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496 a.a.
Key reference
DOI no: 10.1073/pnas.132060599 Proc Natl Acad Sci U S A 99:9127-9132 (2002) PubMed id: 12093900
High-resolution structures of a chitinase complexed with natural product cyclopentapeptide inhibitors: mimicry of carbohydrate substrate. D.R.Houston, K.Shiomi, N.Arai, S.Omura, M.G.Peter, A.Turberg, B.Synstad, V.G.Eijsink, D.M.van Aalten. ABSTRACT
Over the past years, family 18 chitinases have been validated as potential targets for the design of drugs against human pathogens that contain or interact with chitin during their normal life cycles. Thus far, only one potent chitinase inhibitor has been described in detail, the pseudotrisaccharide allosamidin. Recently, however, two potent natural-product cyclopentapeptide chitinase inhibitors, argifin and argadin, were reported. Here, we describe high-resolution crystal structures that reveal the details of the interactions of these cyclopeptides with a family 18 chitinase. The structures are examples of complexes of a carbohydrate-processing enzyme with high-affinity peptide-based inhibitors and show in detail how the peptide backbone and side chains mimic the interactions of the enzyme with chitooligosaccharides. Together with enzymological characterization, the structures explain why argadin shows an order of magnitude stronger inhibition than allosamidin, whereas argifin shows weaker inhibition. The peptides bind to the chitinase in remarkably different ways, which may explain the differences in inhibition constants. The two complexes provide a basis for structure-based design of potent chitinase inhibitors, accessible by standard peptide chemistry.
Selected figure(s)
Figure 2.
Fig. 2. Argifin and argadin complexed to ChiB. The previously published structure of mutationally inactivated ChiB (where the catalytic Glu-144 has been replaced with a glutamine) in complex with GlcNAc[5] (NAG[5]; ref. 17) is shown as a stereo stick model and compared with the ChiB-argifin and ChiB-argadin complexes. Unbiased (i.e., before including any inhibitor model) |F[o]F[c]|,
[calc] (contoured at 2.5
) maps are shown in orange. Ligand carbon atoms are colored purple. Side chains interacting with the cyclopentapeptides are shown in a sticks representation with carbons colored gray except for the catalytic residue 144, for which carbons are shown in yellow. Tyr-145 (which only hydrogen-bonds to GlcNAc[5]; see also Fig. 3) has been omitted to improve clarity. Water molecules hydrogen-bonding to both protein and inhibitor are shown as green spheres (hydrogen bonds are not shown). Hydrogen bonds between the ligands and the protein side chains are shown as black dotted lines. Argifin/argadin intramolecular hydrogens bonds are shown as green dotted lines. In the complex with GlcNAc[5], the sugar subsites are indicated by green labels.
Figure 3.
Fig. 3. Further details of inhibitor-ChiB interactions. Schematic protein-ligand interactions (Left, calculated with LIGPLOT; ref. 37) and surface plots are shown for three ChiB complexes. The ChiB-GlcNAc[5] (NAG[5]) complex (17) is shown, for comparison purposes, together with the ChiB-argifin and ChiB-argadin complexes described here. In the schematic drawings, only protein-ligand hydrogen bonds are shown (see key). For the complex with GlcNAc[5], only the central three sugars are shown. In the surface representations, the protein surface is colored gray with the exception of Trp-97 and Trp-220 (blue) and the catalytic acid Glu-144 (red). The ligands are shown in a sticks representation with carbons colored green. The sugar subsites are labeled in the GlcNAc[5] complex.Figures were selected by an automated process.
Literature references that cite this PDB file's key reference
PubMed id Reference
19329983 T.Hirose, T.Sunazuka, A.Sugawara, A.Endo, K.Iguchi, T.Yamamoto, H.Ui, K.Shiomi, T.Watanabe, K.B.Sharpless, and S.Omura (2009).
Chitinase inhibitors: extraction of the active framework from natural argifin and use of in situ click chemistry.J Antibiot (Tokyo), 62, 277-282.
19703025 V.Kairys, M.K.Gilson, V.Lather, C.A.Schiffer, and M.X.Fernandes (2009).
Toward the design of mutation-resistant enzyme inhibitors: further evaluation of the substrate envelope hypothesis.Chem Biol Drug Des, 74, 234-245.
18680214 C.Petter, C.Scholz, H.Wessner, G.Hansen, P.Henklein, T.Watanabe, and W.Höhne (2008).
Phage display screening for peptidic chitinase inhibitors.J Mol Recognit, 21, 401-409.
16526080 F.H.Cederkvist, A.D.Zamfir, S.Bahrke, V.G.Eijsink, M.Sørlie, J.Peter-Katalinić, and M.G.Peter (2006).
Identification of a high-affinity-binding oligosaccharide by (+) nanoelectrospray quadrupole time-of-flight tandem mass spectrometry of a noncovalent enzyme-ligand complex.Angew Chem Int Ed Engl, 45, 2429-2434.
16193156 O.A.Andersen, M.J.Dixon, I.M.Eggleston, and D.M.van Aalten (2005).
Natural product family 18 chitinase inhibitors.Nat Prod Rep, 22, 563-579.
14717693 B.Synstad, S.Gåseidnes, D.M.Van Aalten, G.Vriend, J.E.Nielsen, and V.G.Eijsink (2004).
Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase.Eur J Biochem, 271, 253-262.
15103145 H.Hu, G.Wang, H.Yang, J.Zhou, L.Mo, K.Yang, C.Jin, C.Jin, and Z.Rao (2004).
Crystallization and preliminary crystallographic analysis of a native chitinase from the fungal pathogen Aspergillus fumigatus YJ-407.Acta Crystallogr D Biol Crystallogr, 60, 939-940. The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.
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