Publications archive

  • 2017

    Article

    • Arsic, B., Aguilar Malavia, J., Bryce, R., & Barber, J. (2017). Conformational study of tylosin A in water and full assignments of 1H and 13C spectra of tylosin A in D2O and tylosin B in CDCl3. Magnetic Resonance in Chemistry, 55(4). DOI: 10.1002/mrc.4537. Publication link: c5114230-c3f5-46ef-8772-1bc1d799bee4
    • Patutina, O. A., Bichenkova, E., Miroshnichenko, S. K., Mironova, N. L., Trivoluzzi, L., Burusco-Goni, K., ... Zenkova, M. A. (2017). miRNases: Novel peptide-oligonucleotide bioconjugates that silence miR-21 in lymphosarcoma cells. Biomaterials, 122, 163-178. DOI: 10.1016/j.biomaterials.2017.01.018. Publication link: 5f4a69bd-c4be-491a-a613-c0040872c5b3

  • 2016

    Article

    • Alnabulsi, S., Santina, E., Russo, I., Hussein, B., Kadirvel, M., Chadwick, A., ... Freeman, S. (2016). Non-symmetrical furan-amidines as novel leads for the treatment of cancer and malaria. European Journal of Medicinal Chemistry, 111, 33-45. DOI: 10.1016/j.ejmech.2016.01.022. Publication link: 8b784583-8154-433a-b2bf-52483d66b835 | PubMed:26854376
    • Ghattas, M. A., Mansour, R. A., Atatreh, N., & Bryce, R. A. (2016). Analysis of Enoyl-Acyl Carrier Protein Reductase Structure and Interactions Yields an Efficient Virtual Screening Approach and Suggests a Potential Allosteric Site.Chemical biology & drug design, 87(1), 131-142. DOI: 10.1111/cbdd.12635. Publication link: 6926bf78-4e87-4697-bb5a-da07a65d3ec3 | PubMed:26259619

  • 2015

    Article

  • 2014

    Article

  • 2013

    Article

  • 2012

    Article

    • Bonnet, P., Mucs, D., & Bryce, R. A. (2012). Targeting the inactive conformation of protein kinases: Computational screening based on ligand conformation. MedChemComm, 3(4), 434-440. DOI: 10.1039/c1md00256b. Publication link: e98deed7-0b54-4906-abf1-0f36dc5cdef7
    • Manickam Achari, V., Nguan, H. S., Heidelberg, T., Bryce, R. A., & Hashim, R. (2012). Molecular dynamics study of anhydrous lamellar structures of synthetic glycolipids: Effects of chain branching and disaccharide headgroup. Journal of Physical Chemistry B, 116(38), 11626-11634. DOI: 10.1021/jp302292s. Publication link: 48805c66-0c96-4577-8083-5a0ac2cccec3 | PubMed:22967067

  • 2011

    Article

    • Bryce, R. A. (2011). Stoichiometry and folding of linear polypeptides - Reading between the lines. Journal of Biomolecular Structure and Dynamics, 28(4), 647-648. DOI: 10.1080/073911011010524976. Publication link: 495efbf5-397e-4f6a-83a5-75a588a81dd3
    • Dunstan, M. S., Barnes, J., Humphries, M., Whitehead, R. C., Bryce, R. A., Leys, D., ... Nolan, K. A. (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(19), 6597-6611. DOI: 10.1021/jm200416e. Publication link: a173c10d-9814-498f-a63a-94bf7a454fea | PubMed:21859103
    • Mucs, D., Bryce, R. A., & Bonnet, P. (2011). Application of shape-based and pharmacophore-based in silico screens for identification of Type II protein kinase inhibitors. Journal of Computer-Aided Molecular Design, 25(6), 569-581. DOI: 10.1007/s10822-011-9442-0. Publication link: 110d1665-04dd-4c4b-9b4b-e5882f105268
    • Rajabi, M., Mansell, D., Freeman, S., & Bryce, R. A. (2011). Structure-activity relationship of 2,4,5-trioxoimidazolidines as inhibitors of thymidine phosphorylase. European Journal of Medicinal Chemistry, 46(4), 1165-1171. DOI: 10.1016/j.ejmech.2011.01.035. Publication link: df97467e-a8fd-40eb-8c79-227c0ec7f5f7
    • Wang, Q., & Bryce, R. A. (2011). Accounting for non-optimal interactions in molecular recognition: A study of ion-π complexes using a QM/MM model with a dipole-polarisable MM region. Physical Chemistry Chemical Physics, 13(43), 19401-19408. DOI: 10.1039/c1cp21944h. Publication link: ceceb2d9-de00-4e0e-b8f5-5019caf7ab21

