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Bryce Group: Computational Biophysics and Drug Design is part
of the School of Pharmacy and Pharmaceutical Sciences
Bryce Group: Computational Biophysics and Drug Design

Publications

  • 2011

    Journal article

    • Daniel Mucs, Richard A. Bryce, Pascal Bonnet. (2011). Application of shape-based and pharmacophore-based in silico screens for identification of Type II protein kinase inhibitors. J Comput Aided Mol Des, eScholarID:144158 | DOI:10.1007/s10822-011-9442-0
    • Mark S. Dunstan, John Barnes, Matthew Humphries, Roger C. Whitehead, Richard A. Bryce. (2011). Novel Inhibitors of NRH:Quinone Oxidoreductase 2 (NQO2): Crystal Structures, Biochemical Activity, and Intracellular Effects of Imidazoacridin-6-ones. Journal of Medicinal Chemistry, 54, 6597-6611. eScholarID:144151 | DOI:10.1021/jm200416e
    • Mehdi Rajabi, David Mansell, Sally Freeman and Richard A. Bryce. (2011). Structure-activity relationship of 2,4,5-trioxoimidazolidines as inhibitors of thymidine phosphorylase. European Journal of Medicinal Chemistry, 46, 1165-1171. eScholarID:126029 | DOI:10.1016/j.ejmech.2011.01.035
    • Qiantao Wang and Richard A. Bryce. (2011). Accounting for non-optimal interactions in molecular recognition: a study of ion–p complexes using a QM/MM model with a dipole-polarisable MM region. Phys. Chem. Chem. Phys, 13, 19401-19408. eScholarID:144162 | DOI:10.1039/C1CP21944H
    • Richard A Bryce. (2011). Physics-based scoring of protein-ligand interactions: explicit polarizability, quantum mechanics and free energies. Future Med Chem, 3(6), 683-698. eScholarID:132535 | DOI:10.1007/s10822-011-9442-0
    • Richard A Bryce. (2011). Stoichiometry and Folding of Linear Polypeptides – Reading Between the Lines. Journal of Biomolecular Structure & Dynamics, 28(4), 647-648. eScholarID:98760

    Journal contribution

    • Richard A Bryce. (2011). Ask the experts: focus on computational chemistry. Future Med Chem, 3(8), 911. eScholarID:144188 | DOI:10.4155/FMC.11.57

  • 2010

    Journal article

    • Anitha Ramraj, Rajesh K. Rajua Qiantao Wang, Ian H. Hillier, Richard A. Bryce, Mark A. Vincenta. (2010). An evaluation of the GLYCAM06 and MM3 force fields, and the PM3-D* molecular orbital method for modelling prototype carbohydrate-aromatic interactions. Journal of Molecular Graphics and Modelling, 29, 321-325. eScholarID:98235 | DOI:10.1016/j.jmgm.2010.07.004
    • Christopher J. Morrow, Mohammad Ghattas, Christopher Smith, Heinz Bönisch, Richard A. Bryce,D. Mark Hickinson, Tim P. Green, and Caroline Dive. (2010). Src Family Kinase Inhibitor Saracatinib (AZD0530) Impairs Oxaliplatin Uptake in Colorectal Cancer Cells and Blocks Organic Cation Transporters. Cancer Research: American Association for Cancer Research, 70(14), 5931-5941. eScholarID:86921 | DOI:10.1158/0008-5472.CAN-10-0694
    • David Mansell, Nicolás Veiga, Julia Torres, Laura L. Etchells, Richard A. Bryce, Carlos Kremer, Sally Freeman. (2010). Conformational Study Of The Natural Iron Chelator Myo-Inositol 1,2,3-Trisphosphate Using Restrained/Flexible Analogues And Computational Analysis. Tetrahedron, 66, 8949-8957. eScholarID:93003 | DOI:10.1016/j.tet.2010.09.033
    • F.L. Mitchell, S.M. Miles, J. Neres, E.V. Bichenkova, R.A. Bryce. (2010). Tryptophan as a molecular shovel in the glycosyl transfer activity of Trypanosoma cruzi Trans-sialidase. Biophysical Journal, 98, L38-L40. eScholarID:83668 | DOI:10.1016/j.bpj.2010.01.006
    • KA Nolan, MP Humphries, J Barnes, JR Doncaster, MC Caraher, N Tirelli, RA Bryce, RC Whitehead, IJ Stratford. (2010). Triazoloacridin-6-ones as novel inhibitors of the Quinone Oxidoreductases NQO1 and NQO2. Bioorg. Med. Chem, 18, 696-706. eScholarID:79039 | DOI:10.1016/j.bmc.2009.11.059
    • KA Nolan, MP Humphries, RA Bryce, IJ Stratford. (2010). Imidazoacridin-6-ones as novel inhibitors of the quinone oxidoreductase NQO2. Bioorg. Med Chem Lett, 20, 2832-2836. eScholarID:85097 | DOI:10.1016/j.bmcl.2010.03.051
    • Neil J. Bruce and Richard A. Bryce. (2010). Ab Initio Protein Folding Using a Cooperative Swarm of Molecular Dynamics Trajectories. J. Chem. Theory Comput, 6, 1925-1930. eScholarID:86920 | DOI:10.1021/ct100060t
    • Neil J. Bruce, Deliang Chen, Shubhra G. Dastidar,Gabriel E. Marks,Catherine H. Schein, Richard A. Bryce. (2010). Molecular dynamics simulations of A-beta fibril interactions with beta-sheet breaker peptides. Peptides, 31, 2100-2108. eScholarID:92836 | DOI:10.1016/j.peptides.2010.07.015
    • RK Raju, IH Hillier, NA Burton, MA Vincent, S Doudou, RA Bryce. (2010). The effects of Perfluorination on Carbohydrate-pi Interactions: computational studies of the interaction of Benzene and Hexafluorobenzene with Fucose and Cyclodextrin. Phys.Chem. Chem Phys, 12, 7959-7967. eScholarID:85094 | DOI:10.1039/c002058c

