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Riccardo  Baron
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Phone: 801-585-7117
Office: L .S. Skaggs Pharmacy Research Building, Room 1962

Riccardo Baron

Adjunct Assistant Professor, Bioengineering
Assistant Professor of Medicinal Chemistry, College of Pharmacy
The Henry Eyring Center for Theoretical Chemistry
Center for High Performance Computing
Ph.D. in Sciences, Swiss Federal Institute of Technology – ETH Zurich
2010 “Alfredo di Braccio” Prize for Chemistry, Accademia Nazionale dei Lincei
2010 Postdoctoral Research Award, American Chemical Society, Physical Chemistry Division

Research

Biomolecular Simulation, Computational Chemistry, Molecular Recognition, Biomaterials, Biophysics


Current Research

Our ultimate goal is to address problems of outstanding relevance for public health using chemical theory and computation. To achieve this goal as a team, we develop and apply computational chemistry to investigate the coupling among biomolecular structure, (thermo)dynamics, and function at diverse spatiotemporal scales. This is crucial for understanding and predicting molecular recognition and computational drug discovery. Special emphasis in our research is placed on the role of water in biomolecular association, entropic effects, and epigenetic drugs. A key component of our collaborative research is the integration and interplay between simulation and biophysical or biochemical experiments. Our group benefits from excellent computational facilities within the Center for High Performance Computing and interdisciplinary interactions within The Henry Eyring Center for Theoretical Chemistry.


Selected Publications

Ratnapriya R, Zhan X, Fariss RN, Branham KE, Zipprer D, Chakarova CF, Sergeev YV, Campos MM, Othman M, Friedman JS, Maminishkis A, Waseem NH, Brooks M, Rajasimha HK, Edwards AO, Lotery A, Klein BE, Truitt BJ, Li B, Schaumberg DA, Morgan DJ, Morrison MA, S, Rare and common variants in extracellular matrix gene Fibrillin 2 (FBN2) are associated with macular degeneration. Hum Mol Genet 2014 Nov 1;23(21):5827-37

Zabriskie MS, Eide CA, Tantravahi SK, Vellore NA, Estrada J, Nicolini FE, Khoury HJ, Larson RA, Konopleva M, Cortes JE, Kantarjian H, Jabbour EJ, Kornblau SM, Lipton JH, Rea D, Stenke L, Barbany G, Lange T, Hernández-Boluda JC, Ossenkoppele GJ, Press RD, , BCR-ABL1 compound mutations combining key kinase domain positions confer clinical resistance to ponatinib in Ph chromosome-positive leukemia. Cancer Cell 2014 Sep 8;26(3):428-42

Eiring AM, Page BD, Kraft IL, Mason CC, Vellore NA, Resetca D, Zabriskie MS, Zhang TY, Khorashad JS, Engar AJ, Reynolds KR, Anderson DJ, Senina A, Pomicter AD, Arpin CC, Ahmad S, Heaton WL, Tantravahi SK, Todic A, Colaguori R, Moriggl R, Wilson DJ, Baron , Combined STAT3 and BCR-ABL1 inhibition induces synthetic lethality in therapy-resistant chronic myeloid leukemia. Leukemia 2014 Aug 19;:

Vellore NA, Baron R, Epigenetic molecular recognition: a biomolecular modeling perspective. ChemMedChem 2014 Mar;9(3):484-94

Rusu VH, Horta VA, Horta BA, Lins RD, Baron R, MDWiZ: a platform for the automated translation of molecular dynamics simulations. J Mol Graph Model 2014 Mar;48:80-6

Baron R, Fast sampling of A-to-B protein global conformational transitions: from Galileo Galilei to Monte Carlo anisotropic network modeling. Biophys J 2013 Oct 1;105(7):1545-6

Kulkarni RA, Vellore NA, Bliss MR, Stanford SM, Falk MD, Bottini N, Baron R, Barrios AM, Substrate selection influences molecular recognition in a screen for lymphoid tyrosine phosphatase inhibitors. Chembiochem 2013 Sep 2;14(13):1640-7

