Computational Investigation into Catalytic Mechanisms of Disease-Causing Enzymes and Biocatalysts

Abstract

Computational chemistry, namely the ONIOM method, is used to investigate areas of interest to drug design, including malaria and inflammation, as well as biocatalysts for the hydration of nitrile substrates.

With the risk of malarial resistance reaching catastrophic levels, novel methods into the inhibition of this disease need to be prioritized. The current work uses high performance docking methods to model different substrates binding into the active sites of varying homo sapien and Plasmodium peptidyl-prolyl cis/trans isomerase enzymes and compares their subsequent docking scores. This approach has shown that the substrates ILS-920 and WYE-592 will bind less-favourably with hFKBP12 and PfFKBP35 compared to a competing substrate rapamycin; however, the binding appears to be more favourable in PvFKBP35. This could suggest a possible target for inhibition of the Plasmodium vivax parasite. Alternatively, the exploitation of active site differences between parasitic and human peptidyl-prolyl cis/trans isomerases can be used for suicide inhibition of malaria, effectively poisoning the parasite without affecting the patient. This method of inhibition was explored using Plasmodium falciparum and Homo sapien Fk506-binding proteins as templates for quantum mechanics/molecular mechanics calculations. Modification of the natural substrate has shown suicide inhibition is a valid approach for novel anti-malarials with little risk for parasitic resistance.

Leukotrienes are a family of drug-like molecules involved in the pathobiology of bronchial asthma and are responsible for smooth muscle contraction. Leukotriene C4 synthase is a nuclear-membrane enzyme responsible for the conjugation of leukotriene A4 (LTA4) to glutathione to form LTC4, a cysteinyl leukotriene. The mechanism of LTA4 binding by LTC4S has been computationally examined. Within the present computational methodology the ‘tail-to-head’ orientation appears to be the most likely substrate orientation. The mechanism by which LTB4 is synthesized by LTA4 hydrolase is also studied. The current proposed mechanism is unable to provide realistic Gibbs energy barriers for LTB4 synthesis.

The catalytic mechanisms for nitrile hydratase is explored, involving cysteine-sulfenic acid acting as a nucleophile, activating a water molecule to attack nitrile and isonitrile substrates. For the nitrile substrate, the iminol intermediate undergoes tautomerization to form the amide product. The computed enthalpies are closely related to experimental values, suggesting the current mechanism with two water molecules should be further investigated. For the isonitrile substrate, the first steps offer realistic enthalpy values for enzymatic mechanisms; however, the calculations should be repeated with a second water molecule, as it will likely lower enthalpy barriers further.