Background: HIV-1 is the most virulent type, causing most AIDS cases worldwide. Therapeutics like NRTIs and NNRTIs terminate replication by terminating polymerization reactions. Natural-based therapeutics are increasingly being used to reduce side effects and combat disease. Method: The study focuses on identifying phytochemical compounds that effectively inhibit the HIV-1 reverse transcriptase process using molecular docking and molecular dynamic simulations. Result: Molecular docking results show anisomelolide has a significantly stronger binding affinity (-29.9992KJ/mol) compared to nevirapine (-13.34696 KJ/mol), forming more hydrogen bonds and hydrophilic interactions, indicating a more stable and specific binding. MD simulations further support these findings, with anisomelolide exhibiting lower RMSD and RMSF values, suggesting greater structural stability and lower flexibility. Interaction energy analysis reveals robust binding and stability for anisomelolide over time. Additionally, hydrogen bond analysis indicates more frequent and stronger interactions for anisomelolide. Conclusion: The phytochemical compound anisomelolide exhibits superior binding affinity, structural stability, and interaction dynamics, making it a promising candidate for drug development against HIV-1 RT.
{"title":"Exploring Phytochemical Compounds: A Computational Study for HIV-1 Reverse Transcriptase Inhibition","authors":"Jyotsna Bandi, Madhan Chunduru, Satya Tulasi Mangamuri, Anand Kumar Nelapati, Jalaja Naravula, Viswajit Mulpuru","doi":"10.2174/0115701646316517240901091407","DOIUrl":"https://doi.org/10.2174/0115701646316517240901091407","url":null,"abstract":"Background: HIV-1 is the most virulent type, causing most AIDS cases worldwide. Therapeutics like NRTIs and NNRTIs terminate replication by terminating polymerization reactions. Natural-based therapeutics are increasingly being used to reduce side effects and combat disease. Method: The study focuses on identifying phytochemical compounds that effectively inhibit the HIV-1 reverse transcriptase process using molecular docking and molecular dynamic simulations. Result: Molecular docking results show anisomelolide has a significantly stronger binding affinity (-29.9992KJ/mol) compared to nevirapine (-13.34696 KJ/mol), forming more hydrogen bonds and hydrophilic interactions, indicating a more stable and specific binding. MD simulations further support these findings, with anisomelolide exhibiting lower RMSD and RMSF values, suggesting greater structural stability and lower flexibility. Interaction energy analysis reveals robust binding and stability for anisomelolide over time. Additionally, hydrogen bond analysis indicates more frequent and stronger interactions for anisomelolide. Conclusion: The phytochemical compound anisomelolide exhibits superior binding affinity, structural stability, and interaction dynamics, making it a promising candidate for drug development against HIV-1 RT.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"203 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142258651","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}
Pub Date : 2024-09-05DOI: 10.2174/0115701646323264240821072359
Anuradha Mehra, Amit Mittal, Divya Thakur
Background: A pivotal impetus has led to the development of numerous small molecules to develop therapeutic strategies for type 2 diabetes. Novel heterocyclic derivatives are now available with expansive pharmacological activity designed specifically to activate Glucokinase (GK) in the body. This target is of particular significance in antidiabetic drug design since it is a newly validated target. Individuals with type 2 diabetes are unable to maintain blood glucose homeostasis due to impaired glucokinase function. The novel approach to managing type 2 diabetes relies on utilizing heterocyclic derivatives to activate the GK enzyme, also known as a metabolic enzyme. Objective: In this research endeavor, the primary objective was to improve drug delivery while minimizing adverse effects by using molecules that activate glucokinase Methods: There are 53,000 compounds included in Maybridge's online repository, which has been subjected to rigorous scrutiny. Eight two compounds that encompass the specific oxadiazole core were selectively extracted from this extensive collection. ChemBioDraw Ultra was used for structural drawing, and AutoDock Vina 1.5.6 was used to perform docking analysis. For the online prediction of log P, the SwissADME algorithm was employed. A PKCSM software program was used to predict toxicity for leading compounds. Results: Among all of the compounds, AD80 and AD27 displayed the highest affinity for GK receptors. These compounds, by adhering to Lipinski’s Rule of Five, exhibited good absorption and excretion profiles through the gastrointestinal (GI) tract. Lipinski’s Rule of Five refers to physicochemical properties that favor good oral bioavailability, and these specifications are zero to five hydrogen bond donors, zero to ten hydrogen bond acceptors, molecular weight below 500, and log P no more than five. These criteria ensure that the compounds of the invention have acceptable solubility and permeability, which are vital prerequisites when given orally, to be absorbed via the gastrointestinal wall, metabolized, and found in the urine. Therefore, the chance of drug candidates exhibiting favorable pharmacokinetic characteristics is increased, enhancing their chances of being developed for oral administration. In comparison with standard drugs Dorzagliatin as a glucokinase activator (GKA) and MRK (co-crystallized ligand), these compounds exhibit no skin sensitization, AMES toxicity, or hepatotoxicity. Conclusion: The recently designed lead molecules exhibit an improved pharmacokinetic profile, enhanced binding affinity, and minimal toxicity based on the computational study, potentially making them suitable candidates for further optimization as glucokinase activators.
