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Wray J, Whitmore A. Network-Driven Drug Discovery. Methods Mol Biol 2022; 2390:177-190. [PMID: 34731469 DOI: 10.1007/978-1-0716-1787-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We describe an approach to early stage drug discovery that explicitly engages with the complexities of human biology. The combined computational and experimental approach is formulated on a conceptual framework in which network biology is used to bridge between individual molecular entities and the cellular phenotype that emerges when those entities interact in a network. Multiple aspects of early stage discovery are addressed including the data-driven elucidation of biological processes implicated in disease, target identification and validation, phenotypic discovery of active molecules and their mechanism of action, and extraction of genetic target support from human population genetics data. Validation is described via summary of a number of discovery projects and details from a project aimed at COVID-19 disease.
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Affiliation(s)
- Jonny Wray
- e-therapeutics plc, Long Hanborough, UK.
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52
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Barbosa MAG, Xavier CPR, Pereira RF, Petrikaitė V, Vasconcelos MH. 3D Cell Culture Models as Recapitulators of the Tumor Microenvironment for the Screening of Anti-Cancer Drugs. Cancers (Basel) 2021; 14:190. [PMID: 35008353 PMCID: PMC8749977 DOI: 10.3390/cancers14010190] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022] Open
Abstract
Today, innovative three-dimensional (3D) cell culture models have been proposed as viable and biomimetic alternatives for initial drug screening, allowing the improvement of the efficiency of drug development. These models are gaining popularity, given their ability to reproduce key aspects of the tumor microenvironment, concerning the 3D tumor architecture as well as the interactions of tumor cells with the extracellular matrix and surrounding non-tumor cells. The development of accurate 3D models may become beneficial to decrease the use of laboratory animals in scientific research, in accordance with the European Union's regulation on the 3R rule (Replacement, Reduction, Refinement). This review focuses on the impact of 3D cell culture models on cancer research, discussing their advantages, limitations, and compatibility with high-throughput screenings and automated systems. An insight is also given on the adequacy of the available readouts for the interpretation of the data obtained from the 3D cell culture models. Importantly, we also emphasize the need for the incorporation of additional and complementary microenvironment elements on the design of 3D cell culture models, towards improved predictive value of drug efficacy.
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Affiliation(s)
- Mélanie A. G. Barbosa
- Cancer Drug Resistance Group, IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal; (M.A.G.B.); (C.P.R.X.)
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal;
| | - Cristina P. R. Xavier
- Cancer Drug Resistance Group, IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal; (M.A.G.B.); (C.P.R.X.)
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal;
| | - Rúben F. Pereira
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal;
- Biofabrication Group, INEB—Instituto de Engenharia Biomédica, Universidade do Porto, 4200-135 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Vilma Petrikaitė
- Laboratory of Drug Targets Histopathology, Institute of Cardiology, Lithuanian University of Health Sciences, A. Mickevičiaus g 9, LT-44307 Kaunas, Lithuania;
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257 Vilnius, Lithuania
| | - M. Helena Vasconcelos
- Cancer Drug Resistance Group, IPATIMUP—Institute of Molecular Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal; (M.A.G.B.); (C.P.R.X.)
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal;
- Department of Biological Sciences, FFUP—Faculty of Pharmacy of the University of Porto, 4050-313 Porto, Portugal
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53
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Bai X, Yin Y. Exploration and augmentation of pharmacological space via adversarial auto-encoder model for facilitating kinase-centric drug development. J Cheminform 2021; 13:95. [PMID: 34872613 PMCID: PMC8650415 DOI: 10.1186/s13321-021-00574-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 11/20/2021] [Indexed: 11/10/2022] Open
Abstract
Predicting compound-protein interactions (CPIs) is of great importance for drug discovery and repositioning, yet still challenging mainly due to the sparse nature of CPI matrixes, resulting in poor generalization performance. Hence, unlike typical CPI prediction models focused on representation learning or model selection, we propose a deep neural network-based strategy, PCM-AAE, that re-explores and augments the pharmacological space of kinase inhibitors by introducing the adversarial auto-encoder model (AAE) to improve the generalization of the prediction model. To complete the data space, we constructed Ensemble of PCM-AAE (EPA), an ensemble model that quickly and accurately yields quantitative predictions of binding affinity between any human kinase and inhibitor. In rigorous internal validation, EPA showed excellent performance, consistently outperforming the model trained with the imbalanced set, especially for targets with relatively fewer training data points. Improved prediction accuracy of EPA for external datasets enhances its generalization ability, making it possible to gracefully handle previously unseen kinases and inhibitors. EPA showed promising potential when directly applied to virtual screening and off-target prediction, exhibiting its practicality in hit prediction. Our strategy is expected to facilitate kinase-centric drug development, as well as to solve more challenging prediction problems with insufficient data points.
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Affiliation(s)
- Xinyu Bai
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, People's Republic of China
| | - Yuxin Yin
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, People's Republic of China.
- Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing, 100191, China.
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54
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Olías-Molero AI, de la Fuente C, Cuquerella M, Torrado JJ, Alunda JM. Antileishmanial Drug Discovery and Development: Time to Reset the Model? Microorganisms 2021; 9:2500. [PMID: 34946102 PMCID: PMC8703564 DOI: 10.3390/microorganisms9122500] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 01/27/2023] Open
Abstract
Leishmaniasis is a vector-borne parasitic disease caused by Leishmania species. The disease affects humans and animals, particularly dogs, provoking cutaneous, mucocutaneous, or visceral processes depending on the Leishmania sp. and the host immune response. No vaccine for humans is available, and the control relies mainly on chemotherapy. However, currently used drugs are old, some are toxic, and the safer presentations are largely unaffordable by the most severely affected human populations. Moreover, its efficacy has shortcomings, and it has been challenged by the growing reports of resistance and therapeutic failure. This manuscript presents an overview of the currently used drugs, the prevailing model to develop new antileishmanial drugs and its low efficiency, and the impact of deconstruction of the drug pipeline on the high failure rate of potential drugs. To improve the predictive value of preclinical research in the chemotherapy of leishmaniasis, several proposals are presented to circumvent critical hurdles-namely, lack of common goals of collaborative research, particularly in public-private partnership; fragmented efforts; use of inadequate surrogate models, especially for in vivo trials; shortcomings of target product profile (TPP) guides.
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Affiliation(s)
- Ana Isabel Olías-Molero
- Department of Animal Health, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.I.O.-M.); (C.d.l.F.); (M.C.)
| | - Concepción de la Fuente
- Department of Animal Health, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.I.O.-M.); (C.d.l.F.); (M.C.)
| | - Montserrat Cuquerella
- Department of Animal Health, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.I.O.-M.); (C.d.l.F.); (M.C.)
| | - Juan J. Torrado
- Department of Pharmaceutics and Food Technology, Faculty of Pharmacy, Universidad Complutense de Madrid, 28040 Madrid, Spain;
| | - José M. Alunda
- Department of Animal Health, Faculty of Veterinary Medicine, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.I.O.-M.); (C.d.l.F.); (M.C.)
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55
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Tuffin J, Chesor M, Kuzmuk V, Johnson T, Satchell SC, Welsh GI, Saleem MA. GlomSpheres as a 3D co-culture spheroid model of the kidney glomerulus for rapid drug-screening. Commun Biol 2021; 4:1351. [PMID: 34857869 PMCID: PMC8640035 DOI: 10.1038/s42003-021-02868-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 10/28/2021] [Indexed: 01/28/2023] Open
Abstract
The glomerulus is the filtration unit of the kidney. Injury to any component of this specialised structure leads to impaired filtration and eventually fibrosis and chronic kidney disease. Current two and three dimensional (2D and 3D) models that attempt to recreate structure and interplay between glomerular cells are imperfect. Most 2D models are simplistic and unrepresentative, and 3D organoid approaches are currently difficult to reproduce at scale and do not fit well with current industrial drug-screening approaches. Here we report a rapidly generated and highly reproducible 3D co-culture spheroid model (GlomSpheres), better demonstrating the specialised physical and molecular structure of a glomerulus. Co-cultured using a magnetic spheroid formation approach, conditionally immortalised (CI) human podocytes and glomerular endothelial cells (GEnCs) deposited mature, organized isoforms of collagen IV and Laminin. We demonstrate a dramatic upregulation of key podocyte (podocin, nephrin and podocalyxin) and GEnC (pecam-1) markers. Electron microscopy revealed podocyte foot process interdigitation and endothelial vessel formation. Incubation with pro-fibrotic agents (TGF-β1, Adriamycin) induced extracellular matrix (ECM) dysregulation and podocyte loss, which were attenuated by the anti-fibrotic agent Nintedanib. Incubation with plasma from patients with kidney disease induced acute podocyte loss and ECM dysregulation relative to patient matched remission plasma, and Nintedanib reduced podocyte loss. Finally, we developed a rapid imaging approach to demonstrate the model's usefulness in higher throughput pharmaceutical screening. GlomSpheres therefore represent a robust, scalable, replacement for 2D in vitro glomerular disease models.
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Affiliation(s)
- Jack Tuffin
- Bristol Renal, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS1 3NY, UK.
| | - Musleeha Chesor
- Bristol Renal, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS1 3NY, UK.,Faculty of Medicine, Princess of Naradhiwas University, Narathiwat, Thailand
| | - Valeryia Kuzmuk
- Bristol Renal, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS1 3NY, UK
| | | | - Simon C Satchell
- Bristol Renal, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS1 3NY, UK
| | - Gavin I Welsh
- Bristol Renal, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS1 3NY, UK
| | - Moin A Saleem
- Bristol Renal, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS1 3NY, UK
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56
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Thomas M, Boardman A, Garcia-Ortegon M, Yang H, de Graaf C, Bender A. Applications of Artificial Intelligence in Drug Design: Opportunities and Challenges. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2390:1-59. [PMID: 34731463 DOI: 10.1007/978-1-0716-1787-8_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Artificial intelligence (AI) has undergone rapid development in recent years and has been successfully applied to real-world problems such as drug design. In this chapter, we review recent applications of AI to problems in drug design including virtual screening, computer-aided synthesis planning, and de novo molecule generation, with a focus on the limitations of the application of AI therein and opportunities for improvement. Furthermore, we discuss the broader challenges imposed by AI in translating theoretical practice to real-world drug design; including quantifying prediction uncertainty and explaining model behavior.
