Publications
Books
Ekins S. Winning Grants Springer 2023
Magazine articles
A Very Brief Introduction to “Winning Grants” AAPS News magazine 2023
Papers
ANTIVIRALS
Kazakova E, Lane TR, Jones T, Puhl AC, Riabova O, Makarov V, Ekins S. 1-Sulfonyl-3-amino-1H-1,2,4-triazoles as Yellow Fever Virus Inhibitors: Synthesis and Structure-Activity Relationship. ACS Omega. 2023 Nov 1;8(45):42951-42965. doi: 10.1021/acsomega.3c06106. PMID: 38024733; PMCID: PMC10653066.
Jones T, Monakhova N, Guivel-Benhassine F, Lepioshkin A, Bruel T, Lane TR, Schwartz O, Puhl AC, Makarov V, Ekins S. Synthesis and Evaluation of 9-Aminoacridines with SARS-CoV-2 Antiviral Activity. ACS Omega. 2023 Oct 19;8(43):40817-40822. doi: 10.1021/acsomega.3c05900. PMID: 37929131; PMCID: PMC10620940.
Jones T, Tavis JE, Li Q, Riabova O, Monakhova N, Bradley DP, Lane TR, Makarov V, Ekins S. Antiviral Evaluation of Dispirotripiperazines against Hepatitis B Virus. J Med Chem. 2023 Aug 23. doi: 10.1021/acs.jmedchem.3c00974. Epub ahead of print. PMID: 37611244.
Puhl AC, Lane TR, Ekins S. Learning from COVID-19: How drug hunters can prepare for the next pandemic. Drug Discov Today. 2023 Jul 22;28(10):103723. doi: 10.1016/j.drudis.2023.103723. Epub ahead of print. PMID: 37482237.
Puhl AC, Godoy AS, Noske GD, Nakamura AM, Gawriljuk VO, Fernandes RS, Oliva G, Ekins S. Discovery of PLpro and Mpro Inhibitors for SARS-CoV-2. ACS Omega. 2023 Jun 14;8(25):22603-22612. doi: 10.1021/acsomega.3c01110. PMID: 37387790; PMCID: PMC10275482.
Lane TR, Fu J, Sherry B, Tarbet B, Hurst BL, Riabova O, Kazakova E, Egorova A, Clarke P, Leser JS, Frost J, Rudy M, Tyler KL, Klose T, Volobueva AS, Belyaevskaya SV, Zarubaev VV, Kuhn RJ, Makarov V, Ekins S. Efficacy of an isoxazole-3-carboxamide analog of pleconaril in mouse models of Enterovirus-D68 and Coxsackie B5. Antiviral Res. 2023 Jun 14;216:105654. doi: 10.1016/j.antiviral.2023.105654. Epub ahead of print. PMID: 37327878.
Lane T, Makarov V, Nelson JAE, Meeker RB, Sanna G, Riabova O, Kazakova E, Monakhova N, Tsedilin A, Urbina F, Jones T, Suchy A, Ekins S. N-Phenyl-1-(phenylsulfonyl)-1H-1,2,4-triazol-3-amine as a New Class of HIV-1 Non-nucleoside Reverse Transcriptase Inhibitor. J Med Chem. 2023 May 2. doi: 10.1021/acs.jmedchem.2c02055.
Vignaux PA, Lane TR, Puhl AC, Hau RK, Wright SH, Cherrington NJ, Ekins S. Transporter Inhibition Profile for the Antivirals Tilorone, Quinacrine and Pyronaridine. ACS Omega. 2023 Mar 24;8(13):12532-12537. doi: 10.1021/acsomega.3c00724. eCollection 2023 Apr 4.PMID: 37033868
Puhl AC, Fernandes RS, Godoy AS, Gil LHVG, Oliva G, Ekins S. The protein disulfide isomerase inhibitor 3-methyltoxoflavin inhibits Chikungunya virus. Bioorg Med Chem. 2023 Apr 1;83:117239. doi: 10.1016/j.bmc.2023.117239. Epub 2023 Mar 15.PMID: 36940609
Mottin M, de Paula Sousa BK, de Moraes Roso Mesquita NC, de Oliveira KIZ, Noske GD, Sartori GR, de Oliveira Albuquerque A, Urbina F, Puhl AC, Moreira-Filho JT, Souza GE, Guido RVC, Muratov E, Neves BJ, Martins da Silva JH, Clark AE, Siqueira-Neto JL, Perryman AL, Oliva G, Ekins S, Andrade CH. Discovery of New Zika Protease and Polymerase Inhibitors through the Open Science Collaboration Project OpenZika. J Chem Inf Model. 2022 Oct 14. doi: 10.1021/acs.jcim.2c00596. Online ahead of print.PMID: 36239304
Puhl AC, Gomes GF, Damasceno S, Fritch EJ, Levi JA, Johnson NJ, Scholle F, Premkumar L, Hurst BL, Lee-Montiel F, Veras FP, Batah SS, Fabro AT, Moorman NJ, Yount BL, Dickmander RJ, Baric RS, Pearce KH, Cunha FQ, Alves-Filho JC, Cunha TM, Ekins S. Vandetanib Blocks the Cytokine Storm in SARS-CoV-2-Infected Mice. ACS Omega. 2022 Aug 29;7(36):31935-31944. doi: 10.1021/acsomega.2c02794. eCollection 2022 Sep 13.
