Biological Evaluation of Coronaviruses and the Study of Molecular Docking, Linalool, and Thymol as orf1ab Protein Inhibitors and
 the Role of SARS-CoV-2 Virus in Bioterrorism

Fazeli nasab, Bahman

doi:10.29252/sjimu.28.6.77

[Home ] [Archive]

[ فارسی ]

Journal of Ilam University of Medical Sciences

Main Menu

Home

Journal Information

Articles archive

Publication Ethics

Peer Review Process

Indexing Databases

For Authors

For Reviewers

Subscription

Contact us

Site Facilities

Google Scholar Metrics

	All	Since 2019
Citations	6870	4104
h-index	28	22
i10-index	206	99

Search in website

Receive site information

Registered in

Volume 28, Issue 6 (1-2021)

Journal of Ilam University of Medical Sciences 2021, 28(6): 77-96

Back to browse issues page

Biological Evaluation of Coronaviruses and the Study of Molecular Docking, Linalool, and Thymol as orf1ab Protein Inhibitors and the Role of SARS-CoV-2 Virus in Bioterrorism

Bahman Fazeli nasab ^*

Research Dept of Agronomy and Plant Breeding, Agricultural Research Institute, University of Zabol, Zabol, Iran , bfazelinasab@gmail.com

Abstract: (3081 Views)

Introduction: Coronaviruses are animal-derived enveloped viruses that in addition to respiratory and digestive diseases have also been found in neurological diseases, some of which have caused nephritis or have been observed in patients with Multiple Sclerosis and mouse hepatitis. However, in general, the most important effect of coronaviruses is on the respiratory and digestive systems. This study aimed to compare the genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-28) with that of other viruses of the coronavirus family. Moreover, it was attempted to investigate the possibility of its falsification and finally evaluate the effect of linalool and thymol on the inactivity of the orf1ab protein of SARS-CoV-2.

Materials & Methods: The Coronaviridae family virus genome sequence was obtained from the NCBI database. After alignment, the number of mutations, nucleotide diversity, number of sites in which the same substitution occurred, clustering, similarity and genetic distance, as well as dN/dS index were evaluated in this study. The three-dimensional structure of the orf1ab protein prediction and the accuracy of the predicted model was also investigated. Furthermore, this study examined the motif and the domains conserved for the orf1ab gene in all viruses of the Coronaviridae family, as well as the membrane, cytoplasm, and kinase domains in the orf1ab virus of SARS-CoV-2. Regarding the molecular docking, linalool (the most important thirst-suppressing substance of Scrophularia striata) of the model plant (i.e., araboidopsis) and thymol (the most important ingredient of Trachyspermum ammi L.) were used to prevent the inactivation of the orf1ab protein of SARS-CoV-2.Ethics code: IR.UOZ.REC.1399.003

Findings: The SARS-CoV-2 virus has 11 conserved domains and 11 genes. The presence of the NSP13 superfamily and SUD-M superfamily in the SARS-CoV-2 virus genome indicate the ability and effort of this virus to be more stable in the environment. Based on the numerical value of dN/dS (1.036) and Tajima´s D (4.39) for orf1ab, the slope of the changes during evolution for the orf1ab gene is very slow, and there is no choice of direction in virus changes. Based on the highest interaction between linalool protein and orf1ab protein (-41.0), the highest accuracy (0.172), lowest energy level (ΔG=-6.23Kcal/mol), and the best combination (Full Fitness=-1340.18 Kcal/mol) between thymol phytochemical and orf1ab protein, molecular docking results showed that both linalool protein and thymol substance bound to orf1ab protein and inhibited its activity.

Discussions & Conclusions: Linalol and thymol affected the inactivity of the orf1ab protein in the SARS-CoV-2 virus. However, clinical trials on linalool and thymol should be performed to confirm these hypotheses. If the hypothesis approves, it is suggested to use them in this regard. In addition, by examining the dN/dS indices, as well as evaluating the singletons, domains, and conserved areas of all viruses, it was found that the SARS-CoV-2 virus could not be purposefully manipulated.

Keywords: Carum copticum, COVID-19, Scrophularia striata, Zataria multiflora

Full-Text [PDF 1400 kb] (1258 Downloads)

Type of Study: Research | Subject: environmental healt
Received: 2020/04/8 | Accepted: 2020/10/3 | Published: 2021/02/28

References

1. Li W, Shi Z, Yu M, Ren W, Smith C, Epstein JH, et al. Bats are natural reservoirs of SARS like coronaviruses. Science 2005; 310: 676-79. doi.10.1126/science.1118391

2. Lai MM, Cavanagh D. The molecular biology of coronaviruses. 1 th ed. Adv Virus Res Elsevier Publication. 1997; P.1-100.

