Rommie E Amaro

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Toward understanding the conformational dynamics of RNA ligation
    Robert V Swift
    Department of Chemistry and Biochemistry, NSF Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093 0365, USA
    Biochemistry 48:709-19. 2009
  2. pmc Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
    Lily S Cheng
    National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093, USA
    J Med Chem 51:3878-94. 2008
  3. pmc Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations
    Rommie E Amaro
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093 0365, USA
    J Am Chem Soc 131:4702-9. 2009
  4. ncbi request reprint Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design
    Rommie E Amaro
    Department of Chemistry and Biochemistry, NSF Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California 92093 0365, USA
    J Am Chem Soc 129:7764-5. 2007
  5. pmc Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei
    Rommie E Amaro
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
    PLoS Negl Trop Dis 1:e68. 2007
  6. pmc An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
    Rommie E Amaro
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093 0365, USA
    J Comput Aided Mol Des 22:693-705. 2008
  7. pmc Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei
    Rommie E Amaro
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093 0365, USA
    Proc Natl Acad Sci U S A 105:17278-83. 2008
  8. pmc Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1
    Jacob D Durrant
    Biomedical Sciences Program, University of California San Diego, La Jolla, California, United States of America
    PLoS Negl Trop Dis 4:e803. 2010
  9. pmc Distinct glycan topology for avian and human sialopentasaccharide receptor analogues upon binding different hemagglutinins: a molecular dynamics perspective
    Dong Xu
    National Biomedical Computation Resource, University of California San Diego, La Jolla, CA 92093 0505, USA
    J Mol Biol 387:465-91. 2009
  10. pmc Mechanism of 150-cavity formation in influenza neuraminidase
    Rommie E Amaro
    Department of Pharmaceutical Sciences, Computer Science and Chemistry, University of California, Irvine, California 92697, USA
    Nat Commun 2:388. 2011

