Protein-protein interactions are involved in many biological events and the development of molecules targeting PPIs is one of the main goals of contemporary medicinal chemistry. Recently, much attention has been paid to the design of peptides containing non-natural amino acids (nnAAs) able to stabilize a certain secondary structure, often the right-handed helical one, in order to combine the high selectivity and specificity and low toxicity of well-designed peptides with the stability toward peptidases and proteases provided by the nnAAs. One of the most exploited classes of nnAAs is that of chiral Cα-tetrasubistuted amino acids (cCTAAs), which stabilize the helical secondary structure by limiting the backbone conformational freedom and induce a preferential helical screw sense in otherwise achiral peptides thanks to their side chains. However, although these cCTAAs are commonly used, rationales explaining the mechanisms of their helical stabilization and stereoselectivity are not well clarified. We started to fill this knowledge gap by performing REMD simulations, PMF and QTAIM calculations on selected Ac-L-Ala-cCTAA-L-Ala-Aib-L-Ala-NHMe and Ac-Aib2-cCTAA-Aib2-NHMe model peptides for the study of the mechanism of helical stabilization and helical stereoselectivity, respectively. We found that the inclusion of the selected cCTAAs in the former peptide model limits the backbone conformational freedom thanks to a steric hindrance predominantly located in the (+x,+y,-z) sector of a right-handed 3D-Cartesian space, where the +z → -z axis coincides with the N → C helical axis and the Cα of the cCTAA lies on the +y axis (0,+y,0), and the generation of additional intramolecular C-H···O interactions. Analogously, the stereoselectivity toward a particular screw sense of Ac-Aib2-cCTAA-Aib2-NHMe peptides is achieved thanks to the positioning of the cCTAAs' side chains in the (-x,+y,+z) and, at minor extent, in the (+x,+y,-z) sectors and to the presence of a strong C-H···O H-bonds network.

Use of Chiral Cα-Tetrasubstituted Amino Acids For Stabilizing The Geometry and Screw Sense of Helical Secondary Structures / I. Maffucci, S. Pellegrino, A. Contini - In: SBDD2015 - Computational Advances in Drug Discovery[s.l] : Ecole Polytecnique Fédérale de Lausanne, 2015 Sep.

Use of Chiral Cα-Tetrasubstituted Amino Acids For Stabilizing The Geometry and Screw Sense of Helical Secondary Structures.

I. Maffucci
Primo
;
S. Pellegrino
Secondo
;
A. Contini
Ultimo
2015-09

Abstract

Protein-protein interactions are involved in many biological events and the development of molecules targeting PPIs is one of the main goals of contemporary medicinal chemistry. Recently, much attention has been paid to the design of peptides containing non-natural amino acids (nnAAs) able to stabilize a certain secondary structure, often the right-handed helical one, in order to combine the high selectivity and specificity and low toxicity of well-designed peptides with the stability toward peptidases and proteases provided by the nnAAs. One of the most exploited classes of nnAAs is that of chiral Cα-tetrasubistuted amino acids (cCTAAs), which stabilize the helical secondary structure by limiting the backbone conformational freedom and induce a preferential helical screw sense in otherwise achiral peptides thanks to their side chains. However, although these cCTAAs are commonly used, rationales explaining the mechanisms of their helical stabilization and stereoselectivity are not well clarified. We started to fill this knowledge gap by performing REMD simulations, PMF and QTAIM calculations on selected Ac-L-Ala-cCTAA-L-Ala-Aib-L-Ala-NHMe and Ac-Aib2-cCTAA-Aib2-NHMe model peptides for the study of the mechanism of helical stabilization and helical stereoselectivity, respectively. We found that the inclusion of the selected cCTAAs in the former peptide model limits the backbone conformational freedom thanks to a steric hindrance predominantly located in the (+x,+y,-z) sector of a right-handed 3D-Cartesian space, where the +z → -z axis coincides with the N → C helical axis and the Cα of the cCTAA lies on the +y axis (0,+y,0), and the generation of additional intramolecular C-H···O interactions. Analogously, the stereoselectivity toward a particular screw sense of Ac-Aib2-cCTAA-Aib2-NHMe peptides is achieved thanks to the positioning of the cCTAAs' side chains in the (-x,+y,+z) and, at minor extent, in the (+x,+y,-z) sectors and to the presence of a strong C-H···O H-bonds network.
Settore CHIM/06 - Chimica Organica
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2434/325670
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