Journal of Biomolecular Structure & Dynamics最新文献_第10页

Identification of novel nuclear pore complex associated proteins in esophageal carcinoma by an integrated bioinformatics analysis. 通过综合生物信息学分析鉴定食管癌中的新型核孔复合体相关蛋白

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2024-09-01 Epub Date: 2023-07-28 DOI: 10.1080/07391102.2023.2240414

Parisa Mohamadynejad, Mehdi Moghanibashi, Kambiz Bagheri

引用次数: 0

Cefmetazole sodium as an allosteric effector that regulates the oxygen supply efficiency of adult hemoglobin. 头孢美唑钠是一种调节成人血红蛋白供氧效率的异位效应器。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2024-09-01 Epub Date: 2023-08-09 DOI: 10.1080/07391102.2023.2245043

Peilin Shu, Guoxing You, Weidan Li, Yuzhi Chen, Zongtang Chu, Dong Qin, Ying Wang, Hong Zhou, Lian Zhao

{"title":"Cefmetazole sodium as an allosteric effector that regulates the oxygen supply efficiency of adult hemoglobin.","authors":"Peilin Shu, Guoxing You, Weidan Li, Yuzhi Chen, Zongtang Chu, Dong Qin, Ying Wang, Hong Zhou, Lian Zhao","doi":"10.1080/07391102.2023.2245043","DOIUrl":"10.1080/07391102.2023.2245043","url":null,"abstract":"Allosteric effectors play an important role in regulating the oxygen supply efficiency of hemoglobin for blood storage and disease treatment. However, allosteric effectors that are approved by the US FDA are limited. In this study, cefmetazole sodium (CS) was found to bind adult hemoglobin (HbA) from FDA library (1338 compounds) using surface plasmon resonance imaging high-throughput screening. Using surface plasmon resonance (SPR), the interaction between CS and HbA was verified. The oxygen dissociation curve of HbA after CS interaction showed a significant increase in P50 and theoretical oxygen-release capacity. Acid-base sensitivity (SI) exhibited a decreasing trend, although not significantly different. An oxygen dissociation assay indicated that CS accelerated HbA deoxygenation. Microfluidic modulated spectroscopy showed that CS changed the ratio of the alpha-helix to the beta-sheet of HbA. Molecular docking suggested CS bound to HbA's β-chains via hydrogen bonds, with key amino acids being N282, K225, H545, K625, K675, and V544.The results of molecular dynamics simulations (MD) revealed a stable orientation of the HbA-CS complex. CS did not significantly affect the P50 of bovine hemoglobin, possibly due to the lack of Valβ1 and Hisβ2, indicating that these were the crucial amino acids involved in HbA's oxygen affinity. Competition between the 2,3-Diphosphoglycerate (2,3-DPG) and CS in the HbA interaction was also determined by SPR, molecular docking and MD. In summary, CS could interact with HbA and regulate the oxygen supply efficiency via forming stable hydrogen bonds with the β-chains of HbA, and showed competition with 2,3-DPG.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10339600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring the chemical space for potential inhibitors against cell surface binding protein of Mpox virus using molecular fingerprint based screening approach. 利用基于分子指纹的筛选方法，探索 Mpox 病毒细胞表面结合蛋白潜在抑制剂的化学空间。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2024-09-01 Epub Date: 2023-07-22 DOI: 10.1080/07391102.2023.2238087

