Advances in cancer biology have underscored the central role of kinases in tumorigenesis. As recognized therapeutic agents, small-molecule kinase inhibitors are classified into five types (I–V), based on their binding modes [1]. Type II inhibitors, in particular, target the inactive form of kinases, which feature gatekeeper residues and a DFG-out conformation [2]. By binding reversibly to a hydrophobic pocket adjacent to the ATP-binding site, accessible only after rearrangement of the activation loop (A-loop) and DFG motif, these inhibitors sterically hinder ATP access and disrupt kinase activity [3]. Unlike Type I inhibitors that bind to the active DFG-in conformation, Type II inhibitors exploit less conserved regions of the kinase cleft, enhancing selectivity across the kinome.
Life Chemicals presents a specialized screening library of over 1,800 structurally diverse small molecules designed to selectively inhibit kinases in their inactive DFG-out conformation, offering significant potential for the discovery of highly selective kinase inhibitors with improved therapeutic profiles. This Library contains potential kinase type II inhibitors identified by structure-based virtual screening against the following targets:
- Receptor-type tyrosine-protein kinase FLT3 (996 compounds)
- Tyrosine-protein kinase ABL1 (816 compounds)
Furthermore, compound selections can be customized upon request to include specific protein targets or be filtered based on physicochemical properties, biological activity, metabolic stability, toxicity profiles, and other factors.
For your convenience, in addition to customer-tailored selections, also available is cherry picking.
Please, contact us at orders@lifechemicals.com for any additional information and price quotations.
Representative screening compounds from the Screening Library
Background information
Key structural determinants for Type II binding include an outward-displaced C-helix and the DFG-out orientation positioning of the activation loop. Many compounds in this library mimic the binding mode of imatinib to ABL1, which stabilizes a DFG-out, C-out conformation. However, variations, such as Gly-rich loop (P-loop) positioning and side-chain rotamers like Met290 in ABL1, critically influence binding [4], especially in crystals with high B-factors indicating local flexibility or instability.
Resistance often emerges through mutations in regulatory regions like the P-loop (GXGXXG motif), which promote the active conformation and diminish inhibitor binding. The compounds in this set are selected for compatibility with diverse kinase structures, particularly those exhibiting dynamic inactive conformations [5-6].
By focusing on conformational flexibility and fine structural motifs of kinase regulatory elements, this Library serves as a powerful tool for the discovery of highly selective and potent Type II kinase inhibitors suitable for both biochemical screening and structure-based drug design. The collection prioritizes clinically relevant targets, such as the ABL T315I mutant, a gatekeeper mutation responsible for resistance to first- and second-generation TKIs in chronic myeloid leukemia, and the FLT3 kinase domain, frequently mutated in acute myeloid leukemia and associated with poor prognosis [7-8]. Targeting these kinases enables the discovery of next-generation inhibitors with the potential to overcome drug resistance and improve therapeutic outcomes.
Figure 1. Types of kinase inhibitors. Adapted from Rahul Kumar, et al. 2024 [1]
Compound selection
This Screening Library was designed using structure-based virtual screening, taking advantage of Phase (receptor-ligand complex) and the Life Chemicals proprietary HTS Compound Collection and Kinase Targeted Libraries. The results were filtered based on similarity parameters related to the pharmacophore hypothesis in structure-based virtual screening (PhaseScreenScore). After that, the obtained compounds were filtered based on structural diversity, resulting in over 1,800 potential type II inhibitors.
Receptor-type tyrosine-protein kinase FLT3 - Key features:
- Method: structure-based virtual screening using Phase (receptor-ligand complex)
- X-Ray data used: 4XUF
- Filters used: no
- Number of compounds selected: 998
Fig. 2. Compound F2680-0243 (white) in the binding site of FLT3 kinase domain with the inhibitor quizartinib (pink) complex. The complex has been obtained by structure-based virtual screening.
Tyrosine-protein kinase ABL1 - Key features:
- Method: structure-based virtual screening using Phase (receptor-ligand complex)
- X-Ray data used: 3OY3
- Filters used: no
- Number of compounds selected: 816
Fig. 3. Compound F2823-0228 (white) in the binding site of ABL T315I mutant kinase with a DFG-out inhibitor (pink) complex. The complex has been obtained by structure-based virtual screening.
Reference:
- Rahul Kumar, et al. Recent developments in receptor tyrosine kinase inhibitors: A promising mainstay in targeted cancer therapy. Medicine in Drug Discovery, 2024 Sept 23, 100195. DOI: 10.1016/j.medidd.2024.100195
- Vijayan RS, He P, Modi V, Duong-Ly KC, Ma H, Peterson JR, Dunbrack RL Jr, Levy RM. Conformational analysis of the DFG-out kinase motif and biochemical profiling of structurally validated type II inhibitors. J Med Chem. 2015 Jan 8;58(1):466-79. Doi: 10.1021/jm501603h.
- Eshaq, A.M.; Flanagan, T.W.; Hassan, S.-Y.; Al Asheikh, S.A.; Al-Amoudi, W.A.; Santourlidis, S.; Hassan, S.-L.; Alamodi, M.O.; Bendhack, M.L.; Alamodi, M.O.; et al. Non-Receptor Tyrosine Kinases: Their Structure and Mechanistic Role in Tumor Progression and Resistance. Cancers 2024, 16, 2754. https://doi.org/10.3390/cancers16152754.
- Kufareva I, Abagyan R. Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. J Med Chem. 2008 Dec 25;51(24):7921-32. doi: 10.1021/jm8010299.
- Kim P, Li H, Wang J, Zhao Z. Landscape of drug-resistance mutations in kinase regulatory hotspots. Brief Bioinform. 2021 May 20;22(3):bbaa108. doi: 10.1093/bib/bbaa108.
- Alam KA, Gani Osman A. S. B. M., Engh RA. Inhibitor binding to mutants of protein kinase A with GGGxxG and GxGxxA glycine-rich loop motifs. J Mol Recognit. 2021; 34:e2882. https://doi.org/10.1002/jmr.2882.
- Sulaibi, M.A., Zahra, J., Bardaweel, S. et al. Docking-guided exploration of the anti-FLT3 potential of isoindigo derivatives towards potential treatments of acute myeloid leukemia. Med Chem Res 33, 1242–1266 (2024). https://doi.org/10.1007/s00044-024-03259-3.
- Gao C, Zhang L, Xu Y, Ma X, Chen P, Chen ZS, Wei L. I13 overrides resistance mediated by the T315I mutation in chronic myeloid leukemia by direct BCR-ABL inhibition. Front Pharmacol. 2023 Apr 12;14:1183052. Doi: 10.3389/fphar.2023.1183052.