Beyond Rule of Five and PROTACs in Modern Drug Discovery: Polarity Reducers, Chameleonicity, and the Evolving Physicochemical Landscape

Developing orally bioavailable drugs demands an understanding of absorption in early drug development. Traditional methods and physicochemical properties optimize absorption for rule of five (Ro5) compounds; beyond rule of five (bRo5) drugs necessitate advanced tools like the experimental measure of exposed polarity (EPSA) and the AbbVie multiparametric score (AB-MPS). Analyzing AB-MPS and EPSA against ∼1000 compounds with human absorption data and ∼10,000 AbbVie tool compounds (∼1000 proteolysis targeting chimeras or PROTACs, ∼7000 Ro5s, and ∼2000 bRo5s) revealed new patterns of physicochemical trends. We introduced a high-throughput "polarity reduction" descriptor: ETR, the EPSA-to-topological polar surface area (TPSA) ratio, highlights unique bRo5 and PROTAC subsets for specialized drug design strategies for effective absorption. Our methods and guidelines refine drug design by providing innovative in vitro approaches, enhancing physicochemical property optimization, and enabling accurate predictions of intestinal absorption in the complex bRo5 domain.

Targeting IRAK3 for Degradation to Enhance IL-12 Pro-inflammatory Cytokine Production

Interleukin-1 receptor-associated kinase 3 (IRAK3) is a pseudokinase mediator in the human inflammatory pathway, and ablation of its function is associated with enhanced antitumor immunity. Traditionally, pseudokinases have eluded "druggability" and have not been considered tractable targets in the pharmaceutical industry. Herein we disclose a CRISPR/Cas9-mediated knockout of IRAK3 in monocyte-derived dendritic cells that results in an increase in IL-12 production upon lipopolysaccharide (LPS) stimulation. Furthermore, we disclose and characterize Degradomer D-1, which displays selective proteasomal degradation of IRAK3 and reproduces the 1L-12p40 increases observed in the CRISPR/Cas9 knockout.

Discovery and Optimization of DNA Gyrase and Topoisomerase IV Inhibitors with Potent Activity against Fluoroquinolone-Resistant Gram-Positive Bacteria

Herein, we describe the discovery and optimization of a novel series that inhibits bacterial DNA gyrase and topoisomerase IV via binding to, and stabilization of, DNA cleavage complexes. Optimization of this series led to the identification of compound 25, which has potent activity against Gram-positive bacteria, a favorable in vitro safety profile, and excellent in vivo pharmacokinetic properties. Compound 25 was found to be efficacious against fluoroquinolone-sensitive Staphylococcus aureus infection in a mouse thigh model at lower doses than moxifloxacin. An X-ray crystal structure of the ternary complex formed by topoisomerase IV from Klebsiella pneumoniae, compound 25, and cleaved DNA indicates that this compound does not engage in a water-metal ion bridge interaction and forms no direct contacts with residues in the quinolone resistance determining region (QRDR). This suggests a structural basis for the reduced impact of QRDR mutations on antibacterial activity of 25 compared to fluoroquinolones.

Topoisomerase Inhibitors Addressing Fluoroquinolone Resistance in Gram-Negative Bacteria

Since their discovery over 5 decades ago, quinolone antibiotics have found enormous success as broad spectrum agents that exert their activity through dual inhibition of bacterial DNA gyrase and topoisomerase IV. Increasing rates of resistance, driven largely by target-based mutations in the GyrA/ParC quinolone resistance determining region, have eroded the utility and threaten the future use of this vital class of antibiotics. Herein we describe the discovery and optimization of a series of 4-(aminomethyl)quinolin-2(1H)-ones, exemplified by 34, that inhibit bacterial DNA gyrase and topoisomerase IV and display potent activity against ciprofloxacin-resistant Gram-negative pathogens. X-ray crystallography reveals that 34 occupies the classical quinolone binding site in the topoisomerase IV-DNA cleavage complex but does not form significant contacts with residues in the quinolone resistance determining region.

