E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies

The pandemic of the COVID-19 disease caused by SARS-CoV-2 has led to more than 100 million infections and over 2 million deaths worldwide. The progress in the developments of effective vaccines and neutralizing antibody therapeutics brings hopes to eliminate the threat of COVID-19. However, SARS-CoV-2 continues to mutate, and several new variants have been emerged. Among the various naturally-occurring mutations, the E484K mutation shared by both the 501Y.V2 and 501Y.V3 variants attracted serious concerns, which may potentially enhance the receptor binding affinity and reduce the immune response. In the present study, the molecular mechanism behind the impacts of E484K mutation on the binding affinity of the receptor-binding domain (RBD) with the receptor human angiotensin-converting enzyme 2 (hACE2) was investigated by using the molecular dynamics (MD) simulations combined with the molecular mechanics-generalized Born surface area (MMGBSA) method. Our results indicate that the E484K mutation results in more favorable electrostatic interactions compensating the burial of the charged and polar groups upon the binding of RBD with hACE2, which significantly improves the RBD-hACE2 binding affinity. Besides that, the E484K mutation also causes the conformational rearrangements of the loop region containing the mutant residue, which leads to more tight binding interface of RBD with hACE2 and formation of some new hydrogen bonds. The more tight binding interface and the new hydrogen bonds formation also contribute to the improved binding affinity of RBD to the receptor hACE2. In addition, six neutralizing antibodies and nanobodies complexed with RBD were selected to explore the effects of E484K mutation on the recognition of these antibodies to RBD. The simulation results show that the E484K mutation significantly reduces the binding affinities to RBD for most of the studied neutralizing antibodies, and the decrease in the binding affinities is mainly owing to the unfavorable electrostatic interactions caused by the mutation. Our studies revealed that the E484K mutation may improve the binding affinity between RBD and the receptor hACE2, implying more transmissibility of the E484K-containing variants, and weaken the binding affinities between RBD and the studied neutralizing antibodies, indicating reduced effectiveness of these antibodies. Our results provide valuable information for the effective vaccine development and antibody drugs design.

Effect of up-regulation of miR-92a on the proliferation and angiogenesis of non-small cell lung cancer / 临床与实验病理学杂志

Purpose To investigate the effect of down-regulation of miR-92 a on the proliferation and angiogenesis of nonsmall cell lung cancer (NSCLC). Methods Human NSCLC cell A549 was divided into three groups: A549 group (non-transfected A549 cells), sc-siRNA group (A549 cells transfected with sc-siRNA) and miR-92a-siRNA group (A 5 4 9 cells trans-fected with miR-92a-siRNA). The relative expression level of miR-92 a, PTEN and vascular endothelial growth factor (VEGF) in A549 cells and human bronchial epithelial (HBE) cells were detected by RT-PCR and Western blot respectively. The proliferation ability of A549 cells in each group was detected by living cell count and crystal violet staining experiment. Results The relative expression of miR-92 a in A549 cells was significantly higher than that in HBE cells (P < 0.05), the expression level of PTEN protein in A549 cells was significantly lower than that in HBE cells (P < 0.05), and the expression level of VEGF protein was significantly higher than that in HBE cells (P < 0.05).In the miR-92a-siRNA group, the relative expression of miR-92 a decreased (P < 0.05), the expression level of PTEN protein in-creased (P < 0.05), and the expression level of VEGF protein decreased (P < 0.05). The expression levels of PI3 K and Akt in miR-92a-siRNA group decreased (P < 0.05). the number of cells and cell proliferation ability in miR-92a-siRNA group reduced. Conclusion The expression of miR-92 a in NSCLC A549 cells is up-regulated, miR-92 a gene silencing can significantly inhibit cell proliferation and inhibit cell angiogenesis, PTEN and VEGF related PI3K/Akt signaling pathways may play an important role in this process.

