Molecular docking studies of phytochemicals against trehalose–6–phosphate phosphatases of pathogenic microbes

Targeted Drug Designing for Treating Masticatory Myofascial Pain Dysfunction Syndrome: An In Silico Simulation Study

Background Masticatory Myofascial Pain Dysfunction Syndrome (MMPDS) is a musculoligamentous disorder that shares similarities with temporomandibular joint pain and odontogenic pain. It manifests as dull or aching pain in masticatory muscles, influenced by jaw movement. Computer-aided drug design (CADD) encompasses various theoretical and computational approaches used in modern drug discovery. Molecular docking is a prominent method in CADD that facilitates the understanding of drug-bimolecular interactions for rational drug design, mechanistic studies & the formation of stable complexes with increased specificity and potential efficacy. The docking technique provides valuable insights into binding energy, free energy, and complex stability predictions. Aim The aim of this study was to use the docking technique for myosin inhibitors. Materials and methods Four inhibitors of myosin were chosen from the literature. These compound structures were retrieved from the Zinc15 database. Myosin protein was chosen as the target and was optimized using the RCSB Protein Data Bank. After pharmacophore modeling, 20 novel compounds were found and the SwissDock was used to dock them with the target protein. We compared the binding energies of the newly discovered compounds to those of the previously published molecules with the target. Results The results indicated that among the 20 molecules ZINC035924607 and ZINC5110352 exhibited the highest binding energy and displayed superior properties compared to the other molecules. Conclusion The study concluded that ZINC035924607 and ZINC5110352 exhibited greater binding affinity than the reported inhibitors of myosin. Therefore, these two molecules can be used as a potential and promising lead for the treatment of MMPDS and could be employed in targeted drug therapy.

Phytochemical profiling and cytotoxic potential of Arnebia nobilis root extracts against hepatocellular carcinoma using in-vitro and in-silico approaches

Hepatocellular carcinoma is the fifth most prevalent cancer worldwide. The emergence of drug resistance and other adverse effects in available anticancer options are challenging to explore natural sources. The current study was designed to decipher the Arnebia nobilis (A. nobilis) extracts for detecting phytochemicals, in-vitro evaluation of antioxidative and cytotoxic potentials, and in-silico prediction of potent anticancer compounds. The phytochemical analysis revealed the presence of flavonoids, phenols, tannins, alkaloids, quinones, and cardiac glycosides, in the ethanol (ANE) and n-hexane (ANH) extracts of A. nobilis. ANH extract exhibited a better antioxidant potential to scavenge DPPH, nitric oxide and superoxide anion radicals than ANE extract, which showed better potential only against H2O2 radicals. In 24 h treatment, ANH extract revealed higher cytotoxicity (IC50 value: 22.77 µg/mL) than ANH extract (IC50 value: 46.74 µg/mL) on cancer (HepG2) cells without intoxicating the normal (BHK) cells using MTT assay. A better apoptotic potential was observed in ANH extract (49.10%) compared to ANE extract (41.35%) on HepG2 cells using the annexin V/PI method. GCMS analysis of ANH extract identified 35 phytocompounds, from which only 14 bioactive compounds were selected for molecular docking based on druggability criteria and toxicity filters. Among the five top scorers, deoxyshikonin exhibited the best binding affinities of - 7.2, - 9.2, - 7.2 and - 9.2 kcal/mol against TNF-α, TGF-βR1, Bcl-2 and iNOS, respectively, followed by ethyl cholate and 2-Methyl-6-(4-methylphenyl)hept-2-en-4-one along with their desirable ADMET properties. The phytochemicals of ANH extract could be used as a promising drug candidate for liver cancer after further validations.

In Vitro Antibacterial Efficacy of Cymbopogon flexuosus Essential Oil against Aeromonas hydrophila of Fish Origin and in Silico Molecular Docking of the Essential Oil Components against DNA Gyrase-B and Their Drug-Likeness