Puhl AC, Mottin M, Sacramento CQ, Tavella TA, Dias GG, Fintelman-Rodrigues N, Temerozo JR, Dias SSG, Ramos PRPDS, Merten EM, Pearce KH, Costa FTM, Premkumar L, Souza TML, Andrade CH, Ekins S. Computational and Experimental Approaches Identify Beta-Blockers as Potential SARS-CoV-2 Spike Inhibitors. ACS Omega. 2022 Aug 8;7(32):27950-27958. doi: 10.1021/acsomega.2c01707. eCollection 2022 Aug 16.
Puhl AC, Gomes GF, Damasceno S, Godoy AS, Noske GD, Nakamura AM, Gawriljuk VO, Fernandes RS, Monakhova N, Riabova O, Lane TR, Makarov V, Veras FP, Batah SS, Fabro AT, Oliva G, Cunha FQ, Alves-Filho JC, Cunha TM, Ekins S. Pyronaridine Protects against SARS-CoV-2 Infection in Mouse.ACS Infect Dis. 2022 May 24. doi: 10.1021/acsinfecdis.2c00091..PMID: 35609344
Puhl AC, Lane TR, Urbina F and Ekins S. The need for speed and efficiency: A brief review of small molecule antivirals for COVID-19. Frontiers in Drug Discovery. 2022 Mar 30 https://doi.org/10.3389/fddsv.2022.837587
Mottin M, Caesar LK, Brodsky D, Mesquita NCMR, de Oliveira KZ, Noske GD, Sousa BKP, Ramos PRPS, Jarmer H, Loh B, Zorn KM, Foil DH, Torres PM, Guido RVC, Oliva G, Scholle F, Ekins S, Cech NB, Andrade CH, Laster SM. Chalcones from Angelica keiskei (ashitaba) inhibit key Zika virus replication proteins. Bioorg Chem. 2022 Jan 31;120:105649. doi: 10.1016/j.bioorg.2022.105649. Epub ahead of print. PMID: 35124513.
Lane TR, Ekins S. Defending Antiviral Cationic Amphiphilic Drugs That May Cause Drug-Induced Phospholipidosis. J Chem Inf Model. 2021 Sep 27;61(9):4125-4130. doi: 10.1021/acs.jcim.1c00903. Epub 2021 Sep 13. PMID: 34516123.
Puhl AC, Lane TR, Ekins S et al. “Repurposing the Ebola and Marburg Virus Inhibitors Tilorone, Quinacrine and Pyronaridine: In Vitro Activity Against SARS-CoV-2 and Potential Mechanisms.” ACS Omega, 2021 Mar 11. DOI: 10.1021/acsomega.0c05996
Vignaux PA, Minerali E, Lane TR, Foil DH, Madrid PB, Puhl AC, Ekins S. “The Antiviral Drug Tilorone Is A Potent and Selective Inhibitor of Acetylcholinesterase.” Chemical Research in Toxicology, 2021 Jan 5. DOI: 10.1021/acs.chemrestox.0c00466
Zorn KM, Ekins S. “Flavonoids from Pterogyne nitens as Zika virus NS2B-NS3 protease inhibitors.” Bioorganic Chemistry, Volume 109, 2021. DOI: 10.1016/j.bioorg.2021.104719.
Lima CS, Mottin M, de Assis LR, Mesquita NCMR, Sousa BKP, Coimbra LD, Santos KB, Zorn KM, Guido RVC, Ekins S, Marques RE, Proença-Modena JL, Oliva G, Andrade CH, Regasini LO. Flavonoids from Pterogyne nitens as Zika virus NS2B-NS3 protease inhibitors. Bioorg Chem. 2021 Apr;109:104719. doi: 10.1016/j.bioorg.2021.104719. Epub 2021 Feb 11.
Ekins S. “The Past, Present and Future of RNA Respiratory Viruses: Influenza and Coronaviruses.” Pathogens and Disease, 2020 Oct. DOI: 10.1093/femspd/ftaa046
Ekins S, Zorn KM, Puhl AC. “déjà vu: Stimulating Open Drug Discovery for SARS CoV 2.” Drug Discovery Today, 2020 May. DOI: 10.1016/j.drudis.2020.03.019
Ekins S. “Repurposing Quaternary Ammonium Compounds as Potential Treatments for COVID-19.” Springer Link, 2020 May 25. DOI: 10.1007/s11095-020-02842-8
Lane TR, et al. “Pyronaridine Tetraphosphate Efficacy Against Ebola Virus Infection in Guinea Pig.” Antiviral Res. 2020 Jul 16:104863. doi: 10.1016/j.antiviral.2020.104863.
