Integrated bioinformatics analysis reveals upregulated extracellular matrix hub genes in pancreatic cancer: Implications for diagnosis, prognosis, immune infiltration, and therapeutic strategies

BACKGROUND

Pancreatic cancer (PC) stands out as one of the most formidable malignancies and exhibits an exceptionally unfavorable clinical prognosis due to the absence of well-defined diagnostic indicators and its tendency to develop resistance to therapeutic interventions. The primary objective of this present study was to identify extracellular matrix (ECM)-related hub genes (HGs) and their corresponding molecular signatures, with the intent of potentially utilizing them as biomarkers for diagnostic, prognostic, and therapeutic applications.

METHODS

Three microarray datasets were sourced from the NCBI database to acquire upregulated differentially expressed genes (DEGs), while MatrisomeDB was employed for filtering ECM-related genes. Subsequently, a protein-protein interaction (PPI) network was established using the STRING database. The created network was visually inspected through Cytoscape, and HGs were identified using the CytoHubba plugin tool. Furthermore, enrichment analysis, expression pattern analysis, clinicopathological correlation, survival analysis, immune cell infiltration analysis, and examination of chemical compounds were carried out using Enrichr, GEPIA2, ULCAN, Kaplan Meier plotter, TIMER2.0, and CTD web platforms, respectively. The diagnostic and prognostic significance of HGs was evaluated through the ROC curve analysis.

RESULTS

Ten genes associated with ECM functions were identified as HGs among 131 DEGs obtained from microarray datasets. Notably, the expression of these HGs exhibited significantly (p < 0.05) higher in PC, demonstrating a clear association with tumor advancement. Remarkably, higher expression levels of these HGs were inversely correlated with the likelihood of patient survival. Moreover, ROC curve analysis revealed that identified HGs are promising biomarkers for both diagnostic (AUC > 0.75) and prognostic (AUC > 0.64) purposes. Furthermore, we observed a positive correlation between immune cell infiltration and the expression of most HGs. Lastly, our study identified nine compounds with significant interaction profiles that could potentially act as effective chemical agents targeting the identified HGs.

CONCLUSION

Taken together, our findings suggest that COL1A1, KRT19, MMP1, COL11A1, SDC1, ITGA2, COL1A2, POSTN, FN1, and COL5A1 hold promise as innovative biomarkers for both the diagnosis and prognosis of PC, and they present as prospective targets for therapeutic interventions aimed at impeding the progression PC.

Therapeutic potential of clinically proven natural products in the management of dementia

Dementia is a common neurodegenerative disorder connected to damage to nerve cells in the brain. Although some conventional drugs are available for dementia treatments and are still sanctified for dementia patients, their short- and long-term side effects and other limitations make treating patients more challenging. The authors aimed to explain novel options for treating dementia with natural products and unravel some clinically proven natural products. This article systematically reviewed recent studies that have investigated the role of natural products and their bioactive compounds for dementia. PubMed Central, Scopus, and Google Scholar databases of articles were collected, and abstracts were reviewed for relevance to the subject matter.In this review, we provide mechanistic insights of clinically validated natural products, including like- Yokukansan, Souvenaid, BDW, Hupergene, Bacopa monnier, Omega-3, Tramiprostate and Palmitoylethanolamide with which have therapeutic efficacy against dementia in the management of dementia. As shown by studies, certain natural ingredients could be used to treat and prevent dementia. We strongly believe that the medicinal plants and phytoconstituents alone or in combination with other compounds would be effective treatments against dementia with lesser side effects as compared to currently available treatments. Moreover, these products should be studied further in order to develop novel dementia medications.

Genome-Wide Investigation Reveals Potential Therapeutic Targets in Shigella spp

Shigella stands as a major contributor to bacterial dysentery worldwide scale, particularly in developing countries with inadequate sanitation and hygiene. The emergence of multidrug-resistant strains exacerbates the challenge of treating Shigella infections, particularly in regions where access to healthcare and alternative antibiotics is limited. Therefore, investigations on how bacteria evade antibiotics and eventually develop resistance could open new avenues for research to develop novel therapeutics. The aim of this study was to analyze whole genome sequence (WGS) of human pathogenic Shigella spp. to elucidate the antibiotic resistance genes (ARGs) and their mechanism of resistance, gene-drug interactions, protein-protein interactions, and functional pathways to screen potential therapeutic candidate(s). We comprehensively analyzed 45 WGS of Shigella, including S. flexneri (n = 17), S. dysenteriae (n = 14), S. boydii (n = 11), and S. sonnei (n = 13), through different bioinformatics tools. Evolutionary phylogenetic analysis showed three distinct clades among the circulating strains of Shigella worldwide, with less genomic diversity. In this study, 2,146 ARGs were predicted in 45 genomes (average 47.69 ARGs/genome), of which only 91 ARGs were found to be shared across the genomes. Majority of these ARGs conferred their resistance through antibiotic efflux pump (51.0%) followed by antibiotic target alteration (23%) and antibiotic target replacement (18%). We identified 13 hub proteins, of which four proteins (e.g., tolC, acrR, mdtA, and gyrA) were detected as potential hub proteins to be associated with antibiotic efflux pump and target alteration mechanisms. These hub proteins were significantly (p < 0.05) enriched in biological process, molecular function, and cellular components. Therefore, the finding of this study suggests that human pathogenic Shigella strains harbored a wide range of ARGs that confer resistance through antibiotic efflux pumps and antibiotic target modification mechanisms, which must be taken into account to devise and formulate treatment strategy against this pathogen. Moreover, the identified hub proteins could be exploited to design and develop novel therapeutics against MDR pathogens like Shigella.

Screening out molecular pathways and prognostic biomarkers of ultraviolet-mediated melanoma through computational techniques

PURPOSE

Ultraviolet radiation causes skin cancer, but the exact mechanism by which it occurs and the most effective methods of intervention to prevent it are yet unknown. For this purpose, our study will use bioinformatics and systems biology approaches to discover potential biomarkers of skin cancer for early diagnosis and prevention of disease with applicable clinical treatments.