    Comment/debate

    • Bajorath, J., Barreca, M. L., Bender, A., Bryce, R., Hutter, M., Laggner, C., ... Willett, P. (2011). Ask the experts: focus on computational chemistry.Future medicinal chemistry, 3(8), 909-921. DOI: 10.4155/fmc.11.57. Publication link: db0358c2-f23a-4823-9286-b9e10d2e2f22

  • 2010

    Article

    • Bruce, N. J., & Bryce, R. A. (2010). Ab initio protein folding using a cooperative swarm of molecular dynamics trajectories. Journal of Chemical Theory and Computation, 6(7), 1925-1930. DOI: 10.1021/ct100060t. Publication link: 678baf9a-3b4a-4364-8fbd-200d0de6b544
    • Bruce, N. J., Chen, D., Dastidar, S. G., Marks, G. E., Schein, C. H., & Bryce, R. A. (2010). Molecular dynamics simulations of Aβ fibril interactions with β-sheet breaker peptides. Peptides, 31(11), 2100-2108. DOI: 10.1016/j.peptides.2010.07.015. Publication link: 8de6ee26-a76d-4d27-8254-2d7b2d0f3e4d
    • Mansell, D., Veiga, N., Torres, J., Etchells, L. L., Bryce, R. A., Kremer, C., & Freeman, S. (2010). Conformational study of the natural iron chelator myo-inositol 1,2,3-trisphosphate using restrained/flexible analogues and computational analysis. Tetrahedron, 66(46), 8949-8957. DOI: 10.1016/j.tet.2010.09.033. Publication link: 81d53140-0719-4c54-aa17-ed63110f004a
    • Mitchell, F. L., Miles, S. M., Neres, J., Bichenkova, E. V., & Bryce, R. A. (2010). Tryptophan as a molecular shovel in the glycosyl transfer activity of Trypanosoma cruzi trans-sialidase. Biophysical Journal, 98(9), L38-L40. DOI: 10.1016/j.bpj.2010.01.006. Publication link: 59ebe22a-7436-461b-a3e6-766b02b1f1c6
    • Morrow, C. J., Ghattas, M., Smith, C., Bönisch, H., Bryce, R. A., Hickinson, D. M., ... Dive, C. (2010). Src family kinase inhibitor saracatinib (AZD0530) impairs oxaliplatin uptake in colorectal cancer cells and blocks organic cation transporters. Cancer Research, 70(14), 5931-5941. DOI: 10.1158/0008-5472.CAN-10-0694. Publication link: b642943f-f3b2-4e3b-8466-a4998fa5c59f
    • Nolan, K. A., Caraher, M. C., Humphries, M. P., Bettley, H. A. A., Bryce, R. A., & Stratford, I. J. (2010). In silico identification and biochemical evaluation of novel inhibitors of NRH:quinone oxidoreductase 2 (NQO2). Bioorganic and Medicinal Chemistry Letters, 20(24), 7331-7336. DOI: 10.1016/j.bmcl.2010.10.070. Publication link: ce8756f0-ecad-4e39-919c-bb231e64e3e5 | PubMed:21074425
    • Nolan, K. A., Humphries, M. P., Barnes, J., Doncaster, J. R., Caraher, M. C., Tirelli, N., ... Stratford, I. J. (2010). Triazoloacridin-6-ones as novel inhibitors of the quinone oxidoreductases NQO1 and NQO2. Bioorganic and Medicinal Chemistry, 18(2), 696-706. DOI: 10.1016/j.bmc.2009.11.059. Publication link: 23c18530-0779-4f6c-8e70-879fed4871a5 | PubMed:20036559
    • Nolan, K. A., Humphries, M. P., Bryce, R. A., & Stratford, I. J. (2010). Imidazoacridin-6-ones as novel inhibitors of the quinone oxidoreductase NQO2. Bioorganic and Medicinal Chemistry Letters, 20(9), 2832-2836. DOI: 10.1016/j.bmcl.2010.03.051. Publication link: b99852af-d132-445b-b26a-6a96623b63c1 | PubMed:20356739
    • Raju, R. K., Hillier, I. H., Burton, N. A., Vincent, M. A., Doudou, S., & Bryce, R. A. (2010). The effects of perfluorination on carbohydrate-π interactions: Computational studies of the interaction of benzene and hexafluorobenzene with fucose and cyclodextrin. Physical Chemistry Chemical Physics, 12(28), 7959-7967. DOI: 10.1039/c002058c. Publication link: 08a3a956-d21b-4336-bdb1-457331d6d08a
    • Ramraj, A., Raju, R. K., Wang, Q., Hillier, I. H., Bryce, R. A., & Vincent, M. A. (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(3), 321-325. DOI: 10.1016/j.jmgm.2010.07.004. Publication link: b5b164da-0473-4d31-9f8c-61651d628ae7