Lane TR, Ekins S. “Toward the Target: Tilorone, Quinacrine, and Pyronaridine Bind to Ebola Virus Glycoprotein.” ACS Med. Chem. Lett. 2020, 11, 8, 1653–1658
Lane TR, Dyall J, Mercer L, Goodin C, Foil DH, Zhou H, Postnikova E, Liang JY, Holbrook MR, Madrid PB, Ekins S. “Repurposing Pyramax®, quinacrine and tilorone as treatments for Ebola virus disease.” Antiviral Res. 2020 Oct;182:104908. doi: 10.1016/j.antiviral.2020.104908.
Egorova A, Bogner E, Novoselova E, Zorn KM, Ekins S, Makarov V. “Dispirotripiperazine-core compounds, their biological activity with a focus on broad antiviral property, and perspectives in drug design.” European Journal of Medicinal Chemistry, 2020 Nov 13. doi: 10.1016/j.ejmech.2020.113014.
Lane TR, Comer JE, Freiberg AN, Madrid PB, Ekins S. “Repurposing Quinacrine against Ebola Virus Infection In Vivo.” Antimicrob Agents Chemother. 2019 Aug 23;63(9):e01142-19. doi: 10.1128/AAC.01142-19.
Lane TR, Massey C, Comer JE, Anantpadma M, Freundlich JS, Davey RA, Madrid PB, Ekins S. “Repurposing the antimalarial pyronaridine tetraphosphate to protect against Ebola virus infection.” PLoS Negl Trop Dis. 2019 Nov 21;13(11):e0007890. doi: 10.1371/journal.pntd.0007890.
Lane T, Anantpadma M, Freundlich JS, Davey RA, Madrid PB, Ekins S. “The Natural Product Eugenol Is an Inhibitor of the Ebola Virus In Vitro.” Pharm Res. 2019 May 17;36(7):104. doi: 10.1007/s11095-019-2629-0.
RARE OR NEGLECTED DISEASES
Puhl AC, Negri S, Hupcey AZ M and Ekins S, Developing treatments for rare diseases on a shoestring. GEN Biotechnology Published Online:16 Oct 2023
Rank L, Puhl AC, Havener TM, Anderson E, Foil DH, Zorn KM, Monakhova N, Riabova O, Hickey AJ, Makarov V, Ekins S.Multiple approaches to repurposing drugs for neuroblastoma. Bioorg Med Chem. 2022 Nov 1;73:117043. doi: 10.1016/j.bmc.2022.117043. Epub 2022 Oct 4.PMID: 36208544
Nelvagal HR, Eaton SL, Wang SH, Eultgen EM, Takahashi K, Le SQ, Nesbitt R, Dearborn JT, Siano N, Puhl AC, Dickson PI, Thompson G, Murdoch F, Brennan PM, Gray M, Greenhalgh SN, Tennant P, Gregson R, Clutton E, Nixon J, Proudfoot C, Guido S, Lillico SG, Whitelaw CBA, Lu J-Y, Hofmann SL, Ekins S, Sands MS, Wishart TM, and Cooper JD. Cross-species efficacy of enzyme replacement therapy for CLN1 disease in mice and sheep. J Clin Invest. 2022 Oct 17;132(20):e163107. doi: 10.1172/JCI163107.
Puhl AC and Ekins S. Advancing the Research and Development of Enzyme Replacement Therapies for Lysosomal Storage Diseases. GEN Biotechnology. 2022 1 (2)
Alves VM, Korn D, Pervitsky V, Thieme A, Capuzzi S, Baker N, Chirkova R, Ekins S, Muratov EN, Hickey A, Tropsha A. Knowledge-based approaches to drug discovery for rare diseases. Drug Discov Today. 2021 Oct 27:S1359-6446(21)00452-9. doi: 10.1016/j.drudis.2021.10.014. Epub ahead of print. PMID: 34718207.
Klein JJ, Baker NC, Foil DH, Zorn KM, Urbina F, Puhl AC, Ekins S. “Using Bibliometric Analysis and Machine Learning to Identify Compounds Binding to Sialidase-1.” ACS Omega. 2021 Jan 20. doi: 10.1021/acsomega.0c05591
Ekins S, Puhl AC, Davidow A. “Repurposing the Dihydropyridine Calcium Channel Inhibitor Nicardipine as a Nav1.8 Inhibitor In Vivo for Pitt Hopkins Syndrome.” Pharm Res. 2020;37(7):127.
