title: Understanding the molecular mechanism of aryl acylamidase activity of acetylcholinesterase - An in silico study.
abstract: Acetylcholinesterase (AChE) exhibits two different activities, namely esterase and aryl acylamidase (AAA). Unlike esterase, AAA activity of AChE is inhibited by the active site inhibitors while remaining unaffected by the peripheral anionic site inhibitors. This differential inhibitory pattern of active and peripheral anionic site inhibitors on the AAA activity remains unanswered. To answer this, we investigated the mechanism of binding and trafficking of AAA substrates using in silico tools. Molecular docking of serotonin and AAA substrates (o-nitroacetanilide, and o-nitrotrifluoroacetanilide,) onto AChE shows that these compounds bind at the side door of AChE. Thus, we conceived that the AAA substrates prefer the side door to reach the active site for their catalysis. Further, steered molecular dynamics simulations show that the force required for binding and trafficking of the AAA substrate through the side door is comparatively lesser than their dissociation (900kJ/mol/nm). Among the two substrates, o-nitrotrifluoroacetanilide required lesser force (380kJ/mol/nm) than o-nitroacetanilide the (550kJ/mol/nm) for its binding, thus validating o-nitrotrifluoroacetanilide as a better substrate. With these observations, we resolve that the AAA activity of AChE is mediated through its side door. Therefore, binding of PAS inhibitors at the main door of AChE remain ineffective against AAA activity.
authors.affiliation: Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India.
authors.forename: Raj Kumar
authors.initials: RK
authors.lastname: Chinnadurai
authors.affiliation: Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India.
authors.forename: Ponne
authors.initials: P
authors.lastname: Saravanaraman
authors.affiliation: Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India. Electronic address: boopathybiotech@gmail.com.
authors.forename: Rathanam
authors.initials: R
authors.lastname: Boopathy
mesh_terms: D000083:Acetanilides / Q000737:chemistry*; D000110:Acetylcholinesterase / Q000737:chemistry*; D000581:Amidohydrolases / Q000737:chemistry*; D002093:Benzenaminium, 4,4'-(3-oxo-1,5-pentanediyl)bis(N,N-dimethyl-N-2-propenyl-), Dibromide / Q000737:chemistry; D020134:Catalytic Domain; D002800:Cholinesterase Inhibitors / Q000737:chemistry*; D006801:Humans; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011419:Propidium / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D012701:Serotonin / Q000737:chemistry; D040681:Structural Homology, Protein; D013816:Thermodynamics
chemical_list: C539847:2-nitrotrifluoroacetanilide; D000083:Acetanilides; D002800:Cholinesterase Inhibitors; D012701:Serotonin; D011419:Propidium; D002093:Benzenaminium, 4,4'-(3-oxo-1,5-pentanediyl)bis(N,N-dimethyl-N-2-propenyl-), Dibromide; D000110:Acetylcholinesterase; D000581:Amidohydrolases; C019732:aryl acylamidase; C539848:2-nitroacetanilide
keywords: Acetylcholinesterase; Aryl acylamidase; Side door; Steered molecular dynamics; o-Nitroacetanilide; o-Nitrotrifluoroacetanilide