Identification by molecular dynamic simulation and in vitro validation of SISB-A1, N-[1-(4-bromophenyl)-3-methyl-1H-pyrazol-5-yl]-2-[(2-oxo-4-phenyl-2H-chromen-7-yl) oxy], as an inhibitor of the AblT315I mutant kinase to combat imatinib resistance in chronic myeloid leukemia

The discovery of imatinib, a specific inhibitor of Abl kinase, revolutionized the therapeutic approach to chronic myeloid leukemia (CML); however, its efficacy can be impeded by the emergence of novel mutations within the kinase domain, particularly AblT315I, that lead to the development of drug resistance. It therefore remains necessary to identify specific inhibitors that can effectively target imatinib-resistant CML harboring the AblT315I mutation. A natural product library sourced from the ZINC database was screened against the experimental structure of AblT315I kinase to identify compounds that selectively target the mutated kinase. The top-scoring compound was empirically tested for inhibition of AblT315I kinase using a luminescence-based kit and for impact on cellular proliferation using the BaF3-BCR-ABL-T315I stable cell line. Computational docking and molecular dynamic simulations identified the compound SISB-A1, N-[1-(4-bromophenyl)-3-methyl-1H-pyrazol-5-yl]-2-[(2-oxo-4-phenyl-2H-chromen-7-yl)oxy] acetamide, to effectively bind the catalytic domain of the mutant AblT315I kinase. Moreover, SISB-A1 exhibited greater preference than imatinib for amino acid residues of the mutant kinase's active site, including isoleucine 315. MMPBSA-based Gibbs binding free energy estimation predicted SISB-A1 to have a free energy of -51.5 versus -65.0 kcal/mol for the conventional AblT315I inhibitor ponatinib. Cell proliferation assays showed SISB-A1 to have a GI50 of 164.0 nM against the ABL-T315I stable cell line, whereas imatinib had a GI50 of 5035 nM. The IC50 value obtained for SISB-A1 against the AblT315I kinase was 197.9 nM. The results indicate SISB-A1 to have a notable ability to bind the catalytic domain of the AblT315I mutant kinase and effectively suppress its activity, thereby surpassing the associated resistance to imatinib. Continued advancement of this lead compound has the potential to yield innovative therapeutics for imatinib-resistant CML.

Computational analysis and in vitro evaluation of TMF 104, for its antioxidant, antimicrobial, and anticancer efficacies

Benzylidene chromanones are small molecules, structurally similar to active phytochemicals. Herein, we report one novel benzylidene chromanone, TMF 104, for its bio-efficacies. Its computational docking for Vanin-1, antioxidant, free radical scavenging capacities, antimicrobial effects, and anticancer efficacy were analyzed. TMF 104 predicated strong binging to Vanin-1 protein with a docking energy of -8.1 kcal/mol. The compound dose-dependently exhibited free-radical scavenging and antioxidant activities when tested in vitro. The compound also had remarkable activity against Salmonella typhimurium, Enterococcus faecalis, Staphylococcus aureus, and Escherichia coli with minimum inhibitory concentration values of 1.5, 2.0, 12.5, and 13.5 μg/ml, respectively. The compound was also effective against Bacillus cereus and Pseudomonas aeruginosa albeit at higher concentrations. TMF 104 dose-dependently inhibited the proliferation of MCF-7, NCI H460, and Caki-1 cells with respective GI₅₀ values of 24.51, 21.95, and 32.95 μg/ml, whereas the compound was toxic to normal Vero cells at much higher concentration of 264.70 μg/ml. The compound also aided in apoptosis and increased the sub G₀ /G₁ phase of the cell cycle in all three cancer cells tested. Our study identified a novel, potent benzylidene analogue with potent antioxidant, antimicrobial, and anticancer activities, which drives further attention for further research.

