Sean Ekins

Sean Ekins
Born Cleethorpes, England
Residence United States
Nationality United Kingdom, United States
Fields Pharmacology
Cheminformatics
Scientific collaborations
Alternatives to animal testing
Institutions Collaborations in Chemistry
Alma mater The University of Aberdeen
Nottingham Trent University
Doctoral advisor Gabrielle M. Hawksworth and M. Danny Burke
Known for ADME/Tox models
Pharmacophores
New technologies for pharmaceutical R&D

Sean Ekins is a British pharmacologist and expert in the fields of ADME/Tox, computational toxicology and cheminformatics at Collaborations in Chemistry, a division of corporate communications firm Collaborations in Communications. He is also the editor of four books and a book series for John Wiley & Sons.

Biography

Sean Ekins was born in Cleethorpes, England, on 2 March 1970 to John Ekins and Elsie May Ekins. He grew up in Grimsby. Ekins attended Edward Street Primary and Middle School followed by Havelock School. Ekins then earned his HND Science Applied Biology from Nottingham Trent University (formerly Polytechnic, 1988–1991), graduating in 1991, with a sandwich year (1989–1990) at the pharmaceutical company Servier in Fulmer, UK where his interest in drug discovery was established. Ekins then earned his M.Sc. in Clinical Pharmacology (1991–1992) at the University of Aberdeen with a dissertation entitled “Speculations on the relative roles of cytochrome P450 and flavin containing monooxygenase in the metabolism of S12363”[1] he then earned a Ph.D. in clinical pharmacology, at the University of Aberdeen in 1996, funded by Servier, and wrote a thesis entitled “Maintenance and cryopreservation of xenobiotic metabolism in precision-cut liver slices. Evaluation of an alternative in vitro model to isolated hepatocytes”. During his PhD he developed an interest in predicting drug-drug interactions computationally as an alternative to using animal models.

From 1996-1998 Ekins continued his research as a Postdoc at Eli Lilly and Company laboratories characterizing the little-known CYP2B6 and applied computational methods to this enzyme. He collected drug-drug interaction Ki data for other P450s and generated pharmacophores. He created test sets to test the models, that were ultimately published.[2][3][4][5][6] He published seminal ideas on how such models could be used to profile libraries of compounds for predicted drug-drug interactions.[7][8]

In late 1998 Ekins joined Pfizer and continued his interest in predicting drug-drug interactions and ADME properties. In 1999 he moved to Lilly to build a predictive ADME/Tox group. Between 1999 and late 2001 he generated pharmacophores and statistical models for various proteins including P-glycoprotein,[9][10][11][12] PXR[13] and enzymes.[14][15]

In December 2001 he started work for a start-up company, Concurrent Pharmaceuticals (now Vitae Pharmaceuticals)[16] as the Associate Director, Computational Drug Discovery. He was responsible for developing computational models for ADME/Tox and targets of interest. During this time he developed an interest in the polypharmacology of ADME/Tox proteins. In 2004 he joined GeneGo (now owned by Thomson Reuters) as Vice President, Computational Biology and developed the MetaDrug product (patent pending).[17][18][19][20]

In 2005 he earned his D.Sc. in Science from the University of Aberdeen with a thesis entitled “Computational and in vitro models for predicting drug interactions in humans”.

Since 2006 Ekins has consulted for several companies including on pharmacoeconomics and performing research on Tuberculosis Drug Discovery for Collaborative Drug Discovery.[21][22][23]

Ekins has also carried out independent research and collaborative research on topics including pharmacophores for drug transporters, cheminformatics for predicting immunoassay cross reactivity, models for studying nuclear receptor-ligand co-evolution, computational models for PXR agonists and antagonists as well as analyses of large datasets and crowdsourcing data.

Making Pharmaceutical Data Open

In 2010 Sean Ekins was the co-author of seminal papers around data sharing and making pharmaceutical data more open. In these papers he opinions:

1. on the long overdue need for making preclinical ADME/Tox data precompetitive [24]

2. how crowdsourcing could be used in the pharmaceutical industry [25]

3. how computational models for pharmacoeconomics could be shared by the scientific community[26]

4. what tools are still needed in cheminformatics and how methods for model sharing will be important[27]

5. How pharmaceutical companies could use open source molecular descriptors and algorithms which would facilitate computational model sharing with the academic and neglected disease community[28]

This work is important because it is the first prominent advocacy for making a broad array of approaches to make preclinical and postmarketing data and models available as well as the demonstration of the feasibility of such approaches. Ekins has served on the advisory group for ChemSpider and provided an array of pharmaceutical data sets to the database to make it available to the community.

