Discovery of benzo[d]isothiazole derivatives as novel scaffold inhibitors targeting the programmed cell death-1/programmed cell death-ligand 1 (PD-1/PD-L1) interaction through "ring fusion" strategy.

The inhibition of programmed cell death-1/programmed cell death-ligand 1 (PD-1/PD-L1) interaction by monoclonal antibodies (mAbs) has achieved promising outcomes in cancer immunotherapy. Due to the inherent deficiencies of mAbs drugs, such as high cost of treatment, immunogenicity, poor pharmacokinetics and penetration of solid tumors, researchers are encouraged to develop small molecule inhibitors, to overcome mAbs drugs' deficiencies and change the situation where small molecule drugs are not available on the market. Herein, we reported a series of benzo[d]isothiazole derivatives targeting the PD-1/PD-L1 interaction through "ring fusion" strategy using BMS-202 as a starting point. Among them, compound D7 exhibited the best inhibitory activity with an IC50 value of 5.7 nM by homogeneous time-resolved fluorescence (HTRF) binding assay. In immunotoxicity analysis, D7 showed low cytotoxicity to Jurkat T cells in CCK-8 assay compared to BMS-202. The binding mode between D7 and PD-L1 protein was explored by molecular docking and molecular dynamics (MD) simulations, which revealed crucial chemical groups, such as biphenyl group interacting with Ile54A, Tyr56A, Met115A, Ala121A, Ile54B, Met115B, Ala121B and Tyr123B by hydrophobic interactions, bromobenzene moiety forming π-π stacking interaction with Tyr56B, as well as l-serine moiety forming hydrogen bond (H-bond) and salt bridge interactions with Asp122A and Lys124A. Furthermore, molecular modeling studies showed that D7 is likely to bind to the FA8 (fatty acid 8) binding site of human serum albumin (HSA). Taken together, D7 significantly inhibits the PD-1/PD-L1 interaction with low cytotoxicity, indicating that D7 is a promising starting point for further drug development in cancer immunotherapy.

Quinone-thioether metabolites of hydroquinone play a dual role in promoting a vicious cycle of ROS generation: in vitro and in silico insights.

Humans are exposed to hydroquinone (HQ) via diet, smoking, occupation, and even via inhalation of polluted air. Given its preferential distribution in kidney and liver, the impact of biotransformation on the nephrotoxicity and hepatotoxicity of HQ was evaluated. Indeed, HQ and its metabolites, benzoquinone, and quinone-thioethers (50, 100, 200, and 400 µM) all induced ROS-dependent cell death in both HK-2, a human kidney proximal epithelial cell line, and THLE-2, a human liver epithelial cell line, in a concentration-dependent manner. For a deeper insight into the biological mechanism of ROS stimulation, the bioinformatics database was reviewed. Intriguingly, 163 proteins were currently reported to form co-crystal complex with benzoquinone analogs, a large proportion of which are closely related to ROS generation. After a thorough assessment of the interaction affinity and binding energy, three key mitochondrial proteins that are particularly involved in electric transport, namely, cytochrome BC1, succinate dehydrogenase, and sulfide:quinone oxidoreductase, were highlighted for further verification. Their binding affinity and the action pattern were explored and validated by molecular docking and molecular dynamics simulations. Remarkably, quinone-thioether metabolites of HQ afforded high affinity to the above proteins that purportedly cause a surge in the generation of ROS. Therefore, HQ can be further converted into quinone-thioethers, which on one hand can function as substrates for redox cycling, and on the other hand may afford high affinity with key proteins evolved in mitochondrial electron transport system, leading to a vicious cycle of ROS generation. The combined data provide a prospective insight into the mechanisms of ROS motivation, expanding HQ-mediated toxicology profiles.

[Status analysis on child neglect of rural pupils aged 6-11 year-old in China].

