Open Access Open Access  Restricted Access Subscription Access

Recommendations for developing predictive and systems medicine for drug discovery in India


Affiliations
1 Centre for Predictive Human Model Systems, Atal Incubation Centre, Centre for Cellular and Molecular Biology, Hyderabad 500 039, India, India
 

Biological phenomena often emerge based on the inter­action between pathways, cells and tissues, rather than a single set of genes or proteins. This has led to the emergence of systems medicine. Predictive medicine is another emerging field that aims to predict the disease onset, progression, deterioration, risk and treatment strategies. In this article, we review how systems and computational tools are being used globally in the drug discovery pipeline. With increase in the amount of biological data being generated, data integration is also a critical aspect in systems biology. Towards this, we describe the use of various data integration frameworks. We also analyse the global and local funding patterns, regulations and challenges and propose recommendations to enable India as a key player in this area

Keywords

Adverse outcome pathways, computational tools, drug discovery, predictive medicine, systems biology.
User
Notifications
Font Size

  • Berlin, J. A., Glasser, S. C. and Ellenberg, S. S., Adverse event de-tection in drug development: recommendations and obligations be-yond phase 3. Am. J. Public Health, 2008, 98, 1366–1371.
  • Ahmed, S., Zhou, Z., Zhou, J. and Chen, S.-Q., Pharmacogenomics of drug metabolizing enzymes and transporters: relevance to precision medicine. Genomics, Proteom. Bioinform., 2016, 14, 298–313.
  • Batta, A., Kalra, B. S. and Khirasaria, R., Trends in FDA drug ap-provals over last 2 decades: an observational study. J. Family Med.Primary Care, 2020, 9, 105–114.
  • Xing, J. et al., Genetic diversity in India and the inference of Eura-sian population expansion. Genome Biol., 2010, 11, R113.
  • Tätte, K. et al., The genetic legacy of continental scale admixture in Indian Austroasiatic speakers. Sci. Rep., 2019, 9, 3818.
  • Morgan, A. A., Mooney, S. D., Aronow, B. J. and Brenner, S. E., Precision medicine: data and discovery for improved health and therapy. Pac. Symp. Biocomput., 2016, 21, 243–248.
  • Cardinal-Fernández, P., Nin, N., Ruíz-Cabello, J. and Lorente, J. A., Systems medicine: a new approach to clinical practice. Arch. Bron-coneumol., 2014, 50, 444–451.
  • Marshall, L. J., Austin, C. P., Casey, W., Fitzpatrick, S. C. and Willett, C., Recommendations toward a human pathway-based approach to disease research. Drug Discov. Today, 2018, 23, 1824–1832.
  • Berikol, G. B. and Berikol, G., Predictive models in precision medi-cine. In Artificial Intelligence in Precision Health (ed. Barh, D.), Academic Press, USA, 2020, pp. 177–188; doi:10.1016/B978-0-12-817133-2.00007-0.
  • Andreu-Perez, J., Poon, C. C. Y., Merrifield, R. D., Wong, S. T. C. and Yang, G.-Z., Big data for health. IEEE J. Biomed. Health In-format., 2015, 19, 1193–1208.
  • Ristevski, B. and Chen, M., Big data analytics in medicine and healthcare. J. Integr. Bioinformat., 2018, 15.
  • Lillo-Castellano, J. M., Mora-Jiménez, I., Santiago-Mozos, R., Chavarría-Asso, F., Cano-González, A., García-Alberola, A. and Rojo-Álvarez, J. L., Symmetrical compression distance for arrhythmia discrimination in cloud-based big-data services. IEEE J. Biomed.Health Informat., 2015, 19(4), 1253–1263.
  • van de Vijver, M. J. et al., A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med., 2002, 347, 1999–2009.
  • van’t Veer, L. J. et al., Gene expression profiling predicts clinical outcome of breast cancer. Nature, 2002, 415, 530–536.
  • Ma, J., Sheridan, R. P., Liaw, A., Dahl, G. E. and Svetnik, V., Deep neural nets as a method for quantitative structure–activity relation-ships. J. Chem. Inf. Model., 2015, 55(2), 263–274.
  • Newby, D., Freitas, A. A. and Ghafourian, T., Decision trees to characterise the roles of permeability and solubility on the predic-tion of oral absorption. Eur. J. Med. Chem., 2015, 90, 751–765.
  • Hinton, G. E., Osindero, S. and Teh, Y.-W., A fast learning algo-rithm for deep belief nets. Neural Comput., 2006, 18, 1527–1554.
  • Li, Y. and Agarwal, P., A pathway-based view of human diseases and disease relationships. PLoS ONE, 2009, 4, e4346.
  • Sander, J., Ester, M., Kriegel, H.-P. and Xu, X., Density-based clu-stering in spatial databases: the algorithm GDBSCAN and its appli-cations. Data Min. Knowl. Discov., 1998, 2, 169–194.
  • Chen, B., Ding, Y. and Wild, D. J., Assessing drug target associa-tion using semantic linked data. PLoS Comput. Biol., 2012, 8(7), e1002574.
  • Xue, H., Li, J., Xie, H. and Wang, Y., Review of drug repositioning approaches and resources. Int. J. Biol. Sci., 2018, 14, 1232–1244.