Ekins S, Gerlach J, Zorn KM, Antonio BM, Lin Z, Gerlach A. “Repurposing Approved Drugs as Inhibitors of Kv7.1 and Nav1.8 to Treat Pitt Hopkins Syndrome.” Pharm Res. 2019 Jul 22;36(9):137.
Ekins S and Perlstein EO. “Doing it All - How Families are Reshaping Rare Disease Research.” Pharm Res, 35: 192, 2018
Ekins S. “Industrializing rare disease therapy discovery and development.” Nat Biotechnol, 35: 117-118, 2017
Ekins S and Wood J. “Incentives for starting small companies focused on rare and neglected diseases.” Pharm Res, 33: 809-815, 2016Ekins S. “Collecting Rare Diseases.” F1000Research, 3:260, 2014
Litterman NK, Rhee, M, Swinney DC and Ekins S. “Collaboration for rare disease drug discovery research.” F1000Research 3:261, 2014
Sames L, Moore A, Arnold R and Ekins S. “Recommendations to enable drug development for the inherited neuropathies: Charco-Marie-Tooth and Giant Axonal Neuropathy.” F1000Research 3: 83, 2014
Wood J, Sames L, Moore A, Ekins S. “The multifaceted roles of rare disease parent / patient advocates in drug discovery.” Drug Disc Today, 18: 1043–1051, 2013.
Beaulieu CL, Samuels ME, Ekins S, McMaster CR, Edwards AM, Krainer AR, Hicks GG, Frey BJ, Boycott KM, Mackenzie AE. “A generalizable pre-clinical research approach for orphan disease therapy.” Orphanet 7:39, 2012
MACHINE LEARNING
Ekins S, Brackmann M, Invernizzi C, Lentzos F. Generative Artificial Intelligence-Assisted Protein Design Must Consider Repurposing Potential. GEN Biotechnol. 2023 Aug 1;2(4):296-300. doi: 10.1089/genbio.2023.0025. Epub 2023 Aug 17. PMID: 37928405; PMCID: PMC10623615.
Linciano P, Quotadamo A, Luciani R, Santucci M, Zorn KM, Foil DH, Lane TR, Cordeiro da Silva A, Santarem N, B Moraes C, Freitas-Junior L, Wittig U, Mueller W, Tonelli M, Ferrari S, Venturelli A, Gul S, Kuzikov M, Ellinger B, Reinshagen J, Ekins S, Costi MP. High-Throughput Phenotypic Screening and Machine Learning Methods Enabled the Selection of Broad-Spectrum Low-Toxicity Antitrypanosomatidic Agents. J Med Chem. 2023 Nov 23;66(22):15230-15255. doi: 10.1021/acs.jmedchem.3c01322. Epub 2023 Nov 3. PMID: 37921561; PMCID: PMC10683024.
Ekins S, Lentzos F, Brackmann M, Invernizzi, C, There’s a ‘ChatGPT’ for biology. What could go wrong?, Bulletin of the Atomic Scientists, March 24, 2023
Lane TR, Harris J, Urbina F and Ekins S, Comparing LD50/LC50 Machine Learning Models for Multiple Species. ACS Chem Health Saf 2023, In press.
Vignaux PA, Lane TR, Urbina F, Gerlach J, Puhl AC, Snyder SH, Ekins S. Validation of Acetylcholinesterase Inhibition Machine Learning Models for Multiple Species. Chem Res Toxicol. 2023 Feb 20;36(2):188-201. doi: 10.1021/acs.chemrestox.2c00283. Epub 2023 Feb 3.PMID: 36737043
Urbina F, Lentzos F, Invernizzi C, Ekins S. Preventing AI From Creating Biochemical Threats. J Chem Inf Model. 2023 Feb 13;63(3):691-694. doi: 10.1021/acs.jcim.2c01616. Epub 2023 Jan 25. PMID: 36696568.
Ekins S and Urbina F in James Revill, Vivienne Zhang and María Garzón Maceda (eds.) “Stakeholder perspectives on the Biological Weapons Convention”, UNIDIR, Geneva, 2022. https://doi.org/10.37559/WMD/22/BWC/03.