Potent nonimmunosuppressive cyclophilin inhibitors with improved pharmaceutical properties and decreased transporter inhibition

Nonimmunosuppressive cyclophilin inhibitors have demonstrated efficacy for the treatment of hepatitis C infection (HCV). However, alisporivir, cyclosporin A, and most other cyclosporins are potent inhibitors of OATP1B1, MRP2, MDR1, and other important drug transporters. Reduction of the side chain hydrophobicity of the P4 residue preserves cyclophilin binding and antiviral potency while decreasing transporter inhibition. Representative inhibitor 33 (NIM258) is a less potent transporter inhibitor relative to previously described cyclosporins, retains anti-HCV activity in cell culture, and has an acceptable pharmacokinetic profile in rats and dogs. An X-ray structure of 33 bound to rat cyclophilin D is reported.

Purine derivatives as potent gamma-secretase modulators

The development of a novel series of purines as gamma-secretase modulators for potential use in the treatment of Alzheimer's disease is disclosed herein. Optimization of a previously disclosed pyrimidine series afforded a series of potent purine-based gamma-secretase modulators with 300- to 2000-fold in vitro selectivity over inhibition of Notch cleavage and that selectively reduces Alphabeta42 in an APP-YAC transgenic mouse model.

3-Aryl-4-hydroxyquinolin-2(1H)-one derivatives as type I fatty acid synthase inhibitors

A series of 3-aryl-4-hydroxyquinolin-2(1H)-ones with fatty acid synthase inhibitory activity was prepared. Starting from a derivative with an IC(50) = 1.4 microM, SAR studies led to compounds with more than 70-fold increase in potency (IC(50) < 20 nM).

On the Remarkable Antitumor Properties of Fludelone: How We Got There

Small-molecule natural products are presumably often biosynthesized with a view to optimizing their ability to bind to strategic proteins or other biomolecular targets. Although the ultimate setting in which a drug must function may be very different, the use of such natural products as lead compounds can serve as a significant head start in the hunt for new agents of clinical value. Herein we reveal the synergistic relationship between chemical synthesis and drug optimization in the context of our research program around the epothilones: how synthesis led to the discovery of more-potent epothilone derivatives, and discovery inspired the development of new synthetic routes, thus demonstrating the value of target-directed total synthesis in the quest for new substances of material clinical benefit.

Discovery of (E)-9,10-dehydroepothilones through chemical synthesis: on the emergence of 26-trifluoro-(E)-9,10-dehydro-12,13-desoxyepothilone B as a promising anticancer drug candidate

We provide a full account of the discovery of the (E)-9,10-dehydro derivatives of 12,13-desoxyepothilone B (dEpoB), a new class of antitumor agents with promising in vivo preclinical properties. The compounds, which are to date not available by modification of any of the naturally occurring epothilones, were discovered through total chemical synthesis. We describe how our investigations of ring-closing metathesis reactions in epothilone settings led to the first and second generation syntheses of (E)-9,10-dehydro-12,13-desoxyepothilone congener 6. With further modifications, the synthesis was applied to reach a 26-trifluoro derivative compound (see compound 7). To conduct such studies and in anticipation of future development needs, the total synthesis which led to the initial discovery of compound 7 was simplified significantly. The total synthesis methodology used to reach compound 7 was then applied to reach more readily formulated compounds, bearing hydroxy and amino functionality on the 21-position (see compounds 45, 62, and 63). Following extensive in vitro evaluations of these new congeners, compound 7 was nominated for in vivo evaluations in xenograft models. The data provided herein demonstrate a promising therapeutic efficacy, activity against large tumors, nonrelapseability, and oral activity. These results have identified compound 7 as a particularly promising compound for clinical development. The excellent, totally synthetic, route to 7 makes such a program quite feasible.

Radical and Palladium-Catalyzed Cyclizations to Cyclobutenes: An Entry to the BCD Ring System of Penitrem D

A novel approach toward the synthesis of the BCD ring system of penitrem D is described. The strategy capitalizes on the fast cyclization rates of aryl radicals into cyclobutenes and allows access to a variety of fused tricyclic structures. Radical/polar crossover reactions of precursors 24-29 promoted by samarium diiodide in the presence of HMPA and acetone allow access to the fully functionalized BCD ring system of penitrem D. The stereochemical implications of these processes are evaluated, and a Pd-mediated cyclization approach toward the penitrems is also introduced.