  • 2009

    Article

    • Fong, P., McNamara, J. P., Hillier, I. H., & Bryce, R. A. (2009). Assessment of QM/MM scoring functions for molecular docking to HIV-1 protease. Journal of Chemical Information and Modeling, 49(4), 913-924. DOI: 10.1021/ci800432s. Publication link: f82bd784-088d-435c-858a-016b529dec46
    • Mitchell, F. L., Frank, F., Marks, G. E., Suzuki, M., Douglas, K. T., & Bryce, R. A. (2009). Molecular dynamics study of chemically engineered green fluorescent protein mutants: Comparison of intramolecular fluorescence resonance energy transfer rate. Proteins: Structure, Function and Bioinformatics, 75(1), 28-39. DOI: 10.1002/prot.22218. Publication link: c282b18d-447e-4a0d-a078-3b0e34c0eb31
    • Neres, J., Brewer, M. L., Ratier, L., Botti, H., Buschiazzo, A., Edwards, P. N., ... Douglas, K. T. (2009). Discovery of novel inhibitors of Trypanosoma cruzi trans-sialidase from in silico screening. Bioorganic and Medicinal Chemistry Letters, 19(3), 589-596. DOI: 10.1016/j.bmcl.2008.12.065. Publication link: a9b6c0f7-bd2e-49f5-81cd-e879e947ec41
    • Nolan, K. A., Doncaster, J. R., Dunstan, M. S., Scott, K. A., Frenkel, A. D., Siegel, D., ... Bryce, R. A. (2009). Synthesis and biological evaluation of coumarin-based inhibitors of NAD(P)H: Quinone oxidoreductase-1 (NQO1). Journal of Medicinal Chemistry, 52(22), 7142-7156. DOI: 10.1021/jm9011609. Publication link: 38d0b392-2aa7-4441-8127-6329b33edfca | PubMed:19877692
    • Wang, Q., & Bryce, R. A. (2009). Improved hydrogen bonding at the NDDO-type semiempirical quantum mechanical/molecular mechanical interface. Journal of Chemical Theory and Computation, 5(9), 2206-2211. DOI: 10.1021/ct9002674. Publication link: 05fa36ab-32a3-426a-a111-96d649611e09

  • 2008

    Article

    • Chong, T. T., Heidelberg, T., Hashim, R., & Bryce, R. A. (2008). Computer simulation of a hexagonal assembly for a branched chain glycolipid. Malaysian Journal of Science, 27(2), 75-82. . Publication link: 10480431-83e3-4458-9b46-70ce228e6546
    • Kadirvel, M., Gbaj, A., Mansell, D., Miles, S. M., Arsic, B., Bichenkova, E. V., ... Douglas, K. (2008). Conformational probe: static quenching is reduced upon acid triggered ring flip of a myo-inositol derivative. Tetrahedron, 64(23), 5598-5603. DOI: 10.1016/j.tet.2008.03.045. Publication link: 948b0afa-507f-40ef-b554-cb2343684dba
    • Mansell, D., Rattray, N., Etchells, L. L., Schwalbe, C. H., Blake, A. J., Bichenkova, E. V., ... Freeman, S. (2008). Fluorescent probe: Complexation of Fe3+with the myo-inositol 1,2,3-trisphosphate motif. Chemical Communications, (41), 5161-5163. DOI: 10.1039/b809238a. Publication link: 3bb447d8-0e90-4fce-b071-fc3451af4ece
    • Neres, J., Bryce, R. A., & Douglas, K. T. (2008). Rational drug design in parasitology: trans-sialidase as a case study for Chagas disease. Drug Discovery Today, 13(3-4), 110-117. DOI: 10.1016/j.drudis.2007.12.004. Publication link: 57e502b3-3e6a-4f1a-a706-3736f62a0251
    • Reigan, P., Gbaj, A., Stratford, I. J., Bryce, R. A., & Freeman, S. (2008). Xanthine oxidase-activated prodrugs of thymidine phosphorylase inhibitors. European Journal of Medicinal Chemistry, 43(6), 1248-1260. DOI: 10.1016/j.ejmech.2007.07.015. Publication link: f2af9e84-31fe-4e0d-8902-70642337881f

