1
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Axtman AD, Brennan PE, Frappier‐Brinton T, Betarbet R, Carter GW, Fu H, Gileadi O, Greenwood AK, Leal K, Longo FM, Mangravite LM, Edwards AM, Levey AI. Open drug discovery in Alzheimer's disease. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2023; 9:e12394. [PMID: 37215505 PMCID: PMC10192886 DOI: 10.1002/trc2.12394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 05/24/2023]
Abstract
Alzheimer's disease (AD) drug discovery has focused on a set of highly studied therapeutic hypotheses, with limited success. The heterogeneous nature of AD processes suggests that a more diverse, systems-integrated strategy may identify new therapeutic hypotheses. Although many target hypotheses have arisen from systems-level modeling of human disease, in practice and for many reasons, it has proven challenging to translate them into drug discovery pipelines. First, many hypotheses implicate protein targets and/or biological mechanisms that are under-studied, meaning there is a paucity of evidence to inform experimental strategies as well as high-quality reagents to perform them. Second, systems-level targets are predicted to act in concert, requiring adaptations in how we characterize new drug targets. Here we posit that the development and open distribution of high-quality experimental reagents and informatic outputs-termed target enabling packages (TEPs)-will catalyze rapid evaluation of emerging systems-integrated targets in AD by enabling parallel, independent, and unencumbered research.
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Affiliation(s)
- Alison D. Axtman
- University of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | | | | | | | | | - Haian Fu
- Emory University School of MedicineAtlantaGeorgiaUSA
| | - Opher Gileadi
- Structural Genomics ConsortiumKarolinska InstituteStockholmSweden
| | | | | | - Frank M. Longo
- Stanford University School of MedicineStanfordCaliforniaUSA
| | | | - Aled M. Edwards
- Structural Genomics ConsortiumUniversity of TorontoTorontoOntarioCanada
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2
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Ross-Hellauer T, Reichmann S, Cole NL, Fessl A, Klebel T, Pontika N. Dynamics of cumulative advantage and threats to equity in open science: a scoping review. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211032. [PMID: 35116143 PMCID: PMC8767192 DOI: 10.1098/rsos.211032] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Open Science holds the promise to make scientific endeavours more inclusive, participatory, understandable, accessible and re-usable for large audiences. However, making processes open will not per se drive wide reuse or participation unless also accompanied by the capacity (in terms of knowledge, skills, financial resources, technological readiness and motivation) to do so. These capacities vary considerably across regions, institutions and demographics. Those advantaged by such factors will remain potentially privileged, putting Open Science's agenda of inclusivity at risk of propagating conditions of 'cumulative advantage'. With this paper, we systematically scope existing research addressing the question: 'What evidence and discourse exists in the literature about the ways in which dynamics and structures of inequality could persist or be exacerbated in the transition to Open Science, across disciplines, regions and demographics?' Aiming to synthesize findings, identify gaps in the literature and inform future research and policy, our results identify threats to equity associated with all aspects of Open Science, including Open Access, Open and FAIR Data, Open Methods, Open Evaluation, Citizen Science, as well as its interfaces with society, industry and policy. Key threats include: stratifications of publishing due to the exclusionary nature of the author-pays model of Open Access; potential widening of the digital divide due to the infrastructure-dependent, highly situated nature of open data practices; risks of diminishing qualitative methodologies as 'reproducibility' becomes synonymous with quality; new risks of bias and exclusion in means of transparent evaluation; and crucial asymmetries in the Open Science relationships with industry and the public, which privileges the former and fails to fully include the latter.
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Affiliation(s)
- Tony Ross-Hellauer
- Know-Center GmbH, Graz, Austria
- Open and Reproducible Research Group, Graz University of Technology, Inffeldgasse 13, 8010 Graz, Austria
| | - Stefan Reichmann
- Open and Reproducible Research Group, Graz University of Technology, Inffeldgasse 13, 8010 Graz, Austria
| | - Nicki Lisa Cole
- Know-Center GmbH, Graz, Austria
- Open and Reproducible Research Group, Graz University of Technology, Inffeldgasse 13, 8010 Graz, Austria
| | - Angela Fessl
- Know-Center GmbH, Graz, Austria
- Open and Reproducible Research Group, Graz University of Technology, Inffeldgasse 13, 8010 Graz, Austria
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3
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4
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Quinlan RBA, Brennan PE. Chemogenomics for drug discovery: clinical molecules from open access chemical probes. RSC Chem Biol 2021; 2:759-795. [PMID: 34458810 PMCID: PMC8341094 DOI: 10.1039/d1cb00016k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
In recent years chemical probes have proved valuable tools for the validation of disease-modifying targets, facilitating investigation of target function, safety, and translation. Whilst probes and drugs often differ in their properties, there is a belief that chemical probes are useful for translational studies and can accelerate the drug discovery process by providing a starting point for small molecule drugs. This review seeks to describe clinical candidates that have been inspired by, or derived from, chemical probes, and the process behind their development. By focusing primarily on examples of probes developed by the Structural Genomics Consortium, we examine a variety of epigenetic modulators along with other classes of probe.
