In a previous study, a catalyst (A) was discovered for oxidative decarboxylation of melanin-concentrating hormone (MCH). To explain the catalytic action and to predict the structure of a new catalyst with improved activity, docking simulations were carried out for the complex formed between A and MCH. The simulations suggested that the three terminal groups of A form a hydrophobic pocket and that van der Waals interactions between the hydrophobic pocket and MCH play a role in stabilizing the MCH-A complex. Consequently, a new catalyst (B) was designed and synthesized in expectation of improved catalytic activity resulting from enhanced van der Waals interactions. The new catalyst, however, showed slightly lower catalytic activity. Lack of the accurate solution structure of MCH may be one of the factors associated with difficulties in prediction of improvement in catalytic activity by purely theoretical means. The results, however, revealed that variation of the acyl portion of the hydroxyproline portion may lead to improved catalysts.