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Affiliation(s)
- Morgan Thomas
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Andrew Boardman
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Miguel Garcia-Ortegon
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK.,Department of Pure Mathematics and Mathematical Statistics, University of Cambridge, Cambridge, UK
| | - Hongbin Yang
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK.
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57
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Anderson JM, Measom ND, Murphy JA, Poole DL. Bridge Functionalisation of Bicyclo[1.1.1]pentane Derivatives. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Joseph M. Anderson
- GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
- Department of Pure and Applied Chemistry WestCHEM University of Strathclyde 295 Cathedral Street Glasgow Scotland G1 1XL UK
| | - Nicholas D. Measom
- GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - John A. Murphy
- Department of Pure and Applied Chemistry WestCHEM University of Strathclyde 295 Cathedral Street Glasgow Scotland G1 1XL UK
| | - Darren L. Poole
- GlaxoSmithKline Medicines Research Centre Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
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Anderson JM, Measom ND, Murphy JA, Poole DL. Bridge Functionalisation of Bicyclo[1.1.1]pentane Derivatives. Angew Chem Int Ed Engl 2021; 60:24754-24769. [PMID: 34151501 PMCID: PMC9291545 DOI: 10.1002/anie.202106352] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Indexed: 12/30/2022]
Abstract
"Escaping from flatland", by increasing the saturation level and three-dimensionality of drug-like compounds, can enhance their potency, selectivity and pharmacokinetic profile. One approach that has attracted considerable recent attention is the bioisosteric replacement of aromatic rings, internal alkynes and tert-butyl groups with bicyclo[1.1.1]pentane (BCP) units. While functionalisation of the tertiary bridgehead positions of BCP derivatives is well-documented, functionalisation of the three concyclic secondary bridge positions remains an emerging field. The unique properties of the BCP core present considerable synthetic challenges to the development of such transformations. However, the bridge positions provide novel vectors for drug discovery and applications in materials science, providing entry to novel chemical and intellectual property space. This Minireview aims to consolidate the major advances in the field, serving as a useful reference to guide further work that is expected in the coming years.
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Affiliation(s)
- Joseph M. Anderson
- GlaxoSmithKline Medicines Research CentreGunnels Wood RoadStevenageHertfordshireSG1 2NYUK
- Department of Pure and Applied ChemistryWestCHEMUniversity of Strathclyde295 Cathedral StreetGlasgowScotlandG1 1XLUK
| | - Nicholas D. Measom
- GlaxoSmithKline Medicines Research CentreGunnels Wood RoadStevenageHertfordshireSG1 2NYUK
| | - John A. Murphy
- Department of Pure and Applied ChemistryWestCHEMUniversity of Strathclyde295 Cathedral StreetGlasgowScotlandG1 1XLUK
| | - Darren L. Poole
- GlaxoSmithKline Medicines Research CentreGunnels Wood RoadStevenageHertfordshireSG1 2NYUK
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59
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Williams M. Improving Translational Paradigms in Drug Discovery and Development. Curr Protoc 2021; 1:e273. [PMID: 34780124 DOI: 10.1002/cpz1.273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Despite improved knowledge regarding disease causality, new drug targets, and enabling technologies, the attrition rate for compounds entering clinical trials has remained consistently high for several decades, with an average 90% failure rate. These failures are manifested in an inability to reproduce efficacy findings from animal models in humans and/or the occurrence of unexpected safety issues, and reflect failures in T1 translation. Similarly, an inability to sequentially demonstrate compound efficacy and safety in Phase IIa, IIb, and III clinical trials represents failures in T2 translation. Accordingly, T1 and T2 translation are colloquially termed 'valleys of death'. Since T2 translation dealt almost exclusively with clinical trials, T3 and T4 translational steps were added, with the former focused on facilitating interactions between laboratory- and population-based research and the latter on 'real world' health outcomes. Factors that potentially lead to T1/T2 compound attrition include: the absence of biomarkers to allow compound effects to be consistently tracked through development; a lack of integration/'de-siloing' of the diverse discipline-based and technical skill sets involved in drug discovery; the industrialization of drug discovery, which via volume-based goals often results in quantity being prioritized over quality; inadequate project governance and strategic oversight; and flawed decision making based on unreliable/irreproducible or incomplete data. A variety of initiatives have addressed this problem, including the NIH National Center for Advancing Translational Sciences (NCATS), which has focused on bringing an unbiased academic perspective to translation, to potentially revitalize the process. This commentary provides an overview of the basic concepts involved in translation, along with suggested changes in the conduct of biomedical research to avoid valleys of death, including the use of Translational Scoring as a tool to avoid translational attrition and the impact of the FDA Accelerated Approval Pathway in lowering the hurdle for drug approval. © 2021 Wiley Periodicals LLC.
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Affiliation(s)
- Michael Williams
- Department of Biological Chemistry and Pharmacology, College of Medicine, Ohio State University, Columbus, Ohio
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Boissel JP, Pérol D, Décousus H, Klingmann I, Hommel M. Using numerical modeling and simulation to assess the ethical burden in clinical trials and how it relates to the proportion of responders in a trial sample. PLoS One 2021; 16:e0258093. [PMID: 34634062 PMCID: PMC8504716 DOI: 10.1371/journal.pone.0258093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 09/21/2021] [Indexed: 01/24/2023] Open
Abstract
In order to propose a more precise definition and explore how to reduce ethical losses in randomized controlled clinical trials (RCTs), we set out to identify trial participants who do not contribute to demonstrating that the treatment in the experimental arm is superior to that in the control arm. RCTs emerged mid-last century as the gold standard for assessing efficacy, becoming the cornerstone of the value of new therapies, yet their ethical grounds are a matter of debate. We introduce the concept of unnecessary participants in RCTs, the sum of non-informative participants and non-responders. The non-informative participants are considered not informative with respect to the efficacy measured in the trial in contrast to responders who carry all the information required to conclude on the treatment's efficacy. The non-responders present the event whether or not they are treated with the experimental treatment. The unnecessary participants carry the burden of having to participate in a clinical trial without benefiting from it, which might include experiencing side effects. Thus, these unnecessary participants carry the ethical loss that is inherent to the RCT methodology. On the contrary, responders to the experimental treatment bear its entire efficacy in the RCT. Starting from the proportions observed in a real placebo-controlled trial from the literature, we carried out simulations of RCTs progressively increasing the proportion of responders up to 100%. We show that the number of unnecessary participants decreases steadily until the RCT's ethical loss reaches a minimum. In parallel, the trial sample size decreases (presumably its cost as well), although the trial's statistical power increases as shown by the increase of the chi-square comparing the event rates between the two arms. Thus, we expect that increasing the proportion of responders in RCTs would contribute to making them more ethically acceptable, with less false negative outcomes.
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Affiliation(s)
| | - David Pérol
- Department of Biostatistics, Centre Léon Bérard, Lyon, France
| | - Hervé Décousus
- INSERM, CIC 1408—F Crin, INNOVTE, CHU Saint-Etienne, Hôpital Nord, Service Médecine Vasculaire et Thérapeutique, Saint Etienne, France
| | - Ingrid Klingmann
- European Forum for Good Clinical Practice (EFGCP), Brussels, Belgium
| | - Marc Hommel
- Novadiscovery, Lyon, France
- University Hospital Grenoble, Grenoble, EA 4407 AGEIS UGA, France
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Personalization of medical treatments in oncology: time for rethinking the disease concept to improve individual outcomes. EPMA J 2021; 12:545-558. [PMID: 34642594 PMCID: PMC8495186 DOI: 10.1007/s13167-021-00254-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/01/2021] [Indexed: 12/12/2022]
Abstract
The agenda of pharmacology discovery in the field of personalized oncology was dictated by the search of molecular targets assumed to deterministically drive tumor development. In this perspective, genes play a fundamental "causal" role while cells simply act as causal proxies, i.e., an intermediate between the molecular input and the organismal output. However, the ceaseless genomic change occurring across time within the same primary and metastatic tumor has broken the hope of a personalized treatment based only upon genomic fingerprint. Indeed, current models are unable in capturing the unfathomable complexity behind the outbreak of a disease, as they discard the contribution of non-genetic factors, environment constraints, and the interplay among different tiers of organization. Herein, we posit that a comprehensive personalized model should view at the disease as a "historical" process, in which different spatially and timely distributed factors interact with each other across multiple levels of organization, which collectively interact with a dynamic gene-expression pattern. Given that a disease is a dynamic, non-linear process - and not a static-stable condition - treatments should be tailored according to the "timing-frame" of each condition. This approach can help in detecting those critical transitions through which the system can access different attractors leading ultimately to diverse outcomes - from a pre-disease state to an overt illness or, alternatively, to recovery. Identification of such tipping points can substantiate the predictive and the preventive ambition of the Predictive, Preventive and Personalized Medicine (PPPM/3PM). However, an unusual effort is required to conjugate multi-omics approaches, data collection, and network analysis reconstruction (eventually involving innovative Artificial Intelligent tools) to recognize the critical phases and the relevant targets, which could help in patient stratification and therapy personalization.
