Computational Analysis of Non-synonymous SNPs in ATM Kinase: Structural Insights, Functional Implications, and Inhibitor Discovery.

Ataxia telangiectasia-mutated (ATM) protein kinase, a key player in cellular integrity regulation, is known for its role in DNA damage response. This study investigates the broader impact of ATM on cellular processes and potential clinical manifestations arising from mutations, aiming to expand our understanding of ATM's diverse functions beyond conventional roles. The research employs a comprehensive set of computational techniques for a thorough analysis of ATM mutations. The mutation data are curated from dbSNP and HuVarBase databases. A meticulous assessment is conducted, considering factors such as deleterious effects, protein stability, oncogenic potential, and biophysical characteristics of the identified mutations. Conservation analysis, utilizing diverse computational tools, provides insights into the evolutionary significance of these mutations. Molecular docking and dynamic simulation analyses are carried out for selected mutations, investigating their interactions with Y2080D, AZD0156, and quercetin inhibitors to gauge potential therapeutic implications. Among the 419 mutations scrutinized, five (V1913C, Y2080D, L2656P, C2770G, and C2930G) are identified as both disease causing and protein destabilizing. The study reveals the oncogenic potential of these mutations, supported by findings from the COSMIC database. Notably, Y2080D is associated with haematopoietic and lymphoid cancers, while C2770G shows a correlation with squamous cell carcinomas. Molecular docking and dynamic simulation analyses highlight strong binding affinities of quercetin for Y2080D and AZD0156 for C2770G, suggesting potential therapeutic options. In summary, this computational analysis provides a comprehensive understanding of ATM mutations, revealing their potential implications in cellular integrity and cancer development. The study underscores the significance of Y2080D and C2770G mutations, offering valuable insights for future precision medicine targeting-specific ATM. Despite informative computational analyses, a significant research gap exists, necessitating essential in vitro and in vivo studies to validate the predicted effects of ATM mutations on protein structure and function.

Selective blockade of IL-21 by myricetin impedes T follicular helper cell differentiation by negatively regulating the JAK/STAT/Bcl-6 pathway in a rheumatoid arthritis animal model.

Interleukin (IL)-21 is a major lineage-defining factor that promotes Tfh cell differentiation. The current study investigated the molecular basis of myricetin, a flavonoid that impedes IL-21-mediated differentiation of Tfh cells in RA. Through high-throughput virtual screening of natural compounds that inhibit IL-21, we found that myricetin binds to IL-21 and hampers its interaction with IL-21 receptor (IL-21R). Our in vivo studies demonstrated that myricetin treatment ameliorated the clinical manifestations in adjuvant-induced arthritis (AIA) mice by reducing paw thickness and cellular infiltration. In addition, myricetin inhibited splenic Tfh cell differentiation and IL-21 production in AIA mice. Myricetin negatively regulates JAK/STAT signaling and the downstream Bcl-6 transcription factor at the molecular level, which arrests Tfh cell differentiation. Our current research proposal to target IL-21 with myricetin inevitably represents a new molecular approach that expedites new alternative drugs for rheumatoid arthritis therapy. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03880-w.

Computational insights into NIMA-related kinase 6: unraveling mutational effects on structure and function.

The NEK6 (NIMA-related kinase 6) serine/threonine kinase is a pivotal player in a multitude of cellular processes, including the regulation of the cell cycle and the response to DNA damage. Its significance extends to disease pathogenesis, as changes in NEK6 activity have been linked to the development of cancer. Non-synonymous single nucleotide polymorphisms (nsSNPs) in NEK6 have been linked to cancer as they alter the protein's native structure and function. The association between NEK6 activity and cancer development has prompted researchers to explore the effects of genetic variations within the NEK6 gene. Therefore, we utilized advanced computational tools to analyze 155 high-confidence nsSNPs in the NEK6 gene. From this analysis, 21 nsSNPs were identified as potentially harmful, raising concerns about their impact on NEK6 activity and cancer risk. These 21 mutations were then examined for structural alterations, and eight of nsSNPs (I51M, V76A, I134N, Y152D, R171Q, V186G, L237R, and C285S) were found to destabilize the protein. Among the destabilizing mutations screened, a specific mutation, R171Q, stood out due to its conserved nature. To understand its impact on the protein and conformation, all-atom molecular dynamics simulations (MDS) for 100 ns were performed for both Wildtype NEK6 (WT-NEK6) and R171Q. The simulations revealed that the R171Q variant was unstable and led to significant conformational changes in NEK6. This study provides valuable insights into NEK6 dysfunction caused by single amino acid alterations, offering a novel understanding of the molecular mechanisms underlying NEK6-related cancer progression.

