Although modulating GPCRs with orthosteric selective drug candidates has numerous success stories, in many cases, allosteric GPCR ligands are more effective for these biological targets. The small molecule allosteric modulation of GPCRs can promote a conformational change in the receptor that often has no noticeable effects, but can have a strong impact on the signaling pathway in the presence of an orthosteric endogenous ligand. On the other hand, GPCRs actuated by intractable stimuli can be modulated allosterically, opening a new opportunity for these currently unassailable targets. Two allosteric GPCRs modulators that have been introduced in the clinic (Cinacalcet and Maraviroc) are excellent evidence of prospects of investigation in this area. Another benefit of these ligands is their relatively low molecular weight and hence higher potential for oral bioavailability, in contrast to most orthosteric ligands. Moreover, allosteric sites are generally less conserved enabling development of actives with greater subtype selectivity than drugs targeting the conserved binding site.

Enamine’s Allosteric GPCR Library is a utile starting point for the drug discovery in the field of allosteric GPCR modulators.

Library design

Both ligand- and structure-based methods were used in design of the library. Ligand-based approach relied on using 3D pharmacophore search to the reference set of known ligands with high activity values (over 200 compounds from ChEMBL and BindingDB). The main emphasis has been done on allosteric modulators of class B GPCRs that are well established in drug discovery. Two pharmacophore models were created using the reference compounds sets and then validated with the training sets of actives and non-active ligands (Figure 1). Finally, over 6 200 small molecules were selected into Pharmacophore-based allosteric GPCR subset starting from Enamine MedChem set (710 K).

Fig. 1. Pharmacophore superposition of a reference active compound (in green) and a hit compound from the Library (in grey).

Structure-based approach was applied to human Glucagon receptor (GCGR) and human Corticotropin-releasing factor 1 receptor (CRF1R). The corresponding protein structures recorded in 5EE7 and 4K5Y PDB entries were optimized and used for the docking calculation with Glide (Schrödinger software). Compounds with at least 50% score-based efficacy as compared to the co-crystallized ligands were selected as hits and included in the targeted sets: h-GCGR set – 200 compounds; h-CRF1R set: 7 200 compounds (Figures 2 and 3).

Fig. 2. Binding mode of a hit (in red) obtained from the docking and the co-crystallized ligand (in green) of human Glucagon receptor.
 

Fig. 3. Superposition of a hit compound obtained after docking of CRF1R allosteric site with Enamine MedChem screening compounds (in green) and the co-crystallized ligand CP-376395 (in orange).

Examples of the molecules

Z2052759665

Z1256586621

Z2052158874

Z1299484172

Z2234781168

Z1192156186

Z1572741745

Z2326994277

The most straightforward approach to the design of kinase inhibitors relies on targeting ATP pocket. In fact, all compounds of this class approved by FDA (Copanlisib, Neratinib, Brigatinib, and Ribociclib) demonstrate this binding mode. The standard kinase interaction pattern consists of a hydrogen bond acceptor for the hinge region, heteroaromatic core with various substituents, and a second hydrogen acceptor for the conserved Lysine residue. This type of Inhibitors can be considered as ATP mimetics in the sense that they make interactions similar to that of ATP. Hydrogen bonds with Hinge Region formed by the adenosine moiety of ATP are crucial for effective binding (Figure 1, left). Analysis of a broad number of the kinase-inhibitor interactions has shown that similar hydrogen bonding patter is necessary for high inhibitory potency.

Fig. 1. ATP binding mode with hinge region (left) and examples of core structures that can mimic that mode (right).

Library design

Starting from the results of our previous study (Anticancer Agents Med. Chem. 2007, 7, 171–188) and detailed structure analysis of known and most potent kinase inhibitors, we have developed a series of unique structure filters aimed to identify potential inhibitors targeting ATP pocket. Molecular fragments able to form at least two hydrogen bonds with hinge region (Figure 1, right) have been analyzed, and appropriate topological models were developed for searching of directed inhibitors. The screening models were evaluated with a reference set of known kinase inhibitors (over 2 000 molecules with high inhibitory activity). Validated topological models were applied to over 3.2 M Enamine stock collection to produce Kinase Hinge Binders Libarary. The resulting set of compounds was evaluated with main emphasis on novel chemotypes. MedChem filters including PAINS and Ro5 PhysChem restrictions were applied as a prerequisite.

Examples of the molecules

Z1082776814

Z4521999208

Z1757787998

In response to high demand for new and small carboxylic acid we have created set of carefully selected specific molecules that strictly respond to FBDD requirements. Our carboxylic acid fragments are mainly consist from the compounds derived in the last three years from previously established at Enamine in-house program for design and producing diverse carboxylic acids to enlarge core Building Blocks Collection and diversification of decorating reagents.

Mainly this type of fragments has great potential for hit finding on new and difficult targets, e.g. protein-protein interaction, due to binding affinity to so called “hot-spot” residues. In addition there is probability of high solubility and good membrane permeability of discovered initial hit that often could be a limiting factor for phenotypic screening or in vivo activity of following investigation.

Key features

• High novelty and core diversity
• Fast follow-up with stock available analogues & synthesis
• Cherry-picking is available, customer preferred delivery format

Examples of the molecules in the library

Z2010010696

Z1201621939

Z234897401

Z963458200

Z2418194212

Z785812168

Z1445591040

Z1410957296

Ion channels are most widely distributed in organism tissues and play an important role in numerous cell types as large families of related genes with cell-specific expression pattern. This type of therapeutic targets is most important in developing of new highly effective medical treatments in the same time being one of the most difficult tasks in Medicinal Chemistry.

Examples of the molecules

Using our Libraries for hit identification you receive multiple benefits allowing you to save on time and costs in lead generation:

• Resupply from dry powders for hit confirmation, hit expansion from in-stock analogs.
• Straightforward and low-cost synthesis of analogues through our REAL Database technology.
• Medicinal chemistry support enhanced with on-site broad ADME/T panel.

Library design

We applied multipronged approach in rational library design to gain a qualitative set of molecules focused on ion channel targets. A major contribution was made in the lead-oriented synthesis program at Enamine focused on increasing novelty and structural diversity. The project has already yielded 36 800 lead-like compounds built on novel scaffolds featuring saturated rings that have been recognized as potential ion channel blockers. Pharmacophore ligand-based biased analysis was performed on the reference set of over 1 000 highly active ligands (≤10 nM) resulting in three main pharmacophore motifs frequently occurring in reported ligands. Optimized models were used in searching a lead-like part of Enamine Screening Collection and a lead-like part of REAL database. One of the common features of derived pharmacophores was presence of tertiary/secondary amino group. Additional compounds were added to the library after analysis of privileged motives of known ion channel blockers and after morphing of some recently discovered ion channel and TRPV1 modulators. General Medicinal Chemistry overview finalized the library profile: favorable physicochemical parameters and solubility requirements.