Construction and conformational behavior of peptoids with cis-amide bond geometry: design of a peptoid with alternate φ, ψ values of inverse PP-II/PP-II and PP-I structures.

In peptoids due to the absence of amide protons, the backbone is devoid of hydrogen bond donor, linked by tertiary amide, which can be iso-energetic between cis and trans-amide bond geometry. The peptoids can be realized with cis amide bond if the side chain of ith residue can engage the carbonyl group of ith-1 residue in CH--O interactions. Simulations studies both in water and DMSO have been carried out. The peptoid Ac-(N(tle))(7) -NMe(2) can adopt degenerate conformations with alternate φ, ψ values of inverse PP-I and PP-I type structure's, or vice versa in water. In DMSO, Ac-(N(tle))(7)-NMe(2) also adopts inverse PP-I type structure. Like polyproline, molecule adopting a rigid structure can be used as molecular markers or spacers in biological studies.The peptoid Ac-(N(ala)-N(tle))(3)-NMe(2) with alternate trans and cis amide bond geometry for N(ala) and N(tle) residue corresponding to inverse PP-II/PP-II type and for N(tle) residue of PP-I type.