title: Genetically encoded fragment-based discovery of glycopeptide ligands for carbohydrate-binding proteins.
abstract: We describe an approach to accelerate the search for competitive inhibitors for carbohydrate-recognition domains (CRDs). Genetically encoded fragment-based discovery (GE-FBD) uses selection of phage-displayed glycopeptides to dock a glycan fragment at the CRD and guide selection of synergistic peptide motifs adjacent to the CRD. Starting from concanavalin A (ConA), a mannose (Man)-binding protein, as a bait, we narrowed a library of 10(8) glycopeptides to 86 leads that share a consensus motif, Man-WYD. Validation of synthetic leads yielded Man-WYDLF that exhibited 40-50-fold enhancement in affinity over methyl α-d-mannopyranoside (MeMan). Lectin array suggested specificity: Man-WYD derivative bound only to 3 out of 17 proteins—ConA, LcH, and PSA—that bind to Man. An X-ray structure of ConA:Man-WYD proved that the trimannoside core and Man-WYD exhibit identical CRD docking, but their extra-CRD binding modes are significantly different. Still, they have comparable affinity and selectivity for various Man-binding proteins. The intriguing observation provides new insight into functional mimicry of carbohydrates by peptide ligands. GE-FBD may provide an alternative to rapidly search for competitive inhibitors for lectins.
authors: †Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
authors: Simon
authors: S
authors: Ng
authors: †Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
authors: Edith
authors: E
authors: Lin
authors: †Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
authors: Pavel I
authors: PI
authors: Kitov
authors: †Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
authors: Katrina F
authors: KF
authors: Tjhung
authors: ‡Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6475, United States.
authors: Oksana O
authors: OO
authors: Gerlits
authors: †Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
authors: Lu
authors: L
authors: Deng
authors: §Biomedical Chemistry Institute, Department of Chemistry, New York University, New York, New York 10003, United States.
authors: Brian
authors: B
authors: Kasper
authors: ∥Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602,United States.
authors: Amika
authors: A
authors: Sood
authors: ⊥New England Biolabs, Ipswich, Massachusetts 01938, United States.
authors: Beth M
authors: BM
authors: Paschal
authors: #Alberta Glycomics Centre, Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
authors: Ping
authors: P
authors: Zhang
authors: #Alberta Glycomics Centre, Department of Chemistry, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
authors: Chang-Chun
authors: CC
authors: Ling
authors: †Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
authors: John S
authors: JS
authors: Klassen
authors: ⊥New England Biolabs, Ipswich, Massachusetts 01938, United States.
authors: Christopher J
authors: CJ
authors: Noren
authors: §Biomedical Chemistry Institute, Department of Chemistry, New York University, New York, New York 10003, United States.
authors: Lara K
authors: LK
authors: Mahal
authors: ∥Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602,United States.|∇School of Chemistry, National University of Ireland, Galway, University Road, Galway, Ireland.
authors: Robert J
authors: RJ
authors: Woods
authors: ‡Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6475, United States.
authors: Leighton
authors: L
authors: Coates
authors: †Alberta Glycomics Centre, Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada.
authors: Ratmir
authors: R
authors: Derda
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001665:Binding Sites; D032449:Canavalia / Q000737:chemistry / Q000378:metabolism*; D003208:Concanavalin A / Q000737:chemistry / Q000378:metabolism*; D018360:Crystallography, X-Ray; D006020:Glycopeptides / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D008024:Ligands; D008358:Mannose / Q000031:analogs & derivatives / Q000378:metabolism; D062105:Molecular Docking Simulation; D019151:Peptide Library; D011485:Protein Binding
chemical_list: D006020:Glycopeptides; D008024:Ligands; D019151:Peptide Library; D003208:Concanavalin A; D008358:Mannose