• 2321 Citations
  • 28 h-Index
1994 …2024

Research output per year

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Research Output

2020

JSF-3285, A Novel KasA Inhibitor for Tuberculosis

Freundlich, J., Alland, D., Neiditch, M., Capodagli, G., Inoyama, D., Kumar, P. & Awasthi, D., Jan 2020

Research output: Innovation

2019

Ebola Virus Bayesian Machine Learning Models Enable New in Vitro Leads

Anantpadma, M., Lane, T., Zorn, K. M., Lingerfelt, M. A., Clark, A. M., Freundlich, J. S., Davey, R. A., Madrid, P. B. & Ekins, S., Jan 30 2019, In : ACS Omega. 4, 1, p. 2353-2361 9 p.

Research output: Contribution to journalArticle

3 Scopus citations

Intrabacterial Metabolism Obscures the Successful Prediction of an InhA Inhibitor of Mycobacterium tuberculosis

Wang, X., Perryman, A. L., Li, S. G., Paget, S. D., Stratton, T. P., Lemenze, A., Olson, A. J., Ekins, S., Kumar, P. & Freundlich, J. S., Jan 1 2019, In : ACS Infectious Diseases.

Research output: Contribution to journalArticle

Optimization of N-benzyl-5-nitrofuran-2-carboxamide as an antitubercular agent

Gallardo-Macias, R., Kumar, P., Jaskowski, M., Richmann, T., Shrestha, R., Russo, R., Singleton, E., Zimmerman, M. D., Ho, H. P., Dartois, V., Connell, N., Alland, D. & Freundlich, J. S., Feb 15 2019, In : Bioorganic and Medicinal Chemistry Letters. 29, 4, p. 601-606 6 p.

Research output: Contribution to journalArticle

2 Scopus citations

Radiosynthesis and PET Bioimaging of 76Br-Bedaquiline in a Murine Model of Tuberculosis

Ordonez, A. A., Carroll, L. S., Abhishek, S., Mota, F., Ruiz-Bedoya, C. A., Klunk, M. H., Singh, A. K., Freundlich, J. S., Mease, R. C. & Jain, S. K., Dec 13 2019, In : ACS Infectious Diseases. 5, 12, p. 1996-2002 7 p.

Research output: Contribution to journalArticle

2 Scopus citations

Repurposing the antimalarial pyronaridine tetraphosphate to protect against Ebola virus infection

Lane, T. R., Massey, C., Comer, J. E., Anantpadma, M., Freundlich, J. S., Davey, R. A., Madrid, P. B. & Ekins, S., Jan 1 2019, In : PLoS neglected tropical diseases. 13, 11, e0007890.

Research output: Contribution to journalArticle

Open Access

Structural basis of DSF recognition by its receptor rpfr and its regulatory interaction with the DSF synthase RpfF

Waldron, E. J., Snyder, D., Fernandez, N. L., Sileo, E., Inoyama, D., Freundlich, J. S., Waters, C. M., Cooper, V. S. & Neiditch, M. B., Feb 2019, In : PLoS biology. 17, 2, e3000123.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Synthesis and biological evaluation of solithromycin analogs against multidrug resistant pathogens

Daher, S. S., Jin, X., Patel, J., Freundlich, J. S., Buttaro, B. & Andrade, R. B., Jun 1 2019, In : Bioorganic and Medicinal Chemistry Letters. 29, 11, p. 1386-1389 4 p.

Research output: Contribution to journalArticle

The Natural Product Eugenol Is an Inhibitor of the Ebola Virus In Vitro

Lane, T., Anantpadma, M., Freundlich, J. S., Davey, R. A., Madrid, P. B. & Ekins, S., Jul 1 2019, In : Pharmaceutical research. 36, 7, 104.

Research output: Contribution to journalComment/debate

2018

Accessible Machine Learning Approaches for Toxicology

Ekins, S., Clark, A. M., Perryman, A. L., Freundlich, J., Korotcov, A. & Tkachenko, V., Feb 14 2018, Computational Toxicology: Risk Assessment for Chemicals. wiley, p. 1-29 29 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Scopus citations

Comparing and Validating Machine Learning Models for Mycobacterium tuberculosis Drug Discovery

Lane, T., Russo, D. P., Zorn, K. M., Clark, A. M., Korotcov, A., Tkachenko, V., Reynolds, R. C., Perryman, A. L., Freundlich, J. S. & Ekins, S., Oct 1 2018, In : Molecular pharmaceutics. 15, 10, p. 4346-4360 15 p.