In aquaculture, diseases caused by the Aeromonads with high antibiotic resistance are among the most common and troublesome diseases. Application of herbs is emerging as a tool in controlling these diseases. Plant extracts besides disease control, favor various physiological activities in fish. In this study, essential oil of Cymbopogon flexuosus (Poaceae family) was studied in vitro for its antibacterial efficacy against two oxytetracycline (OTC) resistant and one sensitive strains of Aeromonas hydrophila. The oil was found rich (86.93 %) in oxygenated terpenoids containing 74.15 % of citral. The oil exhibited dose dependent growth inhibition of the bacteria. Mean MIC value of the oil against the sensitive strain was recorded as 2.0 mg mL^-1 whereas MBC value was recorded as 4.0 mg mL^-1 . The oil was found effective against the OTC resistant isolates with the MIC and MBC values ranging from 2.67-3.33 and 4.0-6.67 mg mL^-1 , respectively. In silico molecular docking of the essential oil components against DNA gyrase-B, a vital macromolecule in bacterial cell, was carried out to computationally asses the efficacy of the oil against the bacteria. Some of the components of the essential oil strongly bonded with the enzyme to inhibit its efficacy. Binding energy of some components of the oil was comparable to that of the conventional antibiotic, OTC. The identified phytochemicals exhibited favorable physicochemical and pharmacokinetic properties and satisfied the rule of five (Ro5).

Molecular docking investigation of anti-inflammatory herbal compounds as potential LOX-5 and COX-2 inhibitors

According to the World Journal of Gastroenterology, more than 5 million people worldwide suffer from inflammatory bowel disease. The use of phytotherapeutic remedies in treatment of chronic inflammatory processes can be an effective alternative in patient’s therapy. The advantage of herbal medicines is the ability to influence various links of pathogenesis, lack of addiction, and the absence of withdrawal syndrome with long-term use in chronic pathology. In order to develop a new combined remedy with anti-inflammatory activity for the treatment of colitis, thirteen herbs, which are used in official or traditional medicine in inflammatory processes, were selected among the Ukrainian flora members. To select the most promising drugs and optimize further pharmacological research, molecular docking of the main active substances of the selected herbs to the fundamental pro-inflammatory enzymes – lipoxygenase-5 (LOX-5) and cyclooxygenase-2 (COX-2) – was carried out. Native inhibitors AKBA and celecoxib, respectively, were used as the reference ligands. The selection of candidate structures for in silico research was carried out according to the bibliosemantic research and logical-structural analysis concerning anti-inflammatory effect of the substances, which are part of chemical composition of the selected herbs. Molecular docking results have shown a high affinity level for the active site of the LOX-5 inhibitor gallotannin, quercetin, inulin, sitosterine, and moderate for ellagic acid. High affinity level for the active site of the COX-2 inhibitor was found for inulin, quercetin, gallotannin, ellagic acid and urticin A, moderate one – for gallic acid. For the further pharmacological in vitro and in vivo studies for anti-inflammatory activity, medicinal herbs with the highest content of the mentioned compounds were selected: Inula helenium, Cichorium intybus, Capsella bursa-pastoris, Foeniculum vulgare, Equisetum arvense, Veronica officinalis. Besides, it is recommended to use aqueous extracts of the selected herbs for the further pharmacological studies.

Carpaine Promotes Proliferation and Repair of H9c2 Cardiomyocytes after Oxidative Insults

Carpaine has long been identified as the major alkaloid in Carica papaya leaves that possess muscle relaxant properties. Limited study on the molecular signaling properties of carpaine urges us to conduct this study that aims to elucidate the mechanism underlying the cardioprotective effect of carpaine in embryonic cardiomyocytes of the H9c2 cell line. The 50% inhibitory concentration (IC₅₀) of carpaine was first determined using a colorimetric MTT assay to establish the minimum inhibitory concentration for the subsequent test. Using a 1 µM carpaine treatment, a significant increase in the H9c2 proliferation rate was observed following 24 and 48 h of incubation. A Western blot analysis also revealed that carpaine promotes the upregulation of the cell cycle marker proteins cyclin D1 and PCNA. Carpaine-induced H9c2 cell proliferation is mediated by the activation of the FAK-ERK1/2 and FAK-AKT signaling pathways. In the setting of ischemia-reperfusion injury (IRI), carpaine provided a significant protective role to recover the wounded area affected by the hydrogen peroxide (H₂O₂) treatment. Furthermore, the oxidative-stress-induced reduction in mitochondrial membrane potential (MMP) and overproduction of reactive oxygen species (ROS) were attenuated by carpaine treatment. The current study revealed a novel therapeutic potential of carpaine in promoting in vitro cardiomyocyte proliferation and repair following injury.

In-silico characterization of phytochemicals identified from Vitex negundo (L) extract as potential therapy for Wnt-signaling proteins

Background

Colorectal cancer is the third most diagnosed disease in the world population and current chemotherapy has been used for targeting the cell proliferation and metastasizing ability of tumor cells. Potent chemotherapeutic drugs for colorectal cancer are capecitabine, fluorouracil, irinotecan, etc. which have toxic effects in normal tissues and adverse effects in multiple organs leading to major obstacles in clinical use. The aim of the study is the use of plant-derived compounds that improve the effectiveness of chemotherapeutics with lower and alleviate toxic side effects and reduce the risk of tumor progression.

