Protein and Peptide Letters最新文献

Bacteriophages, or phages, have emerged as powerful platforms in synthetic biology, offering innovative solutions for therapeutic and environmental challenges through advanced genome redesign strategies. This review explores a wide range of phage engineering techniques, including CRISPR (clustered regularly-interspaced short palindromic repeats)-Cas systems, phage display, random and site-directed mutagenesis, retrons, and rebooting approaches, highlighting their potential to create phages with tailored functionalities. CRISPR-Cas systems enable precise genome editing, allowing the development of phages with expanded host ranges, biofilm degradation capabilities, and targeted antimicrobial activity. Phage display facilitates the presentation of peptides on phage surfaces, enabling applications in targeted drug delivery, tumor imaging, and bioremediation. Beyond these, techniques like retron-mediated recombination and homologous recombination offer additional avenues for precise phage genome modification. In the therapeutic realm, engineered phages show promise in combating drug-resistant infections, modulating the microbiome, and delivering targeted therapies for cancer and other diseases. Environmentally, phage-based strategies, such as the use of phage-displayed metal-binding peptides, provide innovative solutions for bioremediation and reducing exposure to toxic heavy metals. This review also addresses challenges, such as phage resistance, immune responses, and the limitations of current engineering methods, while exploring future directions, including the development of improved CRISPR systems, phage-based biosensors, and high-throughput screening platforms. By integrating cutting-edge genome redesign strategies with diverse applications, this review underscores the transformative potential of engineered bacteriophages in addressing global healthcare and environmental sustainability challenges.

Introduction: Mycobacterium tuberculosis (Mtb) is a Gram-positive bacterium that causes tuberculosis (TB). It remains viable for extended periods within host macrophages by entering a dormant state. Alpha crystallin 1 (Acr1) is a 16 kDa protein of Mtb and is reported to be highly upregulated in latent TB. Acr1 suppresses the host's immune system by impairing the differentiation and maturation of dendritic cells and macrophages. We hypothesize that Mtb judiciously utilizes its Acr1 protein to paralyse the immune system of the host by inducing the release of IL-10 and generating an immunosuppressive environment.

Methods: We employed in silico tools to identify highly promiscuous, IL-10-inducing and IL-6- non-inducing epitopes of Mtb. Moreover, the selected epitope was synthesized and tested for its suppressive activity and generation of Tregs.

Results: We identified the presence of a specific epitope in Acr1 (F18) that is responsible for bolstering the release of IL-10 and Tregs through in silico tools and verified the activity by in vitro assays. In hPBMCs, the F18 epitope could suppress the proliferation of CD4 T cells stimulated with PHA and expand the pool of Tregs in a dose-dependent manner.

Discussion: The F18 epitope from Mtb's Acr1 protein promotes IL-10 and Treg responses without triggering pro-inflammatory IL-6, suggesting its probable immunoregulatory role. While it holds potential for treating autoimmune diseases, its impact on infection in tuberculosis should be further investigated.

Conclusion: Our findings suggest that the F18 epitope induces IL-10 production and Treg differentiation while inhibiting CD4+ T cell proliferation and IL-6 secretion, thereby promoting an immunosuppressive environment. Furthermore, this study highlights the possible role of Acr1 and its immunosuppressive epitope F18 as therapeutic agents for inducing suppressive Tregs, which may help in the management of autoimmune diseases.

Introduction: Dysregulation of mevalonate metabolism is a hallmark of tumorigenesis and therapy resistance across malignancies, though its role in bladder cancer remains unclear. This study aimed to elucidate its impact on prognosis and cisplatin chemosensitivity in bladder cancer.

Methods: Transcriptomic data and clinical information of bladder cancer patients were obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Non-negative matrix factorization (NMF) was used to cluster mevalonate metabolism-related genes into distinct metabolic subtypes (C1 and C2). Associations between mevalonate metabolism, clinical characteristics, immune infiltration, and cisplatin resistance were analyzed using Gene Set Variation Analysis (GSVA), Kaplan-Meier survival analysis, single-sample Gene Set Enrichment Analysis (ssGSEA), and in vitro experiments.

Results: NMF clustering classified bladder cancer patients into two metabolic subtypes (C1/C2). The C1, characterized by higher mevalonate metabolism (MVAscore), was associated with a poorer prognosis, shorter overall survival (OS), and higher T-stage and pathological grades. Immune analysis showed lower immune cell infiltration in C1. Immune infiltration analysis revealed significantly lower immune infiltration levels in the C1. Further analysis revealed a positive correlation between mevalonate metabolism and platinum resistance, with a notable increase in mevalonate metabolism observed in cisplatin-resistant bladder cancer cells. In vitro, simvastatin inhibited the proliferation of bladder cancer cells and enhanced their sensitivity to cisplatin.

