Recent technological innovations have led to the development of methods for the rapid identification of high-affinity macrocyclic peptides for a wide range of targets; however, it is still challenging to achieve the desired activity and membrane permeability at the same time. Here, we propose a novel small molecule lead discovery strategy, ″Peptide-to-Small Molecule″, which is a combination of rapid identification of high-affinity macrocyclic peptides <i>via</i> peptide display screening followed by pharmacophore-guided <i>de novo</i> design of small molecules, and demonstrate the applicability using nicotinamide <i>N</i>-methyltransferase (NNMT) as a target. Affinity selection by peptide display technology identified macrocyclic peptide <b>1</b> that exhibited good enzymatic inhibitory activity but no cell-based activity. Thereafter, a peptide pharmacophore-guided <i>de novo</i> design and further structure-based optimization resulted in highly potent and cell-active small molecule <b>14</b> (cell-free IC<sub>50</sub> = 0.0011 μM, cell-based IC<sub>50</sub> = 0.40 μM), indicating that this strategy could be a new option for drug discovery.