3. Cavanagh D, Macnaughton M. Coronaviruses in principles and practice of clinical virology. 2 th ed. Wiley Chichester Publication.1995; P.325-36.

4. Talbot PJ, Paquette JS, Ciurli C, Antel JP, Ouellet F. Myelin basic protein and human coronavirus 229E cross reactive T cells in multiple sclerosis. Annal Neurol 1996; 3: 233-40. doi. 10.1002/ana.410390213

5. Tavakoli A, Vahdat K, Keshavarz M. Novel coronavirus disease 2019 an emerging infectious disease in the 21st century. Iranian South Med J 2020; 22: 432-50.

6. Danesh F, Ghavidel S. Coronavirus scientometrics of 50 years of global scientific productions. Iranian J Med Microbiol 2020; 14: 1-16.

7. Siddell S. The small membrane protein in the coronaviridae. 2 th ed. Plenum NY Publication. 1995; P.1-86.

8. Groot RJ, Baker S, Baric R, Enjuanes L, Gorbalenya A, Holmes K, et al. Family coronaviridae. Virus Tax 2012;2: 806-28.

9. Cavanagh D, Brian DA, Brinton MA, Enjuanes L, Holmes KV, Horzinek MC, et al. In virus taxonomy. 6 th ed. Springer Verlag Vienna NY Publication.1995; P. 407-11..

10. Snijder EJ, Spaan WJ. The coronaviruslike superfamily. 1 th ed. Springer Publication. 1995; P.239-55.

11. Risco C, Antón IM, Enjuanes L, Carrascosa JL. The transmissible gastroenteritis coronavirus contains a spherical core shell consisting of M and N proteins. J Virol 1996; 70: 4773-77.

12. Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Dempsey DM, et al. Changes to virus taxonomy and the statutes ratified by the international committee on taxonomy of viruses. 1 th ed. Springer Publication. 2020;P.111-20.

13. Fazelinasab B, Mirzaei N. [Evaluation of total phenol and flavonoid content in a wide variety of native and imported plants]. Sci J Ilam Uni Medical Sci 2018; 26: 141-54. (Persian) doi.10.29252/sjimu.26.2.141

14. Keikhaie KR, Fazelinasab B, Jahantigh HR, Hassanshahian M. Antibacterial activity of ethyl acetate and methanol extracts of securigera securidaca withania sominefra rosmarinus officinalis and Aloe vera plants against important human pathogens. J Med Bacteriol 2018; 7: 13-21.

15. Valizadeh M, Beigomi M, Fazelinasab B. Antibacterial and Anti biofilm effects of ethanol and aceton leaf extract of Momordica charantia and Tecomella undulata against Acinetobacter baumannii. Int J Adv Biol Biomed Res 2020; 8: 403-18. doi.10.33945/sami/ijabbr.2020.4.6

16. Rezaeinasab M, Komeili G, Fazelinasab B. Gastroprotective effects of aqueous and hydroalcholic extract of Scrophularia striata on ethanol induced gastric ulcers in Rats. Der Pharm Lett 2017; 9: 84-93.

17. Khan R, Zakir M, Khanam Z, Shakil S, Khan AU. Novel compound from Trachyspermum ammi seeds with antibiofilm and antiadherence activities against Streptococcus mutans a potential chemotherapeutic agent against dental caries. J Appl Microbiol 2010; 109: 2151-9. doi.10.1111/j.1365-2672.2010.04847.x

18. Moazeni M, Saharkhiz MJ, Hosseini AA. In vitro lethal effect of ajowan Trachyspermum ammi L. essential oil on hydatid cyst protoscoleces. Vet Parasitol 2012; 187: 203-8. doi.10.1016/j.vetpar.2011.12.025

19. Ashraf M, Orooj A. Salt stress effects on growth, ion accumulation and seed oil concentration in an arid zone traditional medicinal plant ajwain Trachyspermum ammi L sprague. J Ar Environ2006; 64: 209-20.