背景：为开发 2 型糖尿病的治疗策略，人们开发出了许多小分子药物。目前，新型杂环衍生物具有广泛的药理活性，专门用于激活体内的葡萄糖激酶（GK）。这一靶点是新近验证的靶点，因此在抗糖尿病药物设计中具有特别重要的意义。由于葡萄糖激酶功能受损，2 型糖尿病患者无法维持血糖平衡。控制 2 型糖尿病的新方法是利用杂环衍生物激活 GK 酶（也称为代谢酶）。研究目的在这项研究工作中，主要目标是利用能激活葡萄糖激酶的分子来改善给药方式，同时尽量减少不良反应：Maybridge 在线资源库中包含 53,000 种化合物，这些化合物都经过了严格的审查。我们从这个庞大的数据库中选择性地提取了包含特定噁二唑核心的 8 种化合物。ChemBioDraw Ultra 用于绘制结构图，AutoDock Vina 1.5.6 用于进行对接分析。在线预测对数 P 时，使用了 SwissADME 算法。PKCSM 软件用于预测主要化合物的毒性。结果显示在所有化合物中，AD80 和 AD27 与 GK 受体的亲和力最高。这些化合物符合利宾斯基五项原则，通过胃肠道（GI）的吸收和排泄情况良好。Lipinski's Rule of Five 指的是有利于良好口服生物利用度的理化性质，这些规格包括零到五个氢键供体、零到十个氢键受体、分子量低于 500 和对数 P 不超过 5。这些标准确保本发明的化合物具有可接受的溶解性和渗透性，这是口服时通过胃肠壁吸收、代谢并在尿液中发现的重要前提条件。因此，候选药物表现出良好的药代动力学特征的几率增加，从而提高了开发用于口服给药的机会。与作为葡萄糖激酶激活剂（GKA）的标准药物Dorzagliatin和MRK（共晶体配体）相比，这些化合物没有皮肤过敏、AMES毒性或肝毒性。结论根据计算研究，最近设计的先导分子显示出更好的药代动力学特征、更强的结合亲和力和最小的毒性，可能使它们成为进一步优化葡萄糖激酶激活剂的合适候选化合物。
{"title":"Molecular Docking, Pharmacophore Mapping, and Virtual Screening of Novel Glucokinase Activators as Antidiabetic Agents","authors":"Anuradha Mehra, Amit Mittal, Divya Thakur","doi":"10.2174/0115701646323264240821072359","DOIUrl":"https://doi.org/10.2174/0115701646323264240821072359","url":null,"abstract":"Background: A pivotal impetus has led to the development of numerous small molecules to develop therapeutic strategies for type 2 diabetes. Novel heterocyclic derivatives are now available with expansive pharmacological activity designed specifically to activate Glucokinase (GK) in the body. This target is of particular significance in antidiabetic drug design since it is a newly validated target. Individuals with type 2 diabetes are unable to maintain blood glucose homeostasis due to impaired glucokinase function. The novel approach to managing type 2 diabetes relies on utilizing heterocyclic derivatives to activate the GK enzyme, also known as a metabolic enzyme. Objective: In this research endeavor, the primary objective was to improve drug delivery while minimizing adverse effects by using molecules that activate glucokinase Methods: There are 53,000 compounds included in Maybridge's online repository, which has been subjected to rigorous scrutiny. Eight two compounds that encompass the specific oxadiazole core were selectively extracted from this extensive collection. ChemBioDraw Ultra was used for structural drawing, and AutoDock Vina 1.5.6 was used to perform docking analysis. For the online prediction of log P, the SwissADME algorithm was employed. A PKCSM software program was used to predict toxicity for leading compounds. Results: Among all of the compounds, AD80 and AD27 displayed the highest affinity for GK receptors. These compounds, by adhering to Lipinski’s Rule of Five, exhibited good absorption and excretion profiles through the gastrointestinal (GI) tract. Lipinski’s Rule of Five refers to physicochemical properties that favor good oral bioavailability, and these specifications are zero to five hydrogen bond donors, zero to ten hydrogen bond acceptors, molecular weight below 500, and log P no more than five. These criteria ensure that the compounds of the invention have acceptable solubility and permeability, which are vital prerequisites when given orally, to be absorbed via the gastrointestinal wall, metabolized, and found in the urine. Therefore, the chance of drug candidates exhibiting favorable pharmacokinetic characteristics is increased, enhancing their chances of being developed for oral administration. In comparison with standard drugs Dorzagliatin as a glucokinase activator (GKA) and MRK (co-crystallized ligand), these compounds exhibit no skin sensitization, AMES toxicity, or hepatotoxicity. Conclusion: The recently designed lead molecules exhibit an improved pharmacokinetic profile, enhanced binding affinity, and minimal toxicity based on the computational study, potentially making them suitable candidates for further optimization as glucokinase activators.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"24 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142217975","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}
Pub Date : 2024-09-02DOI: 10.2174/0115701646317271240821071544
Jiana Fang, Jingru Huang, Jiazhong Zhang, Lin Chen, Jin Deng
Purpose: The molecular properties of TLSs in pancreatic cancer are still not well comprehended. This research delved into the molecular properties of intratumoral TLSs in pancreatic cancer through the exploration of multi-omics data. Methods: Seven key genes were identified through Cox regression analysis and random survival forest analysis from a total of 5908 genes related to TLSs. These genes were utilized to construct a prognosis model, which was subsequently validated in two independent cohorts. Additionally, the study investigated the molecular features of different populations of TLSs from multiple perspectives. The model’ s forecasting accuracy was verified by analyzing column-line graphs and decision curves, taking into account the patients’ clinical traits. Results: The analysis of immune cell infiltration showed a notably greater presence of Macrophage M0 cells in the group at high risk than in the low-risk group. The pathway enrichment analysis demonstrated the activation among common cancer-related pathways, including ECM receptor interaction, pathways in cancer, and focal adhesion, in the high-risk group. Additionally, the methylation study revealed notable disparities in DNA methylation between two TLS groups across four regions: TSS200, 5’ UTR, 1stExon, and Body. A variety of notably distinct sites were linked with PVT1. Furthermore, by constructing a competing endogenous RNA network, several mRNAs and lncRNAs were identified that compete for the binding of