Discussion: Mevalonate metabolism drives BCa heterogeneity and chemoresistance while suppressing anti-tumor immunity. Its dysregulation serves as both a prognostic biomarker and a target for therapeutic intervention.

Conclusion: Mevalonate metabolism contributes to cisplatin resistance in bladder cancer and represents a potential therapeutic target. Simvastatin targeting this pathway enhances the efficacy of cisplatin, providing a novel personalized chemotherapy strategy.

Introduction: Neurodegenerative disorders such as Alzheimer's, Parkinson's, and ALS are characterized by progressive neuronal dysfunction with limited therapeutic options. Recent advances in molecular biology and drug development have highlighted the therapeutic promise of precision enzyme targeting, offering novel strategies for disease modulation and symptom management.

Methods: A comprehensive literature review spanning recent/current was conducted using PubMed, Scopus, and ScienceDirect. Studies focusing on enzyme-based targets, high-throughput screening, and molecular docking in neurodegeneration were included. Thematic synthesis was employed to categorize findings based on enzyme class, disease relevance, and therapeutic outcomes.

Results: Key enzyme families such as kinases, proteases, and oxidoreductases were identified as pivotal modulators in disease progression. Emerging enzyme-targeted compounds demonstrated enhanced bioavailability, blood-brain barrier permeability, and disease-specific efficacy. Novel screening platforms and computational modeling enabled the precise selection of inhibitors, significantly improving the therapeutic index and reducing off-target effects.

Discussion: Targeting enzymes implicated in neuroinflammation, oxidative stress, and protein misfolding has shown disease-modifying potential. Integrating precision drug discovery tools, such as AI-assisted modeling and enzyme kinetics, supports rational drug design. However, translational challenges persist due to variability in enzyme expression and disease heterogeneity.

Conclusion: Future research should focus on refining enzyme inhibitors and integrating biomarkers to facilitate personalized treatment strategies for neurodegenerative disorders. As the understanding of enzymatic roles in neurodegeneration deepens, precision enzyme-targeted drug discovery holds significant promise in transforming neurotherapeutic approaches.

Background: COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a highly pathogenic human coronavirus (CoV). For the treatment of COVID-19, various drugs, ayurvedic formulations, used for other diseases, were repurposed. Ayurveda and yoga exhibited a pivotal role in the treatment of COVID-19. Various medicinal plants, including garlic, tulsi, clove, cinnamon, ginger, black pepper, and turmeric, are recommended for the prevention of COVID-19 as immunity boosters along with their antiviral property.

Objective: In view of the drug repurposing approach, the present work has been initiated with the broader objectives of screening and identification of phytoconstituents of Indian spices against targets, namely furin, 3C-like protease (3CL-PRO), NSP-9 RNA binding protein, papain-like protease, RNA dependent RNA polymerase (RDRP), spike protein concerned with life cycle of SARS-CoV-2 using in-silico tools.

Methods: The phytoconstituents of Indian spices were screened for interaction with several targets using a molecular docking approach with the help of Discovery Studio 4.5 software. Furthermore, the pharmacokinetic analyses of selected ligands using ADMET and Lipinski's rule of five were also performed.

Results: In the present study, a total of 37 active phytoconstituents of Indian spices were screened for interaction with several identified targets of COVID-19 using a molecular docking approach. The ligands, namely morin, gingerol, myristic acid, quercetin, gallic acid and alliin were found to be the top interacting ligands with the targets analyzed.

Conclusion: Based on the present in-silico finding, the active components of spices could be considered for drug-lead compounds against COVID-19.

Background: The role of ZNF165 in only a few tumors has been reported. ZNF165 plays an important role in liver cancer, gastric cancer, and breast cancer, especially in regulating the immune microenvironment, promoting tumor cell proliferation and migration, and serving as a potential target for immunotherapy.

Objective: This study aimed to enhance an understanding of how the ZNF165 gene functions and influences cancer development.

