A Novel Inhibitor of Poly(ADP-Ribose) Polymerase-1 Inhibits Proliferation of a BRCA-Deficient Breast Cancer Cell Line via the DNA Damage-Activated cGAS-STING Pathway.

Loss-of-function mutations in the Breast Cancer Susceptibility Gene (BRCA1 and BRCA2) are often detected in patients with breast cancer. Poly(ADP-ribose) polymerase-1 (PARP1) plays a key role in the repair of DNA strand breaks, and PARP inhibitors have been shown to induce highly selective killing of BRCA1/2-deficient tumor cells, a mechanism termed synthetic lethality. In our previous study, a novel PARP1 inhibitor─(E)-2-(2,3-dibromo-4,5-dimethoxybenzylidene)-N-(4-fluorophenyl) hydrazine-1-carbothioamide (4F-DDC)─was synthesized, which significantly inhibited PARP1 activity with an IC50 value of 82 ± 9 nM. The current study aimed to explore the mechanism(s) underlying the antitumor activity of 4F-DDC under in vivo and in vitro conditions. 4F-DDC was found to selectively inhibit the proliferation of BRCA mutant cells, with highly potent effects on HCC-1937 (BRCA1-/-) cells. Furthermore, 4F-DDC was found to induce apoptosis and G2/M cell cycle arrest in HCC-1937 cells. Interestingly, immunofluorescence and Western blot results showed that 4F-DDC induced DNA double strand breaks and further activated the cGAS-STING pathway in HCC-1937 cells. In vivo analysis results revealed that 4F-DDC inhibited the growth of HCC-1937-derived tumor xenografts, possibly via the induction of DNA damage and activation of the cGAS-STING pathway. In summary, the current study provides a new perspective on the antitumor mechanism of PARP inhibitors and showcases the therapeutic potential of 4F-DDC in the treatment of breast cancer.

Design and Screening of New Lead Compounds for Autism Based on QSAR Model and Molecular Docking Studies.

The purpose of the present study aims to develop a satisfactory model for predicting pro-social and pro-cognitive effects on azinesulfonamides of cyclic amine derivatives as potential antipsychotics. The three dimensional-quantitative structure affinity relationship (3D-QSAR) study was performed on a series of azinesulfonamides of cyclic amine derivative using comparative molecular similarity indices analysis (CoMSIA). The best statistical model of CoMSIA q2, r2, SEE and F values are 0.664, 0.973, 0.087, and 82.344, respectively. Based on the model contour maps and the highest activity structure of the 43rd compound, serial new structures were designed and the 43k1 compound was selected as the best structure. The dock results showed a good binding of 43k1 with the protein (PDB ID: 6A93). The QSAR model analysis of the contour maps can help us to provide guidelines for finding novel potential antipsychotics.

Dietary epicatechin improves survival and delays skeletal muscle degeneration in aged mice.

We recently reported that epicatechin, a bioactive compound that occurs naturally in various common foods, promoted general health and survival of obese diabetic mice. It remains to be determined whether epicatechin extends health span and delays the process of aging. In the present study, epicatechin or its analogue epigallocatechin gallate (EGCG) (0.25% w/v in drinking water) was administered to 20-mo-old male C57BL mice fed a standard chow. The goal was to determine the antiaging effect. The results showed that supplementation with epicatechin for 37 wk strikingly increased the survival rate from 39 to 69%, whereas EGCG had no significant effect. Consistently, epicatechin improved physical activity, delayed degeneration of skeletal muscle (quadriceps), and shifted the profiles of the serum metabolites and skeletal muscle general mRNA expressions in aging mice toward the profiles observed in young mice. In particular, we found that dietary epicatechin significantly reversed age-altered mRNA and protein expressions of extracellular matrix and peroxisome proliferator-activated receptor pathways in skeletal muscle, and reversed the age-induced declines of the nicotinate and nicotinamide pathway both in serum and skeletal muscle. The present study provides evidence that epicatechin supplementation can exert an antiaging effect, including an increase in survival, an attenuation of the aging-related deterioration of skeletal muscles, and a protection against the aging-related decline in nicotinate and nicotinamide metabolism.-Si, H., Wang, X., Zhang, L., Parnell, L. D., Admed, B., LeRoith, T., Ansah, T.-A., Zhang, L., Li, J., Ordovás, J. M., Si, H., Liu, D., Lai, C.-Q. Dietary epicatechin improves survival and delays skeletal muscle degeneration in aged mice.