Results

The current study is performed using Vitex negundo leaf which has been demonstrated to have positive effects against colorectal cancer. The use of computational approaches will help improve the identification and screening of lead molecules using AutoDock 4.2 and AutoDock Vina. Using computational approaches will help to improve lead identification and screening. Herein, we have retrieved six phytochemicals from published literature and investigated their inhibitory effect with Wnt-associated signaling proteins. Authentication of phytocompounds and Wnt-associated signaling proteins was done using AutoDock.4.2.

Conclusions

The results are screened based on the number of hydrogen bonds, binding energy, and interacting amino acids. The Isoorientin, luteolin, and Chrysophanol get the highest binding energy with target receptors. The binding energy is calculated with all target receptors from the range of − 6.0 to − 8.9 kcal/mol. The In-silico drug likeliness properties are predicted to be the best interacting compounds based on Lipinski Rule of 5 and ADMET analysis. Hence, we propose that Isoorientin, luteolin, and Chrysophanol are the potential inhibitors of Wnt signaling inhibitors, and preclinical studies are needed to confirm the promising therapeutic ability of colorectal cancer.

Structural Diversity and Role of Phytochemicals against P38-α Mitogen-activated Protein Kinase and Epidermal Growth Factor Receptor Kinase Domain: A Privileged Computational Approach

Computational databases and tools in recent times have been proved to provide an essential aid for anticancer studies in the field of oncology. Molecular docking studies facilitate the structural diversity of plant-derived phytomolecules having anticancer properties against receptor proteins involved in cancer signaling pathways. The current study involves the investigation of phytocompounds-agasthisflavone, anacardic acid, zoapatanolide A, a purified product of the plant extract Amarogopinois546 were subjected to docking studies on p38-α MAPK and EGFR Kinase domain. The effectiveness of this study was evaluated by comparing the docking interactions of a standard drug, doxorubicin against the receptor molecules. The docking study is analyzed by compound estimated with lowest binding energy is considered to have the highest affinity towards the active site of the receptor proteins. The isolated plant compound Amarogopinois546 displayed the least binding score with a large number of hydrogen bonds and hydrophobic interactions towards the P38α MAP kinase receptor in comparison with the EGFR kinase domain. This preliminary result can strongly be supported for carrying out experimental evaluation in near future.

The In Vitro α-Glucosidase Inhibition Activity of Various Solvent Fractions of Tamarix dioica and 1H-NMR Based Metabolite Identification and Molecular Docking Analysis

The Tamarix dioica (T. dioica) is widely used medicinal plant to cure many chronic ailments. T. dioica is being used to manage diabetes mellitus in traditional medicinal system; however, very little scientific evidence is available on this plant in this context. The current study involves the fractionation of crude methanolic extract of T. dioica using n-hexane, ethyl acetate, chloroform, and n-butanol. The screening for antioxidant activity using 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay was carried out. The in vitro antidiabetic potential was assessed by measuring α-glucosidase inhibition. Total phenolic and flavonoid contents were also determined for each fraction. The metabolites were identified using highly sensitive and emerging ¹H-NMR technique. The results revealed the ethyl acetate fraction as the most potent with DPPH scavenging activity of 84.44 ± 0.21% and α-glucosidase inhibition with IC₅₀ value of 122.81 ± 2.05 µg/mL. The total phenolic and flavonoid content values of 205.45 ± 1.36 mg gallic acid equivalent per gram dried extract and 156.85 ± 1.33 mg quercetin equivalent per gram dried extract were obtained for ethyl acetate fraction. The bucketing of ¹H-NMR spectra identified 22 metabolites including some pharmacologically important like tamarixetin, tamaridone, quercetin, rutin, apigenin, catechin, kaempferol, myricetin and isorhamnetin. Leucine, lysine, glutamic acid, aspartic acid, serine, and tyrosine were the major amino acids identified in ethyl acetate fraction. The molecular docking analysis provided significant information on the binding affinity among secondary metabolites and α-glucosidase. These metabolites were most probably responsible for the antioxidant activity and α-glucosidase inhibitory potential of ethyl acetate fraction. The study ascertained the ethnomedicinal use of T. dioica to manage diabetes mellitus and may be a helpful lead towards naturopathic mode for anti-hyperglycemia.