Numerous heterocycles occur as recurring motifs in the design of kinase inhibitors. Pyrazolo3,4-bpyridine has proved particularly versatile due to its ability to interact with kinases via multiple ...binding modes. As such, this scaffold has been claimed for kinase inhibition in many patents originating from several companies and universities, and these cover a broad range of kinase targets.
Patents from 2008 to the present in which pyrazolo3,4-b pyridine is utilized as a key element for inhibitor binding are included. This scaffold typically binds to the hinge region of the kinase, but examples in which other key interactions are formed are included in this review. Articles published in peer-reviewed journals that supplement information provided in the patent literature are highlighted.
Several bicyclic heterocycles are capable of forming a hydrogen bond donor-acceptor pair. This interaction is common among kinase inhibitors, particularly at the hinge region. These heterocycles are elaborated to form additional interactions in the kinase pocket which provide potency and selectivity, and thus serve as key scaffolds in kinase inhibitor design. Pyrazolo3,4-bpyridine can be viewed as having elements of both pyrrolo2,3-bpyridine and indazole and can therefore achieve multiple kinase binding modes. This scaffold is often encountered in kinase inhibitors as a result. Examination of the patent literature suggests that in some cases this group is simply one of several hinge binders examined for a particular series. In other cases, the pyrazolo3,4-bpyridine appears to provide an advantage, either in terms of intellectual property, inhibitor activity, physical properties or synthetic flexibility.
The macrocyclic core of gymnodimine has been constructed via an intramolecular Diels−Alder reaction of an α,β-unsaturated iminium dienophile in water. The cycloaddition furnished a single ...exo-product, along with two endo-products. Through X-ray analysis of a suitable derivative, the stereochemistry of the exo-product was established, thereby demonstrating that its stereochemistry matches that of gymnodimine. In contrast, macrocyclization of an analogous α,β-unsaturated ketone dienophile gave only undesired endo-products. Interestingly, the imine dienophile shows remarkable stability in water.
Cell potent inhibitors of B-RafV600E that bind to the kinase in the DFG-out conformation are reported. These compounds utilize the hinge-binding group and lipophilic linker from a previously ...disclosed series of B-RafV600E inhibitors that bind to the kinase in an atypical DFG-in, αC-helix-out conformation. This new series demonstrates that DFG-out kinase inhibitors can be rationally designed from related inhibitors which utilize an unconventional binding mode. Kinase selectivity profiles are compared. The pattern of kinase selectivity was found to be determined by the feature of the inhibitor which extends into the back pocket of the kinase and leads to the kinase conformation, rather than by the hinge-binding group or other minor modifications.
A single crystal was obtained of a lead B-RafV600E inhibitor with low aqueous solubility. The X-ray crystal structure revealed hydrogen-bonded head-to-tail dimers formed by the pyrazolopyridine and ...sulfonamide groups of a pair of molecules. This observation suggested a medicinal chemistry strategy to disrupt crystal packing and reduce the high crystal lattice energy of alternative inhibitors. Both a bulkier group at the interface of the dimer and an out-of-plane substituent were required to decrease the compound’s melting point and increase aqueous solubility. These substituents were selected based on previously developed structure–activity relationships so as to concurrently maintain good enzymatic and cellular activity against B-RafV600E.
Structure–activity relationships around a novel series of B-RafV600E inhibitors are reported. The enzymatic and cellular potencies of inhibitors derived from two related hinge-binding groups were ...compared and3-methoxypyrazolopyridine proved to be superior. The 3-alkoxy group of lead B-RafV600E inhibitor 1 was extended and minimally affected potency. The propyl sulfonamide tail of compound 1, which occupies the small lipophilic pocket formed by an outward shift of the αC-helix, was expanded to a series of arylsulfonamides. X-ray crystallography revealed that this lipophilic pocket unexpectedly enlarges to accommodate the bulkier aryl group.