OBJECTIVE: To analyze pupils' neglect status aged 6-11 years in China's rural. METHODS: According to the principle of multi-stage stratified cluster sampling, to extract 7,943 pupils aged 6-11 years for the survey from 56 primary schools in 28 counties in nine provinces, from December 2012 to March 2013. Proceed questionnaire survey by the scale from "Neglect Evaluation Norms for pupils aged 6-8 years in Rural Areas of China" and "Neglect Evaluation Norms for pupils aged 9-11 years in Rural Areas of China". And analyze neglect rates and neglect degrees of the different grades, gender, family types and different levels of neglect. RESULTS: The total neglect rate of China's rural pupils aged 6-8 and 9-11 years was 40.2% (1,258/3,130) and 42.5% (1,498/3,526) respectively, which differences had no statistical significant (χ2=3.59, P=0.058); the total neglect degree was 46.04±8.87 and 44.78±10.43 respectively, which differences had statistical significant (t=5.01, P<0.001); the differences of neglect rates and neglect degrees between male (41.4% (657/1,587) and 46.28±8.76) and female (39.0% (601/1,543) and 45.78±8.97) of aged 6-8 were all no statistical significant (χ2=1.87, P=0.171; t=1.49, P=0.136); the neglect rates and neglect degrees of male (46.3% (816/1,763) and 45.53±10.11) were higher than female (38.7% (682/1,763) and 44.06±10.69) in the group of aged 9-11, which differences were all statistical significant (χ2=20.84, t=3.97, P<0.001); the male neglect rate in the group of aged 6-8 in social neglect (11.7% (198/1,691)) and the neglect degree in educational neglect (48.09±9.70) were higher than female (9.4% (155/1,648) and 47.37±9.89), which differences were all statistical significance (χ2=14.55, P<0.001, t=2.22, P=0.026), the male neglect rate in the group of aged 9-11 in physical neglect (20.4% (398/1,954)) was higher than female (16.7% (326/1 957)), which differences had statistical significance (χ2=8.92, P=0.003). CONCLUSION: The neglect status of Chinese pupils aged 6-11 years in rural was serious, and we should find out risk factors and provide efficient prevention measures.

[Development of Neglect Evaluation Scale for primary school students aged 6-11 years old in rural areas of China].

OBJECTIVE: To develop a standard Neglect Evaluation Scale which is suitable for rural primary school students in China. METHODS: According to the principle of multi-stage stratified cluster sampling, a field investigation was conducted among primary school students in 28 counties from 7 provinces and 2 municipalities. The questionnaires were self-designed, and determined by multiple rounds of pilots and revisions. Among 5 862 students, 2 792 (6-8 years' old) and 3 070 (9-11 years' old) were investigated by using two kinds of Neglect Evaluation questionnaires, respectively. After project analysis, factor analysis, reliability and validity analysis, the reliability and stability of the scale were tested. Then percentile method was used to determine the evaluation standard to develop and finalize the formal scale. RESULTS: The numbers of the remaining items for 6-8 year-old group and 9-11 year-old group is 69 and 58, respectively, both of which contain six levels of neglect, including body, emotion, health care, education, security, and society. 4 times of factor analysis were conducted in both of the two groups. The factor loadings in these two groups were 0.290-0.700 and 0.276-0.729 respectively. Reliability test results showed that the two kinds of scales' Cronbach alpha coefficient were 0.924 and 0.929 respectively, split-half reliability were 0.891 and 0.904 respectively, the retest reliability were 0.559 and 0.892 respectively, the differences were statistically significant (P < 0.05). The retest reliability among 6-8 year-old group in medical neglect level had no statistical significance, but was close to the cut-off point (P = 0.054). The test results of external validity indicated that both of the two scales could reflect the neglect status of the subjects (P < 0.05), but the subjective and objective evaluation towards neglect were not consistent. The cut-off points for judging whether the children were neglected or not among 6-8 year-old and 9-11 year-old groups were 159 and 137 respectively; and the adjusted values were 160 and 135 respectively. CONCLUSION: The two norm scales developed by this study showed good discriminability, reliability, validity, and stability. The norms developed on the basis of the scales was suitable for the situation of rural students in primary schools in China.

A patent review on hypoxia-inducible factor (HIF) modulators (2021-2023).

INTRODUCTION: Hypoxia-inducible factor (HIF) is a central regulatory factor in detecting and adapting to cellular oxygen stress. Dysregulation of HIF is associated with various human diseases. Seven HIF modulators, including six prolyl hydroxylase (PHD) inhibitors and one HIF-2α inhibitor, have already been approved for the treatment of renal anemia and cancer, respectively. AREAS COVERED: This review summarizes HIF modulators patented in the 2021-2023 period. This review provides an overview of HIF downregulators, including HIF-1α inhibitors, HIF-2α inhibitors, and HIF-2α degraders, as well as HIF upregulators, including PHD, FIH, and VHL inhibitors, and HIF-2α and HIF-3α agonists. EXPERT OPINION: Efforts should be made to address the adverse clinical effects associated with approved HIF-modulating drugs, including PHD inhibitors and HIF-2α inhibitors. Identification of the specific buried cavity in the HIF-2α and an opened pocket in HIF-3α offer an avenue for designing novel modulators for HIF-2α or HIF-3α. Given the similarities observed in the binding cavities of HIF-2α and HIF-3α, it should be considered whether the approved HIF-2α inhibitors also inhibit HIF-3α. A comprehensive understanding of the HIF signaling pathway biology would lead to the development of novel small-molecule HIF modulators as innovative therapeutic approaches for a wide range of human diseases.