A Systems Biology-Based Approach to Uncovering Molecular Mechanisms Underlying Effects of Traditional Chinese Medicine Qingdai in Chronic Myelogenous Leukemia, Involving Integration of Network Pharmacology and Molecular Docking Technology.

BACKGROUND The method of multiple targets overall control is increasingly used to predict the main active ingredient and potential target group of Chinese traditional medicines and to determine the mechanisms involved in their curative effects. Qingdai is the main traditional Chinese medicine used in the treatment of chronic myelogenous leukemia (CML), but the complex active ingredients and antitumor targets in treatment of CML have not been clearly defined in previous studies. MATERIAL AND METHODS We constructed a protein-protein interaction network diagram of CML with 638 nodes (proteins) and 1830 edges, based on the biological function of chronic myelocytic leukemia by use of Cytoscape, and we determined 19 key gene nodes in the CML molecule by network topological properties analysis in a data bank. Then, we used the Surflex-dock plugin in SYBYL7.3 docking and acquired the protein crystal structures of key genes involved in CML from the chemical composition of the traditional Chinese medicine Qingdai with key proteins in CML networks. RESULTS According to the score and the spatial structure, the pharmacodynamically active ingredients of Qingdai are Isdirubin, Isoindigo, N-phenyl-2-naphthylamine, and Isatin, among which Isdirubin is the most important. We further screened the most effective activity key protein structures of CML to find the best pharmacodynamically active ingredients of Qingdai, according to the binding interactions of the inhibitors at the catalytic site performed in best docking combinations. CONCLUSIONS The results suggest that Isdirubin plays a role in resistance to CML by altering the expressions of PIK3CA, MYC, JAK2, and TP53 target proteins. Network pharmacology and molecular docking technology can be used to search for possible reactive molecules in traditional chinese medicines (TCM) and to elucidate their molecular mechanisms.

The evaluation of acute toxicity, antimicrobial activity of 1-phenyl-5-p-tolyl-1H-1, 2, 3-triazole, and binding to human serum albumin.

1-Phenyl-5-p-tolyl-1H-1, 2, 3-triazole (PPTA) was a synthesized compound. The result of acute toxicities to mice of PPTA by intragastric administration indicated that PPTA did not produce any significant acute toxic effect on Kunming strain mice. It exhibited the various potent inhibitory activities against two kinds of bananas pathogenic bacteria, black sigatoka and freckle, when compared with that of control drugs and the inhibitory rates were up to 64.14% and 43.46%, respectively, with the same concentration of 7.06 mM. The interaction of PPTA with human serum albumin (HSA) was studied using fluorescence polarization, absorption spectra, 3D fluorescence, and synchronous spectra in combination with quantum chemistry and molecular modeling. Multiple modes of interaction between PPTA and HSA were suggested to stabilize the PPTA-HSA complex, based on thermodynamic data and molecular modeling. Binding of PPTA to HSA induced perturbation in the microenvironment around HSA as well as secondary structural changes in the protein.

3D-QSAR modeling and molecular docking study on Mer kinase inhibitors of pyridine-substituted pyrimidines.

Mer kinase is a novel therapeutic target for many cancers, and overexpression of Mer receptor tyrosine kinase has been observed in several kinds of tumors. To deeply understand the structure-activity correlation of a series of pyridine/pyrimidine analogs as potent Mer inhibitors, a combined molecular docking and three-dimensional quantitative structure-activity relationship modeling was carried out. A comparative molecular similarity indices analysis model was developed based on the maximum common substructure alignment. The optimum model exhibited statistically significant results: the cross-validated correlation coefficient q2 was 0.599, and non-cross-validated r2 value was 0.984. Furthermore, the results of internal validation such as bootstrapping, Y-randomization as well as external validation (the external predictive correlation coefficient r2 ext = 0.728) confirmed the rationality and good predictive ability of the model. Using the crystal structure of Mer kinase, the selected pyridine/pyrimidine compounds were docked into the enzyme active site. Some key amino acid residues were determined, and hydrogen bonding and hydrophobic interactions between Mer kinase and inhibitors were identified. The satisfactory results from this study may aid in the research and development of novel potent Mer kinase inhibitors.