hsa-mir-221. Conclusion: Overall, this research sheds light on the molecular properties of TLSs across various pancreatic cancer stages and suggests possible focal points for the treatment of pancreatic cancer. result: The analysis of immune cell infiltration showed a notably greater presence of Macrophage M0 cells in the group at high-risk than in the low-risk group. Pathway enrichment analysis demonstrated the activation among common cancer-related pathways, including ECM receptor interaction, pathways in cancer, and focal adhesion, in the high-risk group. Additionally, the methylation study revealed notable disparities in DNA methylation between two TLSs groups across four regions: TSS200, 5’ UTR, 1stExon, and Body. A variety of notably distinct sites were linked with PVT1. By constructing a competing endogenous RNA network, multiple mRNAs and lncRNAs competing for the binding of hsa-mir-221 were identified.
{"title":"Comprehensive Analysis of Tertiary Lymphoid Structures in Pancreatic Cancer: Molecular Characteristics and Prognostic Implications","authors":"Jiana Fang, Jingru Huang, Jiazhong Zhang, Lin Chen, Jin Deng","doi":"10.2174/0115701646317271240821071544","DOIUrl":"https://doi.org/10.2174/0115701646317271240821071544","url":null,"abstract":"Purpose: The molecular properties of TLSs in pancreatic cancer are still not well comprehended. This research delved into the molecular properties of intratumoral TLSs in pancreatic cancer through the exploration of multi-omics data. Methods: Seven key genes were identified through Cox regression analysis and random survival forest analysis from a total of 5908 genes related to TLSs. These genes were utilized to construct a prognosis model, which was subsequently validated in two independent cohorts. Additionally, the study investigated the molecular features of different populations of TLSs from multiple perspectives. The model’ s forecasting accuracy was verified by analyzing column-line graphs and decision curves, taking into account the patients’ clinical traits. Results: The analysis of immune cell infiltration showed a notably greater presence of Macrophage M0 cells in the group at high risk than in the low-risk group. The pathway enrichment analysis demonstrated the activation among common cancer-related pathways, including ECM receptor interaction, pathways in cancer, and focal adhesion, in the high-risk group. Additionally, the methylation study revealed notable disparities in DNA methylation between two TLS groups across four regions: TSS200, 5’ UTR, 1stExon, and Body. A variety of notably distinct sites were linked with PVT1. Furthermore, by constructing a competing endogenous RNA network, several mRNAs and lncRNAs were identified that compete for the binding of hsa-mir-221. Conclusion: Overall, this research sheds light on the molecular properties of TLSs across various pancreatic cancer stages and suggests possible focal points for the treatment of pancreatic cancer. result: The analysis of immune cell infiltration showed a notably greater presence of Macrophage M0 cells in the group at high-risk than in the low-risk group. Pathway enrichment analysis demonstrated the activation among common cancer-related pathways, including ECM receptor interaction, pathways in cancer, and focal adhesion, in the high-risk group. Additionally, the methylation study revealed notable disparities in DNA methylation between two TLSs groups across four regions: TSS200, 5’ UTR, 1stExon, and Body. A variety of notably distinct sites were linked with PVT1. By constructing a competing endogenous RNA network, multiple mRNAs and lncRNAs competing for the binding of hsa-mir-221 were identified.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"5 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142217977","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}
Pub Date : 2024-08-28DOI: 10.2174/0115701646331003240821061517
K M Monisha, Dhanu A S, D Mutthuraj, G Nandini, Sridhar Muthusami, Kanthesh M. Basalingappa
: Neuroblastoma, a malignancy predominantly affecting young children, originates from neural crest cells in the sympathetic nervous system. It primarily appears in the adrenal gland but can also affect nerve tissues in regions, such as the chest, neck, abdomen, and pelvis. Despite advancements in treatment, high-risk neuroblastoma patients often face poor prognoses, underscoring the need for ongoing research. This review paper examines the numerous factors responsible for neuroblastoma, emphasizing the importance of approaching the disorder with more strategic therapeutic methods. MicroRNAs, particularly miR-124, play critical roles in gene regulation and cancer pathogenesis. Abundant in the brain, miR-124 functions as a tumor suppressor by inhibiting cell growth, migration, and invasion and is often dysregulated in neuroblastoma. This study investigates the molecular functions of miR-124 in neuroblastoma, its potential as a biomarker, and its application in targeted therapy. MiR-124 regulates key pathways in neuroblastoma, including PI3K/AKT, TGF-β, and p53 signaling, impacting cell proliferation, apoptosis, and metastasis. The study also explores the promise of miR-124 as a biomarker for neuroblastoma through liquid biopsy, enabling non-invasive diagnosis and disease monitoring. Therapeutic strategies targeting miR-124 pathways show potential for overcoming chemotherapy resistance and improving treatment efficacy. The research underscores the significance of miR-124 in neuroblastoma, aiming to enhance early diagnosis, identify specific drug targets, and expand treatment options, ultimately improving patient outcomes.