Methods: Using a suite of online resources, including TIMER, TCGA, GTEx, GEPIA2, cBioPortal, TIMER2, STRING, DAVID, RNAactDrug, CancerSEA, and UCSC, along with comprehensive statistical analyses, we conducted a thorough investigation of the pan-cancer landscape of ZNF165. This study encompassed an assessment of ZNF165 levels, their associations with patient outcomes, and clinical correlates. We examined the interplay between ZNF165 and key cancer biomarkers, such as Microsatellite Instability (MSI), Tumor Mutational Burden (TMB), immune cell infiltration, and the expression of immune checkpoint genes. We delved into the genetic variations of ZNF165, its biological roles across various cancer types, and its potential links to drug responsiveness. We analyzed single-cell expression patterns of ZNF165 and their implications for the functional dynamics of cancer. We employed quantitative Reverse Transcription PCR (qRT-PCR) to measure ZNF165 levels in Ovarian Cancer (OC) cell lines.

Results: ZNF165 expression displayed aberrations across a diverse range of human cancers and exhibited correlations with clinical stages. High ZNF165 expression in KIRC, KIRP, STAD, and UCEC was significantly associated with poor overall survival. ZNF165 has encouraging diagnostic value in specific tumor types, with gene amplification identified as the predominant genetic alteration. Our analysis further uncovered significant associations between ZNF165 levels and MSI across three distinct cancer types, as well as with TMB in six different malignancies. We detected substantial correlations between ZNF165 levels and immune cell infiltration, as well as the expression of immune checkpoint genes. ZNF165 was found to be involved in several prevalent signaling pathways across various cancer types. ZNF165 may potentially contribute to chemotherapy and chemoresistance, and was observed to be involved in cancer progression. A ceRNA regulatory network involving AFDN-DT, miR-191-5p, and ZNF165 was constructed for OC, revealing significantly elevated ZNF165 levels in OC cell lines. Dysregulated ZNF165 expression across a spectrum of malignancies might play a role in cancer initiation and advancement via multiple biological pathways.

Conclusion: ZNF165 may serve as a promising therapeutic target for the treatment of cancer in human patients.

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a significant and prevalent pathogen that poses a major challenge in healthcare environments. In light of the growing threat posed by multidrug-resistant organisms like MRSA, there is an urgent need for alternative therapeutic strategies. One promising avenue of research involves the use of antimicrobial peptides (AMPs). These naturally occurring molecules, which are part of the innate immune response in many organisms, have garnered attention for their ability to combat a wide range of pathogens.

Objectives: This study aimed to produce recombinant versions of Ib-AMP₄ and Oncorhyncin II and to evaluate their combined effects against MRSA (NCTC10442).

Methods: Escherichia coli BL21(DE₃) served as the expression host for the synthesized variants of the Ib-AMP₄ and Oncorhyncin II genes. The antimicrobial efficacy of these peptides against MRSA S. aureus (NCTC1042) was evaluated using a comprehensive methodology that encompassed the determination of the minimum inhibitory concentration (MIC), the performance of time-kill assays, and the analysis of growth kinetics.

Results: The individual antimicrobial activities of Ib-AMP₄ and Oncorhyncin II were assessed, revealing minimum inhibitory concentrations (MICs) of 27.75 μg/mL and 40.125 μg/mL against S. aureus (MRSA) (NCTC10442), respectively. The application of a checkerboard assay to evaluate the combination of these antimicrobial peptides (AMPs) demonstrated a synergistic interaction, which was further validated through time-kill and growth kinetic studies. When administered at double the MIC, a significant reduction in the log₁₀ CFU/mL of MRSA (NCTC 10442) was observed, underscoring the synergistic bacteriostatic effect mediated by the fractional inhibitory concentration (FIC) index of the two peptides.

Conclusion: Antimicrobial peptides (AMPs) have attracted significant interest owing to the growing intricacy of microbial infections. They constitute a promising category of novel antibiotics that warrant further investigation for the treatment of S. aureus infections and the enhancement of wound healing. Although certain AMPs can operate autonomously, others may necessitate a synergistic approach alongside conventional antibiotics. Studies examining the combined efficacy of Oncorhyncin II and Ib-AMP₄ against MRSA in vitro have revealed their effectiveness.

Introduction: This study aimed to investigate the anti-carcinogenic effects of recombinant L- methioninase (rBlmet) on the pancreatic cancer cell line MiaPaCa-2.

