Molecular Docking, Metal Substitution and Hydrolysis Reaction of Chiral Substrates of Phosphotriesterase

Abstract

During World War II, organophosphorus compounds with neurotoxic action were developed and used as the basis for the development of structures currently used as pesticides in the agricultural industry. Among the nerve agents, Tabun, Sarin, Soman and VX are the most important. The factor responsible for the high toxicity of organophosphorus (OP) is the acetylcholinesterase inhibition. However, one of the characterized enzymes capable of degrading OP is Phosphotriesterase (PTE). This enzyme has generated considerable interest for applications of rapid and complete detoxification. Due to the importance of bioremediation methods for the poisoning caused by OP, this work aims to study the interaction mode between the PTE enzyme and organophosphorus compounds, in this case, Sarin, Soman, Tabun and VX have been used, which are potent acetylcholinesterase inhibitors, taking into account the enantiomers "Rp" and " Sp" of each compound, with the Sp-enantiomers presenting the higher toxicity. With that, we were able to demonstrate the existence of the stereochemical preference by PTE in these compounds. With the purpose of increasing the speed of the hydrolysis mechanism, we have proposed a modification in the enzyme active site structure, where Zn(2+) ions were substituted by Al(3+) ions. To analyze the stability of Al(3+) ions in the wild-type PTE active site, MD simulations were also performed. This mutation brought relevant results; in this case, there was a reduction of the reaction energy barrier for all the compounds, mainly for VX in which the reaction presented lower activation energy values, and consequently, a faster hydrolysis process.

Microbial Phosphotriesterase: Structure, Function, and Biotechnological Applications

“…The active site pocket of the PTE in a hydrophobic condition contains two metal ions (Zn 2+ Mn 2+ , Co 2+ , and Cd 2+ ) bridged with side-chains of histidine residues that are clustered around the metal atoms [22,27]. A number of the crystal structures of PTE isolated from bacteria such as Pseudomonas pseudoalcaligenes (2.1 Å), Pseudomonas diminuta (2.0 Å), Mycobacterium tuberculosis (2.27 Å), Agrobacterium radiobacter (1.99 Å), Geobacillus stearothermophilus (2.09 Å), and Geobacillus kaustophilus HTA426 (2.05 Å) have been determined [4,7,16,28,29]. In this review, three crystal structures of PTEs from Pseudomonas diminuta, Sphingobium fuliginis strain ATCC 27551, and Geobacillus stearothermophilus (PLL) are used as examples in this section to shown the similarities and differences in their 3D structure Figure 2.…”

“…In addition, mutation near the small pocket of PTE or Loop 7 using error prone PCR has also given reliable results where the mutant L7ep-3a enhanced a 600-fold (2.6 × 10 3 M −1 s −1 ) faster action in the detoxification of VR and VX nerve agents [40]. The substitution of the metal ion has also been done to identify the influence of the metal ion towards selectivity and stability of the PTE [4,22] Zinc is the native metal ion for PTE but can be substituted with other metals such as Co 2+ , Ni 2+ , Cd 2+ , or Mn 2+ to retain the catalytic activity [17]. The value of k cat /K m has been shown to decrease when the Zn 2+ /Zn 2+ (6.8 × 10 6 M −1 s −1 ) was substituted with Cd 2+ /Cd 2+ (1.32 × 10 6 M −1 s −1 ) and Zn 2+ /Cd 2+ (2.8 × 10 6 M −1 s −1 ) with paraoxon as the substrate, but not for parathion.…”

“…Contamination by these compounds may occur because of terrorist attacks, unsafe disposal methods, and spillage from poor handling by agricultural workers [2]. OP compounds are known to inhibit mammalian acetylcholinesterases (AChE) [3][4][5]. Acetylcholinesterase (AChE) is an enzyme that hydrolyzes the neurotransmitter acetylcholine (ACh) and serves as a regulator of neurotransmission [3].…”

Biotransformation of disperse dyes using nitroreductase immobilized on magnetic particles modified with tosyl group: Identification of products by LC-MS-MS and theoretical studies conducted with DNA

“…This methodology has exhibited significantly good performance in the treatment of large systems with high level of theory. The QM part was carried out at DFT level, with B3LYP functional density and 6-31G (d, p) basis set (de Castro et al, 2016;Sartorelli et al, 2016).…”

Theoretical Studies Applied to the Evaluation of the DFPase Bioremediation Potential against Chemical Warfare Agents Intoxication

“…Although there are certain resources available for treatment, there is not a universal antidote efficient against all existing OP agents. In this context, considering that the bioremediation is an expanding field, and that the knowledge about the wild-type DFPase enzyme has brought significant contributions for the medicinal chemistry, more studies become necessary [ 10 , 14 , 15 ]. Thus, this work uses theoretical molecular docking studies, supported by chemometric analyzes, along with computations such as quantum mechanics/molecular mechanics (QM/MM) to investigate the OP degradation through DFPase enzyme.…”