  • 2007

    Article

    • Gould, I. R., Bettley, H. A. A., & Bryce, R. A. (2007). Correlated Ab Initio quantum chemical calculations of Di- and trisaccharide conformations. Journal of Computational Chemistry, 28(12), 1965-1973. DOI: 10.1002/jcc.20738. Publication link: 6090fd27-734f-480e-ace5-894b21dce5b1
    • McNally, V. A., Rajabi, M., Gbaj, A., Stratford, I. J., Edwards, P. N., Douglas, K. T., ... Freeman, S. (2007). Design, synthesis and enzymatic evaluation of 6-bridged imidazolyluracil derivatives as inhibitors of human thymidine phosphorylase. Journal of Pharmacy and Pharmacology, 59(4), 537-547. DOI: 10.1211/jpp.59.4.0008. Publication link: a3e652ca-e646-4533-b1bf-3ba2b01bebe4
    • Neres, J., Bonnet, P., Edwards, P. N., Kotian, P. L., Buschiazzo, A., Alzari, P. M., ... Douglas, K. T. (2007). Benzoic acid and pyridine derivatives as inhibitors of Trypanosoma cruzi trans-sialidase. Bioorganic and Medicinal Chemistry, 15(5), 2106-2119. DOI: 10.1016/j.bmc.2006.12.024. Publication link: 5dd91914-58e3-49a8-9aa2-4234583544b6
    • Nolan, K. A., Zhao, H., Faulder, P. F., Frenkel, A. D., Timson, D. J., Siegel, D., ... Bryce, R. A. (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. Journal of Medicinal Chemistry, 50(25), 6316-6325. DOI: 10.1021/jm070472p. Publication link: 7641c2ce-0333-48c3-9a8a-9abef20c4f09 | PubMed:17999461

  • 2006

    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. Organic and Biomolecular Chemistry, 4(2), 367-378. DOI: 10.1039/b511707k. Publication link: ac850076-8d13-4cd6-a29c-f561d8e4a4e1
    • Bryce, D. L., & Sward, G. D. (2006). Chlorine-35/37 NMR spectroscopy of solid amino acid hydrochlorides: Refinement of hydrogen-bonded proton positions using experiment and theory. Journal of Physical Chemistry B, 110(51), 26461-26470. DOI: 10.1021/jp065878c. Publication link: ed92d22d-1c70-458f-a4f3-20070e7937f0
    • Dimelow, R. J., Bryce, R. A., Masters, A. J., Hillier, I. H., & Burton, N. A. (2006). Exploring reaction pathways with transition path and umbrella sampling: Application to methyl maltoside. Journal of Chemical Physics, 124(11), [114113]. DOI: 10.1063/1.2172604. Publication link: 36f10499-6e32-4615-8227-f51965c242c9
    • Nolan, K. A., Timson, D. J., Stratford, I. J., & Bryce, R. A. (2006). In silico identification and biochemical characterization of novel inhibitors of NQO1. Bioorganic and Medicinal Chemistry Letters, 16(24), 6246-6254. DOI: 10.1016/j.bmcl.2006.09.015. Publication link: 8a90921f-6cb9-4401-a129-1371ece482d3

    Chapter

    • Bryce, R. A., Muslim, A., McNamara, J., Abdel-aal, H., & Hillier, I. (2006). Hybrid QM/MM simulation of carbohydrates in aqueous solution. In NMR Spectroscopy and Modeling of Carbohydrates, H. Vliegenhart, R.J. Woods eds. (Washington, American Chemical Society) Washington, DC. (Vol. 930). Publication link: 966945b2-0ee3-419c-ae9a-5db7d5897f13
    • Muslim, A. M., McNamara, J. P., Abdel-Aal, H., Hillier, I. H., & Bryce, R. A. (2006). QM/MM simulations of carbohydrates. In ACS Symposium Series|ACS Symp. Ser.. (Vol. 930, pp. 186-202). Publication link: 6b2821be-6ff1-45b8-8b15-31a7051450d6

