Synthesis, molecular docking studies, and in vitro evaluation of 1,3,5-triazine derivatives as promising antimicrobial agents

Bioinformatic investigation of Nipah virus surface protein mutations: Molecular docking with Ephrin B2 receptor, molecular dynamics simulation, and structural impact analysis

The SARS-CoV-2 outbreak resulted in significant challenges and loss of life. The Nipah virus, known for its high infectivity and severity, was designated an emergency concern by the World Health Organization. To understand its mutations, the Nipah virus proteins were analyzed extensively, with a focus on the essential G and F proteins responsible for viral entry into host cells. Our bioinformatics analysis unveiled multiple mutations, including simultaneous mutations within a single sequence. Notably, the G273S mutation in the F protein was identified as a potential cause of structural damage, which carries significant implications for vaccine development. Comparing the docking scores of G and F proteins with the Ephrin B2 receptor, it was found that the Y228H mutation in the G protein and the D252G mutation in the F protein likely affect virus entry into host cells. Moreover, our investigation into stability and deformability highlighted the impact of the Y228H mutation in the G protein complex. Molecular dynamics simulations revealed increased flexibility and conformational changes in the G protein complex with the Y228H mutation compared with the known complex. Furthermore, evaluating the root mean square deviation variation demonstrated greater dynamic behavior in the G protein complex and the Ephrin B2 receptor complex. This comprehensive study provides valuable insights into Nipah virus mutations, their significance for vaccine development, and the importance of understanding protein complex behavior in drug discovery. The identified mutations, especially G273S and Y228H, hold crucial implications for future research and potential interventions against the Nipah virus.

s-Triazine Derivatives Functionalized with Alkylating 2-Chloroethylamine Fragments as Promising Antimicrobial Agents: Inhibition of Bacterial DNA Gyrases, Molecular Docking Studies, and Antibacterial and Antifungal Activity

The spectrum of biological properties of s-triazine derivatives is broad and includes anti-microbial, anti-cancer, and anti-neurodegenerative activities, among others. The s-triazine molecule, due to the possibility of substituting three substituents, offers many opportunities to obtain hybrid compounds with a wide variety of activities. A group of 1,3,5 triazine derivatives containing a dipeptide, 2-ethylpiperazine, and a methoxy group as substituents was screened for their antimicrobial activity. An in vitro study was conducted on pathogenic bacteria (E. coli, S. aureus, B. subtilis, and M. luteus), yeasts (C. albicans), and filamentous fungi (A. fumigatus, A. flavus, F. solani, and P. citrinum) via microdilution in broth, and the results were compared with antibacterial (Streptomycin) and antifungal (Ketoconazole and Nystatin) antibiotics. Several s-triazine analogues have minimal inhibitory concentrations lower than the standard. To confirm the inhibitory potential of the most active compounds against gyrases E. coli and S. aureus, a bacterial gyrases inhibition assay, and molecular docking studies were performed. The most active s-triazine derivatives contained the -NH-Trp(Boc)-AlaOMe, -NH-Asp(OtBu)-AlaOMe, and -NH-PheOMe moieties in their structures.

Synthesis and Antitumor Activity of Panaxadiol Pyrazole and Isooxazole Derivatives

In this study, we designed and synthesized 19 nitrogen-containing heterocyclic derivatives of panaxadiol (PD). We first reported the antiproliferative activity of these compounds against four different tumor cells. The results of the MTT assay showed that the PD pyrazole derivative (compound 12b) had the best antitumor activity and could significantly inhibit the proliferation of four tested tumor cells. For A549 cells, the IC50 value was as low as 13.44±1.23 μM. Western blot analysis showed that the PD pyrazole derivative was a bifunctional regulator. On the one hand, it can down-regulate the expression of HIF-1α by acting on PI3 K/AKT signaling pathway in A549 cells. On the other hand, it can induce the decrease of CDKs protein family and E2F1 protein expression levels, thus playing a crucial role in cell cycle arrest. According to the results of molecular docking, we found that multiple hydrogen bonds were formed between the PD pyrazole derivative and two related proteins, and the docking score of the derivative was also significantly higher than that of the crude drug. In summary, the study of the PD pyrazole derivative laid a foundation for the development of ginsenoside as an antitumor agent.

Synthesis and Antiproliferative Activity of a New Series of Mono- and Bis(dimethylpyrazolyl)-s-triazine Derivatives Targeting EGFR/PI3K/AKT/mTOR Signaling Cascades

