DISTANT HOMOLOGY
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FUNCTIONAL SIMILARITY

Overview

Our interest is in how nature uses and re-uses the same approaches and to apply this knowledge to research. This case study shows the structural similarity between the ATP binding domains of four proteins that have all been considered potential drug discovery targets;

  • DNA gyrase B : Novobiocin target.

  • HSP-90 : Oncology

  • Histidine Kinase EnvZ: Antibmicrobial

  • Pyruvate Dehydrogenase Kinase: Hyperglycaemia

For more detailed information see our original Nature publication: Tanaka et al., 1998, 396, 88-92.

Structural Similarity

None of these protein relationships can be identified with a simple sequence alignment. More advanced profile based methods such as PSI-Blast and GenThreader or alphafold are required. After confirmation of the EnvZ, HSP90 and DNA gyraseB 3D structures a detailed structure-based sequence alignment could be generated.

Alignment

The structure based sequence alignment shown below (colours emphasise the structural relationship observed in 3D) is adapted from our original publication. Two key elements of distant relationships are apparent;

  • Low overall sequence identity

  • Clustering of the few residue identities at functionally critical locations.  

Conserved residues are involved with the ATP binding site especially the key DxGxG motif. 

Subsequent to our work being published, other proteins such as Pyruvate Dehydrogenase Kinase for Type 2 diabetes were also found to have the same ATP binding domain, suggesting opportunities to design directly with AI using known inhibitors and hits rather than starting from a conventional HTS.

Fragment Based Drug Discovery

The aspartate of the conserved DxGxG motif occurs in publications FBDD by two companies; Vernalis and Astex. The following image shows four fragments from these publications interacting with the Asp.

Vernalis structures are: (a) 2wi1 and (b) 2wi7; Astex structures are: (c) 2xdl and (d) 2xab. 

For more details see our subsequent publication and references therein. LigPlot+: Multiple Ligand-Protein Interaction Diagrams for Drug Discovery, Roman A. Laskowski and Mark B. Swindells. Journal of Chemical Information and Modelling. 2011, 51, 2778–2786