METHODS

This study compared gene expression and protein levels in ultraviolet-mediated cultured keratinocytes and adjacent normal skin tissue using RNA sequencing data from the National Center for Biotechnology Information-Gene Expression Omnibus (NCBI-GEO) database. Then, pathway analysis was employed with a selection of hub genes from the protein-protein interaction (PPI) network and the survival and expression profiles. Finally, potential clinical biomarkers were validated by receiver operating characteristic (ROC) curve analysis.

RESULTS

We identified 32 shared differentially expressed genes (DEGs) by analyzing three different subsets of the GSE85443 dataset. Skin cancer development is related to the control of several DEGs through cyclin-dependent protein serine/threonine kinase activity, cell cycle regulation, and activation of the NIMA kinase pathways. The cytoHubba plugin in Cytoscape identified 12 hub genes from PPI; among these 3 DEGs, namely, AURKA, CDK4, and PLK1 were significantly associated with survival (P < 0.05) and highly expressed in skin cancer tissues. For validation purposes, ROC curve analysis indicated two biomarkers: AURKA (area under the curve (AUC) value = 0.8) and PLK1 (AUC value = 0.7), which were in an acceptable range.

CONCLUSIONS

Further translational research, including clinical experiments, teratogenicity tests, and in-vitro or in-vivo studies, will be performed to evaluate the expression of these identified biomarkers regarding the prognosis of skin cancer patients.

Comprehensive exploration of Biochanin A as an oncotherapeutics potential in the treatment of multivarious cancers with molecular insights

Cancer is considered a leading cause of mortality. This rising cancer death rate and several existing limitations like side effects, poor efficacies, and high cost of the present chemotherapeutic agents have increased the demand for more potent and alternative cancer treatments. This review elucidated a brief overview of Biochanin A (BCA) and its potentiality on various cancers with details of anticancer mechanism. According to our review, a number of studies including in silico, in vitro, pre-clinical, and clinical trials have tested to evaluate the efficacy of BCA. This compound is effective against 15 types of cancer, including breast, cervical, colorectal, gastric, glioblastoma, liver, lung, melanoma, oral, osteosarcoma, ovarian, pancreatic, pharynx, prostate, and umbilical vein cancer. The general anticancer activities of this compound are mediated via several molecular processes, including regulation of apoptosis, cell proliferation, metastasis and angiogenesis, signaling, enzymatic pathways, and other mechanisms. Targeting both therapeutic and oncogenic proteins, as well as different pathways, makes up the molecular mechanism underlying the anticancer action. Many signaling networks and their components, such as EFGR, PI3K/Akt/mTOR, MAPK, MMP-2, MMP-9, PARP, Caspase-3/8/9, Bax, Bcl2, PDL-1, NF-κB, TNF-α, IL-6, JAK, STAT3, VEGFR, VEGF, c-MY, Cyclin B1, D1, E1 and CDKs, Snail, and E-cadherin proteins, can be regulated in cancer cells by BCA. Such kind of anticancer properties of BCA could be a result of its correct structural chemistry. The use of BCA-based therapies as nano-carriers for the delivery of chemotherapeutic medicines has the potential to be very effective. This natural compound synergises with other natural compounds and standard drugs, including sorafenib, 5-fluorouracil, temozolomide, doxorubicin, apigenin, and genistein. Moreover, proper use of this compound can reverse multidrug resistance through numerous mechanisms. BCA has better drug-likeness and pharmacokinetic properties and is nontoxic (eye, liver, kidney, skin, cardio) in human bodies. As having a wide range of cancer-fighting mechanisms, synergistic effects, and good pharmacokinetic properties, BCA can be used as a supplementary food until standard drugs are available at pharma markets.

Unveiling the potential anti-cancer activity of calycosin against multivarious cancers with molecular insights: A promising frontier in cancer research

BACKGROUND

Calycosin may be a potential candidate regarding chemotherapeutic agent, because already some studies against multivarious cancer have been made with this natural compound.

AIM

This review elucidated a brief overview of previous studies on calycosin potential effects on various cancers and its potential mechanism of action.

METHODOLOGY

Data retrieved by systematic searches of Google Scholar, PubMed, Science Direct, Web of Science, and Scopus by using keywords including calycosin, cancer types, anti-cancer mechanism, synergistic, and pharmacokinetic and commonly used tools are BioRender, ChemDraw Professional 16.0, and ADMETlab 2.0.

RESULTS

Based on our review, calycosin is available in nature and effective against around 15 different types of cancer. Generally, the anti-cancer mechanism of this compound is mediated through a variety of processes, including regulation of apoptotic pathways, cell cycle, angiogenesis and metastasis, oncogenes, enzymatic pathways, and signal transduction process. These study conducted in various study models, including in silico, in vitro, preclinical and clinical models. The molecular framework behind the anti-cancer effect is targeting some oncogenic and therapeutic proteins and multiple signaling cascades. Therapies based on nano-formulated calycosin may make excellent nanocarriers for the delivery of this compound to targeted tissue as well as particular organ. This natural compound becomes very effective when combined with other natural compounds and some standard drugs. Moreover, proper use of this compound can reverse resistance to existing anti-cancer drugs through a variety of strategies. Calycosin showed better pharmacokinetic properties with less toxicity in human bodies.

CONCLUSION

Calycosin exhibits excellent potential as a therapeutic drug against several cancer types and should be consumed until standard chemotherapeutics are available in pharma markets.

Esculetin unveiled: Decoding its anti-tumor potential through molecular mechanisms-A comprehensive review

BACKGROUND

The growing complexity of cancer has made it a significant concern in the medical community. Although cancer research has advanced, it is still challenging to create new effective medications due to the limitations and side effects of existing treatment strategies. These are enforcing the development of some alternative drugs from natural compounds with fewer drawbacks and side effects.