  • 2009

    Journal article

    • Fong P, McNamara J, Hillier I, Bryce RA. (2009). Assessment of QM/MM scoring functions for molecular docking to HIV-1 protease. J Chem Inf Model, 49( 4), 913-24. eScholarID:1d19298 | DOI:10.1021/ci800432s
    • KA Nolan, JR Doncaster, M Dunstan, KA Scott, AD Frenkel, D Siegel, D Ross, J Barnes, C Levy, D Leys, RC Whitehead, IJ Stratford, RA Bryce. (2009). Synthesis and biological evaluation of coumarin-based inhibitors of NAD(P)H: Quinone Oxidoreductase-1 (NQO1). J Med. Chem, 52, 7142-7156. eScholarID:79035 | DOI:10.1021/jm9011609
    • Mitchell F, Frank F, Marks G, Suzuki M, Douglas KT, Bryce RA. (2009). Molecular dynamics study of chemically engineered green fluorescent protein mutants: Comparison of intramolecular fluorescence resonance energy transfer rate. Proteins, 75( 1), 28-39. eScholarID:1d18711 | DOI:10.1002/prot.22218
    • Neres, J, Brewer, M, Ratier, L, Botti, H, Buschiazzo, A, Edwards, P, Mortenson, P, Charlton, M, Alzari, P, Frasch, A, Bryce, RA, Douglas, KT. (2009). Discovery of novel inhibitors of Trypanosoma cruzitrans-sialidase from in silico screening. Bioorg Med Chem Lett, 19( 3), 589-96. eScholarID:1d18710 | DOI:10.1016/j.bmcl.2008.12.065
    • Q Wang, RA Bryce. (2009). Improved hydrogen bonding at the NDDO-type semiempirical quantum mechanical/molecular mechanical interface. J. Chem Theory Comput, 5, 2206-2211. eScholarID:79034 | DOI:10.1021/ct9002674

  • 2008

    Journal article

    • Atatreh N, Stojkoski C, Smith P, Booker G.W, Dive C, Frenkel. A.D, Freeman S, Bryce RA. (2008). In silico screening and biological evaluation of inhibitors of Src-SH3 domain interaction with a proline-rich ligand. Bioorg Med Chem Lett, 18[3], 1217-1222. eScholarID:1d17285
    • Mansell D., Rattray N., Etchells L., Schwalbe C., Blake A., Bichenkova E.V., Bryce R.A., Barker C., Díaz A., Kremer C., Freeman S. (2008). Fluorescent probe: complexation of Fe(3+) with the myo-inositol 1,2,3-trisphosphate motif. Chem. Comm. (Camb), 41, 5161-5163 . eScholarID:1d18030 | DOI:10.1039/b809238a
    • Mitchell F.L., Marks G.E., Bichenkova E.V., Douglas K.T., Bryce R.A. (2008). Molecular probes: insights into design and analysis from computational and physical chemistry. Biochem. Soc. Trans, 36 (1), 5598-5603. eScholarID:1d17010 | DOI:10.1016/j.tet.2008.03.045
    • Neres J, Bryce RA, Douglas KT. (2008). Rational drug design in parasitology: trans-sialidase as a case study for Chagas disease. Drug Discovery Today, 13[3/4], 110-117. eScholarID:1d16969
    • Reigan P, Gbaj A, Stratford IJ, Bryce RA, Freeman S. (2008). Xanthine oxidase-activated prodrugs of thymidine phosphorylase inhibitors. Eur J Med Chem, 43( 6), 1248-60. eScholarID:1d17756 | DOI:10.1016/j.ejmech.2007.07.015

