Starting in the 1980's DeGrado's group developed the approach of
de novo protein design, a term they coined to describe the design of proteins from first principles rather than through modification of natural protein sequences. They pioneered parametric approaches to the design of water-soluble 4-helix (alpha4) and 3-helix bundles (alpha3D), and ion channel peptides. The protein, alpha3D, was notable at the time, because it was the premier example of a
de novo protein, which was biologically expressed, structurally validated, and whose sequence and structure were not based on the sequence or the precise tertiary structure of a natural protein. The sequence of alpha3D was designed using the computational sidechain repacking algorithms that had recently been developed by Ponders & Richards, Desjarlais & Handel, Dahiyat & Mayo. The folding kinetics of alpha3D are among the most extensively characterized of single-domain proteins, and it has been used as a template for design of metalloproteins. The company Arcellx used alpha3D as a starting point for design of chimeric antigen receptors (CARs). Clinical data announced in 2020 showed deep and durable responses of multiple myeloma, illustrating the potential of
de novo proteins for treatment of human disease. With Angela Lombardi (
University of Naples),
Les Dutton and
Michael Therien (
Duke University) DeGrado has also designed numerous proteins that mimic many of the catalytic and electron relay properties of heme and non-heme iron proteins, including a transmembrane protein capable of shuttling electrons across membranes. His group has also designed the first examples of
de novo ion and proton channels. Because the original approaches to de novo protein design focused on physical chemical principles it was easily extended to design biologically active polymers and foldamers (short homogeneous, sequence-specific polymers that fold into unique structures). This work led to the design of Brilacidin, which is currently in phase II clinical trials. == Contributions to Pharmaceutical Chemistry ==