Kulkarni RA, Stanford SM, Vellore NA, Krishnamurthy D, Bliss MR, Baron R, Bottini N, Barrios AM, Thiuram disulfides as pseudo-irreversible inhibitors of lymphoid tyrosine phosphatase. ChemMedChem 2013 Sep;8(9):1561-8

Vellore NA, Baron R, Molecular dynamics simulations indicate an induced-fit mechanism for LSD1/CoREST-H3-histone molecular recognition. BMC Biophys 2013 Nov 25;6(1):15

Robertson JC, Hurley NC, Tortorici M, Ciossani G, Borrello MT, Vellore NA, Ganesan A, Mattevi A, Baron R, Expanding the druggable space of the LSD1/CoREST epigenetic target: new potential binding regions for drug-like molecules, peptides, protein partners, and chromatin. PLoS Comput Biol 2013;9(7):e1003158

Baron R, McCammon JA, Molecular recognition and ligand association. Annu Rev Phys Chem 2013;64:151-75

Baron R, Setny P, Paesani F, Water structure, dynamics, and spectral signatures: changes upon model cavity-ligand recognition. J Phys Chem B 2012 Nov 26;116(46):13774-80

Baron R, Vellore NA, LSD1/CoREST is an allosteric nanoscale clamp regulated by H3-histone-tail molecular recognition. Proc Natl Acad Sci U S A 2012 Jul 31;109(31):12509-14

Baron R, Vellore NA, LSD1/CoREST reversible opening-closing dynamics: discovery of a nanoscale clamp for chromatin and protein binding. Biochemistry 2012 Apr 17;51(15):3151-3

Lawrenz M, Baron R, Wang Y, McCammon JA, Independent-trajectory thermodynamic integration: a practical guide to protein-drug binding free energy calculations using distributed computing. Methods Mol Biol 2012;819:469-86

Nichols SE, Baron R, McCammon JA, On the use of molecular dynamics receptor conformations for virtual screening. Methods Mol Biol 2012;819:93-103

Lawrenz M, Baron R, Wang Y, McCammon JA, Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies. J Chem Theory Comput 2011 Jun 2;7(7):2224-2232

Nichols SE, Baron R, Ivetac A, McCammon JA, Predictive power of molecular dynamics receptor structures in virtual screening. J Chem Inf Model 2011 Jun 27;51(6):1439-46

Baron R, Binda C, Tortorici M, McCammon JA, Mattevi A, Molecular mimicry and ligand recognition in binding and catalysis by the histone demethylase LSD1-CoREST complex. Structure 2011 Feb 9;19(2):212-20

Setny P, Baron R, McCammon JA, How Can Hydrophobic Association Be Enthalpy Driven? J Chem Theory Comput 2010 Sep 14;6(9):2866-2871

Baron R, Setny P, McCammon JA, Water in cavity-ligand recognition. J Am Chem Soc 2010 Sep 1;132(34):12091-7

Peric-Hassler L, Hansen HS, Baron R, Hünenberger PH, Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling. Carbohydr Res 2010 Aug 16;345(12):1781-801

Baron R, Hünenberger PH, McCammon JA, Absolute Single-Molecule Entropies from Quasi-Harmonic Analysis of Microsecond Molecular Dynamics: Correction Terms and Convergence Properties. J Chem Theory Comput 2009 Dec 8;5(12):3150-3160

Baron R, McCammon JA, Mattevi A, The oxygen-binding vs. oxygen-consuming paradigm in biocatalysis: structural biology and biomolecular simulation. Curr Opin Struct Biol 2009 Dec;19(6):672-9

Baron R, Riley C, Chenprakhon P, Thotsaporn K, Winter RT, Alfieri A, Forneris F, van Berkel WJ, Chaiyen P, Fraaije MW, Mattevi A, McCammon JA, Multiple pathways guide oxygen diffusion into flavoenzyme active sites. Proc Natl Acad Sci U S A 2009 Jun 30;106(26):10603-8

Lawrenz M, Baron R, McCammon JA, Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. J Chem Theory Comput 2009 Apr 14;5(4):1106-1116

Winger M, Trzesniak D, Baron R, van Gunsteren WF, On using a too large integration time step in molecular dynamics simulations of coarse-grained molecular models. Phys Chem Chem Phys 2009 Mar 28;11(12):1934-41