Urbina F, Lentzos F, Invernizzi C, Ekins S. A teachable moment for dual-use. Nat Mach Intell. 2022 Jul;4(7):607. doi: 10.1038/s42256-022-00511-6. Epub 2022 Jul 12.PMID: 36393980
Hamm J, Mahapatra D, Knuth MM, Abedini J, Lingerfelt M, Ekins S, Kullman SW. Confirmation of high-throughput screening data and novel mechanistic insights into FXR-xenobiotic interactions by orthogonal assays. Curr Res Toxicol. 2022 Nov 1;3:100092. doi: 10.1016/j.crtox.2022.100092. eCollection 2022.PMID: 36353521
Ekins S, Al-novation: Finding New Uses for Artificial Intelligence Across Industries. GEN Biotechnology, https://doi.org/10.1089/genbio.2022.0025
Urbina F, Lentzos F, Invernizzi C, Ekins S. AI in drug discovery: A wake-up call. Drug Discov Today. 2022 Oct 18;28(1):103410. doi: 10.1016/j.drudis.2022.103410. PMID: 36270472
Lane TR, Urbina F, Zhang X, Fye M, Gerlach J, Wright SH, Ekins S. Machine Learning Models Identify New Inhibitors for Human OATP1B1.Mol Pharm. 2022 Nov 7;19(11):4320-4332. doi: 10.1021/acs.molpharmaceut.2c00662. Epub 2022 Oct 21.PMID: 36269563
Blay V, Li X, Gerlach J, Urbina F, Ekins S. Combining DELs and machine learning for toxicology prediction. Drug Discov Today. 2022 Sep 9:103351. doi: 10.1016/j.drudis.2022.103351. Online ahead of print.PMID: 36096360
Puhl AC, Gao ZG, Jacobson KA, Ekins S. Machine Learning for Discovery of New ADORA Modulators. Front Pharmacol. 2022 Jun 22;13:920643. doi: 10.3389/fphar.2022.920643. eCollection 2022.PMID: 35814244
Lemenze A, Mittal N, Perryman AL, Daher SS, Ekins S, Occi J, Ahn YM, Wang X, Russo R, Patel JS, Daugherty RM, Wood DO, Connell N, Freundlich JS. Rickettsia Aglow: A Fluorescence Assay and Machine Learning Model to Identify Inhibitors of Intracellular Infection. ACS Infect Dis. 2022 Jul 8;8(7):1280-1290. doi: 10.1021/acsinfecdis.2c00014. Epub 2022 Jun 24.
Urbina F, Lowden CT, Culberson JC, and Ekins S, MegaSyn: Integrating Generative Molecular Design, Automated Analog Designer, and Synthetic Viability Prediction, ACS Omega 2022, Publication Date:May 27, 2022, https://doi.org/10.1021/acsomega.2c01404
Urbina F, Ekins S. The Commoditization of AI for Molecule Design. Artif Intell Life Sci. 2022 Dec;2:100031. doi: 10.1016/j.ailsci.2022.100031. Epub 2022 Jan 24.PMID: 36211981
Urbina F, Lentzos F, Invernizzi C, Ekins S. Dual use of artificial-intelligence-powered drug discovery. Nature Machine Intelligence. 2022 Mar; 4: 189-191
Schmalstig AA, Zorn KM, Murcia S, Robinson A, Savina S, Komarova E, Makarov V, Braunstein M, Ekins S. Mycobacterium abscessus drug discovery using machine learning. Tuberculosis (Edinb). 2022 Jan;132:102168. doi: 10.1016/j.tube.2022.102168. Epub 2022 Jan 20. PMID: 35077930.
Lane TR, Urbina F, Rank L, Gerlach J, Riabova O, Lepioshkin A, Kazakova E, Vocat A, Tkachenko V, Cole S, Makarov V, Ekins S. Machine Learning Models for Mycobacterium tuberculosis In VitroActivity: Prediction and Target Visualization. Mol Pharm. 2022 Feb 7;19(2):674-689. doi: 10.1021/acs.molpharmaceut.1c00791. Epub 2021 Dec 29. PMID: 34964633.
Urbina F, Batra K, Luebke KJ, White JD, Matsiev D, Olson LL, Malerich JP, Hupcey MAZ, Madrid PB, Ekins S. UV-adVISor: Attention-Based Recurrent Neural Networks to Predict UV-Vis Spectra. Anal Chem. 2021 Dec 7;93(48):16076-16085. doi: 10.1021/acs.analchem.1c03741. Epub 2021 Nov 23. PMID: 34812602.
Miller SR, McGrath ME, Zorn KM, Ekins S, Wright SH, Cherrington NJ. Remdesivir and EIDD-1931 Interact with Human Equilibrative Nucleoside Transporters 1 and 2: Implications for Reaching SARS-CoV-2 Viral Sanctuary Sites. Mol Pharmacol. 2021 Sep 9:MOLPHARM-AR-2021-000333. doi: 10.1124/molpharm.121.000333. Epub ahead of print. PMID: 34503974.
Gawriljuk VO, Zin PPK, Puhl AC, Zorn KM, Foil DH, Lane TR, Hurst B, Tavella TA, Costa FTM, Lakshmanane P, Bernatchez J, Godoy AS, Oliva G, Siqueira-Neto JL, Madrid PB, Ekins S. Machine Learning Models Identify Inhibitors of SARS-CoV-2. J Chem Inf Model. 2021 Sep 27;61(9):4224-4235. doi: 10.1021/acs.jcim.1c00683. Epub 2021 Aug 13. PMID: 34387990.