Research output: Contribution to journalArticle

15 Scopus citations

Human Microbiome Inspired Antibiotics with Improved β-Lactam Synergy against MDR Staphylococcus aureus

Chu, J., Vila-Farres, X., Inoyama, D., Gallardo-Macias, R., Jaskowski, M., Satish, S., Freundlich, J. S. & Brady, S. F., Jan 12 2018, In : ACS Infectious Diseases. 4, 1, p. 33-38 6 p.

Research output: Contribution to journalArticle

5 Scopus citations

Naïve Bayesian Models for Vero Cell Cytotoxicity

Perryman, A. L., Patel, J. S., Russo, R., Singleton, E., Connell, N., Ekins, S. & Freundlich, J. S., Sep 1 2018, In : Pharmaceutical research. 35, 9, 170.

Research output: Contribution to journalArticle

3 Scopus citations

Synergistic lethality of a binary inhibitor of mycobacterium tuberculosis kasA

Kumar, P., Capodagli, G. C., Awasthi, D., Shrestha, R., Maharaja, K., Sukheja, P., Li, S. G., Inoyama, D., Zimmerman, M., Liang, H. P. H., Sarathy, J., Mina, M., Rasic, G., Russo, R., Perryman, A. L., Richmann, T., Gupta, A., Singleton, E., Verma, S., Husain, S. & 13 others, Soteropoulos, P., Wang, Z., Morris, R., Porter, G., Agnihotri, G., Salgame, P., Ekins, S., Rhee, K. Y., Connell, N., Dartois, V., Neiditch, M. B., Freundlich, J. S. & Alland, D., Nov 1 2018, In : mBio. 9, 6, e02101-17.

Research output: Contribution to journalArticle

2 Scopus citations

The EU approved antimalarial pyronaridine shows antitubercular activity and synergy with rifampicin, targeting RNA polymerase

Mori, G., Orena, B. S., Franch, C., Mitchenall, L. A., Godbole, A. A., Rodrigues, L., Aguilar-Pérez, C., Zemanová, J., Huszár, S., Forbak, M., Lane, T. R., Sabbah, M., Deboosere, N., Frita, R., Vandeputte, A., Hoffmann, E., Russo, R., Connell, N., Veilleux, C., Kumar, R. & 9 others, Kumar, P., Freundlich, J. S., Brodin, P., Aínsa, J. A., Nagaraja, V., Maxwell, A., Mikušová, K., Pasca, M. R. & Ekins, S., Sep 2018, In : Tuberculosis. 112, p. 98-109 12 p.

Research output: Contribution to journalArticle

2 Scopus citations
2017

Addressing the Metabolic Stability of Antituberculars through Machine Learning

Stratton, T. P., Perryman, A. L., Vilchèze, C., Russo, R., Li, S. G., Patel, J. S., Singleton, E., Ekins, S., Connell, N., Jacobs, W. R. & Freundlich, J. S., Oct 12 2017, In : ACS Medicinal Chemistry Letters. 8, 10, p. 1099-1104 6 p.

Research output: Contribution to journalArticle

5 Scopus citations

A novel small-molecule inhibitor of the mycobacterium tuberculosis demethylmenaquinone methyltransferase meng is bactericidal to both growing and nutritionally deprived persister cells

Sukheja, P., Kumar, P., Mittal, N., Li, S. G., Singleton, E., Russo, R., Perryman, A. L., Shrestha, R., Awasthi, D., Husain, S., Soteropoulos, P., Brukh, R., Connell, N., Freundlich, J. S. & Alland, D., Jan 1 2017, In : mBio. 8, 1, e02022-16.

Research output: Contribution to journalArticle

19 Scopus citations

Antimicrobials inspired by nonribosomal peptide synthetase gene clusters

Vila-Farres, X., Chu, J., Inoyama, D., Ternei, M. A., Lemetre, C., Cohen, L. J., Cho, W., Reddy, B. V. B., Zebroski, H. A., Freundlich, J. S., Perlin, D. S. & Brady, S. F., Feb 1 2017, In : Journal of the American Chemical Society. 139, 4, p. 1404-1407 4 p.

Research output: Contribution to journalArticle

18 Scopus citations

Antimycobacterial Metabolism: Illuminating Mycobacterium tuberculosis Biology and Drug Discovery

Awasthi, D. & Freundlich, J. S., Sep 2017, In : Trends in Microbiology. 25, 9, p. 756-767 12 p.