{"title":"miR-124 in Neuroblastoma: Mechanistic Insights, Biomarker Potential, and Therapeutic Prospects","authors":"K M Monisha, Dhanu A S, D Mutthuraj, G Nandini, Sridhar Muthusami, Kanthesh M. Basalingappa","doi":"10.2174/0115701646331003240821061517","DOIUrl":"https://doi.org/10.2174/0115701646331003240821061517","url":null,"abstract":": Neuroblastoma, a malignancy predominantly affecting young children, originates from neural crest cells in the sympathetic nervous system. It primarily appears in the adrenal gland but can also affect nerve tissues in regions, such as the chest, neck, abdomen, and pelvis. Despite advancements in treatment, high-risk neuroblastoma patients often face poor prognoses, underscoring the need for ongoing research. This review paper examines the numerous factors responsible for neuroblastoma, emphasizing the importance of approaching the disorder with more strategic therapeutic methods. MicroRNAs, particularly miR-124, play critical roles in gene regulation and cancer pathogenesis. Abundant in the brain, miR-124 functions as a tumor suppressor by inhibiting cell growth, migration, and invasion and is often dysregulated in neuroblastoma. This study investigates the molecular functions of miR-124 in neuroblastoma, its potential as a biomarker, and its application in targeted therapy. MiR-124 regulates key pathways in neuroblastoma, including PI3K/AKT, TGF-β, and p53 signaling, impacting cell proliferation, apoptosis, and metastasis. The study also explores the promise of miR-124 as a biomarker for neuroblastoma through liquid biopsy, enabling non-invasive diagnosis and disease monitoring. Therapeutic strategies targeting miR-124 pathways show potential for overcoming chemotherapy resistance and improving treatment efficacy. The research underscores the significance of miR-124 in neuroblastoma, aiming to enhance early diagnosis, identify specific drug targets, and expand treatment options, ultimately improving patient outcomes.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"163 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142217976","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}
Pub Date : 2024-08-13DOI: 10.2174/0115701646319572240805103747
Rustam Nailevich Mustafin
Transposable elements are the oldest structural and functional units that were formed during the emergence of life on Earth. The most ancient properties of transposable elements are the multifunctionality of their transcription and translation products and the formation of their many variants through processing, due to which transposable elements are key evolutionary sources of long non-coding RNAs, circular RNAs, microRNAs, proteins and peptides formation. Moreover, the same type of transposon can simultaneously serve as the source of the origin of all these molecules, providing the adaptive properties of living organisms, especially complex eukaryotes, including humans. The ancient ability of transposable elements for mutual integration due to their protein products interacting with DNA and RNA molecules, as well as for mutual regulation due to the functionality of their RNA, is the basis for the origin of many proteins and non-coding RNAs characterized by the same properties. This can explain the emergence of transcription factors from transposable elements, that is, proteins capable of interacting with the structures of DNA molecules due to the presence of specific amino acid sequences derived from transposable elements. This article presents facts about the origin during the evolution of many protein and non-- coding RNA genes from transposable elements. Specific proteins and peptides translated from long non-coding RNAs, pri-microRNAs and circular RNAs are described, which reflect the origin of non-coding RNAs from transposable elements in evolution. These proteins and peptides are promising tools for the treatment of viral infections and drug-resistant tumors, since, together with non-coding RNAs, they are involved in antiviral and antitumor responses.
