Sialidase crystal structure

Importantly, the crystal structure of 34 complexed with N9 sialidase (Fig. 8) indicated differences in the orientation of the guanidino group in subsite S2, and in its interaction with the active site residues, compared to that of zanamivir (Babu et al. 2000). These differences have implications for cross-reactivity of 34 with zanamivir-resistant influenza viruses that have Glul 19 mutations in the sialidase S2 subsite (see Sect. 5.1). 

Fig. 8 Superimposition of inhibitors and key active site residues in influenza A virus sialidase cyclopentane-based inhibitor peramivir 34 (brown carbons, PDB - 117f), Neu5Ac2en 4 (green carbons, PDB - lf8b). Note the overlap of the carboxyl and acetamido-methyl groups of the inhibitors, and the alternative conformations of the side-chain of Glu276. To the right is shown peramivir 34 oriented as in the crystal structure...

Chavas LMG, Tringah C, Fusi P, Venerando B, Tettamanti G, Kato R, Monti E, Wakatsuki S (2005) Crystal structure of the human cytosolic sialidase Neu2. Evidence for the dynamic nature of substrate recognition. J Biol Chem 280 469-475... 

The X-ray crystal structure of virus sialidase was first solved in early 1980s.24,25 While the active site could be identified, resolution was insufficient to determine the orientation of the bound ligand (Neu5Ac) within the catalytic center. Subsequent efforts in protein crystallography allowed further refinement... 

Fig. 5. The important interactions of Zanamivir (1) with the active site of influenza virus A sialidase.70 This figure was generated from crystal structure data (PDB-1NNC) using LIGPLOT.63...

The lipase-catalysed hydrolysis of methyl 2-fluoro-2-arylpropionates was proposed to proceed via a mechanism whereby, after ester hydrolysis, the enzyme facilitates the elimination of fluoride ion with the formation of a carbocation stabilized by the adjacent C02 group.230 Determination of the crystal structure of human sialidase Neu2, an enzyme that catalyses the hydrolysis of sialic acids, reveals a tyrosine residue that is positioned in the active site to stabilize the carbocation proposed as an intermediate in the hydrolysis.231 ll-Fluoro-all-frans-retinol is found to undergo isomerization to its 11 -cis form in the presence of visual cycle enzymes, in contrast to a previous study where no isomerization was reported.232 The result of the prior study was taken as evidence for a carbonium ion pathway in the isomerization. Although the authors of the present study do not rule out such a mechanism, they suggest that the isomerization mechanism remains unknown. Data obtained in a study of the oxidation of... 

X-ray crystal structure studies of influenza A/N2, A/N9, and B sialidases bound with a-Neu5Ac [66] show that the active site contains 18 invariant amino acid residues that either interact with the bound a-Neu5Ac or support these residues. These residues are conserved in all strains of influenza A and B viruses, suggesting their involvement in the enzymatic activity [65,66], The residues helped define the topology of the active site [66, 67], Of those conserved amino acids interacting with the substrate, many are polar, but there are also a number of nonpolar residues... 

X-ray crystal structures of a-Neu5Ac and 11 in complex with influenza virus sialidases in the 1980s and early 1990s led to the opportunity for structure-based design and development of influenza virus sialidase inhibitors [66, 85],... 

An X-ray crystal structure of peramivir (24) in complex with influenza A N9 showed interactions of the 3-pentyl group with S4 and S5 [117]. Due to the different stereochemistry of the guanidino moiety of 24 compared to zanamivir, a water molecule was displaced from S2 when 24 was bound. The different binding mode of the guanidine moiety within the active site provided the reason by which 24 showed inhibitory activity also for zanamivir-resistant influenza virus sialidase strains [117,120], Compound 24, which showed comparable or better efficacy in vivo than zanamivir and oseltamivir [121, 122], successfully completed animal studies and is in phase III clinical trials. 

A number of C-4-substituted 2,3-didehydro derivatives show significant inhibition of influenza A and B virus sialidase. The C-4 amino derivative (163) was originally targeted as a potential inhibitor of influenza virus sialidase based on molecular modelling studies of the X-ray crystal structure of influenza A virus sialidase [189-191]. 

A. Buschiazzo, M. F. Amaya, M. L. Cremona, A. C. C. Frasch, and P. M. Alzari, The crystal structure and mode of action of trans-sialidase, a key enzyme in Trypanosoma cruzi pathogenesis, Mol. Cell,... 

The computer-aided design of potent inhibitors of influenza virus sialidase based on a crystal structure of the enzyme has been described. A combination of manual molecular graphics analysis and the de novo ligand design tool GRID was used to identify modifications to the... 

Sialidases (Neuraminidases). The three sialidase families (GH 33, 34 and 83) all have the same catalytic machinery, an aspartate, which appears to act as a proton donor, and a probable nucleophilic tyrosine, rather than a carboxylate, activated in all likelihood by a glutamate. GH 33 contains all transialidases as well as simple hydrolytic enzymes, whereas GH 34 and GH 83 contain only enzymes from viruses which are mammalian or avian pathogens. GH 33 and GH 34 act with retention of the anomeric configuration and it is currently assumed that GH 83 is similar. Obtaining crystal structures with mechanistically informative ligands bound is complicated by the facility with which sialidases dehydrate A -acetylneuraminic acid to its 2,3-dehydro derivative, DANA the process is most facile with GH 33 enzymes. The influenza sialidase in GH 34 was more amenable and not only bound the minor anomer of NANA, but bound it in the conformation. Structures of GH 83 sialidases are available only with uninformative ligands such as p-NANA bound. 

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