BTK
December 2022
Bruton’s Tyrosine Kinase (BTK)
There is a bonus at the very bottom of the article, so be sure to read to the very end.
Bruton’s Tyrosine Kinase (BTK) is essential for the development and activation of B cells, so it has been extensively studied as a therapeutic target for blood cancer. Currently, three covalent BTK inhibitors (ibrutinib, acalabrutinib and zanubrutinib) are used in clinical treatments. In addition, BTK has emerged as a promising target for autoimmune diseases. Many small-molecule inhibitors have been developed with this aim and are currently under clinical trials for non-oncological applications.
Researchers at Takeda have recently investigated the use of BTK as a target for rheumatoid arthritis, a chronic incurable autoimmune disease that strongly needs the development of novel treatments.
Using a fragment-based drug discovery (FBDD) approach supported by X-ray crystal structures, they managed to develop a new covalent BTK inhibitor in only 6 months, from the beginning of the optimization to the identification of the final clinical candidate (TAK-020).
Scientists started their campaign by screening a library of small compounds (11098 fragments) and then crystallizing the most promising ones with BTK (20 structures). From the analysis of the 3D structures obtained, they selected triazolone fragment 6 as a starting point for designing a new covalent inhibitor because:
A) it forms an extended network of electrostatic interactions (with the hinge region and with the gatekeeper Thr-474), providing a solid anchoring to the protein (Image 1A)
B) it gives the possibility to grow the size of the molecule toward an adjacent pocket in the binding site, which would increase the number of interactions with the protein (Image 1B)
Image 1. 3D structure of fragment 6 (green) in complex with BTK (yellow; PDB: 7N5R). A: electrostatic interactions network with the protein hinge region and gatekeeper Thr 474 (red) (interactions automatically calculated by 3decision® software). B: in the black circle, the adjacent pocket in the binding site which can be exploited for further expansion of the molecule. Pictures are produced with 3decision® software.
They modified the phenyl ring of the starting fragment 6, to expand the molecule towards the nearby pocket. In this way, they developed compound 18. The 3D structure of the BTK-compound 18 complex confirmed that the newly designed portion of the molecule was pointing toward the desired pocket. Moreover, this structure helped them in selecting a chemical group that could be directed toward the Cys-481, to form the desired covalent bond. These structural insights led to the final clinical candidate -TAK-020, which preserves all the interactions of the original fragment (Image 2).
Image 2. Overlay of the 3D structures of compounds 18 and TAK-020. Measurement of the distance between compound 18 and Cys 481 helped to select the proper chemical moiety to fill the space in the pocket (BTK complex with: 18 in white, PDB: 7N5X; TAK-020 in blue, PDB: 7N5Y). Pictures produced with 3decision® software.
Supported at every step by the 3D structural information, researchers at Takeda managed to develop a new oral covalent BTK inhibitor with high potency and selectivity in an impressively short time. This success serves as a good example that the FBDD can reduce the time needed to identify chemical leads compared to high-throughput screening approaches.
Reference:
Sabat M, Dougan DR, Ermolieff J, Halkowycz P, Knight B, Lawson JD, Scorah N, Smith CR, Taylor ER, Vu P, Wyrick C, Wang H, Balakrishna D, Hixon M, Madakamutil L, McConn D. Correction to "Discovery of the Bruton's Tyrosine Kinase Inhibitor Clinical Candidate TAK-020 (S)-5-(1-((1-Acryloylpyrrolidin-3-yl)oxy)isoquinolin-3-yl)-2,4-dihydro-3H-1,2,4-triazol-3-one, by Fragment-Based Drug Design". J Med Chem. 2021 Nov 11;64(21):16318. doi: 10.1021/acs.jmedchem.1c01685. Epub 2021 Oct 28. Erratum for: J Med Chem. 2021 Sep 9;64(17):12893-12902. PMID: 34708652.
BONUS
BTK is one of the many proteins that have been recently predicted by MetaAI. MetaAI models can be integrated into the 3decision database, together with others produced in-house or from public sources (e.g. AlphaFold). See below how is done.
Superposition on experimental and MetaAI predicted structures of BTK