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Pritam M, Dutta S, Medicherla KM, Kumar R, Singh SP. Computational analysis of spike protein of SARS-CoV-2 (Omicron variant) for development of peptide-based therapeutics and diagnostics. J Biomol Struct Dyn 2023:1-19. [PMID: 37498146 DOI: 10.1080/07391102.2023.2239932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/17/2023] [Indexed: 07/28/2023]
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.
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Affiliation(s)
- Manisha Pritam
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
| | - Somenath Dutta
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
- Department of Bioinformatics, Pondicherry Central University, Puducherry, India
| | - Krishna Mohan Medicherla
- Department of Biotechnology and Bioinformatics, Birla Institute of Scientific Research, Jaipur, India
| | - Rajnish Kumar
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
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Anurans against SARS-CoV-2: A review of the potential antiviral action of anurans cutaneous peptides. Virus Res 2022; 315:198769. [PMID: 35430319 PMCID: PMC9008983 DOI: 10.1016/j.virusres.2022.198769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/17/2023]
Abstract
At the end of 2019, in China, clinical signs and symptoms of unknown etiology have been reported in several patients whose sample sequencing revealed pneumonia caused by the SARS-CoV-2 virus. COVID-19 is a disease triggered by this virus, and in 2020, the World Health Organization declared it a pandemic. Since then, efforts have been made to find effective therapeutic agents against this disease. Identifying novel natural antiviral drugs can be an alternative to treatment. For this reason, antimicrobial peptides secreted by anurans' skin have gained attention for showing a promissory antiviral effect. Hence, this review aimed to elucidate how and which peptides secreted by anurans' skin can be considered therapeutic agents to treat or prevent human viral infectious diseases. Through a literature review, we attempted to identify potential antiviral frogs' peptides to combat COVID-19. As a result, the Magainin-1 and -2 peptides, from the Magainin family, the Dermaseptin-S9, from the Dermaseptin family, and Caerin 1.6 and 1.10, from the Caerin family, are molecules that already showed antiviral effects against SARS-CoV-2 in silico. In addition to these peptides, this review suggests that future studies should use other families that already have antiviral action against other viruses, such as Brevinins, Maculatins, Esculentins, Temporins, and Urumins. To apply these peptides as therapeutic agents, experimental studies with peptides already tested in silico and new studies with other families not tested yet should be considered.
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Bacterial expression of a snake venom metalloproteinase inhibitory protein from the North American opossum (D.virginiana). Toxicon 2021; 194:1-10. [PMID: 33581173 DOI: 10.1016/j.toxicon.2021.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/21/2020] [Accepted: 01/20/2021] [Indexed: 11/20/2022]
Abstract
A variety of opossum species are resistant to snake venoms due to the presence of antihemorrhagic and antimyotoxic acidic serum glycoproteins that inhibit several toxic venom components. Two virtually identical antihemorrhagic proteins isolated from either the North American opossum (D. virginiana) or the South American big-eared opossum (D. aurita), termed oprin or DM43 respectively, inhibit specific snake venom metalloproteinases (SVMPs). A better understanding of the structure of these proteins may provide useful insight to determine their mechanism of action and for the development of therapeutics against the global health concern of snake-bite envenomation. The aim of this work is to produce a recombinant snake venom metalloproteinase inhibitor (SVMPI) similar to the above opossum proteins in Escherichia coli and determine if this bacterially produced protein inhibits the proteolytic properties of Western Diamondback rattlesnake (C. atrox) venom. The resulting heterologous SVMPI was produced with either a 6-Histidine or maltose binding protein (MBP) affinity tag on either the C-terminus or N-terminus of the protein, respectively. The presence of the solubility enhancing MBP affinity tag resulted in significantly more soluble protein expression. The inhibitory activity was measured using two complementary assays and the MBP labeled SVMPI showed 7-fold less activity as compared to the 6-Histidine labeled SVMPI. Thus, the bacterially derived SVMPI with an unlabeled N-terminus showed high inhibitory activity (IC50 = 4.5 μM). The use of a solubility enhancing MBP fusion protein construct appears to be a productive way to express sufficient quantities of this mammalian protein in E. coli for further study.
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Zhao Q, Bai Y, Liu D, Zhao N, Gao H, Zhang X. Quinetides: diverse posttranslational modified peptides of ribonuclease-like storage protein from Panax quinquefolius as markers for differentiating ginseng species. J Ginseng Res 2020; 44:680-689. [PMID: 32913397 PMCID: PMC7471211 DOI: 10.1016/j.jgr.2019.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 05/13/2019] [Accepted: 05/23/2019] [Indexed: 10/27/2022] Open
Abstract
Background Peptides have diverse and important physiological roles in plants and are ideal markers for species identification. It is unclear whether there are specific peptides in Panax quinquefolius L. (PQ). The aims of this study were to identify Quinetides, a series of diverse posttranslational modified native peptides of the ribonuclease-like storage protein (ginseng major protein), from PQ to explore novel peptide markers and develop a new method to distinguish PQ from Panax ginseng. Methods We used different fragmentation modes in the LTQ Orbitrap analysis to identify the enriched Quinetide targets of PQ, and we discovered Quinetide markers of PQ and P. ginseng using ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry analysis. These "peptide markers" were validated by simultaneously monitoring Rf and F11 as standard ginsenosides. Results We discovered 100 Quinetides of PQ with various post-translational modifications (PTMs), including a series of glycopeptides, all of which originated from the protein ginseng major protein. We effectively distinguished PQ from P. ginseng using new "peptide markers." Four unique peptides (Quinetides TP6 and TP7 as markers of PQ and Quinetides TP8 and TP9 as markers of P. ginseng) and their associated glycosylation products were discovered in PQ and P. ginseng. Conclusion We provide specific information on PQ peptides and propose the clinical application of peptide markers to distinguish PQ from P. ginseng.
