Structure-Based Optimization and Biological Evaluation of Potent and Selective MMP-7 Inhibitors for Kidney Fibrosis.

Matrix metalloproteinase-7 (MMP-7) has been shown to play important roles in pathophysiological processes involved in the development/progression of diseases such as cancer and fibrosis. We discovered selective MMP-7 inhibitors composed of arylsulfonamide, carboxylate, and short peptides by a molecular hybridization approach. These compounds interacted with MMP-7 via multiple hydrogen bonds in the cocrystal structures. To obtain compounds for in vivo evaluation, we attempted structural optimization, particularly targeting Tyr167 at the S3 subsite through structure-based drug design, and identified compound 15 as showing improved MMP-7 potency and MMP subtype selectivity. A novel π-π stacking interaction with Tyr167 was achieved when 4-pyridylalanine was introduced as the P3 residue. Compound 15 suppressed the progression of kidney fibrosis in a dose-dependent manner in a mouse model of unilateral ureteral obstruction. Thus, we demonstrated, for the first time, that potent and selective MMP-7 inhibitors could prevent the progression of kidney fibrosis.

Lead generation from N-[benzyl(4-phenylbutyl)carbamoyl]amino acid as a novel LPA1 antagonist for the treatment of systemic sclerosis.

Lysophosphatidic acid (LPA), a bioactive phospholipid, binds to the G protein-coupled LPA1 receptor on the surfaces of immune cells, to promote progression of fibrosis of the skin and organs through inducing infiltration of immune cells into tissues, chemokine production, inflammatory cytokine production, and fibroblast transformation. Anti-fibrotic effects of LPA1 blockade have been reported in animal models of scleroderma and scleroderma patients. In the study reported herein, we identified the novel urea compound 5 as a hit compound with LPA1 antagonist activity from our in-house library and synthesized the lead compound TP0541640 (18) by structural transformation utilizing a structure-based drug design (SBDD) approach. Compound 18 possessed potent in vitro LPA1 antagonist activity and exhibited a dose-dependent inhibitory effect against LPA-induced histamine release in mice. Furthermore, 18 significantly suppressed collagen production and skin thickening in a mouse model of bleomycin-induced skin fibrosis. Herein, we describe the compound design strategies and in vivo studies in greater detail.

Discovery of a potent dual inhibitor of wild-type and mutant respiratory syncytial virus fusion proteins through the modulation of atropisomer interconversion properties.

The development of effective respiratory syncytial virus (RSV) fusion glycoprotein (F protein) inhibitors against both wild-type and the D486N-mutant F protein is urgently required. We recently reported a 15-membered macrocyclic pyrazolo[1,5-a]pyrimidine derivative 4 that exhibited potent anti-RSV activities against not only wild-type, but also D486N-mutant F protein. However, NMR studies revealed that the 15-membered derivative 4 existed as a mixture of atropisomers. An optimization study of the linker moiety between the 2-position of the benzoyl moiety and the 7-position of the pyrazolo[1,5-a]pyrimidine scaffold identified a 16-membered derivative 42c with an amide linker that showed a rapid interconversion of atropisomers. Subsequent optimization of the 5-position of the pyrazolo[1,5-a]pyrimidine scaffold and the 5-position of the benzoyl moiety resulted in the discovery of a potent clinical candidate 60b for the treatment of RSV infections.

Discovery of a Potent Dual Inhibitor of Wild-Type and Mutant Respiratory Syncytial Virus Fusion Proteins.

A novel series of macrocyclic pyrazolo[1,5-a]pyrimidine derivatives as respiratory syncytial virus (RSV) fusion glycoprotein (F protein) inhibitors were designed and synthesized based on docking studies of acyclic inhibitors. This effort resulted in the discovery of several macrocyclic compounds, such as 12b, 12f, and 12h, with low nanomolar to subnanomolar activities against the wild-type RSV F protein A2. In addition, 12h showed a single-digit nanomolar potency against the previously reported drug-resistant mutant D486N. Molecular modeling and computational analyses suggested that 12h binds to the D486N mutant while maintaining a rigid bioactive conformation via macrocyclization and that it interacts with a hydrophobic cavity of the mutant using a new interaction surface of 12h. This report describes the rational design of macrocyclic compounds with dual inhibitory activities against wild-type and mutant RSV F proteins.

