Prevalence of Trichomonas vaginalis infection among Sudanese patients with different genders in Khartoum state, Sudan

Background:  Trichomonas vaginalis infection is one of the major health problems in   the world, Trichomonas vaginalis infection is a common sexually transmitted protozoal infection, with an estimated 180 million prevalent cases worldwide. Objective: This study aims to estimate the prevalence of Trichomonas vaginalis infection among Sudanese patients according to sex and age in Bashaeir Hospital –Khartoum state. Methods: This study was a retrospective descriptive study of pre-collected urine samples, included male and female patients attending the outpatient, requested for urine general examination, samples were selected by systemic random sampling. One hundred-twenty five (125) samples have been taken; wet preparation has been done for all samples in Bashaeir Hospital lab. Result: 125 urine samples was examined. The number of females was 95 and males was 30. All samples were examined for T. vaginalis. Only 15 were positive. We could not collect data for all subjects; because it was not available. There was an available data about sex and age for 23 cases. Conclusion:Femalewas more affected by Trichomonas vaginalis than in males. The most affected age was ranging from (31-40) years

Integrating computational methods guided the discovery of phytochemicals as potential Pin1 inhibitors for cancer: pharmacophore modeling, molecular docking, MM-GBSA calculations and molecular dynamics studies

Pin1 is a pivotal player in interactions with a diverse array of phosphorylated proteins closely linked to critical processes such as carcinogenesis and tumor suppression. Its axial role in cancer initiation and progression, coupled with its overexpression and activation in various cancers render it a potential candidate for the development of targeted therapeutics. While several known Pin1 inhibitors possess favorable enzymatic profiles, their cellular efficacy often falls short. Consequently, the pursuit of novel Pin1 inhibitors has gained considerable attention in the field of medicinal chemistry. In this study, we employed the Phase tool from Schrödinger to construct a structure-based pharmacophore model. Subsequently, 449,008 natural products (NPs) from the SN3 database underwent screening to identify compounds sharing pharmacophoric features with the native ligand. This resulted in 650 compounds, which then underwent molecular docking and binding free energy calculations. Among them, SN0021307, SN0449787 and SN0079231 showed better docking scores with values of −9.891, −7.579 and −7.097 kcal/mol, respectively than the reference compound (−6.064 kcal/mol). Also, SN0021307, SN0449787 and SN0079231 exhibited lower free binding energies (−57.12, −49.81 and −46.05 kcal/mol, respectively) than the reference ligand (−37.75 kcal/mol). Based on these studies, SN0021307, SN0449787, and SN0079231 showed better binding affinity that the reference compound. Further the validation of these findings, molecular dynamics simulations confirmed the stability of the ligand-receptor complex for 100 ns with RMSD ranging from 0.6 to 1.8 Å. Based on these promising results, these three phytochemicals emerge as promising lead compounds warranting comprehensive biological screening in future investigations. These compounds hold great potential for further exploration regarding their efficacy and safety as Pin1 inhibitors, which could usher in new avenues for combating cancer

Repurposing of approved drugs for targeting CDK4/6 and aromatase protein using molecular docking and molecular dynamics studies.

Breast cancer is a leading cause of cancer-related morbidity and mortality worldwide, with the highest incidence among women. Among the various subtypes of breast cancer, estrogen-receptor positive (ER+) is the most diagnosed. Estrogen upregulates cyclin D1, which in turn promotes the activity of CDK4/6 and facilitates cell cycle progression. To address this, the first-line treatment for ER+ breast cancer focuses on inhibiting estrogen production by targeting aromatase, the enzyme responsible for the rate-limiting step in estrogen synthesis. Thus, combining CDK4/6 inhibitors with aromatase inhibitors has emerged as a crucial treatment strategy for this type of breast cancer. This approach effectively suppresses estrogen biosynthesis and controls uncontrolled cell proliferation, significantly improving overall survival rates and delayed disease progression. This study aimed to identify compounds that are likely to inhibit CDK4/6 and aromatase simultaneously by using a structure-based drug design strategy. 12,432 approved and investigational drugs were prepared and docked into the active site of CDK6 using HTVS and XP docking modes of Glide resulting in 277 compounds with docking scores ≤ -7 kcal/mol. These compounds were docked into aromatase enzyme using XP mode to give seven drugs with docking scores≤ -6.001 kcal/mol. Furthermore, the shortlisted drugs were docked against CDK4 showing docking scores ranging from -3.254 to -8.254 kcal/mol. Moreover, MM-GBSA for the top seven drugs was calculated. Four drugs, namely ellagic acid, carazolol, dantron, and apomorphine, demonstrated good binding affinity to all three protein targets CDK4/6 and aromatase. Specifically, they exhibited favourable binding free energy with CDK6, with values of -51.92, -53.90, -50.22, and -60.97 kcal/mol, respectively. Among these drugs, apomorphine displayed the most favourable binding free energy with all three protein targets. To further evaluate the stability of the interaction, apomorphine was subjected to a 100 ns molecular dynamics simulation with CDK6. The results indicated the formation of a stable ligand-protein complex. While the results obtained from the MM-GBSA calculation of the binding free energies of the MD conformations of apomorphine showed less favourable binding free energy compared to that obtained post-docking. All these computational findings will provide better structural insight for the development of CDK4/6 and aromatase multi-target inhibitors

