Difference between revisions of "Rizzo Lab Publications"

Latest revision as of 11:20, 22 April 2024

Complete List of Published Work in MyBibliography:

http://www.ncbi.nlm.nih.gov/myncbi/browse/collection/40578611/?sort=date&direction=descending

Complete List of Published Work in Google Scholar:

http://scholar.google.com/citations?hl=en&user=zSmJOOAAAAAJ&view_op=list_works&sortby=citations

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 DOI 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 DOI
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 DOI
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 DOI 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 DOI 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 DOI
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 DOI 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 DOI 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 DOI 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 DOI
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 DOI 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 DOI 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 DOI 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 DOI 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 DOI
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 DOI 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 DOI PMID: 19369428
19. Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. Biochemistry, 2009, 48, 8435-8448 DOI 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 DOI 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 DOI 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 DOI 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 DOI 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 DOI 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 DOI 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 DOI PMID: 22569593
27. Allen, W. J.; Rizzo, R. C. Computer-Aided Approaches for Targeting HIVgp41, Biology, 2012, 1, 311-338 DOI PMID: 23730525
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 DOI PMID: 23236415
29. Balius, T. E.; Allen, W. J.; Mukherjee, S.; Rizzo, R. C. Grid-based Molecular Footprint Comparison Method for Docking and De Novo Design: Application to HIVgp41, J. Comput. Chem., 2013, 34, 1226-1240 DOI PMID: 23436713
30. Furt, F.; Allen, W. J.; Widhalm, J. R.; Madzelan, P.; Rizzo, R. C.; Basset, G.; Wilson, M. A. Functional Convergence of Structurally Distinct Thioesterases from Cyanobacteria and Plants Involved in Phylloquinone Biosynthesis, Acta Cryst., 2013, D69, 1876-1888 DOI PMID: 24100308
31. Holden, P. M.; Allen, W. J.; Gochin, M.; Rizzo, R. C. Strategies for Lead Discovery: Application of Footprint Similarity Targeting HIVgp41, Bioorg. Med. Chem., 2014, 22, 651-661 DOI PMID: 24315195
32. Allen, W. J.; Rizzo, R. C. Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design, J. Chem. Inf. Model., 2014, 54, 518-529 DOI PMID: 24410429
33. Kaczocha, M.; Rebecchi, M. J.; Ralph, B. P.; Teng, Y. G.; Berger, W. T.; Galbavy, W.; Elmes, M. W.; Glaser, S. T.; Wang, L.; Rizzo, R. C.; Deutsch, D. G.; Ojima, I. Inhibition of Fatty Acid Binding Proteins Elevates Brain Anandamide Levels and Produces Analgesia, PLoS One, 2014, 9, e94200 DOI PMID: 24705380