Identification of highly selective and potent orexin receptor 1 antagonists derived from a dual orexin receptor 1/2 antagonist based on the structural framework of pyrazoylethylbenzamide.

The design, synthesis, and structure activity relationships of the novel class of pyrazolylethylbenzamide orexin receptor 1-selective antagonists are described. Further derivatization of the prototype dual orexin receptor 1/2 antagonist lead (1) by installing a (S)-methyl group into the ethyl linker moiety between the pyrazole ring and benzamide resulted in an increase of the antagonist potency against orexin receptor 1/2 receptors. Optimization of the benzamide and pyrazole parts of compounds 2 and 9b led to the identification of N-ethyl-5-fluoro-N-{(2S)-1-[5-(4-fluorophenyl)-2H-tetrazol-2-yl]propan-2-yl}-2-(pyrimidin-2-yl)benzamide (24), which exhibited excellent antagonistic activity against orexin receptor 1 with an IC50 of 2.01nM and a 265-fold selectivity for orexin receptor 1 over orexin receptor 2.

Discovery and in vitro and in vivo profiles of N-ethyl-N-[2-[3-(5-fluoro-2-pyridinyl)-1H-pyrazol-1-yl]ethyl]-2-(2H-1,2,3-triazol-2-yl)-benzamide as a novel class of dual orexin receptor antagonist.

Orexins play an important role in sleep/wake regulation, and orexin receptor antagonists are a focus of novel therapy for the treatment of insomnia. We identified 27e (TASP0428980) as a potent dual orexin receptor antagonist through the systematic modification of our original designed lead A. We demonstrated the potent sleep-promoting effects of 27e at ip dose of 3mg/kg in a rat polysomnogram study. 27e exhibited relatively short half-life profiles in rats and dogs. Furthermore, accumulating evidence regarding ADME profiles indicates that the predicted human half-life of 27e should be 1.2-1.4h. These data indicated that 27e has a short-acting hypnotic property, suggesting that 27e might be useful for treating primary insomnia while exhibiting a low risk of next-day residual somnolence. Thus, 27e and its related compounds should be further evaluated to enable advancement to clinical trials.

A dual-level state-specific time-dependent density-functional theory.

A highly efficient new algorithm for time-dependent density-functional theory (TDDFT) calculations is presented. In this algorithm, a dual-level approach to speed up DFT calculations (Nakajima and Hirao, J Chem Phys 2006, 124, 184108) is combined with a state-specific (SS) algorithm for TDDFT (Chiba et al., Chem Phys Lett 2006, 420, 391). The dual-level SS-TDDFT algorithm was applied to excitation energy calculations of typical small molecules, the Q bands of the chlorophyll A molecule, the charge-transfer energy of the zincbacteriochlorin-bacteriochlorin model system, and the lowest-lying excitation of the circumcoronene molecule. As a result, it was found that the dual-level SS-TDDFT gave correct excitation energies with errors of 0.2-0.3 eV from the standard TDDFT approach, with much lower CPU times for various types of excitation energies of large-scale molecules.

An improved long-range corrected hybrid exchange-correlation functional including a short-range Gaussian attenuation (LCgau-BOP).

A new hybrid exchange-correlation functional is presented based on the long-range correction (LC) scheme [H. Iikura et al., J. Chem. Phys. 115, 3540 (2001); Tawada et al., J. Chem. Phys. 120, 8425 (2004)], named LCgau-BOP. The key feature is the use of a two-parameter Gaussian correction to the Coulomb attenuation, which allows a more flexible description of exact exchange at short-range interelectronic separations. The new partitioning preserves 100% exact exchange in the long range, which is known to be important for the success of the LC scheme, with an asymptotic attenuation described by a standard error function with a parameter of 0.42. The LCgau partitioning was optimized for the reproduction of atomization energies over the G2 set and reaction barrier heights over Database/3, and produced results which are superior to B3LYP, CAM-BLYP, and the best LC functionals we are aware of. The results highlight the importance of including a substantial portion of exact exchange in the short range. Using the same parameters, the new functional was tested for the reproduction of geometries, as well as valence, Rydberg and charge-transfer excitations which are known challenges for conventional density functional theory. Our conclusion is that LCgau-BOP can provide a consistently more accurate description of thermochemistries, chemical reactions, and excitation energies than other existing long-range corrected functionals.