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Upadhyay A. Natural compounds in the regulation of proteostatic pathways: An invincible artillery against stress, ageing, and diseases. Acta Pharm Sin B 2021; 11:2995-3014. [PMID: 34729300 PMCID: PMC8546668 DOI: 10.1016/j.apsb.2021.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/12/2020] [Accepted: 11/03/2020] [Indexed: 01/13/2023] Open
Abstract
Cells have different sets of molecules for performing an array of physiological functions. Nucleic acids have stored and carried the information throughout evolution, whereas proteins have been attributed to performing most of the cellular functions. To perform these functions, proteins need to have a unique conformation and a definite lifespan. These attributes are achieved by a highly coordinated protein quality control (PQC) system comprising chaperones to fold the proteins in a proper three-dimensional structure, ubiquitin-proteasome system for selective degradation of proteins, and autophagy for bulk clearance of cell debris. Many kinds of stresses and perturbations may lead to the weakening of these protective cellular machinery, leading to the unfolding and aggregation of cellular proteins and the occurrence of numerous pathological conditions. However, modulating the expression and functional efficiency of molecular chaperones, E3 ubiquitin ligases, and autophagic proteins may diminish cellular proteotoxic load and mitigate various pathological effects. Natural medicine and small molecule-based therapies have been well-documented for their effectiveness in modulating these pathways and reestablishing the lost proteostasis inside the cells to combat disease conditions. The present article summarizes various similar reports and highlights the importance of the molecules obtained from natural sources in disease therapeutics.
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Key Words
- 17-AAG, 17-allylamino-geldanamycin
- APC, anaphase-promoting complex
- Ageing
- Autophagy
- BAG, BCL2-associated athanogene
- CAP, chaperone-assisted proteasomal degradation
- CASA, chaperone-assisted selective autophagy
- CHIP, carboxy-terminus of HSC70 interacting protein
- CMA, chaperone-mediated autophagy
- Cancer
- Chaperones
- DUBs, deubiquitinases
- Drug discovery
- EGCG, epigallocatechin-3-gallate
- ESCRT, endosomal sorting complexes required for transport
- HECT, homologous to the E6-AP carboxyl terminus
- HSC70, heat shock cognate 70
- HSF1, heat shock factor 1
- HSP, heat shock protein
- KFERQ, lysine-phenylalanine-glutamate-arginine-glutamine
- LAMP2a, lysosome-associated membrane protein 2a
- LC3, light chain 3
- NBR1, next to BRCA1 gene 1
- Natural molecules
- Neurodegeneration
- PQC, protein quality control
- Proteinopathies
- Proteostasis
- RING, really interesting new gene
- UPS, ubiquitin–proteasome system
- Ub, ubiquitin
- Ubiquitin proteasome system
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Affiliation(s)
- Arun Upadhyay
- Department of Biochemistry, Central University of Rajasthan, Bandar Sindari, Kishangarh, Ajmer, Rajasthan 305817, India
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63
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In vivo inducible reverse genetics in patients' tumors to identify individual therapeutic targets. Nat Commun 2021; 12:5655. [PMID: 34580292 PMCID: PMC8476619 DOI: 10.1038/s41467-021-25963-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/09/2021] [Indexed: 01/18/2023] Open
Abstract
High-throughput sequencing describes multiple alterations in individual tumors, but their functional relevance is often unclear. Clinic-close, individualized molecular model systems are required for functional validation and to identify therapeutic targets of high significance for each patient. Here, we establish a Cre-ERT2-loxP (causes recombination, estrogen receptor mutant T2, locus of X-over P1) based inducible RNAi- (ribonucleic acid interference) mediated gene silencing system in patient-derived xenograft (PDX) models of acute leukemias in vivo. Mimicking anti-cancer therapy in patients, gene inhibition is initiated in mice harboring orthotopic tumors. In fluorochrome guided, competitive in vivo trials, silencing of the apoptosis regulator MCL1 (myeloid cell leukemia sequence 1) correlates to pharmacological MCL1 inhibition in patients´ tumors, demonstrating the ability of the method to detect therapeutic vulnerabilities. The technique identifies a major tumor-maintaining potency of the MLL-AF4 (mixed lineage leukemia, ALL1-fused gene from chromosome 4) fusion, restricted to samples carrying the translocation. DUX4 (double homeobox 4) plays an essential role in patients’ leukemias carrying the recently described DUX4-IGH (immunoglobulin heavy chain) translocation, while the downstream mediator DDIT4L (DNA-damage-inducible transcript 4 like) is identified as therapeutic vulnerability. By individualizing functional genomics in established tumors in vivo, our technique decisively complements the value chain of precision oncology. Being broadly applicable to tumors of all kinds, it will considerably reinforce personalizing anti-cancer treatment in the future. Preclinical molecular models are useful that mimic a patient´s response to targeted therapy. Here, the authors establish an in vivo inducible RNAi-mediated gene silencing system in patient-derived xenograft models of acute leukemia to identify individual vulnerabilities and therapeutic targets.
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König H, Frank D, Baumann M, Heil R. AI models and the future of genomic research and medicine: True sons of knowledge?: Artificial intelligence needs to be integrated with causal conceptions in biomedicine to harness its societal benefits for the field. Bioessays 2021; 43:e2100025. [PMID: 34382215 DOI: 10.1002/bies.202100025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 11/10/2022]
Abstract
The increasing availability of large-scale, complex data has made research into how human genomes determine physiology in health and disease, as well as its application to drug development and medicine, an attractive field for artificial intelligence (AI) approaches. Looking at recent developments, we explore how such approaches interconnect and may conflict with needs for and notions of causal knowledge in molecular genetics and genomic medicine. We provide reasons to suggest that-while capable of generating predictive knowledge at unprecedented pace and scale-if and how these approaches will be integrated with prevailing causal concepts will not only determine the future of scientific understanding and self-conceptions in these fields. But these questions will also be key to develop differentiated policies, such as for education and regulation, in order to harness societal benefits of AI for genomic research and medicine.
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Affiliation(s)
- Harald König
- Karlsruhe Institute of Technology, Institute for Technology Assessment and Systems Analysis (ITAS), Karlsruhe, Germany
| | - Daniel Frank
- Chair for Ethics, Theory, and History of the Life Sciences, University of Tübingen, Tübingen, Germany
| | - Martina Baumann
- Karlsruhe Institute of Technology, Institute for Technology Assessment and Systems Analysis (ITAS), Karlsruhe, Germany
| | - Reinhard Heil
- Karlsruhe Institute of Technology, Institute for Technology Assessment and Systems Analysis (ITAS), Karlsruhe, Germany
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65
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Grafton F, Ho J, Ranjbarvaziri S, Farshidfar F, Budan A, Steltzer S, Maddah M, Loewke KE, Green K, Patel S, Hoey T, Mandegar MA. Deep learning detects cardiotoxicity in a high-content screen with induced pluripotent stem cell-derived cardiomyocytes. eLife 2021; 10:68714. [PMID: 34338636 PMCID: PMC8367386 DOI: 10.7554/elife.68714] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/27/2021] [Indexed: 12/15/2022] Open
Abstract
Drug-induced cardiotoxicity and hepatotoxicity are major causes of drug attrition. To decrease late-stage drug attrition, pharmaceutical and biotechnology industries need to establish biologically relevant models that use phenotypic screening to detect drug-induced toxicity in vitro. In this study, we sought to rapidly detect patterns of cardiotoxicity using high-content image analysis with deep learning and induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). We screened a library of 1280 bioactive compounds and identified those with potential cardiotoxic liabilities in iPSC-CMs using a single-parameter score based on deep learning. Compounds demonstrating cardiotoxicity in iPSC-CMs included DNA intercalators, ion channel blockers, epidermal growth factor receptor, cyclin-dependent kinase, and multi-kinase inhibitors. We also screened a diverse library of molecules with unknown targets and identified chemical frameworks that show cardiotoxic signal in iPSC-CMs. By using this screening approach during target discovery and lead optimization, we can de-risk early-stage drug discovery. We show that the broad applicability of combining deep learning with iPSC technology is an effective way to interrogate cellular phenotypes and identify drugs that may protect against diseased phenotypes and deleterious mutations.
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Affiliation(s)
| | - Jaclyn Ho
- Tenaya Therapeutics, South San Francisco, United States
| | - Sara Ranjbarvaziri
- Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, United States
| | | | | | | | | | | | | | - Snahel Patel
- Tenaya Therapeutics, South San Francisco, United States
| | - Tim Hoey
- Tenaya Therapeutics, South San Francisco, United States
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66
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Jung O, Song MJ, Ferrer M. Operationalizing the Use of Biofabricated Tissue Models as Preclinical Screening Platforms for Drug Discovery and Development. SLAS DISCOVERY 2021; 26:1164-1176. [PMID: 34269079 DOI: 10.1177/24725552211030903] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
A wide range of complex in vitro models (CIVMs) are being developed for scientific research and preclinical drug efficacy and safety testing. The hope is that these CIVMs will mimic human physiology and pathology and predict clinical responses more accurately than the current cellular models. The integration of these CIVMs into the drug discovery and development pipeline requires rigorous scientific validation, including cellular, morphological, and functional characterization; benchmarking of clinical biomarkers; and operationalization as robust and reproducible screening platforms. It will be critical to establish the degree of physiological complexity that is needed in each CIVM to accurately reproduce native-like homeostasis and disease phenotypes, as well as clinical pharmacological responses. Choosing which CIVM to use at each stage of the drug discovery and development pipeline will be driven by a fit-for-purpose approach, based on the specific disease pathomechanism to model and screening throughput needed. Among the different CIVMs, biofabricated tissue equivalents are emerging as robust and versatile cellular assay platforms. Biofabrication technologies, including bioprinting approaches with hydrogels and biomaterials, have enabled the production of tissues with a range of physiological complexity and controlled spatial arrangements in multiwell plate platforms, which make them amenable for medium-throughput screening. However, operationalization of such 3D biofabricated models using existing automation screening platforms comes with a unique set of challenges. These challenges will be discussed in this perspective, including examples and thoughts coming from a laboratory dedicated to designing and developing assays for automated screening.