34. Jiang, L.; Rizzo, R. C. Pharmacophore-Based Similarity Scoring for DOCK, J. Phys. Chem. B., 2015, 119, 1083-1102 DOI PMID: 25229837
35. Allen, W. J.; Balius, T. E.; Mukherjee, S.; Brozell, S. R.; Moustakas, D. T.; Lang, P. T.; Case, D. A.; Kuntz, I. D.; Rizzo, R. C. DOCK 6: Impact of New Features and Current Docking Performance, J. Comput. Chem., 2015, 36, 1132-1156 DOI PMID: 25914306
36. Allen, W. J.; Yi, H. A.; Gochin, M.; Jacobs, A.; Rizzo, R. C. Small Molecule Inhibitors of HIVgp41 N-heptad Repeat Trimer Formation, Bioorg. Med. Chem. Lett., 2015, 25, 2853-2859. DOI PMID: 26013847
37. Airola, M. V.; Allen, W. J.; Pulkoski-Gross, M. J.; Obeid, L. M.; Rizzo, R. C.; Hannun, Y. A. Structural Basis for Ceramide Recognition and Hydrolysis by Human Neutral Ceramidase, Structure, 2015, 23, 1482-1491. DOI PMID: 26190575
38. Teng, Y. H.; Berger, W. T.; Nesbitt, N. M.; Kumar, K.; Balius, T. E.; Rizzo, R. C.; Tonge, P. J.; Ojima, I.; Swaminathan, S. Computer-aided identification, synthesis, and biological evaluation of novel inhibitors for botulinum neurotoxin serotypr A, Bioorg. Med. Chem., 2015, 23(17), 5489-95. DOI PMID: 26275678
39. Yi, H. A.; Fochtman, B. C.; Rizzo, R. C.; Jacobs, A. Inhibition of HIV entry by targeting the envelope transmembrane subunit gp41, Curr. HIV Res., 2016, 14, 283-294. DOI PMCID: PMC4909398
40. Zhou, Y.; McGillick, B. E.; Teng, Y. H.; Haranahalli, K; Ojima, I; Subramanyam, S.; Rizzo, R. C. Identification of Small Molecule Inhibitors of Botulinum Neurotoxin Serotype E via Footprint Similarity, Bioorg. Med. Chem., 2016, 24, 4875–4889 DOI PMID: 27543389
41. Peng, X.; Studholme, K.; Kanjiya, M. P.; Luk, J.; Bogdan, D.; Elmes, M. W.; Carbonetti, G.; Tong, S.; Teng, Y. H.; Rizzo, R.C.; Li, H.; Deutsch, D. G.; Ojima, I.; Rebecchi, M. J.; Puopolo, M.; Kaczocha, M. Fatty acid binding protein inhibition produces analgesic effects through peripheral and central mechanisms. Molecular Pain, 2017, 13, 1-16 DOI PMCID: PMC5407663
42. McGee, T. D.; Yi, H. A.; Allen, W. J.; Jacobs, A.; Rizzo, R. C. Structure-based identification of inhibitors targeting obstruction of the HIVgp41 N-Heptad repeat trimer, Bioorg. Med. Chem. Lett., 2017, 27, 3177–3184 DOI PMCID: PMC5551449
43. Hsu, Hao-Chi; Tong, S; Zhou, Y; Elmes, M; Wang, L; Yan, S; Kaczocha, M; Deutsch, D. G.; Rizzo, R. C.; Ojima, I; Li, H The Antinociceptive Agent SBFI-26 Binds to Anandamide Transporters FABP5 and FABP7 at Two Different Sites, Biochemistry, 2017, 56, 3454–3462 DOI PMCID: PMC5884075
44. Allen, W. J.; Fochtman, B. C.; Balius, T. E.; Rizzo, R. C. Customizable de novo Design Strategies for DOCK: Application to HIVgp41 and Other Therapeutic Targets, J. Comput. Chem., 2017, 38, 2641–2663 DOI PMCID: PMC5659719
45. Yan, S.; Elmes, M. W.; Tong, S.; Hu, K.; Awwa, M.; Teng, Y. H.; Jing, Y. Freitag, M.; Gan, Q.; Clement, T.; Wei, L.; Sweeney, J. M.; Joseph, O. M.; Che, J.; Carbonetti, G. S.; Wang, L.; Bogdan, D. M.; Falcone, J.; Smietalo, N.; Zhou, Y.; Ralph, B. P.; Hsu, Hao-Chi; Li, H.; Rizzo, R. C.; Deutsch, D. G.; Kaczocha, M.; Ojima, I. SAR Studies on Truxillic Acid Mono Esters as a New Class of Antinociceptive Agents Targeting Fatty Acid Binding Proteins, European Journal of Medicinal Chemistry, 2018, 154, 233–252 DOI PMID: 29803996