3D-QSAR Studies on High-affinity Phosphodiestera.

BACKGROUND: Recent studies have found that Phosphodiesterase-4 (PDE4) is closely related to the pathogenesis of depression, cognitive impairment and neurological impairment. OBJECTIVE: Our objective is to develop potent inhibitors of the high-affinity phosphodiesterase 4D isoform (PDE4D) that can serve as radioligands for Positron Emission Tomography (PET) imaging, thereby advancing research in the field of neurological diseases. METHODS: We employed a multi-step approach combining three-dimensional quantitative structure-activity relationship (3D-QSAR) modeling, molecular docking, classification techniques, and CoMSIA analysis to investigate the conformational relationship of highaffinity PDE4D inhibitors as PET ligands. ADMET and Drug-likeness predictions were also conducted. By utilizing these methods, our aim was to identify more potent PDE4D inhibitors. RESULTS: The results showed that the CoMSIA model with the best principal component scores (n=7) had a cross-validated Q2 value of 0.602 and a non-cross-validated R2 value of 0.976. These results affirmed the excellent predictive capability of the established CoMSIA model. Analysis of the generated 3D-QSAR contour plots highlighted specific regions in the molecular structure of the compounds that can be further optimized and modified. Guided by the contour plots, we designed 100 novel PDE4D inhibitors, and molecular docking was performed for the top 4 compounds with high activity. The molecular docking scores were promising, and ADMET and drug similarity predictions yielded satisfactory results. Taking into consideration these factors, compound 51c was determined to be the optimal compound, laying a solid foundation for further research. CONCLUSION: For the continued development of PDE4D PET radioligand, these models and new compounds' developing methodology offer a theoretical foundation and crucial references.

Study on interaction with high-abundant blood proteins and identification of low-abundant proteins to 5-phenyl-1-(p-tolyl)-1 H-1,2,3-triazole by serum proteomics.

In this study, a comprehensive investigation was undertaken to elucidate a simple triazole compound, 5-phenyl-1-(p-tolyl)-1 H-1,2,3-triazole (PPTT), its interactions with high-abundant proteins and identification of low-abundant proteins by serum proteomics. Employing a combination of spectroscopic techniques and computational chemistry, the interactions between PPTT and three high-abundance blood globular proteins, namely human serum albumin (HSA), human immunoglobulin G (HIgG), and hemoglobin (BHb), were explored, thereby ascertaining their binding constants and thermodynamic parameters at the molecular level. Subsequently, based on the differential proteomics, utilizing two-dimensional gel electrophoresis (2-DE) in conjunction with matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS), the research team isolated and identified differentially expressed low-abundance proteins in human blood serum samples following exposure to PPTT. The results showed that there were twenty highly expressed proteins identified from blood serum samples intervened by PPTT. Combining bioinformatics techniques, these proteins were classified, providing preliminary insights like preproprotein or precursors inhibiting the activity of elastase, defending and regulating the immune system, carrying lipid, and other functions into their biological functionalities. One of the differential proteins, apolipoprotein A-1 (ApoA-1) protein, was selected as a possible target to explore the mechanism of action of PPTT intervention on the related signaling pathways involved in human hepatocellular carcinomas(Hep G2) cells. These research findings offer scientifically sound guidance for further in-depth exploration, development, and application of the 1,2,3-triazole compound.

Tit Structure-activity Relationship Study and Design of Novel 1, 8- Naphthimide Derivatives as Potential DNA-targeting Chemotherapeutic Agents for Osteosarcoma.

