Identification of novel natural drug candidates against BRAF mutated carcinoma; An integrative in-silico structure-based pharmacophore modeling and virtual screening process

In-vitro and in-silico evaluation of rue herb for SARS-CoV-2 treatment

SARS-CoV-2, a β-coronavirus responsible for the COVID-19 pandemic, has resulted in approximately 4.9 million fatalities worldwide. Despite the urgent need, there is currently no specific therapeutic developed for treating or preventing SARS-CoV-2 infections. The virus enters the host by engaging in a molecular interaction between the viral Spike glycoprotein (S protein) and the host ACE2 receptor, facilitating membrane fusion and initiating infection. Inhibiting this interaction could impede viral activity. Therefore, this study aimed to identify natural small molecules from perennial rue herb (Ruta graveolens) as potential inhibitors against the S protein, thus preventing virus infection. Initially, a screening process was conducted on 53 compounds identified from rue herbs, utilizing pharmacophore-based virtual screening approaches. This analysis resulted in the identification of 12 hit compounds. Four compounds, namely Amentoflavone (CID: 5281600), Agathisflavone (CID: 5281599), Vitamin P (CID: 24832108), and Daphnoretin (CID: 5281406), emerged as potential S protein inhibitors through molecular docking simulations, exhibiting binding energies in kcal/mol of -9.2, -8.8, -8.2, and -8.0, respectively. ADMET analysis revealed favorable pharmacokinetics and toxicity profiles for these compounds. The compounds' stability with respect to the target S protein was evaluated using MD simulation and MM-GBSA approaches. The analysis revealed the stability of the selected compounds with the target protein. Also, PCA revealed distinctive movement patterns in four selected compounds, offered valuable insights into their functional behaviors and potential interactions. In-vitro assays revealed that rue herb extracts containing these compounds displayed potential inhibitory properties against the virus, with an IC50 value of 1.299 mg/mL and a cytotoxic concentration (CC50) value of 11.991 mg/mL. The compounds derived from rue herb, specifically Amentoflavone, Agathisflavone, Vitamin P, and Daphnoretin, show promise as candidates for the therapeutic intervention of SARS-CoV-2-related complications.

Identification of Critical Amino Acid Residues of a Two-Component Sensor Protein for Signal Sensing in Porphyromonas gingivalis Fimbriation via Random Mutant Library Construction

Porphyromonas gingivalis (Pg) utilizes FimA fimbriae to colonize the gingival sulcus and evade the host immune system. The biogenesis of all FimA-related components is positively regulated by the FimS-FimR two-component system, making the FimS sensory protein an attractive target for preventing Pg infection. However, the specific environmental signal received by FimS remains unknown. We constructed random Pg mutant libraries to identify critical amino acid residues for signal sensing by FimS. Optimized error-prone polymerase chain reaction (PCR) was used to introduce a limited number of random mutations in the periplasmic-domain-coding sequence of fimS, and expression vectors carrying various mutants were generated by inverse PCR. More than 500 transformants were obtained from the fimS-knockout Pg strain using the Escherichia coli-Pg conjugal transfer system, whereas only ~100 transformants were obtained using electroporation. Four and six transformant strains showed increased and decreased fimA expression, respectively. Six strains had single amino acid substitutions in the periplasmic domain, indicating critical residues for signal sensing by FimS. This newly developed strategy should be generally applicable and contribute to molecular genetics studies of Pg, including the elucidation of structure-function relationships of proteins of interest.

Identification of potentially high drug-like VEGFR2/c-Met dual-target type II kinase inhibitors with symmetric skeletons based on structural screening

