Molecular Biotechnology最新文献

{"title":"Scaffold Hopping Method for Design and Development of Potential Allosteric AKT Inhibitors.","authors":"Alireza Poustforoosh","doi":"10.1007/s12033-024-01307-2","DOIUrl":"https://doi.org/10.1007/s12033-024-01307-2","url":null,"abstract":"<p><p>Targeting AKT is a practical strategy for cancer therapy in many cancer types. Targeted inhibitors of AKT are attractive solutions for inhibiting the interconnected signaling pathways, like PI3K/Akt/mTOR. Allosteric inhibitors are more desirable among different classes of AKT inhibitors as they could be more specific with fewer off-target proteins. In this study, a ligand/structure-based pipeline was developed to design new allosteric AKT inhibitors by employing the core hopping method. Triciribine, a traditional allosteric AKT inhibitor was used as the template, and the FDA-approved kinase inhibitors for cancer treatment were considered as the cores. The allosteric site in the crystal structure of AKT1 was used to screen the designed compounds. The results were further evaluated using molecular docking, ADME/T analysis, molecular dynamics (MD) simulation, and binding free energy calculations. The outcomes introduced 24 newly designed inhibitors, amongst which three compounds C6, C20, and C16 showed remarkable binding affinity to AKT1. While the docking scores for triciribine was around - 8.6 kcal/mol, the docking scores of these compounds were about - 11 to - 13 kcal/mol. The MD results indicated that designed compounds target the essential residues of the PH domain and kinase domain of AKT, such as Trp80, Thr211, Tyr272, Asp274, and Asp292. Scaffold hopping is a tremendous tool for designing novel anti-cancer agents by improving already known and potential drug compounds. The designed compounds are worth to be examined by experimental investigation in vitro and in vivo.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142504423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nanotechnology and CRISPR/Cas-Mediated Gene Therapy Strategies: Potential Role for Treating Genetic Disorders.","authors":"Guneet Kaur, Jasnoor Arora, Abhinashi Singh Sodhi, Sonu Bhatia, Navneet Batra","doi":"10.1007/s12033-024-01301-8","DOIUrl":"https://doi.org/10.1007/s12033-024-01301-8","url":null,"abstract":"<p><p>Gene therapy has made substantial progress in the treatment of the genetic diseases, focussing on the reduction of characteristics of recessive/dominant disorders, as well as various cancers. Extensive research has been conducted in the past few decades to investigate the application of nanotechnology and CRISPR/Cas technology in gene therapy. Nanotechnology due to attributes such has targeted drug delivery, controlled release, scalability and low toxicity has gained attention of the medical world. CRISPR/Cas9 system is considered as an impactful genome editing tool in the area of next-generation therapeutics and molecular diagnostics. CRISPR technology emphasises on gene editing, gene regulation modulation, and formulation of defined genetic changes. Its applications in treatment of the genetic disorders are extended beyond traditional therapies. These techniques are being explored as treatment of several genetic disorders including Duchenne muscular dystrophy, cystic fibrosis, Alzheimer's disease, Parkinson's disease, and Huntington disease. Despite considerable therapeutic potential of gene therapy, several obstacles must be addressed before it can be widely adopted in clinical practice, particularly in terms of ensuring safety and effectiveness. As research advances in this captivating field, these therapies will become the primary treatments and will have significant beneficial effects on the lives of patients with genetic disorders.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142504422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Indicator for Distinguishing Multi-drug-Resistant Tuberculosis from Drug Sensitivity Tuberculosis and Potential Medications for Treatment.","authors":"Shulin Song, Donghui Gan, Di Wu, Ting Li, Shiqian Zhang, Yibo Lu, Guanqiao Jin","doi":"10.1007/s12033-024-01299-z","DOIUrl":"https://doi.org/10.1007/s12033-024-01299-z","url":null,"abstract":"<p><p>The issue of multi-drug-resistant tuberculosis (MDR-TB) presents a substantial challenge to global public health. Regrettably, the diagnosis of drug-resistant tuberculosis (DR-TB) frequently necessitates an extended period or more extensive laboratory resources. The swift identification of MDR-TB poses a particularly challenging endeavor. To identify the biomarkers indicative of multi-drug resistance, we conducted a screening