BACKGROUND: 1, 8-naphthimide is a novel tumor inhibitor targeting nuclear DNA, which makes it applicable to the design and development of anti-osteosarcoma drugs. OBJECTIVE: The aim of this study is to establish a satisfactory model based on 1, 8-naphthimide derivatives that makes reliable prediction as DNA-targeted chemotherapy agents for osteosarcoma. METHODS: All compounds are constructed using ChemDraw software and subsequently optimized using Sybyl software. COMSIA method is used to construct QSAR model with the optimized compound in Sybyl software package. A series of new 1, 8-naphthalimide derivatives are designed and their IC50 values are predicted using the QSAR model. Finally, the newly designed compounds are screened according to IC50 values, and molecular docking experiments are conducted on the top ten compounds of IC50. RESULTS: The COMSIA model shows that q2 is 0.529 and the optimum number of components is 6. The model has a high r2 value of 0.993 and a low SEE of 0.033, with the F value and the r2 predicted to be 495.841 and 0.996 respectively. The statistical results and verification results of the model are satisfactory. In addition, analyzing the contour maps is conducive to finding the structural requirements. CONCLUSION: The results of this study can provide guidance for medical chemists and other related workers to develop targeted chemotherapy drugs for osteosarcoma.

Network Pharmacology and Integrated Molecular Docking Study on the Mechanism of the Therapeutic Effect of Fangfeng Decoction in Osteoarthritis.

BACKGROUND: At present, there are no effective pharmacologic therapies for attenuating the course of osteoarthritis (OA) in humans and current therapies are geared to mitigating symptoms. Fangfeng decoction (FFD) is a traditional Chinese medicine prescribed for the treatment of OA. In the past, FFD has achieved positive clinical outcomes in alleviating the symptoms of OA in China. However, its mechanism of action has not yet been clarified. OBJECTIVE: The objective of this study is to investigate and explore the mechanism of FFD and how the compound interacts with the target of OA; network pharmacology and molecular docking methods were applied in this study. METHODS: The active components of FFD were screened by Traditional Chinese Medicine Systems Pharmacology (TCMSP) database according to the inclusion criteria as oral bioactivity (OB) ≥ 30% and drug likeness (DL) ≥ 0.18. Then, gene name conversion was performed through the UniProt website. The related target genes of OA were obtained from the Genecards database. Core components, targets, and signaling pathways were obtained through compound-target-pathway (C-T-P) and protein-protein interaction (PPI) networks were built using Cytoscape 3.8.2 software. Matescape database was utilized to get gene ontology (GO) function enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment of gene targets. The interactions of key targets and components were analyzed by molecular docking in Sybyl 2.1 software. RESULTS: A total of 166 potential effective components, 148 FFD-related targets, and 3786 OA-related targets were obtained. Finally, 89 common potential target genes were confirmed. Pathway enrichment results showed that HIF-1 and CAMP signaling pathways were considered key pathways. The screening of core components and targets was achieved through the CTP network. The core targets and active components were obtained according to the CTP network. The molecular docking results showed that quercetin, medicarpin, and wogonin of FFD could bind to NOS2, PTGS2, and AR, respectively. CONCLUSION: FFD is effective in the treatment of OA. It may be caused by the effective binding of the relevant active components of FFD to the targets of OA.

Proton therapy (PT) combined with concurrent chemotherapy for locally advanced non-small cell lung cancer with negative driver genes.