Research output: Contribution to journalReview article

12 Scopus citations

Enhanced respiration prevents drug tolerance and drug resistance in Mycobacterium tuberculosis

Vilchèze, C., Hartman, T., Weinrick, B., Jain, P., Weisbrod, T. R., Leung, L. W., Freundlich, J. S. & Jacobs, W. R., Apr 25 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 17, p. 4495-4500 6 p.

Research output: Contribution to journalArticle

43 Scopus citations

Machine learning models identify molecules active against the Ebola virus in vitro

Ekins, S., Freundlich, J. S., Clark, A. M., Anantpadma, M., Davey, R. A. & Madrid, P., Jan 1 2017, In : F1000Research. 4, 1091.

Research output: Contribution to journalArticle

6 Scopus citations

Mycobacterium abscessus L,D-transpeptidases are susceptible to inactivation by carbapenems and cephalosporins but not penicillins

Kumar, P., Chauhan, V., Silva, J. R. A., Lameira, J., D’Andrea, F. B., Li, S. G., Ginell, S. L., Freundlich, J. S., Alves, C. N., Bailey, S., Cohen, K. A. & Lamichhane, G., Jan 1 2017, In : Antimicrobial agents and chemotherapy. 61, 10

Research output: Contribution to journalArticle

9 Scopus citations

Non-classical transpeptidases yield insight into new antibacterials

Kumar, P., Kaushik, A., Lloyd, E. P., Li, S. G., Mattoo, R., Ammerman, N. C., Bell, D. T., Perryman, A. L., Zandi, T. A., Ekins, S., Ginell, S. L., Townsend, C. A., Freundlich, J. S. & Lamichhane, G., Jan 1 2017, In : Nature Chemical Biology. 13, 1, p. 54-61 8 p.

Research output: Contribution to journalArticle

40 Scopus citations
2016

Discovery of MRSA active antibiotics using primary sequence from the human microbiome

Chu, J., Vila-Farres, X., Inoyama, D., Ternei, M., Cohen, L. J., Gordon, E. A., Reddy, B. V. B., Charlop-Powers, Z., Zebroski, H. A., Gallardo-Macias, R., Jaskowski, M., Satish, S., Park, S., Perlin, D. S., Freundlich, J. S. & Brady, S. F., Dec 1 2016, In : Nature Chemical Biology. 12, 12, p. 1004-1006 3 p.

Research output: Contribution to journalArticle

55 Scopus citations

Machine Learning Model Analysis and Data Visualization with Small Molecules Tested in a Mouse Model of Mycobacterium tuberculosis Infection (2014-2015)

Ekins, S., Perryman, A. L., Clark, A. M., Reynolds, R. C. & Freundlich, J. S., Jul 25 2016, In : Journal of Chemical Information and Modeling. 56, 7, p. 1332-1343 12 p.

Research output: Contribution to journalArticle

10 Scopus citations

Machine learning models identify molecules active against the Ebola virus in vitro

Ekins, S., Freundlich, J. S., Clark, A. M., Anantpadma, M., Davey, R. A. & Madrid, P., Jan 1 2016, In : F1000Research. 4, 1091.

Research output: Contribution to journalArticle

19 Scopus citations

Open drug discovery for the Zika virus

Ekins, S., Mietchen, D., Coffee, M., Stratton, T. P., Freundlich, J. S., Freitas-Junior, L., Muratov, E., Siqueira-Neto, J., Williams, A. J. & Andrade, C., Jan 1 2016, In : F1000Research. 5, 150.

Research output: Contribution to journalArticle

34 Scopus citations

Predicting Mouse Liver Microsomal Stability with "pruned" Machine Learning Models and Public Data

Perryman, A. L., Stratton, T. P., Ekins, S. & Freundlich, J. S., Feb 1 2016, In : Pharmaceutical research. 33, 2, p. 433-449 17 p.

