Accurate de novo design of hyperstable constrained peptides.
Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks generally have shapes that have evolved to fit precisely into binding pockets on their targets. Such peptides can have excellent pharmaceutical properties, combining the stability and tissue penetration of small-molecule drugs with the specificity of much larger protein therapeutics. The ability to design constrained peptides with precisely specified tertiary structures would enable the design of shape-complementary inhibitors of arbitrary targets. Here we describe the development of computational methods for accurate de novo design of conformationally restricted peptides, and the use of these methods to design 18-47 residue, disulfide-crosslinked peptides, a subset of which are heterochiral and/or N-C backbone-cyclized. Both genetically encodable and non-canonical peptides are exceptionally stable to thermal and chemical denaturation, and 12 experimentally determined X-ray and NMR structures are nearly identical to the computational design models. The computational design methods and stable scaffolds presented here provide the basis for development of a new generation of peptide-based drugs.
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.|Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.
Gaurav
G
Bhardwaj
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.|Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.
Vikram Khipple
VK
Mulligan
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.|Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.
Christopher D
CD
Bahl
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.|Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.
Jason M
JM
Gilmore
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
Peta J
PJ
Harvey
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
Olivier
O
Cheneval
Seattle Structural Genomics Center for Infectious Diseases, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.
Garry W
GW
Buchko
Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA.
Surya V S R K
SV
Pulavarti
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
Quentin
Q
Kaas
Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA.
Alexander
A
Eletsky
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.|Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.
Po-Ssu
PS
Huang
Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
William A
WA
Johnsen
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.|Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.|Global Research, Novo Nordisk A/S, DK-2760 Måløv, Denmark.
Per Jr
PJ
Greisen
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.|Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.
Gabriel J
GJ
Rocklin
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.|Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.|Cyrus Biotechnology, Seattle, Washington 98109, USA.
Yifan
Y
Song
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.|Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.
Thomas W
TW
Linsky
Department of Chemistry, New York University, New York, New York 10003, USA.
Andrew
A
Watkins
Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.
Stephen A
SA
Rettie
Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA.
Xianzhong
X
Xu
Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.
Lauren P
LP
Carter
Department of Biology, New York University, New York, New York 10003, USA.|Center for Computational Biology, Simons Foundation, New York, New York 10010, USA.
Richard
R
Bonneau
Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
James M
JM
Olson
Applied Mathematics and Statistics and Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA.
Evangelos
E
Coutsias
Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
Colin E
CE
Correnti
Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260, USA.
Thomas
T
Szyperski
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
David J
DJ
Craik
Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.|Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA.|Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.
David
D
Baker
D020816:Amino Acid Motifs; D017076:Computer-Aided Design; D018360:Crystallography, X-Ray; D003500:Cyclization; D004220:Disulfides / Q000737:chemistry; D015195:Drug Design; D006358:Hot Temperature; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D010455:Peptides / Q000138:chemical synthesis* / Q000737:chemistry* / Q000235:genetics; D010456:Peptides, Cyclic / Q000737:chemistry / Q000235:genetics; D011489:Protein Denaturation; D055550:Protein Stability; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013237:Stereoisomerism
D004220:Disulfides; D010455:Peptides; D010456:Peptides, Cyclic