PURPOSE: To discuss the optimal treatment modality for inoperable locally advanced Non-Small Cell Lung Cancer patients with poor physical status, impaired cardio-pulmonary function, and negative driver genes, and provide clinical evidence. MATERIALS AND METHODS: Retrospective analysis of 62 cases of locally advanced non-small cell lung cancer patients with negative driver genes treated at Tsukuba University Hospital(Japan) and Qingdao University Affiliated Hospital(China).The former received proton therapy with concurrent chemotherapy, referred to as the proton group, with 25 cases included; while the latter underwent X-ray therapy with concurrent chemoradiotherapy followed by 1 year of sequential immunomodulatory maintenance therapy, referred to as the X-ray group, with 37 cases included.The treatment response and adverse reactions were assessed using RECIST v1.1 criteria and CTCAE v3.0, and radiotherapy planning and evaluation of organs at risk were performed using the CB-CHOP method.All data were subjected to statistical analysis using GraphPad Prism v9.0, with a T-test using P < 0.05 considered statistically significant. RESULTS: (1)Target dose distribution: compared to the X-ray group, the proton group exhibited smaller CTV and field sizes, with a more pronounced bragg peak.(2)Organs at risk dose: When comparing the proton group to the X-ray group, lung doses (V5, V20, MLD) and heart doses (V40, Dmax) were lower, with statistical significance (P < 0.05), while spinal cord and esophagus doses showed no significant differences between the two groups (P > 0.05).(3)Treatment-related toxicities: The incidence of grade 3 or higher adverse events in the proton group and X-ray group was 28.6% and 4.2%, respectively, with a statistically significant difference (P < 0.05). In terms of the types of adverse events, the proton group primarily experienced esophagitis and pneumonia, while the X-ray group primarily experienced pneumonia, esophagitis, and myocarditis. Both groups did not experience radiation myelitis or esophagotracheal fistula.(4)Efficacy evaluation: The RR in the proton group and X-ray group was 68.1% and 70.2%, respectively (P > 0.05), and the DCR was 92.2% and 86.4%, respectively (P > 0.05), indicating no significant difference in short-term efficacy between the two treatment modalities.(5)Survival status: The PFS in the proton group and X-ray group was 31.6 ± 3.5 months (95% CI: 24.7 ~ 38.5) and 24.9 ± 1.55 months (95% CI: 21.9 ~ 27.9), respectively (P > 0.05), while the OS was 51.6 ± 4.62 months (95% CI: 42.5 ~ 60.7) and 33.1 ± 1.99 months (95% CI: 29.2 ~ 37.1), respectively (P < 0.05).According to the annual-specific analysis, the PFS rates for the first to third years in both groups were as follows: 100%, 56.1% and 32.5% for the proton group vs. 100%, 54.3% and 26.3% for the X-ray group. No statistical differences were observed at each time point (P > 0.05).The OS rates for the first to third years in both groups were as follows: 100%, 88.2%, 76.4% for the proton group vs. 100%, 91.4%, 46.3% for the X-ray group. There was no significant difference in the first to second years (P > 0.05), but the third year showed a significant difference (P < 0.05). Survival curve graphs also depicted a similar trend. CONCLUSION: There were no significant statistical differences observed between the two groups in terms of PFS and OS within the first two years. However, the proton group demonstrated a clear advantage over the X-ray group in terms of adverse reactions and OS in the third year. This suggests a more suitable treatment modality and clinical evidence for populations with frail health, compromised cardio-pulmonary function, post-COVID-19 sequelae, and underlying comorbidities.

A computational study on thiourea analogs as potent MK-2 inhibitors.

Mitogen-activated protein kinase-activated protein kinase 2 (MK-2) has been identified as a drug target for the treatment of inflammatory diseases. Currently, a series of thiourea analogs as potent MK-2 inhibitors were studied using comprehensive computational methods by 3D-QSAR, molecular docking and molecular dynamics simulations for a further improvement in activities. The optimal 3D models exhibit high statistical significance of the results, especially for the CoMFA results with r(2) (ncv), q(2) values of 0.974, 0.536 for the internal validation, and r(2) (pred), r(2) (m) values of 0.910, 0.723 for the external validation and Roy's index, respectively. In addition, more rigorous validation criteria suggested by Tropsha were also employed to check the built models. Graphic representation of the results, as contoured 3D coefficient plots, also provides a clue to the reasonable modification of molecules: (i) The substituent with a bulky size and electron-rich group at the C5 position of the pyrazine ring is required to enhance the potency; (ii) The H-bond acceptor group in the C3 position of the pyrazine ring is likely to be helpful to increase MK-2 inhibition; (iii) The small and electropositive substituent as a hydrogen bond donor of the C2 position in the oxazolone ring is favored; In addition, several important amino acid residues were also identified as playing an important role in MK-2 inhibition. The agreement between 3D-QSAR, molecular docking and molecular dynamics simulations also proves the rationality of the developed models. These results, we hope, may be helpful in designing novel and potential MK-2 inhibitors.

