Targeted drug delivery to the thrombus by fusing streptokinase with a fibrin-binding peptide (CREKA): an in silico study.

Aim: Streptokinase has poor selectivity and provokes the immune response. In this study, we used in silico studies to design a fusion protein to achieve targeted delivery to the thrombus. Materials & methods: Streptokinase was analyzed computationally for mapping. The fusion protein modeling and quality assessment were carried out on several servers. The enzymatic activity and the stability of the fusion protein and its complex with plasminogen were assessed through molecular docking analysis and molecular dynamics simulation respectively. Results: Physicochemical properties analysis, protein quality assessments, protein-protein docking and molecular dynamics simulations predicted that the designed fusion protein is functionally active. Conclusion: Our results showed that this fusion protein might be a prospective candidate as a novel thrombolytic agent with better selectivity.

Unveiling promising breast cancer biomarkers: an integrative approach combining bioinformatics analysis and experimental verification.

BACKGROUND: Breast cancer remains a significant health challenge worldwide, necessitating the identification of reliable biomarkers for early detection, accurate prognosis, and targeted therapy. MATERIALS AND METHODS: Breast cancer RNA expression data from the TCGA database were analyzed to identify differentially expressed genes (DEGs). The top 500 up-regulated DEGs were selected for further investigation using random forest analysis to identify important genes. These genes were evaluated based on their potential as diagnostic biomarkers, their overexpression in breast cancer tissues, and their low median expression in normal female tissues. Various validation methods, including online tools and quantitative Real-Time PCR (qRT-PCR), were used to confirm the potential of the identified genes as breast cancer biomarkers. RESULTS: The study identified four overexpressed genes (CACNG4, PKMYT1, EPYC, and CHRNA6) among 100 genes with higher importance scores. qRT-PCR analysis confirmed the significant upregulation of these genes in breast cancer patients compared to normal samples. CONCLUSIONS: These findings suggest that CACNG4, PKMYT1, EPYC, and CHRNA6 may serve as valuable biomarkers for breast cancer diagnosis, and PKMYT1 may also have prognostic significance. Furthermore, CACNG4, CHRNA6, and PKMYT1 show promise as potential therapeutic targets. These findings have the potential to advance diagnostic methods and therapeutic approaches for breast cancer.

Harnessing the Power of CAR-NK Cells: A Promising Off-the-Shelf Therapeutic Strategy for CD38-Positive Malignancies.

Background: CD38 is highly expressed on multiple myeloma (MM) cells and has been successfully targeted by different target therapy methods. This molecule is a critical prognostic marker in both diffuse large B-cell lymphoma and chronic lymphocytic leukemia. Objective: We have designed and generated an anti-CD38 CAR-NK cell applying NK 92 cell line. The approach has potential application as an off-the-shelf strategy for treatment of CD38 positive malignancies. Methods: A second generation of anti-CD38 CAR-NK cell was designed and generated, and their efficacy against CD38-positive cell lines was assessed in vitro. The PE-Annexin V and 7-AAD methods were used to determine the percentage of apoptotic target cells. Flow cytometry was used to measure IFN-γ, Perforin, and Granzyme-B production following intracellular staining. Using in silico analyses, the binding capacity and interaction interface were evaluated. Results: Using Lentivirus, cells were transduced with anti-CD38 construct and were expanded. The expression of anti-CD38 CAR on the surface of NK 92 cells was approximately 25%. As we expected from in silico analysis, our designed CD38-chimeric antigen receptor was bound appropriately to the CD38 protein. NK 92 cells that transduced with the CD38 chimeric antigen receptor, generated significantly more IFN-γ, perforin, and granzyme than Mock cells, and successfully lysed Daudi and Jurkat malignant cells in a CD38-dependent manner. Conclusion: The in vitro findings indicated that the anti-CD38 CAR-NK cells have the potential to be used as an off-the-shelf therapeutic strategy against CD38-positive malignancies. It is recommended that the present engineered NK cells undergo additional preclinical investigations before they can be considered for subsequent clinical trial studies.

Bioinformatics analysis for the purpose of designing a novel multi-epitope DNA vaccine against Leishmania major.

