Thalidomide-based inhibitor for TNF-α: designing and Insilico evaluation

Background Inflammatory diseases are the vast array of disorders caused by inflammation. During most inflammatory events, many cytokines expressions were modulated, and one such cytokine is tumor necrosis factor-alpha (TNF-α). TNF-α is mainly secreted by monocytes and macrophages. Notably, it has been proposed as a therapeutic target for several diseases. The anti-TNF biology approach is mainly based on monoclonal antibodies. The fusion protein and biosimilars are prevalent in treating inflammation for decades. Only a few small molecule inhibitors are available to inhibit the expression of TNF-α, and one such promising drug was thalidomide. Therefore, the study was carried out to design thalidomide-based small molecule inhibitors for TNF-α. The main objective of our study is to design thalidomide analogs to inhibit TNF-α using the insilico approach. Results Several thalidomide analogs were designed using chemsketch. After filtration of compounds through ‘Lipinski rule of 5’ by Molinspiration tool, as a result, five compounds were selected. All these compounds were subjected to molecular docking, and the study showed that all five compounds had good binding energy. However, based on ADMET predictions, two compounds (S3 and S5) were eliminated. Conclusions Our preliminary results suggest that S1, S2, S4 compounds showed potential ligand binding capacity with TNF-α and, interestingly, with limited or no toxicity. Our preliminary investigation and obtained results have fashioned more interest for further in vitro studies.

Delineation of colorectal cancer ligand-receptor interactions and their roles in the tumor microenvironment and prognosis

Background Immunotherapies targeting ligand-receptor interactions (LRIs) are advancing rapidly in the treatment of colorectal cancer (CRC), and LRIs also affect many aspects of CRC development. However, the pattern of LRIs in CRC and their effect on tumor microenvironment and clinical value are still unclear. Methods We delineated the pattern of LRIs in 55,539 single-cell RNA sequencing (scRNA-seq) samples from 29 patients with CRC and three bulk RNA-seq datasets containing data from 1411 CRC patients. Then the influence of tumor microenvironment, immunotherapy and prognosis of CRC patients were comprehensively investigated. Results We calculated the strength of 1893 ligand-receptor pairs between 25 cell types to reconstruct the spatial structure of CRC. We identified tumor subtypes based on LRIs, revealed the relationship between the subtypes and immunotherapy efficacy and explored the ligand-receptor pairs and specific targets affecting the abundance of tumor-infiltrating lymphocytes. Finally, a prognostic model based on ligand-receptor pairs was constructed and validated. Conclusion Overall, through the comprehensive and in-depth investigation of the existing ligand-receptor pairs, this study provides new ideas for CRC subtype classification, a new risk screening tool for CRC patients, and potential ligand-receptor pair targets and pathways for CRC therapy.

Proteome wide screening for identification of putative drug target gene in Nautella italica and structure-based ligand screening for therapeutic candidates

In silico based subtractive genomic approaches were employed to identify the key drug targets for an opportunistic pathogen Nautella italica, a member of the marine Roseobacter clade that causes bleaching disease in the temperate-marine red macro algae, Delisea pulchra. The aim of this study is to propose new active ligands against bleaching disease seen in algae. Using comparative and subtractive genomic approach, a set of 21 proteins were identified as the therapeutic drug target proteins for algal bleaching. This core set of drug targets has been analyzed for network topology using string network analysis and major hub gene identified by CytoHubba was rpoB (DNA directed RNA Polymerase subunit beta). The three-dimensional structure of rpoB was built by comparative modelling and used to perform a virtual screening of Zinc database by DOCK Blaster server. The 50 top scored compounds were screened for toxicity analysis by OSIRIS Data Warrior and ECOSAR tool. Further refinement by autodock program revealed two compounds ZINC49821385 and ZINC97218938 with the best binding energy of -7.07 and -6.79 respectively. These results indicated that 5-(4- isopropylphenyl)furan-2-carboxamide (ZINC ID 49821385) could be one of the potential ligand to treat bleaching disease in algae.

Identification of Iron-Sulfur (Fe-S) and Zn-binding Sites Within Proteomes Predicted by DeepMind′s AlphaFold2 Program Dramatically Expands the Metalloproteome

DeepMind′s AlphaFold2 software has ushered in a revolution in high quality, 3D protein structure prediction. In very recent work by the DeepMind team, structure predictions have been made for entire proteomes of twenty-one organisms, with >360,000 structures made available for download. Here we show that thousands of novel binding sites for iron-sulfur (Fe-S) clusters and zinc ions can be identified within these predicted structures by exhaustive enumeration of all potential ligand-binding orientations. We demonstrate that AlphaFold2 routinely makes highly specific predictions of ligand binding sites: for example, binding sites that are comprised exclusively of four cysteine sidechains fall into three clusters, representing binding sites for 4Fe-4S clusters, 2Fe-2S clusters, or individual Zn ions. We show further: (a) that the majority of known Fe-S cluster and Zn-binding sites documented in UniProt are recovered by the AlphaFold2 structures, (b) that there are occasional disputes between AlphaFold2 and UniProt with AlphaFold2 predicting highly plausible alternative binding sites, (c) that the Fe-S cluster binding sites that we identify in E. coli agree well with previous bioinformatics predictions, (d) that cysteines predicted here to be part of Fe-S cluster or Zn-binding sites show little overlap with those shown via chemoproteomics techniques to be highly reactive, and (e) that AlphaFold2 occasionally appears to build erroneous disulfide bonds between cysteines that should instead coordinate a ligand. These results suggest that AlphaFold2 could be an important tool for the functional annotation of proteomes, and the methodology presented here is likely to be useful for predicting other ligand-binding sites.