Novel hypoxia features with appealing implications in discriminating the prognosis, immune escape and drug responses of 947 hepatocellular carcinoma patients.

Background: Hypoxia has a profound impact on the development and progression of hepatocellular carcinoma (HCC). This study aimed to explore and elucidate how hypoxia affect prognosis, immune escape and drug responses in HCC. Methods: HCC-specific hypoxia signatures were identified based on the intersect of differentially expressed genes (DEGs) of GSE41666 and GSE15366. The hypoxia score was calculated using the gene set variation analysis (GSVA) function and validated on GSE18494. We collected five cohorts [The Cancer Genome Atlas (TCGA), GSE14520, GSE39791, GSE36376, GSE57957] for further analysis. First, we analyzed the effect of the hypoxia score on prognosis. Next, we systematically analyzed the potential hypoxia-related immune escape mechanisms and the effect of hypoxia upon immunotherapy. Then, we predicted and screened potential sensitive drugs for HCC patients with high hypoxia levels using machine learning and docking. Results: We constructed a novel HCC-specific hypoxia score and undertook further analysis in five cohorts (TCGA, GSE14520, GSE39791, GSE36376, GSE57957). We observed that patients with high hypoxia scores exhibited worse overall survival (OS) in TCGA and GSE14520. We also constructed a hypoxia-related nomogram that had good performance in predicting HCC patients' prognosis. Furthermore, patients with lower hypoxia scores had a lower risk of immune escape and thus may benefit from immunotherapy. Finally, we predicted and screened VLX600 as the candidate drug for HCC patients with high hypoxia scores. We further explored and elucidated why VLX600 was more sensitive in HCC patients with high hypoxia than with low hypoxia HCC patients using weighted gene co-expression network analysis (WGCNA). Conclusions: This study provides further evidence of the link between hypoxia and prognosis and immune escape in HCC patients. Moreover, our research screened VLX600 as a potential drug for HCC patients with high hypoxia levels and elucidated the potential mechanism.

Network Pharmacology Integrated Molecular Docking to Reveal the Autism and Mechanism of Baohewan Heshiwei Wen Dan Tang.

BACKGROUND: In recent years, the prevalence and mortality of autism spectrum disorder (ASD) have been increasing. The clinical features are different with different cases, so the treatment ways are different for each one. OBJECTIVE: Baohewan Heshiwei Wen Dan Tang (BHWDT) has been recommended for treating autistic spectrum disorder. To investigate the mechanism of action and how the compounds interact with ASD targets, network pharmacology and molecular docking methods were used in this study. METHODS: Traditional Chinese Medicine Systems Pharmacology (TCMSP) was used to screen the active components according to index of oral bio-activity and drug-likeness. Then, TCMSP and Swiss Target Prediction databases were used to screen potential target genes of active components. The related target genes of ASD were obtained from the Gene Cards database. Matescape database was utilized to get gene ontology (GO) function enrichment and Kyoto Encyclopedia of Genes and Genomes pathway annotation of gene targets. Composition- target-pathway (C-T-P) and a protein-protein interaction (PPI) networks were built with Cytoscape 3.8.2 software. RESULTS: The interaction of the main active components of BHWDT was verified by molecular docking. The key targets of MAPK1, IL6, CXCL8 and TP53 of BHWDT were obtained. The key active components Quercetin, Kaempferol and Iuteolin of BHWDT could bind with MAPK1, IL6, CXCL8 and TP53 of BHWDT, respectively. CONCLUSION: BHWDT can be highly effective for treating ASD and this study can help us to understand multiple targets and multiple pathways mechanism.

Location of Si vacancies and [Ti(OSi)4] and [Ti(OSi)3OH] sites in the MFI framework: a large cluster and full ab initio study.