Leishmaniasis is one of the main infectious diseases worldwide. In the midst of all the different forms of the disease, Cutaneous Leishmania (CL) has the highest incidence in the world. Many trial vaccines have been developed with the purpose of generating long-term cell-mediated immunity to Leishmania(L) major. As there is not any multi-epitope DNA vaccine with high efficacy against L.major, the aim of this study is to design a new multi-epitope DNA vaccine in order to have effective control upon this infectious disease through the immune bioinformatics. The L.major antigens: Gp63, LACK, TSA, LmSTI1and KMP11 were selected to design a multi-epitope DNA vaccine. The initial structure of the DNA vaccine was designed, benefiting from Gen Bank's website information. Epitopes of MHC-I antigens were predicted through the Immune Epitope Database (IEDB), and the selected epitopes were used to make vaccines construct along with linkers. New multi-epitope vaccine including 459 nucleic acids designed, and inserted between BamH1 and HindIII restriction sites of pCDNA3.1 mammalian expression vector. 12 epitopes among the chosen antigens were selected by two servers (IEDB and ANTIGEN). They had high stability and high antigenic power. Physicochemical features of vaccine measured by ProtParam server, and this structure was thermostable and hydrophilic. it's a suitable model to study on the animal and human phases. The designed vaccine is expected to be an effective candidate through development of (CL) vaccines. However, the effectiveness of this vaccine should also evaluate in vivo model.

Contamination of breast milk with lead, mercury, arsenic, and cadmium in Iran: a systematic review and meta-analysis.

Breast milk is a complete food for the development of the newborn, but it can also be an important route for environmental pollutants transmission to the infants. This study was aimed to evaluate the status of heavy metals including lead (Pb), mercury (Hg), cadmium (Cd) and arsenic (As) in the breast milk of Iranian mothers. The international databases including Scopus, PubMed, Web of Science and the Persian electronic databases including Scientific Information Database, IranMedex and Magiran were examined to find relevant articles published until July 2021. A total of 23 studies examined the levels of toxic metals in Iranian breast milk samples. According to the findings, the pooled average concentrations (µg/L) of Pb, Cd, Hg and As were 25.61, 2.40, 1.29 and 1.16, respectively. The concentration of Hg and Pb in colostrum milk was more than twice of mature milk. The Hg mean concentration in the breast milk of mothers with at least one amalgam-filled tooth was approximately three times that of mothers without amalgam-filled teeth. Risk assessment analysis indicated that the intake of Pb and Hg by infants through breastfeeding can be considered a health concern in Iran. It seems necessary to reduce the Pb exposure of pregnant and lactating women in Iran. However, more extensive studies are needed to clarify the toxic metals' exposure status of infants through breast milk in other parts of the country.

Novel single-chain antibodies against highly conserved epitopes in the hemagglutinin of influenza A viruses: Promising agents for universal therapies.

OBJECTIVES: Development of new antibodies with broad activity would provide anti-influenza prophylaxis and treatment. Human single-chain variable fragments (scFvs) are considered effective agents against viruses. In this study specific human scFvs against highly conserved epitopes in the hemagglutinin (HA) of influenza A viruses were selected and their neutralizing activity was evaluated. MATERIALS AND METHODS: Bioinformatic methods were used to evaluate HA epitopes. The panning process selected specific clones from a scFv library. PCR and DNA fingerprinting differentiated the common patterns. Soluble forms of scFvs were produced and evaluated using Western blot analysis. The neutralizing effects of anti-HA scFvs were assessed by microneutralization assay using MDCK cells. Real-time PCR was done to determine the exact copy number of the virus following neutralization. RESULTS: Bioinformatic evaluation confirmed the antigenicity and accessibility of the epitopes. Four specific anti-HA scFvs, scFvs I, II, I', and II' were selected. The scFvs neutralized 2009 H1N1 pandemic and 83.34%, 79.17%, 75%, and 62.5% reduction in the virus titers were obtained following treatments with scFv-II', I, I', and II, respectively. Real-time PCR demonstrated 98.6%, 95.7%, 95.26%, and 91.19% reductions in virus numbers following neutralization with scFv-II', I, I', and II, respectively. CONCLUSION: Anti-HA scFvs selected against highly conserved HA of influenza A virus with high neutralizing effects, offer novel human antibodies for prophylaxis and treatment of a wide range of influenza viruses including different subtypes of H1N1, H3N2, and H5N1 influenza A virus. The antibodies have the potential to be used for universal therapy.

Design and characterization of a recombinant immunotoxin for targeted therapy of breast cancer cells: In vitro and in silico analyses.

