A Degron Blocking Strategy Towards Improved CRL4CRBN Recruiting PROTAC Selectivity.

Small molecules inducing protein degradation are important pharmacological tools to interrogate complex biology and are rapidly translating into clinical agents. However, to fully realise the potential of these molecules, selectivity remains a limiting challenge. Herein, we addressed the issue of selectivity in the design of CRL4CRBN recruiting PROteolysis TArgeting Chimeras (PROTACs). Thalidomide derivatives used to generate CRL4CRBN recruiting PROTACs have well described intrinsic monovalent degradation profiles by inducing the recruitment of neo-substrates, such as GSPT1, Ikaros and Aiolos. We leveraged structural insights from known CRL4CRBN neo-substrates to attenuate and indeed remove this monovalent degradation function in well-known CRL4CRBN molecular glues degraders, namely CC-885 and Pomalidomide. We then applied these design principles on a previously published BRD9 PROTAC (dBRD9-A) and generated an analogue with improved selectivity profile. Finally, we implemented a computational modelling pipeline to show that our degron blocking design does not impact PROTAC-induced ternary complex formation. We believe that the tools and principles presented in this work will be valuable to support the development of targeted protein degradation.

Metagenomic analysis of soybean endosphere microbiome to reveal signatures of microbes for health and disease.

BACKGROUND: Soil metagenomics is a cultivation-independent molecular strategy for investigating and exploiting the diversity of soil microbial communities. Soil microbial diversity is essential because it is critical to sustaining soil health for agricultural productivity and protection against harmful organisms. This study aimed to perform a metagenomic analysis of the soybean endosphere (all microbial communities found in plant leaves) to reveal signatures of microbes for health and disease. RESULTS: The dataset is based on the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) release "microbial diversity in soybean". The quality control process rejected 21 of the evaluated sequences (0.03% of the total sequences). Dereplication determined that 68,994 sequences were artificial duplicate readings, and removed them from consideration. Ribosomal Ribonucleic acid (RNA) genes were present in 72,747 sequences that successfully passed quality control (QC). Finally, we found that hierarchical classification for taxonomic assignment was conducted using MG-RAST, and the considered dataset of the metagenome domain of bacteria (99.68%) dominated the other groups. In Eukaryotes (0.31%) and unclassified sequence 2 (0.00%) in the taxonomic classification of bacteria in the genus group, Streptomyces, Chryseobacterium, Ppaenibacillus, Bacillus, and Mitsuaria were found. We also found some biological pathways, such as CMP-KDO biosynthesis II (from D-arabinose 5-phosphate), tricarboxylic acid cycle (TCA) cycle (plant), citrate cycle (TCA cycle), fatty acid biosynthesis, and glyoxylate and dicarboxylate metabolism. Gene prediction uncovered 1,180 sequences, 15,172 of which included gene products, with the shortest sequence being 131 bases and maximum length 3829 base pairs. The gene list was additionally annotated using Integrated Microbial Genomes and Microbiomes. The annotation process yielded a total of 240 genes found in 177 bacterial strains. These gene products were found in the genome of strain 7598. Large volumes of data are generated using modern sequencing technology to sample all genes in all species present in a given complex sample. CONCLUSIONS: These data revealed that it is a rich source of potential biomarkers for soybean plants. The results of this study will help us to understand the role of the endosphere microbiome in plant health and identify the microbial signatures of health and disease. The MG-RAST is a public resource for the automated phylogenetic and functional study of metagenomes. This is a powerful tool for investigating the diversity and function of microbial communities.

An in silico approach for prediction of B cell and T cell epitope candidates against Chikungunya virus.

Several outbreaks of Chikungunya virus (CHIKV) had been reported since 1952 when mankind had his first encounter against the virus in Tanzania. Although these reports designate the CHIKV to be rarely fatal, cases of outbreaks in the last decade accompanied by severe complications and death poses a challenge to the development of effective treatment methods. Several attempts to vaccine development against CHIKV still remains unsuccessful. In this study, we aimed at the prediction of B-cell and T cell epitopes against CHIKV by using immunoinformatics. This, in turn, can contribute to development of an epitope based vaccine against CHIKV. Both linear and discontinuous B-cell epitopes, as well as Cytotoxic T-lymphocyte epitopes, were predicted for the CHIKV Envelope (E1 and E2) glycoproteins and (NS2). The antigenic CTL epitopes with highest binding affinities with type-1 MHC were selected and the peptides were docked to them. Docking followed by molecular dynamics simulations were performed to assess the stability of the docked complexes.

Glaucoma-TrEl: A web-based interactive database to build evidence-based hypotheses on the role of trace elements in glaucoma.

OBJECTIVE: Glaucoma is a chronic neurological disease that is associated with high intraocular pressure (IOP), causes gradual damage to retinal ganglion cells, and often culminates in vision loss. Recent research suggests that glaucoma is a complex multifactorial disease in which multiple interlinked genes and pathways play a role during onset and development. Also, differential availability of trace elements seems to play a role in glaucoma pathophysiology, although their mechanism of action is unknown. The aim of this work is to disseminate a web-based repository on interactions between trace elements and protein-coding genes linked to glaucoma pathophysiology. RESULTS: In this study, we present Glaucoma-TrEl, a web database containing information about interactions between trace elements and protein-coding genes that are linked to glaucoma. In the database, we include interactions between 437 unique genes and eight trace elements. Our analysis found a large number of interactions between trace elements and protein-coding genes mutated or linked to the pathophysiology of glaucoma. We associated genes interacting with multiple trace elements to pathways known to play a role in glaucoma. The web-based platform provides an easy-to-use and interactive tool, which serves as an information hub facilitating future research work on trace elements in glaucoma.

Respiratory cancer database: An open access database of respiratory cancer gene and miRNA.

