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
Category Archives: Computer-Aided Drug Design
152.
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
151.
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
148.
E. A. Coutsias, K. W. Lexa, M. J. Wester, S. N. Pollock, and M. P. Jacobson. “Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics”, J. Chem. Theory. Comput., 12 (2016) 4674-4687. Pubmed PMC5465426
147.
F. de Jesus Cortez, M. Suzawa, S. Irvy, J. M. Bruning, E. Sablin, M. P. Jacobson, R. J. Fletterick, H. A. Ingraham, and P. M. England. “Disulfide-Trapping Identifies a New, Effective Chemical Probe for Activating the Nuclear Receptor Human LRH-1 (NR5A2)”, PLoS One, 11 (2016) e0159316. PMC4965143
146.
M. M. Armstrong, C. J. Freedman, J. E. Jung, Y. Zheng, C. Kalyanaraman, M. P. Jacobson, A. Simeonov, D. J. Maloney, K. van Leyen, A. Jadhav, and T. R. Holman. “A potent and selective inhibitor targeting human and murine 12/15-LOX”, Bioorg. Med. Chem., 24 (2016) 1183-1190. PMC4778748
144.
S. S. Leung, D. Sindhikara, M. P. Jacobson. “Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition”, J. Chem. Inf. Model., 56 (2016) 924-949. Pubmed
142.
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
141.
C. L. Ahlbach, K. W. Lexa, A. T. Bockus, V. Chen, P. Crews, M. P. Jacobson, and R. S. Lokey. “Beyond cyclosporine A: conformation-dependent passive membrane permeabilities of cyclic peptide natural products”, Future Medicinal Chemistry, 7 (2015) 2121-2130. Pubmed
140.
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
139.
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
134.
133.
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
131.
S. Krishnan, R. M. Miller, B. Tian, I. M. Serafimova, R. D. Mullins, M. P. Jacobson, and J. Taunton. “Reversibility by design: activated acrylonitriles for cysteine targeting applications”, JACS, 136 (2014) 12624-12630. PMC4160273
129.
A. M. Mathiowetz, S. S. F. Leung, and M. P. Jacobson. “Optimizing the permeability and oral bioavailability of macrocycles”, in Macrocycles in Drug Discovery (2015), 367-397.
128.
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
123.
K. Lexa, E. Dolghih, A. Wiser, and M. P. Jacobson. “A Structure-Based Model for Predicting Serum Albumin Binding”, PLoS ONE, 9 (2014) e93323. PMC3972100
121.
B. M. Silber, J. R. Gever, S. Rao, Z. Li, A. R. Renslo, K. Widjaja, C. Wong, K. Giles, Y. Freyman, M. Elepano, J. J. Irwin, M. P. Jacobson, and S. B. Prusiner. “Novel compounds lowering the cellular isoform of the human prion protein in cultured human cells”, Bioorg. Med Chem., 22 (2014) 1960-1972. PMC3984052
117.
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
116.
B. M. Silber, J. R. Gever, Z. Li, A. Gallardo-Godoy, A. R. Renslo, K. Widjaja, J. J. Irwin, S. Rao, M. P. Jacobson, S. Ghaemmaghami, and S. B. Prusiner. “Antiprion compounds that reduce PrPSc levels in dividing and stationary-phase cells”, Bioorg. Med. Chem., 21 (2013) 7999-8012. Online PMC3984054
115.
D. Lu, K. Giles, Z. Li, S. Rao, E. Dolghih, J. R. Gever, M. Geva, M. Elepano, A. Oehler, C. Bryant, A. Renslo, M. P. Jacobson, S. J. DeArmond, B. M. Silber, and S. B. Prusiner. “Biaryl amides and hydrazones as therapeutics for prion disease in transgenic mice”, J. Pharmacol. Exp. Ther., 347 (2013) 325-338. Online PMC3807058
109.
M. Spreafico and M. P. Jacobson. “In silico prediction of brain exposure: drug free fraction, unbound brain to plasma concentration ratio and equilibrium half-life”, Current Topics in Medicinal Chemistry, 13 (2013) 813-820. Online PMC4005893
106.
Z. Li, B. M. Silber, S. Rao, J. Gever, C. Bryant, A. Gallardo-Godoy, E. Dolghih, K. Widjaja, M. Elepano, M. P. Jacobson, S. B. Prusiner and A. R. Renslo. “2-Aminothiazoles with Improved Pharmacotherapeutic Properties for Treatment of Prion Disease”, ChemMedChem, 8 (2013) 847-857. PMC3984044
105.
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
103.
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
101.
E. Dolghih and M. P. Jacobson. “Predicting efflux ratios and blood-brain barrier penetration from chemical structure: combining passive permeability with active efflux by P-glycoprotein”, ACS Chemical Neuroscience, 4 (2013) 361-367. Online PMC3582291
100.
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
98.
S. S. F. Leung, J. Mijalkovic, K. Borrelli, and M. P. Jacobson. “Testing Physical Models of Passive Membrane Permeation”, Journal of Chemical Information and Modeling, 52 (2012) 1621-1636. Online PMC3383340
95.