Non-steroidal anti-inflammatory drugs (NSAIDs): A current insight into its molecular mechanism eliciting organ toxicities.

Non-steroidal anti-inflammatory drugs (NSAIDs) are a class of medications that are routinely been used across the world. Their analgesic, anti-inflammatory, and antipyretic effects have all been well-documented. Moreover, they are been deliberated to have a protective role against various critical diseases such as cancer and cardiovascular diseases. However, the data presented by numerous studies in past have signified the adverse effects of NSAIDs due to overdosing on various systems such as cardiovascular, gastrointestinal, hepatic, renal, neural, etc. Despite substantial studies representing the mechanism behind the clinical risk of NSAIDs, there are very few reviews that have collated comprehensive records of various toxicities caused by overdosing on NSAIDs. As a result, we have presented a comprehensive overview of existing information on NSAIDs in this review. In addition to that, we have concentrated on presenting our understanding of various organ-based toxicities caused due to NSAID's prolonged use/overdosage.

NIMA-related kinase-6 (NEK6) as an executable target in cancer

Cancer is a disease that develops when cells begin to divide uncontrollably and spreads to other parts of the body. Proliferation and invasion of cancerous cells are generally known to be influenced by cell cycle-related proteins in human malignancies. Therefore, in this review, we have emphasized on the serine/threonine kinase named NEK6. NEK6 is been deliberated to play a critical role in mitosis progression that includes mitotic spindle formation, metaphase to anaphase transition, and centrosome separation. Moreover, it has a mechanistic role in DNA repair and can cause apoptosis when inhibited. Past studies have connected NEK6 protein expression to cancer cell senescence. Besides, there are reports relating NEK6 to a range of malignancies including breast, lung, ovarian, prostate, kidney, liver, and others. Given its significance, this review attempts to describe the structural and functional aspects of NEK6 in various cellular processes, as well as how it is linked to different forms of cancer. Lastly, we have accentuated, on some of the plausible inhibitors that have been explored against NEK6 overexpression (AU)

The NEK family of serine/threonine kinases as a biomarker for cancer.

Cancer is defined by unrestrained cell proliferation due to impaired protein activity. Cell cycle-related proteins are likely to play a role in human cancers, including proliferation, invasion, and therapeutic resistance. The serine/threonine NEK kinases are the part of Never In Mitosis A Kinases (NIMA) family, which are less explored kinase family involved in the cell cycle, checkpoint regulation, and cilia biology. They comprise of eleven members, namely NEK1, NEK2, NEK3, NEK4, NEK5, NEK6, NEK7, NEK8, NEK9, NEK10, and NEK11, located in different cellular regions. Recent research has shown the role of NEK family in various cancers by perversely expressing. Therefore, this review aimed to provide a systematic account of our understanding of NEK kinases; structural details; and its role in the cell cycle regulation. Furthermore, we have comprehensively reviewed the NEK kinases in terms of their expression and regulation in different cancers. Lastly, we have emphasized on some of the potential NEK inhibitors reported so far.

NIMA-related kinase-6 (NEK6) as an executable target in cancer.

Cancer is a disease that develops when cells begin to divide uncontrollably and spreads to other parts of the body. Proliferation and invasion of cancerous cells are generally known to be influenced by cell cycle-related proteins in human malignancies. Therefore, in this review, we have emphasized on the serine/threonine kinase named NEK6. NEK6 is been deliberated to play a critical role in mitosis progression that includes mitotic spindle formation, metaphase to anaphase transition, and centrosome separation. Moreover, it has a mechanistic role in DNA repair and can cause apoptosis when inhibited. Past studies have connected NEK6 protein expression to cancer cell senescence. Besides, there are reports relating NEK6 to a range of malignancies including breast, lung, ovarian, prostate, kidney, liver, and others. Given its significance, this review attempts to describe the structural and functional aspects of NEK6 in various cellular processes, as well as how it is linked to different forms of cancer. Lastly, we have accentuated, on some of the plausible inhibitors that have been explored against NEK6 overexpression.

Trichopus zeylanicus ameliorates ibuprofen inebriated hepatotoxicity and enteropathy: an insight into its modulatory impact on pro/anti-inflammatory cytokines and apoptotic signaling pathways.