Vascular endothelial growth factor receptor 2 (VEGFR2) and c-Mesenchymal epithelial transition factor (c-Met) are tyrosine kinase receptors associated with the occurrence of malignant tumors. Studies have shown that inhibition of VEGFR2 promotes a feedback increase in c-Met, a mechanism linked to the emergence of resistance to VEGFR2 inhibitors. Therefore, treatment targeting both VEGFR2 and c-Met will have better application prospects. In this study, hierarchical virtual screening was performed on ZINC15, Molport and Mcule-ULTIMATE databases to identify potential VEGFR2/c-Met dual inhibitors. Firstly, the best pharmacophore model for each target was used to cross-screen the three databases, and the compounds that could match the two pharmacophore models were then retained based on the Fit Value of the respective crystal ligands. Compounds ZINC, MOL, and MLB named after their database sources were retained by binding pattern analysis and docking assessment. ADMET predictions indicated that ZINC had significantly higher oral bioavailability compared to the approved drug cabozantinib. This is likely due to ZINC's unique symmetrical backbone with less structure complexity, which may reduce the occurrence of adverse effects. Molecular dynamics simulations and binding free energy analysis showed that all three hit compounds were able to stably bind at the active site, but only ZINC could form high occupancy of hydrogen bonds with both VEGFR2 and c-Met, and also only ZINC had a higher binding free energy than crystal ligands, suggesting that ZINC was the most likely potential VEGFR2/c-Met dual-target inhibitor. This finding provides a promising starting point for the development of VEGFR2/c-Met dual-target inhibitors.Communicated by Ramaswamy H. Sarma.

Marine-derived sea urchin compounds as potential anti-cancer drug candidate against colorectal cancer: In silico and in vitro studies

Sea urchin-derived compounds are potential candidates for the development of effective drugs for the treatment of cancer diseases. In this study, 19 compounds derived from sea urchin (Diadema savignyi) were used to treat colorectal cancer using the HCT116 cell line. However, molecular docking, ADME (absorption, distribution, metabolism, and excretion), toxicity, molecular dynamic (MD) simulation, and molecular mechanics generalized Born surface area (MM-GBSA) were used to confirm the ligand-protein interaction. Interactions of Importin-11 receptor with sea urchin compounds reveal that four compounds have higher binding affinities (ranging from -8.6 to -7.1 kcal/mol). In vitro testing revealed that the CID 6432458 compound was effective (docking score of -8.6 kcal/mol) against the HCT116 cell line. The cytotoxicity of HCT116 has been documented, with an IC50 value of 6.885 ± 4. MTT assay, apoptosis analysis, and cell cycle assay were utilized to examine cell death in colorectal cancer. In the MTT experiment, 15 µM and 20 µM dosages were associated with 77% cell death; however, flow cytometry analysis using the IC50 value revealed that the selected chemical induced greater apoptosis in the HCT116 cell line (58.5%). The gene expression data revealed that the apoptotic gene BAX is expressed at a higher level than the BCL-2 gene. The IPO11 gene was downregulated during treatment. In the experiment involving the cell cycle, the S phase for the 30  µM dose showed 75.1% apoptosis, which was greater than the other concentrations used alone. These in silico and in vitro analysis will not only provide new information about Importin-11 receptor and insight into colorectal cancer but will also facilitate the development of natural compounds in a significant and worthwhile manner.

Younger Than 55 Years Old and BRAF V600E Mutation are Risk Factors for Lymph Node Metastasis in Papillary Thyroid Carcinomas ≤1.0 cm but Not in >1.0 cm

Background

Studies on the relationship between BRAF V600E mutation and the clinicopathologic features of papillary thyroid carcinoma (PTC), risk of lymph node metastasis in papillary thyroid microcarcinoma (PTMC) have shown inconsistent results.

Methods

In this retrospective analysis, clinicopathological data of the patients were collected, and molecular testing was done for BRAF V600E mutation. PTC patients are divided into PTC≤1.0cm (PTMC) and PTC>1.0cm, and the relationship between BRAF V600E mutation and clinicopathologic features was analyzed respectively.

Results

Of the 520 PTC patients, 432 (83.1%) were female and 416 (80.0%) were <55 years old. BRAF V600E mutation was detected in 422 (81.2%) tumour samples of PTC. There was no significant difference in the frequency of BRAF V600E mutation between different age groups. There were 250 (48.1%) patients with PTMC and 270 (51.9%) patients with PTC>1.0cm. BRAF V600E mutation was significantly associated with bilateral cancer (23.0% vs 4.9%, P=0.005) and lymph node metastasis (61.7% vs 39.0%, P=0.009) in PTMC patients, while BRAF V600E mutation was significantly associated with bilateral cancer (24.9% vs 12.3%, P=0.048) in PTC>1.0cm patients. Logistic regression analysis showed that, after adjusting for gender, Hashimoto's thyroiditis and calcification, we found that younger age (<55 years old) (OR: 2.384, 95% CI: 1.241-4.579, P=0.009) and BRAF V600E mutation (OR: 2.213, 95% CI: 1.085-4.512, P=0.029) were significantly associated with lymph node metastasis in PTMC, similar results were not obtained in PTC>1.0cm.

