Fragment Libraries for Small-Molecule Drug Discovery

For libraries containing fluorine, bromine, or pre-fragments, see Specialty fragment libraries below.
 

For complete convenience, all libraries are custom weighed to your requirements in milligram or micromolar quantities. They may be ordered neat or in DMSO or D6DMSO, in plates or vials.

Fluorine is frequently substituted in drug molecules to help modulate potency and improve physiochemical and pharmacokinetic properties of compounds, with about 20% of known drug molecules containing a fluorine atom. In fragment screening, fluorine labels offer advantages for biophysical screening using NMR as well as crystallography, enabling unambiguous orientation of fragments in observed electron density. We offer a complete Maybridge fluorine compound collection and a novel fluorine-labeled fragment library, as well as libraries of bromine-labeled fragments and “pre-fragments.”
 

Complex sample NMR spectrum vs far simpler ¹⁹F fluorine-labeled NMR spectrum. (left) NMR spectrum for the fragment (1-Methyl-1H-imidazol-4-yl) methylamine (CC03613) in PBS with the chemically encoded shift data of all compounds in the fragment library. 1H-NMR spectra in aqueous conditions with full structural information are available on request to accelerate your screening workflow by avoiding having to run an 1H-NMR baseline. (right) ¹⁹F NMR spectrum for 1-Methyl-5-(trifluoromethyl)-2,3-dihydro-1Hbenzo[d]imidazole-2-thione (TG00013). The far simpler ¹⁹F NMR spectrum simplifies interpretation, facilitating the use of “cocktailing” and allowing multiple compounds to be screened together.

In fragment-based drug screening, the Rule of 3 (Ro3) is equivalent to Lipinski’s Rule of 5 for compound screening.¹ The Ro3 proposes that molecular weight should be <300 Da, the calculated partition coefficient (cLogP) should be £3, and the number of hydrogen bond donors and acceptors should each be £3. In addition to Ro3 criteria, the Maybridge fragment collection has been filtered for purity and potential “false leads” to allow you complete freedom to design a library that meets your specific needs.
 

¹Jhoti H, Williams G, Rees DC, Murray CW. The ‘rule of three’ for fragment-based drug discovery: Where are we now? Nat Rev Drug Discov. 2013; 12: 644. PubMed

Several key antituberculosis drugs, including pyrazinamide, with a molecular mass of 123.1 g/mol, are smaller than the usual drug-like molecules. Current drug discovery efforts focus on the screening of larger compounds with molecular masses centered around 400 to 500 g/mol. Fragment (molecular mass <300 g/mol) libraries have not been systematically explored for antitubercular activity. Here we screened a collection of 1,000 fragments, present in the Maybridge Ro3 library, for whole-cell activity against Mycobacterium tuberculosis.

Twenty-nine primary hits showed dose-dependent growth inhibition equal to or better than that of pyrazinamide. The most potent hit, indole propionic acid [IPA; 3-(1H-indol-3-yl)propanoic acid], a metabolite produced by the gut microbiota, was profiled in vivo. The molecule was well tolerated in mice and showed adequate pharmacokinetic properties. In a mouse model of acute M. tuberculosis infection, IPA reduced the bacterial load in the spleen 7-fold. Our results suggest that IPA should be evaluated as an add-on to current regimens and that fragment libraries should be further explored to identify antimycobacterial lead candidates.