In molecular communication, the heavy tail nature of molecular signals causes inter-symbol interference (ISI). Because of this, it is difficult to decrease symbol periods and achieve high data rate. As a probable solution for ISI mitigation, enzymes were proposed to be used since they are capable of degrading ISI molecules without deteriorating the molecular communication. While most prior work has assumed an infinite amount of enzymes deployed around the channel, from a resource perspective, it is more efficient to deploy a limited amount of enzymes at particular locations and structures. This paper considers carrying out such deployment at two structures-around the receiver (Rx) and/or the transmitter (Tx) site. For both of the deployment scenarios, channels with different system environment parameters, Tx-to-Rx distance, size of enzyme area, and symbol period, are compared with each other for analyzing an optimized system environment for ISI mitigation when a limited amount of enzymes are available.