School of Chemistry

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Peter Johnson

Research Professor
Member of the Chemical Biology and Medicinal Chemistry group

Contact details

Room: 1.10b
Tel: +44 (0)113 3436515


Synthetic methods
Structure based drug design
Software development
Computational chemistry
Total synthesis

Photograph of Peter Johnson

Research interests

Total synthesis of natural products; development of new synthetic methods; synthesis of designed catalysts and synthetic receptors; development of software for structure based drug design eg SPROUT for de novo ligand design, CAESA for estimation of synthetic accessibility; development of software for automatic extraction of chemical information from scanned images of chemistry journals.


Cunningham F, McPhillie MJ, Johnson AP, Fishwick CW An in silico structure-based approach to anti-infective drug discovery. Parasitology 141 17-27, 2014
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Simmons KJ, Gotfryd K, Billesbølle CB, Loland CJ, Gether U, Fishwick CW, Johnson AP A virtual high-throughput screening approach to the discovery of novel inhibitors of the bacterial leucine transporter, LeuT. Mol Membr Biol 30 184-194, 2013
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Fishwick CWG, Chadwick J, Kellet K, Casas_Arce E, Hooper N, Johnson AP, Mok Y Discovery of biphenylacetamide-derived inhibitors of BACE1 using de novo structure-based molecular design Journal of Medicinal Chemistry 56 1843-1852, 2013
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Wacker SJ, Jurkowski W, Simmons KJ, Fishwick CWG, Johnson AP, Madge D, Lindahl E, Rolland JF, deGroot BL Identification of Selective Inhibitors of the Potassium Channel Kv1.1-1.2(3) by High-Throughput Virtual Screening and Automated Patch Clamp ChemMedChem 7 1775-1783, 2012
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Bedingfield PT, Cowen D, Acklam P, Cunningham F, Parsons MR, McConkey GA, Fishwick CW, Johnson AP Factors influencing the specificity of inhibitor binding to the human and malaria parasite dihydroorotate dehydrogenases. J Med Chem 55 5841-5850, 2012
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Kankanala J, Latham AM, Johnson AP, Homer-Vanniasinkam S, Fishwick CW, Ponnambalam S A combinatorial in silico and cellular approach to identify a new class of compounds that target VEGFR2 receptor tyrosine kinase activity and angiogenesis. Br J Pharmacol 166 737-748, 2012
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Cook A, Johnson AP, Law J, Mirzazadeh M, Ravitz O, Simon A Computer-aided synthesis design: 40 years on WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2 79-107, 2012

Latham AM, Bruns AF, Kankanala J, Johnson AP, Fishwick CW, Homer-Vanniasinkam S, Ponnambalam S Indolinones and anilinophthalazines differentially target VEGF-A- and basic fibroblast growth factor-mediated responses in primary human endothelial cells. Br J Pharmacol 165 245-259, 2012
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McPhillie MJ, Trowbridge R, Mariner KR, O'Neill AJ, Johnson AP, Chopra I, Fishwick CWG Structure-Based Ligand Design of Novel Bacterial RNA Polymerase Inhibitors ACS MED CHEM LETT 2 729-734, 2011

Cowen D, Bedingfield P, McConkey GA, Fishwick CW, Johnson AP A study of the effects of substituents on the selectivity of the binding of N-arylaminomethylene malonate inhibitors to DHODH. Bioorg Med Chem Lett 20 1284-1287, 2010
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Yi Mok N, Chadwick J, Kellett KA, Hooper NM, Johnson AP, Fishwick CW Discovery of novel non-peptide inhibitors of BACE-1 using virtual high-throughput screening. Bioorg Med Chem Lett 19 6770-6774, 2009
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Davies M, Heikkilä T, McConkey GA, Fishwick CW, Parsons MR, Johnson AP Structure-based design, synthesis, and characterization of inhibitors of human and Plasmodium falciparum dihydroorotate dehydrogenases. J Med Chem 52 2683-2693, 2009
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Valko AT, Johnson AP CLiDE Pro: the latest generation of CLiDE, a tool for optical chemical structure recognition. J Chem Inf Model 49 780-787, 2009
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Brozic P, Cesar J, Kovac A, Davies M, Johnson AP, Fishwick CWG, Rizner TL, Gobec S Derivatives of pyrimidine, phthalimide and anthranilic acid as inhibitors of human hydroxysteroid dehydrogenase AKR1C1, 2009