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Affiliation(s)
- Robert B A Quinlan
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
| | - Paul E Brennan
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
- Alzheimer's Research (UK) Oxford Drug Discovery Institute, Nuffield Department of Medicine, University of Oxford Oxford OX3 7FZ UK
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5
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Yeung AWK, Atanasov AG, Sheridan H, Klager E, Eibensteiner F, Völkl-Kernsock S, Kletecka-Pulker M, Willschke H, Schaden E. Open Innovation in Medical and Pharmaceutical Research: A Literature Landscape Analysis. Front Pharmacol 2021; 11:587526. [PMID: 33519448 PMCID: PMC7840485 DOI: 10.3389/fphar.2020.587526] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022] Open
Abstract
Open innovation in medical and pharmaceutical research has grown steadily over the last decade. However, the performance of the published literature in terms of the scientific impact and gaining social media attention remains largely unexplored. The scientific literature of open innovation was examined by means of bibliometric analyses to identify the most prolific authors, organizations, countries, journals, research areas, and recurring terms. By accessing the Web of Science Core Collection and Altmetric electronic databases, citation-related and Altmetric data were evaluated. Public-private partnerships and a selection of newly introduced potential novel drugs in the analyzed publications were identified. North America and Europe were the major literature contributors. Research outputs were mainly published in journals focused on business and economics, pharmacology and pharmacy, and engineering. Many pharmaceutical and biotechnological companies contributed to the analyzed publications, with higher mean citation counts and social media attention (Altmetric score) than nonindustry articles. Public-private partnerships fostered financial support, sharing of expertise and intellectual property, and research collaborations. In summary, open innovation might serve as a powerful strategy to both benefit the involved industry entities and accelerate the development of solutions and products for the betterment of human health.
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Affiliation(s)
- Andy Wai Kan Yeung
- Oral and Maxillofacial Radiology, Applied Oral Sciences and Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China.,Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria
| | - Atanas G Atanasov
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria.,Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Magdalenka, Poland.,Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia, Bulgaria.,Department of Pharmacognosy, University of Vienna, Vienna, Austria
| | - Helen Sheridan
- NatPro Centre. School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, Dublin, Ireland
| | - Elisabeth Klager
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria
| | - Fabian Eibensteiner
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria.,Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Sabine Völkl-Kernsock
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria
| | - Maria Kletecka-Pulker
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria
| | - Harald Willschke
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria.,Department of Anaesthesia, Intensive Care Medicine and Pain Medicine, Medical University Vienna, Vienna, Austria
| | - Eva Schaden
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria.,Department of Anaesthesia, Intensive Care Medicine and Pain Medicine, Medical University Vienna, Vienna, Austria
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6
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Advances in antibiotic drug discovery: reducing the barriers for antibiotic development. Future Med Chem 2020; 12:2067-2087. [PMID: 33124460 DOI: 10.4155/fmc-2020-0247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Antibiotic drug discovery has been an essential field of research since the early 1900s, but the threat from infectious bacteria has only increased over the decades because of the emergence of widespread multidrug resistance. In this review, we discuss the recent advances in natural product, computational and medicinal chemistry that have reinvigorated the field of antibiotic drug discovery while giving perspective on how easily, both in cost and in expertise, these methods can be implemented by other researchers with the goal of increasing the number of scientists contributing to this public health crisis.
