Comprehensive computational design of ordered peptide macrocycles

Abstract

Mixed-chirality peptide macrocycles such as cyclosporine are among the most potent therapeutics identified to date, but there is currently no way to systematically search the structural space spanned by such compounds. Natural proteins do not provide a useful guide: Peptide macrocycles lack regular secondary structures and hydrophobic cores, and can contain local structures not accessible with L-amino acids. Here, we enumerate the stable structures that can be adopted by macrocyclic peptides composed of L- and D-amino acids by near-exhaustive backbone sampling followed by sequence design and energy landscape calculations. We identify more than 200 designs predicted to fold into single stable structures, many times more than the number of currently available unbound peptide macrocycle structures. Nuclear magnetic resonance structures of 9 of 12 designed 7- to 10-residue macrocycles, and three 11- to 14-residue bicyclic designs, are close to the computational models. Our results provide a nearly complete coverage of the rich space of structures possible for short peptide macrocycles and vastly increase the available starting scaffolds for both rational drug design and library selection methods.

Ordered and Isomerically Stable Bicyclic Peptide Scaffolds Constrained through Cystine Bridges and Proline Turns

“…These peptides have ac onserved cysteine/prolinef ramework for directing the oxidative folding into af used bicyclic structure that consists of four irregular turns and a3 10 helix (characterized by NMRs pectroscopy). [5] Our work demonstrates the feasibility of mutuallym anipulatingp recise disulfide pairing and proline residues to design ordered peptideb icycles withoutr egular secondary structures and hydrophobic cores, which thus could inspiret he design of novel bicyclic peptides caffolds and the selection of new bicyclic peptide ligands and therapeutics.We serendipitously discovered that ag roup of sequences from the selection of ap hage-encoded peptide library [8] of the format CXCX 5 CX 5 Ca gainst ap rotein target MDM2 can regioselectively fold into as ingle isomer (i.e.,r ibbon-typed isulfide connectivity;i dentified by orthogonal protecting group synthesis and NMR characterization) with > 90 %y ields (Figure 1, Figures S1 and S2 in the Supporting Information). In turn, this could inspire the design and engineering of multicyclic peptides with new structures and benefit the development of novel protein binders and therapeutics.…”

“…[5] Our work demonstrates the feasibility of mutuallym anipulatingp recise disulfide pairing and proline residues to design ordered peptideb icycles withoutr egular secondary structures and hydrophobic cores, which thus could inspiret he design of novel bicyclic peptides caffolds and the selection of new bicyclic peptide ligands and therapeutics. We show that the uniquef ramework of cysteine and proline( i.e., CPCX 5 CPX 4 C; Xi sa ny residue except cysteine) can precisely direct the oxidative folding of peptides into ar ibbon-type disulfidec onnectivity.N MR structural characterizations and mutational analyses unveiled ak ey role for proline-stabilized structures in the precise pairing of cysteiner esidues andt he ultimate ordered bicyclic structure.…”

“…The variable regions( i.e.,n onconserved residues) contain residues covering almost all typeso fa mino acids (Figure 5A), thus indicating that these residues are tolerant to mutations. [2][3][4][5][6][7][8][9][10][11][12][13][14][15][16]. Therefore, we examined whether substituting these residues in pb-13 to alaninea ffected the oxidative fold- Figure 2.…”

“…[8] The second benefits from recent developments in computational peptided esigns [5] that mightb ea ble to de novo designp otent bicyclic bindersb yt aking advantage of structural informationa tp rotein-protein binding interfaces. There are two promising paths forwards for development.…”

Neue Methoden und Designprinzipien für zellgängige Peptide

“…[68,75,82,[134][135][136] Kürzlich verwendeten die Autoren diesen Ansatz, um eine obere Grenze fürdie passive Zellpenetration zu ermitteln, die bei einem Molekülvolumen von etwa 1500 3 liegt, entsprechend 1000-1200 Da, je nach Kompaktheit der Struktur. [138][139][140] In welchem Umfang kçnnen polare Seitenketten in diese strukturierten Makrocyclen eingebaut werden, ohne dass die passiven Zellpenetration leidet? [135] Bemerkenswerterweise deckt sich dieses Ergebnis mit den Tr ends,d ie bei oral absorbierten "beyond-rule-of-5"-Wirkstoffen sowie bei zellgängigen, nicht-peptidischen Makrocyclen beobachtet wurden.…”