Is There a Covalent Intermediate in the Viral Neuraminidase Reaction? A Hybrid Potential Free-Energy Study

Abstract

The neuraminidase from the influenza virus is essential for maintaining viral infectivity as it aids in the transmission of the virus between cells. Although there are large variations in the amino acid sequences of neuraminidases from different influenza strains, there are several amino acids in the active site region of the protein that are strictly conserved. This has raised hopes that a single neuraminidase inhibitor and, hence a drug, can be found that is effective against all influenza strains. In this paper, we examine with theoretical simulation techniques one aspect of the reaction catalyzed by the viral neuraminidase that could be important for inhibitor design studiesnamely, whether a covalently bound complex can be formed between the enzyme and the sialosyl cation intermediate that occurs during the reaction. We used a hybrid semiempirical quantum mechanical/molecular mechanical (QM/MM) potential in conjunction with potential of mean force calculations to determine the free-energy profiles for formation of the covalent intermediate and its hydrolysis to sialic acid and for the direct hydroxylation of the sialosyl cation to sialic acid. Ab initio QM calculations were used to check the validity of the semiempirical results. We find that direct hydroxylation of the sialosyl cation is the energetically preferred pathway but not by so much that the possibility of being able to design covalently bound inhibitors need be completely abandoned.

Multidimensional Tunneling, Recrossing, and the Transmission Coefficient for Enzymatic Reactions

“…65,66,70,71,79,98,106,157 Enzyme applications have been based on Warshel's quantized classical path (QCP) algorithm. 66 This is similar in many respects to MQCMD, but it is easier to quantize more than one atom.…”

“…The concept of potential of mean force 98,167,205,[387][388][389][390][391][392][393][394][395][396][397][398][399][400][401] (PMF) plays an important role in condensed-phase TST. The PMF is usually computed by classical mechanics as a function of a single coordinate, called the distinguished coordinate and here denoted z.…”

A microscopic view of substitution reactions solvated by ionic liquids

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Simulating enzyme reactions: Challenges and perspectives

“…59 for details), but they are computationally expensive and so further applications of this technique to enzyme reactions have been limited, although a study of a hydrogen transfer in the reaction catalyzed by the flu virus neuraminidase has also been published. 154 A number of techniques, other than path-integral methods, have been used to investigate quantum dynamical effects in enzyme reactions. Thus, in two recent articles, Alhambra et al employed semiempirical QM/MM potentials in conjunction with semiclassical variational TST to calculate the rates and the kinetic isotope effects (KIEs) for the proton transfer in the yeast enolase reaction 155 and the hydride transfer in liver alcohol dehydrogenase (LADH).…”