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Affiliation(s)
- Olive Jung
- 3D Tissue Bioprinting Laboratory (3DTBL), Division of Pre-clinical Innovation (DPI), National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD, USA.,Biomedical Ultrasonics, Biotherapy and Biopharmaceuticals Laboratory, Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Min Jae Song
- 3D Tissue Bioprinting Laboratory (3DTBL), Division of Pre-clinical Innovation (DPI), National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD, USA
| | - Marc Ferrer
- 3D Tissue Bioprinting Laboratory (3DTBL), Division of Pre-clinical Innovation (DPI), National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD, USA
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67
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Artificial intelligence guided discovery of a barrier-protective therapy in inflammatory bowel disease. Nat Commun 2021; 12:4246. [PMID: 34253728 PMCID: PMC8275683 DOI: 10.1038/s41467-021-24470-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/21/2021] [Indexed: 12/19/2022] Open
Abstract
Modeling human diseases as networks simplify complex multi-cellular processes, helps understand patterns in noisy data that humans cannot find, and thereby improves precision in prediction. Using Inflammatory Bowel Disease (IBD) as an example, here we outline an unbiased AI-assisted approach for target identification and validation. A network was built in which clusters of genes are connected by directed edges that highlight asymmetric Boolean relationships. Using machine-learning, a path of continuum states was pinpointed, which most effectively predicted disease outcome. This path was enriched in gene-clusters that maintain the integrity of the gut epithelial barrier. We exploit this insight to prioritize one target, choose appropriate pre-clinical murine models for target validation and design patient-derived organoid models. Potential for treatment efficacy is confirmed in patient-derived organoids using multivariate analyses. This AI-assisted approach identifies a first-in-class gut barrier-protective agent in IBD and predicted Phase-III success of candidate agents. Traditional drug discovery process use differential, Bayesian and other network based approaches. We developed a Boolean approach for building disease maps and prioritizing pre-clinical models to discover a first-in-class therapy to restore and protect the leaky gut barrier in inflammatory bowel disease.
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68
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Palano G, Foinquinos A, Müllers E. In vitro Assays and Imaging Methods for Drug Discovery for Cardiac Fibrosis. Front Physiol 2021; 12:697270. [PMID: 34305651 PMCID: PMC8298031 DOI: 10.3389/fphys.2021.697270] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 12/20/2022] Open
Abstract
As a result of stress, injury, or aging, cardiac fibrosis is characterized by excessive deposition of extracellular matrix (ECM) components resulting in pathological remodeling, tissue stiffening, ventricular dilatation, and cardiac dysfunction that contribute to heart failure (HF) and eventually death. Currently, there are no effective therapies specifically targeting cardiac fibrosis, partially due to limited understanding of the pathological mechanisms and the lack of predictive in vitro models for high-throughput screening of antifibrotic compounds. The use of more relevant cell models, three-dimensional (3D) models, and coculture systems, together with high-content imaging (HCI) and machine learning (ML)-based image analysis, is expected to improve predictivity and throughput of in vitro models for cardiac fibrosis. In this review, we present an overview of available in vitro assays for cardiac fibrosis. We highlight the potential of more physiological 3D cardiac organoids and coculture systems and discuss HCI and automated artificial intelligence (AI)-based image analysis as key methods able to capture the complexity of cardiac fibrosis in vitro. As 3D and coculture models will soon be sufficiently mature for application in large-scale preclinical drug discovery, we expect the combination of more relevant models and high-content analysis to greatly increase translation from in vitro to in vivo models and facilitate the discovery of novel targets and drugs against cardiac fibrosis.
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Affiliation(s)
- Giorgia Palano
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ariana Foinquinos
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Erik Müllers
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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69
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Meyers J, Fabian B, Brown N. De novo molecular design and generative models. Drug Discov Today 2021; 26:2707-2715. [PMID: 34082136 DOI: 10.1016/j.drudis.2021.05.019] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/21/2021] [Accepted: 05/26/2021] [Indexed: 02/09/2023]
Abstract
Molecular design strategies are integral to therapeutic progress in drug discovery. Computational approaches for de novo molecular design have been developed over the past three decades and, recently, thanks in part to advances in machine learning (ML) and artificial intelligence (AI), the drug discovery field has gained practical experience. Here, we review these learnings and present de novo approaches according to the coarseness of their molecular representation: that is, whether molecular design is modeled on an atom-based, fragment-based, or reaction-based paradigm. Furthermore, we emphasize the value of strong benchmarks, describe the main challenges to using these methods in practice, and provide a viewpoint on further opportunities for exploration and challenges to be tackled in the upcoming years.
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Affiliation(s)
| | | | - Nathan Brown
- BenevolentAI, 4-8 Maple Street, London W1T 5HD, UK
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70
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Treherne JM, Langley GR. Converging global crises are forcing the rapid adoption of disruptive changes in drug discovery. Drug Discov Today 2021; 26:2489-2495. [PMID: 34015541 PMCID: PMC8129828 DOI: 10.1016/j.drudis.2021.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/25/2021] [Accepted: 05/10/2021] [Indexed: 02/07/2023]
Abstract
Spiralling research costs combined with urgent pressures from the Coronavirus 2019 (COVID-19) pandemic and the consequences of climate disruption are forcing changes in drug discovery. Increasing the predictive power of in vitro human assays and using them earlier in discovery would refocus resources on more successful research strategies and reduce animal studies. Increasing laboratory automation enables effective social distancing for researchers, while allowing integrated data capture from remote laboratory networks. Such disruptive changes would not only enable more cost-effective drug discovery, but could also reduce the overall carbon footprint of discovering new drugs.
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Affiliation(s)
- J Mark Treherne
- Talisman Therapeutics Limited, Babraham Research Campus, Cambridge CB22 3AT, UK.
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71
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Breen CP, Nambiar AM, Jamison TF, Jensen KF. Ready, Set, Flow! Automated Continuous Synthesis and Optimization. TRENDS IN CHEMISTRY 2021. [DOI: 10.1016/j.trechm.2021.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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72
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Abstract
Affective bias – a propensity to focus on negative information at the expense of positive information – is a core feature of many mental health problems. However, it can be caused by wide range of possible underlying cognitive mechanisms. Here we illustrate this by focusing on one particular behavioural signature of affective bias – increased tendency of anxious/depressed individuals to predict lower rewards – in the context of the Signal Detection Theory (SDT) modelling framework. Specifically, we show how to apply this framework to measure affective bias and compare it to the behaviour of an optimal observer. We also show how to extend the framework to make predictions about bias when the individual holds incorrect assumptions about the decision context. Building on this theoretical foundation, we propose five experiments to test five hypothetical sources of this affective bias: beliefs about prior probabilities, beliefs about performance, subjective value of reward, learning differences, and need for accuracy differences. We argue that greater precision about the mechanisms driving affective bias may eventually enable us to better understand the mechanisms underlying mood and anxiety disorders.
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73
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Biswas S, Khimulya G, Alley EC, Esvelt KM, Church GM. Low-N protein engineering with data-efficient deep learning. Nat Methods 2021; 18:389-396. [PMID: 33828272 DOI: 10.1038/s41592-021-01100-y] [Citation(s) in RCA: 196] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/22/2021] [Indexed: 11/09/2022]
Abstract
Protein engineering has enormous academic and industrial potential. However, it is limited by the lack of experimental assays that are consistent with the design goal and sufficiently high throughput to find rare, enhanced variants. Here we introduce a machine learning-guided paradigm that can use as few as 24 functionally assayed mutant sequences to build an accurate virtual fitness landscape and screen ten million sequences via in silico directed evolution. As demonstrated in two dissimilar proteins, GFP from Aequorea victoria (avGFP) and E. coli strain TEM-1 β-lactamase, top candidates from a single round are diverse and as active as engineered mutants obtained from previous high-throughput efforts. By distilling information from natural protein sequence landscapes, our model learns a latent representation of 'unnaturalness', which helps to guide search away from nonfunctional sequence neighborhoods. Subsequent low-N supervision then identifies improvements to the activity of interest. In sum, our approach enables efficient use of resource-intensive high-fidelity assays without sacrificing throughput, and helps to accelerate engineered proteins into the fermenter, field and clinic.
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Affiliation(s)
- Surojit Biswas
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.,Nabla Bio, Inc., Boston, MA, USA
| | | | - Ethan C Alley
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kevin M Esvelt
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA.
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74
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Hnatiuk AP, Briganti F, Staudt DW, Mercola M. Human iPSC modeling of heart disease for drug development. Cell Chem Biol 2021; 28:271-282. [PMID: 33740432 PMCID: PMC8054828 DOI: 10.1016/j.chembiol.2021.02.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 01/26/2021] [Accepted: 02/19/2021] [Indexed: 02/08/2023]
Abstract
Human induced pluripotent stem cells (hiPSCs) have emerged as a promising platform for pharmacogenomics and drug development. In cardiology, they make it possible to produce unlimited numbers of patient-specific human cells that reproduce hallmark features of heart disease in the culture dish. Their potential applications include the discovery of mechanism-specific therapeutics, the evaluation of safety and efficacy in a human context before a drug candidate reaches patients, and the stratification of patients for clinical trials. Although this new technology has the potential to revolutionize drug discovery, translational hurdles have hindered its widespread adoption for pharmaceutical development. Here we discuss recent progress in overcoming these hurdles that should facilitate the use of hiPSCs to develop new medicines and individualize therapies for heart disease.
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Affiliation(s)
- Anna P Hnatiuk
- Stanford Cardiovascular Institute, 240 Pasteur Drive, Biomedical Innovation Building, Palo Alto, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Francesca Briganti
- Stanford Cardiovascular Institute, 240 Pasteur Drive, Biomedical Innovation Building, Palo Alto, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - David W Staudt
- Stanford Cardiovascular Institute, 240 Pasteur Drive, Biomedical Innovation Building, Palo Alto, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Mark Mercola
- Stanford Cardiovascular Institute, 240 Pasteur Drive, Biomedical Innovation Building, Palo Alto, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA.
