Non-coding RNA's prevalence as biomarkers for prognostic, diagnostic, and clinical utility in breast cancer.

Noncoding RNAs (ncRNAs), which make up a significant portion of the mammalian transcriptome and plays crucial regulatory roles in expression of genes and other biological processes, have recently been found. The most extensively researched of the sncRNAs, microRNAs (miRNAs), have been characterized in terms of their synthesis, roles, and significance in the tumor development. Its crucial function in the stem cell regulation, another class of sncRNAs known as aspirRNAs, has attracted attention in cancer research. The investigations have shown that long non-coding RNAs have a crucial role in controlling developmental stages, such as mammary gland development. Additionally, it has been discovered that lncRNA dysregulation precedes the development of several malignancies, including breast cancer. The functions of sncRNAs (including miRNAs and piRNAs) and lncRNAs in the onset and development of the breast cancer are described in this study. Additionally, future perspectives of various ncRNA-based diagnostic, prognostic, and therapeutic approaches also discussed.

An unnatural amino acid modified human insulin derivative for visual monitoring of insulin aggregation.

Insulin often forms toxic fibrils during production and transportation, which are deposited as amyloids at repeated injection sites in diabetic patients. Distinguishing early fibrils from non-fibrillated insulin is difficult. Herein, we introduce a chemically modified human insulin derivative with a distinct visual colour transition upon aggregation, facilitating insulin quality assessment.

Strategies for Interference of Insulin Fibrillogenesis: Challenges and Advances.

The discovery of insulin came with very high hopes for diabetic patients. In 2021, the world celebrated the 100th anniversary of the discovery of this vital hormone. However, external use of insulin is highly affected by its aggregating tendency that occurs during its manufacturing, transportation, and improper handling which ultimately leads to its pharmaceutically and biologically ineffective form. In this review, we aim to discuss the various approaches used for decelerating insulin aggregation which results in the enhancement of its overall structural stability and usage. The approaches that are discussed are broadly classified as either a measure through excipient additions or by intrinsic modifications in the insulin native structure.

Z-Guggulsterone Is a Potential Lead Molecule of Dawa-ul-Kurkum against Hepatocellular Carcinoma.

An ancient saffron-based polyherbal formulation, Dawa-ul-Kurkum (DuK), has been used to treat liver ailments and other diseases and was recently evaluated for its anticancer potential against hepatocellular carcinoma (HCC) by our research team. To gain further insight into the lead molecule of DuK, we selected ten active constituents belonging to its seven herbal constituents (crocin, crocetin, safranal, jatamansone, isovaleric acid, cinnamaldehyde, coumaric acid, citral, guggulsterone and dehydrocostus lactone). We docked them with 32 prominent proteins that play important roles in the development, progression and suppression of HCC and those involved in endoplasmic reticulum (ER) stress to identify the binding interactions between them. Three reference drugs for HCC (sorafenib, regorafenib, and nivolumab) were also examined for comparison. The in silico studies revealed that, out of the ten compounds, three of them-viz., Z-guggulsterone, dehydrocostus lactone and crocin-showed good binding efficiency with the HCC and ER stress proteins. Comparison of binding affinity with standard drugs was followed by preliminary in vitro screening of these selected compounds in human liver cancer cell lines. The results provided the basis for selecting Z-guggulsterone as the best-acting phytoconstituent amongst the 10 studied. Further validation of the binding efficiency of Z-guggulsterone was undertaking using molecular dynamics (MD) simulation studies. The effects of Z-guggulsterone on clone formation and cell cycle progression were also assessed. The anti-oxidant potential of Z-guggulsterone was analyzed through DPPH and FRAP assays. qRTPCR was utilized to check the results at the in vitro level. These results indicate that Z-guggulsterone should be considered as the main constituent of DuK instead of the crocin in saffron, as previously hypothesized.

Facile synthesis of rapamycin-peptide conjugates as mTOR and Akt inhibitors.

A simple and straightforward process for the synthesis of rapamycin peptide conjugates in a regio and chemoselective manner was developed. The methodology comprises the tagging of chemoselective functionalities to rapamycin and peptides which enables the conjugation of free peptides, without protecting the functionality of the side chain amino acids, in high yield and purity. From this methodology, we successfully conjugate free peptides containing up to 15 amino acids. Rapamycin is also conjugated to the peptides known for inhibiting the kinase activity of Akt protein. These conjugates act as dual target inhibitors and inhibit the kinase activity of both mTOR and Akt.