AIM

Therefore, this review aims to provide up-to-date, crucial, and all-encompassing data on esculetin's anticancer activity, including all relevant molecular and cellular processes based on in vivo and in vitro investigations.

RESULTS

According to the literature review, esculetin is available in nature and is effective against 16 different types of cancer. The general mechanism shown by esculetin is modulating signaling cascades and its related pathways, like cell proliferation, cell growth, autophagy, apoptosis, necrosis, inflammation, angiogenesis, metastasis, invasion, and DNA damage. Nanoformulation of esculetin improves this natural product's efficacy by improving water solubility. Esculetin's synergistic effects with both natural substances and conventional treatments have been shown, and this method aids in reversing resistance mechanisms by modulating resistance-related proteins. In addition, it has fewer side effects on humans than other phytochemicals and standard drugs with some good pharmacokinetic features.

CONCLUSION

Therefore, until standard chemotherapeutics are available in pharmaceutical markets, esculetin should be used as a therapeutic drug against various cancer types.

Serum creatinine phosphokinase: A potential prognostic marker in assessing clinical severity with organophosphorus poisoning

INTRODUCTION

Organophosphorus compound (OPC) poisoning undoubtedly being a major concern in cultivation sites of the developing world, including Bangladesh. Two potential biomarkers, for example, serum creatine phosphokinase (CPK) and lactate dehydrogenase (LDH), are widely used in OPC poisoning severity indicators in patients. In this study, we sought to correlate the severity score of acute OPC poisoning with CPK or LDH level and subsequently explore their prognostic value.

METHODS

This study was performed on a total of 70 patients with OPC poisoning admitted to the inpatient care unit at a territory-based hospital in Bangladesh. Sociodemographics and poison types were recorded, and severity was assessed according to Peradeniya Organophosphorus Poisoning (POP) scale. Serum CPK and LDH levels were measured and recorded.

RESULTS

A total of seventy OPC patients were included with male to female ratio of 1.33:1, respectively, with a mean age of 28.7 ± 12.8 years. Chlorpyrifos and methylparathion were the most commonly utilized OP compounds, accounting for 42.9% and 28.6%, respectively. Among the OPC patients, the majority were married homemakers from rural areas. According to POP score, 55.7% and 37.1% of patients were categorized as mild and moderate, whereas very few were found to be severe. The mean serum CPK and LDH of OPC-patients at admission time were 235.6 ± 79.8 IU/L and 348.3 ± 154.1 IU/L, respectively. Serum CPK, atropine dose and hospital stay strongly correlated with clinical severity.

CONCLUSION

We conclude that the serum CPK level strongly correlates with the degree of OPC poisoning and can be used as a predictor of the clinical intervention approaches.

Unraveling the signaling mechanism behind astrocytoma and possible therapeutics strategies: A comprehensive review

BACKGROUND

A form of cancer called astrocytoma can develop in the brain or spinal cord and sometimes causes death. A detailed overview of the precise signaling cascade underlying astrocytoma formation has not yet been revealed, although various factors have been investigated. Therefore, our objective was to unravel and summarize our current understanding of molecular genetics and associated signaling pathways with some possible therapeutic strategies for astrocytoma.

RECENT FINDINGS

In general, four different forms of astrocytoma have been identified in individuals, including circumscribed, diffuse, anaplastic, and multiforme glioblastoma, according to a recent literature review. All types of astrocytoma have a direct connection with some oncogenic signaling cascade. Common signaling is MAPK cascade, including Ras-Raf-ERK, up-regulated with activating EGFR/AKT/PTEN/mTOR and PDGFR. Recent breakthrough studies found that BRAF mutations, including KIAA1549: BRAF and BRAF V600E are responsible for astrocytoma progression. Additionally, cancer progression is influenced by mutations in some tumor suppressor genes, such as the Tp53/ATRX and MGMT mutant. As synthetic medications must cross the blood-brain barrier (BBB), modulating signal systems such as miRNA is the primary option for treating patients with astrocytoma. However, available surgery, radiation therapy, and experimental therapies such as adjuvant therapy, anti-angiogenic therapy, and EGFR-targeting antibody drug are the usual treatment for most types of astrocytoma. Similar to conventional anticancer medications, some phytochemicals slow tumor growth by simultaneously controlling several cellular proteins, including those involved in cell cycle regulation, apoptosis, metastatic spread, tyrosine kinase, growth factor receptor, and antioxidant-related proteins.

CONCLUSION

In conclusion, cellular and molecular signaling is directly associated with the development of astrocytoma, and a combination of conventional and alternative therapies can improve the malignancy of cancer patients.

Study of kaempferol in the treatment of COVID-19 combined with Chikungunya co-infection by network pharmacology and molecular docking technology

Chikungunya (CHIK) patients may be vulnerable to coronavirus disease (COVID-19). However, presently there are no anti-COVID-19/CHIK therapeutic alternatives available. The purpose of this research was to determine the pharmacological mechanism through which kaempferol functions in the treatment of COVID-19-associated CHIK co-infection. We have used a series of network pharmacology and computational analysis-based techniques to decipher and define the binding capacity, biological functions, pharmacological targets, and treatment processes in COVID-19-mediated CHIK co-infection. We identified key therapeutic targets for COVID-19/CHIK, including TP53, MAPK1, MAPK3, MAPK8, TNF, IL6 and NFKB1. Gene ontology, molecular and upstream pathway analysis of kaempferol against COVID-19 and CHIK showed that DEGs were confined mainly to the cytokine-mediated signalling pathway, MAP kinase activity, negative regulation of the apoptotic process, lipid and atherosclerosis, TNF signalling pathway, hepatitis B, toll-like receptor signaling, IL-17 and IL-18 signaling pathways. The study of the gene regulatory network revealed several significant TFs including KLF16, GATA2, YY1 and FOXC1 and miRNAs such as let-7b-5p, mir-16-5p, mir-34a-5p, and mir-155-5p that target differential-expressed genes (DEG). According to the molecular coupling results, kaempferol exhibited a high affinity for 5 receptor proteins (TP53, MAPK1, MAPK3, MAPK8, and TNF) compared to control inhibitors. In combination, our results identified significant targets and pharmacological mechanisms of kaempferol in the treatment of COVID-19/CHIK and recommended that core targets be used as potential biomarkers against COVID-19/CHIK viruses. Before conducting clinical studies for the intervention of COVID-19 and CHIK, kaempferol might be evaluated in wet lab tests at the molecular level.