46. Guo, J.; Collins, S.; Miller, W.T.; Rizzo, R. C. Identification of a water-coordinating HER2 inhibitor by virtual screening using similarity-based scoring, Biochemistry, 2018, 57, 4934-4951 DOI PMCID: PMC6110523
47. Elmes, M.W.; Prentis, L.E.; McGoldrick, L.L.; Giuliano, C.J.; Sweeney, J.M.; Joseph, O.M.; Che, J.; Carbonetti, G.S.; Studholme, K.; Deutsch, D.G.; Rizzo, R.C.; Glynn, S.E.; Kaczocha, M.; FABP1 controls hepatic transport and metabolism of Δ9-THC, Scientific Reports, 2019, 9, 7588 DOI PMCID: PMC6527858
48. Kim, J.; Bogdan, D. M.; Elmes, M. W.; Awwa, M.; Yan, S.; Che, J.; Lee, G. Deutsch, D. G.; Rizzo, R. C.; Kaczocha, M.; and Ojima, I. Incarvillateine produces antinociceptive and motor suppressive effects via adenosine receptor activation, PLoS ONE, 2019, 14, e0218619 DOI PMCID: PMC6592529
49. Singleton, C. S.; Humbly, M.S.; Yi, H. A.; Rizzo, R. C.; Jacobs, A. Identification of Ebola Virus Inhibitors Targeting GP2 using Principles of Molecular Mimicry, J Virology 2019, 93, e00676-19 DOI PMCID: PMC6639268
50. Zhou, Y; Elmes, M. W.; Sweeney, J. M.; Joseph, O. M.; Kaczocha, M; Li, H.; Ojima, I; Deutsch, D. G.; Rizzo, R. C. Identification of Fatty Acid Binding Protein 5 Inhibitors Through Similarity-Based Screening, Biochemistry, 2019, 58, 4304-4316 DOI PMCID: PMC6812325
51. Telehany, S. M.; Humby, M. S.; McGee, T. D., Jr.; Riley, S. P.; Jacobs, A.; Rizzo, R. C. Identification of Zika Virus Inhibitors Using Homology Modeling and Similarity-based Screening to Target Glycoprotein E. Biochemistry 2020, 59, 3709−3724 DOI PMCID: PMC7598728
52. Prentis, L. E.*; Singleton, C. D.*; Bickel, J. D.; Allen, W. J.; Rizzo, R.C.; A molecular evolution algorithm for ligand design in DOCK J. Comput. Chem 2022, 43, 1942-1963 DOI PMCID: 36073674
53. Collins, S.J.; Guo, J; Rizzo, R.C.; Miller, W.T.; Inhibition of mutationally activated HER2, Chem. Biol. Drug Des., 2023, 101, 87-102 DOI PMCID: PMC9879383
54. Duarte Ramos Matos, G.*; Pak, S.*; Rizzo, R.C.; Descriptor-Driven de Novo Design for DOCK6 Using RDKit, J. Chem. Inf. Model., 2023, 63, 5803-5822 DOI PMCID: PMC10694857
55. Coant, N.*; Bickel, J.D.*; Rahaim, R.; Otsuka, Y.; Choi, Y.M.; Xu, R.; Simoes, M.; Cariello, C.; Mao, C.; Saied, E.M.; Arenz, C.; Spicer, T.P.; Bannister, T.D.; Tonge, P.J.; Airola, M.V.; Scampavia, L.; Hannun, Y.A.; Rizzo, R.C.; Haley, J.D.; Neutral ceramidase-active site inhibitor chemotypes and binding modes, Bioorg. Chem., 2023, 139, 106747 DOI PMCID: PMC10681040
56. Hillowe, A.; Gordon, C.; Wang, Liqun; Rizzo, R.C.; Trotman, L.C.; Ojima, I.; Bialkowska, A.; Kaczocha, M.; Fatty acid protein binding 5 regulates docetaxal sensitivity in taxane-resistant prostate cancer cells, PLoS One, 2023, 18, e029483 DOI PMCID: PMC10553314
57. Alcantara, J.; Chiu, K.; Bickel, J.D.; Rizzo, R.C.; Simmerling, C.; Rapid Rescoring and Refinement of Ligand-Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir, J. Chem. Theory Comput., 2023, 19, 7934-7945 DOI PMCID: PMC10702174
58. Swamynathan, M.M.; Mathew, G.; Aziz, A.; Gordon, C.; Hillowe, A.; Wang, H.; Jhaveri, A.; Kendall, J.; Cox, H.; Giarrizzo, M.; Azabdaftari, G.; Rizzo, R.C.; Diermeier, S.D.; Ojima, I; Bialkowska, A.B.; Kaczocham M.; Trotman, L.C.; FABP5 Inhibition against PTEN-Mutant Therapy Resistant Prostate Cancer Cancers, 2023, 16, 60 DOI PMCID: PMC10871093

* Denotes equal contribution