Research output: Contribution to journalArticle

17 Scopus citations
2015

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

Ekins, S., Litterman, N. K., Arnold, R. J. G., Burgess, R. W., Freundlich, J. S., Gray, S. J., Higgins, J. J., Langley, B., Willis, D. E., Notterpek, L., Pleasure, D., Sereda, M. W. & Moore, A., Feb 26 2015, In : F1000Research. 4

Research output: Contribution to journalReview article

19 Scopus citations

A high throughput screening assay for anti-mycobacterial small molecules based on adenylate kinase release as a reporter of cell lysis

Forbes, L., Ebsworth-Mojica, K., DiDone, L., Li, S. G., Freundlich, J. S., Connell, N., Dunman, P. M. & Krysan, D. J., Jun 22 2015, In : PloS one. 10, 6, e0129234.

Research output: Contribution to journalArticle

9 Scopus citations

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

Perryman, A. L., Yu, W., Wang, X., Ekins, S., Forli, S., Li, S. G., Freundlich, J. S., Tonge, P. J. & Olson, A. J., Mar 23 2015, In : Journal of Chemical Information and Modeling. 55, 3, p. 645-659 15 p.

Research output: Contribution to journalArticle

26 Scopus citations

Combining metabolite-based pharmacophores with Bayesian machine learning models for mycobacterium tuberculosis drug discovery

Ekins, S., Madrid, P. B., Sarker, M., Li, S. G., Mittal, N., Kumar, P., Wang, X., Stratton, T. P., Zimmerman, M., Talcott, C., Bourbon, P., Travers, M., Yadav, M. & Freundlich, J. S., Oct 30 2015, In : PloS one. 10, 10, e0141076.

Research output: Contribution to journalArticle

6 Scopus citations

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

Li, S. G., Vilchèze, C., Chakraborty, S., Wang, X., Kim, H., Anisetti, M., Ekins, S., Rhee, K. Y., Jacobs, W. R. & Freundlich, J. S., May 25 2015, In : Tetrahedron Letters. 56, 23, p. 3246-3250 5 p.

Research output: Contribution to journalArticle

10 Scopus citations

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

Clark, A. M., Dole, K., Coulon-Spektor, A., McNutt, A., Grass, G., Freundlich, J. S., Reynolds, R. C. & Ekins, S., Jun 22 2015, In : Journal of Chemical Information and Modeling. 55, 6, p. 1231-1245 15 p.

Research output: Contribution to journalArticle

42 Scopus citations
2014

A common feature pharmacophore for FDA-approved drugs inhibiting the Ebola virus

Ekins, S., Freundlich, J. & Coffee, M., Dec 12 2014, In : F1000Research. 3

Research output: Contribution to journalArticle

33 Scopus citations
24 Scopus citations

Biological evaluation of potent triclosan-derived inhibitors of the enoyl-acyl carrier protein reductase InhA in drug-sensitive and drug-resistant strains of mycobacterium tuberculosis

Stec, J., Vilchèze, C., Lun, S., Perryman, A. L., Wang, X., Freundlich, J. S., Bishai, W., Jacobs, W. R. & Kozikowski, A. P., Nov 1 2014, In : ChemMedChem. 9, 11, p. 2528-2537 10 p.

Research output: Contribution to journalArticle

16 Scopus citations

Combining computational methods for hit to lead optimization in mycobacterium tuberculosis drug discovery

Ekins, S., Freundlich, J. S., Hobrath, J. V., Lucile White, E. & Reynolds, R. C., Feb 1 2014, In : Pharmaceutical research. 31, 2, p. 414-435 22 p.

Research output: Contribution to journalArticle

37 Scopus citations

Computational models for neglected diseases: Gaps and opportunities

Ponder, E. L., Freundlich, J., Sarker, M. & Ekins, S., Feb 1 2014, In : Pharmaceutical research. 31, 2, p. 271-277 7 p.

Research output: Contribution to journalReview article

14 Scopus citations

Folate pathway disruption leads to critical disruption of methionine derivatives in mycobacterium tuberculosis

Nixon, M. R., Saionz, K. W., Koo, M. S., Szymonifka, M. J., Jung, H., Roberts, J. P., Nandakumar, M., Kumar, A., Liao, R., Rustad, T., Sacchettini, J. C., Rhee, K. Y., Freundlich, J. S. & Sherman, D. R., Jul 17 2014, In : Chemistry and Biology. 21, 7, p. 819-830 12 p.

Research output: Contribution to journalArticle

25 Scopus citations

Identification of a novel drug lead that inhibits HCV infection and cell-to-cell transmission by targeting the HCV E2 glycoprotein

Al Olaby, R. R., Cocquerel, L., Zemla, A., Saas, L., Dubuisson, J., Vielmetter, J., Marcotrigiano, J., Khan, A. G., Catalan, F. V., Perryman, A. L., Freundlich, J. S., Forli, S., Levy, S., Balhorn, R. & Azzazy, H. M., Oct 30 2014, In : PloS one. 9, 10, e111333.