Patel JS, Norambuena J, Al-Tameemi H, Ahn YM, Perryman AL, Wang X, Daher SS, Occi J, Russo R, Park S, Zimmerman M, Ho HP, Perlin DS, Dartois V, Ekins S, Kumar P, Connell N, Boyd JM, Freundlich JS. Bayesian Modeling and Intrabacterial Drug Metabolism Applied to Drug-Resistant Staphylococcus aureus. ACS Infect Dis. 2021 Aug 3. doi: 10.1021/acsinfecdis.1c00265. Epub ahead of print. PMID: 34342426.
Gawriljuk VO, Foil DH, Puhl AC, Zorn KM, Lane TR, Riabova O, Makarov V, Godoy AS, Oliva G, Ekins S. Development of Machine Learning Models and the Discovery of a New Antiviral Compound against Yellow Fever Virus. J Chem Inf Model. 2021 Jul 21. doi: 10.1021/acs.jcim.1c00460. Epub ahead of print. PMID: 34286575.
Urbina F, Puhl AC, Ekins S. Recent advances in drug repurposing using machine learning. Curr Opin Chem Biol. 2021 Jul 15;65:74-84. doi: 10.1016/j.cbpa.2021.06.001. Epub ahead of print. PMID: 34274565.
Martinez Guerrero LJ, Zhang X, Zorn KM, Ekins S, Wright SH. Cationic Compounds with SARS-CoV-2 Antiviral Activity and their Interaction with OCT/MATE Secretory Transporters. J Pharmacol Exp Ther. 2021 Jul 12:JPET-AR-2021-000619. doi: 10.1124/jpet.121.000619. Epub ahead of print. PMID: 34253645.
Urbina F, Zorn KM, Brunner D, Ekins S. Comparing the Pfizer Central Nervous System Multiparameter Optimization Calculator and a BBB Machine Learning Model. ACS Chem Neurosci. 2021 Jun 16;12(12):2247-2253. doi: 10.1021/acschemneuro.1c00265. Epub 2021 May 24.
Batra K, Zorn KM, Foil DH, Minerali E, Gawriljuk VO, Lane TR, Ekins S. Quantum Machine Learning Algorithms for Drug Discovery Applications. J Chem Inf Model. 2021 May 25. doi: 10.1021/acs.jcim.1c00166.
Miller SR, Lane TR, Zorn KM, Ekins S, Wright SH, Cherrington N. Multiple Computational Approaches for Predicting Drug Interactions with Human Equilibrative Nucleoside Transporter 1. Drug Metab Dispos. 2021 May 12:DMD-AR-2021-000423. doi: 10.1124/dmd.121.000423.
Mansouri K, Karmaus AL, Fitzpatrick J, Patlewicz G, Pradeep P, Alberga D, Alepee N, Allen TEH, Allen D, Alves VM, Andrade CH, Auernhammer TR, Ballabio D, Bell S, Benfenati E, Bhattacharya S, Bastos JV, Boyd S, Brown JB, Capuzzi SJ, Chushak Y, Ciallella H, Clark AM, Consonni V, Daga PR, Ekins S, Farag S, Fedorov M, Fourches D, Gadaleta D, Gao F, Gearhart JM, Goh G, Goodman JM, Grisoni F, Grulke CM, Hartung T, Hirn M, Karpov P, Korotcov A, Lavado GJ, Lawless M, Li X, Luechtefeld T, Lunghini F, Mangiatordi GF, Marcou G, Marsh D, Martin T, Mauri A, Muratov EN, Myatt GJ, Nguyen DT, Nicolotti O, Note R, Pande P, Parks AK, Peryea T, Polash AH, Rallo R, Roncaglioni A, Rowlands C, Ruiz P, Russo DP, Sayed A, Sayre R, Sheils T, Siegel C, Silva AC, Simeonov A, Sosnin S, Southall N, Strickland J, Tang Y, Teppen B, Tetko IV, Thomas D, Tkachenko V, Todeschini R, Toma C, Tripodi I, Trisciuzzi D, Tropsha A, Varnek A, Vukovic K, Wang Z, Wang L, Waters KM, Wedlake AJ, Wijeyesakere SJ, Wilson D, Xiao Z, Yang H, Zahoranszky-Kohalmi G, Zakharov AV, Zhang FF, Zhang Z, Zhao T, Zhu H, Zorn KM, Casey W, Kleinstreuer NC. CATMoS: Collaborative Acute Toxicity Modeling Suite. Environ Health Perspect. 2021 Apr;129(4):47013. doi: 10.1289/EHP8495. Epub 2021 Apr 30.
Donlin MJ, Lane TR, Riabova O, Lepioshkin A, Xu E, Lin J, Makarov V, Ekins S. Discovery of 5-Nitro-6-thiocyanatopyrimidines as Inhibitors of Cryptococcus neoformans and Cryptococcus gattii. ACS Med Chem Lett. 2021 Apr 7;12(5):774-781. doi: 10.1021/acsmedchemlett.1c00038.
