ABSTRACT
Bioactive compounds oftentimes bind to several target proteins, thereby exhibiting polypharmacology. Experimentally determining these interactions is however laborious, and structure-based virtual screening (SBVS) of bioactive compounds could expedite drug discovery by prioritizing hits for experimental validation. Here, we present ePharmaLib, a library of 15,148 e-pharmacophores modeled from solved structures of pharmaceutically relevant protein-ligand complexes of the screening Protein Data Bank (sc-PDB). ePharmaLib can be used for target fishing of phenotypic hits, side effect predictions, drug repurposing, and scaffold hopping. In retrospective SBVS, a good balance was obtained between computational efficiency and predictive accuracy. As a proof of concept, we carried out prospective SBVS in conjunction with a photometric assay, which inferred that the mechanism of action of neopterin (an endogenous immunomodulator) putatively stems from its inhibition (IC50 = 18 µM) of the human purine nucleoside phosphorylase. This ready-to-use library is freely available at http://www.pharmbioinf.uni-freiburg.de/epharmalib.
Subject(s)
Drug Discovery , Polypharmacology , Databases, Protein , Humans , Ligands , Prospective Studies , Retrospective StudiesABSTRACT
Polyphosphate kinases (PPKs) are involved in many metabolic processes; enzymes of the second family (PPK2) are responsible for nucleotide synthesis fuelled by the consumption of inorganic polyphosphate. They catalyse the phosphorylation of nucleotides with various numbers of phosphate residues, such as monophosphates or diphosphates. Hence, these enzymes are promising candidates for cofactor regeneration systems. Besides adenosine 5'-triphosphate, PPK2s also catalyse the synthesis of highly phosphorylated nucleotides in vitro, as shown here for adenosine 5'-tetraphosphate and adenosine 5'-pentaphosphate. These unusually phosphorylated adenosine 5'-polyphosphates add up to 50 % of the whole adenosine nucleotides in the assay. The two new products were chemically synthesised to serve as standards and compared with the two enzymatically produced compounds by high-performance ion chromatography and 31 Pâ NMR analysis. This study shows that PPK2s are highly suitable for biocatalytic synthesis of different phosphorylated nucleotides.
Subject(s)
Adenosine Monophosphate/metabolism , Phosphotransferases (Phosphate Group Acceptor)/metabolism , Polyphosphates/metabolism , Adenosine Monophosphate/chemistry , Catalysis , Substrate SpecificityABSTRACT
Most Gram-negative phytopathogenic bacteria inject type III effector (T3E) proteins into plant cells to manipulate signaling pathways to the pathogen's benefit. In resistant plants, specialized immune receptors recognize single T3Es or their biochemical activities, thus halting pathogen ingress. However, molecular function and mode of recognition for most T3Es remains elusive. Here, we show that the Xanthomonas T3E XopH possesses phytase activity, i.e., dephosphorylates phytate (myo-inositol-hexakisphosphate, InsP6), the major phosphate storage compound in plants, which is also involved in pathogen defense. A combination of biochemical approaches, including a new NMR-based method to discriminate inositol polyphosphate enantiomers, identifies XopH as a naturally occurring 1-phytase that dephosphorylates InsP6 at C1. Infection of Nicotiana benthamiana and pepper by Xanthomonas results in a XopH-dependent conversion of InsP6 to InsP5. 1-phytase activity is required for XopH-mediated immunity of plants carrying the Bs7 resistance gene, and for induction of jasmonate- and ethylene-responsive genes in N. benthamiana.
Subject(s)
6-Phytase/metabolism , Bacterial Proteins/metabolism , Phytic Acid/metabolism , Xanthomonas campestris/metabolism , 6-Phytase/genetics , Amino Acid Sequence , Bacterial Proteins/genetics , Bacterial Secretion Systems/genetics , Bacterial Secretion Systems/metabolism , Biocatalysis , Disease Resistance/genetics , Inositol Phosphates/metabolism , Kinetics , Phosphorylation , Plant Cells/metabolism , Plant Cells/microbiology , Plant Diseases/genetics , Plant Diseases/microbiology , Sequence Homology, Amino Acid , Substrate Specificity , Xanthomonas campestris/genetics , Xanthomonas campestris/physiologyABSTRACT
A series of [5]helicenes difunctionalized in the fjord region with either fluoro, methoxy, or methyl groups was synthesized via photochemical and benzylic coupling route. Resolution of each compound into enantiomers and determination of the Gibbs activation energies of enantiomerization (ΔG⧧(T)) revealed high configurational stability in all three cases. The ΔG⧧(T) values of difunctionalized [5]helicenes were compared with those of their monofunctionalized analogues and the parent [5]helicene. Within this series, an exponential correlation between the torsional twist and ΔG⧧(T) was found. The dimethyl derivative exhibits one of the highest configurational stabilities among [n]helicenes reported to date, comparable to that of [9]helicene.
