4-Amino-7,8-dihydro-1,6-naphthyridin-5(6 H)-ones as Inhaled Phosphodiesterase Type 4 (PDE4) Inhibitors: Structural Biology and Structure-Activity Relationships

Accelerating and Automating the Free Energy Perturbation Absolute Binding Free Energy Calculation with the RED-E Function

The accurate prediction of the binding affinities between small molecules and biological macromolecules plays a fundamental role in structure-based drug design, which is still challenging. The free energy perturbation-based absolute binding free energy (FEP-ABFE) approach has shown potential in its reliability. To correctly calculate the energy related to the ligand being restrained by the receptor, additional restraints between the ligand and the receptor are needed. However, determining the restraint parameters for individual ligands empirically is too trivial to be automated, and usually gives rise to numerical instabilities, which set back the applications of FEP-ABFE. To address these issues, we derived the analytical expression for the probability distribution of energy differences, P(ΔU), during the process of restraint addition, which is called the RED-E (restraint energy distribution at equilibrium position) function. Simulations indicated that the RED-E function can accurately describe P(ΔU) when restraints are added at the equilibrium position. Based on the RED-E function, an automatic restraint selection method was proposed to select the best restraint. With this method, there is a high phase-space overlap between the free and restrained states, such that using a 2-λ perturbation can accurately calculate the free energy of the restraint addition, which is a nearly 6 times acceleration compared with current widely used 12-λ perturbation method. The RED-E function gives insight into the non-Gaussian behavior of the sampled P(ΔU) in certain FEP processes in an analytical way. The highly automated and accelerated restraint selection also makes it possible for the large-scale application of FEP-ABFE in real drug discovery practices.

Advances in the development of phosphodiesterase-4 inhibitors

Phosphodiesterase 4 (PDE4) hydrolyzes cyclic adenosine monophosphate (cAMP) and plays a vital roles in many biological processes. PDE4 inhibitors have been widely studied as therapeutics for the treatment of various diseases, including asthma, chronic obstructive pulmonary disease (COPD) and psoriasis. Many PDE4 inhibitors have progressed to clinical trials and some have been approved as therapeutic drugs. Although many PDE4 inhibitors have been approved to enter clinical trials, however, the development of PDE4 inhibitors for the treatment of COPD or psoriasis has been hampered by their side effects of emesis. Herein, this review summarizes advances in the development of PDE4 inhibitors over the last ten years, focusing on PDE4 sub-family selectivity, dual target drugs, and therapeutic potential. Hopefully, this review will contribute to the development of novel PDE4 inhibitors as potential drugs.

A General Synthesis of Dihydronaphthyridinones with Aryl-Substituted Quaternary Benzylic Centers

A variety of 7,8-dihydro-1,6-naphthyridin-5(6H)-ones and 3,4-dihydro-2,7-naphthyridin-1(2H)-ones with quaternary centers and aryl substitutions at the benzylic carbon were synthesized with a new 3-step, 2-pot method. The first step is an S_NAr using widely available 2- and 4-chloronicotinate esters and tertiary benzylic nitriles. The last two steps are a one-pot selective nitrile reduction in the presence of various heterocycles followed by a lactam ring closure of the free amine on the ester.

A straightforward coupling of 4-sulfonylpyridines with Grignard reagents

A straightforward synthesis of alkyl-sulfonylpyridines and aryl-sulfonylpyridines is developed by coupling of sulfonylpyridines with the Grignard reagents. The protocol proceeds through a catalyst- and oxidant-free coupling of sulfonylpyridines as substrates via a Chichibabin-type reaction mechanism.

Promising heterocycle-based scaffolds in recent (2019-2021) anti-Alzheimer's drug design and discovery

Alzheimer's disease (AD) is one of the neurodegenerative diseases that led to morbidity and mortality world-wide. It is a complex disease whose etiology is not completely known that leads to difficulty in prevent or cure of the AD. Also, there are only few approved drugs for AD treatment. Apart from deaths due to AD, expenditure of treatment and care of AD patients is higher than that of treatment of HIV and cancer diseases combined. Hence, it leads to an economic burden also. Although research is being carried out on designing drugs for AD, most of them have ended up in poor inhibitors with high toxicity. Hence, researchers should shoulder a great responsibility of discovery of efficient drugs for AD treatment. In the field of drug discovery, heterocycles played an important role. Also, most of the heterocyclic scaffolds have been used in design of potent anti-AD agents. In view of this, heterocyclic molecules reported recently are compiled and evaluated comprehensively. Especially, the molecules which exhibited pronounced activity are emphasized and described with respect to structure-activity relationship (SAR) in brief.