Tuberculosis and Malaria Research

While working for Collaborative Drug Discovery, (funded by the Bill and Melinda Gates Foundation) he analyzed data provided to the public domain by the pharmaceutical industry. Specifically this was malaria screening data from GlaxoSmithKline for over 13,000 compounds. As a result of this work an important caution was provided to the scientific community in accepting such data at face value.[29] These data were compared to other malaria and tuberculosis data.[30]

In addition he has provided analyses of very large libraries of tuberculosis data which highlight important physicochemical properties,.[31][32]

Ekins has highlighted gaps in TB research, specifically in how cheminformatics and other computational tools could be integrated to improve efficiency[33] and provided examples of how computational methods can be used to assist in screening for compounds active against TB[34]

In February 2011 Ekins began participating in the MM4TB project as part of Collaborative Drug Discovery [35] led by Professor Stewart Cole.[36]

Science Mobile Applications

Ekins co-developed a Wiki with Antony John Williams called Science Mobile Applications[37] launched June 21, 2011.[38] Initially this grew out of a desire to track chemistry Apps [39] (for a paper submitted) and then Apps for science in the chemistry classroom.[40]

Database quality

Using their respective blogs, Ekins and Antony Williams alerted the scientific community within days of the release of the NCGC NPC browser [41] that there were significant errors in molecule structures. These observations were later published as an editorial in Drug Discovery Today.[42]

Editorships

Ekins has edited or co-edited 4 books for Wiley including: Computer Applications in Pharmaceutical Research and Development (2006), Computational Toxicology: Risk Assessment For Pharmaceutical and Environmental Chemicals(1007), Drug Efficacy, Safety, and Biologics Discovery(2009) and Collaborative Computational Technologies for Biomedical Research (2011) All the books have an underlying connection with computational technologies and their application for pharmaceutical R&D.

Ekins is the Editor of Expert Reviews for the Journal of Pharmaceutical Research,[43][44] a Springer Journal. He solicits reviews, commentaries and perspectives for the field of pharmaceutical research. He is on the editorial board for Drug Metabolism and Disposition,[45] Journal of Pharmacological and Toxicological Methods,[46] Mutation Research - Reviews,[47] and Drug Discovery Today [48]

Patents

Ekins is inventor on two issued US patents,[49] and [50]

