Rizzo Lab Publications

Publications (in chronological order)

1. Bausch, J. W.; Rizzo, R. C.; Sneddon, L. G.; Wille, A. E.; Williams, R. E. An Ab Initio/IGLO/NMR Investigation of nido-C₄B₇H₁₁ Configurations: Structural Assignment of the Three Known Isomers and Reconfirmation of Empirical Carbon Placement Patterns. Inorg. Chem., 1996, 35, 131-135 WEB PMID: 11666174

2. Rizzo, R. C.; Jorgensen, W. L. OPLS All-Atom Model for Amines: Resolution of the Amine Hydration Problem. J. Am. Chem. Soc., 1999, 121, 4827-4836 dx.doi.org/10.1021/ja984106u

3. Rizzo, R. C.; Wang, D.-P.; Tirado-Rives, J.; Jorgensen, W. L. Validation of a Model for the Complex of HIV-1 Reverse Transcriptase with Sustiva through Computation of Resistance Profiles. J. Am. Chem. Soc., 2000, 122, 12898-12900 dx.doi.org/10.1021/ja003113r

4. Rizzo, R. C.; Tirado-Rives, J.; Jorgensen, W. L. Estimation of Binding Affinities for HEPT and Nevirapine Analogues with HIV-1 Reverse Transcriptase via Monte Carlo Simulations. J. Med. Chem., 2001, 44, 145-154 dx.doi.org/10.1021/jm000255n PMID: 11170624 5. Jorgensen, W. L.; Plount-Price, M. L.; Price, D. J.; Rizzo, R. C.; Wang, D.-P.; Pierce, A. C.; Tirado-Rives, J. COX-2, SRC SH2 Domain, HIV Reverse Transcriptase, and Thrombin: Computational Approaches to Drug Design., In Free Energy Calculations in Rational Drug Design, M. R. Reddy and M. D. Elion, Eds., Kluwer: New York, 2001; Chapter 15, 299-316

6. Wang, D.-P.; Rizzo, R. C.; Tirado-Rives, J.; Jorgensen, W. L. Antiviral Drug Design: Computational Analyses of the Effects of the L100I Mutation for HIV-RT on the Binding of NNRTIs. Bioorg. Med. Chem. Lett., 2001, 11, 2799-2802 dx.doi.org/10.1016/S0960-894X(01)00510-8 PMID: 11597403

7. Zhou, R.; Friesner, R. A.; Ghosh, A.; Rizzo, R. C.; Jorgensen, W. L.; Levy, R. M. New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model. J. Phys. Chem. B, 2001, 105, 10388-10397 dx.doi.org/10.1021/jp011480z

8. Rizzo, R. C.; Blagović, M. U.; Wang, D.-P.; Watkins, E. K.; Smith, M. B. K.; Smith, R. H. Jr.; Tirado-Rives, J.; Jorgensen, W. L. Prediction of Activity for Nonnucleoside Inhibitors with HIV-1 Reverse Transcriptase Based on Monte Carlo Simulations. J. Med. Chem., 2002, 45, 2970-2987 dx.doi.org/10.1021/jm010580q PMID: 12086483

9. Smith, M. B. K.; Hose, B. M.; Hawkins, A.; Lipchock, J.; Farnsworth, D. W.; Rizzo, R. C.; Tirado-Rives, J.; Arnold, E.; Zhang, W.; Hughes, S. H.; Jorgensen, W. L.; Michejda, C. J.; Smith, R. H. Jr. Molecular Modeling Calculations of HIV-1 Reverse Transcriptase Nonnucleoside Inhibitors: Correlation of Binding Energy with Biological Activity for Novel 2-Aryl-Substituted Benzimidazole Analogues. J. Med. Chem., 2003, 46, 1940-1947 dx.doi.org/10.1021/jm020271f PMID: 12723956

10. Rizzo, R. C.; Toba, S.; Kuntz, I. D. A Molecular Basis for the Selectivity of Thiadiazole Urea Inhibitors with Stromelysin-1 and Gelatinase-A from Generalized Born Molecular Dynamics Simulations. J. Med. Chem., 2004, 47, 3065-3074 dx.doi.org/10.1021/jm030570k PMID: 15163188

11. Rizzo, R. C.; Aynechi, T.; Case, D. A.; Kuntz, I. D. Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions. J. Chem. Theory Comput., 2006, 2, 128-139 dx.doi.org/10.1021/ct050097l

12. Hornak, V.; Okur, A.; Rizzo, R. C.; Simmerling, C. HIV-1 Protease Flaps Spontaneously Open and Reclose in Molecular Dynamics Simulations. Proc. Natl. Acad. Sci. U.S.A., 2006, 103, 915-920 dx.doi.org/10.1073/pnas.0508452103 PMID: 16418268

13. Hornak, V.; Okur, A.; Rizzo, R. C.; Simmerling, C. HIV-1 Protease Flaps Spontaneously Close to the Correct Structure in Simulations Following Manual Placement of an Inhibitor into the Open State. J. Am. Chem. Soc., 2006, 128, 2812-2813 dx.doi.org/10.1021/ja058211x PMID: 16506755