HCV serine protease NS3 represents an attractive drug target because it is not only essential for viral replication but also implicated in the viral evasion of the host immune response pathway ...through direct cleavage of key proteins in the human innate immune system. Through structure-based drug design and optimization, macrocyclic peptidomimetic molecules bearing both a lipophilic P2 isoindoline carbamate and a P1/P1′ acylsulfonamide/acylsulfamide carboxylic acid bioisostere were prepared that possessed subnanomolar potency against the NS3 protease in a subgenomic replicon-based cellular assay (Huh-7). Danoprevir (compound 49) was selected as the clinical development candidate for its favorable potency profile across multiple HCV genotypes and key mutant strains and for its good in vitro ADME profiles and in vivo target tissue (liver) exposures across multiple animal species. X-ray crystallographic studies elucidated several key features in the binding of danoprevir to HCV NS3 protease and proved invaluable to our iterative structure-based design strategy.
A single crystal was obtained of a lead B-Raf(V600E) inhibitor with low aqueous solubility. The X-ray crystal structure revealed hydrogen-bonded head-to-tail dimers formed by the pyrazolopyridine and ...sulfonamide groups of a pair of molecules. This observation suggested a medicinal chemistry strategy to disrupt crystal packing and reduce the high crystal lattice energy of alternative inhibitors. Both a bulkier group at the interface of the dimer and an out-of-plane substituent were required to decrease the compound's melting point and increase aqueous solubility. These substituents were selected based on previously developed structure-activity relationships so as to concurrently maintain good enzymatic and cellular activity against B-Raf(V600E).
Cell potent inhibitors of B-Raf(V600E) that bind to the kinase in the DFG-out conformation are reported. These compounds utilize the hinge-binding group and lipophilic linker from a previously ...disclosed series of B-Raf(V600E) inhibitors that bind to the kinase in an atypical DFG-in, αC-helix-out conformation. This new series demonstrates that DFG-out kinase inhibitors can be rationally designed from related inhibitors which utilize an unconventional binding mode. Kinase selectivity profiles are compared. The pattern of kinase selectivity was found to be determined by the feature of the inhibitor which extends into the back pocket of the kinase and leads to the kinase conformation, rather than by the hinge-binding group or other minor modifications.
•Solubility enhancement predication (about 200 fold) of amorphous form of G–F by using thermal approach.•Making spray-dried amorphous dispersion (SDD) of G–F based on favorable solubility ...prediction.•In vitro dissolution of G–F SDD shows about 20 fold increase compared with crystalline form.•In vivo, G–F SDD shows about 3.5 fold improvement of AUC and Cmax at 100mg/kg dose in rat.•From thermal prediction to in vitro and in vivo tests, this systematic approach provides the success of SDD of G–F to enable efficacy and safety studies.
It is well acknowledged that oral bioavailability of a drug candidate is often influenced by factors such as the permeability, physico-chemical properties, and metabolism of the drug. Among the physico-chemical properties, solubility and dissolution rate are considered the most critical factors affecting the oral bioavailability of a compound G–F is a potent and selective B-Raf inhibitor with poor solubility and adsorption is limited by solubility at high doses. In order to overcome this issue using a spray-dried amorphous dispersion (SDD) formulation was evaluated. A combination of theoretical solubility prediction and in vitro dissolution, were used to predict the in vivo exposure of G–F. The predicted value was found to have good agreement with the in vivo exposure from dosing the crystalline and amorphous form of G–F.
In general, this combined approach demonstrated that the amorphous form of G–F offers an advantage over the crystalline form of G–F in terms of solubility; in vitro dissolution and in vivo absorption were predictable and consistent with the literature. This systemic approach provides a great value for compound development.
Recent clinical data provided proof-of-concept for selective B-Raf inhibitors in treatment of B-RafV600E mutant melanoma. Pyrazolopyridine-type B-Raf inhibitors previously described by the authors ...are potent and selective but exhibit low solubility requiring the use of amorphous dispersion-based formulation for achieving efficacious drug exposures. Through structure-based design, we discovered a new class of highly potent aminopyrimidine-based B-Raf inhibitors with improved solubility and pharmacokinetic profiles. The hinge binding moiety possesses a basic center imparting high solubility at gastric pH, addressing the dissolution limitation observed with our previous series. In our search for an optimal linker-hinge binding moiety system, amide-linked thieno3,2-dpyrimidine analogues 32 and 35 (G945), molecules with desirable physicochemical properties, emerged as lead compounds with strong efficacy in a B-RafV600E mutant mouse xenograft model. Synthesis, SAR, lead selection, and evaluation of key compounds in animal studies will be described.