of the GSE147689 dataset for differentially expressed genes (DEGs) and subsequently conducted a gene enrichment analysis. Our analysis identified a total of 117 DEGs, concentrated in pathways related to the immune response. Three machine learning methods, namely random forest, decision tree, and support vector machine recursive feature elimination (SVM-RFE), were implemented to identify the top 10 genes according to their feature importance scores. A4GALT and S1PR1, which were identified as common genes among the three methods, were selected as potential molecular markers for distinguishing between MDR-TB and drug-susceptible tuberculosis (DS-TB). These markers were subsequently validated using the GSE147690 dataset. The findings suggested that A4GALT exhibited area under the curve (AUC) values of 0.8571 and 0.7121 in the training and test datasets, respectively, for distinguishing between MDR-TB and DS-TB. S1PR1 demonstrated AUC values of 0.8163 and 0.5404 in the training and test datasets, respectively. When A4GALT and S1PR1 were combined, the AUC values in the training and test datasets were 0.881 and 0.7551, respectively. The relationship between hub genes and 28 immune cells infiltrating MDR-TB was investigated using single sample gene enrichment analysis (ssGSEA). The findings indicated that MDR-TB samples exhibited a higher proportion of type 1 T helper cells and a lower proportion of activated dendritic cells in contrast to DS-TB samples. A negative correlation was observed between A4GALT and type 1 T helper cells, whereas a positive correlation was found with activated dendritic cells. S1PR1 exhibited a positive correlation with type 1 T helper cells and a negative correlation with activated dendritic cells. Furthermore, our study utilized connectivity map analysis to identify nine potential medications, including verapamil, for treating MDR-TB. In conclusion, our research identified two molecular indicators for the differentiation between MDR-TB and DS-TB and identified a total of nine potential medications for MDR-TB.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142504421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Expression Profile and Prognostic Significance of Pivotal Regulators for N7-Methylguanosine Methylation in Diffuse Large B-Cell Lymphoma.","authors":"Cong Wang, Ran Kong, Guangcai Zhong, Peipei Li, Na Wang, Ganyu Feng, Mei Ding, Xiangxiang Zhou","doi":"10.1007/s12033-024-01264-w","DOIUrl":"https://doi.org/10.1007/s12033-024-01264-w","url":null,"abstract":"<p><p>N7-methylguanosine (m7G) occurs by adding a methyl group to the N7 atom of the RNA guanine. Emerging evidence suggests that m7G modification has emerged as a crucial regulator of tumorigenesis, progression, invasion, and metastasis in multiple cancers. Nevertheless, the utility of m7G modification in diffuse large B-cell lymphoma (DLBCL) remains undefined, notably the interaction with the tumor microenvironment (TME). Here, we aimed to identify the expression profile of m7G regulators in DLBCL, construct a novel risk model, and explore their connection with TME. We initially investigated the difference and correlation in m7G regulators' expression in normal and tumor groups, classified patients by consistent clustering analysis, investigated the functional and prognostic significance of the resulting subtypes, and identified prognosis-associated genes by one-way Cox and least absolute shrinkage and selection operator (LASSO) regression calculations, and constructed a risk model. Further analysis showed that correlation among immune cell infiltration with m7G risk score and determined that it impacts the prognosis of DLBCL patients. Our research demonstrated the relevance of m7G regulators to DLBCL prognosis, providing theoretical support for precise prognostic stratification and immunotherapeutic assessment in DLBCL.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessment the Efficacy of the CRISPR System for Inducing Mutations in the AIMP2 Gene to Create a Cell Line Model of HLD17 Disease.","authors":"Shima Farrokhi, Atieh Eslahi, Farzaneh Alizadeh, Mohammad Amin Kerachian, Majid Mojarrad","doi":"10.1007/s12033-024-01257-9","DOIUrl":"https://doi.org/10.1007/s12033-024-01257-9","url":null,"abstract":"<p><p>Hypomyelinating leukodystrophy-17 is a neurodevelopmental disorder caused by autosomal recessive mutations in the AIMP2 gene, resulting in a lack of myelin deposition during brain development, leading to variable neurological symptoms. Research on brain function in these disorders is challenging due to the lack of access to brain tissue. To overcome this problem, researchers have utilized