可转座元件是地球生命出现过程中形成的最古老的结构和功能单元。可转座元件最古老的特性是其转录和翻译产物的多功能性以及通过加工形成的多种变体，因此，可转座元件是长非编码 RNA、环状 RNA、microRNA、蛋白质和肽形成的关键进化源。此外，同一类型的转座子可以同时作为所有这些分子的起源，为生物体，尤其是包括人类在内的复杂真核生物提供适应特性。转座子因其蛋白质产物与 DNA 和 RNA 分子相互作用而具有相互整合的古老能力，也因其 RNA 的功能而具有相互调控的能力，这是许多具有相同特性的蛋白质和非编码 RNA 的起源基础。这可以解释转录因子从可转座元件中产生的原因，即由于存在来自可转座元件的特定氨基酸序列而能够与 DNA 分子结构相互作用的蛋白质。本文介绍了许多蛋白质和非编码RNA基因在进化过程中源自转座元件的事实。文章描述了由长非编码RNA、前微RNA和环状RNA翻译而来的特定蛋白质和肽，反映了非编码RNA在进化过程中起源于转座元件。这些蛋白质和肽是治疗病毒感染和耐药性肿瘤的有前途的工具，因为它们与非编码 RNA 一起参与了抗病毒和抗肿瘤反应。
{"title":"The Relationship of Transposable Elements with Non-Coding RNAs in the Emergence of Human Proteins and Peptides","authors":"Rustam Nailevich Mustafin","doi":"10.2174/0115701646319572240805103747","DOIUrl":"https://doi.org/10.2174/0115701646319572240805103747","url":null,"abstract":"Transposable elements are the oldest structural and functional units that were formed during the emergence of life on Earth. The most ancient properties of transposable elements are the multifunctionality of their transcription and translation products and the formation of their many variants through processing, due to which transposable elements are key evolutionary sources of long non-coding RNAs, circular RNAs, microRNAs, proteins and peptides formation. Moreover, the same type of transposon can simultaneously serve as the source of the origin of all these molecules, providing the adaptive properties of living organisms, especially complex eukaryotes, including humans. The ancient ability of transposable elements for mutual integration due to their protein products interacting with DNA and RNA molecules, as well as for mutual regulation due to the functionality of their RNA, is the basis for the origin of many proteins and non-coding RNAs characterized by the same properties. This can explain the emergence of transcription factors from transposable elements, that is, proteins capable of interacting with the structures of DNA molecules due to the presence of specific amino acid sequences derived from transposable elements. This article presents facts about the origin during the evolution of many protein and non-- coding RNA genes from transposable elements. Specific proteins and peptides translated from long non-coding RNAs, pri-microRNAs and circular RNAs are described, which reflect the origin of non-coding RNAs from transposable elements in evolution. These proteins and peptides are promising tools for the treatment of viral infections and drug-resistant tumors, since, together with non-coding RNAs, they are involved in antiviral and antitumor responses.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"9 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142217978","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}
Background: Hypothetical proteins (HPs) are those proteins whose functions are unknown; therefore, the present study was carried out to predict similarity-based functionality of HPs in selected bacteria Streptomyces coelicolor A3(2) and Neisseria meningitidis. Methods: Annotation-based approaches using Pfam, orthology, String, Bi-directional Best Blast Hit, PSLpred, Subloc, Cello, homology modeling, and computational tools were used in evaluating the functionality of HPs. Results: Thirty-one domains in both bacterial species were retrieved based on the E-value score and compared with bacterial species already existing in databases. Statistical analysis was duly done to check which features performed well. Conclusion: Out of 31 HPs found in Streptomyces coleicolor strain A3(2), 14 domains were found to be uncharacterized in their functionality, while 2 uncharacterized domains in the case of Neisseria meningitidis were assigned a function on similarity-based approaches. The annotation of HPs is a challenge in bacteria as these are based on the similarity of proteins in other species.
