Discovery of novel DAPY-IAS hybrid derivatives as potential HIV-1 inhibitors using molecular hybridization based on crystallographic overlays

Diastereoselective Synthesis of Dihydrobenzofuran-Fused Spiroindolizidines via Double-Dearomative [3 + 2] Cycloadditions

Spiroindolizidine oxindoles represent a kind of privileged scaffold in many biologically active natural alkaloids. 2,3-Dihydrobenzofuran derivatives exhibit significant bioactivities in a variety of pharmaceuticals. Herein, we assembled these two privileged fragments into a small molecule via double-dearomative [3 + 2] cycloadditions with pyridinium ylides and 2-nitrobenzofurans. This protocol features remarkable advantages including wide substrate scope, mild condition, high level of diastereoselectivities and yields. Thus, a collection of spiroindolizidine-fused dihydrobenzofurans/indolines were facilely produced efficiently.

Current medicinal chemistry strategies in the discovery of novel HIV-1 ribonuclease H inhibitors

During HIV-1 genome replication, the viral reverse transcriptase-associated ribonuclease H (RT-associated RNase H) activity hydrolyzes the RNA strand of RNA/DNA heteroduplex intermediates. As of today, HIV-1 RNase H inhibitors (RHIs) remain at an investigational level, although none of them reached clinical trials. Therefore, RNase H remains as an attractive target for drug design and development. In this paper, we review the current status of medicinal chemistry strategies aimed at the discovery of novel RHIs, while discussing problems encountered in their characterization and further development, thereby providing an update on recent progress in the field.

Tandem 1,6-addition/cyclopropanation/rearrangement reaction of vinylogous para-quinone methides with 3-chlorooxindoles: construction of vicinal quaternary carbon centers

A novel tandem 1,6-addition/cyclopropanation/rearrangement reaction of vinylogous para-quinone methides with 3-chlorooxindoles has been developed, providing dispirooxindole–cyclopentane–cyclohexadienones with vicinal quaternary carbon centers.

Indolylarylsulfones bearing phenylboronic acid and phenylboronate ester functionalities as potent HIV‑1 non-nucleoside reverse transcriptase inhibitors

To explore the chemical space around the entrance channel of the HIV-1 reverse transcriptase (RT) binding pocket, we innovatively designed and synthesized a series of novel indolylarylsulfones (IASs) bearing phenylboronic acid and phenylboronate ester functionalities at the indole-2-carboxamide as new HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) through structure-based drug design. All the newly synthesized compounds exhibited excellent to moderate potency against wild-type (WT) HIV-1 with EC₅₀ values ranging from 6.7 to 42.6 nM. Among all, (3-ethylphenyl)boronic acid substituted indole-2-carboxamide and (4-ethylphenyl) boronate ester substituted indole-2-carboxamide were found to be the most potent inhibitors (EC₅₀ = 8.5 nM, SI = 3310; EC₅₀ = 6.7 nM, SI = 3549, respectively). Notably, (3-ethylphenyl)boronic acid substituted indole-2-carboxamide maintained excellent activities against the single HIV-1 mutants L100I (EC₅₀ = 7.3 nM), K103N (EC₅₀ = 9.2 nM), as well as the double mutant V106A/F227L (EC₅₀ = 21.1 nM). Preliminary SARs and molecular modelling studies are also discussed in detail.

Druggability modification strategies of the diarylpyrimidine-type non-nucleoside reverse transcriptase inhibitors

Drug discovery of human immunodeficiency virus (HIV) is a hot field in medicinal chemistry community for many years. The diarylpyrimidines (DAPYs) are the second-generation non-nucleoside reverse transcriptase inhibitors (NNRTIs) targeting reverse transcriptase, playing a great irreplaceable role in HIV transcriptional therapy. However, fast-growing drug-resistant mutations as nonnegligible challenge are still unpredictably appeared in the clinical practice, leading to deactivate or reduce the existing drugs. In the last 20 years, more and more novel DAPY derivatives have developed with the purpose to counter the mutants. Nevertheless, most of them have dissatisfactory pharmacokinetics (PK) or poor antiviral activity toward resistant mutant strains. In this article, we will analyze the NNRTI derivatives with promising druggability, and summarize a series of druggability modification strategies to improve the antiviral activity, reduce toxicity and improve the PK properties in recent years. The prospects of DAPYs and the directions for future efforts will be discussed.