Inhaled Phosphodiesterase 4 (PDE4) Inhibitors for Inflammatory Respiratory Diseases

PDE4 inhibitors can suppress a variety of inflammatory cell functions that contribute to their anti-inflammatory actions in respiratory diseases like chronic obstructive pulmonary disease (COPD) and asthma. The systemically delivered PDE4 inhibitor roflumilast has been approved for use in a subset of patients with severe COPD with chronic bronchitis and a history of exacerbations. Use of systemically delivered PDE4 inhibitors has been limited by systemic side effects. Inhaled PDE4 inhibitors have been considered as a viable alternative to increase tolerability and determine the maximum therapeutic potential of PDE4 inhibition in respiratory diseases.

Construction of piperidine-2,4-dione-type azaheterocycles and their application in modern drug development and natural product synthesis

The review surveys the existing routes to piperidine-2,4-dione-type heterocycles including derivatives with the most vital types of biological activity. This heterocyclic platform is ideal for the construction of modern drugs and natural products.

Targeted Treatments for Chronic Obstructive Pulmonary Disease (COPD) Using Low-Molecular-Weight Drugs (LMWDs)

Chronic obstructive pulmonary disease (COPD) is a very common and frequently fatal airway disease. Current therapies for COPD depend mainly on long-acting bronchodilators, which cannot target the pathogenic mechanisms of chronic inflammation in COPD. New pharmaceutical therapies for the inflammatory processes of COPD are urgently needed. Several anti-inflammatory targets have been identified based on increased understanding of the pathogenesis of COPD, which raises new hopes for targeted treatment of this fatal respiratory disease. In this review, we discuss the recent advances in bioactive low-molecular-weight drugs (LMWDs) for the treatment of COPD and, in addition to the first-line drug bronchodilators, focus particularly on low-molecular-weight anti-inflammatory agents, including modulators of inflammatory mediators, inflammasome inhibitors, protease inhibitors, antioxidants, PDE4 inhibitors, kinase inhibitors, and other agents. We also provide new insights into targeted COPD treatments using LMWDs, particularly small-molecule agents.

A New Approach for Drug Target and Bioactivity Prediction: The Multifingerprint Similarity Search Algorithm (MuSSeL)

We present MuSSeL, a multifingerprint similarity search algorithm, able to predict putative drug targets for a given query small molecule as well as to return a quantitative assessment of its bioactivity in terms of K_i or IC₅₀ values. Predictions are automatically made exploiting a large collection of high quality experimental bioactivity data available from ChEMBL (version 22.1) combining, in a consensus-like approach, predictions resulting from a similarity search performed using 13 different fingerprint definitions. Importantly, the herein proposed algorithm is also effective in detecting and handling activity cliffs. A calibration set including small molecules present in the last updated version of ChEMBL (version 23) was employed to properly tune the algorithm parameters. Three randomly built external sets were instead challenged for model performances. The potential use of MuSSeL was also challenged by a prospective exercise for the prediction of five bioactive compounds taken from articles published in the Journal of Medicinal Chemistry just few months ago. The paper emphasizes the importance of implementing multifingerprint consensus strategies to increase the confidence in prediction of similarity search algorithms and provides a fast and easy-to-run tool for drug target and bioactivity prediction.

Efficient drug discovery by rational lead hybridization based on crystallographic overlay

In this review, we provide an overview of recent applications of crystallographic overlay-based molecular structure hybridization of lead compounds as a rational strategy for efficient drug discovery, with selected examples, and briefly discuss its advantages compared with other ligand-based methodologies.

Diastereoselective synthesis and profiling of bicyclic imidazolidinone derivatives bearing a difluoromethylated catechol unit as potent phosphodiesterase 4 inhibitors

Metal-mediated C–H functionalization of cyclic N-oxides was exploited to access new highly potent analogs of the phosphodiesterase 4 inhibitor Ro-20-1724.