Law J, Zsoldos Z, Simon A, Reid D, Liu Y, Khew SY, Johnson AP, Major S, Wade RA, Ando HY Route Designer: A Retrosynthetic Analysis Tool Utilizing Automated Retrosynthetic Rule Generation. J Chem Inf Model -, 2009
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Agarwal AK, Johnson AP, Fishwick CWG Synthesis of de novo designed small-molecule inhibitors of bacterial RNA polymerase (vol 64, pg 10049, 2008) TETRAHEDRON 65 1077-1077, 2009

Agarwal AK, Johnson AP, Fishwick CWG Synthesis of de novo designed small-molecule inhibitors of bacterial RNA polymerase TETRAHEDRON 64 10049-10054, 2008

Johnson AP, Law J, Zsoldos Z, Simon A, Williams AJ CINF 78-A new, automated retrosynthetic search engine: ARChem, 2008

Valko A, Johnson AP, Simon A CINF 54-Introducing CLiDE Pro, 2008

Reid D, Zsoldos Z, Johnson AP COMP 57-Fragment based de novo design using an existing fragment based docking program, eHiTS, 2008

Johnson AP, Valko V, Valko A, Zsoldos Z, Boda K, Reid D SynSPROUT and SPROUT-LeadOpt: De novo ligand design and optimization guided by virtual synthesis ABSTR PAP AM CHEM S 233 259-259, 2007

Heikkila T, Ramsey C, Davies M, Galtier C, Stead AMW, Johnson AP, Fishwick CWG, Boa AN, McConkey GA Design and synthesis of potent inhibitors of the malaria parasite dihydroorotate dehydrogenase J MED CHEM 50 186-191, 2007

Boda K, Johnson AP Molecular complexity analysis of de novo designed ligands J MED CHEM 49 5869-5879, 2006

Zsoldos Z, Reid D, Aniko S, Sadjad BS, Johnson AP eHITS: an Innovative Approach to the Docking and Scoring Function Problems Current Protein and Peptide Sciences 7 421-435, 2006

Agarwal AK, Hurdle JG, AlOmar AI, Chopra I, Johnson AP, Fishwick CWG MEDI 326-De Novo design and synthesis of novel RNA polymerase inhibitors as potential anti-tuberculosis agents ABSTR PAP AM CHEM S 232 -, 2006

Johnson AP, Boda K, Weaver S, Valko A, Valko V DeNovo design tools for the generation of synthetically accessible ligands, 2006

Boda K, Johnson AP Molecular Complexity Analysis of de Novo Designed Ligands Journal of Medicinal Chemistry 49 5869-5872, 2006

Heikkila T, Thirumalairajan S, Davies M, Parsons MR, McConkey AG, Fishwick CWG, Johnson AP The first de novo designed inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase BIOORG MED CHEM LETT 16 88-92, 2006

Besong GE, Bostock JM, Stubbings WJ, Chopra I, Roper DI, Lloyd AJ, Fishwick CWG, Johnson AP A De Novo Designed Inhibitor of D-Ala-D-Ala Ligase from E. coli Angewandte Chemie - International Edition 44 6403-6406, 2005

Besong GE, Bostock JM, Stubbings W, Chopra I, Roper DI, Lloyd AJ, Fishwick CWG, Johnson AP A de Novo designed inhibitor of D-Ala-D-Ala ligase from E-coli ANGEW CHEM INT EDIT 44 6403-6406, 2005

