H. L. Tran, K. W. Lexa, O. Julien, T. S. Young, C. T. Walsh, M. P. Jacobson, and J. A. Wells.  “Structure-Activity Relationship and Molecular Mechanics Reveal the Importance of Ring Entropy in the Biosynthesis and Activity of a Natural Product.”  JACS, 139 (2017) 2541-2544.  Pubmed



Q. Wang, S. Sciabola, G. Barreiro, X. Hou, G. Bai, M. J. Shapiro, F. E. Koehn, A. Villalobos, and M. P. Jacobson.  “Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction”, J. Chem. Inf. Model., 56 (2016) 2194-2206.  Pubmed


M. Armstrong, C. van Hoorebeke, T. Horn, J. Deschamps, J. C. Freedman, C. Kalyanaraman, M. P. Jacobson, and T. Holman.  “Human 15-LOX-1 active site mutations alter inhibitor binding and decrease potency”, Bioorg. Med. Chem., 24 (2016) 5380-5387.  PMC5065787


T. Long, R. J. Neitz, R. Beasley, C. Kalyanaraman, B. M. Suzuki, M. P. Jacobson, C. Dissous, J. H. McKerrow, D. H. Drewry, W. J. Zuercher, R. Singh, and C. R. Caffrey.  “Structure-Bioactivity Relationship for Benzimidazole Thiophene Inhibitors of Polo-Like Kinase 1 (PLK1), a Potential Drug Target in Schistosoma mansoni”,  PLoS Negl. Trop. Dis., 10 (2016) e0004356.  Open Access


J. Schwochert, R. Turner, M. Thang, R. Berkeley, A. Ponkey, K. M. Rodriguez, S. S. S. Leung, B. Khunte, C. Limberakis, A. S. Kalgutkar, H. Eng, M. J. Shapiro, A. M. Mathiowetz, D. A. Price, S. Liras, M. P. Jacobson, and R. S. Lokey.  “Peptide to peptoid substitutions increase cellular permeability in cyclic hexapeptides”, Org. Lett., 17 (2015) 2928-2931.  Pubmed


A. T. Bockus, K. Lexa, C. Pye, A. Kalgutkar, J. Garden, K. Hund, W. M. Hewitt, J. Schwochert, E. Glassey, D. A. Price, A. M. Mathiowetz, S. Liras, M. P. Jacobson, and R. S. Lokey.  “Probing the Physicochemical Boundaries of Cell Permeability and Oral Bioavailability in Lipophilic Macrocycles Inspired by Natural Products”, J. Med. Chem., 58 (2015) 4581-4589.  Pubmed


M. C. Chimenti, S. L. Bulfer, R. J. Neitz, A. R. Renslo, M. P. Jacobson, T. L. James, M. R. Arkin, and M. J. S. Kelly.  “A Fragment-Based Ligand Screen Against Part of a Large Protein Machine; the ND1 Domains of the AAA+ ATPase p97/VCP”, J. Biomolecular Screening, 20 (2015) 788-800.  Pubmed


J. B. Jameson, A. Kantz, L. Schultz, C. Kalyanaraman, M. P. Jacobson, D. J. Maloney, A. Jadhav, A. Simeonov, and T. R. Holman.  “A high throughput screen identifies potent and selective inhibitors to human epithelial 15-lipoxygenase-2”.  PLoS One, 9 (2014) e104094.  PMC4128814


M. Ndao, M. Nath-Chowdhury, M. Sajid, V. Marcus, S. T. Mashiyama, J. Sakanari, E. Chow, Z. Mackey, K. M. Land, M. P. Jacobson, C. Kalyanaraman, J. H. McKerrow, M. J. Arrowood, C. R. Caffrey. “A cysteine protease inhibitor rescues mice from a lethal Cryptosporidium parvum infection”, Antimicrobial Agents and Chemotherapy, 57 (2013) 6063-6073.  Online  PMC3837922


J. W. Choy, C. Bryant, C. M. Calvet, P. S. Doyle, S. S. Gunatilleke, S. S. F. Leung, K. K. H. Ang, S. Chen, J. Gut, J. A. Oses-Prieto, J. B. Johnston, M. R. Arkin, A. L. Burlingame, J. Taunton, M. P. Jacobson, J. M. McKerrow, L. M. Podust, and A. R. Renslo.  “Chemical-Biological Characterization of a Cruzain Inhibitor Reveals a Second Target and a Mammalian Off-Target”.  Beilstein J. Org. Chem, 9 (2013) 15-25.  PMC3566858


B. M. Silber, S. Rao, K. L. Fife, A. Gallardo-Godoy, A. R. Renslo, D. K. Dalvie, K. Giles, Y. Freyman, M. Elepano, J. R. Gever, B. Lam, M. P. Jacobson, Y. Huang, L. Z. Benet, S. B. Prusiner.  “Pharmacokinetics and metabolism of 2-aminothiazoles with antiprion activity in mice”, Pharmaceutical Research, 30 (2013) 932-950.  PMC3640342


A. C. Rand, S. S. F. Leung, H. Eng, C. J. Rotter, R. Sharma, A. S. Kalgutkar, Y. Zhang, M. V. Varma, K. Farley, C. Limberakis, A. M. Mathiowetz, D. A. Price, S. Liras, M. P. Jacobson and R. S. Lokey.  “Optimizing PK properties of cyclic peptides: the effect of side chain substitutions on permeability and clearance” (invited article).  MedChemComm, 3 (2012) 1282-1289.  Online  PMC3488302


C. S. Rapp, C. Kalyanaraman, A. Schiffmiller, E. L. Schoenbrun, and M. P. Jacobson.  “A Molecular Mechanics Approach to Modeling Protein-Ligand Interactions:  Relative Binding Affinities in Congeneric Series”, Journal of Chemical Information and Modeling, 51 (2011) 2082-2089.  PMC3183355


T. R. White, C. M. Renzelman, A. C. Rand, T. Rezai, C. M. McEwen, V. M. Gelev, R. A. Turner, A. C. Rand, R. G. Linington, S. S. F. Leung, A. S. Kalgutkar, J. N. Bauman, Y. Zhang, S. Liras, D. A. Price, A. M. Mathiowetz, M. P. Jacobson, and R. S. Lokey. “On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds”, Nature Chemical Biology, 7 (2011) 810-817.  PMC3210067.  [Discussed in SciBX 4 (2011).]  F1000


N. Huang, C. Kalyanaraman, K. Bernacki, and M. P. Jacobson.  “Molecular Mechanics Methods for Predicting Protein-Ligand Binding” (invited feature article), Physical Chemistry Chemical Physics, 8 (2006) 5166–5177.  [PCCP “hot paper”; top downloaded papers in 2006.]  Online


W. Sherman, T. Day, M. P. Jacobson, R. A. Friesner, and R. Farid. “Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects”, Journal of Medicinal Chemistry, 49 (2006) 534–553.  [#3 most cited article in J Med Chem in 2006]  Online


N. Huang, C. Kalyanaraman, J. J. Irwin, and M. P. Jacobson.  “Physics-Based Scoring of Protein-Ligand Complexes:  Enrichment of Known Inhibitors in Large-Scale Virtual Screening”, Journal of Chemical Information and Modeling, 46 (2006) 243–253.  Online


K. Bernacki, C. Kalyanaraman, and M. P. Jacobson.  “Virtual ligand Screening against E. coli Dihydrofolate Reductase:  Improving Docking Enrichment Using Physics-Based Methods” (invited paper), Journal of Biomolecular Screening, 10 (2005) 675–681.  Online