Riccardo Baron

Summary

Affiliation: University of Utah
Country: USA

Publications

  1. doi request reprint Molecular recognition and ligand association
    Riccardo Baron
    Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112 5820, USA
    Annu Rev Phys Chem 64:151-75. 2013
  2. pmc Molecular dynamics simulations indicate an induced-fit mechanism for LSD1/CoREST-H3-histone molecular recognition
    Nadeem A Vellore
    Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112 5820, USA
    BMC Biophys 6:15. 2013
  3. doi request reprint Water structure, dynamics, and spectral signatures: changes upon model cavity-ligand recognition
    Riccardo Baron
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
    J Phys Chem B 116:13774-80. 2012
  4. doi request reprint LSD1/CoREST reversible opening-closing dynamics: discovery of a nanoscale clamp for chromatin and protein binding
    Riccardo Baron
    Department of Medicinal Chemistry, College of Pharmacy, The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, United States
    Biochemistry 51:3151-3. 2012
  5. pmc LSD1/CoREST is an allosteric nanoscale clamp regulated by H3-histone-tail molecular recognition
    Riccardo Baron
    Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, UT 84112 5820, USA
    Proc Natl Acad Sci U S A 109:12509-14. 2012
  6. pmc Molecular mimicry and ligand recognition in binding and catalysis by the histone demethylase LSD1-CoREST complex
    Riccardo Baron
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, and Department of Pharmacology, Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093 0365, USA
    Structure 19:212-20. 2011
  7. pmc Substrate selection influences molecular recognition in a screen for lymphoid tyrosine phosphatase inhibitors
    Rhushikesh A Kulkarni
    Department of Medicinal Chemistry, University of Utah, 30 South 2000 East, Salt Lake City, UT 84112 USA
    Chembiochem 14:1640-7. 2013
  8. pmc Expanding the druggable space of the LSD1/CoREST epigenetic target: new potential binding regions for drug-like molecules, peptides, protein partners, and chromatin
    James C Robertson
    Department of Medicinal Chemistry, College of Pharmacy, The University of Utah, Salt Lake City, Utah, USA
    PLoS Comput Biol 9:e1003158. 2013
  9. doi request reprint (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding
    Riccardo Baron
    Department of Chemistry and Biochemistry and Center for Theoretical and Biological Physics, University of California at San Diego, La Jolla, CA 92093 0365, USA
    Chemphyschem 9:983-8. 2008
  10. doi request reprint Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing
    Morgan Lawrenz
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA, USA
    Methods Mol Biol 819:469-86. 2012