  • Qian, T., Zhu, S. and Hoshida, Y., Use of big data in drug develop-ment for precision medicine: an update. Expert Rev. Precis. Med.Drug Dev., 2019, 4, 189–200.
  • Ankley, G. T. et al., Adverse outcome pathways: a conceptual framework to support ecotoxicology research and risk assessment. Environ. Toxicol. Chem., 2010, 29, 730–741.
  • Hecker, M. and LaLone, C. A., Adverse outcome pathways: moving from a scientific concept to an internationally accepted framework. Environ. Toxicol. Chem., 2019, 38, 1152–1163.
  • Knapen, D. et al., Adverse outcome pathway networks I: develop-ment and applications. Environ. Toxicol. Chem., 2018, 37, 1723–1733.
  • OECD, Guidance document on the reporting of defined approaches and individual information sources to be used within integrated appro-aches to testing and assessment (IATA) for skin sensitisation, Orga-nization for Economic Cooperation Development, 2017; doi:10.1787/9789264279285-en.
  • Tollefsen, K. E. et al., Applying adverse outcome pathways (AOPs) to support integrated approaches to testing and assessment (IATA). Regul. Toxicol. Pharmacol., 2014, 70, 629–640.
  • LaLone, C. A. et al., Weight of evidence evaluation of a network of adverse outcome pathways linking activation of the nicotinic acetyl-choline receptor in honey bees to colony death. Sci. Total Environ. 2017, 584–585, 751–775.
  • Wittwehr, C. et al., How adverse outcome pathways can aid the deve-lopment and use of computational prediction models for regulatory toxicology. Toxicol. Sci., 2017, 155, 326–336.
  • Bal-Price, A. et al., Developing and applying the adverse outcome pathway concept for understanding and predicting neurotoxicity. NeuroToxicology, 2017, 59, 240–255.
  • Conolly, R. B. et al., Quantitative adverse outcome pathways and their application to predictive toxicology. Environ. Sci. Technol., 2017, 51, 4661–4672.
  • Perkins, E. J. et al., Building and applying quantitative adverse outcome pathway models for chemical hazard and risk assessment. Environ. Toxicol. Chem., 2019, 38, 1850–1865.
  • Shipman, M., EPA high-tech ‘virtual embryo project’ will target developmental risk. Inside EPA’s Risk Policy Report 15, no. 2,2008, pp. 1–6; https://www.jstor.org/stable/26727372.
  • Amunts, K., Ebell, C., Muller, J., Telefont, M., Knoll, A. and Lip-pert, T., The human brain project: creating a European research in-frastructure decode the human brain. Neuron, 2016, 96(3), 574–581; doi:10.1016/j.neuron.2016.10.046; PMID: 27809997.
  • Wang, Z., Jensen, M. A. and Zenklusen, J. C., A practical guide to The Cancer Genome Atlas (TCGA). Methods Mol. Biol., 2016, 1418, 111–141.
  • Mazein, A. et al., Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms. NPJ Syst. Biol.Appl., 2018, 4, 1–10.
  • Eckhardt, M., Hultquist, J. F., Kaake, R. M., Hüttenhain, R. and Krogan, N. J., A systems approach to infectious disease. Nature Rev. Genet., 2020, 21, 339–354.
  • Fisher, C. K., Smith, A. M. and Walsh, J. R., Machine learning for comprehensive forecasting of Alzheimer’s disease progression. Sci.Rep., 2019, 9, 13622.
  • Computational biology market size worth $13.6 billion by 2026. March 2019; https://www.grandviewresearch.com/press-release/global-computational-biology-market (accessed on 17 March 2020).
  • Margolis, R. et al., The National Institutes of Health’s Big Data to Knowledge (BD2K) initiative: capitalizing on biomedical big data. J. Am. Med. Informat. Assoc., 2014, 21, 957–958.
  • Hodge, R. D. et al., Conserved cell types with divergent features in human versus mouse cortex. Nature, 2019, 573, 61–68.
  • Parvatam, S. et al., The need to develop a framework for human-relevant research in India: towards better disease models and drug discovery. J. Biosci., 2020, 45, 144.
  • Tripathi, B. et al., Adapting community detection algorithms for disease module identification in heterogeneous biological networks.Front. Genet., 2019, 10, 164.
  • Chauhan, S. and Ahmad, S., Enabling full-length evolutionary pro-files based deep convolutional neural network for predicting DNA-binding proteins from sequence. Proteins, 2020, 88, 15–30.
  • Sahu, A. et al., Integrative network analysis identifies differential regulation of neuroimmune system in schizophrenia and bipolar disorder. Brain, Behav. Immun. – Health, 2020, 2, 100023.
  • DBT, Biological data storage, access and sharing policy of India –draft 1, Department of Biotechnology, New Delhi, 2019; https://www.nhp.gov.in/NHPfiles/Draft1-Biological_Data_Policy.pdf (ac-cessed on 14 February 2021).
  • Koshy, J., What is ‘IndiGen’ project that is sequencing Indian genes? The Hindu, 3 November 2019; https://www.thehindu.com/sci-tech/sequencing-indian-genes/article29865310.ece#:%7E:text=The%20project%20ties%20in%20with,every%20State%20and%-20diverse%20ethnicities (accessed on 25 May 2021).