Application of ring-closing metathesis reactions in the synthesis of epothilones

There is wide interest in the epothilones, which like the taxoids initiate cytotoxicity through microtubule stabilization. Briefly described is an application of a ring-closing metathesis reaction toward the synthesis of epothilones as carried out in our laboratory. This has led to the discovery of the (E)-9,10-dehydroepothilones as second-generation anticancer drug candidates.

Complex target-oriented total synthesis in the drug discovery process: the discovery of a highly promising family of second generation epothilones

The total synthesis of a family of (E)-9,10-dehydro derivatives of epothilone D (i.e., 12,13-desoxyepothilone B) is described. The route is particularly concise and amenable to production of new congeners. Furthermore, the chemistry described herein constitutes a major simplification in the total synthesis of EpoD, which is in human clinical trials. This new family of epothilones shows major advantages in terms of their potency and pharmacostability relative to the wild-type saturated analogues in the D series. From the perspective of compound availability through synthesis, potency, and pharmacokinetic properties, these compounds could well warrant advancement to clinical evaluation in humans.

Samarium(II) iodide mediated radical/polar crossover reactions of cyclobutenes. An efficient approach to the BCD ring system of the penitrems

[reaction: see text] Radical/polar crossover reactions of derivatives of 1-(2-cyclobutenyl)-2-(2-iodoaryl)ethanones with acetone promoted by samarium diiodide and HMPA provide 1-(1-hydroxy-1-methylethyl)-2,2a,4,8b-tetrahydro-1H-cyclobuta[a]naphthalen-3-one derivatives in about 50% isolated yield. This reaction shows promise for construction of the BCD ring fragment of the penitrems.

On the introduction of a trifluoromethyl substituent in the epothilone setting: chemical issues related to ring forming olefin metathesis and earliest biological findings

The disclosure herein describes the synthesis of 10,11-dehydro-13,14-desoxy-27-trifluoro-[17]epothilone B via a stereoselective ring-closing metathesis and provides early biological evaluation data pertinent to this compound. [reaction: see text]

Total syntheses of [17]- and [18]dehydrodesoxyepothilones B via a concise ring-closing metathesis-based strategy: correlation of ring size with biological activity in the epothilone series

A convergent ring-closing metathesis strategy has been employed for the highly concise syntheses of 10,11-dehydro-13,14-[17]desoxyepothilone B ([17]ddEpoB) and 10,11-dehydro-14,15-[18]desoxyepothilone B ([18]ddEpoB), which are 17- and 18-membered ring homologues of 10,11-dehydro-12,13-desoxyepothilone B ([16]ddEpoB or epothilone 490). We have demonstrated that the ring-closing metathesis (RCM) provides [17]ddEpoB or [18]ddEpoB with a high level of stereocontrol in the generation of the desired olefin in the products. These analogues were evaluated for antitumor activity. The results from the in vitro assays revealed that the [17]ddEpoB analogue is highly active against various tumor cell lines with a potency comparable to that of [16]ddEpoB. This is the first example of a 17-membered ring macrolactone epothilone that has retained its antitumor activity. In contrast, the biological data revealed that [18]ddEpoB is significantly less active than either [17]ddEpoB or the parent [16]ddEpoB.

Quasiracemic synthesis: concepts and implementation with a fluorous tagging strategy to make both enantiomers of pyridovericin and mappicine

The concept of quasiracemic synthesis is introduced and illustrated with syntheses of both enantiomers of pyridovericin (whose absolute configuration is assigned as R) and mappicine. Like racemic synthesis, quasiracemic synthesis provides both enantiomers in a single synthetic sequence; however, separation tagging is used to ensure that quasiracemic mixtures can be analyzed, separated, and identified on demand. Fluorous tags of differing chain lengths are used to tag two enantiomeric starting materials. The resulting quasienantiomers are mixed to make a quasiracemate, which is then treated like a true racemate in successive steps of the synthesis. Fluorous chromatography is used to separate, or demix, the final quasiracemate into its two components, which are then detagged to provide (true) enantiomeric products. Quasiracemic synthesis is portrayed as the first and simplest of a series of mixture synthesis techniques based on separation tagging, and the prospects for using other types of separation tags are briefly evaluated.