14. Moustakas, D. T.; Lang, P. T.; Pegg, S.; Pettersen, E.; Kuntz, I. D.; Broojimans, N.; Rizzo, R. C. Development and Validation of a Modular, Extensible Docking Program: DOCK 5. J. Comput. Aided Mol. Des., 2006, 20, 601-619 dx.doi.org/10.1007/s10822-006-9060-4 PMID: 17149653

15. Strockbine, B.; Rizzo, R. C. Binding of Anti-Fusion Peptides with HIVgp41 from Molecular Dynamics Simulations: Quantitative Correlation with Experiment. Proteins: Struct. Func. Bioinformatics, 2007, 67, 630-642 dx.doi.org/10.1002/prot.21301 PMID: 17335007

16. Chachra, R.; Rizzo, R. C. Origins of Resistance Conferred by the R292K Neuraminidase Mutation via Molecular Dynamics and Free Energy Calculations. J. Chem. Theory Comput., 2008, 4, 1526-1540 dx.doi.org/10.1021/ct800068v

17. Carrascal, N.; Rizzo, R. C. Calculation of Binding Free Energies for Non-zinc Chelating Pyrimidine Dicarboxamide Inhibitors with MMP-13. Bioorg. Med. Chem. Lett., 2009, 19, 47-50 dx.doi.org/10.1016/j.bmcl.2008.11.038 PMID: 19042129

18. Lang, P.T.; Brozell, S.R.; Mukherjee, S.; Pettersen, E.; Meng, E.; Thomas, V.; Rizzo, R. C.; Case, D. A.; James, T. L.; Kuntz, I. D. DOCK 6: Combining Techniques to Model RNA-Small Molecule Complexes. RNA, 2009, 15, 1219-1230 dx.doi.org/10.1261/rna.1563609 PMID: 19369428

19. Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. Biochemistry, 2009, 48, 8435-8448 dx.doi.org/10.1021/bi900729a PMID: 19627157

20. McGillick, B. E.; Balius, T.E.; Mukherjee, S.; Rizzo, R. C. Origins of Resistance to the HIVgp41 Viral Entry Inhibitor T20. Biochemistry, 2010, 49, 3575-3592 dx.doi.org/10.1021/bi901915g PMID: 20230061

21. Mukherjee, S.; Balius, T.E.; Rizzo, R. C. Docking Validation Resources: Protein Family and Ligand Flexibility Experiments. J. Chem. Inf. Model, 2010, 50, 1986-2000 dx.doi.org/10.1021/ci1001982 PMID: 21033739

22. Balius, T. E.; Mukherjee, S.; Rizzo, R. C. Implementation and Evaluation of a Docking-rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32, 2273-2289 dx.doi.org/10.1002/jcc.21814 PMID: 21541962

23. Dufour, A.; Sampson, N. S.; Li, J.; Kuscu, C.; Rizzo, R. C.; DeLeon, J. L.; Zhi, J.; Jaber, N.; Liu, E.; Zucker, S.; Cao, J. Small-molecule anticancer compounds selectively target the hemopexin domain of matrix metalloproteinase-9. Cancer Res., 2011, 71, 4977-4988 dx.doi.org/10.1158/0008-5472.CAN-10-4552 PMID: 21646471

24. Huang, Y.; Rizzo, R. C. A Water-based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases, Biochemistry, 2012, 51, 2390-2406 dx.doi.org/10.1021/bi2016553 PMID: 22352796

25. Holden, P. M.; Kaur, H.; Gochin, M.; Rizzo, R. C. Footprint-based identification of HIVgp41 inhibitors, Bioorg. Med. Chem. Lett., 2012, 22, 3011–3016 dx.doi.org/10.1016/j.bmcl.2012.02.017 PMID: 22425565

26. Brozell, S. R.; Mukherjee, S.; Balius, T. E.; Roe, D. R.; Case, D. A.; Rizzo, R. C. Evaluation of DOCK 6 as a Pose Generation and Database Enrichment Tool, J. Comput-Aided Mol. Des., 2012, 26, 749-773 dx.doi.org/10.1007/s10822-012-9565-y PMID: 22569593

27. Allen, W. L.; Rizzo, R. C. Computer-Aided Approaches for Targeting HIVgp41, Biology, 2012, 1, 311-338 dx.doi.org/10.3390/biology1020311

28. Berger, W. T.; Ralph, B. P.; Kaczocha, M.; Sun, J.; Balius. T. E.; Rizzo, R. C.; Haj-Dahmane, S.; Ojima, I.; Deutsch, D. G. Targeting Fatty Acid Binding Protein (FABP) Anandamide Transporters - A Novel Strategy for Development of Anti-Inflammatory and Anti-Nociceptive Drugs, PLoS ONE, 2012, 7, e50968 dx.doi.org/10.1371/journal.pone.0050968 PMID: 23236415

29. Balius, T. E.; Allen, W. L.; Mukherjee, S.; Rizzo, R. C. Grid-based Molecular Footprint Comparison Method for Docking and De Novo Design: Application to HIVgp41, J. Comput. Chem., 2013, In Press

30. Mukherjee, S.; Balius, T. E.; Allen, W. L.; Rizzo, R. C. Algorithmic Updates and Improvements in DOCK6, In Preparation