Titanium silicalite-1 (TS-1) is an important catalyst for selective oxidation reactions. However, the nature and structure of the active sites and the mechanistic details of the catalytic reactions over TS-1 have not been well-understood, leaving a continuous debate on the genesis of active sites on the TS-1 surface in the literature. In this work, the location of Si vacancies and [Ti(OSi)(4)] and [Ti(OSi)(3)OH] sites in the MFI (Framework Type Code of ZSM-5 (Zeolite Socony Mobile-Five)) framework has been studied using a full ab initio method with 40T clusters with a Si:Ti molar ratio of 39:1. It was shown that the former four energetically favorable sites for Si vacancies are T6, T12, T4, and T8 and for Ti centers of [Ti(OSi)(4)] are T10, T4, T8 and T11, being partially the same sites. Whether by replacing Si vacancies or substituting the fully coordinated Si sites, the most preferential site for Ti is T10, which indicates that the insertion mechanism does not affect the favorable sites of Ti in the MFI lattice. For the defective [Ti(OSi)(3)OH] sites, it was found that the Si vacancy at T6 with a Ti at its neighboring T9 site (T6-def-T9-Ti pair) is the most energetically favorable one, followed by a T6-def-T5-Ti pair with a small energy gap. These findings are significant to elucidate the nature of the active sites and the mechanism of reactions catalyzed by TS-1 and to design the TS-1 catalyst.

Novel quantitative structure-activity relationship model to predict activities of natural products against COVID-19.

Currently, COVID-19 is spreading in a large scale while no efficient vaccine has been produced. A high-effective drug for COVID-19 is very necessary now. We established a satisfied quantitative structure-activity relationship model by gene expression programming to predict the IC50 value of natural compounds. A total of 27 natural products were optimized by heuristic method in CODESSA program to build a liner model. Based on it, only two descriptors were selected and utilized to build a nonlinear model in gene expression programming. The square of correlation coefficient and s2 of heuristic method were 0.80 and 0.10, respectively. In gene expression programming, the square of correlation coefficient and mean square error for training set were 0.91 and 0.04. The square of correlation coefficient and mean square error for test set are 0.86 and 0.1. This nonlinear model has stronger predictive ability to develop the targeted drugs of COVID-19.

Combined Luteolin and Indole-3-Carbinol Synergistically Constrains ERα-Positive Breast Cancer by Dual Inhibiting Estrogen Receptor Alpha and Cyclin-Dependent Kinase 4/6 Pathway in Cultured Cells and Xenograft Mice.

The high concentrations of individual phytochemicals in vitro studies cannot be physiologically achieved in humans. Our solution for this concentration gap between in vitro and human studies is to combine two or more phytochemicals. We screened 12 phytochemicals by pairwise combining two compounds at a low level to select combinations exerting the synergistic inhibitory effect of breast cancer cell proliferation. A novel combination of luteolin at 30 µM (LUT30) and indole-3-carbinol 40 µM (I3C40) identified that this combination (L30I40) synergistically constrains ERα+ breast cancer cell (MCF7 and T47D) proliferation only, but not triple-negative breast cancer cells. At the same time, the individual LUT30 and I3C40 do not have this anti-proliferative effect in ERα+ breast cancer cells. Moreover, this combination L30I40 does not have toxicity on endothelial cells compared to the current commercial drugs. Similarly, the combination of LUT and I3C (LUT10 mg + I3C10 mg/kg/day) (IP injection) synergistically suppresses tumor growth in MCF7 cells-derived xenograft mice, but the individual LUT (10 mg/kg/day) and I3C (20 mg/kg/day) do not show an inhibitory effect. This combination synergistically downregulates two major therapeutic targets ERα and cyclin dependent kinase (CDK) 4/6/retinoblastoma (Rb) pathway, both in cultured cells and xenograft tumors. These results provide a solid foundation that a combination of LUT and I3C may be a practical approach to treat ERα+ breast cancer cells after clinical trials.

Identifying the potential regulators of neutrophils recruitment in hepatocellular carcinoma using bioinformatics method.