Design, synthesis, pharmacological evaluation, and computational study of benzo[d] isothiazol-based small molecule inhibitors targeting PD-1/PD-l1 interaction.

Blockade of the programmed cell death-1 (PD-1)/programmed cell death ligand 1 (PD-L1) pathway is an attractive strategy for immunotherapy, but the clinical application of small molecule PD-1/PD-L1 inhibitors remains unclear. In this work, based on BMS-202 and our previous work YLW-106, a series of compounds with benzo[d]isothiazol structure as scaffold were designed and synthesized. Their inhibitory activity against PD-1/PD-L1 interaction was evaluated by a homogeneous time-resolved fluorescence (HTRF) assay. Among them, LLW-018 (27c) exhibited the most potent inhibitory activity with an IC50 value of 2.61 nM. The cellular level assays demonstrated that LLW-018 exhibited low cytotoxicity against Jurkat T and MDA-MB-231. Further cell-based PD-1/PD-L1 blockade bioassays based on PD-1 NFAT-Luc Jurkat cells and PD-L1 TCR Activator CHO cells indicated that LLW-018 could interrupt PD-1/PD-L1 interaction with an IC50 value of 0.88 µM. Multi-computational methods, including molecular docking, molecular dynamics, MM/GBSA, MM/PBSA, Metadynamics, and QM/MM MD were utilized on PD-L1 dimer complexes, which revealed the binding modes and dissociation process of LLW-018 and C2-symmetric small molecule inhibitor LCH1307. These results suggested that LLW-018 exhibited promising potency as a PD-1/PD-L1 inhibitor for further investigation.

Structural requirement of RARγ agonism through computational aspects.

CONTEXT: RARγ is a therapeutic target for many skin diseases and has potential in cancer treatment. In the current study, we put forward a comprehensive structure-activity relationship study of third and fourth generations of RARγ agonists, addressing multiple crystal structures of RARγ complexes and approved drugs. Adapalene and Trifarotene, through hybrid strategies including protein contacts Atlas analysis, molecular docking, dynamics simulations, MM-GBSA, ASM, and pharmacophore modeling. Our result revealed crucial amino acids Arg267, Ser278, Phe288, Phe230, Met272, Leu271, and Leu268 within the RARγ pocket, as well as pharmacophore features such as two hydrophobic groups, two aromatic rings, and negative ionic features, which are essential for the binding of RARγ agonists. Based on this study, the binding mechanism of RARγ agonists was elucidated, which will be helpful for the rational design of new RARγ agonists for skin diseases and cancer treatment. METHODS: In this study, Schrödinger suite 2021-2 with OPLS_4 force field, Discovery Studio program 3.0, LigandScout 4.3, and PyMOL are utilized in the investigation.

Synthesis of selective PAK4 inhibitors for lung metastasis of lung cancer and melanoma cells.

The p21 activated kinase 4 (PAK4) is serine/threonine protein kinase that is critical for cancer progression. Guided by X-ray crystallography and structure-based optimization, we report a novel subseries of C-3-substituted 6-ethynyl-1H-indole derivatives that display high potential and specificity towards group II PAKs. Among these inhibitors, compound 55 exhibited excellent inhibitory activity and kinase selectivity, displayed superior anti-migratory and anti-invasive properties against the lung cancer cell line A549 and the melanoma cell line B16. Compound 55 exhibited potent in vivo antitumor metastatic efficacy, with over 80% and 90% inhibition of lung metastasis in A549 or B16-BL6 lung metastasis models, respectively. Further mechanistic studies demonstrated that compound 55 mitigated TGF-ß1-induced epithelial-mesenchymal transition (EMT).

Structure-based discovery of 1-(3-fluoro-5-(5-(3-(methylsulfonyl)phenyl)-1H-pyrazolo[3,4-b]pyridin-3-yl)phenyl)-3-(pyrimidin-5-yl)urea as a potent and selective nanomolar type-II PLK4 inhibitor.