AIMS: Respiratory cancer database (RespCanDB) is a genomic and proteomic database of cancer of respiratory organ. It also includes the information of medicinal plants used for the treatment of various respiratory cancers with structure of its active constituents as well as pharmacological and chemical information of drug associated with various respiratory cancers. MATERIALS AND METHODS: Data in RespCanDB has been manually collected from published research article and from other databases. Data has been integrated using MySQL an object-relational database management system. MySQL manages all data in the back-end and provides commands to retrieve and store the data into the database. The web interface of database has been built in ASP. RESULTS AND CONCLUSIONS: RespCanDB is expected to contribute to the understanding of scientific community regarding respiratory cancer biology as well as developments of new way of diagnosing and treating respiratory cancer. Currently, the database consist the oncogenomic information of lung cancer, laryngeal cancer, and nasopharyngeal cancer. Data for other cancers, such as oral and tracheal cancers, will be added in the near future. The URL of RespCanDB is http://ridb.subdic-bioinformatics-nitrr.in/.

Estradiol affects androgen-binding protein expression and fertilizing ability of spermatozoa in adult male rats.

The estrogenicity of certain environmental pollutants is being increasingly correlated to decline in sperm counts and fertility of the males. Qualitative effects, if any, of estrogen(s) on terminal differentiation of spermatids have been less reported. The present study suggests that exposure to estrogen(s) can also alter the status of condensed chromatin in testicular spermatozoa and reduce their fertilizing potential. A significant reduction was evident in the serum gonadotropins, testosterone, weights of reproductive organs, sperm counts and litters sired by male rats after 10 days of estradiol exposure to a dose of 0.1mg/kg/day. Estradiol treatment led to retardation of in vitro decondensation rates of sperm chromatin, reduction in the uptake of acridine orange dye by chromatin, reduction in susceptibility of chromatin to acid denaturation in vitro, reduced uptake of thiol reactive monobromobimane dye and reduced levels of immunoreactive protamine 1 in caput epididymal sperms. Concomitantly, testicular levels of immunoreactive protamine 1, transition proteins 1/2 and cyclic adenosyl response element modulator-tau (CREMtau) were significantly reduced whilst their mRNA levels were unaffected after estradiol treatment. A significant increase was observed in the testicular mRNA levels of androgen-binding protein (ABP) in estradiol treated sires. An inverse correlation was observed between ABP mRNA levels and uptake of acridine orange by estradiol treated caput sperm chromatin. The results suggest that estradiol-induced increase in ABP mRNA underlies the mechanism(s) involved in the reduction in levels of certain proteins involved in nuclear chromatin condensation during spermiogenesis.

Cyproterone acetate affects protamine gene expression in the testis of adult male rat.

The temporal effects of oral administration of cyproterone acetate (CPA), a progestational androgen receptor blocker, were studied on the fertility of adult male rat sires, at a dose of 20 mg kg-1 day-1 after 15 days of gavage. The treatment reduced the fertility and weights of accessory sex glands, without altering the serum levels of luteinizing hormone, follicle-stimulating hormone (FSH) and testosterone (T). Sperm counts were significantly reduced after treatment. Several changes were evident in caput epididymal sperm chromatin in treated rats. The in vitro decondensation rates of sperm chromatin and total fluorescent acridine orange (AO) dye uptake were enhanced. The fluorescent AO dye uptake by the double- and single-stranded sperm chromatin increased. The uptake of thiol-specific monobromobimane fluorescent dye by sperm chromatin was significantly reduced. Sperm of treated rats exhibited hypoprotamination. Protamine levels in the testis were significantly reduced after treatment. Androgen-binding protein (ABP) expression was significantly reduced in testis after treatment. A slight but significant increase was observed in cyclic AMP immunoexpression in testis after treatment. The expression and levels of transition proteins 1 (TP1) and 2 (TP2) as well as cyclic AMP response element modulator protein-tau were maintained at control levels in the testis of treated rats. The present study reports that androgen receptor occupation by CPA preferentially reduces the levels of spermatidal protamine in testis and spermatozoa involved in nuclear chromatin condensation. It is inferred that ABP could be mediating the effects of T in modulating the sequential expression of TPs and protamines during nuclear chromatin condensation. It is likely that indirect effects of T involve its aromatization in spermatids.

Effects of tamoxifen citrate on gene expression during nuclear chromatin condensation in male rats.

AIM: To evaluate the effects of tamoxifen citrate on gene expression during nuclear chromatin condensation in male rats. METHODS: The effects of an oral dose of 0.4 kg/(kg.d) tamoxifen citrate on rates of in vitro chromatin decondensation, acridine orange (AO) dye uptake, concentration of thiol-groups, levels and/or expression of transition proteins 1, 2 (TP1, TP2), protamine 1 (P1), cyclic AMP response element modulator-tau (CREMtau), androgen-binding protein (ABP) and cyclic adenosine 3',5' monophosphate (cAMP) were evaluated after 60 days of exposure in adult male rats. Controls received the vehicle. RESULTS: Tamoxifen citrate enhanced the rates of chromatin decondensation, increased AO dye uptake and reduced free thiols in caput epididymal sperms and reduced the levels of TP1, TP2, P1, and CREMtau in the testis, while cAMP was unaffected. P1 deposition was absent in the sperm. The transcripts of TP1, TP2 were increased, of P1 and ABP decreased, while those of CREMtau unaffected in the testis. CONCLUSION: Tamoxifen citrate reduced caput epididymal sperm chromatin compaction by reducing the testicular levels of proteins TP1, TP2 and P1 and the CREMtau involved in chromatin condensation during spermiogenesis. Tamoxifen citrate affects the expression of these genes at both the transcriptional and post-transcriptional levels.