different cell and animal models. The CRISPR-Cas9 system is considered the most optimal and effective method for genetic modification and developing cell models. We studied the efficacy of the CRISPR-Cas9 technology in inducing mutations in the AIMP2 gene in HEK293 cell lines. The study involved transfecting HEK293 cells with recombinant PX458 plasmids targeting spCas-9 and AIMP2 sgRNA. The cells were evaluated using fluorescent microscopy and enriched using serial dilution. The CRISPR/Cas9 plasmids were validated through PCR and Sanger sequencing. After serial dilution, AS-PCR, Sanger sequencing, and TIDE program analysis showed the construct successfully induces an indel mutation in HEK cells. Our findings demonstrated the great efficacy of the CRISPR system and produced a construct for inducing mutations in the AIMP2 gene, which can be utilized to edit the AIMP2 gene in nerve cells and create a cellular model of the HLD17 disease.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Targeting PilA in Acinetobacter baumannii: A Computational Approach for Anti-Virulent Compound Discovery.","authors":"Mohanraj Gopikrishnan, George Priya C Doss","doi":"10.1007/s12033-024-01300-9","DOIUrl":"https://doi.org/10.1007/s12033-024-01300-9","url":null,"abstract":"<p><p>Acinetobacter baumannii (A. baumannii) has emerged as a critical global pathogen due to its ability to acquire resistance traits. This bacterium exhibits two distinct forms of motility: twitching, mediated by type IV pili (T4P), and surface-associated motility, independent of appendages. T4P is crucial in various bacterial species, facilitating twitching motility, biofilm formation, and host-cell adhesion. The synthesis of T4P is a common feature among Gram-negative pathogens, particularly A. baumannii, suggesting that PilA could be a viable target for biofilm-related treatments. This study aims to develop drug molecules to mitigate A. baumannii virulence by targeting PilA. Using Schrodinger software, we screened 60,766 compounds from the CMNPD, ChemDiv, and Enamine antibacterial databases through high-throughput virtual screening. The top two compounds from each database, identified through extra precision (XP) mode, were subjected to further studies. Among the six compounds identified (CMNPD18469, CMNPD20698, Z2377302405, Z2378175729, N039-0021, and N098-0051), docking scores ranged from - 5.0 to - 7.5 kcal/mol. Subsequently, we conducted 300 ns molecular dynamics simulations and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) analysis of the PilA-ligand complexes. Analysis of the simulation trajectories indicated structural stability and consistent behavior of the PilA-ligand complexes in a dynamic environment. Notably, the PilA-N098-0051 complex exhibited enhanced stability and robust binding interactions, underscoring its potential as a therapeutic agent. These findings suggest that the identified compounds, particularly N098-0051, hold promise as potent molecules targeting PilA, necessitating further validation through in vitro and in vivo studies.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470312","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exosomal miR-494 Regulates the Biological Behavior of Trophoblasts by Targeting mTOR in Unexplained Recurrent Spontaneous Abortion.","authors":"Yihong Guo, Lujing Chen, Qiulin Ma, Peiyu Liu","doi":"10.1007/s12033-024-01298-0","DOIUrl":"https://doi.org/10.1007/s12033-024-01298-0","url":null,"abstract":"<p><p>Recurrent spontaneous abortion (RSA) is a pregnancy disorder, and trophoblasts are involved in its complex pathogenesis. This study aimed to identify the functional role of exosomal miR-494 in promoting the development of unexplained RSA (uRSA). 15 uRSA tissues and 15 healthy controls were collected to compare the exosomal miR-494 expression. The ultracentrifugation method was used for serum exosome isolation, and exosome characteristics were examined using transmission electron microscopy (TEM). The affection of exosomal miR-494 on HTR-8/SVneo cells were determined by CCK-8, EdU, Wound healing, and Transwell assays. Our findings demonstrated that miR-494 levels were markedly lower in placental tissue and plasma exosomes from patients with uRSA than in normal pregnant women. Furthermore, treatment with miR-494-overexpressing exosomes reduced the viability, invasion, and migration of HTR-8/SVneo cells. In terms of regulation, exosomal miR-494 downregulated mTOR levels in HTR-8/SVneo cells. Mechanism research suggested that exosomal miR-494 reduces the viability, invasion, and migration of trophoblasts by targeting mTOR. Exosomal miR-494 and mTOR are potential predicative biomarkers and therapeutic targets for uRSA patients.