Identification and characterization of domain-specific inhibitors of DENV NS3 and NS5 proteins by in silico screening methods

The dengue virus (DENV) infects approximately 400 million people annually worldwide causing significant morbidity and mortality. Despite advances in understanding the virus life cycle and infectivity, no specific treatment for this disease exists due to the lack of therapeutic drugs. In addition, vaccines available currently are ineffective with severe side effects. Therefore, there is an urgent need for developing therapeutics suitable for effective management of DENV infection. In this study, we adopted a drug repurposing strategy to identify new therapeutic use of existing FDA approved drug molecules to target DENV2 non-structural proteins NS3 and NS5 using computational approaches. We used Drugbank database molecules for virtual screening and multiple docking analysis against a total of four domains, the NS3 protease and helicase domains and NS5 MTase and RdRp domains. Subsequently, MD simulations and MM-PBSA analysis were performed to validate the intrinsic atomic interactions and the binding affinities. Furthermore, the internal dynamics in all four protein domains, in presence of drug molecule binding were assessed using essential dynamics and free energy landscape analyses, which were further coupled with conformational dynamics-based clustering studies and cross-correlation analysis to map the regions that exhibit these structural variations. Our comprehensive analysis identified tolcapone, cefprozil, delavirdine and indinavir as potential inhibitors of NS5 MTase, NS5 RdRp, NS3 protease and NS3 helicase functions, respectively. These high-confidence candidate molecules will be useful for developing effective anti-DENV therapy to combat dengue infection.Communicated by Ramaswamy H. Sarma.

[Characteristics of PIK3CA gene mutations in Her2-low breast cancer]

BACKGROUND

Mutations in the PIK3CA gene, encoding the catalytic subunit of the PI3K class IA p110α, is a common mechanism of activating of PI3K/AKT/mTOR pathway in breast cancer (BC). The detection of these mutations in patients with hormone-positive Her2-negative BC is of important clinical value, since they are the predictor of the sensitivity of the tumor to the PI3K inhibitor - alpelisib. According to the status of the Her2/neu expression, all patients with hormone-positive Her2-negative BC can be divided into two groups - with low expression of Her2/neu (IHC 1+; 2+, ISH-) and with a complete lack of expression of this protein (IHC 0).

OBJECTIVE

Establish whether there are differences of the PIK3CA gene mutations charasteristics in BC with luminal immunophenotype and low expression of Her2/neu in comparison with tumors in which Her2/neu expression is absent.

MATERIAL AND METHODS

The presence of PIK3CA mutations was determined using real-time PCR on 96 patient tissues of hormone-positive Her2-negative BC. Commercially available cobas PIK3CA Mutation Kit (Roche) and cobas z480 analyzer were used.

RESULTS

PIK3CA gene mutations were detected in 40 of 96 cases studied (41.6%). Most of them were localized in the exons 9 and 20, encoding helicase (p.E542K, p.E545X) or kinase (p.H1047X) domains of PI3K, respectively. The frequency of mutations in the exon 9 (p.E542K+p.E545X) was 2.6 times higher in Her2-low BC compared to tumors in which the Her2/neu expression was absent (p<0.05). There were no statistically significant differences in mutation frequency in the exon 20.

CONCLUSION

Statistically significant increase in the frequency of exon 9 mutations of the PIK3CA gene is specific for the group of patients with Her2-low BC. Our results supported the concept of Her2-low BCs as the unique entity and pointed out the need of their further study.

A Glimpse of "Dicer Biology" Through the Structural and Functional Perspective

The RNA interference pathway (RNAi) is executed by two core enzymes, Dicer and Argonaute, for accomplishing a tailored transcriptional and post-transcriptional gene regulation. Dicer, an RNase III enzyme, initiates the RNAi pathway, plays a pivotal role in fighting infection against pathogens, and acts as a housekeeping enzyme for cellular homeostasis. Here, we review structure-based functional insights of Dicer and its domains present in a diverse group of organisms. Although Dicer and its domains are evolutionarily conserved from microsporidian parasites to humans, recent cryo-electron microscopy structures of Homo sapiens Dicer and Drosophila melanogaster Dicer-2 suggest characteristic variations in the mechanism of the dsRNA substrate recognition. Interestingly, the necessity for more than one functionally distinct Dicer paralogs in insects and plants compared with a single Dicer in other eukaryotic life forms implies Dicer’s role in the interplay of RNAi and other defense mechanisms. Based on the structural and mechanistic information obtained during the last decade, we aim to highlight the significance of key Dicer domains that are crucial to Dicer specific recognition and precise cleavage of dsRNA substrates. Further, the role of Dicer in the formation of Argonaute-based RNA-induced silencing complex (RISC) assembly formation, Dicer’s ability to regulate a complex protein interaction network, and its role in other cellular processes, as well as its therapeutic potentials, are emphasized.

Structural and functional analysis of the human spliceosomal DEAD-box helicase Prp28

The DEAD-box protein Prp28 is essential for pre-mRNA splicing as it plays a key role in the formation of an active spliceosome. Prp28 participates in the release of the U1 snRNP from the 5'-splice site during association of the U5·U4/U6 tri-snRNP, which is a crucial step in the transition from a pre-catalytic spliceosome to an activated spliceosome. Here, it is demonstrated that the purified helicase domain of human Prp28 (hPrp28ΔN) binds ADP, whereas binding of ATP and ATPase activity could not be detected. ATP binding could not be observed for purified full-length hPrp28 either, but within an assembled spliceosomal complex hPrp28 gains ATP-binding activity. In order to understand the structural basis for the ATP-binding deficiency of isolated hPrp28, the crystal structure of hPrp28ΔN was determined at 2.0 Å resolution. In the crystal the helicase domain adopts a wide-open conformation, as the two RecA-like domains are extraordinarily displaced from the productive ATPase conformation. Binding of ATP is hindered by a closed conformation of the P-loop, which occupies the space required for the γ-phosphate of ATP.