Here, we synthesized a newseries of mono- and bis(dimethylpyrazolyl)-s-triazine derivatives. The synthetic methodology involved the reaction of different mono- and dihydrazinyl-s-triazine derivatives with acetylacetone in the presence of triethylamine to produce the corresponding target products in high yield and purity. The antiproliferative activity of the novel mono- and bis(dimethylpyrazolyl)-s-triazine derivatives was studied against three cancer cell lines, namely, MCF-7, HCT-116, and HepG2. N-(4-Bromophenyl)-4-(3,5-dimethyl-1H-pyrazol-1-yl)-6-morpholino-1,3,5-triazin-2-amine 4f, N-(4-chlorophenyl)-4,6-bis(3,5-dimethyl-1H-pyrazol-1-yl)-1,3,5-triazin-2-amine 5c, and 4,6-bis(3,5-dimethyl-1H-pyrazol-1-yl)-N-(4-methoxyphenyl)-1,3,5-triazin-2-amine 5d showed promising activity against these cancer cells: 4f [(IC₅₀ = 4.53 ± 0.30 μM (MCF-7); 0.50 ± 0.080 μM (HCT-116); and 3.01 ± 0.49 μM (HepG2)]; 5d [(IC₅₀ = 3.66 ± 0.96 μM (HCT-116); and 5.42 ± 0.82 μM (HepG2)]; and 5c [(IC₅₀ = 2.29 ± 0.92 μM (MCF-7)]. Molecular docking studies revealed good binding affinity with the receptor targeting EGFR/PI3K/AKT/mTOR signaling cascades. Compound 4f exhibited potent EGFR inhibitory activity with an IC₅₀ value of 61 nM compared to that of Tamoxifen (IC₅₀ value of 69 nM), with EGFR inhibition of 83 and 84%, respectively, at a concentration of 10 μM. Interestingly, 4f showed remarkable PI3K/AKT/mTOR inhibitory activity with 0.18-, 0.27-, and 0.39-fold decrease in their concentration (reduction in controls from 6.64, 45.39, and 86.39 ng/mL to 1.24, 12.35, and 34.36 ng/mL, respectively). Hence, the synthetic 1,3,5-triazine derivative 4f exhibited promising antiproliferative activity in HCT-116 cells through apoptosis induction by targeting the EGFR and its downstream pathway.

Molecular design, molecular docking and ADMET study of cyclic sulfonamide derivatives as SARS-CoV-2 inhibitors

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) continues to spread globally with more than 172 million confirmed cases and 3.57 million deaths. Cyclic sulfonamide derivative is identified as a successful compound and showed anti-SARS-CoV-2 activity. In this study, the structure and activity relationships of 35 cyclic sulfonamide compound inhibitors are investigated by using three-dimensional quantitative structure-activity relationship (3D-QSAR) and holographic quantitative structure-activity relationship (HQSAR). Two models with good statistical parameters and reliable predictive ability are obtained from the same training set, including Topomer CoMFA (q2= 0.623,r2= 0.938,rpred2= 0.893) model and HQSAR (q2= 0.704,r2= 0.958,rpred2=0.779) model. The established models not only have good stability, but also show good external prediction ability for the test set. The contour and color code maps of the models provide a lot of useful information for determining the structural requirements which might affect the activity; this information paves the way for the design of four novel cyclic sulfonamide compounds, and predictes their pIC₅₀ values. We explore the interaction between the newly designed molecule and SARS-CoV-2 3CLpro by molecular docking. The docking results show that GLU166, GLN192, ALA194, and VAL186 may be the potential active residues of the SARS-CoV-2 inhibitor evaluated in this study. Finally, the oral bioavailability and toxicity of the newly designed cyclic sulfonamide compounds are evaluated and the results show that the four newly designed cyclic sulfonamide compounds have major ADMET properties and can be used as reliable inhibitors against COVID-19. These results may provide useful insights for the design of effective SARS-CoV-2 inhibitors.

Exploring the mechanism of Yixinyin for myocardial infarction by weighted co-expression network and molecular docking

Yixinyin, the traditional Chinese medicine, has the effects of replenishing righteous qi, and promoting blood circulation to eliminate blood stagnation. It is often used to treat patients with acute myocardial infarction (MI). The purpose of our study is to explore the key components and targets of Yixinyin in the treatment of MI. In this study, we analyzed gene expression data and clinical information from 248 samples of MI patients with the GSE34198, GSE29111 and GSE66360 data sets. By constructing a weighted gene co-expression network, gene modules related to myocardial infarction are obtained. These modules can be mapped in Yixinyin PPI network. By integrating differential genes of healthy/MI and unstable angina/MI, key targets of Yixinyin for the treatment of myocardial infarction were screened. We validated the key objectives with external data sets. GSEA analysis is used to identify the biological processes involved in key targets. Through molecular docking screening, active components that can combine with key targets in Yixinyin were obtained. In the treatment of myocardial infarction, we have obtained key targets of Yixinyin, which are ALDH2, C5AR1, FOS, IL1B, TLR2, TXNRD1. External data sets prove that they behave differently in the healthy and MI (P < 0.05). GSEA enrichment analysis revealed that they are mainly involved in pathways associated with myocardial infarction, such as viral myocarditis, VEGF signaling pathway and type I diabetes mellitus. The docking results showed that the components that can be combined with key targets in YixinYin are Supraene, Prostaglandin B1, isomucronulatol-7,2'-di-O-glucosiole, angusifolin B, Linolenic acid ethyl ester, and Mandenol. For that matter, they may be active ingredients of Yixinyin in treating MI. These findings provide a basis for the preliminary research of myocardial infarction therapy in traditional Chinese medicine and provide ideas for the design of related drugs.

A computational approach for designing novel SARS-CoV-2 Mpro inhibitors: combined QSAR, molecular docking, and molecular dynamics simulation techniques

The promising compound T₂₁ for treating COVID-19 at the active site of SARS-CoV-2 M^pro.