2015 in review

2015 saw the continuation of some research themes from 2014, namely some work on Ebola, rare diseases and Bayesian models for neglected diseases. At the end of the year several papers are in press for next year so more to come. As usual there were some ups and downs in getting some of these to see the light of day.

The following lists many collaborations from the last year or so – several were actually written in 2014 and made it out this year. Some are open access. If you need reprints for any of the others please get in touch.

A big thanks to all collaborators old and new that made this possible.

Shedding Light on Synergistic Chemical Genetic Connections with Machine Learning

Sean Ekins Jair Lage Siqueira-Neto
Volume 1, Issue 6, p377–379, 23 December 2015

 Machine learning models identify molecules active against the Ebola virus in vitro [version 1; referees: 2 approved]

Sean Ekins1-3, Joel S. Freundlich4, Alex M. Clark5, Manu Anantpadma6, Robert A. Davey6, Peter Madrid
F1000Research 2015, 4:1091 (doi: 10.12688/f1000research.7217.1)

Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologies.

Hanson SM, Ekins S, Chodera JD.

J Comput Aided Mol Des. 2015 Dec;29(12):1073-86. doi: 10.1007/s10822-015-9888-6. Epub 2015 Dec 17.


Combining Metabolite-Based Pharmacophores with Bayesian Machine Learning Models for Mycobacterium tuberculosis Drug Discovery.

Ekins S, Madrid PB, Sarker M, Li SG, Mittal N, Kumar P, Wang X, Stratton TP, Zimmerman M, Talcott C, Bourbon P, Travers M, Yadav M, Freundlich JS.

PLoS One. 2015 Oct 30;10(10):e0141076. doi: 10.1371/journal.pone.0141076. eCollection 2015.


Free PMC Article

Kelch Domain of Gigaxonin Interacts with Intermediate Filament Proteins Affected in Giant Axonal Neuropathy.

Johnson-Kerner BL, Garcia Diaz A, Ekins S, Wichterle H.

PLoS One. 2015 Oct 13;10(10):e0140157. doi: 10.1371/journal.pone.0140157. eCollection 2015.


Free PMC Article

Predicting Mouse Liver Microsomal Stability with “Pruned” Machine Learning Models and Public Data.

Perryman AL, Stratton TP, Ekins S, Freundlich JS.

Pharm Res. 2015 Sep 28. [Epub ahead of print]


Evolution of a thienopyrimidine antitubercular relying on medicinal chemistry and metabolomics insights.

Li SG, Vilchèze C, Chakraborty S, Wang X, Kim H, Anisetti M, Ekins S, Rhee KY, Jacobs WR Jr, Freundlich JS.

Tetrahedron Lett. 2015 Jun 3;56(23):3246-3250.


Making Transporter Models for Drug-Drug Interaction Prediction Mobile.

Ekins S, Clark AM, Wright SH.

Drug Metab Dispos. 2015 Oct;43(10):1642-5. doi: 10.1124/dmd.115.064956. Epub 2015 Jul 21.


Machine Learning Models and Pathway Genome Data Base for Trypanosoma cruzi Drug Discovery.

Ekins S, de Siqueira-Neto JL, McCall LI, Sarker M, Yadav M, Ponder EL, Kallel EA, Kellar D, Chen S, Arkin M, Bunin BA, McKerrow JH, Talcott C.

PLoS Negl Trop Dis. 2015 Jun 26;9(6):e0003878. doi: 10.1371/journal.pntd.0003878. eCollection 2015 Jun.


Free PMC Article

Thiophenecarboxamide Derivatives Activated by EthA Kill Mycobacterium tuberculosis by Inhibiting the CTP Synthetase PyrG.

Mori G, Chiarelli LR, Esposito M, Makarov V, Bellinzoni M, Hartkoorn RC, Degiacomi G, Boldrin F, Ekins S, de Jesus Lopes Ribeiro AL, Marino LB, Centárová I, Svetlíková Z, Blaško J, Kazakova E, Lepioshkin A, Barilone N, Zanoni G, Porta A, Fondi M, Fani R, Baulard AR, Mikušová K, Alzari PM, Manganelli R, de Carvalho LP, Riccardi G, Cole ST, Pasca MR.

