Small-molecule stabilization of protein-protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design chemical starting points in a "bottom-up" approach is largely unanswered. We report a novel concept for identifying initial chemical matter for PPI stabilization based on imine-forming fragments. The imine bond offers a covalent anchor for sitedirected fragment targeting, whereas its transient nature enables efficient analysis of structure-activity relationships. This bond enables fragment identification and optimisation using protein crystallography. We report novel fragments that bind specifically to a lysine at the PPI interface of the p65subunit-derived peptide of NF-kB with the adapter protein 14-3-3. Those fragments that subsequently establish contacts with the p65-derived peptide, rather than with 14-3-3, efficiently stabilize the 14-3-3/p65 complex and offer novel starting points for molecular glues.

Small-molecule stabilization of protein-protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design chemical starting points in a "bottom-up" approach is largely unanswered. We report a novel concept for identifying initial chemical matter for PPI stabilization based on imine-forming fragments. The imine bond offers a covalent anchor for sitedirected fragment targeting, whereas its transient nature enables efficient analysis of structure-activity relationships. This bond enables fragment identification and optimisation using protein crystallography. We report novel fragments that bind specifically to a lysine at the PPI interface of the p65subunit-derived peptide of NF-kB with the adapter protein 14-3-3. Those fragments that subsequently establish contacts with the p65-derived peptide, rather than with 14-3-3, efficiently stabilize the 14-3-3/p65 complex and offer novel starting points for molecular glues.

In order to examine the influence of the alkyl chain length on some physical properties of guanidinium salts, the synthesis of a homologous series of new N″-n-alkylsubstituted N,N-diethyl-N′ ,N′- di-n-propyl-N″-n-hexyl guanidinium ionic liquids (gILs), containing chloride (Cl), tetrafluoroborate (BF4), acesulfamate (Ace), saccharinate (Sac), and tosylate (Tos) as anions, is reported. Cn-gILAce, Cn-gILSac, and Cn-gILBF4 were obtained by ion exchange reaction of the corresponding hexasubstituted guanidinium chlorides (Cn-gCl, n = 3, 4, 6, 8, 10), which were synthesized by a quaternization reaction of the pentaalkyl-substituted guanidine 3 and the corresponding alkylchloride in DMF. The tosylates gILs Cn-gTos (n = 1, 2, 4, 6, 8, 10) were synthesized by alkylation of 3 with the corresponding alkyltosylates. Some physical properties, such as solubility in water and organic solvents, refractive index and density, are considered as a function of the length of the n-alkyl substituent R and the nature of the anion

Forward-synthetic databases are an efficient way to enumerate chemical space. We explored here whether these databases are good sources of novel protein ligands and how many molecules are obtainable and in which time frame. Based on docking calculations, series of molecules were selected to gain insights into the ligand structure-activity relationship. To evaluate the novelty of compounds in a challenging way, we chose the β 2 -adrenergic receptor, for which a large number of ligands is already known. Finding dissimilar ligands is thus the exception rather than the rule. Here we report on the results, the successful synthesis of 127/240 molecules in just 2 weeks, the discovery of previously unreported dissimilar ligands of the β 2 -adrenergic receptor, and the optimization of one series to a K D of 519 nM in only one round. Moreover, the finding that only 3 of 240 molecules had ever been synthesized before indicates that large parts of chemical space are unexplored.de novo design | parallel synthesis | highly designed libraries | docking | forward synthetic libraries