Exploring the anti-cancer potential of dietary phytochemicals for the patients with breast cancer: A comprehensive review

BACKGROUND

The most common and deadly cancer in female is breast cancer (BC) and new incidence and deaths related to this cancer are rising.

AIMS

Several issues, that is, high cost, toxicity, allergic reactions, less efficacy, multidrug resistance, and the economic cost of conventional anti-cancer therapies, has prompted scientists to discover innovative approaches and new chemo-preventive agents.

MATERIALS

Numerous studies are being conducted on plant-based and dietary phytochemicals to discover new-fangled and more advanced therapeutic approaches for BC management.

RESULT

We have identified that natural compounds modulated many molecular mechanisms and cellular phenomena, including apoptosis, cell cycle progression, cell proliferation, angiogenesis and metastasis, up-regulation of tumor-suppressive genes, and down-regulation of oncogenes, modulation of hypoxia, mammosphere formation, onco-inflammation, enzymatic regulation, and epigenetic modifications in BC. We found that a number of signaling networks and their components such as PI3K/Akt/mTOR, MMP-2 and 9, Wnt/-catenin, PARP, MAPK, NF-κB, Caspase-3/8/9, Bax, Bcl2, Smad4, Notch1, STAT3, Nrf2, and ROS signaling can be regulated in cancer cells by phytochemicals. They induce up-regulation of tumor inhibitor microRNAs, which have been highlighted as a key player for ani-BC treatments followed by phytochemical supplementation.

CONCLUSION

Therefore, this collection offers a sound foundation for further investigation into phytochemicals as a potential route for the development of anti-cancer drugs in treating patients with BC.

A comprehensive review on clinically proven natural products in the management of nerve pain, with mechanistic insights

Introduction

People are treating their neuropathic pain with several approved and licensed pharmacological drugs. But due to having existing limitations like low efficacy with some side effects, there needs to be a more effective alternative and complementary therapeutic options.

Purpose

s: The study was designed to discuss the mechanistic role of several clinically proven natural products that have been shown to play a significant role against different nerve pain or neuropathic pain.

Method

ology: Information for this review article was salvaged using several accessible searching databases like SciVerse Scopus ® (Elsevier Properties S. A, USA), Web of Science® (Thomson Reuters, USA), and PubMed® (U.S. National Library of Medicine, USA) considering some search items like - nerve pain, natural products in pain/nerve pain management, clinically proven natural products in pain management, pain-reducing agents and so on.

Result

Our study reported the therapeutic efficacy of natural products and their possible mechanism against neuropathic pain in the human body. Natural products widely used to treat neuropathic pain include comfrey root extract ointment, lavender oil, Rose Oil, aromatic essential oil, ginger oil, vitex agnus-castus, peganum oil, and ajwain 10%. Some common pathways are involved in pain relief through sensory stimulation, enzymatic, anti-inflammatory, and pain-related receptor regulation.

Conclusion

The present study suggests that the mentioned natural products can be an appropriate choice for the treatment and management of neuropathic pain.

Baicalein as Promising Anticancer Agent: A Comprehensive Analysis on Molecular Mechanisms and Therapeutic Perspectives

Despite significant therapeutic advancements for cancer, an atrocious global burden (for example, health and economic) and radio- and chemo-resistance limit their effectiveness and result in unfavorable health consequences. Natural compounds are generally considered safer than synthetic drugs, and their use in cancer treatment alone, or in combination with conventional therapies, is increasingly becoming accepted. Interesting outcomes from pre-clinical trials using Baicalein in combination with conventional medicines have been reported, and some of them have also undergone clinical trials in later stages. As a result, we investigated the prospects of Baicalein, a naturally occurring substance extracted from the stems of Scutellaria baicalensis Georgi and Oroxylum indicum Kurz, which targets a wide range of molecular changes that are involved in cancer development. In other words, this review is primarily driven by the findings from studies of Baicalein therapy in several cancer cell populations based on promising pre-clinical research. The modifications of numerous signal transduction mechanisms and transcriptional agents have been highlighted as the major players for Baicalein’s anti-malignant properties at the micro level. These include AKT serine/threonine protein kinase B (AKT) as well as PI3K/Akt/mTOR, matrix metalloproteinases-2 & 9 (MMP-2 & 9), Wnt/-catenin, Poly(ADP-ribose) polymerase (PARP), Mitogen-activated protein kinase (MAPK), NF-κB, Caspase-3/8/9, Smad4, Notch 1/Hes, Signal transducer and activator of transcription 3 (STAT3), Nuclear factor erythroid 2-related factor 2 (Nrf2)/Kelch-like ECH-associated protein-1 (Keap 1), Adenosine monophosphate-activated protein kinase (AMPK), Src/Id1, ROS signaling, miR 183/ezrin, and Sonic hedgehog (Shh) signaling cascades. The promise of Baicalein as an anti-inflammatory to anti-apoptotic/anti-angiogenic/anti-metastatic medicinal element for treating various malignancies and its capability to inhibit malignant stem cells, evidence of synergistic effects, and design of nanomedicine-based drugs are altogether well supported by the data presented in this review study.