  • 2007

    Journal article

    • Atatreh N, Barraclough J, Welman A, Cawthorne C, Bryce RA, Dive C, Freeman S. (2007). Difluoro analogue of UCS15A triggers activation of exogenously expressed c-Src in HCT 116 human colorectal carcinoma cells. J Enzyme Inhib Med Chem, 22( 5), 638-46. eScholarID:1d16936
    • Gould IR, Bettley HA, Bryce RA. (2007). Correlated ab initio quantum chemical calculations of di- and trisaccharide conformations. J Comput Chem, 28, 1965-1973. eScholarID:1d15868 | DOI:10.1002/jcc.20738
    • McNally V, Rajabi M, Gbaj A, Stratford IJ, Edwards PN, Douglas KT, Bryce RA, Jaffar M, Freeman S. (2007). Design, synthesis and enzymatic evaluation of 6-bridged imidazolyluracil derivatives as inhibitors of human thymidine phosphorylase. J Pharm Pharmacol, 59( 4), 537-47. eScholarID:1d15563
    • Neres J, Bonnet P, Edwards PN, Kotian P.L, Buschiazzo A, Alzari P.M, Bryce RA, Douglas KT. (2007). Benzoic acid and pyridine derivatives as inhibitors of trypanosoma cruzi trans-sialidase. Bioorg Med Chem, 15, 2106-2119. eScholarID:1d15176
    • Nolan, K, Zhao, H, Faulder, P, Frenkel, A, Timson, D, Siegel, D, Ross, D, Burke, T, Stratford, IJ, Bryce, RA. (2007). Coumarin-based inhibitors of human NAD(P)H: quinone oxidoreductase-1. identification, structure-activity, off-target effects and in vitro human pancreatic cancer toxicity. J Med Chem, 50( 25), 6316-25. eScholarID:1d16934

  • 2006

    Book contribution

    • Muslim A, McNamara J, Abdel-aal H, Hillier I-, Bryce RA. (2006). Hybrid QM/MM simulation of carbohydrates in aqueous solution. NMR Spectroscopy and Modeling of Carbohydrates, H. Vliegenhart, R.J. Woods eds. (Washington, American Chemical Society) Washington, DC. ( 930, pp. 186-202). eScholarID:3d448

    Journal article

    • Bichenkova E.V., Sardarian A.R., Wilton A.N., Bonnet P., Bryce R.A., Douglas K.T. (2006). Exciplex fluorescence emission from simple organic intramolecular constructs in non-polar and highly polar media as model systems for DNA-assembled exciplex detectors. Org. Biomol. Chem, 4(2), 367-378. eScholarID:1d12625
    • Chong TT, Hashim R, Bryce RA. (2006). Molecular dynamics simulation of monoalkyl glycoside micelles in aqueous solution: influence of carbohydrate headgroup stereochemistry. Journal of Physical Chemistry B, 110, 4978-4984. eScholarID:1d13114 | DOI:10.1021/jp065878c
    • Dimelow RJ, Bryce RA, Hillier IH, Burton NA. (2006). Exploring reaction pathways with transition path and umbrella sampling: application to methyl maltoside. Journal of Chemical Physics, 124, eScholarID:1d13113
    • Nolan KA, Timson DJ, Stratford IJ, Bryce RA. (2006). In silico identification and biochemical characterization of novel inhibitors of NQO1. Bioorg Med Chem Lett, eScholarID:1d13879

  • 2005

    Journal article

    • Bonnet P, Bryce RA. (2005). Scoring binding affinity of multiple ligands using implicit solvent and a single molecular dynamics trajectory: Application to Influenza neuraminidase. Journal of Molecular Graphics and Modelling, 24, 147-156. eScholarID:1d11481 | DOI:10.1016/j.jmgm.2005.08.006
    • Marks AHR, Bhadra PK, McDowell DG, French DJ, Bichenkova EV, Bryce RA, Douglas KT. (2005). Molecular Basis of Action of HyBeacon<sup>TM</sup> Fluorogenic Probes: a Spectroscopic and Molecular Dynamics Study. J. Biomol. Struct. Dynam, 23, 49-62. eScholarID:1d11483
    • Reigan P, Edwards, PN, Gbaj A, Cole C, Barry ST, Page KM, Ashton SE, Luke RW, Douglas, KT, Stratford, IJ, Jaffar, M, Bryce, RA, Freeman, S. (2005). Aminoimidazolylmethyluracil analogues as potent inhibitors of thymidine phosphorylase and their bioreductive nitroimidazolyl prodrugs. Journal of Medicinal Chemistry, 48, 392-402. eScholarID:1d11542 | DOI:10.1021/jm049494r