Structure-Activity Relationship Exploration of NNIBP Tolerant Region I Leads to Potent HIV-1 NNRTIs

Previous efforts in our lab have led to the development of human immunodeficiency virus type 1 (HIV-1) non-nucleoside reverse transcriptase inhibitor (NNRTI) thiophene[3,2-d]pyrimidine compound 1 (K-5a2) with promising activity against wild-type and mutant HIV-1 strains. In this work, a series of novel diarylpyrimidines derivatives carrying a structurally diverse motif at the right wing of the lead K-5a2 was designed and synthesized as potential anti-HIV-1 agents. The results demonstrated that 8a yielded exceptionally potent activity against HIV-1 wild-type (50% effective concentration (EC₅₀) = 3.30 nM) and mutant strain RES056 (EC₅₀ = 22.6 nM) in MT-4 cells; in the reverse transcriptase inhibitory assay, 8a (half maximal inhibitory concentration (IC₅₀) = 0.028 μM) was remarkably superior to that of K-5a2 (IC₅₀ = 0.300 μM) and comparable to that of etravirine (ETR; IC₅₀ = 0.011 μM). Notably, 8a exhibited better druggability than that of K-5a2, including significantly reduced CYP enzymatic inhibitory activity (IC₅₀ > 50 μM), lower human ether-à-go-go related gene (hERG) inhibition (IC₅₀ > 30 μM), and improved metabolic stability (short half-life, T_1/2 = 77.5 min) in vitro.

Design, synthesis, and biological evaluation of piperidinyl-substituted [1,2,4]triazolo[1,5-a]pyrimidine derivatives as potential anti-HIV-1 agents with reduced cytotoxicity

Taking the previously reported compound BH-7d as the lead, we designed and synthesized a series of piperidinyl-substituted [1,2,4]triazolo[1,5-a]pyrimidines, and their anti-HIV activities as well as cytotoxicities were evaluated. Several compounds exhibited moderate anti-HIV (IIIB) potency, among which 2b was the most active one (EC₅₀  = 4.29 μM). Structure-activity relationships derived from the antiretroviral results were analyzed. Additionally, most compounds demonstrated reduced cytotoxicity (CC₅₀  > 200 μM) compared with those of BH-7d and etravirine. Molecular docking study further revealed the binding conformation of 2b in the binding pocket of HIV-1 reverse transcriptase.

Isoquinoline Kelch-like ECH-Associated Protein 1-Nuclear Factor (Erythroid-Derived 2)-like 2 (KEAP1-NRF2) Inhibitors with High Metabolic Stability

Pharmacological activation of NRF2 (nuclear factor erythroid 2-related factor 2) arises from blocking the interaction of NRF2 with its negative regulator, KEAP1 (Kelch-like ECH-associated protein 1). We previously reported an isoquinoline-based NRF2 activator, but this compound showed negative logD_7.4 and a -2 charge at physiological pH, which may have limited its membrane permeability. In this work, we report potent, metabolically stable analogs that result from replacing a carboxymethyl group at the 4-position with a fluoroalkyl group.

Discovery of novel indolylarylsulfones as potent HIV-1 NNRTIs via structure-guided scaffold morphing