Dwaipayan Chaudhuri, Satyabrata Majumder, Joyeeta Datta, Kalyan Giri

{"title":"Exploring the chemical space for potential inhibitors against cell surface binding protein of Mpox virus using molecular fingerprint based screening approach.","authors":"Dwaipayan Chaudhuri, Satyabrata Majumder, Joyeeta Datta, Kalyan Giri","doi":"10.1080/07391102.2023.2238087","DOIUrl":"10.1080/07391102.2023.2238087","url":null,"abstract":"Mpox virus is the latest member of the Poxviridae family of which small pox virus is a member. Monekypox virus has led to thousands of infections across the globe. Poxvirus gains entry into the cell making use of glycosaminoglycans like chondroitin sulphate and heparan sulphate. The interaction of the Mpox virus protein E8L also called cell surface binding protein is crucial for host cell attachment, membrane fusion and viral entry into the host cell leading to establishment of infection thus making this protein a very attractive therapeutic target. In this study we have tried to utilize the chondroitin sulphate binding groove present in the protein and identify molecules which are structurally similar to chondroitin sulphate. These molecules can thus occupy the same pocket but with a better binding affinity than chondroitin sulphate in order to outcompete the latter molecule from binding to the E8L protein and thus prevent it from performing its function. This study may pave the way for development of highly efficient therapeutics against the Mpox virus and further curb its infective potential.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9841805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In Vitro and in silico studies to explore potent antidiabetic inhibitor against human pancreatic alpha-amylase from the methanolic extract of the green microalga Chlorella vulgaris. 从绿色微藻 Chlorella vulgaris 的甲醇提取物中探索强效的人体胰腺α-淀粉酶抗糖尿病抑制剂的体外和硅学研究。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2024-09-01 Epub Date: 2023-08-10 DOI: 10.1080/07391102.2023.2244592

Sthitaprajna Sahoo, Mahesh Samantaray, Mrutyunjay Jena, Vijaykumar Gosu, Prajna Paramita Bhuyan, Donghyun Shin, Biswajita Pradhan

{"title":"In Vitro and in silico studies to explore potent antidiabetic inhibitor against human pancreatic alpha-amylase from the methanolic extract of the green microalga Chlorella vulgaris.","authors":"Sthitaprajna Sahoo, Mahesh Samantaray, Mrutyunjay Jena, Vijaykumar Gosu, Prajna Paramita Bhuyan, Donghyun Shin, Biswajita Pradhan","doi":"10.1080/07391102.2023.2244592","DOIUrl":"10.1080/07391102.2023.2244592","url":null,"abstract":"Today's era and lifestyle have led to a quick rise in cases of diabetes. Diabetes mellitus (DM) has risen to the top of the list of serious diseases and stems from different health disorders. Human pancreatic alpha-amylase (HPA) enzyme plays a critical role in the digestion of carbohydrates, and inhibitors of alpha-amylase have been investigated as a way to slow the absorption of carbohydrates and reduce postprandial (after meal) hyperglycemia in patients with diabetes. Recently algal derivatives have been studied for their potential as a new drug against diabetes and other diseases. The study is aimed to find active biochemical compounds from the methanolic extract of Chlorella vulgaris. The in vitro studies were carried out and the results revealed that methanolic extract from C. vulgaris showed abundant inhibition efficacy of the α-amylase (IC50 of about 2.66 µg/mL) compared to acarbose (IC50 of about 2.85 µg/mL), a standard, commercial inhibitor. All the bioactive compounds from the methanolic extract were identified from the GCMS study and considered for in silico evaluation. Out of 14 bioactive compounds from GCMS, compound C3 showed higher docking energy (-8.3 kcal/mol) compared to other compounds. Subsequently, the comparative molecular dynamic simulation of apo and ligand-bound (compound C3 and acarbose) α-amylase complexes showed overall structural stability for compound C3 at the active site of α-amylase from various MD analyses. Hence, we believe, the bioactive compounds identified from GCMS may assist in diabetic therapeutics. Moreover, the compound C3 identified in this study could be a potential antidiabetic therapeutic inhibitor.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10021111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computational insights into the role of structurally diverse plant secondary metabolites as inhibitors against Imidazole Glycerol Phosphate Dehydratase of Mycobacterium tuberculosis. 通过计算深入了解结构多样的植物次生代谢物作为结核分枝杆菌咪唑甘油磷酸脱氢酶抑制剂的作用。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2024-09-01 Epub Date: 2023-08-14 DOI: 10.1080/07391102.2023.2245486

Vasantharaja Raguraman, Leena Chauhan, Priyanka Gehlot, Bhani Kongkham, P Hariprasad