Zorn KM, Sun S, McConnon CL, Ma K, Chen EK, Foil DH, Lane TR, Liu LJ, El-Sakkary N, Skinner DE, Ekins S, Caffrey CR. “A Machine Learning Strategy for Drug Discovery Identifies Anti-Schistosomal Small Molecules.” ACS Infectious Diseases, 2021 Jan 12. DOI: 10.1021/acsinfecdis.0c00754.
Lane TR, Foil DH, Minerali E, Urbina F, Zorn KM, Ekins S. “Bioactivity Comparison across Multiple Machine Learning Algorithms Using over 5000 Datasets for Drug Discovery.” Mol Pharm, 2020 Dec 16. doi: 10.1021/acs.molpharmaceut.0c01013.
Zorn KM, Foil DH, Lane TR, Hillwalker W, Feifarek DJ, Jones F, Klaren WD, Brinkman AM, Ekins S. “Comparing Machine Learning Models for Aromatase (P450 19A1).” Environ Sci Technol, 2020 Dec 1. doi: 10.1021/acs.est.0c05771.
Miller SR, Zhang X, Hau RK, Jilek JL, Jennings EQ, Galligan JJ, Foil DH, Zorn KM, Ekins S, Wright SH, Cherrington NJ. “Predicting Drug Interactions with Human Equilibrative Nucleoside Transporters 1 and 2 Using Functional Knockout Cell Lines and Bayesian Modeling.” Mol Pharmacol, 2020 Dec 1. doi: 10.1124/molpharm.120.000169.
Puhl AC, Lane TR, Vignaux PA, Zorn KM, Capodagli GC, Neiditich MB, Freundlich JS, Ekins S. “Computational Approaches to Identify Molecules Binding to Mycobacterium Tuberculosis KasA.” ACS Omega, 2020 Nov 15. doi: 10.1021/acsomega.0c04271.
Zorn KM, Foil DH, Lane TR, Hillwalker W, Feifarek DJ, Jones F, Klaren WD, Brinkman AM, Ekins S. “Comparison of Machine Learning Models for the Androgen Receptor.” Environmental Science & Technology, 2020 Oct 21. doi: 10.1021/acs.est.0c03984.
Vignaux P, Minerali E, Foil D, Puhl A, Ekins S. “Machine Learning for Discovery of GSK3β Inhibitors.” ACS Omega, 2020 Oct 12. doi: 10.1021/acsomega.0c03302.
Minerali E, Foil D, Zorn K, Ekins S. “Evaluation of Assay Central® Machine Learning Models for Rat Acute Oral Toxicity Prediction.” ACS Sustainable Chemistry & Engineering. 2020 Oct 9. doi: 10.1021/acssuschemeng.0c06348.
Zorn KM, Foil DH, Lane TR, Russo DP, Hillwalker W, Feifarek DJ, Jones F, Klaren WD, Brinkman AM, Ekins S. “Machine Learning Models for Estrogen Receptor Bioactivity and Endocrine Disruption Prediction.” Environ Sci Technol. 2020 Sep 15. doi: 10.1021/acs.est.0c03982.
Anderson E, Havener TM, Zorn KM, Foil DH, Lane TR, Capuzzi SJ, Morris D, Hickey AJ, Drewry DH, Ekins S. “Synergistic drug combinations and machine learning for drug repurposing in chordoma.” Sci Rep. 2020 Jul 31;10(1):12982. doi: 10.1038/s41598-020-70026-w.
Pereira JC, Daher SS, Zorn KM, Sherwood M, Russo R, Perryman AL, Wang X, Freundlich MJ, Ekins S, Freundlich JS. “Machine Learning Platform to Discover Novel Growth Inhibitors of Neisseria gonorrhoeae.” Pharm Res. 2020 Jul 13;37(7):141. doi: 10.1007/s11095-020-02876-y.
Minerali E, Foil DH, Zorn KM, Lane TR, Ekins S. “Comparing Machine Learning Algorithms for Predicting Drug-Induced Liver Injury (DILI).” Mol Pharm. 2020 Jul 6;17(7):2628-2637. doi: 10.1021/acs.molpharmaceut.0c00326
Ekins S. “Pruned Machine Learning Models to Predict Aqueous Solubility.” ACS Omega. 2020 Jul 1. DOI: 10.1021/acsomega.0c01251
Zin PPK, Ekins S. “Cheminformatics Analysis and Modeling with MacrolactoneDB.” Nature. 2020 April 14. DOI: 10.1038/s41598-020-63192-4
Zorn KM, Lane TR, Russo DP, Clark AM, Makarov V, Ekins S. “Multiple Machine Learning Comparisons of HIV Cell-based and Reverse Transcriptase Data Sets.” Mol Pharm. 2019 Apr 1;16(4):1620-1632. doi: 10.1021/acs.molpharmaceut.8b01297.