Polo-like kinase 4 (PLK4) is a serine/threonine protein kinase involved in regulating cell mitosis and centriole duplication, and has emerged as a therapeutic target for treating multiple cancers. At first, the design and in vitro validation of PLK4 inhibitors (12a-12e, 17a-17f, 22a-22e) bearing 1H-pyrazolo[3,4-b]pyridine scaffold was described and lead compound 22a (IC50 = 0.106 µM) was identified. Then, selectivity- and activity-guided development of a series of potent and selective type-II PLK4 inhibitors using a homology model approach was carried out. Further structure-based optimization resulted in a potent type-II PLK4 inhibitor 29u (IC50 = 0.026 µM), which exhibited outstanding selectivity in a panel of 47 kinases at a single concentration of 1.0 µM. Furthermore, compound 29u significantly inhibited the proliferation of breast cancer cell line MCF-7 with an IC50 value of 1.52 µM, while it exhibited no inhibitory effect on normal cell lines (L02 and HUVECs). Meanwhile, the clone formation, senescence and migration abilities of compound 29u were evaluated using MCF-7 cells. The detailed biological evaluation revealed that compound 29u could arrest cell division in S/G2 phase by inhibiting PLK4, and then affect the expression of downstream signalling pathway proteins regulated by PLK4. Moreover, the in vitro preliminary evaluation of the drug-like properties of compound 29u exhibited outstanding plasma stability, moderate liver microsomal stability, and low risk of drug-drug interactions (DDIs). The current discovery will support the further development of compound 29u as a lead compound for PLK4-targeted anticancer drug discovery and as a useful chemical probe for the further biological research of PLK4.

Drug discovery targeting p21-activated kinase 4 (PAK4): a patent review.

Introduction: The Ser/Thr protein kinase PAK4 is a downstream regulator of Cdc42, mediating cytoskeleton remodeling, and cell motility, and inhibiting apoptosis and transcriptional regulation. Nowadays, efforts in PAK4 inhibitor development are focusing on improving inhibitory selectivity, cellular potency, and in vivo pharmacokinetic properties, and identifying the feasibility of immunotherapy combination in oncology therapy.Areas covered: This review summarized the development of PAK4 inhibitors that reported on patents in the past two decades. According to their binding features, these inhibitors were classified into type I, type I 1/2, and PAMs. Their designing ideas and SAR were elucidated in this review. Moreover, synergistic therapy of PAK4 inhibitors with PD-1/PD-L1 or CAR-T were also summarized .Expert opinion: In the past years, preclinical and clinical studies of PAK4 inhibitors ended in failure due to poor selectivity, cellular activity, or pharmacokinetic issues. There are researchers questioning the reliability of PAK4 as a drug target, particularly PAK4-related therapy is concerned with the distinguishment of the non-kinase functions and catalytic functions triggered by PAK4 phosphorylation. Meanwhile, synergistic effects of PAK4 inhibitors with PD-1/PD-L1 and CAR-T immunotherapy shed light for the development of PAK4 inhibitors.

Revealing the interaction modes of 5-HT2A receptor antagonists and the Structure-Based virtual screening from FDA and TCMNP database.

5-hydroxytryptamine 2A (5-HT2A) receptor is emerging as an important target for numerous psychoactive drugs due to its imperative roles in psychological diseases. In fact, multiple 5-HT2A receptor antagonists were developed to treat numerous psychiatric disorders, however, their clinical outcome was far from ideal probably due to a blurry information of the exact interaction modes between the receptor and its antagonists. Impressively, with a recent release of its crystal structure, we carefully analyzed the receptor-ligand interactions with Protein Contacts Atlas, structure-based pharmacophore models, and molecular dynamics (MD) simulations to sum up the chemical features for antagonists interacting with 5-HT2A receptor. Moreover, the molecular docking-based virtual screening was applied to discover potential 5-HT2A receptor antagonists from FDA and TCMNP databases. Intriguingly, after a systematic assessment of the docking scores, binding modes and free energies, as well as their MD simulations performances, three compounds in TCMNP database were highlighted to be potential 5-HT2A receptor antagonists. Fascinatedly, these three hits also exhibited highly binding affinities with dopamine D2 receptor (D2R) due to the similarity of the ligand binding pockets of the receptors, indicating them to be promising dual target molecules that are of great benefit for anti-psychotic-drug research and development. In addition, ADME/Tox predictions were conducted for a primary evaluation of their developing potential. Together, this study not only revealed the exact interaction modes between 5-HT2A receptor and its antagonists, which shed a light on a better access for developing its novel antagonists, but also provided promising dual D2 and 5-HT2A receptor antagonists.Communicated by Ramaswamy H. Sarma.