{"title":"Annotation-Based Study on Hypothetical Proteins in Bacteria Using Classification Features","authors":"Anchita Prasad, Prashanth Suravajhala, Vinod Kumar Nigam","doi":"10.2174/0115701646303687240805072304","DOIUrl":"https://doi.org/10.2174/0115701646303687240805072304","url":null,"abstract":"Background: Hypothetical proteins (HPs) are those proteins whose functions are unknown; therefore, the present study was carried out to predict similarity-based functionality of HPs in selected bacteria Streptomyces coelicolor A3(2) and Neisseria meningitidis. Methods: Annotation-based approaches using Pfam, orthology, String, Bi-directional Best Blast Hit, PSLpred, Subloc, Cello, homology modeling, and computational tools were used in evaluating the functionality of HPs. Results: Thirty-one domains in both bacterial species were retrieved based on the E-value score and compared with bacterial species already existing in databases. Statistical analysis was duly done to check which features performed well. Conclusion: Out of 31 HPs found in Streptomyces coleicolor strain A3(2), 14 domains were found to be uncharacterized in their functionality, while 2 uncharacterized domains in the case of Neisseria meningitidis were assigned a function on similarity-based approaches. The annotation of HPs is a challenge in bacteria as these are based on the similarity of proteins in other species.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"60 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142217979","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}
Pub Date : 2024-08-13DOI: 10.2174/0115701646309538240805093732
Yue Yue, Yiying Tao, Jiaxin Wang, Shidi Zhao, Fan Zhao, Lei Shen, Ling Zhou
Background: Diabetic kidney disease (DKD) is a common microvascular complication of diabetic mellitus (DM). At present, the early diagnosis of DKD mainly depends on microalbuminuria, which is prone to be affected by confounding factors such as urinary tract infections. Methods: To identify the more stable early diagnosis markers, the whole proteome in the circulating exosomes from controls, DM patients, and DKD patients was quantified by label-free proteomics analysis and then validated with parallel reaction monitoring. Results: Three hundred ninety-one quantitative proteins were detected, and the expression trends of 7 proteins in the validation phase were consistent with that in the discovery phase. The expression level assessment results revealed that the expression of EFEMP1 and ApoA4 in the DKD group was significantly higher than those in DM and controls. Correlation analysis showed that EFEMP1 and APOA4 were positively correlated with urinary microalbumin and urinary albumin creatinine ratio and had excellent diagnostic values for distinguishing DKD from DM and controls. Conclusions: ApoA4 and EFEMP1 could serve as the early diagnosis markers of DKD. These findings provide a possibility for the development of a clinical diagnostic index that can efficiently distinguish DKD from DM in the near future.
{"title":"Circulating Exosomes Studied by Label-free Proteomics Analysis Reveal Transition Signatures from Diabetes Mellitus to Diabetic Kidney Disease","authors":"Yue Yue, Yiying Tao, Jiaxin Wang, Shidi Zhao, Fan Zhao, Lei Shen, Ling Zhou","doi":"10.2174/0115701646309538240805093732","DOIUrl":"https://doi.org/10.2174/0115701646309538240805093732","url":null,"abstract":"Background: Diabetic kidney disease (DKD) is a common microvascular complication of diabetic mellitus (DM). At present, the early diagnosis of DKD mainly depends on microalbuminuria, which is prone to be affected by confounding factors such as urinary tract infections. Methods: To identify the more stable early diagnosis markers, the whole proteome in the circulating exosomes from controls, DM patients, and DKD patients was quantified by label-free proteomics analysis and then validated with parallel reaction monitoring. Results: Three hundred ninety-one quantitative proteins were detected, and the expression trends of 7 proteins in the validation phase were consistent with that in the discovery phase. The expression level assessment results revealed that the expression of EFEMP1 and ApoA4 in the DKD group was significantly higher than those in DM and controls. Correlation analysis showed that EFEMP1 and APOA4 were positively correlated with urinary microalbumin and urinary albumin creatinine ratio and had excellent diagnostic values for distinguishing DKD from DM and controls. Conclusions: ApoA4 and EFEMP1 could serve as the early diagnosis markers of DKD. These findings provide a possibility for the development of a clinical diagnostic index that can efficiently distinguish DKD from DM in the near future.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"10 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2024-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142227067","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}
Pub Date : 2024-08-12DOI: 10.2174/0115701646320388240805064243
Karthickeyan Chandrasekar, Parthasarathy Subbiah
Background: The aim of this research is to identify marine natural compounds derived from green, red, and brown algae that might possibly inhibit the Penicillin-Binding Proteins (PBPs) protein, which is responsible for the development of antibiotic resistance in Streptococcus pneumoniae (mutated resistant 5204-PBP2B strain). We obtained this by using virtual screening and molecular docking. In AutoDock Vina and the Schrodinger suite software, we screened a library of marine natural chemicals and discovered four intriguing candidates that had strong binding affinities to the active region of the PBPs protein. Based on our findings, four naturally occurring marine chemicals show great promise as new inhibitors of S. pneumoniae 5204-PBP2B protein. These discoveries reveal important new information on the potential application of marine natural products as a source of new drugs to combat antibiotic resistance in Streptococcus pneumoniae and other bacterial infections. Methods: The 3318 compounds in the Comprehensive Marine Natural Products Database (CMNPD) derived from green algae (293 compounds), brown algae (1212 compounds) and red algae (1813 compounds) were taken into consideration for this study. Through virtual screening and molecular docking investigations, we found the optimum compounds for the Penicillin-Binding Proteins (PBPs) protein