Baron R, Wong SE, de Oliveira CA, McCammon JA, E9-Im9 colicin DNase-immunity protein biomolecular association in water: a multiple-copy and accelerated molecular dynamics simulation study. J Phys Chem B 2008 Dec 25;112(51):16802-14

Wong SE, Baron R, McCammon JA, Hot-spot residues at the E9/Im9 interface help binding via different mechanisms. Biopolymers 2008 Nov;89(11):916-20

Gorfe AA, Baron R, McCammon JA, Water-membrane partition thermodynamics of an amphiphilic lipopeptide: an enthalpy-driven hydrophobic effect. Biophys J 2008 Oct;95(7):3269-77

Amaro RE, Baron R, McCammon JA, An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des 2008 Sep;22(9):693-705

Dolenc J, Baron R, Missimer JH, Steinmetz MO, van Gunsteren WF, Exploring the conserved water site and hydration of a coiled-coil trimerisation motif: a MD simulation study. Chembiochem 2008 Jul 21;9(11):1749-56

Chang CE, McLaughlin WA, Baron R, Wang W, McCammon JA, Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association. Proc Natl Acad Sci U S A 2008 May 27;105(21):7456-61

Baron R, McCammon JA, (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding. Chemphyschem 2008 May 16;9(7):983-8

Landon MR, Amaro RE, Baron R, Ngan CH, Ozonoff D, McCammon JA, Vajda S, Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble. Chem Biol Drug Des 2008 Feb;71(2):106-16

Baron R, McCammon JA, 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. Biochemistry 2007 Sep 18;46(37):10629-42

Missimer JH, Steinmetz MO, Baron R, Winkler FK, Kammerer RA, Daura X, van Gunsteren WF, Configurational entropy elucidates the role of salt-bridge networks in protein thermostability. Protein Sci 2007 Jul;16(7):1349-59

Baron R, Trzesniak D, de Vries AH, Elsener A, Marrink SJ, van Gunsteren WF, Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models. Chemphyschem 2007 Feb 19;8(3):452-61

Baron R, de Vries AH, Hünenberger PH, van Gunsteren WF, Configurational entropies of lipids in pure and mixed bilayers from atomic-level and coarse-grained molecular dynamics simulations. J Phys Chem B 2006 Aug 10;110(31):15602-14

Dolenc J, Baron R, Oostenbrink C, Koller J, van Gunsteren WF, Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding. Biophys J 2006 Aug 15;91(4):1460-70

van Gunsteren WF, Bakowies D, Baron R, Chandrasekhar I, Christen M, Daura X, Gee P, Geerke DP, Glättli A, Hünenberger PH, Kastenholz MA, Oostenbrink C, Schenk M, Trzesniak D, van der Vegt NF, Yu HB, Biomolecular modeling: Goals, problems, perspectives. Angew Chem Int Ed Engl 2006 Jun 19;45(25):4064-92

Pereira CS, Kony D, Baron R, Müller M, van Gunsteren WF, Hünenberger PH, Conformational and dynamical properties of disaccharides in water: a molecular dynamics study. Biophys J 2006 Jun 15;90(12):4337-44

Baron R, de Vries AH, Hünenberger PH, van Gunsteren WF, Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates. J Phys Chem B 2006 Apr 27;110(16):8464-73

Christen M, Hünenberger PH, Bakowies D, Baron R, Bürgi R, Geerke DP, Heinz TN, Kastenholz MA, Kräutler V, Oostenbrink C, Peter C, Trzesniak D, van Gunsteren WF, The GROMOS software for biomolecular simulation: GROMOS05. J Comput Chem 2005 Dec;26(16):1719-51

Baron R, Bakowies D, van Gunsteren WF, Principles of carbopeptoid folding: a molecular dynamics simulation study. J Pept Sci 2005 Feb;11(2):74-84

Baron R, Bakowies D, van Gunsteren WF, Carbopeptoid folding: effects of stereochemistry, chain length, and solvent. Angew Chem Int Ed Engl 2004 Aug 6;43(31):4055-9