PLAbDab-nano: a database of camelid and shark nanobodies from patents and literature

Abstract

Nanobodies are essential proteins of the adaptive immune systems of camelid and shark species, complementing conventional antibodies. Properties such as their relatively small size, solubility and high thermostability make VHH (variable heavy domain of the heavy chain) and VNAR (variable new antigen receptor) modalities a promising therapeutic format and a valuable resource for a wide range of biological applications. The volume of academic literature and patents related to nanobodies has risen significantly over the past decade. Here, we present PLAbDab-nano, a nanobody complement to the Patent and Literature Antibody Database (PLAbDab). PLAbDab-nano is a self-updating, searchable repository containing ∼5000 annotated VHH and VNAR sequences. We describe the methods used to curate the entries in PLAbDab-nano, and highlight how PLAbDab-nano could be used to design diverse libraries, as well as find sequences similar to known patented or therapeutic entries. PLAbDab-nano is freely available as a searchable web server (https://opig.stats.ox.ac.uk/webapps/plabdab-nano/).

Graphical Abstract

Figure 1.

Nanobodies are derived from the antigen-binding portion of heavy-chain antibodies, which lack the light chain pairing possessed by conventional antibodies (shown in yellow). There are two varieties of nanobody: the VHH from camelid species (shown in blue, with the lighter blue denoting the complementarity-determining region (CDR) loops), and the VNAR from sharks (shown in pink, with the CDR loops and hypervariable regions shown in orange). Protein Data Bank (PDB) entries 8HR2 and 7S83 were used to create the VHH and VNAR figures.

Figure 2.

Data are scraped and processed from GenBank (27), SAbDab (19,30) and TheraSAbDab (20) to generate the PLAbDab-nano database.

Figure 3.

There is an increasing number of depositions of nanobody sequences per year to publicly available sources.

Figure 4.

(A) Entries in PLAbDab-nano are sourced relatively evenly from the different sources: patents, literature and crystal structures, with a minority from therapeutic data. (B) Excluding patents due to a lack of species annotation, most VHH entries are sourced from camelid species and synthetic constructs. The total number of nanobody sequences is 4457. (C) For VNARs, entries are split between various shark species and synthetic constructs. The total number of VNAR sequences is 456.

Figure 5.

(A) The distribution of CDR3 loop lengths (by number of residues) from VHH entries in PLAbDab-nano closely matches those from natural VHH immune repertoire data taken from OAS (17,18). (B) For entries included in PLAbDab-nano, the CDR3 loops of VNARs tend to be longer than VHH CDR3 loops.

Figure 6.

(A) VNARs (pink) and VHHs (blue) binding to overlapping epitopes on the RBD of SARS-CoV-2 (yellow). Their CDR3 sequences for two different binding sites are labelled 1 and 2. (B) These nanobodies bind to their epitopes in differing orientations, with the CDR3 (shown in orange for the VNAR and light blue for the VHH) dominant in binding in all cases. Structures 1 and 2 are rotated 180° across the y-axis to produce structures 3 and 4. Data come from PDB entries 7S83 (for the VNARs) and 8HR2 (for the VHHs), with the RBD from both used to align the structures.