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7
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Bubela T, Gold ER, Goel V, Morgan M, Mossman K, Nickerson J, Patrick D, Edwards A. Open drug discovery of anti-virals critical for Canada’s pandemic strategy. Facets (Ott) 2020. [DOI: 10.1139/facets-2020-0079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In the event of the current COVID-19 pandemic and in preparation for future pandemics, open science can support mission-oriented research and development, as well as commercialization. Open science shares skills and resources across sectors; avoids duplication and provides the basis for rapid and effective validation due to full transparency. It is a strategy that can adjust quickly to reflect changing incentives and priorities, because it does not rely on any one actor or sector. While eschewing patents, it can ensure high-quality drugs, low pricing, and access through existing regulatory mechanisms. Open science practices and partnerships decrease transaction costs, increase diversity of actors, reduce overall costs, open new, higher-risk/higher-impact approaches to research, and provide entrepreneurs freedom to operate and freedom to innovate. We argue that it is time to re-open science, not only in its now restricted arena of fundamental research, but throughout clinical translation. Our model and attendant recommendations map onto a strategy to accelerate discovery of novel broad-spectrum anti-viral drugs and clinical trials of those drugs, from first-in-human safety-focused trials to late stage trials for efficacy. The goal is to ensure low-cost and rapid access, globally, and to ensure that Canadians do not pay a premium for drugs developed from Canadian science.
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Affiliation(s)
- Tania Bubela
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - E. Richard Gold
- Faculty of Law, McGill University, Montreal, QC H3A 1W9, Canada
| | - Vivek Goel
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M6, Canada
| | - Max Morgan
- M4K Pharma, Inc., Toronto, ON M5G 1L7, Canada
- Structural Genomics Consortium (SGC), Toronto, ON M5G 1L7, Canada
| | - Karen Mossman
- Pathology and Molecular Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Jason Nickerson
- University of Ottawa, Ottawa, ON K1N 6K5, Canada
- Bruyère Research Institute, Ottawa, ON K1N 5C8, Canada
| | - David Patrick
- British Columbia Centre for Disease Control, Vancouver, BC V5Z 4R4, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Aled Edwards
- Molecular Genetics and Medical Biophysics, University of Toronto, Toronto, ON M5G 1L5, Canada
- SGC, London, UK
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8
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Workman P, Antolin AA, Al-Lazikani B. Transforming cancer drug discovery with Big Data and AI. Expert Opin Drug Discov 2019; 14:1089-1095. [PMID: 31284790 DOI: 10.1080/17460441.2019.1637414] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/25/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Paul Workman
- The Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research , London , UK
| | - Albert A Antolin
- The Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research , London , UK
- The Department of Data Science, The Institute of Cancer Research , London , UK
| | - Bissan Al-Lazikani
- The Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research , London , UK
- The Department of Data Science, The Institute of Cancer Research , London , UK
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9
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Abstract
A common motivation for increasing open access to research findings and data is the potential to create economic benefits—but evidence is patchy and diverse. This study systematically reviewed the evidence on what kinds of economic impacts (positive and negative) open science can have, how these comes about, and how benefits could be maximized. Use of open science outputs often leaves no obvious trace, so most evidence of impacts is based on interviews, surveys, inference based on existing costs, and modelling approaches. There is indicative evidence that open access to findings/data can lead to savings in access costs, labour costs and transaction costs. There are examples of open science enabling new products, services, companies, research and collaborations. Modelling studies suggest higher returns to R&D if open access permits greater accessibility and efficiency of use of findings. Barriers include lack of skills capacity in search, interpretation and text mining, and lack of clarity around where benefits accrue. There are also contextual considerations around who benefits most from open science (e.g., sectors, small vs. larger companies, types of dataset). Recommendations captured in the review include more research, monitoring and evaluation (including developing metrics), promoting benefits, capacity building and making outputs more audience-friendly.
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10
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Tucker JD, Day S, Tang W, Bayus B. Crowdsourcing in medical research: concepts and applications. PeerJ 2019; 7:e6762. [PMID: 30997295 PMCID: PMC6463854 DOI: 10.7717/peerj.6762] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/11/2019] [Indexed: 12/23/2022] Open
Abstract
Crowdsourcing shifts medical research from a closed environment to an open collaboration between the public and researchers. We define crowdsourcing as an approach to problem solving which involves an organization having a large group attempt to solve a problem or part of a problem, then sharing solutions. Crowdsourcing allows large groups of individuals to participate in medical research through innovation challenges, hackathons, and related activities. The purpose of this literature review is to examine the definition, concepts, and applications of crowdsourcing in medicine. This multi-disciplinary review defines crowdsourcing for medicine, identifies conceptual antecedents (collective intelligence and open source models), and explores implications of the approach. Several critiques of crowdsourcing are also examined. Although several crowdsourcing definitions exist, there are two essential elements: (1) having a large group of individuals, including those with skills and those without skills, propose potential solutions; (2) sharing solutions through implementation or open access materials. The public can be a central force in contributing to formative, pre-clinical, and clinical research. A growing evidence base suggests that crowdsourcing in medicine can result in high-quality outcomes, broad community engagement, and more open science.