Application and advantages of tissue engineering technique in the treatment of infected bone defects / 中国组织工程研究

BACKGROUND:There are many treatment methods for infected bone defects,but there is no first stage treatment method,which has the characteristics of sustained-release,anti-inflammation,osteogenic activity,bone conduction and degradable absorption.OBJECTIVE:To investigate the research progress of bone tissue engineering technique in the treatment of infected bone defects.METHODS:A computer-based retrieval of PubMed,WanFang and CNKI databases was conducted for the articles published from 2000 to 2016,concerning the basic and clinical research on the local application of antibiotics;basic research on infected bone defects with sustained-release of antibiotics;basic studies on the source of seed cells and the osteogenic mechanism;and scaffold materials.A total of 55 eligible articles were included for result analysis.RESULTS AND CONCLUSION:Topical application of antibiotics exhibits different effects in the treatment of osteomyelitis.The development of bone tissue engineering has brought new hope for the treatment of bone defects,and in the meanwhile,selection of excellent seed cells has become a hot and difficult research.A rational combination of antibiotics,seed cells and scaffold materials may provide a new treatment strategy for infected bone defects.

[Differential proteins in esophageal squamous cell line EC9706/CDDP identified by SILAC quantitative proteomic approach].

Multidrug resistance (MDR) is one of the main causes leading to the failure in cancer treatment. Differential proteins between esophageal squamous cell carcinoma (ESCC) cell line EC9706 and its cisdiamminedichloroplatinum (CDDP)-resistant subline EC9706/CDDP revealed by quantitative analysis may provide deeper insights into the molecular mechanisms of MDR implicated in ESCC. EC9706/CDDP was generated by exposure of its parental sensitive EC9706 to a step-wise increase of CDDP concentration during EC9706 cultivation. The stable isotope labeling with amino acids in cell culture (SILAC) was used to label EC9706 and EC9706/CDDP with heavy and light medium, separately. Mixed peptides derived from EC9706 and EC9706/CDDP were analyzed by high performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS/MS) and subsequently subjected to bioinformatics analysis to identify differential proteins between EC9706 and EC9706/CDDP. Compared to parental EC9706, EC9706/CDDP manifested phenotypes of slow proliferation, cell pleomorphology, atypia and increased resistant-index 3.23. Seventy-four differential proteins identified in the present study belongs to various families with multiple functions, such as cytoskeleton (20%), energy metabolism (11%), transcription regulation and DNA repair (11%), redox homeostasis (9.5%), protein biosynthesis and mRNA processing (12%), ribosome constituent (8.1%), molecular chaperone (8.1%), immunity/inflammation (5.4%), intracellular transport (5.4%) and nucleosome assembly (2.7%), which indicated that development of MDR is a complicated process involving dysregulation of multiple molecules and pathways. The data is of great value for in-depth elucidation of molecular mechanisms of the MDR implicated in ESCC and may represent potential molecular targets for future therapeutic development.

Influence of electromagnetic irradiation on P450scc mRNA expression in rat testis tissues and protective effect of the shield / 中华男科学杂志

<p><b>OBJECTIVE</b>To study the influence of electromagnetic irradiation on cytochrome P450 cholesterol side chain lyase (P450scc) in adult rat testis tissues and to assess the protective effect of the copper shield.</p><p><b>METHODS</b>Healthy male Wistar rats were randomized into a control group, an electromagnetic irradiation group and a wholly shielded group (with the copper shielding net). The electromagnetic irradiation group and the shielded group were set for 4 phases of 3, 6, 24 and 72 hours after irradiation, 15 rats for each phrase. The testosterone contents in the serum of the irradiated rats at 3, 6, 24 and 72 hours and in that of the controls were measured by radioimmunoassay(RIA), and so was the level of the P450scc mRNA in the testis tissues by semi-quantitative RT-PCR. And the effect of the copper shielding net on testosterone and P450scc mRNA was observed.</p><p><b>RESULTS</b>The contents of testosterone and the P450scc mRNA level in the irradiated group were significantly lower than in the control rats, decreased by 83.9% and 56.9% at 3 hours (P < 0.01), 54.8% and 27.3% at 6 hours (P < 0.01), restored to normal at 24 hours, but again reduced by 60.1% and 56.1% respectively (P < 0.01). While in the shielded group, no significant change was observed either in the testosterone of the serum or in the P450scc mRNA expression in the testis tissues.</p><p><b>CONCLUSION</b>Electromagnetic irradiation may affect the transcription of P450scc in adult rat Leydig cells and thereby decrease the testosterone synthesis. Whole-body shielding with the copper net may achieve satisfactory effect.</p>