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75
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Desjardins E, Kurtz J, Kranke N, Lindeza A, Richter SH. Beyond Standardization: Improving External Validity and Reproducibility in Experimental Evolution. Bioscience 2021. [DOI: 10.1093/biosci/biab008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Discussions of reproducibility are casting doubts on the credibility of experimental outcomes in the life sciences. Although experimental evolution is not typically included in these discussions, this field is also subject to low reproducibility, partly because of the inherent contingencies affecting the evolutionary process. A received view in experimental studies more generally is that standardization (i.e., rigorous homogenization of experimental conditions) is a solution to some issues of significance and internal validity. However, this solution hides several difficulties, including a reduction of external validity and reproducibility. After explaining the meaning of these two notions in the context of experimental evolution, we import from the fields of animal research and ecology and suggests that systematic heterogenization of experimental factors could prove a promising alternative. We also incorporate into our analysis some philosophical reflections on the nature and diversity of research objectives in experimental evolution.
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Affiliation(s)
- Eric Desjardins
- Rotman Institute of Philosophy, Department of Philosophy, University of Western Ontario, London, Ontario, Canada
| | | | | | | | - S Helene Richter
- RG Behavioural Biology and Animal Welfare, Institute of Neuro and Behavioural Biology all at the WWU, Münster, Germany
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76
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Chakravarty K, Antontsev V, Bundey Y, Varshney J. Driving success in personalized medicine through AI-enabled computational modeling. Drug Discov Today 2021; 26:1459-1465. [PMID: 33609781 DOI: 10.1016/j.drudis.2021.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/26/2021] [Accepted: 02/10/2021] [Indexed: 12/29/2022]
Abstract
The development of successful drugs is expensive and time-consuming because of high clinical attrition rates. This is caused partially by the rupture seen in the translatability of the drug from the bench to the clinic in the context of personalized medicine. Artificial intelligence (AI)-driven platforms integrated with mechanistic modeling have become instrumental in accelerating the drug development process by leveraging data ubiquitously across the various phases. AI can counter the deficiencies and ambiguities that arise during the classical drug development process while reducing human intervention and bridging the translational gap in discovering the connections between drugs and diseases.
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Affiliation(s)
| | - Victor Antontsev
- VeriSIM Life Inc., 1 Sansome St. Suite 3500, San Francisco, CA 94104, USA
| | - Yogesh Bundey
- VeriSIM Life Inc., 1 Sansome St. Suite 3500, San Francisco, CA 94104, USA
| | - Jyotika Varshney
- VeriSIM Life Inc., 1 Sansome St. Suite 3500, San Francisco, CA 94104, USA.
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77
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Sen K, Mukherjee R, Sansare S, Halder A, Kashi H, Ma AWK, Chaudhuri B. Impact of powder-binder interactions on 3D printability of pharmaceutical tablets using drop test methodology. Eur J Pharm Sci 2021; 160:105755. [PMID: 33588046 DOI: 10.1016/j.ejps.2021.105755] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 02/01/2021] [Accepted: 02/09/2021] [Indexed: 01/08/2023]
Abstract
In this study, a pre-screening test has been developed for the binder-jet 3D printing process (BJ3DP) which has been validated using statistical analysis. The pre-screening test or drop test has been adapted from the wet granulation field and modified later on to be used for tablet manufacturing in BJ3DP. Initially, a total of eight powders and ten water-based binder solutions have been introduced in the preliminary test to understand the powder-binder interactions. Afterward, based on the preliminary test results, three blends were developed which had undergone the same drop test. All these powder and binder combinations were then used for 3D printing. The key parameters such as mechanical strength and shape factors of the drop test agglomerates and 3D printed tablets were then compared using multiple linear regressions. Few dimensionless parameters were introduced in this study such as binding capacity and binding index to capture the printability properties of the powders used in this study. Significant relations (p<0.05) were found between the drop test and the BJ3DP process. Application of drop test was carried out to establish a prescreening test, ii) to develop new blend formulations as well as iii) to develop a fundamental understanding of powder-binder interaction during BJ3DP process.
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Affiliation(s)
- Koyel Sen
- Department of Pharmaceutical Sciences, University of Connecticut
| | - Raj Mukherjee
- Department of Pharmaceutical Sciences, University of Connecticut
| | - Sameera Sansare
- Department of Pharmaceutical Sciences, University of Connecticut
| | | | - Hooman Kashi
- Department of Pharmaceutical Sciences, University of Connecticut
| | - Anson W K Ma
- Department of Chemical and Biomolecular Engineering, University of Connecticut; Institute of Material Sciences, University of Connecticut
| | - Bodhisattwa Chaudhuri
- Department of Pharmaceutical Sciences, University of Connecticut; Department of Chemical and Biomolecular Engineering, University of Connecticut; Institute of Material Sciences, University of Connecticut.
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78
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Bender A, Cortes-Ciriano I. Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 2: a discussion of chemical and biological data. Drug Discov Today 2021; 26:1040-1052. [PMID: 33508423 PMCID: PMC8132984 DOI: 10.1016/j.drudis.2020.11.037] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/07/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022]
Abstract
'Artificial Intelligence' (AI) has recently had a profound impact on areas such as image and speech recognition, and this progress has already translated into practical applications. However, in the drug discovery field, such advances remains scarce, and one of the reasons is intrinsic to the data used. In this review, we discuss aspects of, and differences in, data from different domains, namely the image, speech, chemical, and biological domains, the amounts of data available, and how relevant they are to drug discovery. Improvements in the future are needed with respect to our understanding of biological systems, and the subsequent generation of practically relevant data in sufficient quantities, to truly advance the field of AI in drug discovery, to enable the discovery of novel chemistry, with novel modes of action, which shows desirable efficacy and safety in the clinic.
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Affiliation(s)
- Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK; Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK.
| | - Isidro Cortes-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
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79
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Long L, Wang R, Chiang HY, Ding W, Li YX, Chen F, Qian PY. Discovery of Antibiofilm Activity of Elasnin against Marine Biofilms and Its Application in the Marine Antifouling Coatings. Mar Drugs 2021; 19:19. [PMID: 33466541 PMCID: PMC7824865 DOI: 10.3390/md19010019] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 12/22/2020] [Accepted: 12/30/2020] [Indexed: 01/27/2023] Open
Abstract
Biofilms are surface-attached multicellular communities that play critical roles in inducing biofouling and biocorrosion in the marine environment. Given the serious economic losses and problems caused by biofouling and biocorrosion, effective biofilm control strategies are highly sought after. In a screening program of antibiofilm compounds against marine biofilms, we discovered the potent biofilm inhibitory activity of elasnin. Elasnin effectively inhibited the biofilm formation of seven strains of bacteria isolated from marine biofilms. With high productivity, elasnin-based coatings were prepared in an easy and cost-effective way, which exhibited great performance in inhibiting the formation of multi-species biofilms and the attachment of large biofouling organisms in the marine environment. The 16S amplicon analysis and anti-larvae assay revealed that elasnin could prevent biofouling by the indirect impact of changed microbial composition of biofilms and direct inhibitory effect on larval settlement with low toxic effects. These findings indicated the potential application of elasnin in biofilm and biofouling control in the marine environment.
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Affiliation(s)
- Lexin Long
- SZU-HKUST Joint PhD Program in Marine Environmental Science, Shenzhen University, Shenzhen 518000, China;
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China; (R.W.); (H.Y.C.)
| | - Ruojun Wang
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China; (R.W.); (H.Y.C.)
| | - Ho Yin Chiang
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China; (R.W.); (H.Y.C.)
| | - Wei Ding
- Colleague of Marine Life Science, Ocean University of China, 5 Yushan Road, Qingdao 266100, China;
| | - Yong-Xin Li
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong 999077, China
| | - Feng Chen
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Pei-Yuan Qian
- Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China; (R.W.); (H.Y.C.)
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80
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Emmerich CH, Gamboa LM, Hofmann MCJ, Bonin-Andresen M, Arbach O, Schendel P, Gerlach B, Hempel K, Bespalov A, Dirnagl U, Parnham MJ. Improving target assessment in biomedical research: the GOT-IT recommendations. Nat Rev Drug Discov 2021; 20:64-81. [PMID: 33199880 PMCID: PMC7667479 DOI: 10.1038/s41573-020-0087-3] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 02/06/2023]
Abstract
Academic research plays a key role in identifying new drug targets, including understanding target biology and links between targets and disease states. To lead to new drugs, however, research must progress from purely academic exploration to the initiation of efforts to identify and test a drug candidate in clinical trials, which are typically conducted by the biopharma industry. This transition can be facilitated by a timely focus on target assessment aspects such as target-related safety issues, druggability and assayability, as well as the potential for target modulation to achieve differentiation from established therapies. Here, we present recommendations from the GOT-IT working group, which have been designed to support academic scientists and funders of translational research in identifying and prioritizing target assessment activities and in defining a critical path to reach scientific goals as well as goals related to licensing, partnering with industry or initiating clinical development programmes. Based on sets of guiding questions for different areas of target assessment, the GOT-IT framework is intended to stimulate academic scientists' awareness of factors that make translational research more robust and efficient, and to facilitate academia-industry collaboration.