Abstract Views: 242

PDF Views: 116




  • Recommendations for developing predictive and systems medicine for drug discovery in India

Abstract Views: 242  |  PDF Views: 116

Authors

Surat Parvatam
Centre for Predictive Human Model Systems, Atal Incubation Centre, Centre for Cellular and Molecular Biology, Hyderabad 500 039, India, India
Sham Bharadwaj
Centre for Predictive Human Model Systems, Atal Incubation Centre, Centre for Cellular and Molecular Biology, Hyderabad 500 039, India, India

Abstract


Biological phenomena often emerge based on the inter­action between pathways, cells and tissues, rather than a single set of genes or proteins. This has led to the emergence of systems medicine. Predictive medicine is another emerging field that aims to predict the disease onset, progression, deterioration, risk and treatment strategies. In this article, we review how systems and computational tools are being used globally in the drug discovery pipeline. With increase in the amount of biological data being generated, data integration is also a critical aspect in systems biology. Towards this, we describe the use of various data integration frameworks. We also analyse the global and local funding patterns, regulations and challenges and propose recommendations to enable India as a key player in this area

Keywords


Adverse outcome pathways, computational tools, drug discovery, predictive medicine, systems biology.

References





DOI: https://doi.org/10.18520/cs%2Fv123%2Fi11%2F1317-1326