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Tubulin binding compounds are key players in orchestrating anticancer effects by modulating microtubule dynamics that in turn disrupts cell motility and promotes apoptosis. However, their clinical application is limited by high toxicity resulting from their lack of specificity for cancer cells. Consequently, identifying microtubule interacting agents that demonstrate higher specificity for tumor cells continues to be a key objective in the search for more effective cancer treatments. In this context, small tubulin binding peptides (22-35 amino acids) from some intermediate filaments (IFs) were reported to bind unassembled tubulin and disrupt microtubules. To date there are no structural studies on these peptides as it is difficult to crystallize IF proteins. To narrow this wide gap in knowledge, two such peptides corresponding to the tubulin binding sites of the IF protein Desmin were studied using molecular mechanics and molecular dynamics based techniques. This is the first report on the structural plasticity of these peptides and sheds light on the imperative role of non-covalent interactions in directing the secondary structures. These findings shall be significant in guiding and facilitating the future efforts of designing peptide based anti-mitotic drugs.