Methods: In this study, rBlmet was initially cloned, expressed, and purified. To increase enzyme activity, the His-tags on the enzyme were removed using thrombin. rBlmet was then applied to MiaPaCa- 2 cells, and the cell viability of MiaPaCa-2 cells was evaluated by neutral red assay after rBlmet treatment. The combined effect of etoposide with rBlmet against MiaPaCa-2 cells was also evaluated for 12 and 24 hours using a neutral red assay. Furthermore, cell morphology was evaluated by Giemsa and DAPI/F-actin staining methods. Survivin and caspase-3 gene expression levels were measured by RT-qPCR.

Results and discussion: The specific activity of the enzyme increased after His-tag elimination to 5.62 μmol/mg per minute. rBlmet showed a significant cytotoxic effect on the MiaPaCa-2 cell line. The IC₅₀ value (24 h) of rBlmet for MiaPaCa-2 cells was 3.02 U/mL. In addition, rBlmet increased the cytotoxic effect of etoposide on the MiaPaCa-2 cell line, while it showed less effect on HaCat, which is a normal human cell line. Furthermore, rBlmet increased caspase-3 expression and downregulated survivin gene expression in MiaPaCa-2 cell lines. It successfully inhibited the growth of Mia-PaCa-2 cells by exploiting exogenous methionine amino acid in the growth medium. This study revealed promising results. However, further studies are needed on additional pancreatic cancer cell lines and in vivo models.

Conclusion: Based on these findings, it can be concluded that rBlmet not only has great potential to treat pancreatic cancer in the future but can also be used as an adjuvant to enhance the effectiveness of chemotherapeutic agents like etoposide.

Like other vertebrates, amphibians possess innate and adaptive immune systems. At the center of the adaptive immune system is the Major Histocompatibility Complex. The important molecules of innate immunity are antimicrobial peptides (AMPs). These peptides are secreted by granular glands in the skin and protect the animal against microorganisms entering its body through the skin. AMPs offer an effective and rapid defense against pathogenic microorganisms and have cationic and amphiphilic structures. These peptides are small gene-encoded molecules of 8-50 amino acid residues synthesized by ribosomes. These small molecules typically exhibit activity against bacteria, viruses, fungi, and even cancer cells. It is known that today's amphibian AMPs originated from a common precursor gene 150 million years ago and that the origin of these peptides is preprodermaseptins. Today, antibiotic resistance has occurred due to the incorrect use of antibiotics. Traditional antibiotics are becoming increasingly inadequate. AMPs are considered promising candidates for the development of new-generation antibiotics. Therefore, new antibiotic discoveries are needed. AMPs are suitable molecules for new-generation antibiotics that are both fast and have different killing mechanisms. One of the biggest problems in the clinical applications of AMPs is their poor stability. AMPs generally have limited tropical applications because they are sensitive to protease degradation. Coating these peptides with nanomaterials to make them more stable can solve this problem.

Introduction: Abelmoschus esculentus (okra) from the Malvaceae family is widely used in culinary applications and is reported to have many potential therapeutic effects attributed to the compounds isolated from it. In this work, we set out to explore its seed proteome for the isolation of lectins and characterize them.

Methods: A protein of about 21kDa was isolated and purified using chromatography techniques from the ammonium sulphate crude protein extract. It was evaluated for hemagglutination activity on rabbit erythrocyte suspension, trypsin inhibitory activity using chemical assay, and evaluation of anti-cancer activity using cell lines. Mass and transcriptome analysis were done to deduce the complete sequence of the isolated protein.

Results: Using functional, mass, and transcriptome analysis, the protein was identified as AEL (Abelmoschus esculentus lectin), which was reported earlier. Only a partial sequence of AEL was known, and in this work, we have deduced its complete sequence. It showed significant anti-- cancer activity against HeLa (cervical cancer) and T84 (colon cancer) with MIC (Minimum inhibitory concentration) of 20μg/ml and 40% and 30% reduction in cell viability at 100μg/ml and insignificant effect on ACHN (adenocarcinoma) cell lines. No significant effect was seen with the tested doses on normal control human cell lines HEK293 (human embryonic kidney cells). The purified protein shows specificity for lactose and galactose in the hemagglutination assay and trypsin inhibition activity.

Discussion: Studies of okra seed proteome lead to purification of AEL, a 21 kDa protein with dual hemagglutination activity and trypsin inhibitory activity. It showed potential anticancer activity in cervical, colon cancer cell lines and minimal effects on adenocarcinoma and control cell lines, suggesting specificity. The complete sequence of AEL was elucidated which will aid in its bioinformatics analysis.

Conclusion: There are very few reported dual-acting lectins with potential anticancer activity, and this work will help understand their mechanistic interactions better.