{"title":"Computational insights into the role of structurally diverse plant secondary metabolites as inhibitors against Imidazole Glycerol Phosphate Dehydratase of Mycobacterium tuberculosis.","authors":"Vasantharaja Raguraman, Leena Chauhan, Priyanka Gehlot, Bhani Kongkham, P Hariprasad","doi":"10.1080/07391102.2023.2245486","DOIUrl":"10.1080/07391102.2023.2245486","url":null,"abstract":"Mycobacterium tuberculosis (Mtb) is one of the major causes of death worldwide and there is a pressing need for the development of novel drug leads. The Imidazole Glycerol Phosphate Dehydratase (IGPD) of Mtb is one of the key enzymes in the histidine biosynthesis pathway and has been recognized as the potentially underexploited drug target for anti-tuberculosis treatment. In the present study, 6063 structurally diverse plant secondary metabolites (PSM) were screened for their efficiency in inhibiting the catalytic activity of IGPD through molecular docking. The top 150 PSMs with the lowest binding energy represent the chemical classes, including Tannins (34%), Flavonoid Glycosides (14%), Terpene Glycosides (10%), Steroid Lactones (9.3%), Flavonoids (6.6%), Steroidal Glycosides (4.6%), etc. Bismahanine, Ashwagandhanolide, and Daurisoline form stable IGPD-inhibitor complexes with binding free energies of -291.3 ± 16.5, -279.0 ± 25.0, and -279.8 ± 17.6 KJ/mol, respectively, as determined by molecular dynamics simulations. These PSM demonstrated strong H-bond interactions with the amino acid residues Ile279, Arg281, and Lys276 in the catalytic region of IGPD, as revealed by structural snapshots. On the basis of our findings, these three PSM could be considered as possible leads against IGPD and should be explored in vitro and in vivo.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10362724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An in silico molecular docking, ADMET and molecular dynamics simulations studies of azolyl-2H-chroman-4-ones as potential inhibitors against pathogenic fungi and bacteria. 对偶氮基-2H-色满-4-酮作为病原真菌和细菌潜在抑制剂的分子对接、ADMET 和分子动力学模拟研究。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2024-09-01 Epub Date: 2023-08-01 DOI: 10.1080/07391102.2023.2241102

K V S Mani Chandrika, Prathyusha V

{"title":"An in silico molecular docking, ADMET and molecular dynamics simulations studies of azolyl-2H-chroman-4-ones as potential inhibitors against pathogenic fungi and bacteria.","authors":"K V S Mani Chandrika, Prathyusha V","doi":"10.1080/07391102.2023.2241102","DOIUrl":"10.1080/07391102.2023.2241102","url":null,"abstract":"Antimicrobial resistance is a major global threat. In an attempt to discover new compounds with improved efficiency and to overcome drug resistance, a library of 3960 compounds was designed as conformationally rigid analogues of oxiconazole with 2H-chroman-4-one, azole and substituted phenyl fragments. The antifungal and antibacterial activity of the compounds was evaluated using molecular docking studies in the active site of six fungal and four bacterial proteins to establish the binding affinity of the designed ligands. In-silico ADME and Lipinski's rule were used to establish the drug-likeness properties of the compounds. This study revealed that all the designed compounds had a high binding affinity with the target proteins and formed H-bond and π-π interactions. The identified hits have been subjected to molecular dynamics simulations to study protein-ligand complex stability. This study has led to the identification of important compounds that can be developed further as therapeutic agents against pathogenic fungi and bacteria.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9908807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computational identification and molecular dynamics simulation of potential circularRNA derived peptide from gene expression profile of Rheumatoid arthritis, Alzheimer's disease, and Atrial fibrillation. 从类风湿关节炎、阿尔茨海默氏症和心房颤动的基因表达谱中计算识别和分子动力学模拟潜在的 circularRNA 衍生多肽。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2024-09-01 Epub Date: 2023-08-01 DOI: 10.1080/07391102.2023.2241535