Clinically proven natural products, vitamins and mineral in boosting up immunity: A comprehensive review

BACKGROUND

and Purposes: The terminology "immune boost-up" was the talk of the topic in this Covid-19 pandemic. A significant number of the people took initiative to increase the body's defense capacity through boosting up immunity worldwide. Considering this, the study was designed to explain the natural products, vitamins and mineral that were proved by clinical trail as immunity enhancer.

METHODS

Information was retrieved from SciVerse Scopus ® (Elsevier Properties S. A, USA), Web of Science® (Thomson Reuters, USA), and PubMed based on immunity, nutrients, natural products in boosting up immunity, minerals and vitamins in boosting up immunity, and immune booster agents.

RESULT

A well-defined immune cells response provide a-well functioning defense system for the human physiological system. Cells of the immune system must require adequate stimulation so that these cells can prepare themselves competent enough to fight against any unintended onslaught. Several pharmacologically active medicinal plants and plants derived probiotics or micronutrients have played a pivotal role in enhancing the immune boost-up process. Their role has been well established from the previous study. Immune stimulating cells, especially cells of acquired immunity are closely associated with the immune-boosting up process because all the immunological reactions and mechanisms are mediated through these cells.

CONCLUSION

This article highlighted the mechanism of action of different natural products, vitamins and mineral in boosting up the immunity of the human body and strengthening the body's defense system. Therefore, it is recommended that until the specific immune-boosting drugs are available in pharma markets, anyone can consider the mentioned products as dietary supplements to boost up the immunity.

An integrated in-silico Pharmaco-BioInformatics approaches to identify synergistic effects of COVID-19 to HIV patients

BACKGROUND

With high inflammatory states from both COVID-19 and HIV conditions further result in complications. The ongoing confrontation between these two viral infections can be avoided by adopting suitable management measures.

PURPOSE

The aim of this study was to figure out the pharmacological mechanism behind apigenin's role in the synergetic effects of COVID-19 to the progression of HIV patients.

METHOD

We employed computer-aided methods to uncover similar biological targets and signaling pathways associated with COVID-19 and HIV, along with bioinformatics and network pharmacology techniques to assess the synergetic effects of apigenin on COVID-19 to the progression of HIV, as well as pharmacokinetics analysis to examine apigenin's safety in the human body.

RESULT

Stress-responsive, membrane receptor, and induction pathways were mostly involved in gene ontology (GO) pathways, whereas apoptosis and inflammatory pathways were significantly associated in the Kyoto encyclopedia of genes and genomes (KEGG). The top 20 hub genes were detected utilizing the shortest path ranked by degree method and protein-protein interaction (PPI), as well as molecular docking and molecular dynamics simulation were performed, revealing apigenin's strong interaction with hub proteins (MAPK3, RELA, MAPK1, EP300, and AKT1). Moreover, the pharmacokinetic features of apigenin revealed that it is an effective therapeutic agent with minimal adverse effects, for instance, hepatoxicity.

CONCLUSION

Synergetic effects of COVID-19 on the progression of HIV may still be a danger to global public health. Consequently, advanced solutions are required to give valid information regarding apigenin as a suitable therapeutic agent for the management of COVID-19 and HIV synergetic effects. However, the findings have yet to be confirmed in patients, suggesting more in vitro and in vivo studies.

Bioinformatics and In silico approaches to identify novel biomarkers and key pathways for cancers that are linked to the progression of female infertility: A comprehensive approach for drug discovery

Despite modern treatment, infertility remains one of the most common gynecologic diseases causing severe health effects worldwide. The clinical and epidemiological data have shown that several cancerous risk factors are strongly linked to Female Infertility (FI) development, but the exact causes remain unknown. Understanding how these risk factors affect FI-affected cell pathways might pave the door for the discovery of critical signaling pathways and hub proteins that may be targeted for therapeutic intervention. To deal with this, we have used a bioinformatics pipeline to build a transcriptome study of FI with four carcinogenic risk factors: Endometrial Cancer (EC), Ovarian Cancer (OC), Cervical Cancer (CC), and Thyroid Cancer (TC). We identified FI sharing 97, 211, 87 and 33 differentially expressed genes (DEGs) with EC, OC, CC, and TC, respectively. We have built gene-disease association networks from the identified genes based on the multilayer network and neighbour-based benchmarking. Identified TNF signalling pathways, ovarian infertility genes, cholesterol metabolic process, and cellular response to cytokine stimulus were significant molecular and GO pathways, both of which improved our understanding the fundamental molecular mechanisms of cancers associated with FI progression. For therapeutic intervention, we have targeted the two most significant hub proteins VEGFA and PIK3R1, out of ten proteins based on Maximal Clique Centrality (MCC) value of cytoscape and literature analysis for molecular docking with 27 phytoestrogenic compounds. Among them, sesamin, galangin and coumestrol showed the highest binding affinity for VEGFA and PIK3R1 proteins together with favourable ADMET properties. We recommended that our identified pathway, hub proteins and phytocompounds may be served as new targets and therapeutic interventions for accurate diagnosis and treatment of multiple diseases.

RLLB/Alb ratio: a promising noninvasive diagnostic marker in assessing esophageal varices in cirrhotic patients

BACKGROUND

Endoscopy has long been widely used to screen for esophageal varices (EV) in cirrhotic patients. Recurrent endoscopy is a significant burden for the healthcare system of the endoscopic unit as well as uncomfortable and high costs for patients. This study intended to prognosticate Right Liver Lobe Diameter/Serum Albumin Ratio (RLLD/Alb) as a non-invasive approach in the early diagnosis of EV among chronic liver disease (CLD) Bangladeshi patients enrolled in a specific hospital.

PARTICIPANTS AND METHODS

A total of 150 admitted patients with CLD were included in the study. Patients were subjected through a comprehensive biochemical checkup and upper digestive endoscopic or ultrasonographic inspection. The correlation was evaluated between the RLLD/Alb ratio and esophageal varices grades.