References

  1. ↑ Ekins, S., et al. (1993) The role of cytochrome P4503A in the metabolism of the vinca alkaloid a-aminophosphonate derivative S12363 by human liver microsomes. Br J Clin. Pharmacol 36, 165-166P
  2. ↑ http://jpet.aspetjournals.org/content/291/1/424.full.pdf+html?sid=99bffa04-48cb-4cbf-bac6-d94e568b5b31 Ekins, S. Bravi, G. Binkley, S. Gillespie, J.S. Ring, B.J. Wikel, J.H. and Wrighton S.A. (1999) Three and four dimensional-quantitative structure activity relationship analyses of CYP3A4 inhibitors. J Pharm Exp Ther 290, 429-438
  3. ↑ Ekins, S.; et al. (1999). "Three and four dimensional-quantitative structure activity relationship (3D / 4D-QSAR) analyses of CYP2D6 inhibitors". Pharmacogenetics 9: 477–489.
  4. ↑ Ekins, S.; et al. (1999). "Three dimensional-quantitative structure activity relationship analyses of substrates for CYP2B6". Pharm Exp Ther 288: 21–29.
  5. ↑ http://jpet.aspetjournals.org/content/291/1/424.full.pdf+html?sid=99bffa04-48cb-4cbf-bac6-d94e568b5b31 Ekins, S. Bravi, G. Wikel J.H. and Wrighton SA (1999) Three dimensional quantitative structure activity relationship (3D-QSAR) analysis of CYP3A4 substrates. J Pharmacol Exp Thera 291, 424-433
  6. ↑ Ekins, S.; Wrighton, S.A. (1999). "The role of CYP2B6 in human xenobiotic metabolism". Drug Metab Rev 31: 719–754. doi:10.1081/dmr-100101942.
  7. ↑ Ekins, S. et al. (2000) Predicting drug-drug interactions in silico using pharmacophores: a paradigm for the next millennium. In Pharmacophore perception, development, and use in drug design (Guner, O.F., ed.), pp. 269-299, IUL
  8. ↑ Ekins, S.; et al. (2000). "Progress in predicting human ADME parameters in silico". J Pharmacol Toxicol Methods 44 (1): 251–272. doi:10.1016/s1056-8719(00)00109-x.
  9. ↑ Ekins, S.; et al. (2002). "Application of three dimensional quantitative structure-activity relationships of P-glycoprotein inhibitors and substrates". Mol Pharmacol 61: 974–981. doi:10.1124/mol.61.5.974.
  10. ↑ Ekins, S.; et al. (2002). "Three dimensional quantitative structure-activity relationships of inhibitors of P-glycoprotein". Mol Pharmacol 61: 964–973. doi:10.1124/mol.61.5.964.
  11. ↑ hERG
  12. ↑ http://jpet.aspetjournals.org/content/301/2/427.full.pdf+html?sid=99bffa04-48cb-4cbf-bac6-d94e568b5b31 Ekins, S. Crumb, W.J. Sarazan, R.D. Wikel, J.H. and Wrigton, S.A. (2002) Three dimensional quantitative structure activity relationship for the inhibition of the hERG (human ether-a-gogo related gene) potassium channel. J Pharmacol Exp Thera 301, 427-434
  13. ↑ Ekins, S.; Erickson, J.A. (2002). "A pharmacophore for human pregnane-X-receptor ligands". Drug Metab Dispos 30: 96–99. doi:10.1124/dmd.30.1.96.
  14. ↑ Ekins, S. et al. (2002) Pharmacophore insights into the active sites of the CYP3A enzymes. The Pharmacologist 44 Supplement, 114.
  15. ↑ Ethell, B.T.; et al. (2002). "Quantitative structure activity relationships for the glucuronidation of simple phenols by expressed human UGT1A6 and UGT1A9". Drug Metab. Dispos 30: 734–738. doi:10.1124/dmd.30.6.734.
  16. ↑ "Concurrent Pharmaceuticals Changes Name To Vitae Pharmaceuticals And Secures $34 Million In Financing". biospace.com. 19 Oct 2005. Retrieved 23 May 2014.
  17. ↑ Ekins, S.; et al. (2005). "Computational Prediction of Human Drug Metabolism". Exp Opin Drug Metab Toxicol 1: 303–324. doi:10.1517/17425255.1.2.303.
  18. ↑ Ekins, S. et al. (2005) Systems biology: applications in drug discovery. In Drug discovery handbook (Gad, S., ed.), pp. 123-183, Wiley
  19. ↑ Ekins, S.; et al. (2005). "A Novel Method for Visualizing Nuclear Hormone Receptor Networks Relevant to Drug Metabolism". Drug Metab Dispos 33: 474–481. doi:10.1124/dmd.104.002717.
  20. ↑ Ekins, S.; et al. (2005). "Techniques: Application of Systems Biology to Absorption, Distribution, Metabolism, Excretion, and Toxicity". Trends Pharmacol Sci 26: 202–209. doi:10.1016/j.tips.2005.02.006.
  21. ↑ Ekins, S.; et al. (2010). "A Collaborative Database And Computational Models For Tuberculosis Drug Discovery". Mol BioSystems 6 (5): 840–851. doi:10.1039/b917766c. PMID 20567770.
