Modeled library of Ganglioside GM3 analogues with structural modification at different R positions were substituted to the original structure of GM3. Their molecular interactions and binding affinities with Staphylococcal Enterotoxin B (SEB) and Endoglycoceramidase II of Rhodococcus Sp. have been computationally studied using the docking-molecular mechanics based generalized Born/surface area (MM-GB/SA) solvation model. The absorption, distribution, metabolism and excretion (ADME) properties are considered for the final screening of these analogues. The proposed GM3 analogues are docked into the active site of Staphylococcal Enterotoxin B (SEB) and Endoglycoceramidase II of Rhodococcus Sp. These analogues qualify ADME properties and showed suitable drugable characters. The present work shed more light to modify the different R substituent in the GM3 scaffold to model and prepare synthetic analogues for drug development against the bacterial toxin Staphylococcal Enterotoxin B and Endoglycoceramide II from Rhodococcus sp.