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Affiliation(s)
| | - Lorena Martinez Gamboa
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- QUEST Center for Transforming Biomedical Research, Berlin Institute of Health, Berlin, Germany
| | - Martine C J Hofmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine & Pharmacology TMP, Frankfurt am Main, Germany
| | - Marc Bonin-Andresen
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Olga Arbach
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- SPARK-Validation Fund, Berlin Institute of Health, Berlin, Germany
| | - Pascal Schendel
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Katja Hempel
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Anton Bespalov
- PAASP GmbH, Heidelberg, Germany
- Valdman Institute of Pharmacology, Pavlov Medical University, St. Petersburg, Russia
| | - Ulrich Dirnagl
- Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- QUEST Center for Transforming Biomedical Research, Berlin Institute of Health, Berlin, Germany
| | - Michael J Parnham
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine & Pharmacology TMP, Frankfurt am Main, Germany
- Faculty of Biochemistry, Chemistry & Pharmacy, J.W. Goethe University Frankfurt, Frankfurt am Main, Germany
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81
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Fuller AA, Dounay AB, Schirch D, Rivera DG, Hansford KA, Elliott AG, Zuegg J, Cooper MA, Blaskovich MAT, Hitchens JR, Burris-Hiday S, Tenorio K, Mendez Y, Samaritoni JG, O’Donnell MJ, Scott WL. Multi-Institution Research and Education Collaboration Identifies New Antimicrobial Compounds. ACS Chem Biol 2020; 15:3187-3196. [PMID: 33242957 PMCID: PMC7928911 DOI: 10.1021/acschembio.0c00732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
New
antibiotics are urgently needed to address increasing rates
of multidrug resistant infections. Seventy-six diversely functionalized
compounds, comprising five structural scaffolds, were synthesized
and tested for their ability to inhibit microbial growth. Twenty-six
compounds showed activity in the primary phenotypic screen at the
Community for Open Antimicrobial Drug Discovery (CO-ADD). Follow-up
testing of active molecules confirmed that two unnatural dipeptides
inhibit the growth of Cryptococcus neoformans with
a minimum inhibitory concentration (MIC) ≤ 8 μg/mL. Syntheses
were carried out by undergraduate students at five schools implementing
Distributed Drug Discovery (D3) programs. This report showcases that
a collaborative research and educational process is a powerful approach
to discover new molecules inhibiting microbial growth. Educational
gains for students engaged in this project are highlighted in parallel
to the research advances. Aspects of D3 that contribute to its success,
including an emphasis on reproducibility of procedures, are discussed
to underscore the power of this approach to solve important research
problems and to inform other coupled chemical biology research and
teaching endeavors.
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Affiliation(s)
- Amelia A. Fuller
- Santa Clara University, Department of Chemistry & Biochemistry, Santa Clara, California 95053, United States
| | - Amy B. Dounay
- Department of Chemistry and Biochemistry, Colorado College, 14 E. Cache La Poudre Street, Colorado Springs, Colorado 80903, United States
| | - Douglas Schirch
- Department of Chemistry, Goshen College, 1700 South Main Street, Goshen, Indiana 46526, United States
| | - Daniel G. Rivera
- Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, 10400, La Habana, Cuba
| | - Karl A. Hansford
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Alysha G. Elliott
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Johannes Zuegg
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Matthew A Cooper
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Mark A. T. Blaskovich
- Community for Open Antimicrobial Drug Discovery, Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jacob R. Hitchens
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - Sarah Burris-Hiday
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - Kristiana Tenorio
- Santa Clara University, Department of Chemistry & Biochemistry, Santa Clara, California 95053, United States
| | - Yanira Mendez
- Center for Natural Products Research, Faculty of Chemistry, University of Havana, Zapata y G, 10400, La Habana, Cuba
| | - J. Geno Samaritoni
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - Martin J. O’Donnell
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
| | - William L. Scott
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, 402 N. Blackford Street, Indianapolis, Indiana 46202, United States
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82
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Bender A, Cortés-Ciriano I. Artificial intelligence in drug discovery: what is realistic, what are illusions? Part 1: Ways to make an impact, and why we are not there yet. Drug Discov Today 2020; 26:511-524. [PMID: 33346134 DOI: 10.1016/j.drudis.2020.12.009] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/07/2020] [Accepted: 12/11/2020] [Indexed: 12/30/2022]
Abstract
Although artificial intelligence (AI) has had a profound impact on areas such as image recognition, comparable advances in drug discovery are rare. This article quantifies the stages of drug discovery in which improvements in the time taken, success rate or affordability will have the most profound overall impact on bringing new drugs to market. Changes in clinical success rates will have the most profound impact on improving success in drug discovery; in other words, the quality of decisions regarding which compound to take forward (and how to conduct clinical trials) are more important than speed or cost. Although current advances in AI focus on how to make a given compound, the question of which compound to make, using clinical efficacy and safety-related end points, has received significantly less attention. As a consequence, current proxy measures and available data cannot fully utilize the potential of AI in drug discovery, in particular when it comes to drug efficacy and safety in vivo. Thus, addressing the questions of which data to generate and which end points to model will be key to improving clinically relevant decision-making in the future.
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Affiliation(s)
- Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road CB2 1EW, UK; Imaging and Data Analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK.
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, UK.
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83
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Long MJC. Time to Get Turned on by Chemical Biology. Chembiochem 2020; 22:814-817. [PMID: 33174365 DOI: 10.1002/cbic.202000497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/07/2020] [Indexed: 11/08/2022]
Abstract
The pressing need for innovation in drug discovery is spurring the emergence of drugs that turn on protein function, as opposed to shutting activity down. Several pharmacophores usher protein target gain-of-function, for instance: PROTACs promote protein target degradation; other drug candidates have been reported to function through dominant-negative inhibition of their target enzyme. Such classes of molecules are typically active at low target occupancy and display numerous advantages relative to canonical inhibitors, whose function is intrinsically tied to achieving, or exceeding a threshold occupancy. However, our ability to generally tap into gain-of-function processes through small molecule interventions is overall in its infancy. Herein, I outline how chemical biology is poised to help us bring this powerful idea to fruition. I further outline means through which gain-of-function events can be identified and harnessed.
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Affiliation(s)
- Marcus J C Long
- Départment de Biologie Moleculaire; Sciences II, 30 Quai Ernest-Ansermet, 1211, Genève 4, Switzerland
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84
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Vincent F, Loria PM, Weston AD, Steppan CM, Doyonnas R, Wang YM, Rockwell KL, Peakman MC. Hit Triage and Validation in Phenotypic Screening: Considerations and Strategies. Cell Chem Biol 2020; 27:1332-1346. [DOI: 10.1016/j.chembiol.2020.08.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 05/31/2020] [Accepted: 08/14/2020] [Indexed: 02/06/2023]
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85
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Abstract
There is a great need for innovative new medicines to treat unmet medical needs. The discovery and development of innovative new medicines is extremely difficult, costly, and inefficient. In the last decade, phenotypic drug discovery (PDD) was reintroduced as a strategy to provide first-in-class medicines. PDD uses empirical, target-agnostic lead generation to identify pharmacologically active molecules and novel therapeutics which work through unprecedented drug mechanisms. The economic and scientific value of PDD is exemplified through game-changing medicines for hepatitis C virus, spinal muscular atrophy, and cystic fibrosis. In this short review, recent advances are noted for the implementation and de-risking of PDD (for compound library selection, biomarker development, mechanism identification, and safety studies) and the potential for artificial intelligence. A significant barrier in the decision to implement PDD is balancing the potential impact of a novel mechanism of drug action with an under-defined scientific path forward, with the desire to provide infrastructure and metrics to optimize return on investment, which a known mechanism provides. A means to address this knowledge gap in the future is to empower precompetitive research utilizing the empirical concepts of PDD to identify new mechanisms and pharmacologically active compounds.
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86
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PiDose: an open-source system for accurate and automated oral drug administration to group-housed mice. Sci Rep 2020; 10:11584. [PMID: 32665577 PMCID: PMC7360602 DOI: 10.1038/s41598-020-68477-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/25/2020] [Indexed: 12/31/2022] Open
Abstract
Drug treatment studies in laboratory mice typically employ manual administration methods such as injection or gavage, which can be time-consuming to perform over long periods and cause substantial stress in animals. These stress responses may mask or enhance treatment effects, increasing the risk of false positive or negative results and decreasing reliability. To address the lack of an automated method for drug treatment in group-housed mice, we have developed PiDose, a home-cage attached device that weighs individual animals and administers a daily dosage of drug solution based on each animal’s bodyweight through their drinking water. Group housed mice are identified through the use of RFID tagging and receive both regular water and drug solution drops by licking at a spout within the PiDose module. This system allows animals to be treated over long periods (weeks to months) in a fully automated fashion, with high accuracy and minimal experimenter interaction. PiDose is low-cost and fully open-source and should prove useful for researchers in both translational and basic research.
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87
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Ekert JE, Deakyne J, Pribul-Allen P, Terry R, Schofield C, Jeong CG, Storey J, Mohamet L, Francis J, Naidoo A, Amador A, Klein JL, Rowan W. Recommended Guidelines for Developing, Qualifying, and Implementing Complex In Vitro Models (CIVMs) for Drug Discovery. SLAS DISCOVERY 2020; 25:1174-1190. [PMID: 32495689 DOI: 10.1177/2472555220923332] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The pharmaceutical industry is continuing to face high research and development (R&D) costs and low overall success rates of clinical compounds during drug development. There is an increasing demand for development and validation of healthy or disease-relevant and physiological human cellular models that can be implemented in early-stage discovery, thereby shifting attrition of future therapeutics to a point in discovery at which the costs are significantly lower. There needs to be a paradigm shift in the early drug discovery phase (which is lengthy and costly), away from simplistic cellular models that show an inability to effectively and efficiently reproduce healthy or human disease-relevant states to steer target and compound selection for safety, pharmacology, and efficacy questions. This perspective article covers the various stages of early drug discovery from target identification (ID) and validation to the hit/lead discovery phase, lead optimization, and preclinical safety. We outline key aspects that should be considered when developing, qualifying, and implementing complex in vitro models (CIVMs) during these phases, because criteria such as cell types (e.g., cell lines, primary cells, stem cells, and tissue), platform (e.g., spheroids, scaffolds or hydrogels, organoids, microphysiological systems, and bioprinting), throughput, automation, and single and multiplexing endpoints will vary. The article emphasizes the need to adequately qualify these CIVMs such that they are suitable for various applications (e.g., context of use) of drug discovery and translational research. The article ends looking to the future, in which there is an increase in combining computational modeling, artificial intelligence and machine learning (AI/ML), and CIVMs.