Ibuprofen is a nonsteroidal anti-inflammatory drug that is commonly used for its analgesic, antipyretic and anti-inflammatory effects worldwide. However ibuprofen comes with serious unavoidable adverse effects on various organs when used for long duration or overdosed. Trichopus zeylanicus is a medicinal plant endemic to India owning various beneficial properties and is been used in treating various ailments. Therefore, the objective of this study was to evaluate the ameliorative effect of aqueous leaves' extract of Trichopus zeylanicus against ibuprofen-induced hepatic toxicity and enteropathy in rats. Overall in this study 30 male albino rats were used, which were divided into five groups (six in each group). Group-I was normal control, Group-II was ibuprofen (400 mg/kg/day) inebriated group, Group-III  was silymarin (25 mg/kg/day) pretreated  + ibuprofen (400 mg/kg/day), Group-IV was  ALETZ (1000 mg/kg/day) pretreated + ibuprofen (400 mg/kg/day), and Group-V was ALETZ alone (1000 mg/kg/day) group. The duration of the administration was for five days, followed by scarifying rats on the sixth day. Later the rats were assessed for liver and intestine enzyme markers, antioxidant parameters along with histopathological changes. In addition the pro-inflammatory markers such as TNF-α, IL-6 and IL-1ß as well as anti-inflammatory cytokine IL-10 levels were measured using ELISA. Lastly the expression pattern of apoptotic signaling markers such as caspase-3, caspase-8 and Bcl-2 was evaluated using western blot. The results obtained from this study showed changes in levels of aforesaid parameter which presented the toxic effect of ibuprofen on liver and small intestine. Pre-treatment of ALETZ in ibuprofen-inebriated group was able to normalize the adverse effect caused due to ibuprofen. The conclusion of the study deduces that pre-treatment with ALETZ alleviates by modulating oxidative stress, inflammation, and apoptosis in ibuprofen inebriated rats, indicating its protective mechanism.

A serine/threonine protein PIM kinase as a biomarker of cancer and a target for anti-tumor therapy.

The PIM Kinases belong to the family of a proto-oncogene that essentially phosphorylates the serine/threonine residues of the target proteins. They are primarily categorized into three types PIM-1, PIM-2, PIM-3 which plays an indispensable regulatory role in signal transduction cascades, by promoting cell survival, proliferation, and drug resistance. These kinases are overexpressed in several solid as well as hematopoietic tumors which supports in vitro and in vivo malignant cell growth along with survival by regulating cell cycle and inhibiting apoptosis. They lack regulatory domain which makes them constitutively active once transcribed. PIM kinases usually appear to be important downstream effectors of oncoproteins which overexpresses and helps in mediating drug resistance to available agents, such as rapamycin. Structural studies of PIM kinases revealed that they have unique hinge regions where two Proline resides and makes ATP binding unique, by offering a target for an increasing number of potent PIM kinase inhibitors. Preclinical studies of those inhibitory compounds in various cancers indicate that these novel agents show promising activity and some of them currently being under examination. In this review, we have outlined PIM kinases molecular mechanism and signaling pathways along with matriculation in various cancer and list of inhibitors often used.

PCR Amplifiable DNA from Breast Disease FFPE Section for Mutational Analysis.

Formalin-fixed paraffin-embedded (FFPE) tissue specimens have been a staple of research, providing precious resources for molecular and genomic studies. However, the biggest challenge is the extraction of high-quality DNA from FFPE tissues, given that the integrity of DNA is critically affected by formalin fixation. Formaldehyde induces crosslinks in DNA that renders single or double-stranded DNA breaks. Such breaks cause extensive fragmentation that directly influences the quality of DNA purified and the number of templates available for PCR amplification. Thus, protocol for DNA purification from FFPE tissues must effectively extract highly fragmented DNA and reverse cross-linking caused by formalin fixation. DNA extraction methods available in the literature were selected and modified at different stages to optimize a protocol that extracts DNA of sufficient quality and fragment size to be detectable by PCR. Archived FFPE tissues belonged to patients with triple negative breast cancer (TNBC) and benign breast disease were used for the protocol optimization. The best optimized protocol was then used to amplify Exon 4 region of Proviral integration site for Moloney murine leukemia virus1 (Pim1) kinase gene to analyze any probable somatic mutations both in TNBCs and benign breast diseases. Of the 12 different protocols developed, best quality DNA in terms of fragment size and purity was obtained when Tween20 lysis buffer was used for both deparaffinization and overnight digestion along with high salt precipitation. Optimized protocol was then validated by extracting DNAs from 10 TNBCs and 5 benign breast disease specimens with consistent purity and fragment size. PCR amplification and subsequent Sanger's sequencing revealed the presence of mutations in the Exon 4 region of Pim1 kinase. Deparaffinization and overnight digestion in Tween20 lysis buffer along with high salt precipitation yielded the best quality PCR amplifiable DNA for mutational analysis.