  • 2005

    Article

    • Bryce, R. A., Burton, N. A., & Gould, I. R. (2005). Towards accurate calculation of biomolecular recognition and reactivity: A special issue in honour of Professor Ian Hillier. Journal of Molecular Graphics and Modelling, 24(2), 81. DOI: 10.1016/j.jmgm.2005.08.006. Publication link: fe59f17d-973e-4316-890e-0f5f2c87843a
    • Marks, A. H. R., Bhadra, P. K., McDowell, D. G., French, D. J., Bichenkova, E. V., Bryce, R. A., & Douglas, K. T. (2005). Molecular Basis of Action of HyBeaconTM Fluorogenic Probes: a Spectroscopic and Molecular Dynamics Study. J. Biomol. Struct. Dynam., 23, 49-62. DOI: 10.1080/07391102.2005.10507046. Publication link: 9fdbd04f-b5c4-4f22-965b-adf6f58e360d
    • Reigan, P., Edwards, P. N., Gbaj, A., Cole, C., Barry, S. T., Page, K. M., ... Freeman, S. (2005). Aminoimidazolylmethyluracil analogues as potent inhibitors of thymidine phosphorylase and their bioreductive nitroimidazolyl prodrugs. Journal of Medicinal Chemistry, 48(2), 392-402. DOI: 10.1021/jm049494r. Publication link: 44e1db48-88cd-4dd0-9e20-d970701ede45

  • 2004

    Article

  • 2003

    Article

    • Bryce, R. A., Charnock, J. M., Pattrick, R. A. D., & Lennie, A. R. (2003). EXAFS and density functional study of gold(I) thiosulfate complex in aqueous solution. Journal of Physical Chemistry A, 107(14), 2516-2523. DOI: 10.1021/jp021403j. Publication link: d24c353f-f7a9-4e01-95e7-22b0d730dc92
    • McNally, V. A., Gbaj, A., Douglas, K. T., Stratford, I. J., Jaffar, M., Freeman, S., & Bryce, R. A. (2003). Identification of a novel class of inhibitor of human and Escherichia coli thymidine phosphorylase by in silico screening. Bioorganic and Medicinal Chemistry Letters, 13(21), 3705-3709. DOI: 10.1016/j.bmcl.2003.08.010. Publication link: 2d5ac797-dbac-4213-a34f-aebdcc18b276

  • 2001

    Article

    • Bryce, R. A., 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(3), 1373-1388. DOI: 10.1016/S0006-3495(01)75793-1. Publication link: ecd1ed57-7b1b-43f1-bc1b-48442bdb982d
    • Mohr, M., Bryce, R. A., & Hillier, I. H. (2001). Quantum chemical studies of carbohydrate reactivity: Acid catalyzed ring opening reactions. Journal of Physical Chemistry A, 105(35), 8216-8222. DOI: 10.1021/jp010901+. Publication link: fcce4eda-fdaa-463b-9b54-b1b155bd85bc

  • 2000

    Article

  • 1999

    Article

    • Bryce, R. A., Vincent, M. A., & Millier, I. H. (1999). Binding energy of F(H2O)- and the simulation of fluoride water clusters using a hybrid QM/MM (fluctuating charge) potential. Journal of Physical Chemistry A, 103(20), 4094-4100. . Publication link: 424fadd2-cf39-42d1-afdb-dabe8451a4cb

    Chapter

    • Dejaegere, A., Bryce, R. A., & Case, D. A. (1999). An empirical analysis of proton chemical shifts in nucleic acids. In ACS Symposium Series|ACS Symp Ser. (Vol. 732, pp. 194-206). Publication link: 831760c0-43c0-4054-958b-e93b4831d2e4

  • 1998

    Article

    • Bryce, R. A., 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. Journal of Chemical Physics, 109(8), 3077-3085. DOI: 10.1063/1.476900. Publication link: 59af5394-a63d-4c3b-9c28-eb201d9fccc5
    • Maw, S. A., Bryce, R. A., 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. Journal of Physical Chemistry B, 102(21), 4089-4095. . Publication link: c66ceae5-3115-435f-9611-ed1e7865ca07

  • 1997

    Article

    • Bryce, R. A., 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(5-6), 367-371. . Publication link: 91671669-ff63-4654-b0dc-7578038c8672