Cook AP, Johnson AP, Thomas DG Novel method for optimizing subgraph isomorphism algorithms such that 2-D stereochemical descriptors are efficiently processed in a molecule or reaction retrieval system., 2004

Johnson AP, Boda K, Lengyel T, Weaver S, Vigh A Role for chemoinformatics in structure-based de novo ligand design., 2004

Zsoldos Z, Szabo I, Szabo Z, Johnson AP Software tools for structure based rational drug design JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM 666 659-665, 2003

Law JMS, Fung DYK, Zsoldos Z, Simon A, Szabo Z, Csizmadia IG, Johnson AP Validation of the SPROUT de novo design program J MOL STRUC-THEOCHEM 666 651-657, 2003
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Horton JR, Bostock JM, Chopra I, Hesse L, Phillips SE, Adams DJ, Johnson AP, Fishwick CW Macrocyclic inhibitors of the bacterial cell wall biosynthesis enzyme MurD. Bioorg Med Chem Lett 13 1557-1560, 2003
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Johnson AP Handbook of Chemoinformatics, 2003

Saunders SM, Pascoe S, Johnson AP, Pilling MJ, Jenkin M Development and preliminary test results of an expert system for the automatic generation of tropospheric VOC degradation mechanisms Atmospheric Environment 37 1723-1735, 2003

Zsoldos Z, Johnson AP, Simon A, Szabo I, Szabo Z eHiTS: Novel algorithm for fast, exhaustive flexible ligand docking and scoring. ABSTR PAP AM CHEM S 224 U339-U339, 2002

Zsoldos Z, Johnson AP, Simon A, Szabo I, Szabo Z eHiTS: Novel algorithm for fast, exhaustive flexible ligand docking and scoring Abstracts of Papers of the American Chemical Society 224 pp.005-, 2002

Cosgrove D, Bayada DM, Johnson AP A novel method of aligning molecules by local surface shape similarity Journal of Computer - Aided Molecular Design 14 573-591, 2000

Szabo Z, Johnson AP, Vargyas M Novel treatment of conformational flexibility using interval analysis. Journal of Chemical Information and Computer Sciences 40 339-346, 2000

Ting A, McGuire R, Johnson AP, Green SM Expert system assisted pharmacophore identification Journal of Chemical Information and Computer Sciences 40 347-353, 2000

Pleynet DPM, Dutton JK, Johnson AP A new synthesis of hindered spiro-oxindoles by photolysis of 1- (1-alkenyl) benzotriazoles and its application to the synthesis of the alkaloid gelsemine Abstracts of Papers of the American Chemical Society 217 pp.538-, 1999

Dutton JK, Pleynet DPM, Johnson AP Synthesis of hindered spiro-oxindoles by photolysis of 1-(1-Alkenyl)benzotriazoles Tetrahedron 55 11927-11942, 1999

Johnson AP, Leach AR, Marchaland JF, Szabo Z, Vargyas M Structure based selection of combinatorial library subsets Abstracts of Papers of the American Chemical Society 217 pp.219-, 1999

Pleynet DPM, Dutton JK, Johnson AP A general synthesis of 1-(1-alkenyl)benzotriazoles Tetrahedron 55 11903-11926, 1999

Green SM, Johnson AP Computational tools for structure-based design In Computer simulation of biomolecular systems, theorectical and experimental applications , 1997

Johnson AP, Simon A Recent advances in the CLiDE project: Logical layout analysis of chemical documents. Journal of Chemical Information and Computer Sciences 37 109-116, 1997

Johnson AP, Luke RWA, Singh G, Boa AN Synthesis and reactions ofN,N-bis(1-trimethyl silyloxyalkyl)formamides: Preparation of (±)-Argemonine and (±)-Norargemonine. Royal Society of Chemistry. Journal: Perkin Transactions 1 9 907-913, 1996