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Affiliation(s)
- Joseph D. Tucker
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, University of London, London, UK
- Social Entrepreneurship to Spur Health (SESH) Global, Guangzhou, China
| | - Suzanne Day
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Social Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Weiming Tang
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of STD Control, Dermatology Hospital of Southern Medical University, Guangzhou, China
| | - Barry Bayus
- Kenan-Flagler School of Business, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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11
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Morgan MR, Roberts OG, Edwards AM. Ideation and implementation of an open science drug discovery business model - M4K Pharma. Wellcome Open Res 2018; 3:154. [PMID: 30705971 PMCID: PMC6346698 DOI: 10.12688/wellcomeopenres.14947.1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2018] [Indexed: 12/04/2022] Open
Abstract
M4K Pharma was incorporated to launch an open science drug discovery program that relies on regulatory exclusivity as its primary intellectual property and commercial asset, in lieu of patents.In many cases and in key markets, using regulatory exclusivity can provide equivalent commercial protection to patents, while also being compatible with open science. The model is proving attractive to government, foundation and individual funders, who collectively have different expectations for returns on investment compared with biotech, pharmaceutical companies, or venture capital investors.In the absence of these investor-driven requirements for returns, it should be possible to commercialize therapeutics at affordable prices.M4K is piloting this open science business model in a rare paediatric brain tumour, but there is no reason it should not be more widely applicable.
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Affiliation(s)
- Maxwell Robert Morgan
- University of Toronto, Toronto, ON, M5G 1L7, Canada.,M4K Pharma, Toronto, ON, M5G 1L7, Canada.,Structural Genomics Consortium, London, UK
| | | | - Aled Morgan Edwards
- University of Toronto, Toronto, ON, M5G 1L7, Canada.,M4K Pharma, Toronto, ON, M5G 1L7, Canada.,Structural Genomics Consortium, London, UK
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12
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From bench to bedside, via desktop. Recent advances in the application of cutting-edge in silico tools in the research of drugs targeting bromodomain modules. Biochem Pharmacol 2018; 159:40-51. [PMID: 30414936 DOI: 10.1016/j.bcp.2018.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 11/07/2018] [Indexed: 11/22/2022]
Abstract
The discipline of drug discovery has greatly benefited by computational tools and in silico algorithms aiming at rationalization of many related processes, from the stage of early hit identification to the preclinical phases of drug candidate validation. The various methodologies referred to as molecular modeling tools span a broad spectrum of applications, from straightforward approaches such as virtual screening of compound libraries to more advanced techniques involving the precise estimation of free energy upon binding of the candidate drug to its macromolecular target. To this end, we report an overview of specific studies where implementation of such sophisticated modeling algorithms has shown to be indispensable for addressing challenging systems and biological questions otherwise difficult to answer. We focus our attention on the emerging field of bromodomain inhibitors. Bromodomains are small modules involved in epigenetic signaling and currently comprise high-priority targets for developing both drug candidates and chemical probes for basic biomedical research. We attempt a critical presentation of selected cases utilizing cutting-edge in silico methodologies, with our main emphasis being on absolute or relative free energy simulations, on implementation of quantum-mechanics level calculations and on characterization of solvent thermodynamics. We discuss the advantages and strengths as well as the drawbacks and weaknesses of computational tools utilized in those works and we attempt to comment on specific issues related to their integration into the regular medicinal chemistry practice. Our conclusion is that while such methods indeed represent highly promising resources for further advancing the discipline, their application is not always trivial.