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Affiliation(s)
- Jason E Ekert
- In Vitro In Vivo Translation, Research, Pharmaceutical R&D, GlaxoSmithKline, Collegeville, PA, USA
| | - Julianna Deakyne
- In Vitro In Vivo Translation, Research, Pharmaceutical R&D, GlaxoSmithKline, Collegeville, PA, USA
| | - Philippa Pribul-Allen
- In Vitro In Vivo Translation, Research, Pharmaceutical R&D, GlaxoSmithKline, Ware, UK
| | - Rebecca Terry
- In Vitro In Vivo Translation, Research, Pharmaceutical R&D, GlaxoSmithKline, Ware, UK
| | - Christopher Schofield
- Functional Genomics, Medicinal Science and Technology, Pharmaceutical R&D, GlaxoSmithKline, Stevenage, UK
| | | | - Joanne Storey
- Research Office of Animal Welfare, Ethics and Strategy, Research, Pharmaceutical R&D, GlaxoSmithKline, Stevenage, UK
| | - Lisa Mohamet
- Functional Genomics, Medicinal Science and Technology, Pharmaceutical R&D, GlaxoSmithKline, Stevenage, UK
| | - Jo Francis
- Screening Profiling and Mechanistic Biology, Medicinal Science and Technology, Pharmaceutical R&D, GlaxoSmithKline, Stevenage, UK
| | - Anita Naidoo
- In Vitro In Vivo Translation, Research, Pharmaceutical R&D, GlaxoSmithKline, Ware, UK
| | - Alejandro Amador
- Functional Genomics, Medicinal Science and Technology, Pharmaceutical R&D, GlaxoSmithKline, Collegeville, PA, USA
| | - Jean-Louis Klein
- Novel Human Genetics, Research, Pharmaceutical R&D, GlaxoSmithKline, Collegeville, PA, USA
| | - Wendy Rowan
- Novel Human Genetics, Research, Pharmaceutical R&D, GlaxoSmithKline, Stevenage, UK
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88
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Rubbini D, Cornet C, Terriente J, Di Donato V. CRISPR Meets Zebrafish: Accelerating the Discovery of New Therapeutic Targets. SLAS DISCOVERY 2020; 25:552-567. [PMID: 32462967 DOI: 10.1177/2472555220926920] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bringing a new drug to the market costs an average of US$2.6 billion and takes more than 10 years from discovery to regulatory approval. Despite the need to reduce cost and time to increase productivity, pharma companies tend to crowd their efforts in the same indications and drug targets. This results in the commercialization of drugs that share the same mechanism of action (MoA) and, in many cases, equivalent efficacies among them-an outcome that helps neither patients nor the balance sheet of the companies trying to bring therapeutics to the same patient population. Indeed, the discovery of new therapeutic targets, based on a deeper understanding of the disease biology, would likely provide more innovative MoAs and potentially greater drug efficacies. It would also bring better chances for identifying appropriate treatments according to the patient's genetic stratification. Nowadays, we count with an enormous amount of unprocessed information on potential disease targets that could be extracted from omics data obtained from patient samples. In addition, hundreds of pharmacological and genetic screenings have been performed to identify innovative drug targets. Traditionally, rodents have been the animal models of choice to perform functional genomic studies. The high experimental cost, combined with the low throughput provided by those models, however, is a bottleneck for discovering and validating novel genetic disease associations. To overcome these limitations, we propose that zebrafish, in conjunction with the use of CRISPR/Cas9 genome-editing tools, could streamline functional genomic processes to bring biologically relevant knowledge on innovative disease targets in a shorter time frame.
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Affiliation(s)
- Davide Rubbini
- ZeClinics SL, IGTP (Germans Trias I Pujol Research Institute), Barcelona, Spain
| | - Carles Cornet
- ZeClinics SL, IGTP (Germans Trias I Pujol Research Institute), Barcelona, Spain
| | - Javier Terriente
- ZeClinics SL, IGTP (Germans Trias I Pujol Research Institute), Barcelona, Spain
| | - Vincenzo Di Donato
- ZeClinics SL, IGTP (Germans Trias I Pujol Research Institute), Barcelona, Spain
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89
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Griffen EJ, Dossetter AG, Leach AG. Chemists: AI Is Here; Unite To Get the Benefits. J Med Chem 2020; 63:8695-8704. [DOI: 10.1021/acs.jmedchem.0c00163] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Edward J. Griffen
- MedChemica Ltd., Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
| | | | - Andrew G. Leach
- MedChemica Ltd., Alderley Park, Macclesfield, Cheshire SK10 4TG, U.K
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90
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Richter SH. Automated Home-Cage Testing as a Tool to Improve Reproducibility of Behavioral Research? Front Neurosci 2020; 14:383. [PMID: 32390795 PMCID: PMC7193758 DOI: 10.3389/fnins.2020.00383] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 03/30/2020] [Indexed: 01/08/2023] Open
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91
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Palano G, Jansson M, Backmark A, Martinsson S, Sabirsh A, Hultenby K, Åkerblad P, Granberg KL, Jennbacken K, Müllers E, Hansson EM. A high-content, in vitro cardiac fibrosis assay for high-throughput, phenotypic identification of compounds with anti-fibrotic activity. J Mol Cell Cardiol 2020; 142:105-117. [PMID: 32277974 DOI: 10.1016/j.yjmcc.2020.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/26/2022]
Abstract
A key feature in the pathogenesis of heart failure is cardiac fibrosis, but effective treatments that specifically target cardiac fibrosis are currently not available. A major impediment to progress has been the lack of reliable in vitro models with sufficient throughput to screen for activity against cardiac fibrosis. Here, we established cell culture conditions in micro-well format that support extracellular deposition of mature collagen from primary human cardiac fibroblasts - a hallmark of cardiac fibrosis. Based on robust biochemical characterization we developed a high-content phenotypic screening platform, that allows for high-throughput identification of compounds with activity against cardiac fibrosis. Our platform correctly identifies compounds acting on known cardiac fibrosis pathways. Moreover, it can detect anti-fibrotic activity for compounds acting on targets that have not previously been reported in in vitro cardiac fibrosis assays. Taken together, our experimental approach provides a powerful platform for high-throughput screening of anti-fibrotic compounds as well as discovery of novel targets to develop new therapeutic strategies for heart failure.
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Affiliation(s)
- G Palano
- Karolinska Institutet/AstraZeneca Integrated Cardio Metabolic Centre (KI/AZ ICMC), Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - M Jansson
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism, R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - A Backmark
- Discovery Biology, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - S Martinsson
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism, R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - A Sabirsh
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - K Hultenby
- Clincal Research Center, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - P Åkerblad
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism, R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - K L Granberg
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - K Jennbacken
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism, R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden
| | - E Müllers
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism, R&D BioPharmaceuticals, AstraZeneca, Gothenburg, Sweden.
| | - E M Hansson
- Karolinska Institutet/AstraZeneca Integrated Cardio Metabolic Centre (KI/AZ ICMC), Department of Medicine, Karolinska Institutet, Huddinge, Sweden.
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92
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Kabadi A, McDonnell E, Frank CL, Drowley L. Applications of Functional Genomics for Drug Discovery. SLAS DISCOVERY 2020; 25:823-842. [PMID: 32026742 DOI: 10.1177/2472555220902092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Many diseases, such as diabetes, autoimmune diseases, cancer, and neurological disorders, are caused by a dysregulation of a complex interplay of genes. Genome-wide association studies have identified thousands of disease-linked polymorphisms in the human population. However, detailing the causative gene expression or functional changes underlying those associations has been elusive in many cases. Functional genomics is an emerging field of research that aims to deconvolute the link between genotype and phenotype by making use of large -omic data sets and next-generation gene and epigenome editing tools to perturb genes of interest. Here we review how functional genomic tools can be used to better understand the biological interplay between genes, improve disease modeling, and identify novel drug targets. Incorporation of functional genomic capabilities into conventional drug development pipelines is predicted to expedite the development of first-in-class therapeutics.
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Affiliation(s)
- Ami Kabadi
- Element Genomics, a UCB company, Durham, NC, USA
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93
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Aylward J, Hales C, Robinson E, Robinson OJ. Translating a rodent measure of negative bias into humans: the impact of induced anxiety and unmedicated mood and anxiety disorders. Psychol Med 2020; 50:237-246. [PMID: 30683161 PMCID: PMC7083556 DOI: 10.1017/s0033291718004117] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 12/06/2018] [Accepted: 12/18/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Mood and anxiety disorders are ubiquitous but current treatment options are ineffective for many sufferers. Moreover, a number of promising pre-clinical interventions have failed to translate into clinical efficacy in humans. Improved treatments are unlikely without better animal-human translational pipelines. Here, we translate a rodent measure of negative affective bias into humans, exploring its relationship with (1) pathological mood and anxiety symptoms and (2) transient induced anxiety. METHODS Adult participants (age = 29 ± 11) who met criteria for mood or anxiety disorder symptomatology according to a face-to-face neuropsychiatric interview were included in the symptomatic group. Study 1 included N = 77 (47 = asymptomatic [female = 21]; 30 = symptomatic [female = 25]), study 2 included N = 47 asymptomatic participants (25 = female). Outcome measures were choice ratios, reaction times and parameters recovered from a computational model of reaction time - the drift diffusion model (DDM) - from a two-alternative-forced-choice task in which ambiguous and unambiguous auditory stimuli were paired with high and low rewards. RESULTS Both groups showed over 93% accuracy on unambiguous tones indicating intact discrimination, but symptomatic individuals demonstrated increased negative affective bias on ambiguous tones [proportion high reward = 0.42 (s.d. = 0.14)] relative to asymptomatic individuals [0.53 (s.d. = 0.17)] as well as a significantly reduced DDM drift rate. No significant effects were observed for the within-subjects anxiety-induction. CONCLUSIONS Humans with pathological anxiety symptoms directly mimic rodents undergoing anxiogenic manipulation. The lack of sensitivity to transient anxiety suggests the paradigm might be more sensitive to clinically relevant symptoms. Our results establish a direct translational pipeline (and candidate therapeutics screen) from negative affective bias in rodents to pathological mood and anxiety symptoms in humans.