Utilization of computational methods for the identification of new natural inhibitors of human neutrophil elastase in inflammation therapy

Human neutrophil elastase (HNE) plays a crucial role in causing tissue damage in various chronic and inflammatory disorders, making it a target for treating inflammatory diseases. While some inhibitors of HNE’s activity have been identified, only a few have made it to clinical trials. In this study, computational methods were employed to identify potential natural products (NPs) capable of targeting the active site of HNE. The protein–ligand complex has been used to generate a pharmacophore model. A library of 449,008 NPs from the SN3 database was screened against the generated model, resulting in 29,613 NPs that matched the pharmacophore hypothesis. These compounds were docked into the protein active site, resulting in the identification of six promising NPs with better docking scores than the bound ligand to HNE. The top two NPs (SN0338951 and SN0436937) were further evaluated for their interaction stability with HNE through molecular dynamics simulations. Further, the pharmacokinetics and toxicity properties of these compounds were predicted. The results indicated that these two compounds have stable interactions with HNE, as well as, acceptable pharmacokinetic properties. These findings pave the path for further in vitro and in vivo studies of SN0338951 and SN0436937 as promising agents against inflammatory diseases

Phytochemical Screening, Antioxidant and Antibacterial Activities of Pollen Extracts from Micromeria fruticosa, Achillea fragrantissima, and Phoenix dactylifera

Pollen is a male flower gametophyte located in the anthers of stamens in angiosperms and a considerable source of compounds with health protective potential. In the present work, phytochemical screening was carried out as well as analysis of the antioxidant and antibacterial properties of pollen extracts from Micromeria fruticosa, Achillea fragrantissima, and Phoenix dactylifera growing wild in Palestine. Phytochemical screening examined the total flavonol, flavone and phenolic content. The DPPH (1,2-Diphenyl-1-Picrylhydrazyl) and FRAP (ferric reducing antioxidant power) methods were used to assess antioxidant propriety, and disc diffusion, minimum inhibitory and bactericidal concentration tests were used to test the pollen extract’s antibacterial activity against multidrug-resistant (MDR) clinical isolates. The highest level of total phenolic was found in the extract of Micromeria fruticosa (56.78 ± 0.49 mg GAE (Gallic Acid Equivalent)/g). The flavone and flavonol content of samples ranged from 2.48 ± 0.05 to 8.03 ± 0.01 mg QE (Quercetin Equivalent)/g. Micromeria fruticosa pollen with IC50 values of 0.047 and 0.039 mg/mL in the DPPH and FRAP assays, respectively, showed the greatest radical scavenging action. In addition, this pollen showed a mild antibacterial action against the microorganisms studied, with MICs varying from 0.625 to 10 mg/mL and inhibition diameters ranging from 13.66 ± 1.5 to 16.33 ± 1.5 mm

Identification of Novel Natural Dual HDAC and Hsp90 Inhibitors for Metastatic TNBC Using e-Pharmacophore Modeling, Molecular Docking, and Molecular Dynamics Studies

Breast cancer (BC) is one of the main types of cancer that endangers women’s lives. The characteristics of triple-negative breast cancer (TNBC) include a high rate of recurrence and the capacity for metastasis; therefore, new therapies are urgently needed to combat TNBC. Dual targeting HDAC6 and Hsp90 has shown good synergistic effects in treating metastatic TNBC. The goal of this study was to find potential HDAC6 and Hsp90 dual inhibitors. Therefore, several in silico approaches have been used. An e-pharmacophore model generation based on the HDAC6-ligand complex and subsequently a pharmacophore-based virtual screening on 270,450 natural compounds from the ZINC were performed, which resulted in 12,663 compounds that corresponded to the obtained pharmacophoric hypothesis. These compounds were docked into HDAC6 and Hsp90. This resulted in the identification of three compounds with good docking scores and favorable free binding energy against the two targets. The top three compounds, namely ZINC000096116556, ZINC000020761262, and ZINC000217668954, were further subjected to ADME prediction and molecular dynamic simulations, which showed promising results in terms of pharmacokinetic properties and stability. As a result, these three compounds can be considered potential HDAC6 and Hsp90 dual inhibitors and are recommended for experimental evaluation