S. B. Rafi, B. R. Hearn, P. Vedantham, M. P. Jacobson, and A. R. Renslo. “Predicting and improving the membrane permeability of peptidic small molecules”, Journal of Medicinal Chemistry, 55 (2012) 3163-3169. [Discussed in SciBX 5 (2012).] Online PMC3325274
94.
J. R. Ingram, S. B. Rafi, L. Lambeth, I. Hsieh, D. Ruelas, K.C. Lim, J. Sakanari, C. S. Craik, M. P. Jacobson and J. H. McKerrow. “Investigation of the proteolytic functions of an expanded cercarial elastase gene family in Schistosoma mansoni“, PLoS Neglected Tropical Diseases, 6 (2012) e1589. PMC3317910 F1000
88.
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
87.
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
85.
E. Dolghih, C. Bryant, A. R. Renslo, and M. P. Jacobson. “Predicting binding to P-glycoprotein by flexible receptor docking”, PLoS Computational Biology, 7 (2011) e1002083. PMC3121697
82.
J. D. Sadowsky, M. A. Burlingame, D. W. Wolan, C. L. McClendon, M. P. Jacobson and J. A. Wells. “Turning a protein kinase (PDK1) on or off from a single allosteric site via disulfide trapping”. PNAS, 108 (2011) 6056-6061. PMC21430264
77.
P. S. Doyle, C.-K. Chen, J. B. Johnston, S. Hopkins, S. S. F. Leung, M. P. Jacobson, J. C. Engel, J. H. McKerrow, L. M. Podust. “A Non-azole CYP51 Inhibitor Cures Chagas Disease in a Mouse Model of Acute Infection”, Antimicrobial Agents and Chemotherapy, 54 (2010) 2480-2488. PMC2876414
76.
N. Huang and M. P. Jacobson. “Virtual Fragment Screening for Binding Site Assessment”, PLoS One, 5 (2010) e10109. PMC2852417
73.
C.-K. Chen, S. S. F. Leung, C. Guilbert, M. P. Jacobson, J. H. McKerrow, and L. M. Podust. “Structural characterization of CYP51 from Trypanosoma cruzi and Trypanosoma brucei bound to the antifungal drugs posaconazole and fluconazole”. PLoS Neglected Tropical Diseases, 4 (2010) e651. PMC2850312
67.
E. S. Tan, J. C. Naylor, E. S. Groban, J. R. Bunzow, M. P. Jacobson, D. K. Grandy, and T. S. Scanlan. “The Molecular Basis of Species-Specific Ligand Activation of Trace Amine-Associated Receptor 1 (TAAR1)”, ACS Chemical Biology, 20 (2009) 209–220. PMC2677188
63.
C. S. Rapp, C. Schonbrun, M. P. Jacobson and Niu Huang. “Automated Site Preparation in Rescoring of Receptor Ligand Complexes”, Proteins, 77 (2009) 52-61. PMC2744578
58.
E. S. Tan, E. S. Groban, M. P. Jacobson, and T. S. Scanlan. “Deciphering the Code to Aminergic G-Protein Coupled Receptor Drug Design.” Chemistry and Biology, 15 (2008) 343–353. Online PMC2713717
57.
J. Nilmeier and M. P. Jacobson. “Multiscale Monte Carlo Sidechain Sampling: Application to Binding Pocket Flexibility”, Journal of Chemical Theory and Computation, 4 (2008) 835–846. PMC2612633
56.
A. P. Graves, D. M. Shivakumar, S. E. Boyce, M. P. Jacobson, D. A. Case, and B. K. Shoichet. “Rescoring docking hit lists for model cavity sites: predictions and experimental testing”, Journal of Molecular Biology, 377 (2008) 914–934. Online PMC2752715
53.
C. Kalyanaraman and M. P. Jacobson. “An atomistic model of passive membrane permeability: Application to a series of FDA approved drugs”, Journal of Computer-Aided Molecular Design, 21 (2007) 675–679. Online
51.
N. Huang and M. P. Jacobson. “New Physics-Based Methods for Studying Protein-Ligand Interactions”, Current Opinion in Drug Discovery & Development, 10 (2007) 325-331.
46.
T. Rezai, J. E. Bock, M. Vong, C. Kalyanaraman, R. S. Lokey, and M. P. Jacobson. “Conformational Flexibility, Internal Hydrogen Bonding, and Passive Membrane Permeability: Successful In Silico Prediction of the Relative Permeabilities of Cyclic Peptides”, JACS, 128 (2006) 14073–14080. Online
45.
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
41.
T. Rezai, B. Yu, G. L. Millhauser, M. P. Jacobson, and R. S. Lokey. “Testing the conformational hypothesis of passive membrane permeability using synthetic cyclic peptide diastereomers”, JACS, 128 (2006) 2510–2511. Online
40.
V. Kenyon, I. Chorny, T. R. Holman, and M. P. Jacobson. “Novel human lipoxygenase inhibitors discovered using virtual screening with homology models”, Journal of Medicinal Chemistry, 49 (2006) 1356–1363. Online
39.
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
38.
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
35.
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
The Jacobson Laboratory at UCSF 