Chem Biol. 2015 Jul 23;22(7):917-27. doi: 10.1016/j.chembiol.2015.05.016. Epub 2015 Jun 18.


Free PMC Article

Open Source Bayesian Models. 2. Mining a “Big Dataset” To Create and Validate Models with ChEMBL.

Clark AM, Ekins S.

J Chem Inf Model. 2015 Jun 22;55(6):1246-60. doi: 10.1021/acs.jcim.5b00144. Epub 2015 Jun 3.


Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets.

Clark AM, Dole K, Coulon-Spektor A, McNutt A, Grass G, Freundlich JS, Reynolds RC, Ekins S.

J Chem Inf Model. 2015 Jun 22;55(6):1231-45. doi: 10.1021/acs.jcim.5b00143. Epub 2015 Jun 3.


Free PMC Article

Finding small molecules for the ‘next Ebola’.

Ekins S, Southan C, Coffee M.

Version 2. F1000Res. 2015 Feb 27 [revised 2015 Jul 7];4:58. doi: 10.12688/f1000research.6181.2. eCollection 2015.


Free PMC Article

A brief review of recent Charcot-Marie-Tooth research and priorities.

Ekins S, Litterman NK, Arnold RJ, Burgess RW, Freundlich JS, Gray SJ, Higgins JJ, Langley B, Willis DE, Notterpek L, Pleasure D, Sereda MW, Moore A.

F1000Res. 2015 Feb 26;4:53. doi: 10.12688/f1000research.6160.1. eCollection 2015. Review.


Free PMC Article

Machines first, humans second: on the importance of algorithmic interpretation of open chemistry data.

Clark AM, Williams AJ, Ekins S.

J Cheminform. 2015 Mar 22;7:9. doi: 10.1186/s13321-015-0057-7. eCollection 2015.


Free PMC Article

In silico methods for predicting drug-drug interactions with cytochrome P-450s, transporters and beyond.

Ai N, Fan X, Ekins S.

Adv Drug Deliv Rev. 2015 Jun 23;86:46-60. doi: 10.1016/j.addr.2015.03.006. Epub 2015 Mar 19. Review.


FDA approved drugs as potential Ebola treatments.

Ekins S, Coffee M.

Version 2. F1000Res. 2015 Feb 19 [revised 2015 Mar 10];4:48. doi: 10.12688/f1000research.6164.2. eCollection 2015.


Free PMC Article

Small molecules with antiviral activity against the Ebola virus.

Litterman N, Lipinski C, Ekins S.

F1000Res. 2015 Feb 9;4:38. doi: 10.12688/f1000research.6120.1. eCollection 2015. Review.


Free PMC Article

A virtual screen discovers novel, fragment-sized inhibitors of Mycobacterium tuberculosis InhA.

Perryman AL, Yu W, Wang X, Ekins S, Forli S, Li SG, Freundlich JS, Tonge PJ, Olson AJ.

J Chem Inf Model. 2015 Mar 23;55(3):645-59. doi: 10.1021/ci500672v. Epub 2015 Feb 17.


Targeting Mycobacterium tuberculosis topoisomerase I by small-molecule inhibitors.

Godbole AA, Ahmed W, Bhat RS, Bradley EK, Ekins S, Nagaraja V.

Antimicrob Agents Chemother. 2015 Mar;59(3):1549-57. doi: 10.1128/AAC.04516-14. Epub 2014 Dec 22.


Free PMC Article

Databases and collaboration require standards for human stem cell research.

Litterman NK, Ekins S.

Drug Discov Today. 2015 Feb;20(2):247-54. doi: 10.1016/j.drudis.2014.10.006. Epub 2014 Oct 25. Review.


A substrate pharmacophore for the human sodium taurocholate co-transporting polypeptide.

Dong Z, Ekins S, Polli JE.

Int J Pharm. 2015 Jan 15;478(1):88-95. doi: 10.1016/j.ijpharm.2014.11.022. Epub 2014 Nov 13.


Parallel worlds of public and commercial bioactive chemistry data.

Lipinski CA, Litterman NK, Southan C, Williams AJ, Clark AM, Ekins S.

J Med Chem. 2015 Mar 12;58(5):2068-76. doi: 10.1021/jm5011308. Epub 2014 Dec 4.


Free PMC Article

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