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1.
Nano Biomedicine and Engineering ; 14(2):173-185, 2022.
Article in English | EMBASE | ID: covidwho-2226033

ABSTRACT

COVID-19 is caused by severe acute respiratory SARS-CoV-2. Regardless of the availability of treatment strategies for COVID-19, effective therapy will remain essential. A promising approach to tackle the SARS-CoV-2 could be small interfering (si) RNAs. Here we designed the small hairpin RNA (named as shRNA688) for targeting the prepared 813 bp Est of the S protein genes (Delta). The conserved and mutated regions of the S protein genes from the genomes of the SARS-CoV-2 variants in the public database were analyzed. A 813 bp fragment encoding the most part of the RBD and partial downstream RBD of the S protein was cloned into the upstream red florescent protein gene (RFP) as a fusing gene in the pCMV-S-Protein RBD-Est-RFP plasmid for expressing a potential target for RNAi. The double stranded of the DNA encoding for shRNA688 was constructed in the downstream human H1 promoter of the plasmid in which CMV promoter drives enhanced green fluorescent protein (EGFP) marker gene expression. These two kinds of the constructed plasmids were co-transfected into HEK293T via Lipofectamine 2000. The degradation of the transcripts of the SARS-CoV-2 S protein fusing gene expressed in the transfected HEK293T treated by RNAi was analyzed by RT-qPCR with a specific probe of the targeted SARS-CoV-2 S protein gene transcripts. Our results showed that shRNA688 targeting the conserved region of the S protein genes could effectively reduce the transcripts of the S protein genes. This study provides a cell model and technical support for the research and development of the broad-spectrum small nucleic acid RNAi drugs against SARS-CoV-2 or the RNAi drugs for the other hazard viruses which cause human diseases. Copyright © Weiwei Zhang, Linjia Huang, Jumei Huang, Xin Jiang, Xiaohong Ren, Xiaojie Shi, Ling Ye, Shuhui Bian, Jianhe Sun, Yufeng Gao, Zehua Hu, Lintin Guo, Suyan Chen, Jiahao Xu, Jie Wu, Jiwen Zhang, Daxiang Cui, and Fangping Dai.

2.
6th International Conference on Biomedical Engineering and Applications, ICBEA 2022 ; : 116-119, 2022.
Article in English | Scopus | ID: covidwho-2020427

ABSTRACT

A global pandemic of SARS-CoV-2 was caused around the world. The virus is highly contagious and rapidly spreads. Early detection of the virus is crucial to prevent its spread and control outbreaks. Owing to the drawbacks of waiting time and high cost involved in polymerase chain reaction (PCR) testing, low-cost and accurate detection setups with the possibility of being realized as portable systems are desirable. In this study, we examined the feasibility of using a small spectrometer in conjunction with optical biosensors as a measurement system. According to the experimental results related to different concentrations of SARS-CoV-2 ranging from 106 to 102 copies/mL, the surface-mounted device (SMD) size spectrometer and benchtop fiber-optic spectrometer showed good agreement, demonstrating the possibility of using tiny spectrometers to detect the virus at different concentrations using optical biosensors. © 2022 ACM.

3.
New Journal of Chemistry ; 45(26):11512-11529, 2021.
Article in English | EMBASE | ID: covidwho-1585752

ABSTRACT

The normal expression of the main protease (Mpro) plays a vital role in the life cycle of coronavirus. Highly active inhibitors could inhibit the normal circulation of the main protease to achieve therapeutic effects as anti-coronavirus agents. In the present research, 48 peptide compounds with SARS-CoV Mproinhibition selected from the literature were used to establish robust Topomer CoMFA (q2= 0.743,r2= 0.938, andrpred2= 0.700) and HQSAR (q2= 0.774,r2= 0.955, andrpred2= 0.723) models. Structural modification information was used for designing new Mproinhibitors. The high contribution-value descriptor generated by Topomer CoMFA was used to screen for the fragments that possess significant inhibitory activities from the ZINC drug database, and 24 new compounds with predicted high inhibitory activity at nanomolar concentration were designed by combining the high contribution value fragments. The molecular docking results further justified that these potential inhibitors could form hydrogen bonds with the residues of CYS145, GLN189, GLU166, HIS163, and GLY143 of target Mpro, which well explains their strong inhibitory effects. The molecular dynamics simulation results indicated that four highly active compounds could stably bond with SARS-CoV-2 Mproand might be promising anti-SARS-CoV-2 Mprocandidates. Finally, all the newly designed compounds showed premium ADMET properties as per the predictions by the server in the public domain. This research work not only provides robust QSAR models as valuable screening tools for future anti-coronavirus drug development but also renders the newly designed SARS-CoV-2 Mproinhibitors with activity at nanomolar concentration, which can be used for further characterization to obtain novel anti-coronavirus drugs for both SARS-CoV and SARS-CoV-2.

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