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13
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Han C, Chaineau M, Chen CXQ, Beitel LK, Durcan TM. Open Science Meets Stem Cells: A New Drug Discovery Approach for Neurodegenerative Disorders. Front Neurosci 2018; 12:47. [PMID: 29467610 PMCID: PMC5808201 DOI: 10.3389/fnins.2018.00047] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 01/19/2018] [Indexed: 12/31/2022] Open
Abstract
Neurodegenerative diseases are a challenge for drug discovery, as the biological mechanisms are complex and poorly understood, with a paucity of models that faithfully recapitulate these disorders. Recent advances in stem cell technology have provided a paradigm shift, providing researchers with tools to generate human induced pluripotent stem cells (iPSCs) from patient cells. With the potential to generate any human cell type, we can now generate human neurons and develop "first-of-their-kind" disease-relevant assays for small molecule screening. Now that the tools are in place, it is imperative that we accelerate discoveries from the bench to the clinic. Using traditional closed-door research systems raises barriers to discovery, by restricting access to cells, data and other research findings. Thus, a new strategy is required, and the Montreal Neurological Institute (MNI) and its partners are piloting an "Open Science" model. One signature initiative will be that the MNI biorepository will curate and disseminate patient samples in a more accessible manner through open transfer agreements. This feeds into the MNI open drug discovery platform, focused on developing industry-standard assays with iPSC-derived neurons. All cell lines, reagents and assay findings developed in this open fashion will be made available to academia and industry. By removing the obstacles many universities and companies face in distributing patient samples and assay results, our goal is to accelerate translational medical research and the development of new therapies for devastating neurodegenerative disorders.
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Affiliation(s)
| | | | | | | | - Thomas M. Durcan
- Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
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14
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Schweizer L, He J. Guiding principles of value creation through collaborative innovation in pharmaceutical research. Drug Discov Today 2018; 23:213-218. [DOI: 10.1016/j.drudis.2017.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 08/22/2017] [Accepted: 09/03/2017] [Indexed: 11/24/2022]
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15
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Zuber V, Bettella F, Witoelar A, Andreassen OA, Mills IG, Urbanucci A. Bromodomain protein 4 discriminates tissue-specific super-enhancers containing disease-specific susceptibility loci in prostate and breast cancer. BMC Genomics 2017; 18:270. [PMID: 28359301 PMCID: PMC5374680 DOI: 10.1186/s12864-017-3620-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 03/11/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Epigenetic information can be used to identify clinically relevant genomic variants single nucleotide polymorphisms (SNPs) of functional importance in cancer development. Super-enhancers are cell-specific DNA elements, acting to determine tissue or cell identity and driving tumor progression. Although previous approaches have been tried to explain risk associated with SNPs in regulatory DNA elements, so far epigenetic readers such as bromodomain containing protein 4 (BRD4) and super-enhancers have not been used to annotate SNPs. In prostate cancer (PC), androgen receptor (AR) binding sites to chromatin have been used to inform functional annotations of SNPs. RESULTS Here we establish criteria for enhancer mapping which are applicable to other diseases and traits to achieve the optimal tissue-specific enrichment of PC risk SNPs. We used stratified Q-Q plots and Fisher test to assess the differential enrichment of SNPs mapping to specific categories of enhancers. We find that BRD4 is the key discriminant of tissue-specific enhancers, showing that it is more powerful than AR binding information to capture PC specific risk loci, and can be used with similar effect in breast cancer (BC) and applied to other diseases such as schizophrenia. CONCLUSIONS This is the first study to evaluate the enrichment of epigenetic readers in genome-wide associations studies for SNPs within enhancers, and provides a powerful tool for enriching and prioritizing PC and BC genetic risk loci. Our study represents a proof of principle applicable to other diseases and traits that can be used to redefine molecular mechanisms of human phenotypic variation.
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Affiliation(s)
- Verena Zuber
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Francesco Bettella
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Aree Witoelar
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - the CRUK GWAS
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- PCUK Movember Centre of Excellence, CCRCB, Queen’s University, Belfast, UK
| | - the TRICL Consortium
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- PCUK Movember Centre of Excellence, CCRCB, Queen’s University, Belfast, UK
| | - Ole A. Andreassen
- NORMENT, KG Jebsen Centre for Psychosis Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Ian G. Mills
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- PCUK Movember Centre of Excellence, CCRCB, Queen’s University, Belfast, UK
| | - Alfonso Urbanucci
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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16
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Smith JA, Arshad Z, Thomas H, Carr AJ, Brindley DA. Evidence of insufficient quality of reporting in patent landscapes in the life sciences. Nat Biotechnol 2017; 35:210-214. [DOI: 10.1038/nbt.3809] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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17
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Carter AJ, Donner A, Lee WH, Bountra C. Establishing a reliable framework for harnessing the creative power of the scientific crowd. PLoS Biol 2017; 15:e2001387. [PMID: 28199324 PMCID: PMC5331949 DOI: 10.1371/journal.pbio.2001387] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Discovering new medicines is difficult and increasingly expensive. The pharmaceutical industry has responded to this challenge by embracing open innovation to access external ideas. Historically, partnerships were usually bilateral, and the drug discovery process was shrouded in secrecy. This model is rapidly changing. With the advent of the Internet, drug discovery has become more decentralised, bottom-up, and scalable than ever before. The term open innovation is now accepted as just one of many terms that capture different but overlapping levels of openness in the drug discovery process. Many pharmaceutical companies recognise the advantages of revealing some proprietary information in the form of results, chemical tools, or unsolved problems in return for valuable insights and ideas. For example, such selective revealing can take the form of openly shared chemical tools to explore new biological mechanisms or by publicly admitting what is not known in the form of an open call. The essential ingredient for addressing these problems is access to the wider scientific crowd. The business of crowdsourcing, a form of outsourcing in which individuals or organisations solicit contributions from Internet users to obtain ideas or desired services, has grown significantly to fill this need and takes many forms today. Here, we posit that open-innovation approaches are more successful when they establish a reliable framework for converting creative ideas of the scientific crowd into practice with actionable plans.