20. Singh G, Kapoor I, Pandey S, Singh U, Singh R. Studies on essential oils part 10 antibacterial activity of volatile oils of some spices. Phytotherapy Res An International J Dev Pharmacol Toxicol Eval Natural Prod 2002; 16: 680-82. doi.10.1002/ptr.951

21. Fazelinasab B. The effect of explant BAP and 2,4-D on callus induction of trachyspermum ammi. Potravinarstvo Slovak J Food Sci 2018; 12: 578-86. doi.10.5219/953

22. Fazelinasab B, Fooladvand Z. A review on Iranian Carum copticum composition and biological activities. European J Med Plant 2016; 12: 1-8. doi.10.9734/EJMP/2016/17584

23. Amiri H, H LY, Esmaeili A, Samsamnia F, Eghbali D, Viskarami G, et al. Essential oil composition and anatomical study of Scrophularia striata boiss. Iranian J Med Arom Plant 2011; 27: 271-78.

24. Bekhechi C, Boti JB, Bekkara FA, Abdelouahid DE, Casanova J, Tomi F. Isothymol in ajowan essential oil. Nat Prod Commun 2010; 5: 1107-10.

25. Nei M, Li WH. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proce National Acad Sci1979; 76: 5269-73.

26. Datta PP, Sharma MR, Qi L, Frank J, Agrawal RK. Interaction of the G domain of elongation factor G and the C terminal domain of ribosomal protein L7/L12 during translocation as revealed by cryo EM. Mole Cell 2005; 20: 723-31. doi.0.1016/j.molcel.2005.10.028

27. Marchlerbauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, et al. CDD NCBI's conserved domain database. Nucle Acids Res 2014; 43: 222-26. doi.10.1093/nar/gku1221

28. Grimanelli D, Ingouff M. DNA methylation readers in plants. J Mole Biol 2020; 432: 1706-17. doi.10.1016/j.jmb.2019.12.043

29. Shoohani B, Hemati AA, Taherimoghadam M. [Effects of Scrophularia striata extract on wound healing in Rabbit]. Sci J Ilam Uni Med Sci 2009; 17: 9-16. (Presian)

30. Kryazhimskiy S, Plotkin JB. The population genetics of dN/dS. PLoS Genet 2008; 4: 1000304.

31. Buschiazzo E, Ritland C, Bohlmann J, Ritland K. Slow but not low genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms. BMC Evol Biol2012; 12: 1-15. doi.10.1186/1471-2148-12-8

32. Ngandu NK, Scheffler K, Moore P, Woodman Z, Martin D, Seoighe C. Extensive purifying selection acting on synonymous sites in HIV-1 group M sequences. Virol J2008; 5: 1-11. doi.10.1186/1743-422X-5-160

33. Monnin A, Nagot N, Peries M, Vallo R, Meda N, Singataet al. Mitochondrial DNA parameters in blood of infants receiving lopinavir ritonavir or lamivudine prophylaxis to prevent breastfeeding transmission of HIV-1. J Clin Med 2020; 9: 2972. doi.10.3390/jcm9092972

34. Manfredi G, Thyagarajan D, Papadopoulou LC, Pallotti F, Schon EA. The fate of human sperm-derived mtDNA in somatic cells. Am J Hum Gen1997; 61: 953-60.

35. Knight RD, Freeland SJ, Landweber LF. A simple model based on mutation and selection explains trends in codon and amino acid usage and GC composition within and across genomes. Gen Biol 2001; 2: 1-10. doi.10.1186/gb-2001-2-4-research0010

36. Levin DE, Ames BN. Classifying mutagens as to their specificity in causing the six possible transitions and transversions a simple analysis using the Salmonella mutagenicity assay. Environ Mutagene 1986; 8: 9-28. doi.10.1002/em.2860080103

37. Sueoka N. Two aspects of DNA base composition G+ C content and translation coupled deviation from intra strand rule of A=T and G=C. J Mol Evol 1999; 49: 49-62. doi.10.1007/PL00006534

38. Nachman MW, Crowell SL. Estimate of the mutation rate per nucleotide in humans. Genetics 2000; 156: 297-304.

39. Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nature Med 2020: 1-3. doi.10.1038/s41591-020-0820-9

Send email to the article author

Add your comments about this article

‎ 10.29252/sjimu.28.6.77

Ethics code: will send it

Mendeley

Zotero

RefWorks

Fazeli nasab B. Biological Evaluation of Coronaviruses and the Study of Molecular Docking, Linalool, and Thymol as orf1ab Protein Inhibitors and the Role of SARS-CoV-2 Virus in Bioterrorism. J. Ilam Uni. Med. Sci. 2021; 28 (6) :77-96
URL: http://sjimu.medilam.ac.ir/article-1-6449-en.html

Rights and permissions
	This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

Volume 28, Issue 6 (1-2021)

Back to browse issues page

Persian site map - English site map - Created in 0.15 seconds with 41 queries by YEKTAWEB 4671