AIMS: GnRH-DFF40 (gonadotropin releasing hormone-DNA fragmentation factor 40) humanized recombinant immunotoxin serves as a prospective candidate for targeted therapy of malignancies with over-expressed gonadotropin releasing hormone receptor (GnRHR). In this study, we attempted to generate a GnRH-based chimeric protein composed of human DFF40 fused with GnRH which encodes an apoptotic nuclease and specifically targets cancer cells displaying GnRH receptor overexpression. MATERIALS AND METHODS: A codon optimized, synthetic GnRH-DFF40 fusion gene and its single counterpart (DFF40) were constructed in pET28a expression vector. Cytotoxicity of these expressed proteins were evaluated on three breast cancer cell lines (MCF7, MDA-MB231, and SKBR3). The stability and biological activity of the recombinant proteins were investigated in the treated cell line and cell-free system. Also, the ability of this fusion and its single form in inducing apoptosis, and inhibiting metastasis and migration were evaluated by flow cytometry, migration assay and wound healing analysis, respectively. In silico analyses were also done to understand the specific interactions between GnRH and its receptor. KEY FINDINGS: GnRH-DFF40 fusion protein and DFF40 were successfully expressed. The purified chimeric protein showed dose-dependent cytotoxicity against all three cell lines. The recombinant fusion protein was biologically active with nucleolytic functionality and apoptosis induction ability. Moreover, the fusion could inhibit the invasion property of MDA-MB-231 cells. In silico analysis also showed that four residues from GnRH domain and 11 GnRHR residues had the most interaction sites for specific targeted delivery of the immunotoxin in cancer cells. SIGNIFICANCE: Fusion construct could be a prospective candidate for targeted therapy of cancers upregulating GnRH receptor.

Effect of Nigella sativa L. supplementation on inflammatory and oxidative stress indicators: A systematic review and meta-analysis of controlled clinical trials.

AIMS: The objective of the present study was to perform a systematic review and meta-analysis on randomized controlled trials (RCTs) assessing the effects of Nigella sativa L. supplementation on the circulating inflammatory and oxidative stress markers, including C-reactive protein (CRP), interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), total antioxidant capacity (TAC) and malondialdehyde (MDA). METHODS: Systematic search was performed up to March 2020 using PubMed, Scopus, and ISI web of science databases. Two reviewers independently assessed study eligibility, extracted data, and evaluated methodological quality of included primary studies. Statistical heterogeneity was assessed using I-square (I2) statistic. Data were pooled by using the random-effect model and standardized mean difference (SMD) was considered as the summary effect size. RESULTS: Twelve trials were identified to be suitable for our meta-analysis. The pooled results using random effects model indicated that Nigella sativa supplementation significantly reduced CRP (SMD: -0.35; 95% CI: -0.59, -0.12, P < 0.001, I2 = 10.5%) and MDA concentrations (SMD: -0.56; 95% CI: -0.98, -0.15, P < 0.001, I2 = 64.7%). Moreover, Nigella sativa supplementation increased TAC (SMD: 0.48; 95% CI: 0.09, 0.87, P = 0.01, I2 = 65.6%) levels; however, it did not affect TNF-α (SMD: -0.35; 95% CI: -0.70, 0.01, P = 0.05, I2 = 58.2%). CONCLUSION: Nigella sativa supplementation is associated with improved inflammation and oxidative status. Additional prospective studies are recommended using higher supplementation doses and longer intervention period.

Generation and characterization of a specific single-chain antibody against DSPP as a prostate cancer biomarker: Involvement of bioinformatics-based design of novel epitopes.

Isolation of specific single chain antibodies (scFvs) against key epitopes of cancer markers are applied for cancer immunotherapy and diagnosis. In this study following the prediction of the 3D structure of the DSP part of Dentin sialophosphoprotein (DSPP), the epitope was chosen using in silico programs. Panning process was applied to isolate specific human scFv against the epitope. PCR and DNA fingerprinting differentiated the specific clones, which were evaluated by phage ELISA. Following DNA sequencing, the 3D structure of isolated scFv was modeled and Docked on DSP. Results demonstrated the selection of a specific anti-DSPP scFv with 40% frequency, which reacted significantly with the predicted epitope and PCa patients' urines in ELISA tests (P-value < 0.05). The VH and VL of the isolated scFv were from VH1 and VL3 gene families with several amino acid changes in CDRs and FRs domains. The scFv tightly bound to the DSP epitope with the lowest energy level by hydrogen bonds, cation-pi, hydrophobic and ionic interactions demonstrating the specificity of Ag-Ab interactions. The anti-DSPP scFv selected in this study with significant specificity to DSPP antigen offers a promising new agent for both PCa early detection and treatment of cancers with DSPP expression.