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Affiliation(s)
- Adrian J. Carter
- Department of Discovery Research Coordination, Boehringer Ingelheim, Ingelheim, Germany
| | - Amy Donner
- The Chemical Probes Portal, Genetics Medicine Research Building, Chapel Hill, North Carolina, United States of America
| | - Wen Hwa Lee
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Chas Bountra
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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Meier A, Faulkner SD, Schoonderbeek C, Jong B, Kung J, Brindley D, Barker R. An assessment of implications of adaptive licensing for pharmaceutical intellectual property and regulatory exclusivity rights in the European Union. Clin Pharmacol Ther 2016; 100:743-753. [PMID: 27626890 DOI: 10.1002/cpt.511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/12/2016] [Accepted: 09/12/2016] [Indexed: 11/10/2022]
Abstract
One of the key advantages of adaptive licensing (AL) is to align the licensing of new medicines more closely with patient needs for earlier access to beneficial treatments. From an innovators perspective, "earlier" market access may seem an obvious incentive to gain earlier revenue generation. However, this is offset with an "earlier" start to patent and regulatory protection periods, which, depending on the technology, disease, population, and timing of subsequent asset protection periods, can present a conflict.
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Affiliation(s)
- A Meier
- Novartis Pharma AG, Basel, Switzerland
| | - S D Faulkner
- Centre for Advancement for Sustainable Medical Innovation (CASMI), Oxford, United Kingdom
| | | | - B Jong
- Hoyng ROKH Monegier (HRM), Amsterdam, The Netherlands
| | - J Kung
- Novartis Pharmaceuticals Corporation, East Hanover, New Jersey, USA
| | - D Brindley
- The Oxford - UCL Centre for the Advancement of Sustainable Medical Innovation (CASMI), The University of Oxford, Oxford, United Kingdom.,Department of Paediatrics, University of Oxford, Children's Hospital, John Radcliffe, Oxford, United Kingdom.,Said Business School, University of Oxford, Park End Street, Oxford, United Kingdom.,Centre for Behavioural Medicine, UCL School of Pharmacy, University College London, London, United Kingdom.,Harvard Stem Cell Institute, Cambridge, Massachusetts, USA.,University of California - San Francisco, Stanford Center of Excellence in Regulatory Science and Innovation (CERSI), San Francisco, California, USA
| | - R Barker
- Centre for Advancement for Sustainable Medical Innovation (CASMI), Oxford, United Kingdom
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Low E, Bountra C, Lee WH. Accelerating target discovery using pre-competitive open science-patients need faster innovation more than anyone else. Ecancermedicalscience 2016; 10:ed57. [PMID: 27594912 PMCID: PMC4990051 DOI: 10.3332/ecancer.2016.ed57] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Indexed: 12/12/2022] Open
Abstract
We are experiencing a new era enabled by unencumbered access to high quality data through the emergence of open science initiatives in the historically challenging area of early stage drug discovery. At the same time, many patient-centric organisations are taking matters into their own hands by participating in, enabling and funding research. Here we present the rationale behind the innovative partnership between the Structural Genomics Consortium (SGC)-an open, pre-competitive pre-clinical research consortium and the research-focused patient organisation Myeloma UK to create a new, comprehensive platform to accelerate the discovery and development of new treatments for multiple myeloma.
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Affiliation(s)
- Eric Low
- Myeloma UK, 22 Logie Mill, Edinburgh EH7 4HG, UK
| | - Chas Bountra
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
| | - Wen Hwa Lee
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Oxford OX3 7DQ, UK
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