Journal of proteins and proteomics最新文献_第8页

In silico molecular docking of SARS-CoV-2 surface proteins with microbial non-ribosomal peptides: identification of potential drugs. SARS-CoV-2表面蛋白与微生物非核糖体肽的硅分子对接:潜在药物的鉴定

Journal of proteins and proteomics Pub Date : 2021-01-01 Epub Date: 2021-08-25 DOI: 10.1007/s42485-021-00072-z

Poonam Bansal, Raman Kumar, Jasbir Singh, Suman Dhanda

{"title":"In silico molecular docking of SARS-CoV-2 surface proteins with microbial non-ribosomal peptides: identification of potential drugs.","authors":"Poonam Bansal, Raman Kumar, Jasbir Singh, Suman Dhanda","doi":"10.1007/s42485-021-00072-z","DOIUrl":"https://doi.org/10.1007/s42485-021-00072-z","url":null,"abstract":"Outbreak of COVID-19 by SARS-CoV-2 infection caused severe acute respiratory syndrome that has been declared a public health emergency of international concern. To control infections, there is urgent need to develop an effective therapeutic strategy. COVID-19 viral spike glycoprotein and proteases play major role in viral entry and mediating virus replication and spread and thus can serve as potential antiviral drug target. Being highly specific, efficacious and safe, peptides hold their place in therapeutics. In present study, molecular docking of 21 pharmacologically active non ribosomal peptides (NRPs) from marine microbes with SARS-CoV-2 spike glycoprotein and papain such as protease was done. Dactinomycin, Tyrocidine A and Gramicidin S showed highest binding interaction with target proteins. The binding affinity of Dactinomycin and Gramicidin S docked with SARS-CoV-2 spike glycoprotein was - 12.4 kcal/mol and - 11.4 kcal/mol, respectively. This suggested their potential to destabilize SARS spike protein binding with human host ACE2 receptor and thus hindering viral entry to the cells. Binding affinity of Tyrocidine A and Gramicidin S with SARS-CoV-2 papain-like protease was - 13.1 kcal/mol and - 11.4 kcal/mol, respectively which might be inhibited COVID-19 by acting on the protease. Gramicidin S showed same binding affinity for both target proteins and thus expected to be most potent. Based on the binding energy score, it was suggested that these pharmacologically active NRPs are potential molecules to be tested against SARS-CoV-2 and used to develop effective antiviral drugs.","PeriodicalId":73910,"journal":{"name":"Journal of proteins and proteomics","volume":" ","pages":"177-184"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s42485-021-00072-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39363418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

The percentages of SARS-CoV-2 protein similarity and identity with SARS-CoV and BatCoV RaTG13 proteins can be used as indicators of virus origin. SARS-CoV-2蛋白与SARS-CoV和BatCoV RaTG13蛋白的相似性和同源性百分比可作为病毒来源的指标。

Journal of proteins and proteomics Pub Date : 2021-01-01 Epub Date: 2021-04-09 DOI: 10.1007/s42485-021-00060-3

Mohammed Elimam Ahamed Mohammed

{"title":"The percentages of SARS-CoV-2 protein similarity and identity with SARS-CoV and BatCoV RaTG13 proteins can be used as indicators of virus origin.","authors":"Mohammed Elimam Ahamed Mohammed","doi":"10.1007/s42485-021-00060-3","DOIUrl":"https://doi.org/10.1007/s42485-021-00060-3","url":null,"abstract":"There are three types of proteins in coronaviruses: nonstructural, structural, and accessory proteins. Coronavirus proteins are essential for viral replication and for the binding and invasion of hosts and the regulation of host cell metabolism and immunity. This study investigated the amino acid sequence similarity and identity percentages of 10 proteins in SARS-CoV-2, SARS-CoV and the Rhinolophus affinis bat coronavirus (BatCoV RaTG13). The investigated proteins were the 1ab polyprotein, spike protein, orf3a, the envelope protein, the membrane protein, orf6, orf7a, orf7b, orf8, and the nucleocapsid protein. The online sequence alignment service of The European Molecular Biology Open Software Suite (EMBOSS) was used to determine the percentages of protein similarity and identity in the three viruses. The results showed that the similarity and identity percentages of the SARS-CoV-2 and BatCoV RaTG13 proteins were both greater than 95%, while the identity and similarity percentages of SARS-CoV-2 and SARS-CoV were both greater than 38%. The proteins of SARS-CoV-2 and BatCoV RaTG13 have high identity and similarity compared to those of SARS-CoV-2 and SARS-CoV.Graphic abstract: The proteins of the SARS-CoV-2 are most identical and similar to those of BatCoV RaTG13 than to the proteins of SARS-CoV.Supplementary information: The online version contains supplementary material available at 10.1007/s42485-021-00060-3.","PeriodicalId":73910,"journal":{"name":"Journal of proteins and proteomics","volume":"12 2","pages":"81-91"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s42485-021-00060-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25589203","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 20

Comments on potential re-purposing of medicines against high-altitude illnesses towards SARS-CoV2: possibilities and pitfalls. 针对 SARS-CoV2 对高海拔地区疾病药物的潜在再利用：可能性与隐患。

Journal of proteins and proteomics Pub Date : 2021-01-01 Epub Date: 2021-01-20 DOI: 10.1007/s42485-020-00055-6