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Affiliation(s)
- Jessica Aylward
- Neuroscience and Mental Health Group, Institute of Cognitive Neuroscience, 17–19 Queen Square, University College London, WC1N 3AZ, London, UK
| | - Claire Hales
- School of Physiology and Pharmacology, Biomedical Sciences Building, University Walk, University of Bristol, BS8 1TD, Bristol, UK
| | - Emma Robinson
- School of Physiology and Pharmacology, Biomedical Sciences Building, University Walk, University of Bristol, BS8 1TD, Bristol, UK
| | - Oliver J. Robinson
- Neuroscience and Mental Health Group, Institute of Cognitive Neuroscience, 17–19 Queen Square, University College London, WC1N 3AZ, London, UK
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94
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Grebner C, Malmerberg E, Shewmaker A, Batista J, Nicholls A, Sadowski J. Virtual Screening in the Cloud: How Big Is Big Enough? J Chem Inf Model 2019; 60:4274-4282. [PMID: 31682421 DOI: 10.1021/acs.jcim.9b00779] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Virtual screening is a standard tool in Computer-Assisted Drug Design (CADD). Early in a project, it is typical to use ligand-based similarity search methods to find suitable hit molecules. However, the number of compounds which can be screened and the time required are usually limited by computational resources. We describe here a high-throughput virtual screening project using 3D similarity (FastROCS) and automated evaluation workflows on Orion, a cloud computing platform. Cloud resources make this approach fully scalable and flexible, allowing the generation and search of billions of virtual molecules, and give access to an explicit 3D virtual chemistry space not available before. We discuss the impact of the size of the search space with respect to finding novel chemical hits and the size of the required hit list, as well as computational and economical aspects of resource scaling.
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Affiliation(s)
- Christoph Grebner
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-43183 Gothenburg, Sweden
| | - Erik Malmerberg
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-43183 Gothenburg, Sweden
| | - Andrew Shewmaker
- OpenEye Scientific Software, Inc., 9 Bisbee Court Suite D, Santa Fe, New Mexico 87508, United States
| | - Jose Batista
- OpenEye Scientific Software, Inc., 9 Bisbee Court Suite D, Santa Fe, New Mexico 87508, United States
| | - Anthony Nicholls
- OpenEye Scientific Software, Inc., 9 Bisbee Court Suite D, Santa Fe, New Mexico 87508, United States
| | - Jens Sadowski
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, SE-43183 Gothenburg, Sweden
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95
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Ren Y, Fagette PH, Hall CL, Broers H, Grainger DW, Van Der Mei HC, Busscher HJ. Clinical translation of the assets of biomedical engineering – a retrospective analysis with looks to the future. Expert Rev Med Devices 2019; 16:913-922. [DOI: 10.1080/17434440.2019.1685869] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yijin Ren
- Department of Orthodontics, University of Groningen and University Medical Center Groningen, W. J. Kolff Institute of Biomedical Engineering and Materials Science, Groningen, The Netherlands
| | - Paul H. Fagette
- Department of Orthodontics, University of Groningen and University Medical Center Groningen, W. J. Kolff Institute of Biomedical Engineering and Materials Science, Groningen, The Netherlands
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, W. J. Kolff Institute of Biomedical Engineering and Materials Science, Groningen, The Netherlands
| | - Connie L. Hall
- Department of Biomedical Engineering, The College of New Jersey, Ewing, NJ, USA
| | - Herman Broers
- Willem Kolff Foundation (Kampen, NL), Zwolle, The Netherlands
| | - David W. Grainger
- Departments of Biomedical Engineering, and of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Henny C. Van Der Mei
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, W. J. Kolff Institute of Biomedical Engineering and Materials Science, Groningen, The Netherlands
| | - Henk J. Busscher
- Department of Biomedical Engineering, University of Groningen and University Medical Center Groningen, W. J. Kolff Institute of Biomedical Engineering and Materials Science, Groningen, The Netherlands
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96
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Howe JR, Bear MF, Golshani P, Klann E, Lipton SA, Mucke L, Sahin M, Silva AJ. The mouse as a model for neuropsychiatric drug development. Curr Biol 2019; 28:R909-R914. [PMID: 30205056 DOI: 10.1016/j.cub.2018.07.046] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Much has been written about the validity of mice as a preclinical model for brain disorders. Critics cite numerous examples of apparently effective treatments in mouse models that failed in human clinical trials, raising the possibility that the two species' neurobiological differences could explain the high translational failure rate in psychiatry and neurology (neuropsychiatry). However, every stage of translation is plagued by complex problems unrelated to neurobiological conservation. Therefore, although these case studies are intriguing, they cannot alone determine whether these differences observed account for translation failures. Our analysis of the literature indicates that most neuropsychiatric treatments used in humans are at least partially effective in mouse models, suggesting that neurobiological differences are unlikely to be the main cause of neuropsychiatric translation failures.
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Affiliation(s)
- James R Howe
- Departments of Neurobiology, Psychiatry & Biobehavioral Sciences and Psychology, Integrative Center for Learning and Memory, Brain Research Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Current address: Neurosciences Graduate Program, Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mark F Bear
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Peyman Golshani
- Departments of Neurology, Psychiatry and Biobehavioral Sciences, Integrative Center for Learning and Memory, Brain Research Institute, University of California, Los Angeles, CA 90095, USA
| | - Eric Klann
- Center for Neural Science, New York University, New York, NY 10003, USA
| | - Stuart A Lipton
- Neuroscience Translational Center and Departments of Molecular Medicine and Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, and Department of Neurosciences, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Lennart Mucke
- Gladstone Institute of Neurological Disease and Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mustafa Sahin
- F.M. Kirby Neurobiology Center, Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Alcino J Silva
- Departments of Neurobiology, Psychiatry & Biobehavioral Sciences and Psychology, Integrative Center for Learning and Memory, Brain Research Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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97
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Cox NJ, Below JE. Critical Evaluation of Data Requires Rigorous but Broadly Based Statistical Inference. Circ Res 2019; 122:1049-1051. [PMID: 29650629 DOI: 10.1161/circresaha.118.312530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Nancy J Cox
- From the Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN
| | - Jennifer E Below
- From the Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN.
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98
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Kaur G, Arora M, Ravi Kumar MNV. Oral Drug Delivery Technologies-A Decade of Developments. J Pharmacol Exp Ther 2019; 370:529-543. [PMID: 31010845 PMCID: PMC6806634 DOI: 10.1124/jpet.118.255828] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/17/2019] [Indexed: 12/17/2022] Open
Abstract
Advanced drug delivery technologies, in general, enable drug reformulation and administration routes, together contributing to life-cycle management and allowing the innovator to maintain the product monopoly. Over the years, there has been a steady shift from mere life-cycle management to drug repurposing-applying delivery technologies to tackle solubility and permeability issues in early stages or safety and efficacy issues in the late stages of drug discovery processes. While the drug and the disease in question primarily drive the choice of route of administration, the oral route, for its compliance and safety attributes, is the most preferred route, particularly when it comes to chronic conditions, including pain, which is not considered a disease but a symptom of a primary cause. Therefore, the attempt of this review is to take a stock of the advances in oral delivery technologies that are applicable for injectable to oral transformation, improve risk-benefit profiles of existing orals, and apply them in the early discovery program to minimize the drug attrition rates.
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Affiliation(s)
- G Kaur
- Department of Pharmaceutical Sciences, College of Pharmacy, Texas A&M University, College Station, Texas
| | - M Arora
- Department of Pharmaceutical Sciences, College of Pharmacy, Texas A&M University, College Station, Texas
| | - M N V Ravi Kumar
- Department of Pharmaceutical Sciences, College of Pharmacy, Texas A&M University, College Station, Texas
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99
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11PS04 is a new chemical entity identified by microRNA-based biosensing with promising therapeutic potential against cancer stem cells. Sci Rep 2019; 9:11916. [PMID: 31417117 PMCID: PMC6695485 DOI: 10.1038/s41598-019-48359-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/31/2019] [Indexed: 02/07/2023] Open
Abstract
Phenotypic drug discovery must take advantage of the large amount of clinical data currently available. In this sense, the impact of microRNAs (miRs) on human disease and clinical therapeutic responses is becoming increasingly well documented. Accordingly, it might be possible to use miR-based signatures as phenotypic read-outs of pathological status, for example in cancer. Here, we propose to use the information accumulating regarding the biology of miRs from clinical research in the preclinical arena, adapting it to the use of miR biosensors in the earliest steps of drug screening. Thus, we have used an amperometric dual magnetosensor capable of monitoring a miR-21/miR-205 signature to screen for new drugs that restore these miRs to non-tumorigenic levels in cell models of breast cancer and glioblastoma. In this way we have been able to identify a new chemical entity, 11PS04 ((3aR,7aS)-2-(3-propoxyphenyl)-7,7a-dihydro-3aH-pyrano[3,4-d]oxazol-6(4H)-one), the therapeutic potential of which was suggested in mechanistic assays of disease models, including 3D cell culture (oncospheres) and xenografts. These assays highlighted the potential of this compound to attack cancer stem cells, reducing the growth of breast and glioblastoma tumors in vivo. These data demonstrate the enhanced chain of translatability of this strategy, opening up new perspectives for drug-discovery pipelines and highlighting the potential of miR-based electro-analytical sensors as efficient tools in modern drug discovery.
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100
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Wiegand C, Banerjee I. Recent advances in the applications of iPSC technology. Curr Opin Biotechnol 2019; 60:250-258. [PMID: 31386977 DOI: 10.1016/j.copbio.2019.05.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/03/2019] [Accepted: 05/11/2019] [Indexed: 12/18/2022]
Abstract
Pluripotent stems cells (PSCs) can be expanded indefinitely and differentiated into almost any organ-specific cell type. This has enabled the generation of disease relevant tissues from patients in scalable quantities. iPSC-derived organs and organoids are currently being evaluated both in regenerative therapy which are proceeding towards clinical trials, and for disease modeling, which are facilitating drug screening efforts for discovery of novel therapeutics. Here we will review the current efforts and advances in iPSC technology and its subsequent applications and provide a brief commentary on future outlook of this promising technology.
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Affiliation(s)
- Connor Wiegand
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, United States
| | - Ipsita Banerjee
- Department of Chemical and Petroleum Engineering, University of Pittsburgh, United States; Department of Bioengineering, University of Pittsburgh, United States; McGowan Institute for Regenerative Medicine, United States.
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