The difficulties experienced during the preparation and administration of oral drugs by parents at home: a cross-sectional study from Palestine.

BACKGROUND: Failure to properly administer drugs to children at home may cause adverse events, which makes it a challenging job for parents or caregivers. The main goal of this study was to investigate the problems and difficulties that parents or caregivers faced when administering oral drugs to their children at home. METHODS: A cross-sectional study was conducted using a questionnaire consisting of 'yes/no' and multiple-response questions to assess parents' experiences and problems with administering medication to their children at home. Data was collected from parents who visited primary health care centres in Nablus. Descriptive analysis was conducted to describe the characteristics of the sample. RESULTS: We interviewed 420 parents. 91.9% of the parents used drugs without prescription from a doctor, and the most commonly used non-prescription medicines were antipyretics (n=386, 100%), influenza drugs (n=142, 36.8%), cough drugs (n=109, 28.2%) and antibiotics (n= 102, 26.4%). The study showed that 21.7% of parents used teaspoon and 7.1% used tablespoon in administering liquid medications to their children. When the children refused taking liquid medications, almost two-thirds of the parents (65.7%) insisted their children take them, 21.5% mixed it with juice, 5.2% mixed it with food and 4.7% mixed it with milk. 12.4% of the parents reported that they gave drugs in doses higher than prescribed by the doctor to treat their children more quickly. Also, our study revealed that 80.5% of the parents gave medications at incorrect intervals. CONCLUSIONS: This study has shown that there is a proportion of caregivers or parents who administer oral drugs to their children incorrectly, which may involve giving them at the wrong intervals or doses, using incorrect instruments, or mixing them with food, juice or milk. The development of educational programs that will provide parents with education about medication administration is therefore recommended.

AzaGly-Appended Peptidomimetics Structurally Related to PTR6154 as Potential PKB/Akt Inhibitors.

We report the synthesis and biological and physiochemical properties of a series of azaGly-appended peptidomimetics. We have developed a simple and facile synthesis for azapeptides on solid support without any side reaction. The azaGly is inserted by in situ reaction of disuccinimidyl carbonate with free amine followed by treatment of hydrazine hydrate at room temperature. The new series of peptidomimetics was prepared by azaGly scanning of heptapeptide Arg-Pro-Arg-Nle-Tyr-Dap-Nle (Akt-01), a GSK-3ß-derived Akt inhibitor. The azaGly-appended peptides showed significant improvement in biological activity and serum stability, with retention of conformation as evidenced by NMR and CD studies. The results clearly demonstrate that azaGly-appended peptides are new peptidomimetics. Their synthesis makes this approach highly useful for the development of novel peptidomimetics of therapeutic potential.

Strategies for gaseous neuromodulator release in chemical neuroscience: Experimental approaches and translational validation.

Gasotransmitters are a group of short-lived gaseous signaling molecules displaying diverse biological functions depending upon their localized concentration. Nitric oxide (NO), hydrogen sulfide (H2S), and carbon monoxide (CO) are three important examples of endogenously produced gasotransmitters that play a crucial role in human neurophysiology and pathogenesis. Alterations in their optimal physiological concentrations can lead to various severe pathophysiological consequences, including neurological disorders. Exogenous administration of gasotransmitters has emerged as a prominent therapeutic approach for treating such neurological diseases. However, their gaseous nature and short half-life limit their therapeutic delivery. Therefore, developing synthetic gasotransmitter-releasing strategies having control over the release and duration of these gaseous molecules has become imperative. However, the complex chemistry of synthesis and the challenges of specific quantified delivery of these gases, make their therapeutic application a challenging task. This review article provides a focused overview of emerging strategies for delivering gasotransmitters in a controlled and sustained manner to re-establish neurophysiological homeostasis.

Anti-proliferative, -migratory and -clonogenic effects of long-lasting nitric oxide release in HepG2 cells.

