Integrated computational and automated flow synthesis platform for the rapid discovery of N-benzylpiperidine acetylcholinesterase inhibitors.
The principal constraint on early-stage medicinal chemistry in an academic setting is rarely the supply of chemical ideas, but the cycle time required to convert them into tested compounds. Here we benchmark an integrated platform that couples ensemble virtual screening, automated continuous-flow library synthesis with inline scavenging, and biological profiling. The platform was evaluated deliberately on a target-scaffold combination for which the pharmacology is already established: the N-benzylpiperidine carboxamide class, identified in our earlier virtual screening campaign against acetylcholinesterase (AChE)[1] and structurally anchored to the approved therapeutic donepezil (1). This choice makes platform performance, the measured variable. An 84-member virtual library was designed, triaged by ensemble docking, and synthesized on an automated flow platform; 54 members were isolated in ≥95% purity. Single-point screening at 5 μM identified ten compounds with ≥70% AChE inhibition, and dose-response determination against electric eel AChE (eeAChE) gave three sub-200 nM inhibitors: 69 (91 nM), 8 (93 nM) and 12 (117 nM), each exceeding galantamine (237 nM) and approaching donepezil (1, 42 nM) under identical assay conditions. Cytotoxicity against VERO cells was uniformly low (IC50 > 250 μM), giving selectivity indices above 2000. Molecular dynamics simulations and twelve single-crystal X-ray structures provide a structural basis for the observed structure-activity relationships, identifying a C-Br···O halogen bond to Asp72 as the origin of the ortho-bromo preference, and a binding-mode reversal that accounts for the loss of potency on benzylpiperazine extension. The complete cycle was executed in under three months by a three-person team. We report this as a measured platform capability rather than as accelerated drug discovery allowing the rapid generation of first-round leads.