Research Grants

  1. The SMD-Relaxed Complex Method for Drug Design
    Rommie Amaro; Fiscal Year: 2007

Collaborators

Detail Information

Publications31

  1. pmc Toward understanding the conformational dynamics of RNA ligation
    Robert V Swift
    Department of Chemistry and Biochemistry, NSF Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093 0365, USA
    Biochemistry 48:709-19. 2009
    ..Important features of RNA binding and specificity are revealed for kinetoplastid ligases and the broader nucleotidyltransferase superfamily...
  2. pmc Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
    Lily S Cheng
    National Biomedical Computation Resource, University of California, San Diego, La Jolla, California 92093, USA
    J Med Chem 51:3878-94. 2008
    ..This ensemble-based VS and RCS approach may offer improvement over existing strategies for structure-based drug discovery...
  3. pmc Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations
    Rommie E Amaro
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093 0365, USA
    J Am Chem Soc 131:4702-9. 2009
    ..We anticipate the findings presented here will have broad implications for the development of novel antiviral compounds against both seasonal and pandemic influenza strains...
  4. ncbi request reprint Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design
    Rommie E Amaro
    Department of Chemistry and Biochemistry, NSF Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California 92093 0365, USA
    J Am Chem Soc 129:7764-5. 2007
  5. pmc Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei
    Rommie E Amaro
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
    PLoS Negl Trop Dis 1:e68. 2007
    ....
  6. pmc An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
    Rommie E Amaro
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093 0365, USA
    J Comput Aided Mol Des 22:693-705. 2008
    ..Finally, we outline potential methodological improvements that we anticipate will assist future development...
  7. pmc Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei
    Rommie E Amaro
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093 0365, USA
    Proc Natl Acad Sci U S A 105:17278-83. 2008
    ..These compounds are promising scaffolds for future drug design and discovery efforts against these important pathogens...
  8. pmc Novel naphthalene-based inhibitors of Trypanosoma brucei RNA editing ligase 1
    Jacob D Durrant
    Biomedical Sciences Program, University of California San Diego, La Jolla, California, United States of America
    PLoS Negl Trop Dis 4:e803. 2010
    ..RNA Editing Ligase 1 (REL1), a protein unique to trypanosomes and other kinetoplastids, was identified recently as a potential drug target...
  9. pmc Distinct glycan topology for avian and human sialopentasaccharide receptor analogues upon binding different hemagglutinins: a molecular dynamics perspective
    Dong Xu
    National Biomedical Computation Resource, University of California San Diego, La Jolla, CA 92093 0505, USA
    J Mol Biol 387:465-91. 2009
    ..Glycan composition and topological changes upon binding different HAs may be important determinants in species-specificity switch...
  10. pmc Mechanism of 150-cavity formation in influenza neuraminidase
    Rommie E Amaro
    Department of Pharmaceutical Sciences, Computer Science and Chemistry, University of California, Irvine, California 92697, USA
    Nat Commun 2:388. 2011
    ..This result provides an atomic-level structural understanding of the recent finding that antiviral compounds designed to take advantage of contacts in the 150-cavity can inactivate both 2009 H1N1 pandemic and avian H5N1 viruses...
  11. pmc A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology
    Jacob D Durrant
    Biomedical Sciences Program, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 6:e1000648. 2010
    ..As it is capable of identifying potential secondary targets, the strategy described here may play a useful role in future efforts to reduce drug side effects and/or to increase polypharmacology...
  12. doi request reprint Designing novel inhibitors of Trypanosoma brucei
    Ozlem Demir
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
    Methods Mol Biol 993:231-43. 2013
    ..As an example target protein of interest, we focus on the essential protein RNA-editing ligase 1 (REL1) in Trypanosoma brucei, the causative agent of human African trypanosomiasis...
  13. pmc Rational prediction with molecular dynamics for hit identification
    Sara E Nichols
    Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
    Curr Top Med Chem 12:2002-12. 2012
    ..With hardware and software advances, molecular dynamics in combination with traditional structure-based prediction methods can potentially reduce the time and costs involved in the hit identification pipeline...
  14. pmc Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53
    Christopher D Wassman
    Department of Computer Science, University of California, Irvine, Irvine, California 92697, USA
    Nat Commun 4:1407. 2013
    ..These results indicate the L1/S3 pocket as a target for pharmaceutical reactivation of p53 mutants...
  15. pmc Back to the future: can physical models of passive membrane permeability help reduce drug candidate attrition and move us beyond QSPR?
    Robert V Swift
    Department of Chemistry and Biochemistry, University of California San Diego, 3234 Urey Hall, 9500 Gilman Drive, Mail Code 0340, La Jolla, CA 92093 0340, USA
    Chem Biol Drug Des 81:61-71. 2013
    ..Here, we review the current state-of-the-art physical models for passive membrane permeability prediction and present a prospective look at promising new directions for all-atom approaches...