On the reduction of tertiary radicals by samarium diiodide (SmI2)

Reduction of o-iodophenyl 3-methylbut-2-enyl ether with samarium diiodide generates mixtures of 3-isopropyl-2,3-dihydrobenzofuran and 3-(2-propenyl)-2,3-dihydrobenzofuran along with a small amount of dimer. If a source of deuterium is present during the reduction, then the 3-isopropyl product predominates and this product is labeled with one deuterium. However, attempts to quench the putative tertiary organosamarium reagent by adding a deuterium source after the reduction were not very successful at room temperature. But at 0°C, the organosamarium reagent was generated (at least to the extent of about 50%, as measured by deuterium quenching), and its decomposition was followed over time by a series of quenching experiments. The results suggest that tertiary radicals are reduced to a significant extent by SmI2 to form an anionic (presumably alkylsamarium) species. This species is thermally unstable and decomposes to the corresponding reduced and eliminated products. The reduced product is consistently formed in slight excess over the eliminated one, and the mechanism of formation of these products is not yet clear.Key words: samarium diiodide, SmI2, reduction, alkyl samarium.

Recovery from blast lung injury: one-year follow-up

BACKGROUND

Blast injury to the lung is one of the devastating threats facing victims of an explosion. Although the pathogenesis of blast injury has been studied, little is known about the long-term effects on lung function in survivors.

OBJECTIVE

To examine the pulmonary function of survivors 1 year after sustaining a blast injury.

DESIGN

Prospective study.

SETTING

Pulmonary function test laboratory at Hadassah Medical Center, Jerusalem.

PARTICIPANTS

Eleven surviving victims of a blast injury sustained during a bus terrorist explosion.

MEASUREMENTS

Twelve months after the injury, physical examinations, lung function tests, and progressive cardiopulmonary exercise examinations were conducted, and chest radiographs were obtained.

RESULTS

The average age was 28 +/- 9.8 years. Most of the victims had multiple injuries in addition to the lung injury. Ten patients received mechanical ventilation, and 6 patients required chest drainage. All patients were treated in the ICU, with an average stay of 11.8 +/- 9 days. The patients were discharged to their homes or to a rehabilitation center 32.4 +/- 27. 3 days after the explosion. One year later, none had any pulmonary-related complaints. Physical examination of the lungs was normal. Most of the patients demonstrated normal lung function tests and complete resolution of the chest radiograph findings.

CONCLUSION

Most patients who survive lung blast injury will regain good lung function within a year.

Squamous cell metastasis from the tongue to the myocardium presenting as pericardial effusion

Cardiac metastasis from head and neck cancer is rarely encountered. We present a base-of-tongue squamous cell carcinoma with metastasis to the heart that was diagnosed antemortem. Autopsy series indicate that tongue cancer may metastasize more frequently to the heart than from other head and neck sites. However, none of these studies was controlled. Most importantly, cardiac metastasis should be suspected in any patient with cancer in whom new cardiac symptoms develop. The diagnosis is best confirmed with two-dimensional echocardiography or cardiac MRI. A myocardial or endocardial biopsy specimen can be obtained with angiographic guidance. Despite the improvement in diagnostic capability, available treatments are only palliative. All patients eventually die of their metastatic disease.

The galanin antagonist, M-15, inhibits growth hormone release in rats

The neuropeptide, galanin, has been implicated in the regulation of rat growth hormone (rGH) release. In the present study, adult male rats were implanted dually with cannulae to the lateral cerebral ventricle and the right atrium. After surgical recovery, rats were infused with M-15, a specific galanin antagonist, into the lateral ventricle. During the course of this brain infusion, rats were subjected to serial blood sampling with red cell and artificial plasma replacement under stress-free conditions. Plasma was saved for rGH assay. Treatment with M-15 reduced rGH pulse amplitude and pulse frequency when compared to vehicle-infused controls. These data suggest that brain galanin participates in the ongoing stimulation of pulsatile rGH release in the adult male rat.