BACKGROUND: Neutrophils play a crucial role in the development and progression of hepatocellular carcinoma (HCC); however, the mechanism underlying neutrophil recruitment is not fully understood. Therefore, we aimed to explore the potential genes or pathways related to neutrophil recruitment in the cancer microenvironment. METHODS: We downloaded TCGA HCC gene expression profiles, the abundance of 22 different immune cells in HCC patients, and patient survival information. We used Kaplan-Meier survival analysis to determine if neutrophils were related to survival. Next, we screened different expression genes (DEGs) between patients with high and low level of neutrophils. We then identified the transcription factor and its targets in the fence of DEGs. Then, we carried out enrichment analysis and gene set variation analysis (GSVA) for targets. Finally, we explored the potential mechanism of targets via calculating correlation scores. RESULTS: Our survival analysis results showed that neutrophils were significantly associated with patient survival. A total of 736 DEGs were screened. Next, we identified transcription factor larger E26 transformation-specific (ETS) homologous factor (EHF) and 702 targets of EHF from 736 DEGs. Among these targets, the level of FGD6 expression had the highest correlation with the level of EHF expression. Enrichment and GSVA analysis for FGD6 showed that the level of GO:0043547 had a positive regulatory effect on GTPase activity and the GO:0007010 cytoskeleton organization was significantly difference between the high and low neutrophils counts. By calculating the correlation between FGD6 and genes in GO:0043547 and GO:0007010, we identified RIC8B and SIPA1L3. CONCLUSIONS: These findings demonstrated that transcription factor EHF can influence recruitment of neutrophils by mediating the transcription of FGD6. Further investigations are needed to shed new light on EHF and its target FGD6.

Quantitative Structure-activity Relationships; Studying the Toxicity of Metal Nanoparticles.

BACKGROUND: Metal nanomaterials are widely used in various fields, including targeted therapy and diagnosis. They are extensively used in targeted drug delivery and local treatments. However, the toxicity associated with these materials could lead to severe adverse health effects. METHODS: In this study, we investigated the relationships between the toxicity and structures of metal nanoparticles by using theoretical calculations and quantitative structure-activity relationships. Twenty four physicochemical descriptors and toxicity data of 23 types of metal nanoparticles were selected as samples, and a multiple linear regression model was established to obtain a toxicity prediction equation with 5 descriptors with an R2 of 0.910. Structures of copper nanoparticles were designed based on the model, and the structure with low toxicity was searched. The multiple nonlinear regression model was used to further improve the prediction accuracy. RESULTS: The R2 values were 0.995 in the training set and 0.988 in the test set, which indicated that the prediction accuracy improved. Based on the result of multiple linear regression, we designed copper nanoparticles with low toxicity. CONCLUSION: The study confirmed that the quantitative structure-activity relationship was a reasonable method for predicting the toxicity and designing the structures with low toxicity of metal nanoparticles.

The computational and experimental studies on a 1, 2, 3-triazole compound and its special binding to three kinds of blood proteins.

A newly synthesized compound, ethyl 5-phenyl-2-(p-tolyl)-2H-1, 2, 3-triazole-4-carboxylate (EPPC) may be considered as a drug candidate and was exploited to study the structural and spectral properties by using quantum chemical calculation and multiple spectroscopic techniques. The results on theoretical spectrum of EPPC were consistent with experimental spectrum in great degree. In addition, EPPC has been as a special probe and investigated on the interactions with three kinds of blood proteins including human serum albumin (HSA), human immunoglobulin (HIgG) and bovine hemoglobin (BHb) by using UV-Vis, fluorescence spectroscopy and molecular modeling, respectively. Changes in various fluorescence and UV-Vis spectra were observed upon ligand binding along with a remarkable degree of fluorescence enhancement on complex formation under physiological condition with binding constant about 105 order of magnitudes, which caused the variations of conformation and microenvironment of these proteins in aqueous solution. The obtained results from the thermodynamic parameters calculated according to the van't Hoff equation indicated that the entropy change ΔS° and enthalpy change ΔH° were found to be 0.168 KJ/mol K and 22.154 KJ/mol for EPPC-HSA system, 0.284 KJ/mol K and 54.408 KJ/mol for EPPC-HIgG system, and 0.228 KJ/mol K and 37.548 KJ/mol for EPPC-BHb system, respectively, which demonstrated that the primary binding pattern is determined by hydrophobic interaction. The results of docking and molecular dynamics simulation using three proteins crystal models revealed that EPPC could bind to three proteins well into hydrophobic cavity, which showed good consistence with the spectroscopic measurements.Communicated by Ramaswamy H. Sarma.