  16. pmc Role of secondary sialic acid binding sites in influenza N1 neuraminidase
    Jeffrey C Sung
    Department of Chemistry, NSF Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California 92093, USA
    J Am Chem Soc 132:2883-5. 2010
    ..Our results indicate possible lowered HA activity for this secondary sialic acid site, which may be an important event in the emergence of the current pandemic strain...
  17. pmc AutoGrow: a novel algorithm for protein inhibitor design
    Jacob D Durrant
    Biomedical Sciences Program, University of California, San Diego, La Jolla, CA 92093 0365, USA
    Chem Biol Drug Des 73:168-78. 2009
    ..To validate AutoGrow, we recreate three crystallographically resolved ligands from their constituent fragments...
  18. pmc Elements of nucleotide specificity in the Trypanosoma brucei mitochondrial RNA editing enzyme RET2
    Ozlem Demir
    Department of Chemistry and Biochemistry, University of California, San Diego, 3234 Urey Hall, 9500 Gilman Drive, MC 0340 La Jolla, California 92093 0332, USA
    J Chem Inf Model 52:1308-18. 2012
    ..TbRET2 reveals different binding pockets in the apo and UTP-bound MD simulations, which could be targeted for inhibitor design...
  19. pmc Emerging methods for ensemble-based virtual screening
    Rommie E Amaro
    Department of Pharmaceutical Sciences and Department of Information and Computer Science, University of California, Irvine, CA 92697, USA
    Curr Top Med Chem 10:3-13. 2010
    ..Finally, technological advances that will help make virtual screening tools more accessible to a wider audience in computer aided drug design are discussed...
  20. pmc Multistructural hot spot characterization with FTProd
    Lane Votapka
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
    Bioinformatics 29:393-4. 2013
    ..Here we present a plug-in for Visual Molecular Dynamics that streamlines the comparison of the binding configurations of several FTMAP-generated structures...
  21. pmc Magnesium-induced nucleophile activation in the guanylyltransferase mRNA capping enzyme
    Robert V Swift
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
    Biochemistry 51:10236-43. 2012
    ....
  22. pmc Modeling the pharmacodynamics of passive membrane permeability
    Robert V Swift
    Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697 3958, USA
    J Comput Aided Mol Des 25:1007-17. 2011
    ..For the set of tested compounds, the best correlation with experiment is obtained when the implicit chloroform global minimum is used to evaluate the solvation free energy difference...
  23. pmc Molecular simulations of aromatase reveal new insights into the mechanism of ligand binding
    Jiho Park
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 0340, USA
    J Chem Inf Model 53:2047-56. 2013
    ..Our results may be particularly relevant in the design of novel drugs, which may be useful therapeutic treatments of cancers such as those of the breast and prostate. ..
  24. pmc Computational approaches to mapping allosteric pathways
    Victoria A Feher
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
    Curr Opin Struct Biol 25:98-103. 2014
    ....
  25. pmc A 3-dimensional trimeric β-barrel model for Chlamydia MOMP contains conserved and novel elements of Gram-negative bacterial porins
    Victoria A Feher
    Department Chemistry and Biochemistry, University of California San Diego, San Diego, California, United States of America
    PLoS ONE 8:e68934. 2013
    ....
  26. pmc Molecular-level simulation of pandemic influenza glycoproteins
    Rommie E Amaro
    Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA
    Methods Mol Biol 819:575-94. 2012
    ....
  27. pmc Ensemble-based computational approach discriminates functional activity of p53 cancer and rescue mutants
    Ozlem Demir
    Department of Pharmaceutical Sciences, University of California, Irvine, California, United States of America
    PLoS Comput Biol 7:e1002238. 2011
    ..This new method reflects the overall stability of the p53 core domain and can discriminate which second-site mutations restore activity to p53 cancer mutants...
  28. pmc WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets
    Jacob D Durrant
    Department of Chemistry and Biochemistry and the National Biomedical Computation Resource, University of California, San Diego, La Jolla, CA 92093, USA
    BMC Bioinformatics 15:159. 2014
    ....
  29. pmc Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble
    Melissa R Landon
    Bioinformatics Graduate Program, Boston University, Boston, MA 02215, USA
    Chem Biol Drug Des 71:106-16. 2008
    ..Our hot spot analysis provides further support for the feasibility of developing high-affinity inhibitors capable of binding these regions, which appear to be unique to the N1 strain...
  30. ncbi request reprint A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase
    Rommie E Amaro
    Department of Chemistry, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    Biochemistry 46:2156-73. 2007
    ....
  31. pmc Structural elements in IGP synthase exclude water to optimize ammonia transfer
    Rommie E Amaro
    Department of Chemistry, University of Illinois, Urbana, Illinois, USA
    Biophys J 89:475-87. 2005
    ....

Research Grants2

  1. The SMD-Relaxed Complex Method for Drug Design
    Rommie Amaro; Fiscal Year: 2007
    ..The success of this new approach will be demonstrated on an essential RNA editing enzyme found in the trypanosomatid pathogens, which are responsible for several devastating tropical diseases. ..