that the majority of HIV-1-infected treatment-naïve and treatment-experienced patients can achieve maximal virologic suppression (less than 50 copies/mL HIV-1 RNA). This article describes the past and current regulatory challenges in the development of new HIV treatments and provides an overview of the drug regulations that were required for the approval of HIV drugs. This article forms part of a special issue of Antiviral Research marking the 25th anniversary of antiretroviral drug discovery and development, Vol 85, issue 1, 2010.
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Affiliation(s)
- Lisa K Naeger
- Division of Antiviral Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States.
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Oprea TI, Bologa CG, Boyer S, Curpan RF, Glen RC, Hopkins AL, Lipinski CA, Marshall GR, Martin YC, Ostopovici-Halip L, Rishton G, Ursu O, Vaz RJ, Waller C, Waldmann H, Sklar LA. A crowdsourcing evaluation of the NIH chemical probes. Nat Chem Biol 2009; 5:441-7. [PMID: 19536101 PMCID: PMC3596119 DOI: 10.1038/nchembio0709-441] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [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: 11/09/2022]
Abstract
Between 2004 and 2008, the US National Institutes of Health Molecular Libraries and Imaging initiative pilot phase funded 10 high-throughput screening centers, resulting in the deposition of 691 assays into PubChem and the nomination of 64 chemical probes. We crowdsourced the Molecular Libraries and Imaging initiative output to 11 experts, who expressed medium or high levels of confidence in 48 of these 64 probes.
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Affiliation(s)
- Tudor I. Oprea
- UNM Center for Molecular Discovery University of New Mexico School of Medicine 2703 Frontier NE Albuquerque NM 87131, USA
| | - Cristian G. Bologa
- UNM Center for Molecular Discovery University of New Mexico School of Medicine 2703 Frontier NE Albuquerque NM 87131, USA
| | - Scott Boyer
- Global Safety Assessment AstraZeneca R&D, S-431 83 Mölndal, Sweden
| | - Ramona F. Curpan
- UNM Center for Molecular Discovery University of New Mexico School of Medicine 2703 Frontier NE Albuquerque NM 87131, USA
- Institute of Chemistry, Romanian Academy, 24 Mihai Viteazul, Timisoara 300223, Romania
| | - Robert C. Glen
- Unilever Centre for Molecular Science Informatics Department of Chemistry Lensfield Road Cambridge CB2 1EW, UK
| | - Andrew L. Hopkins
- Division of Biological Chemistry and Drug Discovery College of Life Science, University of Dundee, Dow Street, Dundee DD1 3DF, UK
| | | | - Garland R. Marshall
- Center for Computational Biology Washington University 700 S. Euclid Ave., Box 8036 St. Louis, MO 63110
| | | | - Liliana Ostopovici-Halip
- UNM Center for Molecular Discovery University of New Mexico School of Medicine 2703 Frontier NE Albuquerque NM 87131, USA
- Institute of Chemistry, Romanian Academy, 24 Mihai Viteazul, Timisoara 300223, Romania
| | - Gilbert Rishton
- Channel Islands Alzheimer’s Institute, California State University, Channel Islands, One University Drive, Camarillo, CA 93012, USA
| | - Oleg Ursu
- UNM Center for Molecular Discovery University of New Mexico School of Medicine 2703 Frontier NE Albuquerque NM 87131, USA
| | - Roy J. Vaz
- Sanofi-Aventis Pharmaceuticals 1041 Route 202-206, PO Box 5915 Bridgewater, NJ 08807, USA
| | - Chris Waller
- Chemistry Informatics Pfizer Global R&D Pfizer, Eastern Point Road, Groton, CT 06340, USA
| | - Herbert Waldmann
- Max-Planck Institut für Molekulare Physiologie Abteilung IV -Chemische Biologie Otto-Hahn-Strasse 11 D-44229 Dortmund, Germany and Technische Universität Dortmund, Faculty of Chemistry, Chemical Biology
| | - Larry A. Sklar
- UNM Center for Molecular Discovery University of New Mexico School of Medicine 2703 Frontier NE Albuquerque NM 87131, USA
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Schneider CK. Introduction to CHMP structures and procedures. Arb Paul Ehrlich Inst Bundesinstitut Impfstoffe Biomed Arzneim Langen Hess 2009; 96:172-177. [PMID: 20799458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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Popov II. ["Non-aging" pearl oyster and aging salmon (about lack of basis for production of medicines based on European pearl oyster Margaritifera margaritifera)]. Adv Gerontol 2009; 22:596-604. [PMID: 20405726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The article focuses on disproof of the claim by Valery Ziuganov, that pearl oyster infection prolongs the lifespan of salmon and that pearl oyster can be used as a source of medicine. His activity on the production of medicine pretending to care cancer and senescence based on the gills of salmon infected by pearl oyster is blamed. The data on pearl oyster and salmon biology are presented: Atlantic salmon survives after spawning irrespectively of oyster infection. The problem of shady medicines production is discussed. It was shown that even Academic editions and formal attributes of the belonging to scientific community do not provide a necessary barrier to frauds in this field. Adaptationist program popularity contributes such a situation, because it provides "grounds" for any speculation concerning advantages of any biological process.
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Abstract
This article provides an introduction to the problem of pharmaceutical research and development of medicinal products for neglected diseases in developing countries. The prevailing market-based intellectual property incentive model of global pharmaceutical innovation has focussed health research priorities mainly on needs of industrialized countries. Increased international attention to the lack of health tools to prevent or treat diseases affecting impoverished regions has raised the discussion on how to encourage sustainable innovation in this area with little or no market. Proposals include models such as for example prize funds, advanced purchase commitments patent pools or creative licensing strategies and seek to complement the current intellectual property based incentive mechanism and government's innovation policy instruments such as tax credits or public research funds. Indispensable requirement to tackle the issue of neglected diseases, however, is a concerted commitment of all stakeholders on national and international levels.
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Adamson PC. Current challenges in pediatric drug development. Clin Adv Hematol Oncol 2008; 6:883-884. [PMID: 19209138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Peter C Adamson
- Division of Clinical Pharmacology and Therapeutics, Clinical and Translational Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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Gustafsson LL, Wettermark B, Kalin M, Korkmaz S, Persson ME, Almkvist H, Hjemdahl P, Julander M, Kristianson K, Ringertz B, Bergen-Dahl GT, Wilking N. [A model for structured introduction of new drugs. The aim is to offer all patients appropriate treatment]. Lakartidningen 2008; 105:2917-2922. [PMID: 19025148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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