Nitric oxide (NO) holds promise as a cytotoxic agent against tumors, but its gaseous nature and short half-life hinder direct administration to tumor tissues. Herein, we present novel 6,9-disubstituted purine derivatives designed to ensure sustained NO release, followed by study of their significant anti-proliferative, anti-migratory, and anti-clonogenic effects on HepG2 cell lines, highlighting NO release as a potent effector for treating hepatocellular carcinoma.

Synthesis of a highly thermostable insulin by phenylalanine conjugation at B29 Lysine.

Globally, millions of diabetic patients require daily life-saving insulin injections. Insulin heat-lability and fibrillation pose significant challenges, especially in parts of the world without ready access to uninterrupted refrigeration. Here, we have synthesized four human insulin analogs by conjugating ε-amine of B29 lysine of insulin with acetic acid, phenylacetic acid, alanine, and phenylalanine residues. Of these, phenylalanine-conjugated insulin, termed FHI, was the most stable under high temperature (65 °C), elevated salt stress (25 mM NaCl), and varying pH levels (ranging from highly acidic pH 1.6 to physiological pH 7.4). It resists fibrillation for a significantly longer duration with sustained biological activity in in vitro, ex vivo, and in vivo and displays prolonged stability over its native counterpart. We further unravel the critical interactions, such as additional aromatic π-π interactions and hydrogen bonding in FHI, that are notably absent in native insulin. These interactions confer enhanced structural stability of FHI and offer a promising solution to the challenges associated with insulin heat sensitivity.

Aß-oligomers: A potential therapeutic target for Alzheimer's disease.

The cascade of amyloid formation relates to multiple complex events at the molecular level. Previous research has established amyloid plaque deposition as the leading cause of Alzheimer's disease (AD) pathogenesis, detected mainly in aged population. The primary components of the plaques are two alloforms of amyloid-beta (Aß), Aß1-42 and Aß1-40 peptides. Recent studies have provided considerable evidence contrary to the previous claim indicating that amyloid-beta oligomers (AßOs) as the main culprit responsible for AD-associated neurotoxicity and pathogenesis. In this review, we have discussed the primary features of AßOs, such as assembly formation, the kinetics of oligomer formation, interactions with various membranes/membrane receptors, the origin of toxicity, and oligomer-specific detection methods. Recently, the discovery of rationally designed antibodies has opened a gateway for using synthesized peptides as a grafting component in the complementarity determining region (CDR) of antibodies. Thus, the Aß sequence motif or the complementary peptide sequence in the opposite strand of the ß-sheet (extracted from the Protein Data Bank: PDB) helps design oligomer-specific inhibitors. The microscopic event responsible for oligomer formation can be targeted, and thus prevention of the overall macroscopic behaviour of the aggregation or the associated toxicity can be achieved. We have carefully reviewed the oligomer formation kinetics and associated parameters. Besides, we have depicted a thorough understanding of how the synthesized peptide inhibitors can impede the early aggregates (oligomers), mature fibrils, monomers, or a mixture of the species. The oligomer-specific inhibitors (peptides or peptide fragments) lack in-depth chemical kinetics and optimization control-based screening. In the present review, we have proposed a hypothesis for effectively screening oligomer-specific inhibitors using the chemical kinetics (determining the kinetic parameters) and optimization control strategy (cost-dependent analysis). Further, it may be possible to implement the structure-kinetic-activity-relationship (SKAR) strategy instead of structure-activity-relationship (SAR) to improve the inhibitor's activity. The controlled optimization of the kinetic parameters and dose usage will be beneficial for narrowing the search window for the inhibitors.

Identification of New Key Genes and Their Association with Breast Cancer Occurrence and Poor Survival Using In Silico and In Vitro Methods.