in Streptococcus pneumoniae. Utilizing AutoDock Vina and Schrodinger Suite software, the 5204-PBP2B protein selected for this investigation was examined. The structure and binding interaction have been displayed using PyMOL software. Results: Through virtual screening and molecular docking investigations for the 5204-PBP2B protein in Streptococcus pneumoniae, we were able to identify four marine natural products that are present in brown algae from the Comprehensive Marine Natural Products Database. Conclusion: The study has indicated that the main cause of bacterial resistance to antibiotics is 5204-PBP2B in S. pneumoniae. This study's methodology has been shown to be effective in identifying four strong inhibitors of the CMNPD. In this work, potent molecules from CMNPD compounds were screened using the 3D structure of mutated resistant 5204 strain, named 5204- PBP2B (PDB ID: 2WAE) of S. pneumoniae. Out of 3318 compounds that showed strong interactions with PBP2B, docking studies revealed that four of the compounds were inhibitory for the protein and could be used to treat PBP2B. These four marine products were selected as a result of our earlier research on Klebsiella pneumonia’s New Delhi metallo-β-lactamase-1 (NDM-1) protein. This study thus reveals the importance of marine natural products for improving the drug development process, as well as the ability of four marine products generated from brown algae to inhibit both the NDM-1 protein of Klebsiella pneumoniae and the 5204-PBP2B protein in Streptococcus pneumoniae. It is also possible to expand this approach by investigating how different receptor inhi
{"title":"Identification of Novel PBP2B Protein Inhibitors against Streptococcus pneumoniae in Marine Natural Products using an In-Silico Approach","authors":"Karthickeyan Chandrasekar, Parthasarathy Subbiah","doi":"10.2174/0115701646320388240805064243","DOIUrl":"https://doi.org/10.2174/0115701646320388240805064243","url":null,"abstract":"Background: The aim of this research is to identify marine natural compounds derived from green, red, and brown algae that might possibly inhibit the Penicillin-Binding Proteins (PBPs) protein, which is responsible for the development of antibiotic resistance in Streptococcus pneumoniae (mutated resistant 5204-PBP2B strain). We obtained this by using virtual screening and molecular docking. In AutoDock Vina and the Schrodinger suite software, we screened a library of marine natural chemicals and discovered four intriguing candidates that had strong binding affinities to the active region of the PBPs protein. Based on our findings, four naturally occurring marine chemicals show great promise as new inhibitors of S. pneumoniae 5204-PBP2B protein. These discoveries reveal important new information on the potential application of marine natural products as a source of new drugs to combat antibiotic resistance in Streptococcus pneumoniae and other bacterial infections. Methods: The 3318 compounds in the Comprehensive Marine Natural Products Database (CMNPD) derived from green algae (293 compounds), brown algae (1212 compounds) and red algae (1813 compounds) were taken into consideration for this study. Through virtual screening and molecular docking investigations, we found the optimum compounds for the Penicillin-Binding Proteins (PBPs) protein in Streptococcus pneumoniae. Utilizing AutoDock Vina and Schrodinger Suite software, the 5204-PBP2B protein selected for this investigation was examined. The structure and binding interaction have been displayed using PyMOL software. Results: Through virtual screening and molecular docking investigations for the 5204-PBP2B protein in Streptococcus pneumoniae, we were able to identify four marine natural products that are present in brown algae from the Comprehensive Marine Natural Products Database. Conclusion: The study has indicated that the main cause of bacterial resistance to antibiotics is 5204-PBP2B in S. pneumoniae. This study's methodology has been shown to be effective in identifying four strong inhibitors of the CMNPD. In this work, potent molecules from CMNPD compounds were screened using the 3D structure of mutated resistant 5204 strain, named 5204- PBP2B (PDB ID: 2WAE) of S. pneumoniae. Out of 3318 compounds that showed strong interactions with PBP2B, docking studies revealed that four of the compounds were inhibitory for the protein and could be used to treat PBP2B. These four marine products were selected as a result of our earlier research on Klebsiella pneumonia’s New Delhi metallo-β-lactamase-1 (NDM-1) protein. This study thus reveals the importance of marine natural products for improving the drug development process, as well as the ability of four marine products generated from brown algae to inhibit both the NDM-1 protein of Klebsiella pneumoniae and the 5204-PBP2B protein in Streptococcus pneumoniae. It is also possible to expand this approach by investigating how different receptor inhi","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"47 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142217980","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}
In E. coli, the production of proteins as inclusion bodies (IBs) caused a decrease in the solubility and activity of these products. Diverse approaches and methods have been used by investigators to overcome this problem. The secretion of recombinant proteins into the periplasmic space by means of suitable signal peptides is a way to resolve these limitations for the production of recombinant proteins in a native form. Secretory production of recombinant proteins in bacterial hosts has many advantages and thus, it is a topic of interest. However, it is hard to achieve due to the difficulty of the process and the need for the choice of appropriate signal peptide for each host and protein. Based on the literature, different signal peptides have experimentally been applied to enhance the solubility of various recombinant proteins. It has been shown that the secretion efficiency of a given protein differs dramatically based on the type of the signal peptide that is attached to the protein. Therefore, the choice and alteration of signal peptides are the two crucial approaches for the improvement of a recombinant protein secretion that have been discussed in this review. Also, different factors affecting the expression and solubility of recombinant proteins have been discussed.