Yasmin Ahmad, Subhojit Paul, Rajeev Varshney, Bhuvnesh Kumar

{"title":"Comments on potential re-purposing of medicines against high-altitude illnesses towards SARS-CoV2: possibilities and pitfalls.","authors":"Yasmin Ahmad, Subhojit Paul, Rajeev Varshney, Bhuvnesh Kumar","doi":"10.1007/s42485-020-00055-6","DOIUrl":"10.1007/s42485-020-00055-6","url":null,"abstract":"In the ongoing COVID-19 pandemic, the global fraternity of researchers has been assiduously investigating pharmacological interventions against the SARS-CoV2. This novel virus is known to gain entry through the ACE 2 receptor of pulmonary epithelial cells lining the respiratory tract. Many of its initial symptoms (e.g. difficulty breathing) resemble acute high altitude illnesses, particularly HAPE. Based on these overt symptoms, a number of high altitude researchers have speculated on repurposing of drugs used to treat acute altitude illnesses (especially HAPE). However, eminent high altitude researchers with medical expertise as well as some studies on the deeper causes underlying the overt symptoms have found that such repurposing maybe counter-productive. Other factors, (e.g. contra-indications of these drugs), make their use in COVID-19 patients hazardous. The fit-for-repurposing options maybe experimental prophylactic interventions (e.g. silymarin, curcumin) which have proven anti-oxidant and anti-inflammatory effects. Another line of thought focuses on proteomics-based investigations of such patients. However, apart from the logistical and safety issues, a targeted proteomics approach based on prior sound molecular investigations is a more logical approach instead of mere shotgun proteomics. In this commentary, we shed light on such issues associated with COVID-19.","PeriodicalId":73910,"journal":{"name":"Journal of proteins and proteomics","volume":"12 1","pages":"15-17"},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7815497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38780942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

In silico docking of natural compounds from plants against Rhizoctonia solani pectate lyase 植物天然化合物抗茄枯丝核菌果胶裂解酶的硅对接

Journal of proteins and proteomics Pub Date : 2020-11-27 DOI: 10.1007/s42485-020-00053-8

A. Mahanty, S. Lenka, P. Rath, S. Raghu, S. R. Prabhukarthikeyan

引用次数: 0

Quantitative proteomics leads to identify dog brain proteins involved in rabies virus infection: implication in understanding viral pathophysiology 定量蛋白质组学鉴定犬脑蛋白参与狂犬病病毒感染:对理解病毒病理生理的意义

Journal of proteins and proteomics Pub Date : 2020-11-02 DOI: 10.1007/s42485-020-00051-w

S. Behera, R. Pharande, R. R. Reddy, S. Majee, S. Mukherjee, A. Suryawanshi

引用次数: 0

Gene set enrichment analysis, network pharmacology and in silico docking approach to understand the molecular mechanism of traditional medicines for the treatment of diabetes mellitus 利用基因集富集分析、网络药理学和计算机对接等方法了解传统药物治疗糖尿病的分子机制

Journal of proteins and proteomics Pub Date : 2020-10-07 DOI: 10.1007/s42485-020-00049-4

Vishal S. Patil, Sanjay H. Deshpande, Darasaguppe R. Harish, Anuradha S. Patil, Rajashri Virge, Sinjini Nandy, Subarna Roy

引用次数: 13

Identification of natural lead compounds for leaf rust of Wheat: a molecular docking and simulation study 小麦叶锈病天然先导化合物鉴定:分子对接与模拟研究

Journal of proteins and proteomics Pub Date : 2020-10-06 DOI: 10.1007/s42485-020-00048-5

K. Sidhu, Sukhwinder Kaur Bhangu, R. Pathak, I. Yadav, P. Chhuneja

引用次数: 13

Spectrin interactome under normal and HbE-disease conditions Spectrin在正常和乙型肝炎条件下相互作用

Journal of proteins and proteomics Pub Date : 2020-10-03 DOI: 10.1007/s42485-020-00050-x

Dipayan Bose, Sk Ramiz Islam, Sutapa Saha, A. Chakrabarti

引用次数: 1

Dysglycaemia and South Asian ethnicity: a proteomic discovery and confirmation analysis highlights differences in ZAG 低血糖和南亚种族:一项蛋白质组学发现和确认分析强调了ZAG的差异

Journal of proteins and proteomics Pub Date : 2020-10-01 DOI: 10.1007/s42485-020-00046-7

Harriet M. Pearsey, J. Henson, J. Sargeant, David Webb, J. Gill, C. Celis-Morales, Toru Suzuki, H. Waller, K. Khunti, L. Ng, Kelly A. Bowden-Davies, D. Cuthbertson, Andrew Jackson, M. Davies, T. Yates

引用次数: 0

Comparative non-targeted metabolomics reveals differentiation of biochemical pathway network among fruits of natural populations and Cv. Alphonso of mango (Mangifera indica L.) 比较非靶向代谢组学揭示了自然群体和Cv果实间生化通路网络的差异。芒果(Mangifera indica L.)

Journal of proteins and proteomics Pub Date : 2020-10-01 DOI: 10.1007/s42485-020-00047-6

M. S. Dar, Yashwant Kumar, S. Punekar, V. Gupta, B. B. Dholakia, A. Giri

引用次数: 2