Systematic analysis of the mechanism of Xiaochaihu decoction in hepatitis B treatment via network pharmacology and molecular docking.

Hepatitis B (HB) is a globally prevalent infectious disease caused by the HB virus. Xiaochaihu decoction (XCHD) is a classic herbal formula with a long history of clinical application in treating HB. Although the anti-HB activity of XCHD has been reported, systematic research on the exact mechanism of action is lacking. Here, a network pharmacology-based approach was used to predict the active components, important targets, and potential mechanism of XCHD in HB treatment. Investigation included drug-likeness evaluation; absorption, distribution, metabolism, and elimination (ADME) screening; protein-protein interaction (PPI) network construction and cluster analysis; Gene Ontology (GO) analysis; and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. Molecular docking was adopted to investigate the interaction between important target proteins and active components. Eighty-seven active components of XCHD and 155 anti-HB targets were selected for further analysis. The GO enrichment and similarity analysis results indicated that XCHD might perform similar or the same GO functions. Glycyrrhizae Radix (GR), one of the seven XCHD herbs, likely exerts some unique GO functions such as the regulation of interleukin-12 production, positive regulation of interleukin-1 beta secretion, and regulation of the I-kappaB/NF-kappaB complex. The PPI network and KEGG pathway analysis results showed that XCHD affects HB mainly through modulating pathways related to viral infection, immunity, cancer, signal transduction, and metabolism. Additionally, molecular docking verified that the active compounds (quercetin, chrysin, and capsaicin) could bind with the key targets. This work systematically explored the anti-HB mechanism of XCHD and provides a novel perspective for future pharmacological research.

In silico studies on p21-activated kinase 4 inhibitors: comprehensive application of 3D-QSAR analysis, molecular docking, molecular dynamics simulations, and MM-GBSA calculation.

P21-activated kinase 4 (PAK4) is a serine/threonine protein kinase, which is associated with many cancer diseases, and thus being considered as a potential drug target. In this study, three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics (MD) simulations were performed to explore the structure-activity relationship of a series of pyrropyrazole PAK4 inhibitors. The statistical parameters of comparative molecular field analysis (CoMFA, Q 2 = 0.837, R 2 = 0.990, and R 2 pred = 0.967) and comparative molecular similarity indices analysis (CoMSIA, Q 2 = 0.720, R 2 = 0.972, and R 2 pred = 0.946) were obtained from 3D-QSAR model, which exhibited good predictive ability and significant statistical reliability. The binding mode of PAK4 with its inhibitors was obtained through molecular docking study, which indicated that the residues of GLU396, LEU398, LYS350, and ASP458 were important for activity. Molecular mechanics generalized born surface area (MM-GBSA) method was performed to calculate the binding free energy, which indicated that the coulomb, lipophilic and van der Waals (vdW) interactions made major contributions to the binding affinity. Furthermore, through 100 ns MD simulations, we obtained the key amino acid residues and the types of interactions they participated in. Based on the constructed 3D-QSAR model, some novel pyrropyrazole derivatives targeting PAK4 were designed with improved predicted activities. Pharmacokinetic and toxicity predictions of the designed PAK4 inhibitors were obtained by the pkCSM, indicating these compounds had better absorption, distribution, metabolism, excretion and toxicity (ADMET) properties. Above research provided a valuable insight for developing novel and effective pyrropyrazole compounds targeting PAK4.

Computational Strategy Revealing the Structural Determinant of Ligand Selectivity towards Highly Similar Protein Targets.

BACKGROUND: Poor selectivity of drug candidates may lead to toxicity and side effects accounting for as high as 60% failure rate, thus, the selectivity is consistently significant and challenging for drug discovery. OBJECTIVE: To find highly specific small molecules towards very similar protein targets, multiple strategies are always employed, including (1) To make use of the diverse shape of binding pocket to avoid steric bump; (2) To increase binding affinities for favorite residues; (3) To achieve selectivity through allosteric regulation of target; (4) To stabalize the inactive conformation of protein target and (5) To occupy dual binding pockets of single target. CONCLUSION: In this review, we summarize computational strategies along with examples of their successful applications in designing selective ligands, with the aim to provide insights into everdiversifying drug development practice and inspire medicinal chemists to utilize computational strategies to avoid potential side effects due to low selectivity of ligands.