Conclusion

Younger age (<55 years old) and BRAF V600E mutation was independent risk factor for lymph node metastasis in PTMC.

Pharmacophore-based virtual screening approaches to identify novel molecular candidates against EGFR through comprehensive computational approaches and in-vitro studies

Alterations to the EGFR (epidermal growth factor receptor) gene, which primarily occur in the axon 18-21 position, have been linked to a variety of cancers, including ovarian, breast, colon, and lung cancer. The use of TK inhibitors (gefitinib, erlotinib, lapatinib, and afatinib) and monoclonal antibodies (cetuximab, panitumumab, and matuzumab) in the treatment of advanced-stage cancer is very common. These drugs are becoming less effective in EGFR targeted cancer treatment and developing resistance to cancer cell eradication, which sometimes necessitates stopping treatment due to the side effects. One in silico study has been conducted to identify EGFR antagonists using other compounds, databases without providing the toxicity profile, comparative analyses, or morphological cell death pattern. The goal of our study was to identify potential lead compounds, and we identified seven compounds based on the docking score and four compounds that were chosen for our study, utilizing toxicity analysis. Molecular docking, virtual screening, dynamic simulation, and in-vitro screening indicated that these compounds' effects were superior to those of already marketed medication (gefitinib). The four compounds obtained, ZINC96937394, ZINC14611940, ZINC103239230, and ZINC96933670, demonstrated improved binding affinity (-9.9 kcal/mol, -9.6 kcal/mol, -9.5 kcal/mol, and -9.2 kcal/mol, respectively), interaction stability, and a lower toxicity profile. In silico toxicity analysis showed that our compounds have a lower toxicity profile and a higher LD50 value. At the same time, a selected compound, i.e., ZINC103239230, was revealed to attach to a particular active site and bind more tightly to the protein, as well as show better in-vitro results when compared to our selected gefitinib medication. MTT assay, gene expression analysis (BAX, BCL-2, and β-catenin), apoptosis analysis, TEM, cell cycle assay, ELISA, and cell migration assays were conducted to perform the cell death analysis of lung cancer and breast cancer, compared to the marketed product. The MTT assay exhibited 80% cell death for 75 µM and 100µM; however, flow cytometry analysis with the IC50 value demonstrated that the selected compound induced higher apoptosis in MCF-7 (30.8%) than in A549.

Pharmacophore-Model-Based Virtual-Screening Approaches Identified Novel Natural Molecular Candidates for Treating Human Neuroblastoma

The mortality of cancer patients with neuroblastoma is increasing due to the limited availability of specific treatment options. Few drug candidates for combating neuroblastoma have been developed, and identifying novel therapeutic candidates against the disease is an urgent issue. It has been found that muc-N protein is amplified in one-third of human neuroblastomas and expressed as an attractive drug target against the disease. The myc-N protein interferes with the bromodomain and extraterminal (BET) family proteins. Pharmacologically inhibition of the protein potently depletes MYCN in neuroblastoma cells. BET inhibitors target MYCN transcription and show therapeutic efficacy against neuroblastoma. Therefore, the study aimed to identify potential inhibitors against the BET family protein, specifically Brd4 (brodamine-containing protein 4), to hinder the activity of neuroblastoma cells. To identify effective molecular candidates against the disease, a structure-based pharmacophore model was created for the binding site of the Brd4 protein. The pharmacophore model generated from the protein Brd4 was validated to screen potential natural active compounds. The compounds identified through the pharmacophore-model-based virtual-screening process were further screened through molecular docking, ADME (absorption, distribution, metabolism, and excretion), toxicity, and molecular dynamics (MD) simulation approach. The pharmacophore-model-based screening process initially identified 136 compounds, further evaluated based on molecular docking, ADME analysis, and toxicity approaches, identifying four compounds with good binding affinity and lower side effects. The stability of the selected compounds was also confirmed by dynamic simulation and molecular mechanics with generalized Born and surface area solvation (MM-GBSA) methods. Finally, the study identified four natural lead compounds, ZINC2509501, ZINC2566088, ZINC1615112, and ZINC4104882, that will potentially inhibit the activity of the desired protein and help to fight against neuroblastoma and related diseases. However, further evaluations through in vitro and in vivo assays are suggested to identify their efficacy against the desired protein and disease.