4TWT: Human Tnfa Dimer In Complex With The Semi-synthetic Bicyclic Peptide M21

Macrocyclic peptides are potentially a source of powerful drugs, but their de novo discovery remains challenging. Here we describe the discovery of a high-affinity (Kd = 10 nM) peptide macrocycle (M21) against human tumor necrosis factor-alpha (hTNFalpha), a key drug target in the treatment of inflammatory disorders, directly from diverse semi-synthetic phage peptide repertoires. The bicyclic peptide M21 (ACPPCLWQVLC) comprises two loops covalently anchored to a 2,4,6-trimethyl-mesitylene core and upon binding induces disassembly of the trimeric TNFalpha cytokine into dimers and monomers. A 2.9 A crystal structure of the M21/hTNFalpha complex reveals the peptide bound to a hTNFalpha dimer at a normally buried epitope in the trimer interface overlapping the binding site of a previously discovered small molecule ligand (SPD304), which also induces TNF trimer dissociation and synergizes with M21 in the inhibition of TNFalpha cytotoxicity. The discovery of M21 underlines the potential of semi-synthetic bicyclic peptides as ligands for the discovery of cryptic epitopes, some of which are poorly accessible to antibodies.
PDB ID: 4TWTDownload
MMDB ID: 126722
PDB Deposition Date: 2014/7/1
Updated in MMDB: 2015/02
Experimental Method:
x-ray diffraction
Resolution: 2.85  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 4TWT: trimeric; determined by software (PISA)
Molecular Components in 4TWT
Label Count Molecule
Proteins (3 molecules)
Tumor Necrosis Factor(Gene symbol: TNF)
Molecule annotation
Molecule annotation
Chemicals (5 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB