Nanosized montmorillonite clay dispersed in small amounts in polymer results in polymer nanocomposites having superior engineering properties compared to those of the native polymer. These nanoinclusions are created by treating clay with an organic modifier which makes clay organophilic and results in intercalation or exfoliation of the montmorillonite. The modifiers used are usually long carbon chains with alkylammonium or alkylphosphonium cations. In this work, we have investigated the use of some alternative molecules which can act as modifiers for clay composites using clay for reinforcing a matrix of biopeptides or proteins. Such composites have potential applications in the fields of biomedical engineering and pharmaceutical science. In this work, the amino acids arginine and lysine are used as modifiers. The intercalation and mechanical behavior of the interlayer spacing with these amino acids as inclusions under compression and tension are studied using molecular dynamics simulations. Significant differences in the responses are observed. This work also provides an insight into the orientation and interaction of amino acids in the interlayer under different stress paths.