  • 2004

    Journal article

    • Bonnet P, Bryce RA. (2004). Molecular dynamics and free energy analysis of neuraminidase-ligand interactions. Protein Science, 13, 946-957. eScholarID:1d8863
    • McNamara JP, Muslim A, Abdel-Aal H, Wang H, Mohr M, Hillier IH, Bryce RA. (2004). Towards a quantum mechanical force field for carbohydrates: a reparametrized semi-empirical MO approach. Chemical Physics Letters, 394, 429-436. eScholarID:1d10188 | DOI:10.1016/j.cplett.2004.07.037
    • Muslim A, Bryce RA. (2004). Carbohydrate conformation in aqueous solution: calculation of a QM/MM potential of mean force. Chemical Physics Letters, 388, 473-478. eScholarID:1d8865

  • 2003

    Journal article

    • Bryce RA, Charnock J.M, Pattrick R.A.D, Lennie A.R. (2003). EXAFS and Density Functional Study of Gold(I) Thiosulfate Complex in Aqueous Solution. J. Phys. Chem. A, 107, 2516-2523. eScholarID:1d5120
    • McNally V.A, Gbaj A, Douglas KT, Stratford IJ, Jaffar M, Freeman S, Bryce RA. (2003). Identification of a Novel Class of Inhibitor of Human and Escherichia coli Thymidine Phosphorylase by In Silico Screening. Bioorganic & Medicinal Chemistry Letters, 13, 3705-3709. eScholarID:1d6884

  • 2001

    Journal article

    • Bryce RA, Hillier I.H, Naismith J.H. (2001). Carbohydrate-Protein Recognition: Molecular Dynamics Simulations and Free Energy Analysis of Oligosaccharide Binding to Concanavalin A. Biophysical Journal, 81, 1373-1388. eScholarID:1d1077
    • Mohr M, Bryce RA, Hillier I.H. (2001). Quantum Chemical Studies of Carbohydrate Reactivity: Acid Catalyzed Ring Opening Reactions. J. Phys. Chem. A, 105, 8216-8222. eScholarID:1d1076

  • 2000

    Journal article

    • Bryce RA, Vincent M.A, Hillier I.H, Hall R.J. (2000). Structure and stability of galena (PbS) at the interface with aqueous solution: a combined embedded cluster/reaction field study. Journal of Molecular Structure (Theochem), 500, 169-180. eScholarID:1d1001
    • Leach A.R, Bryce RA, Robinson A.J. (2000). Synergy between combinatorial chemistry and de novo design. Journal of Molecular Graphics and Modelling, 18, 358-367. eScholarID:1d957

  • 1999

    Book contribution

    • Dejaegere A, Bryce RA, Case D.A. (1999). An Empirical Analysis of Proton Chemical Shifts in Nucleic Acids. Modelling NMR Chemical Shifts: Gaining Insight into Structure and Environment, ACS Symposium Series, J. Facelli and A. C. deDios, Eds. (American Chemical Society, Washington, DC). ( 732, pp. 194-206). eScholarID:3d966

    Journal article

    • Bryce RA, Vincent M.A, Hillier I.H. (1999). Binding Energy of F(H2O)- and the Simulation of Fluoride Water Clusters Using a Hybrid QM/MM (Fluctuating Charge) Potential. J. Phys. Chem. A, 103, eScholarID:1d1002

  • 1998

    Journal article

    • Bryce RA, Vincent M.A, Malcolm N.O.J, Hillier I.H, Burton N.A. (1998). Cooperative effects in the structuring of fluoride water clusters: Ab initio hybrid quantum mechanical/molecular mechanical model incorporating polarizable fluctuating charge solvent. J. Chem. Phys, 109, eScholarID:1d1003
    • Maw S.A, Bryce RA, Hall R.J, Masters A.J, Hillier I.H. (1998). Integral Equation and ab Initio Study of the Effect of Solvation on Anomeric Equilibria in Aqueous Solution: Application to 4,6-Dimethyl-2-methoxytetrahydropyran. J. Phys. Chem. B, 102, eScholarID:1d1004

  • 1997

    Journal article

    • Bryce RA, Buesnel R, Hillier I.H, Burton N.A. (1997). A solvation model using a hybrid quantum mechanical/molecular mechanical potential with fluctuating solvent charges. Chemical Physics Letters, 279, 367-371. eScholarID:1d1005
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