  22. ↑ Ekins, S. et al. (2010) Analysis and hit filtering of a very large library of compounds screened against Mycobacterium tuberculosis Mol BioSyst 6, 2316-2324
  23. ↑ Lamichhane, G.; et al. (2011). "Essential Metabolites of M. tuberculosis and their Mimics". Mbio 2: e00301–00310. doi:10.1128/mbio.00301-10.
  24. ↑ Ekins, S; Williams, AJ (2010). "Precompetitive Preclinical ADME/Tox Data: Set It Free on The Web to Facilitate Computational Model Building to Assist Drug Development". Lab on a Chip 10: 13–22. doi:10.1039/b917760b. PMID 20024044.
  25. ↑ Ekins S. and Williams AJ, Reaching out to collaborators: crowdsourcing for pharmaceutical research, Pharm Res, 27: 393-395, 2010.
  26. ↑ Arnold RJG and Ekins S, Time for cooperation in health economics among the modeling community, PharmacoEconomics, 28(8):609-613, 2010
  27. ↑ Ekins S, Gupta R, Gifford E, Bunin BA, Waller CL, Chemical Space: missing pieces in cheminformatics, Pharm Res, 27: 2035-2039, 2010
  28. ↑ Gupta, Rishi R.; Gifford, EM; Liston, T; Waller, CL; Hohman, M; Bunin, BA; Ekins, S (2010). "Using open source computational tools for predicting human metabolic stability and additional ADME/Tox properties". Drug Metab Dispos 38: 2083–2090. doi:10.1124/dmd.110.034918.
  29. ↑ Ekins, Sean; John Williams, Antony (2010). "When Pharmaceutical Companies Publish Large Datasets: An Abundance of riches or fool's gold?". Drug Disc Today 15 (19-20): 812–815. doi:10.1016/j.drudis.2010.08.010. PMID 20732447.
  30. ↑ Ekins S and Williams AJ, 2010 Meta-analysis of molecular property patterns and filtering of public datasets of antimalarial "hits" and drugs, MedChemComm 1: 325-330,
  31. ↑ Ekins, S; Bradford, J; Dole, K; Spektor, A; Gregory, K; Blondeau, D; Hohman, M; Bunin, BA (2010). "A Collaborative Database and Computational Models for Tuberculosis Drug Discovery". Mol BioSyst 6 (5): 840–851. doi:10.1039/b917766c. PMID 20567770.
  32. ↑ Ekins, S; Kaneko, T; Lipinski, CA; Bradford, J; Dole, K; Spektor, A; Gregory, K; Blondeau, D; Ernst, S; Yang, J; Goncharoff, N; Hohman, M; Bunin, BA (2010). "Analysis and hit filtering of a very large library of compounds screened against Mycobacterium tuberculosis". Mol Biosyst 6 (11): 2316–2324. doi:10.1039/c0mb00104j. PMID 20835433.
  33. ↑ Ekins, S; Freundlich, JS; Choi, I; Sarker, M; Talcott, C (2011). "Computational Databases, Pathway and Cheminformatics Tools for Tuberculosis Drug Discovery, '". Trends In Microbiology 19 (2): 65–74. doi:10.1016/j.tim.2010.10.005. PMC 3034835. PMID 21129975.
  34. ↑ Lamichhane G, Freundlich JS, Ekins S , Wickramaratne N, Nolan, S and Bishai WR (2011). "Essential metabolites of Mycobacterium tuberculosis and their mimics.". mBio 2 (1): e00301–10. doi:10.1128/mBio.00301-10. PMC 3031304. PMID 21285434.
  35. ↑ http://mm4tb.org/
  36. ↑ http://cole-lab.epfl.ch/
  37. ↑ The SciMobileApps Wiki
  38. ↑ Announcement of the SciMobileApps Wiki
  39. ↑ http://www.rsc.org/chemistryworld/Issues/2010/May/MobileChemistryChemistryHandsFace.asp
  40. ↑ http://pubs.acs.org/doi/abs/10.1021/ed200029p Smart Phones, a Powerful Tool in the Chemistry Classroom
  41. ↑ http://tripod.nih.gov/npc/
  42. ↑ "A quality alert and call for improved curation of public chemistry databases". Drug Discov. Today 16 (17-18): 747–50. September 2011. doi:10.1016/j.drudis.2011.07.007. PMID 21871970.
  43. ↑ http://www.springer.com/biomed/pharmaceutical+science/journal/11095
  44. ↑ http://www.springer.com/biomed/pharmaceutical+science/journal/11095?detailsPage=editorialBoard
  45. ↑
  46. ↑
  47. ↑
  48. ↑ <
  49. ↑ U.S. Patent no 6564152: Ekins S and Smith BJ, "Pharmacophore models for, methods of screening for, and identification of the cytochrome P-450 inhibitory potency of neurokinin-1 receptor antagonists."
  50. ↑ U.S. Patent no 6489094: Ekins S, Kelly KG, Johnson DL, "Method and device for drug-drug interaction testing sample preparation" .

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