N-methyl-D-aspartate (NMDA) receptors constitute the major subtype of glutamate receptors and normally participate in rapid excitatory synaptic transmission. Furthermore, the overstimulation of NMDA receptors allows an excessive Ca2+ influx through the receptor channels, contributing to ischemic neuronal death. The complex GluN1/GluN2B containing NMDA receptors plays an important role in ischemia. Here we designed peptides based on the interaction of the GluN2B-subunit with proteins DAPK1, SRC, D2R and the toxin Conantokin G. The DAPK1 protein has a direct interaction with the S1303 of the intracellular carboxyl terminal tail of GluN2B. This interaction causes excessive Ca2+ influx and acts as a central mediator for stroke damage. D2R and SRC have similar functions to DAPK1 by interaction with S1303 and Y1472 respectively. On the other hand, Conantokin G, a cone snail toxin, is an antagonist of NMDA receptor and selective for the residue M739 of GluN2B subunit. The identification of binding sites between the molecules mentioned above and the GluN2B subunit allowed the design of peptides that would block the interaction and toxic effect generated. The peptide sequence was obtained from each area of interaction between the protein and GluN2B subunit. We generated a model for each peptide using the I-Tasser server and also built a model for proteins that did not have PDB structures. The use of in silico High-throughput ligand mutation scanning and receptor-ligand docking protocol allowed the binding energy evaluation of each receptor-ligand pair. The rational selection from the energy ranked pairs provides new putative peptides, which would have a better efficiency of binding to the ischemia related proteins studied herein.