For more in-depth exploration of the chemical space around the entrance channel of HIV-1 reverse transcriptase (RT), a series of novel indolylarylsulfones (IASs) bearing different chiral N-substituted pyrrolidine, azetidine or substituted sulfonamide groups at indole-2-carboxamide were designed and synthesized as potent HIV NNRTIs by structure-guided scaffold morphing approach. All the IASs exhibited moderate to excellent potency against wild-type HIV-1 with EC₅₀ values ranging from 0.0043 μM to 4.42 μM. Notably, compound 27 (EC₅₀ = 4.7 nM, SI = 5183) and 33 (EC₅₀ = 4.3 nM, SI = 7083) were identified as the most potent compounds, which were more active than nevirapine, lamivudine and efavirenz, and also reached the same order of etravirine. Furthermore, some compounds maintained excellent activity against various single HIV-1 mutants (L100I, K103 N, E138K, Y181C) as well as one double mutant (F227L/V106A) with EC₅₀ values in low-micromolar concentration ranges. Notably, 34 displayed outstanding potency against F227L/V106A (EC₅₀ = 0.094 μM), and also showed exceptional activity against E138K (EC₅₀ = 0.014 μM), L100I (EC₅₀ = 0.011 μM) and K103 N (EC₅₀ = 0.025 μM). Additionally, most compounds showed markedly reduced cytotoxicity (CC₅₀) compared to lead compounds, especially 36 (CC₅₀ > 234.91 μM, SI > 18727) and 37 (CC₅₀ > 252.49 μM, SI > 15152). Preliminary SARs and molecular modeling studies were also discussed in detail, which may provide valuable insights for further optimization.

Multiple Machine Learning Comparisons of HIV Cell-based and Reverse Transcriptase Data Sets

The human immunodeficiency virus (HIV) causes over a million deaths every year and has a huge economic impact in many countries. The first class of drugs approved were nucleoside reverse transcriptase inhibitors. A newer generation of reverse transcriptase inhibitors have become susceptible to drug resistant strains of HIV, and hence, alternatives are urgently needed. We have recently pioneered the use of Bayesian machine learning to generate models with public data to identify new compounds for testing against different disease targets. The current study has used the NIAID ChemDB HIV, Opportunistic Infection and Tuberculosis Therapeutics Database for machine learning studies. We curated and cleaned data from HIV-1 wild-type cell-based and reverse transcriptase (RT) DNA polymerase inhibition assays. Compounds from this database with ≤1 μM HIV-1 RT DNA polymerase activity inhibition and cell-based HIV-1 inhibition are correlated (Pearson r = 0.44, n = 1137, p < 0.0001). Models were trained using multiple machine learning approaches (Bernoulli Naive Bayes, AdaBoost Decision Tree, Random Forest, support vector classification, k-Nearest Neighbors, and deep neural networks as well as consensus approaches) and then their predictive abilities were compared. Our comparison of different machine learning methods demonstrated that support vector classification, deep learning, and a consensus were generally comparable and not significantly different from each other using 5-fold cross validation and using 24 training and test set combinations. This study demonstrates findings in line with our previous studies for various targets that training and testing with multiple data sets does not demonstrate a significant difference between support vector machine and deep neural networks.

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.

Contemporary medicinal-chemistry strategies for the discovery of selective butyrylcholinesterase inhibitors

Butyrylcholinesterase (BChE) is considered a promising drug target for the treatment of moderate to severe Alzheimer's disease (AD). Here, we review medicinal-chemistry strategies that are currently available for the discovery of selective BChE inhibitors.

Advances in diarylpyrimidines and related analogues as HIV-1 nonnucleoside reverse transcriptase inhibitors

HIV-1 nonnucleoside reverse transcriptase inhibitors (NNRTIs) have been playing an important role in the fight against acquired immunodeficiency syndrome (AIDS). Diarylpyrimidines (DAPYs) as the second generation NNRTIs, represented by etravirine (TMC125) and rilpivirine (TMC278), have attracted extensive attention due to their extraordinary potency, high specificity and low toxicity. However, the rapid emergence of drug-resistant virus strains and dissatisfactory pharmacokinetics of DAPYs present new challenges. In the past two decades, an increasing number of novel DAPY derivatives have emerged, which significantly enriched the structure-activity relationship of DAPYs. Studies of crystallography and molecular modeling have afforded a lot of useful information on structural requirements of NNRTIs, which contributes greatly to the improvement of their resistance profiles. In this review, we reviewed the discovery history and their evolution of DAPYs including their structural modification, derivatization and scaffold hopping in continuous pursuit of excellent anti-HIV drugs. And also, we discussed the prospect of DAPYs and the directions of future efforts.