Chelator Fragment Library

Fragment-based lead design (FBLD), sometimes referred to as fragment-based drug discovery (FBDD), is an increasingly important strategy for the discovery of biologically active compounds [1-2]. The application of FBLD to metalloprotein targets of medicinal interest has been described in the literature [1-4]. Nonetheless, the design, synthesis, and use of fragment libraries based on metal chelators for FBLD applications have not been studied extensively so far. Several small-molecule chelators were shown to effectively inhibit metalloproteins associated with many diseases such as cancer, inflammatory, infectious, cardiovascular, neurodegenerative, and other diseases [1, 5-9]. The research has identified the following metal-binding groups: picolinic acids, quinolines, pyrimidines, hydroxypyrones, hydroxypyridones, and salicylic acids [10].

At Life Chemicals, we have designed this Chelator Fragment Library of over 4,400 drug-like chelating fragments based on the Life Chemicals Chelator Focused Screening Library, as well as the HTS Compound Collection and General Fragment Library.

The compound selection can be customized based on your requirements, cherry picking is available.

Please, contact us at orders@lifechemicals.com for any additional information and price quotations.

Background

There are four main approaches based on metal chelation principles using different metal-binding groups (Fig. 1) [11]:

1. redistributing a metal across biological membranes via formation of neutral, lipophilic complexes
2. inactivating an enzyme active site by taking advantage of metal chelation to form protein-metal-chelator ternary complexes
3. enhancing the reactivity of a metal ion by forming a chelate complex, for example, that promotes redox cycling and generation of reactive oxygen species or other cytotoxic products
4. inactivating the reactivity of a metal in case of forming a chelate complex that prevents Fenton chemistry where redox cycling catalyzes the formation of reactive oxygen species

FBLD using metal-chelating moieties will be particularly suitable for the discovery of novel metalloenzyme inhibitors as chelator agents [1], namely they can :

• Demonstrate typically high binding affinities
• Provide a diverse range of molecular platforms
• Their propensity to bind metal ions allows better prediction of their probable binding position within a protein active site in the absence of experimental structural data of the complex

Figure 1. The main groups of chelators.

Compound selection

To form a reference set of known chelator fragments, the Chembl, PubChem, and Drug Bank databases, as well as the CFL-1 library of chelating fragments [5], which showed a high frequency of detection in screening studies against various metalloenzymes, were checked.

Then we applied the substructure search method to the HTS Compound Collection, followed by filtering the selected fragments by physicochemical and biological parameters. The proprietary Chelator Focused Screening Librarywas filtered by physicochemical parameters to pick out the fragment-like molecules.

All the selected fragment-like compounds with potential chelating action have passed substructure, similarity, and physicochemical property filters and have been narrowed down according to an expanded Lipinski’s Rule of Three. All compounds containing toxic, bad, and reactive groups have been filtered out from this Screening Library.

Physicochemical parameters are summarized in the table below:

Figure 2. Various approaches that use principles of metal chelation. Picture adapted from Franz, K. J. et al., 2013 [6]

Representative compounds from Chelator Fragment Library

F8881-8908

F9995-1595

F2163-0150

F8889-5596

F1912-1258

F2147-0750

F6548-2344

F2158-0087

F9994-5215

F2198-8595

F8880-3851

F1967-1723

F2163-0012

F2146-0099

F2135-0221

F6125-3196

F2169-1166

F1918-0073

References

1. Agrawal A, Johnson SL, Jacobsen JA, et al. Chelator fragment libraries for targeting metalloproteinases. ChemMedChem. 2010;5(2):195-199. doi:10.1002/cmdc.200900516
2. Balgoname AA, Alomair SM, AlMubirek AK, Khedr MA. Fragment-based Discovery of Potential Anticancer Lead: Computational and in vitro Studies. Curr Comput Aided Drug Des. 2021;17(3):421-428. doi:10.2174/1573409916666200620195025
3. Thorson MK, Puerta DT, Cohen SM, Barrios AM. Inhibition of the lymphoid tyrosine phosphatase: the effect of zinc(II) ions and chelating ligand fragments on enzymatic activity. Bioorg Med Chem Lett. 2014;24(16):4019-4022. doi:10.1016/j.bmcl.2014.06.016
4. Sales TA, Prandi IG, Castro AA, et al. Recent Developments in Metal-Based Drugs and Chelating Agents for Neurodegenerative Diseases Treatments. Int J Mol Sci. 2019;20(8):1829. Published 2019 Apr 12. doi:10.3390/ijms20081829
5. Jacobsen JA, Fullagar JL, Miller MT, Cohen SM. Identifying chelators for metalloprotein inhibitors using a fragment-based approach. J Med Chem. 2011;54(2):591-602. doi:10.1021/jm101266s
6. Franz KJ. Clawing back: broadening the notion of metal chelators in medicine. Curr Opin Chem Biol. 2013;17(2):143-149. doi:10.1016/j.cbpa.2012.12.021
7. Singh SK, Balendra V, Obaid AA, et al. Copper-mediated β-amyloid toxicity and its chelation therapy in Alzheimer's disease. Metallomics. 2022;14(6):mfac018. doi:10.1093/mtomcs/mfac018
8. Ward RJ, Dexter DT, Martin-Bastida A, Crichton RR. Is Chelation Therapy a Potential Treatment for Parkinson's Disease? Int J Mol Sci. 2021;22(7):3338. Published 2021 Mar 24. doi:10.3390/ijms22073338
9. Li S, Zhang X. Iron in Cardiovascular Disease: Challenges and Potentials. Front Cardiovasc Med. 2021;8:707138. Published 2021 Nov 30. doi:10.3389/fcvm.2021.707138
10. Fujisawa K, Takami T, Matsumoto T, Yamamoto N, Yamasaki T, Sakaida I. An iron chelation-based combinatorial anticancer therapy comprising deferoxamine and a lactate excretion inhibitor inhibits the proliferation of cancer cells. Cancer Metab. 2022;10(1):8. Published 2022 May 12. doi:10.1186/s40170-022-00284-x
11. Credille CV, Dick BL, Morrison CN, et al. Structure-Activity Relationships in Metal-Binding Pharmacophores for Influenza Endonuclease. J Med Chem. 2018;61(22):10206-10217. doi:10.1021/acs.jmedchem.8b01363