Breast cancer is one of the most prevalent types of cancer diagnosed globally and continues to have a significant impact on the global number of cancer deaths. Despite all efforts of epidemiological and experimental research, therapeutic concepts in cancer are still unsatisfactory. Gene expression datasets are widely used to discover the new biomarkers and molecular therapeutic targets in diseases. In the present study, we analyzed four datasets using R packages with accession number GSE29044, GSE42568, GSE89116, and GSE109169 retrieved from NCBI-GEO and differential expressed genes (DEGs) were identified. Protein-protein interaction (PPI) network was constructed to screen the key genes. Subsequently, the GO function and KEGG pathways were analyzed to determine the biological function of key genes. Expression profile of key genes was validated in MCF-7 and MDA-MB-231 human breast cancer cell lines using qRT-PCR. Overall expression level and stage wise expression pattern of key genes was determined by GEPIA. The bc-GenExMiner was used to compare expression level of genes among groups of patients with respect to age factor. OncoLnc was used to analyze the effect of expression levels of LAMA2, TIMP4, and TMTC1 on the survival of breast cancer patients. We identified nine key genes, of which COL11A1, MMP11, and COL10A1 were found up-regulated and PCOLCE2, LAMA2, TMTC1, ADAMTS5, TIMP4, and RSPO3 were found down-regulated. Similar expression pattern of seven among nine genes (except ADAMTS5 and RSPO3) was observed in MCF-7 and MDA-MB-231 cells. Further, we found that LAMA2, TMTC1, and TIMP4 were significantly expressed among different age groups of patients. LAMA2 and TIMP4 were found significantly associated and TMTC1 was found less correlated with breast cancer occurrence. We found that the expression level of LAMA2, TIMP4, and TMTC1 was abnormal in all TCGA tumors and significantly associated with poor survival.

Identification of potential inhibitor molecule against MabA protein of Mycobacterium leprae by integrated in silico approach.

Leprosy is one of the chronic diseases with which humanity has struggled globally for millennia. The potent anti-leprosy medications rifampicin, clofazimine and dapsone, among others, are used to treat leprosy. Nevertheless, even in regions of the world where these drugs have been successfully implemented, resistance continues to be observed. Due to the problems with the current treatments, this disease should be fought at every level of society with new drugs. The purpose of this research was to identify natural candidates with the ability to inhibit MabA (gene-fabG1) with fewer negative effects. The work was accomplished through molecular docking, followed by a dynamic investigation of protein-ligand, which play a significant role in the design of pharmaceuticals. After modelling the protein structure with MODELLER 9.21v, AutoDock Vina was used to perform molecular docking with 13 3 D anti-leprosy medicines and a zinc library to determine the optimal protein-ligand interaction. In addition, the docking result was filtered based on binding energy, ADMET characteristics, PASS analysis and the most crucial binding residues. The ZINC08101051 chemical compound was prioritized for further study. Using an all-atom 100 ns MD simulation, the binding pattern and conformational changes in protein upon ligand binding were studied. Recommendation for subsequent validation based on deviation, fluctuation, gyration and hydrogen bond analysis, followed by main component and free energy landscape.Communicated by Ramaswamy H. Sarma.

Inhibitory effect of natural compounds on Dihydropteroate synthase of Mycobacterium leprae: Molecular dynamic study.

Leprosy is a chronic infectious disease caused by a bacillus, Mycobacterium leprae. According to official data from 139 countries in the 6 WHO Regions, there were 127558 new leprosy cases worldwide in 2020. Leprosy mainly affects the skin, the peripheral nerves, mucosa of the upper respiratory tract, and the eyes. If this disease is left untreated, can harm the skin, nerves, limbs, eyes, and skin permanently. The disease is curable with multidrug therapy. Over a period of time Mycobacterium leprae has become resistant to these drugs. Therefore, new therapeutic molecules are warranted. This study was aimed to carry out the in-silico analysis to determine the inhibitory effect of natural compounds on Dihydropteroate synthase (DHPS) of Mycobacterium leprae. The DHPS is a key enzyme in the folate biosynthesis pathway in M. leprae and acts as a competitive inhibitor of PABA. The 3D structure of DHPS protein was modeled using homology modeling and was validated. Molecular docking and simulation along with other in-silico methods were employed to determine the inhibitory effect of ligand molecules towards DHPS target protein. Results revealed ZINC03830554 molecule as a potential inhibitor of DHPS. Binding experiments and bioassays utilizing this strong inhibitor molecule against purified DHPS protein are necessary to validate these early findings.Communicated by Ramaswamy H. Sarma.

Anti-HIV and anti-HCV small molecule protease inhibitors in-silico repurposing against SARS-CoV-2 Mpro for the treatment of COVID-19.

The COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It is a global health emergency warranting development and implementation of targeted treatment. The enzyme main protease (Mpro; also known as 3C-like protease) is emerging as an attractive drug target. This enzyme plays an indispensable role in processing the translated polyproteins of viral RNA. Inhibiting the activity of Mpro would wedge viral replication. To facilitate the discovery of targeted therapy for COVID-19, we carried out the structure-assisted repurposing of existing protease inhibiting small molecules to target SARS-CoV-2 Mpro. Based on the structure of SARS-CoV-2 Mpro, here we report the small drug molecule namely saquinavir as its potent inhibitor. Findings support the premise that this promising antiviral protease inhibiting small drug molecule can be validated and implemented for the treatment and clinical management of COVID-19 pandemic disease.Communicated by Ramaswamy H. Sarma.

Novel Dipeptides Bearing Sulfonamide as Antimalarial and Antitrypanosomal Agents: Synthesis and Molecular Docking.

OBJECTIVE: Currently, there is a problem of ineffective chemotherapy to trypanosomiasis and the increasing emergence of malaria drug-resistant parasites. The research aimed at the development of new dipeptide-sulfonamides as antiprotozoal agents. BACKGROUND: Protozoan parasites cause severe diseases, with African human trypanosomiasis (HAT) and malaria standing on top of the list. The noted deficiencies of existing antitrypanosomal drugs and the worldwide resurgence of malaria, accompanied by the springing up of widespread drug-resistant protozoan parasites, represent a huge challenge in infectious disease treatment in tropical regions. METHODS: To discover new antiprotozoal agents, ten novel p-nitrobenzenesulphonamide derivatives incorporating dipeptide moiety were synthesized by the condensation reaction of 3-methyl-2-(4- nitrophenylsulphonamido)pentanoic acid (6) with substituted acetamides (4a-j) using peptide coupling reagents, characterized using 1H and 13C NMR, FTIR, HRMS and investigated for their antimalarial and antitrypanosomal activities in vivo employing standard methods. RESULTS: At 100 mg/kg body weight, N-(2-(2,6-dimethylphenylamino)-2-oxoethyl)-3-methyl-2-(4- nitrophenylsulfonamido)pentanamide showed the highest activity by inhibiting P. berghei parasite by 79.89%, which was comparable with the standard drug (artemether-lumefantrine 79.77%). In the antitrypanosomal study, N-(2-(4-chlorophenylamino)-2-oxoethyl)-3-methyl-2-(4-nitrophenylsulfonamido) pentanamide, N-(2-(4-fluorophenylamino)-2-oxoethyl)-3-methyl-2-(4-nitrophenylsulfonamido) pentanamide and N-(2-(3-chlorophenylamino)-2-oxoethyl)-3-methyl-2-(4-nitrophenylsulfonamido) pentanamide were most potent in clearing Trypanosome brucei in mice, but they were less active than the standard drug (diminazene aceturate). Molecular docking results demonstrated good binding affinity among the reported derivatives and target proteins in the active place of the protein. The outcome of hematological analysis, liver, and kidney function tests showed that the new compounds had no adverse effect on the blood and organs. CONCLUSION: The results of this research showed that the new compounds demonstrated interesting antitrypanosomal and antimalarial potentials. However, further research should be carried out on the synthesized derivatives as promising drug candidates for trypanosomiasis and malaria.

Multiple Actions of H2S-Releasing Peptides in Human ß-Amyloid Expressing C. elegans.

Alzheimer's disease (AD) is a debilitating progressive neurodegenerative disorder characterized by the loss of cognitive function. A major challenge in treating this ailment fully is its multifactorial nature, as it is associated with effects like deposition of Aß plaques, oxidative distress, inflammation of neuronal cells, and low levels of the neurotransmitter acetylcholine (ACh). In the present work, we demonstrate the design, synthesis, and biological activity of peptide conjugates by coupling a H2S-releasing moiety to the peptides known for their Aß antiaggregating properties. These conjugates release H2S in a slow and sustained manner, due to the formation of self-assembled structures and delivered a significant amount of H2S within Caenorhabditis elegans. These conjugates are shown to target multiple factors responsible for the progression of AD: notably, we observed reduction in oxidative distress, inhibition of Aß aggregation, and significantly increased ACh levels in the C. elegans model expressing human Aß.

Temporal Cortex Microarray Analysis Revealed Impaired Ribosomal Biogenesis and Hyperactivity of the Glutamatergic System: An Early Signature of Asymptomatic Alzheimer's Disease.