Insilco and Invitro approaches identify novel dual PI3K/AKT pathway inhibitors to control acute myeloid leukemia cell proliferations

Acute myeloid leukemia (AML) is characterized by disruption of intracellular signaling due to aberration of extracellular signaling pathways, namely PI3K/AKT cascade, by dysregulating erythropoiesis and myelopoiesis. Therefore, inhibition of PI3K/AKT, either individually, or by dual inhibitors, is shown to be effective in suppression of tumorigenesis. To increase the therapeutic viability and decrease adverse effects, including cytotoxicity due to off-target kinase inhibitions, customized targeted pharmacological agents are needed that would have greater treatment potential. In this work, using an interdisciplinary approach, we have identified dual inhibitors targeted to PI3K and AKT to significantly repress the cell proliferation in AML cancers. Diversity-based high-throughput virtual screening (D-HTVS) technique followed by conventional docking approach identified small molecules from ChemBridge library, having high binding affinity for PI3KCG subunit. Further computational screening of top identified PI3K-specific lead molecules predicts dual inhibitors with high binding affinity for AKT. To rule out the possibility for cross-reaction/off-target effects of identified small molecules, lead compounds having nil or negligible binding to PI3KCA- and PI3KCB subunits were chosen. Computational screening, enzyme inhibition and cell proliferation assays show compound C16,5-{[(1,3-dioxo-1H-benzo[de]isoquinolin-2(3H)-yl)amino]methylene}-1-phenyl-2,4,6(1H,3H,5H)-pyrimidinetrione has better affinity for PI3KCG, delta, and AKT kinases compared to their respective known/established inhibitors, and has significant anti-cell proliferation activity in AML cells with a GI₅₀ values of 77.25 nM and 49.65 nM in THP-1 and HL-60 cells, respectively. This work proposes a novel dual inhibitor that selectively targets PI3K/AKT and suppresses cell proliferation in AML cells as a potential lead molecule for treating AML cancers.

Mitofusin-2 in cancer: Friend or foe?

Cancer is a category of disorders characterized by excessive cell proliferation with the ability to infiltrate or disseminate to other organs of the body. Mitochondrial dysfunction, as one of the most prominent hallmarks of cancer cells, has been related to the onset and development of various cancers. Mitofusin 2 (MFN2) is a major mediator of mitochondrial fusion, endoplasmic reticulum (ER)-mitochondria interaction, mitophagy and axonal transport of mitochondria. Available data have shown that MFN2, which its alterations have been associated with mitochondrial dysfunction, could affect cancer initiation and progression. In fact, it showed that MFN2 may have a double-edged sword effect on cancer fate. Precisely, it demonstrated that MFN2, as a tumor suppressor, induces cancer cell apoptosis and inhibits cell proliferation via Ca²⁺ and Bax-mediated apoptosis and increases P21 and p27 levels, respectively. It also could suppress cell survival via inhibiting PI3K/Akt, Ras-ERK1/2-cyclin D1 and mTORC2/Akt signaling pathways. On the other hand, MFN2, as an oncogene, could increase cancer invasion via snail-mediated epithelial-mesenchymal transition (EMT) and in vivo tumorigenesis. While remarkable progress has been achieved in recent decades, further exploration is required to elucidate whether MFN2 could be a friend or it's an enemy. This study aimed to highlight the different functions of MFN2 in various cancers.

GC/MS characterization and computational kinome-wide screening of pomegranate fruit extract identifies key phytochemicals interacting to CDK kinases implicated in acute myeloid leukemia cells