Santhiya Panchalingam, Govindaraju Kasivelu, Manikandan Jayaraman

{"title":"Computational identification and molecular dynamics simulation of potential circularRNA derived peptide from gene expression profile of Rheumatoid arthritis, Alzheimer's disease, and Atrial fibrillation.","authors":"Santhiya Panchalingam, Govindaraju Kasivelu, Manikandan Jayaraman","doi":"10.1080/07391102.2023.2241535","DOIUrl":"10.1080/07391102.2023.2241535","url":null,"abstract":"The two most serious global health challenges confronting human society today are autoimmune disorders (AIDs) and neurological diseases (NDs), both of which shorten people's lives and worsen the situation. Despite their extensive impact, statistics show that AIDs is associated with a higher risk of ND. Circular RNAs (circRNAs) are critical in several illnesses and disorders, especially AID and ND. Therefore, the present study focused on understanding the underlying causes of the pathophysiology of diseases such as AID and ND through in silico-based research. In order to determine how circRNAs are related to various disease pathways, this study examined the gene expression data sets for Rheumatoid arthritis (RA), Alzheimer's disease (AD), and atrial fibrillation (AF). Our study identified and analyzed two circRNAs, their respective host genes (DHTKD1 and RAN) and their related miRNAs, which could serve as potential markers for treating disorders like myotonic dystrophy type 1, spinocerebellar ataxia and fragile X syndrome. Further, the circRNA-derived peptide was identified and analysed with the molecular dynamics simulation (MDS) followed by a principal component (PC) based free energy landscape (FEL) profile. The computational results obtained here provide a basis for the development of therapeutics against AD, RA and AF. Moreover, further functional studies are needed to validate their role in disease aetiology and to provide a detailed understanding of their association with AID and ND.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9902543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification of potential phytochemicals and their inhibitory effect on the PERK receptor mediated UPR pathway for neuronal disease regulation: an in silico insight. 鉴定潜在的植物化学物质及其对 PERK 受体介导的 UPR 通路的抑制作用，以调控神经元疾病：硅学洞察。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2024-09-01 Epub Date: 2023-08-01 DOI: 10.1080/07391102.2023.2242495

Shabnam Ameenudeen, Mohammad Waseem, Hemalatha S

{"title":"Identification of potential phytochemicals and their inhibitory effect on the PERK receptor mediated UPR pathway for neuronal disease regulation: an in silico insight.","authors":"Shabnam Ameenudeen, Mohammad Waseem, Hemalatha S","doi":"10.1080/07391102.2023.2242495","DOIUrl":"10.1080/07391102.2023.2242495","url":null,"abstract":"The endoplasmic reticulum (ER) has been considered as the key site of protein biosynthesis and maturation in the eukaryotic cell. In recent years, the sequence at the N-terminal region of translated protein has shown a particular emphasis as a signal responsible for site-specific translocation mediated by post-translational modification. Once the native conformation is not achieved, the degradation pathway is activated, and therefore the restoration of the homeostasis of ER function in UPR pathway is initiated. One of the transmembrane proteins, PKR-like ER kinase (PERK) plays a key role in the activation of UPR through the inhibition of the translation process, thus preventing the cells from apoptosis due to chronic ER stress. Dysregulation of the neuronal proteostasis often results in neuronal dysfunction and its crucially associated neurodegenerative diseases or its manifestation of neuropathic pain. The correlation between ER stress and its associated signaling cascade, namely UPR, is well established in context of neuropathological modifications. This furthermore suggests that the proteins of the signaling cascade such as PERK can serve as a potential target during the onset of neuronal damage. The aim of this study was to identify the potential phytocompounds by evaluating the physicochemical properties, Lipinski screening, ADMET and toxicity properties of the selected phytocompounds by using SwissADME, MolInspiration and pKCSM webservers, which could establish a comparatively better affinity and binding energy than the control drug as GSK2606414 in set up the treatment of the neuronal diseases through molecular docking via PyRx and validating their structural stability through simulation using the Sybyl software for over100ns.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9920781","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Binding characteristics and conformational changes in alpha-2-macroglobulin by the dietary flavanone naringenin: biophysical and computational approach. 膳食黄酮柚皮苷在 alpha-2 巨球蛋白中的结合特性和构象变化：生物物理和计算方法。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2024-09-01 Epub Date: 2023-07-27 DOI: 10.1080/07391102.2023.2240420

Sana Ansari, Mohammad Khalid Zia, Haseeb Ahsan, Md Amiruddin Hashmi, Fahim H Khan

