Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking...

Area of Science:

• Biochemistry
• Computational Chemistry
• Enzymology

Background:

• Acetylcholinesterase (AChE) is a crucial enzyme in neurotransmission, responsible for hydrolyzing acetylcholine (ACh).
• Understanding AChE's substrate binding specificity is vital for designing effective inhibitors and understanding its physiological role.

Purpose of the Study:

• To investigate the binding specificity of acetylcholinesterase (AChE) with its natural substrate acetylcholine (ACh) and related molecules.
• To elucidate the roles of the esteratic and anionic subsites in achieving substrate binding specificity.
• To explore the impact of induced fit on substrate binding and catalytic efficiency.

Main Methods:

• Employed a combined molecular dynamics simulation and multiple ligand docking approach.
• Calculated docking energies and correlated them with experimental kinetic and binding affinity data.
• Analyzed the structural changes and interactions within the AChE active site upon substrate binding.

Main Results:

• Docking energies showed good correlation with experimental k(cat)/K(M) values and binding affinities of TMTFA inhibitors.
• The esteratic and anionic subsites cooperatively determine substrate binding specificity.
• ACh binding induces a conformational change in AChE, stabilizing the catalytic triad and enhancing subsite interactions, yielding 0.7 kcal/mol docking energy gain.
• Substrate tailgroup size and positive charge are critical for binding to the anionic subsite, with charge removal weakening binding by 1 kcal/mol.

Conclusions:

• AChE achieves substrate specificity through the synergistic action of its esteratic and anionic subsites.
• Induced fit plays a significant role in optimizing ACh binding and catalytic setup.
• The structural features of the substrate, particularly the tailgroup's charge and size, are crucial for effective binding to the anionic subsite.