Punica granatum (Pomegranate fruit) and its constituents are proven effective against various cancer types. However, a kinome-wide screening for the active phytochemicals against kinases is not reported. This study aims in validating pomegranate fruit extract (PFE) against acute myeloid leukemia (AML) cells, and computationally identifying the phytochemicals interacting with active kinases. PFE was made with Soxhlet extractor using absolute ethanol. Gas-chromatography-mass spectroscopy (GC-MS) for phytochemical identification and MTT assay for cytotoxicity in AML (THP-1, TF-1 and HL-60) cells were performed. Apoptosis, CDK5 and CDK8 were assessed with flow cytometry. Kinase profiling was performed using In silico kinome screening. GC-MS analysis revealed 38 bioactive phytochemicals in PFE including pyrazoles, aldehydes, phenols, esters, pyranosides, and octadecadienoic acids. The extract inhibited the AML cell proliferations with GI₅₀ values of 195.5 μg/ml, 289.1 μg/ml, and 353.5 μg/ml in THP-1, THP-1, and HL-60 cells, respectively. PFE also exhibited a dose-responsive increase in apoptotic cell populations when treated to the AML cells. Computational screening and modeling predicted three critical constituents, viz., Deoxyartemisinin, 3-Methyl-3-phenyl-3H-indazole, and 8-fluoro-5,6-dimethoxy-3,4-dihydro-2H-naphthalen-1-one of pomegranate extract to interact mainly with cyclin-dependent kinases, including CDK5 and CDK8. Proteinand ligand docking predicted binding energies, and binding pose for top candidate lead molecules. In vitro assay exhibited the anticancer properties of PFE in AML cells. Computational kinome screening predicted top three PFE constituents targeting CDKs which may be responsible for the demonstrated anticancer efficacy of the extract against AML. This hypothesis further aligned with observed efficacy of PFE to inhibit CDK5 and CDK8 in all AML cells tested. PRACTICAL APPLICATIONS: Though Punica granatum (Pomegranate fruit) and its constituents are proven effective against various cancer types, a kinome-wide screening for the active phytochemicals against kinases is not reported. In this study, we have conducted GC/MS characterization of the active phytochemicals of PFE and have performed a kinome-wide screening for all the 38 identified compounds toward 310 active kinases commonly expressed in cancers. These observations warrant isolation and further evaluation of these phytochemicals or their analogues as effective CDK inhibitors against AML proliferation. Further, the computational methods used in this study will throw light on literature for new options of kinome panel screening of active phytochemicals or small molecules.

CB-RAF600E-1 exerts efficacy in vemurafenib-resistant and non-resistant-melanoma cells via dual inhibition of RAS/RAF/MEK/ERK and PI3K/Akt signaling pathways

Background and Aim

Predicting novel dual inhibitors to combat adverse effects such as the development of resistance to vemurafenib in melanoma treatment due to the reactivation of MAPK and PI3K/AKT signaling pathways is studied to help in reversal of cancer symptoms.

Reversal of cancer symptoms in melanoma associated with vemurafenib resistance is driven by reactivation of MAPK and PI3K/Akt signaling pathways. Novel dual inhibitors targeting these proteins would be beneficial to combat resistance.

Methods

High-throughput virtual screening of the ChemBridge library against B-RAFV600E and Akt was performed using an automated protocol with the AutoDock VINA program. Luminescence and time-resolved fluorescence kits were used to measure enzyme activities. The MTT assay was used to determine proliferation in normal and vemurafenib-resistant A375 cells. Flow cytometry was used to examine apoptosis, cell cycle, and phosphorylation of ERK/Akt signaling pathway.

Results

High-throughput screening from the ChemBridge library identified 15 compounds with high binding energy towards B-RAFV600E; among these, CB-RAF600E-1 had the highest ΔG_binding score −11.9 kcal/mol. The compound also had a high affinity towards Akt, with a ΔG_binding score of −11.5 kcal/mol. CB-RAF600E-1 dose-dependently inhibited both B-RAFV600E and Akt with IC₅₀ values of 635 nM and 154.3 nM, respectively. The compound effectively controlled the proliferations of normal and vemurafenib-resistant A375 cells, with GI₅₀ values of 222.3 nM and 230.5 nM, respectively. A dose-dependent increase in the sub G₀/G₁ phase of the cell cycle and total apoptosis was observed following compound treatment in both normal and vemurafenib-resistant melanoma cells. Treatment with CB-RAF600E-1 decreased the pERK/pAkt dual-positive populations in normal and vemurafenib-resistant A375 cells.

Conclusion

CB-RAF600E-1, identified as a novel dual inhibitor effective against normal and vemurafenib-resistant melanoma cells, requires further attention for development as an effective chemotherapeutic agent for melanoma management.