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Affiliation(s)
- Qiang Zhao
- KeyLaboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China.,CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yunpeng Bai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Dan Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Nan Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Huiyuan Gao
- KeyLaboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, China
| | - Xiaozhe Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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Kumar V, Sharma P, Bairagya HR, Sharma S, Singh TP, Tiku PK. Inhibition of human 3-hydroxy-3-methylglutaryl CoA reductase by peptides leading to cholesterol homeostasis through SREBP2 pathway in HepG2 cells. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:604-615. [PMID: 30954578 DOI: 10.1016/j.bbapap.2019.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/27/2019] [Accepted: 04/02/2019] [Indexed: 01/02/2023]
Abstract
In mammalian cells, human 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR), a rate-limiting endoplasmic reticulum (ER) bonded enzyme, plays a central role in the cholesterol homeostasis via the negative feedback mechanism. The present study indicates that the interactions of novel peptides with the catalytic domain of HMGCR, provides an alternative therapeutic candidate for reducing cholesterol. The potential natural origin of HMGCR peptide inhibitors were filtered from the peptide library using the molecular docking, which revealed three strong candidates for inhibition. This information was used for synthesizing peptides, which were evaluated for inhibition against HMGCR. The stronger docking interactions were confirmed by experimental dissociation constant (KD) values of 9.1 × 10-9 M, 1.4 × 10-8 M and 1.2 × 10-8 M for peptides NALEPDNRIESEGG (Pep-1), NALEPDNRIES (Pep-2) and PFVKSEPIPETNNE (Pep-3) respectively. The immunological based interactions show a strong evidence of peptide-HMGCR complexes. The LDL uptake showed enhancements after treatments with peptides in the extracellular environment of HepG2 cells, which was further, corroborated through increase in the immunofluorescence signal of the localized LDL-R protein expression on the cell membrane. The results showed that the mRNA and protein expression of transcription factors were significantly up-regulated showing regulation of cholesterol biosynthesis in peptide treated HepG2 cells. The binding of transcription factors, sterol regulatory element (SRE) and cAMP-response element (CRE) on HMGCR promotor further confirms the cholesterol biosynthesis regulation. All the above results suggested a key role of peptide/s in alleviating cholesterol accumulation in tissue via inhibition of rate-limiting HMGCR enzyme.
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Affiliation(s)
- Varun Kumar
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru, 570020, India; Academy of Scientific and Innovative Research, New Delhi, India
| | - P Sharma
- Department of Biophysics, All India Institute of Medical Science, 110029, New Delhi
| | - H R Bairagya
- Department of Biophysics, All India Institute of Medical Science, 110029, New Delhi
| | - S Sharma
- Department of Biophysics, All India Institute of Medical Science, 110029, New Delhi
| | - T P Singh
- Department of Biophysics, All India Institute of Medical Science, 110029, New Delhi
| | - Purnima Kaul Tiku
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru, 570020, India; Academy of Scientific and Innovative Research, New Delhi, India.
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Sharma N, Murali A, Singh SK, Giri R. Epigallocatechin gallate, an active green tea compound inhibits the Zika virus entry into host cells via binding the envelope protein. Int J Biol Macromol 2017; 104:1046-1054. [PMID: 28666829 DOI: 10.1016/j.ijbiomac.2017.06.105] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 06/25/2017] [Accepted: 06/26/2017] [Indexed: 01/08/2023]
Abstract
Emerging infections of Zika virus (ZIKV) are associated with serious consequences like microcephaly and Guillain-Barré syndrome. It leads to a situation of global health emergency and demand an intensive research investigation to develop safe and effective therapeutics. Various efforts have been made to reduce the pathological pressure of ZIKV, but no effective drug has been introduced against ZIKV infections. A recent study has reported the inhibition of ZIKV entry into the host cells by an active green tea ingredient, Epigallocatechin Gallate (EGCG) in Vero E6cells. The effect of EGCG seems remarkable but lacking the information of the mechanism of action. In this study, we have investigated the binding site (Site1) of EGCG on envelope protein and provided the insights into various interactions of molecule with the binding site using molecular docking studies. Further, using molecular dynamics approaches we proposed the possible associated mechanism of inhibition of ZIKV entry by EGCG molecule. EGCG has found to interact with several residues and providing stability to the protein conformations up to 50ns simulations.
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Affiliation(s)
- Nitin Sharma
- Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Aarthy Murali
- Department of Bioinformatics, Computer Aided Drug Design and Molecular Modeling Lab, Alagappa University,Science Block, Karaikudi-630003, Tamilnadu, India
| | - Sanjeev Kumar Singh
- Department of Bioinformatics, Computer Aided Drug Design and Molecular Modeling Lab, Alagappa University,Science Block, Karaikudi-630003, Tamilnadu, India.
| | - Rajanish Giri
- Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India.
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Extensive characterization of peptides from
Panax ginseng
C. A. Meyer using mass spectrometric approach. Proteomics 2016; 16:2788-2791. [DOI: 10.1002/pmic.201600183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/29/2016] [Accepted: 08/25/2016] [Indexed: 12/27/2022]
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