Collaborators

Detail Information

Publications23

  1. doi request reprint Molecular recognition and ligand association
    Riccardo Baron
    Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112 5820, USA
    Annu Rev Phys Chem 64:151-75. 2013
    ..Physics-based approaches are increasingly expanding their power in pharmacology applications...
  2. pmc Molecular dynamics simulations indicate an induced-fit mechanism for LSD1/CoREST-H3-histone molecular recognition
    Nadeem A Vellore
    Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112 5820, USA
    BMC Biophys 6:15. 2013
    ..Here, we quantify the extent to which LSD1/CoREST substrate binding is consistent with these hypothetical models using LSD1/CoREST conformational ensembles obtained through extensive explicit solvent molecular dynamics (MD) simulations...
  3. doi request reprint Water structure, dynamics, and spectral signatures: changes upon model cavity-ligand recognition
    Riccardo Baron
    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
    J Phys Chem B 116:13774-80. 2012
    ..This study demonstrates that computer simulations and vibrational spectroscopy could be integrated to facilitate the direct study of solvent effects in biomolecular association...
  4. doi request reprint LSD1/CoREST reversible opening-closing dynamics: discovery of a nanoscale clamp for chromatin and protein binding
    Riccardo Baron
    Department of Medicinal Chemistry, College of Pharmacy, The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, Utah 84112, United States
    Biochemistry 51:3151-3. 2012
    ..Thus, targeting this site and including receptor flexibility are crucial strategies for future drug discovery...
  5. pmc LSD1/CoREST is an allosteric nanoscale clamp regulated by H3-histone-tail molecular recognition
    Riccardo Baron
    Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, UT 84112 5820, USA
    Proc Natl Acad Sci U S A 109:12509-14. 2012
    ..This study underscores the importance of receptor flexibility for future epigenetic drug discovery...
  6. pmc Molecular mimicry and ligand recognition in binding and catalysis by the histone demethylase LSD1-CoREST complex
    Riccardo Baron
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, and Department of Pharmacology, Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093 0365, USA
    Structure 19:212-20. 2011
    ..The combination of selective histone-modifying activity with the distinct recognition mechanisms underlies the biological complexity of LSD1/2...
  7. pmc Substrate selection influences molecular recognition in a screen for lymphoid tyrosine phosphatase inhibitors
    Rhushikesh A Kulkarni
    Department of Medicinal Chemistry, University of Utah, 30 South 2000 East, Salt Lake City, UT 84112 USA
    Chembiochem 14:1640-7. 2013
    ..Molecular docking simulations provided a first model for binding of this potent inhibitor to LYP; this will constitute the platform for ongoing lead optimization efforts...
  8. pmc Expanding the druggable space of the LSD1/CoREST epigenetic target: new potential binding regions for drug-like molecules, peptides, protein partners, and chromatin
    James C Robertson
    Department of Medicinal Chemistry, College of Pharmacy, The University of Utah, Salt Lake City, Utah, USA
    PLoS Comput Biol 9:e1003158. 2013
    ..This study sets the basis for future virtual screening campaigns targeting the five novel regions reported herein and for the design of LSD1/CoREST mutants to probe LSD1/CoREST binding with chromatin and various protein partners. ..
  9. doi request reprint (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding
    Riccardo Baron
    Department of Chemistry and Biochemistry and Center for Theoretical and Biological Physics, University of California at San Diego, La Jolla, CA 92093 0365, USA
    Chemphyschem 9:983-8. 2008
    ..We find that receptor flexibility plays a generally underestimated role in protein-ligand binding (thermo)dynamics and that changes of receptor motional correlation determine such large entropy contributions...
  10. doi request reprint Independent-Trajectory Thermodynamic Integration: a practical guide to protein-drug binding free energy calculations using distributed computing
    Morgan Lawrenz
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA, USA
    Methods Mol Biol 819:469-86. 2012
    ..Alternative protocols for the practical and general application of IT-TI calculations are investigated. We highlight a protocol that maximizes predictive power and computational efficiency...
  11. pmc E9-Im9 colicin DNase-immunity protein biomolecular association in water: a multiple-copy and accelerated molecular dynamics simulation study
    Riccardo Baron
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, Department of Pharmacology, Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093 0365, USA
    J Phys Chem B 112:16802-14. 2008
    ..The description of key transient biological interactions can be significantly enriched by the dynamic and atomic-level information provided by computer simulations...
  12. pmc Water in cavity-ligand recognition
    Riccardo Baron
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, Howard Hughes Medical Institute, University of California, San Diego, California 92093, USA
    J Am Chem Soc 132:12091-7. 2010
    ..Our study opens appealing perspectives to tackle the challenge of solvent entropy estimation in complex systems and for improving molecular simulation models...
  13. pmc Water-membrane partition thermodynamics of an amphiphilic lipopeptide: an enthalpy-driven hydrophobic effect
    Alemayehu A Gorfe
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093 0365, USA
    Biophys J 95:3269-77. 2008
    ..Furthermore, structural and entropic analysis of molecular dynamics-generated ensembles suggests that conformational selection may play a hitherto unappreciated role in membrane insertion of lipid-modified peptides and proteins...
  14. 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...
  15. pmc Thiuram disulfides as pseudo-irreversible inhibitors of lymphoid tyrosine phosphatase
    Rhushikesh A Kulkarni
    Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
    ChemMedChem 8:1561-8. 2013
    ..Compound 13 also inhibited LYP activity in Jurkat T cells...
  16. doi request reprint The oxygen-binding vs. oxygen-consuming paradigm in biocatalysis: structural biology and biomolecular simulation
    Riccardo Baron
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093 0365, USA
    Curr Opin Struct Biol 19:672-9. 2009
    ....
  17. pmc Predictive power of molecular dynamics receptor structures in virtual screening
    Sara E Nichols
    Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093 0365, United States
    J Chem Inf Model 51:1439-46. 2011
    ..Additionally, MD can move conformations previously not amenable to docking into the predictive range...
  18. pmc Multiple pathways guide oxygen diffusion into flavoenzyme active sites
    Riccardo Baron
    Department of Chemistry and Biochemistry and Pharmacology, Center for Theoretical Biological Physics, and Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093 0365, USA
    Proc Natl Acad Sci U S A 106:10603-8. 2009
    ..The difference in O(2) reactivity among dehydrogenases, monooxygenases, and oxidases ultimately resides in the fine modulation of the local environment embedding the reactive locus of the flavin...
  19. pmc Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association
    Chia en A Chang
    Departments of Chemistry and Biochemistry and Pharmacology, Center for Theoretical Biological Physics Howard Hughes Medical Institute, University of California at San Diego, La Jolla, CA 92093 0365, USA
    Proc Natl Acad Sci U S A 105:7456-61. 2008
    ..Implications are discussed for understanding and treating diseases in which promiscuous protein interactions are used...
  20. doi request reprint On the use of molecular dynamics receptor conformations for virtual screening
    Sara E Nichols
    Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA, USA
    Methods Mol Biol 819:93-103. 2012
    ..Here we highlight some details and nuances of using such snapshots and evaluating them for predictive performance...
  21. ncbi request reprint Dynamics, hydration, and motional averaging of a loop-gated artificial protein cavity: the W191G mutant of cytochrome c peroxidase in water as revealed by molecular dynamics simulations
    Riccardo Baron
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093 0365, USA
    Biochemistry 46:10629-42. 2007
    ....
  22. pmc Hot-spot residues at the E9/Im9 interface help binding via different mechanisms
    Sergio E Wong
    Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA 92093 0365, USA
    Biopolymers 89:916-20. 2008
    ..This type of model may be helpful in engineering hot-spot clusters at protein-protein interfaces and, consequently, the design of specificity...
  23. doi request reprint Epigenetic molecular recognition: a biomolecular modeling perspective
    Nadeem A Vellore
    Department of Medicinal Chemistry, College of Pharmacy and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, 30 South 2000 East, Salt Lake City, UT 84112 USA
    ChemMedChem 9:484-94. 2014
    ..A brief review of the biological background and biomedical relevance is presented for each topic, followed by a detailed discussion of the computational studies and their relevance...