RESULTS

The upper digestive endoscopy demonstration among 150 patients resulted in no EV in 18%, while 24% of patients was identified as EV grade I, 20% as grade II, 20% as grade III, and 18% patients as grade IV. The mean value of the RLLD/Alb ratio was 4.89 ± 1.49 (range from 2.30 to 8.45). The RLLD/Alb ratio diagnosed the EV employing the cut-off value of 4.01 with 85.3% sensitivity and 68.8% specificity. Furthermore, it was positively correlated with the grading of EV, when this ratio increased the grading of EV increases and vice versa (r = 0.630, p < 0.001).

CONCLUSION

The RLLD/Alb ratio is a non-invasive parameter giving exact guidance relevant to the ascertainment of the existence of EV and their grading in chronic liver disease patients.

Chemotherapeutics activities of dietary phytoestrogens against prostate cancer: From observational to clinical studies

Prostate cancer remains one of the most frequent and deadliest malignancies in males, where the rate of disease progression is closely associated with the type of dietary intake, specifically Western-style diet. Indeed intake of the Asian diet, which contains abundant phytoestrogens, is inversely correlated with a higher risk of prostate cancer, suggesting a chemoprotective effect of phytoestrogen against cancer progression. Although the role of phytoestrogens in cancer treatment was well documented, their impact on prostate cancer is not well understood. Therefore, the present review discusses the possible chemopreventive effect of phytoestrogens, emphasizing their efficacy at the different stages of carcinogenesis. Furthermore, phytoestrogens provide a cytoprotective effect in conventional chemotherapy and enhance chemosensitivity to tumor cells, which have also been discussed. This compilation provides a solid basis for future research on phytoestrogens as a promising avenue for anticancer drug development and also recommends these beneficiary compounds in the daily diet to manage and prevent prostate cancer.

Chemotherapeutic potential of hesperetin for cancer treatment, with mechanistic insights: A comprehensive review

BACKGROUND

Cancer has become a significant concern in the medical sector with increasing disease complexity. Although some available conventional treatments are still a blessing for cancer patients, short-and long-term adverse effects and poor efficiency make it more difficult to treat cancer patients, demonstrating the need for new potent and selective anticancer drugs. In search of potent anticancer agents, naturally occurring compounds have always been admired due to their structural diversity, where Hesperetin (HSP) may be one of the potent candidates.

PURPOSE

We aimed to summarize all sources, pharmacological properties, anticancer activities of HSP against numerous cancers types through targeting multiple pathological processes, mechanism of HSP on sensitizing the current anti-cancer agents and other phytochemicals, overcoming resistance pattern and determining absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox).

METHODS

Information was retrieved from PubMed, Science Direct, and Google Scholar based on some key points like Hesperetin, cancer name, anticancer resistance, nanoformulation, and ADME/Tox was determined by in silico approaches.

RESULT

HSP is a phytoestrogen present in citrus fruits in a high concentration (several hundred mg/kg) and exhibited anti-cancer activities through interfering at several pathways. HSP can suppress tumor formation by targeting several cellular proteins such as cell cycle regulatory, apoptosis, metastatic, tyrosine kinase, growth factor receptor, estrogen metabolism, and antioxidant-related protein.HSP has shown remarkable synergistic properties in combination therapy and has been reported to overcome multidrug cancer resistance drugs, leading to an improved defensive mechanism. These anticancer activities of HSP may be due to proper structural chemistry.

CONCLUSION

Overall, HSP showed potential anticancer activities against all cancer and possess better pharmacokinetic properties. So this phytochemical alone or combination with other agents can be an effective alternative drug for cancer treatment.

Increased lipid peroxidation, depleted non-enzymatic antioxidant, and variability in trace elements concentration in serum are correlated with Bangladeshi end-stage renal disease population

INTRODUCTION

End-stage renal disease (ESRD) is an abnormality where the kidneys are not usually working. This case-control study was planned to determine the extent of serum lipid peroxidation, non-enzymatic antioxidant (vitamin c), and trace elements in 50 patients with ESRD as cases and 50 normal healthy individuals as controls.

METHODS

Determination of lipid peroxidation was carried out by ascertaining concentration of malondialdehyde (MDA) and vitamin C in serum using UV spectrophotometry whereas atomic absorption spectroscopy was used for trace elements estimation. The statistical analysis was conducted via the independent t-test samples and Pearson correlation test.

RESULTS

The blood serum study has shown substantially higher MDA values than the control level and lowers vitamin C levels in the patient population (P < .001). A negative correlation was found between the vitamin C in serum with BMI and MDA for both patients (r = -0.017 and r = -0.132, respectively) and the control group (r = -0.014 and r = -0.229, respectively) after Pearson's correlation analysis. Regarding trace elements, significantly (P < .001) lower concentrations of zinc, copper, and manganese were found in the patient group than control subjects. Inter-element-relationship established a strong positive harmonization between these studied elements in both the cases of patients and control subjects.

CONCLUSION

Our results indicate strong associations of the pathogenesis of ESRD with depleted non-enzymatic antioxidant, increased lipid peroxidation, and inconsistency in trace elements concentration in serum, which may provide a prognostic tool for the treatment of this concerning the disease.

Mining the Proteome of Fusobacterium nucleatum subsp. nucleatum ATCC 25586 for Potential Therapeutics Discovery: An In Silico Approach

The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1,499 proteins of F. nucleatum, which have no homolog's in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the Kyoto Encyclopedia of Genes and Genomes (KEGG) Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the three dimensional structure of these three proteins. Finally, determination of ligand binding sites of the 2 key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against F. nucleatum.

In silico structure analysis and epitope prediction of E3 CR1-beta protein of Human Adenovirus E for vaccine design

BACKGROUND

Human Adenoviruses are divided into 7 species of Human Adenovirus A to G based on DNA genome homology. The Human Adenovirus E (HAdVs-E) genome is a linear, double-stranded DNA containing 38 protein-coding genes. Wild-type adenoviruses type E, are linked to a number of slight illnesses. The most important part of HAdVs-E is E3 CR1-beta protein which controls the host immune response and viral attachment.