Mathematical modeling and stability analysis of the COVID-19 with quarantine and isolation

The present paper focuses on the modeling of the COVID-19 infection with the use of hospitalization, isolation and quarantine. Initially, we construct the model by spliting the entire population into different groups. We then rigorously analyze the model by presenting the necessary basic mathematical features including the feasible region and positivity of the problem solution. Further, we evaluate the model possible equilibria. The theoretical expression of the most important mathematical quantity of major public health interest called the basic reproduction number is presented. We are taking into account to study the disease free equilibrium by studying its local and global asymptotical analysis. We considering the cases of the COVID-19 infection of Pakistan population and find the parameters using the estimation with the help of nonlinear least square and have R 0 ≈ 1 . 95 . Further, to determine the influence of the model parameters on disease dynamics we perform the sensitivity analysis. Simulations of the model are presented using estimated parameters and the impact of various non-pharmaceutical interventions on disease dynamics is shown with the help of graphical results. The graphical interpretation justify that the effective utilization of keeping the social-distancing, making the quarantine of people (or contact-tracing policy) and to make hospitalization of confirmed infected people that dramatically reduces the number of infected individuals (enhancing the quarantine or contact-tracing by 50% from its baseline reduces 84% in the predicted number of confirmed infected cases). Moreover, it is observed that without quarantine and hospitalization the scenario of the disease in Pakistan is very worse and the infected cases are raising rapidly. Therefore, the present study suggests that still, a proper and effective application of these non-pharmaceutical interventions are necessary to curtail or minimize the COVID-19 infection in Pakistan.

High-throughput virtual screening and preclinical analysis identifies CB-1, a novel potent dual B-Raf/c-Raf inhibitor, effective against wild and mutant variants of B-Raf expression in colorectal carcinoma

Paradoxical Raf activation via Raf dimerization is a major drawback of wild/mutant B-Raf inhibitors. Herein, we report that CB-1 a novel, potent B-Raf/c-Raf dual inhibitor, effective against colon cancer cells, irrespective of their genetic status. High-throughput virtual screening of the ChemBridge library against wild B-Raf (B-Raf^WT), mutant B-Raf (B-Raf^V600E), and c-Raf was performed using an automated protocol with the AutoDock-VINA. Caco-2 and HT-29 cells were used. Of the 23,365 compounds screened computationally, CB-1 showed the highest binding energy towards B-Raf^WT with a ΔG_binding score of - 13.0 kcal/mol. The compound was also predicted to be effective against B-Raf^V600E and c-Raf molecules with ΔG_binding energies of - 10.6 and - 10.1 kcal/mol, respectively. The compound inhibited B-Raf^WT, B-Raf^V600E and c-Raf kinases with IC₅₀ values of 27.13, 51.70, and 40.23 nM, respectively. The GI₅₀ value of CB-1 was 247.9 nM in B-Raf^WT-expressing Caco-2 cells and 352.4 nM in B-RafV600E-expressing HT-29 cells. Dose-dependent increases in total apoptosis and G₁ cell cycle phase arrest was observed in CB-1-treated colon cancer cells. The compound decreased B-Raf expression in both wild and mutant colon cancer cells. CB-1, a novel, potent dual B-Raf/c-Raf inhibitor was effective against colon cancer cells bearing wild-type and mutant variants of B-Raf expression.

FNF-12, a novel benzylidene-chromanone derivative, attenuates inflammatory response in in vitro and in vivo asthma models mediated by M2-related Th2 cytokines via MAPK and NF-kB signaling

BACKGROUND AND AIM

This study evaluates a novel benzylidene-chromanone derivative, FNF-12, for efficacy in in vitro and in vivo asthma models.

METHODS

Rat basophilic leukemia (RBL-2H3) and acute monocytic leukemia (THP-1)-derived M2 macrophages were used. Human whole blood-derived neutrophils and basophils were employed. Flow cytometry was used for studying key signalling proteins. Platelet activation factor (PAF)-induced asthma model in guinea pigs was used for in vivo studies.

RESULTS

The chemical structure of FNF-12 was confirmed with proton-nuclear mass resonance (NMR) and mass spectroscopy. FNF-12 controlled degranulation in RBL-2H3 cells with an IC₅₀ value of 123.7 nM and inhibited TNF-α release from these cells in a dose-responsive way. The compound effectively controlled the migration and elastase release in activated neutrophils. IC₅₀ value in the FcεRI-basophil activation assay was found to be 205 nM. FNF-12 controlled the release of lipopolysaccharide (LPS)-induced interleukin-10, I-309/CCL1 and MDC/CCL22 in THP-1 derived M2 macrophages. The compound suppressed LPS-induced mitogen activated protein kinase (MAPK)-p-p38 and nuclear factor kappa B(NF-kB)-p-p65 expression in these cells. A dose-dependent decrease in the accumulation of total leucocytes, eosinophils, neutrophils and macrophages was observed in PAF-induced animal models.