Pathogenic aging is regarded as asymptomatic AD when there is no cognitive deficit except for neuropathology consistent with Alzheimer's disease. These individuals are highly susceptible to developing AD. Braak and Braak's theory specific to tau pathology illustrates that the brain's temporal cortex region is an initiation site for early AD progression. So, the hub gene analysis of this region may reveal early altered biological cascades that may be helpful to alleviate AD in an early stage. Meanwhile, cognitive processing also drags its attention because cognitive impairment is the ultimate result of AD. Therefore, this study aimed to explore changes in gene expression of aged control, asymptomatic AD (AsymAD), and symptomatic AD (symAD) in the temporal cortex region. We used microarray data sets to identify differentially expressed genes (DEGs) with the help of the R programming interface. Further, we constructed the protein-protein interaction (PPI) network by performing the STRING plugin in Cytoscape and determined the hub genes via the CytoHubba plugin. Furthermore, we conducted Gene Ontology (GO) enrichment analysis via Bioconductor's cluster profile package. Resultant, the AsymAD transcriptome revealed the early-stage changes of glutamatergic hyperexcitability. Whereas the connectivity of major hub genes in this network indicates a shift from initially reduced rRNA biosynthesis in the AsymAD group to impaired protein synthesis in the symAD group. Both share the phenomenon of breaking tight junctions and others. In conclusion, this study offers new understandings of the early biological vicissitudes that occur in the brain before the manifestation of symAD and gives new promising therapeutic targets for early AD intervention.

Identification of pathogenic genes associated with CKD: An integrated bioinformatics approach.

Chronic kidney disease (CKD) is defined as a persistent abnormality in the structure and function of kidneys and leads to high morbidity and mortality in individuals across the world. Globally, approximately 8%-16% of the population is affected by CKD. Proper screening, staging, diagnosis, and the appropriate management of CKD by primary care clinicians are essential in preventing the adverse outcomes associated with CKD worldwide. In light of this, the identification of biomarkers for the appropriate management of CKD is urgently required. Growing evidence has suggested the role of mRNAs and microRNAs in CKD, however, the gene expression profile of CKD is presently uncertain. The present study aimed to identify diagnostic biomarkers and therapeutic targets for patients with CKD. The human microarray profile datasets, consisting of normal samples and treated samples were analyzed thoroughly to unveil the differentially expressed genes (DEGs). After selection, the interrelationship among DEGs was carried out to identify the overlapping DEGs, which were visualized using the Cytoscape program. Furthermore, the PPI network was constructed from the String database using the selected DEGs. Then, from the PPI network, significant modules and sub-networks were extracted by applying the different centralities methods (closeness, betweenness, stress, etc.) using MCODE, Cytohubba, and Centiserver. After sub-network analysis we identified six overlapped hub genes (RPS5, RPL37A, RPLP0, CXCL8, HLA-A, and ANXA1). Additionally, the enrichment analysis was undertaken on hub genes to determine their significant functions. Furthermore, these six genes were used to find their associated miRNAs and targeted drugs. Finally, two genes CXCL8 and HLA-A were common for Ribavirin drug (the gene-drug interaction), after docking studies HLA-A was selected for further investigation. To conclude our findings, we can say that the identified hub genes and their related miRNAs can serve as potential diagnostic biomarkers and therapeutic targets for CKD treatment strategies.

A colored hydrophobic peptide film based on self-assembled two-fold topology.

Structural colors are abundant in nature and bear advantages over pigment-based colors, such as higher durability, brilliance and often physical hydrophobicity, thus underlying their vast potential for technological applications. Recently, biomimetics of complex natural topologies resulting in such effects has been extensively studied, requiring advanced processing and fabrication techniques. Yet, artificial topologies combining structural coloration and hydrophobicity have not been reported. Herein, we present the bottom-up fabrication of short self-assembling peptides as surface covering films, resulting in an easily achievable multilevel morphology of primary structures in a foam-like enclosure, producing structural colors and hydrophobicity. We demonstrate simple techniques allowing controlled coloration of different surfaces while maintaining an >100° water contact angle (WCA). The new artificial topology is much simpler than the natural counterparts and is not limited to a specific peptide, thus allowing the design of modular materials with unparalleled multifunctionalities and potential for further tuning and modifications.