METHOD

We use numerous bio-informatics and immuno-informatics implements comprising sequence and construction tools for construction of 3D model and epitope prediction for HAdVs-E.

RESULTS

The 3D structure of E3 CR1-beta protein was generated and total of ten antigenic B cell epitopes, 6 MHC class I and 11 MHC class II binding peptides were predicted.

CONCLUSION

The study was carried out to predict antigenic determinants/epitopes of the E3 CR1-beta protein of Human Adenovirus E along with the 3D protein modeling. The study revealed potential T-cell and B-cell epitopes that can raise the desired immune response against E3 CR1-beta protein and useful in developing effective vaccines against HAdVs-E.

In Silico Structural and Functional Annotation of Hypothetical Proteins of Vibrio cholerae O139

In developing countries threat of cholera is a significant health concern whenever water purification and sewage disposal systems are inadequate. Vibrio cholerae is one of the responsible bacteria involved in cholera disease. The complete genome sequence of V. cholerae deciphers the presence of various genes and hypothetical proteins whose function are not yet understood. Hence analyzing and annotating the structure and function of hypothetical proteins is important for understanding the V. cholerae. V. cholerae O139 is the most common and pathogenic bacterial strain among various V. cholerae strains. In this study sequence of six hypothetical proteins of V. cholerae O139 has been annotated from NCBI. Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. The three dimensional structure of two proteins were modeled and their ligand binding sites were identified. We have found domains and families of only one protein. The analysis revealed that these proteins might have antibiotic resistance activity, DNA breaking-rejoining activity, integrase enzyme activity, restriction endonuclease, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against cholera.

A Systematic Study on Structure and Function of ATPase of Wuchereria bancrofti

BACKGROUND

Analyzing the structures and functions of different proteins of Wuchereria bancrofti is very important because till date no effective drug or vaccine has been discovered to treat lymphatic filariasis (LF). ATPase is one of the most important proteins of Wuchereria bancrofti. Adenosine triphosphate (ATP) converts into adenosine diphosphate (ADP) and a free phosphate ion by the action of these ATPase enzymes. Energy releases from these dephosphorylation reactions drive the other chemical reactions in the cell.

MATERIALS AND METHODS

In this study we worked on the protein ATPase of Wuchereria bancrofti which has been annotated from National Center for Biotechnology Information (NCBI). Various computational tools and databases have been used to determine the various characteristics of that enzyme such as physiochemical properties, secondary structure, three-dimensional (3D) structure, conserved domain, epitope, and their molecular evolutionary relationship.

RESULT

Subcellular localization of ATPase was identified and we have found that 55.5% are localized in the cytoplasm. Secondary and 3D structure of this protein was also predicted. Both structure and function analysis of ATPase of Wuchereria bancrofti showed unique nonhomologous epitope sites and nonhomologous antigenicity sites. Moreover, it resulted in 15 ligand drug-binding sites in its tertiary structure.

CONCLUSION

Structure prediction of these proteins and detection of binding sites and antigenicity sites from this study would indicate a potential target aiding docking studies for therapeutic designing against filariasis.

Choline deficiency causes reversible hepatic abnormalities in patients receiving parenteral nutrition: proof of a human choline requirement: a placebo-controlled trial

BACKGROUND

Previous studies have shown that plasma free choline concentrations are significantly decreased in many long-term home total parenteral nutrition (TPN) patients. Furthermore, low choline status has been associated with both hepatic morphologic and hepatic aminotransferase abnormalities. A preliminary pilot study suggested choline-supplemented TPN may be useful in reversal of these hepatic abnormalities.

METHODS

Fifteen patients (10 M, 5 F) who had required TPN for > or =80% of their nutritional needs were randomized to receive their usual TPN (n = 8), or TPN to which 2 g choline chloride had been added (n = 7) for 24 weeks. Baseline demographic data were similar between groups. Patients had CT scans of the liver and spleen, and blood for plasma free and phospholipid-bound choline, alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase, gamma glutamyl transferase (GGT), bilirubin, serum lipids, complete blood count (CBC), and chemistry profile obtained at baseline, and weeks 2, 4, 6, 12, 16, 20, 24, and 34. CT scans were analyzed for Hounsfield unit (HU) densities.

RESULTS

There were no significant differences in any measured parameters after 2 weeks. However, at 4 weeks, a significant difference in liver HU between groups was observed (13.3+/-5.0 HU [choline] vs 5.8+/-5.2 HU [placebo], p = .04). This significant trend continued through week 24. Recurrent hepatic steatosis and decreased HU were observed at week 34, 10 weeks after choline supplementation had been discontinued. A significant increase in the liver-spleen differential HU was also observed in the choline group (10.6+/-6.2 HU [choline] vs 1.3+/-3.3 HU [placebo], p = .01). Serum ALT decreased significantly (p = .01 to .05) in the choline group vs placebo at weeks 6,12, 20, and 24. Serum AST was significantly decreased in the choline group by week 24 (p = .02). The serum alkaline phosphatase was significantly reduced in the choline group at weeks 2, 12, 20, 24, and 34 (p = .02 to 0.07). Total bilirubin was normal in these patients and remained unchanged during the study. Serum GGT tended to decrease more in the choline group, but the greater decrease was not statistically significant.

CONCLUSIONS

Choline deficiency is a significant contributor to the development of TPN-associated liver disease. The data suggest choline is a required nutrient for long-term home TPN patients.

Verbal and visual memory improve after choline supplementation in long-term total parenteral nutrition: a pilot study

BACKGROUND

Previous investigations have demonstrated that choline deficiency, manifested in low plasma-free choline concentration and hepatic injury, may develop in patients who require long-term total parenteral nutrition (TPN). Preliminary studies have suggested lecithin or choline supplementation might lead to improved visual memory in the elderly and reverse abnormal neuropsychological development in children. We sought to determine if choline-supplemented TPN would lead to improvement in neuropsychological test scores in a group of adult, choline-deficient outpatients receiving TPN.