{"title":"The Study of Different Signal Peptides in Improvement of Recombinant Proteins Solubility in E. coli: A Mini-Review Article","authors":"Seyyed Soheil Rahmatabadi, Soudabeh Askari, Fatemeh Khademi, Bijan Soleymani","doi":"10.2174/0115701646305738240730113619","DOIUrl":"https://doi.org/10.2174/0115701646305738240730113619","url":null,"abstract":"In E. coli, the production of proteins as inclusion bodies (IBs) caused a decrease in the solubility and activity of these products. Diverse approaches and methods have been used by investigators to overcome this problem. The secretion of recombinant proteins into the periplasmic space by means of suitable signal peptides is a way to resolve these limitations for the production of recombinant proteins in a native form. Secretory production of recombinant proteins in bacterial hosts has many advantages and thus, it is a topic of interest. However, it is hard to achieve due to the difficulty of the process and the need for the choice of appropriate signal peptide for each host and protein. Based on the literature, different signal peptides have experimentally been applied to enhance the solubility of various recombinant proteins. It has been shown that the secretion efficiency of a given protein differs dramatically based on the type of the signal peptide that is attached to the protein. Therefore, the choice and alteration of signal peptides are the two crucial approaches for the improvement of a recombinant protein secretion that have been discussed in this review. Also, different factors affecting the expression and solubility of recombinant proteins have been discussed.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"57 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141933831","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}
Pub Date : 2024-08-07DOI: 10.2174/0115701646301703240730054408
Hiba K. Almaadani, Venkata Satish Kumar Mattaparthi
Background:: Autism Spectrum Disorder (ASD) is a complex neurodevelopmental condition. The genetic basis of ASD involves numerous loci converging on neural pathways, particularly affecting excitatory synapses. SHANK3, an essential protein in the post-synaptic neurons, has been implicated in ASD, with mutations affecting its N-terminal, including the SPN domain. Objective: This study aims to investigate the impact of the N52R mutation on SHANK3 and assess the dynamics, stability, flexibility, and compactness of the N52R mutant compared to SHANK3 WT. Methods: Molecular dynamics simulations were conducted to investigate the structural dynamics of SHANK3 WT and the N52R mutant. The simulations involved heating dynamics, density equilibrium, and production dynamics. The trajectories were analyzed for RMSD, RMSF, Rg, hydrogen bond analysis, and secondary structure. Results: The simulations revealed that the N52R mutant disrupts the stability and folding of SHANK3, affecting intramolecular contacts between SPN and ARR. This disruption opens up the distance between SPN and ARR domains, potentially influencing the protein's interactions with partners, including αCaMKII and α-Fodrin. The altered conformation of the SPN-ARR tandem in the N52R mutant suggests a potential impact on dendritic spine shape and synaptic plasticity. Conclusion: The findings shed light on the structural consequences of the N52R mutation in SHANK3, emphasizing its role in influencing intramolecular interactions and potential effects on synaptic function. Understanding these molecular dynamics contributes to unraveling the intricate relationship between genetic variations in SHANK3 and clinical traits associated with ASD. Further investigations are warranted to explore the physiological implications of these structural alterations in vivo.
{"title":"The Effect of N52R Mutation at the SPN-ARR Interface on the Conformational Dynamics of SHANK3","authors":"Hiba K. Almaadani, Venkata Satish Kumar Mattaparthi","doi":"10.2174/0115701646301703240730054408","DOIUrl":"https://doi.org/10.2174/0115701646301703240730054408","url":null,"abstract":"Background:: Autism Spectrum Disorder (ASD) is a complex neurodevelopmental condition. The genetic basis of ASD involves numerous loci converging on neural pathways, particularly affecting excitatory synapses. SHANK3, an essential protein in the post-synaptic neurons, has been implicated in ASD, with mutations affecting its N-terminal, including the SPN domain. Objective: This study aims to investigate the impact of the N52R mutation on SHANK3 and assess the dynamics, stability, flexibility, and compactness of the N52R mutant compared to SHANK3 WT. Methods: Molecular dynamics simulations were conducted to investigate the structural dynamics of SHANK3 WT and the N52R mutant. The simulations involved heating dynamics, density equilibrium, and production dynamics. The trajectories were analyzed for RMSD, RMSF, Rg, hydrogen bond analysis, and secondary structure. Results: The simulations revealed that the N52R mutant disrupts the stability and folding of SHANK3, affecting intramolecular contacts between SPN and ARR. This disruption opens up the distance between SPN and ARR domains, potentially influencing the protein's interactions with partners, including αCaMKII and α-Fodrin. The altered conformation of the SPN-ARR tandem in the N52R mutant suggests a potential impact on dendritic spine shape and synaptic plasticity. Conclusion: The findings shed light on the structural consequences of the N52R mutation in SHANK3, emphasizing its role in influencing intramolecular interactions and potential effects on synaptic function. Understanding these molecular dynamics contributes to unraveling the intricate relationship between genetic variations in SHANK3 and clinical traits associated with ASD. Further investigations are warranted to explore the physiological implications of these structural alterations in vivo.","PeriodicalId":50601,"journal":{"name":"Current Proteomics","volume":"370 1","pages":""},"PeriodicalIF":0.8,"publicationDate":"2024-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141933832","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}
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