{"title":"Binding characteristics and conformational changes in alpha-2-macroglobulin by the dietary flavanone naringenin: biophysical and computational approach.","authors":"Sana Ansari, Mohammad Khalid Zia, Haseeb Ahsan, Md Amiruddin Hashmi, Fahim H Khan","doi":"10.1080/07391102.2023.2240420","DOIUrl":"10.1080/07391102.2023.2240420","url":null,"abstract":"In the present study, we investigated the interaction of alpha-2-macroglobulin (α2M) with naringenin using multi-spectroscopic, molecular docking, and molecular simulation approaches to identify the functional changes and structural variations in the α2M structure. Our study suggests that naringenin compromised α2M anti-proteinase activity. The results of absorption spectroscopy and fluorescence measurement showed that naringenin-α2M formed a complex with a binding constant of (kb)∼104, indicative of moderate binding. The value of ΔG° in the binding indicates the process to be spontaneous and the major force responsible to be hydrophobic interaction. The findings of FRET reveal the binding distance between naringenin and the amino acids of α2M was 2.82 nm. The secondary structural analysis of α2M with naringenin using multi-spectroscopic methods like synchronous fluorescence, red-edge excitation shift (REES), FTIR, and CD spectra further confirmed the significant conformational alterations in the protein. Molecular docking approach reveals the interactions between naringenin and α2M to be hydrogen bonds, van der Waals forces, and pi interactions, which considerably favour and stabilise the binding. Molecular dynamics modelling simulations also supported the steady binding with the least RMSD deviations. Our study suggests that naringenin interacts with α2M to alter its confirmation and compromise its activity.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9874270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Computational analysis of spike protein of SARS-CoV-2 (Omicron variant) for development of peptide-based therapeutics and diagnostics. 对 SARS-CoV-2（Omicron 变种）的尖峰蛋白进行计算分析，以开发基于肽的治疗和诊断方法。

IF 2.7 3区生物学

Journal of Biomolecular Structure & Dynamics Pub Date : 2024-09-01 Epub Date: 2023-07-27 DOI: 10.1080/07391102.2023.2239932

Manisha Pritam, Somenath Dutta, Krishna Mohan Medicherla, Rajnish Kumar, Satarudra Prakash Singh

{"title":"Computational analysis of spike protein of SARS-CoV-2 (Omicron variant) for development of peptide-based therapeutics and diagnostics.","authors":"Manisha Pritam, Somenath Dutta, Krishna Mohan Medicherla, Rajnish Kumar, Satarudra Prakash Singh","doi":"10.1080/07391102.2023.2239932","DOIUrl":"10.1080/07391102.2023.2239932","url":null,"abstract":"In the last few years, the worldwide population has suffered from the SARS-CoV-2 pandemic. The WHO dashboard indicated that around 504,079,039 people were infected and 6,204,155 died from COVID-19 caused by different variants of SARS-CoV-2. Recently, a new variant of SARS-CoV-2 (B.1.1.529) was reported by South Africa known as Omicron. The high transmissibility rate and resistance towards available anti-SARS-CoV-2 drugs/vaccines/monoclonal antibodies, make Omicron a variant of concern. Because of various mutations in spike protein, available diagnostic and therapeutic treatments are not reliable. Therefore, the present study explored the development of some therapeutic peptides that can inhibit the SARS-CoV-2 virus interaction with host ACE2 receptors and can also be used for diagnostic purposes. The screened linear B cell epitopes derived from receptor-binding domain of spike protein of Omicron variant were evaluated as peptide inhibitor/vaccine candidates through different bioinformatics tools including molecular docking and simulation to analyze the interaction between Omicron peptide and human ACE2 receptor. Overall, in-silico studies revealed that Omicron peptides OP1-P12, OP14, OP20, OP23, OP24, OP25, OP26, OP27, OP28, OP29, and OP30 have the potential to inhibit Omicron interaction with ACE2 receptor. Moreover, Omicron peptides OP20, OP22, OP23, OP24, OP25, OP26, OP27, and OP30 have shown potential antigenic and immunogenic properties that can be used in design and development vaccines against Omicron. Although the in-silico validation was performed by comparative analysis with the control peptide inhibitor, further validation through wet lab experimentation is required before its use as therapeutic peptides.Communicated by Ramaswamy H. Sarma.","PeriodicalId":15272,"journal":{"name":"Journal of Biomolecular Structure & Dynamics","volume":null,"pages":null},"PeriodicalIF":2.7,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9874269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0