Detecting nanobodies highly suitable for drug development against deadly diseases

Dr. Dina Schneidman's group, in collaboration with researchers from the University of Pittsburgh, has developed an exceptionally fast and effective method for detecting tiny antibody fragments - called nanobodies- with great potential for the development of drugs against deadly diseases such as the SARS-CoV-2 virus - including variants. The findings were published in the Cell Systems March issue and featured on the journal cover.

Nanobodies are produced by animals from the camelid family (lamas, alpacas and camels). They feature high stability and solubility, and can be inhaled, rather than administered through injection, like regular antibodies. After exposing the llama to a piece of pathogen, within two months the animal’s immune system produces an abundance of mature nanobodies. The researchers presented a method for identifying and characterizing high-affinity and high-specificity nanobodies for a range of targets.

Once the sequences of the nanobodies are identified, they are expressed in microbes for further characterization. Dr. Schneidman’s group used algorithms for protein docking and information from cross-linking mass spectrometry to map the epitopes. To explore additional properties of high affinity binders, Lirane Bitton developed a deep learning model for identifying sequence patterns of nanobodies responsible for high affinity binding.

The team found that the CDR3 region of the nanobodies contributes most significantly to the antigen binding. Two properties were identified in nanobodies with strong binding. First, substitutions in charged amino acids indicate electrostatics optimization with respect to the epitope. Second, high-affinity nanobodies often contain an increased number of tyrosines at the central part of the CDR3 loop. Also, glycine and serine - smaller amino acids, tend to be at the edges of the CDR3 to provide it with flexibility. Using deep learning, the researchers identified consecutive patterns of lysine and arginine and a combination of tyrosines and glycines as the most informative properties of CDR3 for high-affinity binding.

This technology is already being used for the development of neutralizing nanobodies for SARS-CoV-2, published last November in Science journal.

Read the paper