بررسی اثر مهاری پپتید clf36 مشتق شده از لاکتوفرین شتری بر مسیر پیام‌رسان nf-кb در محیط شبیه‌سازی شده مولکولی (in silico)

هدف از این مطالعه، بررسی اثرات مهاری لاکتوفرامپین- لاکتوفریسین شتری نوترکیب بر مسیر فاکتور هسته‌ای کاپا b (nf-кb) بود. این پپتید (clf36) که با مطالعه قبلی در آزمایشگاه بیوتکنولوژی گروه علوم دامی دانشکده کشاورزی دانشگاه فردوسی مشهد (شماره دسترسی بانک ژن: mh327768.1) تهیه شده است. اثرات بازدارندگی این پپتید با شبیه‌سازی داکینگ مولکولی (in silico) ارزیابی شد. داده‌های پروتئین برای مسیر پیام‌رسان nf-кb از بانک داده‌های پروتئین (pdb) و uniprot جمع‌آوری شد. سپس، شبیه‌سازی برهم‌کنش (داکینگ) پپتید clf36 با مسیر پیام‌رسان nf-кb در بالادست، سایتوکین‌های پیش‌التهابی (مانند tnf-α و il-6) و در پایین‌دست، ikk-β وnf-κb-p65  سیتوپلاسمی با استفاده از نرم‌افزار آنلاین  cluspro 2.0انجام شد. تجزیه و تحلیل بیوانفورماتیکی بر اساس برهم‌کنش‌های مولکولی این پپتید با جایگاه فعال پروتئین‌های مسیر nf-кb نشان داد که ممکن است نقش تعدیل‌کنندگی و ضدالتهابی در فرآیندهای ایمنی را با اثر مهاری بر روی سایتوکین‌های tnf-α و il-6 در بالادست و ikk-β و nf-κb-p65 در پایین دست مسیر پیام‌رسان nf-кb  داشته باشد. این نتایج مشابه با اثرات مهاری infliximab،camelid fab، nemo و gilz بر روی مسیر پیام‌رسان nf-кb است. علاوه‌براین، این یافته‌ها ممکن است یک مبنای نظری برای مکانیسم‌های درمانی پپتید clf36 فراهم کند.

investigation of the inhibitory effects of clf36 peptide derived from camel lactoferrin on nf-κb signaling pathway in molecular docking simulation (in silico)

introduction: lactoferrin is secreted in the apo-form from epithelial cells in most exocrine fluids, such as saliva, bile, pancreatic and gastric fluids, tears and, particularly, in milk. lactoferrin is the most dominant protein in milk after casein. this protein plays a crucial role in many biological processes including the regulation of iron metabolism, induction and modulation of the immune system, the primary defense against microorganisms, inhibiting lipid peroxidation and presenting antimicrobial activity against various pathogens such as parasites, fungi, bacteria, and viruses. the major antimicrobial effect of lactoferrin is related to its n-terminal tail where different peptides for instance lactoferricin and lactoferrampin which are important for their antimicrobial abilities are present. clf chimera (clf36 peptide ) was derived from camel lactoferrin (clf) consisting of 42 amino acids and has primary sequence of dliwkllvkaqekfgrgkpskrvkkmrrqwqacksshhhhhh. in addition, the results of previous study showed that clfchimera had anti-inflammatory and regulatory activity of the immune system. nuclear factor kappa b (nf-kb) transcription factors regulate several important physiological processes, including inflammation and immune responses, cell growth, apoptosis, and the expression of certain viral genes. nf-kb dimers are located in the cytoplasm in an inactive form through association with any of several ikb inhibitor proteins. the phosphorylation and degradation of ikb have received great attention as key steps for the regulation ofnuclear factor kappa b (nf-kb) complexes. phosphorylation of the ikb by ikk signals it for ubiquitination at specific lysine residues. the aim of this study was to investigate the inhibitory effects of the recombinant camel lactoferrampin-lactoferricin on nuclear factor kappa b (nf-кb) pathway.materials and methods: clf36 peptide was prepared through a previous study in biotechnology laboratory of animal science department, faculty of agriculture, ferdowsi university of mashhad (genbank accession number: mh327768.1). protein data for inhibitory combinations of the nuclear factor kappa b (nf-kb) pathway was collected from the protein data bank (pdb) and uniprot.physico-chemical properties analysis (atomic state, isoelectric point, half-life, hydrophobicity hydrophilicity , barometric and ph) was done using expasy prot param online server. the inhibitory effects of this peptide was assessed by molecular docking simulation (in silico). the simulation of the interaction (docking) of clf36 peptide with nuclear factor kappa b (nf-kb) signaling pathway in upstream, pro-inflammatory cytokines (e.g., tnf-α and il-6) and in downstream, cytoplasmic ikkb and nf-κbp65 was done using cluspro 2.0 software online.interaction diagram created by ligplot+ showing the hydrogen bond network and the hydrophobic interactions of clf36 peptid with the upstream and downstream nuclear factor kappa b (nf-kb) pathways.results and discussion: bioinformatics analysis on the molecular interaction of this peptide with the active site of nf-κb proteins suggested that in may have role of the modulators and anti-inflammatory of immune processes by inhibitory effect on the tnf-α and il-6 cytokines in upstream and ikk-β and nf-κb-p65 in downstream of the nf-κb signaling pathway. this results are similar to the inhibitory effects of infliximab, camelid fab , nemo and  gilz on the nuclear factor kappa b (nf-kb) signaling pathway. infliximab (remicade) is a chimeric maband its use is not very well tolerated in the majority of patients, infliximab therapy leads to the production of antibodies to infliximab in a small subset of patients. the  camelid fab antibody with the highest (femtomolar) potency, displays a very large surface of interaction with il-6. the regulatory role of nemo in the ikk complex, since a number of genetic and biochemical studies clearly demonstrate that proinflammatory ikk activation is absolutely dependent upon the presence of functional nemo. glucocorticoid-induced leucine zipper (gilz) is a glucocorticoid responsive protein that links the nuclear factor-kappa b (nfκb) and the glucocorticoid signaling pathways. func tional and binding studies suggest that the proline-rich region at the carboxy terminus of glucocorticoid-induced leucine zipper (gilz) binds the p65 subunit of nuclear factor kappa b (nf-kb) and suppresses the immunoinflammatory response.conclusion:  the results of the interaction (docking) of clf36 peptide with nuclear factor kappa b (nf-kb) signaling pathway indicates that, in upstream, will be inhibitory effect of clf36 peptide in active site of pro-inflammatory cytokines (e.g., tnf-α and il-6) and in downstream, cfl36 peptide will bind to protein receptors of cytoplasmic ikkb and nf-κb p65. therefore, these findings may provide a theoretical basis for therapeutic mechanisms of clf36 peptide.