c[D‐pro‐Pro‐D‐pro‐N‐methyl‐Ala] adopts a rigid conformation that serves as a scaffold to mimic reverse‐turns

Abstract

Naturally occurring cyclic tetrapeptides (CTPs) such as tentoxin (Halloin et al., Plant Physiol 1970, 45, 310-314; Saad, Phytopathology 1970, 60, 415-418), ampicidin (Darkin-Rattray, Proc Natl Acad Sci USA 1996, 93, 13143-13147), HC-toxin (Walton, Proc Natl Acad Sci USA 1987, 84, 8444-8447), and trapoxin (Yoshida and Sugita, Jpn J Cancer Res 1992, 83, 324-328; Itazaki et al., J Antibiot (Tokyo) 1990, 43, 1524-1532) have a wide range of biological activity and potential use ranging from herbicides (Walton, Proc Natl Acad Sci USA 1987, 84, 8444-8447; Judson, J Agric Food Chem 1987, 35, 451-456) to therapeutics (Loiseau, Biopolymers 2003, 69, 363-385) for malaria (Darkin-Rattray, Proc Natl Acad Sci USA 1996, 93, 13143-13147) and cancer (Yoshida and Sugita, Jpn J Cancer Res 1992, 83, 324-328). To elucidate scaffolds that have few low-energy conformations and could serve as semirigid reverse-turn mimetics, the flexibility of CTPs was determined computationally. Four analogs of cyclic tetraproline c[Pro-pro-Pro-pro] with alternating L- and D-prolines, namely c[pro-Pro-pro-NMe-Ala], c[pip-Pro-pip-Pro], c[pro-Pip-pro-Pro], and c[Ala-Pro-pip-Pro] were synthesized and characterized by NOESY NMR. Both molecular mechanics and Density Functional Theory quantum calculations found these head-to-tail CTPs to be constrained to one or two relatively stable conformations. NMR structures, while not always yielding the same lowest energy conformation as expected by in silico predictions, confirmed only one or two highly populated solution conformations for all four peptides examined. c[pro-Pro-pro-NMe-Ala] was shown to have a single all trans-amide bond conformation from both in silico predictions and NMR characterization, and to be a reverse-turn mimetic by overlapping four Calpha-Cbeta bonds with those for approximately 6.5% (Tran, J Comput Aided Mol Des 2005, 19, 551-566) of reverse-turns in the Protein Data Bank PDB with a RMSD of 0.57 A.

Limiting Assumptions in the Design of Peptidomimetics

“…The all trans c[pro‐Pro‐pro‐NMe‐Ala] is overlapped (0.57 A° RMSD) by all 4 CαCβ bonds in Tran et al's cluster 6 [Tran et al, ] which mainly represents classical β‐turn Type I conformers. Figure adapted from Arbor et al []. [Color figure can be viewed at http://wileyonlinelibrary.com]…”

“…CTPs containing proline and N-Meamino acids with alternating chirality of the amino acids are highly constrained ( Fig. 7) [Arbor et al, 2008].…”

A virtual library of constrained cyclic tetrapeptides that mimics all four side-chain orientations for over half the reverse turns in the protein data bank

“…CTPs have been found useful as reverse-turn mimetics [7,24]. In order to determine if the energy landscape of The reverse turns in the PDB are shown split into categories by which Tran clusters they overlap with best (1-9).…”

“…Turns have been found critical in a range of macromolecular recognition motifs, such as integrin or interferon-c binding in biological systems ranging from cell adhesion [3] to antiviral agents [4], respectively. There has, therefore, been considerable effort to mimic reverse turns which has been accomplished by short linear peptides [5,6], cyclic peptides [7][8][9][10][11], and small molecules [7][8][9][10][11][12][13][14][15][16][17][18][19] such as benzodiazepines [9,[12][13][14][15][16], b-turn dipeptides (BTD) [20], indolizinoindole b-turn mimetic (IBTM) [20], and c and b-lactams [19]. The use of proline has long been known to help a peptide adopt a reverse-turn conformation [8].…”

“…In addition, cyclic tetrapeptides (CTPs) have been found to be inherently good mimics of reverse turns due to their *180°turn in all four of the sequential four-residue segments. Combination of alternating D and L prolines in CTPs have been found to be good reverse-turn mimetics [7,24] and also more synthetically feasible to cyclize head-to-tail due to the alternating D-and L-proline propensity to stabilize reverse turns which causes the backbone of the linear peptide to turn back upon itself.…”