Camel single‐domain antibody inhibits enzyme by mimicking carbohydrate substrate

Whereas antibodies have demonstrated the ability to mimic various compounds, classic heavy/light‐chain antibodies may be limited in their applications. First, they tend not to bind enzyme active site clefts. Second, their size and complexity present problems in identifying key elements for binding and in using these elements to produce clinically valuable compounds. We have previously shown how cAb‐Lys3, a single variable domain fragment derived from a lysozyme‐specific camel antibody naturally lacking light chains, overcomes the first limitation to become the first antibody structure observed penetrating an enzyme active site. We now demonstrate how cAb‐Lys3 mimics the oligosaccharide substrate functionally (inhibition constant for lysozyme, 50 nM) and structurally (lysozyme buried surface areas, hydrogen bond partners, and hydrophobic contacts are similar to those seen in sugar‐complexed structures). Most striking is the mimicry by the antibody complementary determining region 3 (CDR3) loop, especially Ala104, which mimics the subsite C sugar 2‐acetamido group; this group has previously been identified as a key feature in binding lysozyme. Comparative simplicity, high affinity and specificity, potential to reach and interact with active sites, and ability to mimic substrate suggest that camel heavy‐chain antibodies present advantages over classic antibodies in the design, production, and application of clinically valuable compounds. Proteins 32:515–522, 1998. © 1998 Wiley‐Liss, Inc.