METHODS

Eleven subjects (8 males, 3 females) who received nightly TPN for more than 80% of their nutritional needs for at least 12 weeks before entry in the study were enrolled. Exclusion criteria included active drug abuse, mental retardation, cerebral vascular accident, head trauma, hemodialysis or peritoneal dialysis, (prothrombin time [PT] >2x control), or acquired immune deficiency syndrome (AIDS). Patients were randomly assigned to receive their usual TPN regimen (n = 6, aged 34.0 +/- 12.6 years) over a 12-hour nightly infusion or their usual TPN regimen plus choline chloride (2 g) (n = 5, aged 37.3 +/- 7.3 years). The following neuropsychological tests were administered at baseline and after 24 weeks of choline supplementation (or placebo): Weschler Adult Intelligence Scale-Revised (WAIS-R, intellectual functioning), Weschler Memory Scale-Revised (WMS-R, two subtests, verbal and visual memory), Rey-Osterrieth Complex Figure Test (visuospatial functioning and perceptual organization), Controlled Oral Word Association Test (verbal fluency), Grooved Pegboard (manual dexterity and motor speed), California Verbal Learning Test (CVLT, rote verbal learning ability), and Trail Making Parts A & B (visual scanning, psychomotor speed and set shifting). Scores were reported in terms of standard scores including z scores and percentile ranks. Mean absolute changes in raw scores were compared between groups using the Wilcoxon rank sum test, where p values < .05 constituted statistical significance.

RESULTS

Significant improvements were found in the delayed visual recall of the WMS-R (7.0 +/- 2.7 vs -.33 +/- 5.7, p = .028), and borderline improvements in the List B subset of the CVLT (1.0 +/- 0.8 vs -2.0 +/- 2.4, p = .06) and the Trails A test (-3.8 +/- 8.1 vs 3.7 +/- 4.5 seconds, p = .067). No other statistically significant changes were seen.

CONCLUSIONS

This pilot study indicates both verbal and visual memory may be impaired in patients who require long-term TPN and both may be improved with choline supplementation.

Plasma choline in normal newborns, infants, toddlers, and in very-low-birth-weight neonates requiring total parenteral nutrition

Choline deficiency is associated with hepatic abnormalities in adult volunteers and patients administered total parenteral nutrition (TPN). Preliminary investigation has suggested that plasma-free choline concentration (PFCh) is greater in neonatal animals, including humans, than in adults. The aims of this study were to determine the normal PFCh and phospholipid-bound choline concentration (PPLBCh) for newborns, infants, and toddlers and to determine the change during TPN. We also sought to determine the degree of fetal choline extraction, the relation between maternal and newborn plasma choline concentrations, and the relation between plasma choline status and normal newborn length, weight, and gestational age. Blood samples were obtained from 104 full-term newborns in two centers (Ben Taub and Maimonides), 25 mothers, 21 normal infants aged 20.3 +/- 11.8 wk, 12 normal infants aged 62.4 +/- 3.9 wk, and 14 preterm infants (gestational age = 28.9 +/- 2.2 wk) who required TPN. The vein PFChs were 28.1 +/- 13.0 nmol/mL (Ben Taub) and 68.1 +/- 16.9 nmol/mL (Maimonides). The artery PFChs were 27.1 +/- 13.0 nmol/mL (Ben Taub) and 57.9 +/- 11.6 nmol/mL (Maimonides). The vein PPLChs were 1004.7 +/- 246.6 nmol/mL (Ben Taub) and 1121.2 +/- 289.6 nmol/mL (Maimonides). The artery PPLChs were 1065.7 +/- 469.3 nmol/mL (Ben Taub) and 1106.9 +/- 285.8 nmol/mL (Maimonides). The vein-minus-artery differences for PFCh were 1.0 +/- 9.7 nmol/mL (Ben Taub) and 10.2 +/- 10.9 nmol/mL (Maimonides). The vein-minus-artery differences for PPLCh were -51.9 +/- 398.2 nmol/mL (Ben Taub General Hospital, Houston, Texas) and 14.4 +/- 254.3 nmol/mL (Maimonides, New York, New York). Maternal venous PFCh was 8.4 +/- 3.1 nmol/mL. Maternal venous PPLCh was 2592.1 +/- 584.0 nmol/mL (range = 1227.8-3729.0). Maternal venous PFCh correlated with newborn arterial PFCh (r = 0.53, P < 0.05) but not with newborn venous PFCh. No correlation was seen between maternal venous and newborn PPLCh. No significant differences were seen in PPLCh or choline extraction in Ben Taub versus Maimonides patients, although PFCh was significantly greater in the newborns from Maimonides (P < 0.05). The mean venous PFCh and PPLCh in the preterm infants before beginning TPN was 21.2 +/- 6.3 and 1366.8 +/- 339.1 nmol/mL, respectively. Just before initiation of tube feeding (4.0 +/- 2.7 d after TPN had been started), mean venous PFCh and PPLCh was 18.4 +/- 5.3 and 2251.8 +/- 686.9 nmol/mL, respectively. When TPN was discontinued and tube feeding increased to goal, after 10.8 +/- 10.4 d, venous PFCh and PPLCh was 22.6 +/- 8.7 and 2072.5 +/- 540.6 nmol/mL, respectively. Venous PFCh and PPLCh was 13.4 +/- 2.5 and 1827.5 +/- 327.0 nmol/mL, respectively in the older infant group. In conclusion, newborn PFCh is significantly greater than PFCh in adults but falls to adult levels within the first year of life. Low maternal PFCh may be associated with low newborn PFCh. Normal newborn plasma choline status has no bearing on intrauterine growth, although the role of maternal choline deficiency in underweight newborns is unknown. Newborn PPLCh is substantially below that of adults, which suggests its use in membrane synthesis during growth.