Research output: Contribution to journalArticle

9 Scopus citations

Looking back to the future: Predicting in vivo efficacy of small molecules versus Mycobacterium tuberculosis

Ekins, S., Pottorf, R., Reynolds, R. C., Williams, A. J., Clark, A. M. & Freundlich, J. S., Jan 1 2014, In : Journal of Chemical Information and Modeling. 54, 4, p. 1070-1082 13 p.

Research output: Contribution to journalArticle

27 Scopus citations

Minding the gaps in tuberculosis research

Ekins, S., Nuermberger, E. L. & Freundlich, J., Jan 1 2014, In : Drug Discovery Today. 19, 9, p. 1279-1282 4 p.

Research output: Contribution to journalEditorial

5 Scopus citations
2013

Antituberculosis thiophenes define a requirement for Pks13 in mycolic acid biosynthesis

Wilson, R., Kumar, P., Parashar, V., Vilchèze, C., Veyron-Churlet, R., Freundlich, J., Barnes, S. W., Walker, J. R., Szymonifka, M. J., Marchiano, E., Shenai, S., Colangeli, R., Jacobs, W. R., Neiditch, M., Kremer, L. & Alland, D., Aug 2013, In : Nature Chemical Biology. 9, 8, p. 499-506 8 p.

Research output: Contribution to journalArticle

69 Scopus citations

Bayesian models leveraging bioactivity and cytotoxicity information for drug discovery

Ekins, S., Reynolds, R. C., Kim, H., Koo, M. S., Ekonomidis, M., Talaue, M., Paget, S. D., Woolhiser, L. K., Lenaerts, A. J., Bunin, B. A., Connell, N. & Freundlich, J. S., Mar 21 2013, In : Chemistry and Biology. 20, 3, p. 370-378 9 p.

Research output: Contribution to journalArticle

56 Scopus citations

Computational models for tuberculosis drug discovery

Ekins, S. & Freundlich, J., Jan 1 2013, In Silico Models for Drug Discovery. Humana Press Inc., p. 245-262 18 p. (Methods in Molecular Biology; vol. 993).

Research output: Chapter in Book/Report/Conference proceedingChapter

15 Scopus citations

Discrimination of potent inhibitors of toxoplasma gondii Enoyl-Acyl carrier protein reductase by a thermal shift assay

Afanador, G. A., Muench, S. P., McPhillie, M., Fomovska, A., Schön, A., Zhou, Y., Cheng, G., Stec, J., Freundlich, J. S., Shieh, H. M., Anderson, J. W., Jacobus, D. P., Fidock, D. A., Kozikowski, A. P., Fishwick, C. W., Rice, D. W., Freire, E., McLeod, R. & Prigge, S. T., Dec 23 2013, In : Biochemistry. 52, 51, p. 9155-9166 12 p.

Research output: Contribution to journalArticle

7 Scopus citations

Enhancing Hit Identification in Mycobacterium tuberculosis Drug Discovery Using Validated Dual-Event Bayesian Models

Ekins, S., Reynolds, R. C., Franzblau, S. G., Wan, B., Freundlich, J. S. & Bunin, B. A., May 7 2013, In : PloS one. 8, 5, e63240.

Research output: Contribution to journalArticle

40 Scopus citations

Fusing dual-event data sets for mycobacterium tuberculosis machine learning models and their evaluation

Ekins, S., Freundlich, J. S. & Reynolds, R. C., Nov 25 2013, In : Journal of Chemical Information and Modeling. 53, 11, p. 3054-3063 10 p.

Research output: Contribution to journalArticle

17 Scopus citations

Novel diaryl ureas with efficacy in a mouse model of malaria

Anderson, J. W., Sarantakis, D., Terpinski, J., Santha Kumar, T. R., Tsai, H. C., Kuo, M., Ager, A. L., Jacobs, W. R., Schiehser, G. A., Ekins, S., Sacchettini, J. C., Jacobus, D. P., Fidock, D. A. & Freundlich, J. S., Feb 15 2013, In : Bioorganic and Medicinal Chemistry Letters. 23, 4, p. 1022-1025 4 p.

Research output: Contribution to journalArticle

16 Scopus citations