CONCLUSION

FNF-12 was able to control the inflammatory responses in in vitro and in vivo asthma models, which may be driven by controlling M2-related Th2 cytokines via MAPK and NF-kB signaling.

Cassia auriculata leaf extract ameliorates diabetic nephropathy by attenuating autophagic necroptosis via RIP-1/RIP-3-p-p38MAPK signaling

Diabetic nephropathy (DN) is the most common manifestation of high glucose induced diabetes mellitus. In this study, we report the effects of Cassia auriculata ethanol leaf extract (CALE) on DN-associated cell toxicity and complications. The effects of CALE were screened in vitro using RGE cells. Cell viability was assessed using MTT and flow cytometry. Male Sprague-Dawley rats were divided into control, DN and treatment groups (n = 8). The DN and treatment groups received 60 mg/kg/bw of streptozotocin in citrate buffer, while the treatment group was administered 150 mg/kg/bw of CALE for 10 weeks. Biochemical analysis was conducted using spectrophotometry. Kidney tissues were analyzed using hematoxylin and eosin staining and transmission electron microscopy. CD365-KIM-1 expression was assessed using flow cytometry and signalling proteins were detected using western blotting. Treatment with 30-mM glucose reduced the viability of RGE cells in a time-dependent manner and increased the population of dead RGE cells. Cotreatment with CALE reduced cell death and glucose induced protein expression of LC3-II, RIP-1 and RIP-3 in a dose-dependent manner. In addition, CALE improved the biochemical complications, renal dysfunction and pathophysiology of rats with DN and partially or fully restored the expression of key DN-associated signalling proteins, such as KIM-1 LC3-II, RIP-1, RIP-3 and p-p38MAPK in kidney cells. CALE showed protective effects, and improved DN-associated complications in RGE cells under high glucose stress conditions, potentially by inhibiting autophagic-necroptosis signals. Additionally, CALE improved the biochemical and pathological features of kidney injury while reducing autophagic-necroptosis in rat renal cells via the LC3-II-RIP-p38MAPK pathway. PRACTICAL APPLICATIONS: Results from the current investigation will add information to the literature on glucose induced renal toxicity and the protective effects of CALE over the complications of diabetic nephropathy (DN). The mechanistic investigations of the study will add light on the autophagic/necroptosis signals in DN and open new routes of investigations to study the efficacy of CALE in diabetes-related complications.

Computational and in vitro characterization of ICY-5: A potential candidate promoting mitochondrial apoptosis via the c-MET and STAT3 pathways

Targeted chemotherapy remains the primary choice in controlling various forms of breast cancer (BC) due to its heterogenous gene expressions in various subtypes. In silico and in vitro evaluation of ICY-5, a novel arylidene analogue against c-MET, was performed. ICY-5 exhibited a docking score of -9.6 kcal/mol in inactive conformation and, - 8.6 kcal/mol in active conformation for c-MET. ICY-5 inhibited c-MET enzyme with an IC₅₀ of 34.34 nM. The compound effectively inhibited MDA-MB 231 and MCF-7 cell proliferation, with GI₅₀ values of 62.61 and 75.31 nM, respectively, and hepatocyte growth factor (HGF)/R c-MET phosphorylation with IC₅₀ s of 71.41 and 83.77 nM, respectively. ICY-5 dose-dependently inhibited HGF-induced transmigration, cell scattering, invasion and altered cell cycle. An increase in apoptotic populations of these cells, with a dose-dependent decease in phosphorylation of STAT3 protein was observed. Furthermore, ICY-5 upregulated the caspase-3, caspase-9, Bcl-2-associated X and survivin, and downregulated Bcl-2, vascular endothelial growth factor, matrix metalloproteinase-2 (MMP-2), and MMP-9 in both BC cell lines. In summary, ICY-5 exhibited excellent efficacy in BC cells, targeting c-MET/SAT-3-mediated mitochondrial apoptosis. Further research will be required to ascertain ICY-5 suitability as a targeted chemotherapeutic against multiple forms of BC.