Anantpadma M, Lane T, Zorn KM, Lingerfelt MA, Clark AM, Freundlich JS, Davey RA, Madrid PB, Ekins S. “Ebola Virus Bayesian Machine Learning Models Enable New in Vitro Leads.” ACS Omega. 2019 Jan 31;4(1):2353-2361. doi: 10.1021/acsomega.8b02948.
Wang PF, Neiner A, Lane TR, Zorn KM, Ekins S, Kharasch ED. “Halogen Substitution Influences Ketamine Metabolism by Cytochrome P450 2B6: In Vitro and Computational Approaches.” Mol Pharm. 2019 Feb 4;16(2):898-906. doi: 10.1021/acs.molpharmaceut.8b01214.
Bhhatarai, B, Walters P, Hop C, Lanza G, Ekins S. “Opportunities and Challenges Using Artificial Intelligence in ADME/Tox.” Nature Materials, vol. 18, no. 5, 2019, pp. 418–422., doi:10.1038/s41563-019-0332-5.
Ekins S, Puhl AC, Zorn K, Lane T, Russo D, Klein J, Hickey A, Clark A. “Exploiting Machine Learning for End-to-End Drug Discovery and Development.” Nature Materials, vol. 18, no. 5, 2019, pp. 435–441., doi:10.1038/s41563-019-0338-z.
Dalecki, Alex G., et al. “High-Throughput Screening and Bayesian Machine Learning for Copper-Dependent Inhibitors of Staphylococcus Aureus.” Metallomics, vol. 11, no. 3, 2019, pp. 696–706., doi:10.1039/c8mt00342d.
Chiarelli LR, et al. “A multitarget approach to drug discovery inhibiting Mycobacterium tuberculosis PyrG and PanK.” Sci Rep. 2018 Feb 16;8(1):3187. doi: 10.1038/s41598-018-21614-4.
Lane T, Russo DP, Zorn KM, Clark AM, Korotcov A, Tkachenko V, Reynolds RC, Perryman AL, Freundlich JS, Ekins S. “Comparing and Validating Machine Learning Models for Mycobacterium tuberculosis Drug Discovery.” Mol Pharm. 2018 Oct 1;15(10):4346-4360. doi: 10.1021/acs.molpharmaceut.8b00083.
Mori G, et al. “The EU approved antimalarial pyronaridine shows antitubercular activity and synergy with rifampicin, targeting RNA polymerase.” Tuberculosis (Edinb). 2018 Sep;112:98-109. doi: 10.1016/j.tube.2018.08.004.
Hernandez HW, et al. “High Throughput and Computational Repurposing for Neglected Diseases.” Pharm Res. 2018 Dec 17;36(2):27. doi: 10.1007/s11095-018-2558-3.
Russo, Daniel P., et al. “Comparing Multiple Machine Learning Algorithms and Metrics for Estrogen Receptor Binding Prediction.” Molecular Pharmaceutics, vol. 15, no. 10, 2018, pp. 4361–4370., doi:10.1021/acs.molpharmaceut.8b00546.
Sandoval, Philip J., et al. “Assessment of Substrate-Dependent Ligand Interactions at the Organic Cation Transporter OCT2 Using Six Model Substrates.” Molecular Pharmacology, vol. 94, no. 3, 2018, pp. 1057–1068., doi:10.1124/mol.117.111443.
Ekins S. “Comparison of Deep Learning With Multiple Machine Learning Methods and Metrics Using Diverse Drug Discovery Data Sets.” Mol. Pharmaceutics. 2017 Nov 2. DOI: 10.1021/acs.molpharmaceut.7b00578.
TOXICOLOGY
Vignaux PA, Shriwas P, Revnew A, Agarwal G, Lane TR, McElroy CA, Ekins S. Human CYP2C19 Substrate and Inhibitor Characterization of Organophosphate Pesticides. Chem Res Toxicol. 2023 Aug 31. doi: 10.1021/acs.chemrestox.3c00188. Epub ahead of print. PMID: 37650603.
Ekins S, Lane TR, Urbina F, Puhl AC. In silico ADME/tox comes of age: twenty years later. Xenobiotica. 2023 Aug 8:1-7. doi: 10.1080/00498254.2023.2245049. Epub ahead of print. PMID: 37539466.
Agarwal G, Tichenor H, Roo S, Lane TR, Ekins S, McElroy CA. Targeted Metabolomics of Organophosphate Pesticides and Chemical Warfare Nerve Agent Simulants Using High- and Low-Dose Exposure in Human Liver Microsomes. Metabolites. 2023 Mar 29;13(4):495. doi: 10.3390/metabo13040495.PMID: 37110155
Additional Documentation
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