title: Oxime-dipeptides as anticholinesterase, reactivator of phosphonylated-serine of AChE catalytic triad: probing the mechanistic insight by MM-GBSA, dynamics simulations and DFT analysis.
abstract: Neuropathological cascades leading to reduced cholinergic transmission in Alzheimer's disease led to development of AChE-inhibitors. Although lethal dose of some inhibitors cause interruption with AChE mediated mechanism but reversible AChE inhibitors can assist in protection from inhibition of AChE and hence in an aim to probe potential molecules as anticholinesterase and as reactivators, computationally structure-based approach has been exploited in this work for designing new 2-amino-3-pyridoixime-dipeptides conjugates. We have combined MD simulations with flexible ligand docking approach to determine binding specificity of 2-amino-3-pyridoixime dipeptides towards AChE (PDB 2WHP). PAS residues are found to be responsible for oxime-dipeptides binding along with π-π interactions with Trp86 and Tyr286, hydrogen bonding with side chains of Asp74 and Tyr341 (Gscore -10.801 and MM-GBSA free energy -34.89 kcal/mol). The docking results depicted complementary multivalent interactions along with good binding affinity as predicted from MM-GBSA analysis. The 2-amino-3-pyridoxime-(Arg-Asn) AChE systems subjected to MD simulations under explicit solvent systems with NPT and NVT ensemble. MD simulations uncovered dynamic behavior of 2-amino-3-pyridoxime-(Arg-Asn) and exposed its mobile nature and competence to form strong long range-order contacts towards active site residues to approach inhibited serine residue and facilitated via large contribution from hydrogen bonding and water bridges along with slow and large movements of adjacent important residues. In an effort to evaluate the complete potential surface profile, 2-amino-3-pyridoxime induced reactivation pathway of sarin-serine adduct has been investigated by the DFT approach at the vacuum MO6/6-311G (d, p) level along with the Poisson-Boltzmann solvation model and found to be of relatively low energy barrier. The pKa evaluation has revealed the major deprotonated 2-amino-3-pyridoixime species having pKa of 6.47 and hence making 2-amino-3-pyridoxime-(Arg-Asn) potential anticholinesterase and reactivator for AChE under the physiological pH.
authors.affiliation: a Division of Cyclotron and Radiopharmaceutical Sciences , Institute of Nuclear Medicine and Allied Sciences , Brig. S. K. Mazumdar Road, Delhi 110054 , India.
authors.forename: Nidhi
authors.initials: N
authors.lastname: Chadha
authors.forename: Anjani K
authors.initials: AK
authors.lastname: Tiwari
authors.forename: Vikas
authors.initials: V
authors.lastname: Kumar
authors.forename: Sangeeta
authors.initials: S
authors.lastname: Lal
authors.forename: Marilyn D
authors.initials: MD
authors.lastname: Milton
authors.forename: Anil K
authors.initials: AK
authors.lastname: Mishra
mesh_terms: D000110:Acetylcholinesterase / Q000737:chemistry* / Q000378:metabolism; D000465:Algorithms; D001665:Binding Sites; D055162:Biocatalysis / Q000187:drug effects; D020134:Catalytic Domain; D002800:Cholinesterase Inhibitors / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D002801:Cholinesterase Reactivators / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D004151:Dipeptides / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008024:Ligands; D062105:Molecular Docking Simulation; D015394:Molecular Structure; D010091:Oximes / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012694:Serine / Q000737:chemistry / Q000378:metabolism
chemical_list: D002800:Cholinesterase Inhibitors; D002801:Cholinesterase Reactivators; D004151:Dipeptides; D008024:Ligands; D010091:Oximes; D012694:Serine; C022372:phosphonylated acetylcholinesterase; D000110:Acetylcholinesterase
keywords: Alzheimer’s disease; DFT; acetylcholinesterase; molecular dynamics; oxime