Genomics functional analysis and drug screening of SARS-CoV-2
A novel coronavirus appeared in Wuhan, China has led to major outbreaks. Recently, rapid classification of virus species, analysis of genome and screening for effective drugs are the most important tasks. In the present study, through literature review, sequence alignment, ORF identification, motif...
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| Format: | Article |
| Language: | English |
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KeAi Communications Co., Ltd.
2020-12-01
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| Series: | Genes and Diseases |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352304220300544 |
| _version_ | 1797706961892933632 |
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| author | Long Chen Li Zhong |
| author_facet | Long Chen Li Zhong |
| author_sort | Long Chen |
| collection | DOAJ |
| description | A novel coronavirus appeared in Wuhan, China has led to major outbreaks. Recently, rapid classification of virus species, analysis of genome and screening for effective drugs are the most important tasks. In the present study, through literature review, sequence alignment, ORF identification, motif recognition, secondary and tertiary structure prediction, the whole genome of SARS-CoV-2 were comprehensively analyzed. To find effective drugs, the parameters of binding sites were calculated by SeeSAR. In addition, potential miRNAs were predicted according to RNA base-pairing. After prediction by using NCBI, WebMGA and GeneMark and comparison, a total of 8 credible ORFs were detected. Even the whole genome have great difference with other CoVs, each ORF has high homology with SARS-CoVs (>90%). Furthermore, domain composition in each ORFs was also similar to SARS. In the DrugBank database, only 7 potential drugs were screened based on the sequence search module. Further predicted binding sites between drug and ORFs revealed that 2-(N-Morpholino)-ethanesulfonic acid could bind 1# ORF in 4 different regions ideally. Meanwhile, both benzyl (2-oxopropyl) carbamate and 4-(dimehylamina) benzoic acid have bene demonstrated to inhibit SARS-CoV infection effectively. Interestingly, 2 miRNAs (miR-1307-3p and miR-3613-5p) were predicted to prevent virus replication via targeting 3′-UTR of the genome or as biomarkers. In conclusion, the novel coronavirus may have consanguinity with SARS. Drugs used to treat SARS may also be effective against the novel virus. In addition, altering miRNA expression may become a potential therapeutic schedule. |
| first_indexed | 2024-03-12T06:00:09Z |
| format | Article |
| id | doaj.art-f8e70e4e056a4d0ea3913d34f4d0f3d6 |
| institution | Directory Open Access Journal |
| issn | 2352-3042 |
| language | English |
| last_indexed | 2024-03-12T06:00:09Z |
| publishDate | 2020-12-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Genes and Diseases |
| spelling | doaj.art-f8e70e4e056a4d0ea3913d34f4d0f3d62023-09-03T04:18:47ZengKeAi Communications Co., Ltd.Genes and Diseases2352-30422020-12-0174542550Genomics functional analysis and drug screening of SARS-CoV-2Long Chen0Li Zhong1Corresponding author. Bioengineering Institute of Chongqing University, 174 Shazheng Street, Chongqing, 400000, China.; Bioengineering Institute of Chongqing University, 174 Shazheng Street, Chongqing, ChinaBioengineering Institute of Chongqing University, 174 Shazheng Street, Chongqing, ChinaA novel coronavirus appeared in Wuhan, China has led to major outbreaks. Recently, rapid classification of virus species, analysis of genome and screening for effective drugs are the most important tasks. In the present study, through literature review, sequence alignment, ORF identification, motif recognition, secondary and tertiary structure prediction, the whole genome of SARS-CoV-2 were comprehensively analyzed. To find effective drugs, the parameters of binding sites were calculated by SeeSAR. In addition, potential miRNAs were predicted according to RNA base-pairing. After prediction by using NCBI, WebMGA and GeneMark and comparison, a total of 8 credible ORFs were detected. Even the whole genome have great difference with other CoVs, each ORF has high homology with SARS-CoVs (>90%). Furthermore, domain composition in each ORFs was also similar to SARS. In the DrugBank database, only 7 potential drugs were screened based on the sequence search module. Further predicted binding sites between drug and ORFs revealed that 2-(N-Morpholino)-ethanesulfonic acid could bind 1# ORF in 4 different regions ideally. Meanwhile, both benzyl (2-oxopropyl) carbamate and 4-(dimehylamina) benzoic acid have bene demonstrated to inhibit SARS-CoV infection effectively. Interestingly, 2 miRNAs (miR-1307-3p and miR-3613-5p) were predicted to prevent virus replication via targeting 3′-UTR of the genome or as biomarkers. In conclusion, the novel coronavirus may have consanguinity with SARS. Drugs used to treat SARS may also be effective against the novel virus. In addition, altering miRNA expression may become a potential therapeutic schedule.http://www.sciencedirect.com/science/article/pii/S2352304220300544SARS-CoV-2Drug screeningEpitopeGenomicHomologymiRNA |
| spellingShingle | Long Chen Li Zhong Genomics functional analysis and drug screening of SARS-CoV-2 Genes and Diseases SARS-CoV-2 Drug screening Epitope Genomic Homology miRNA |
| title | Genomics functional analysis and drug screening of SARS-CoV-2 |
| title_full | Genomics functional analysis and drug screening of SARS-CoV-2 |
| title_fullStr | Genomics functional analysis and drug screening of SARS-CoV-2 |
| title_full_unstemmed | Genomics functional analysis and drug screening of SARS-CoV-2 |
| title_short | Genomics functional analysis and drug screening of SARS-CoV-2 |
| title_sort | genomics functional analysis and drug screening of sars cov 2 |
| topic | SARS-CoV-2 Drug screening Epitope Genomic Homology miRNA |
| url | http://www.sciencedirect.com/science/article/pii/S2352304220300544 |
| work_keys_str_mv | AT longchen genomicsfunctionalanalysisanddrugscreeningofsarscov2 AT lizhong genomicsfunctionalanalysisanddrugscreeningofsarscov2 |