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470310","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unlocking Hope: Paving the Way for a Cutting-Edge Multi-Epitope Dengue Virus Vaccine.","authors":"Amtul Wadood Wajeeha, Mamuna Mukhtar, Najam Us Sahar Sadaf Zaidi","doi":"10.1007/s12033-024-01294-4","DOIUrl":"https://doi.org/10.1007/s12033-024-01294-4","url":null,"abstract":"<p><p>Dengue fever is a significant health issue in Pakistan, demanding a vaccine effective against all the viral strains. This study employs reverse vaccinology to develop potential dengue vaccine candidates (DVAX I-III). The study thoroughly examined conserved areas of dengue virus serotypes 1-4's structural and non-structural proteins. Key viral proteins were analyzed to find antigenic peptides, which were incorporated into vaccine candidates and potentiated with adjuvants. Computational methods predicted peptide structures and evaluated their binding to immune receptors TLR 2, TLR 4, HLA *A1101, and DRB*401. A molecular dynamics simulation lasting 100 ns of the DVAX II-TLR4 complex at different time intervals clearly indicated that the ligand is attached to the receptor. Normal mode analysis assessed the stability and flexibility of these interactions. Encouragingly, all three vaccine candidates demonstrated favorable interactions with these immune receptors and the potential to induce a robust immune response. These findings suggest their safety and warrant further in vivo studies to evaluate their efficacy for clinical development.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CRISPR-Cas9: Unraveling Genetic Secrets to Enhance Floral and Fruit Traits in Tomato.","authors":"S Bhoomika, Shubham Rajaram Shalunkhe, A R Sakthi, T Saraswathi, S Manonmani, M Raveendran, M Sudha","doi":"10.1007/s12033-024-01290-8","DOIUrl":"https://doi.org/10.1007/s12033-024-01290-8","url":null,"abstract":"<p><p>Tomato, a globally consumed vegetable, possesses vast genetic diversity, making it suitable for genetic manipulation using various genetic improvement techniques. Tomatoes are grown extensively for their market value and health benefits, primarily contributed by enhanced yield and nutritional value respectively, influenced by floral and fruit traits. Floral morphology is maintained by genes involved in meristem size control, regulation of inflorescence transition, and pollen development. SP (SELF-PRUNING) and SP5G (SELF-PRUNING 5G) determine growth habit and flowering time. RIN (RIPENING INHIBITOR) and PG (POLYGALACTURONASE) are responsible for the shelf life of fruits. In addition to this, nutrition-enriched tomatoes have been developed in recent times. In this review, we comprehensively discuss the major genes influencing floral morphology, flowering time, fruit size, fruit shape, shelf life, and nutritional value, ultimately resulting in enhanced yield. Additionally, we address the advances in CRISPR/Cas9 applied for the genetic improvement of tomatoes along with prospects of areas in which research development in terms of tomato genetic improvement has to be advanced.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142391917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances in Metabolic Engineering for the Accumulation of Astaxanthin Biosynthesis.","authors":"Bingxin Yu, Tianyue Ma, Maryam Nawaz, Hailong Chen, Heng Zheng","doi":"10.1007/s12033-024-01289-1","DOIUrl":"https://doi.org/10.1007/s12033-024-01289-1","url":null,"abstract":"<p><p>Astaxanthin, a lipophilic carotenoid renowned for its strong antioxidant activity, holds significant commercial value across industries such as feed, food, and cosmetics. Although astaxanthin can be synthesized through chemical methods, it may contain toxic by-products in the synthesized astaxanthin, limiting its application in medicine or functional food. Natural astaxanthin can be extracted from algae, however, the cultivation cycle of algae is relatively longer compared to microorganisms. With the advancement of synthetic biology and metabolic engineering, the method of microbial fermentation has emerged as a promising strategy for the large-scale production of astaxanthin. This article provides a comprehensive overview of the research progress in astaxanthin biosynthesis, highlighting the use of the natural host Xanthophyllomyces dendrorhous, and the heterologous hosts Yarrowia lipolytica and Saccharomyces cerevisiae. Additionally, future research prospects are also discussed.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142381285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}