Structural Investigations on the SH3b Domains of Clostridium perfringens Autolysin through NMR Spectroscopy and Structure Simulation Enlighten the Cell Wall Binding Function

Clostridium perfringens autolysin (CpAcp) is a peptidoglycan hydrolase associated with cell separation, division, and growth. It consists of a signal peptide, ten SH3b domains, and a catalytic domain. The structure and function mechanisms of the ten SH3bs related to cell wall peptidoglycan binding remain unclear. Here, the structures of CpAcp SH3bs were studied through NMR spectroscopy and structural simulation. The NMR structure of SH3b6 was determined at first, which adopts a typical β-barrel fold and has three potential ligand-binding pockets. The largest pocket containing eight conserved residues was suggested to bind with peptide ligand in a novel model. The structures of the other nine SH3bs were subsequently predicted to have a fold similar to SH3b6. Their ligand pockets are largely similar to those of SH3b6, although with varied size and morphology, except that SH3b1/2 display a third pocket markedly different from those in other SH3bs. Thus, it was supposed that SH3b3-10 possess similar ligand-binding ability, while SH3b1/2 have a different specificity and additional binding site for ligand. As an entirety, ten SH3bs confer a capacity for alternatively binding to various peptidoglycan sites in the cell wall. This study presents an initial insight into the structure and potential function of CpAcp SH3bs.

MUTATIONAL CONSERVATION, EVOLUTIONARY AND FUNCTIONAL UNDERSTANDING OF PROTO-ONCOGENE c-FOS

c-Fos protein has a function in different types of cancers and is expressed mostly in neurons. It is a human homolog of the viral oncogene. c-Fos is a member of the FOS gene family, these genes interact with the JUN family member to form transcription factors and play a major role in neurons cell development. These genes were also used as an early marker, in neuronal cells to determine early growth and functional features of the neuroendocrine system. Losses in gene function due to mutation leads to neuronal death and have a function in apoptosis. This study has performed mutational conservation in the c-Fos gene across different species. the c-Fos protein sequence was retrieved from the UniProt database (P01100). Total forty nine (49) homologous sequences with the c-Fos protein sequence were identified using the BLASTp tool. Multiple sequence alignment (MSA) and phylogenetic tree construction was done using the MEGA tool. The phylogenetic tree shows that the c-Fos protein of Homosapiens was closely related to Pan troglodytes. UPGMA tree also shows the evolutionary relationship between c-Fos proteins and with the other 49 species included in the dataset. Evolutionary study shows that Myotis species was the common evolutionary species and predicted as root for all other species hence c-Fos gene might have an evolutionary link with these species. Myotis are the most wide diverged species and belongs to the genus of bats. This study highlights the similarity and evolutionary relationship of the c-Fos gene. In this research detailed analysis of evolutionary analysis, PPI, GO, Disease Enrichment was done to understand the functional and evolutionary aspects of c-FOS protein. This study identifies the evolutionary relationship, protein-protein interaction and pathway enrichment of the c-FOS protein. This research can be further extended to include ligand screening and identification of potential ligand against c-FOS protein for drug development and discovery.

3-hydroxykynurenine as a Potential Ligand for Hsp70 Proteins and its Effects on Drosophila Memory After Heat Shock

Kynurenine products of tryptophan metabolism are modifiers of the nervous activity and oxidative processes in mammals and invertebrates. 3-hydroxykynurenine (3HOK) in moderate concentrations is a lipid peroxidation inhibitor. However, its accumulation and oxidative auto dimerization lead to oxidative stress development manifested in age-related neurodegenerative diseases (NDDs) and neurologic disorders provoked by acute stress. Different forms of stress, the mostly studied being heat shock response, rely on functioning of heat shock proteins of Hsp70 superfamily. Since kynurenines are called “kids of stress”, we performed computational estimation of affinity of 3HOK and other kynurenines binding to predicted ATP site of Drosophila Hsp70 cognate 71 protein (Dhsp71) using Autodock Vina. The binding energy of 3HOK dimer is -9.4 kcal/mol, its orientation within the active site is close to that of ATP. This might be a new mechanism of producing a competitive inhibitor of Hsp70 chaperones that decreases organism ability to adapt to heat shock. We also showed that the Drosophila melanogaster cardinal (cd1) mutant with 3HOK excess, serving as a model for Huntington's disease (HD), manifests severe defects of short-term memory after heat shock applied either in adults, or at the prepupal stage.

Repurposing statins as a potential ligand for estrogen receptor alpha via molecular docking

Computational drug repurposing is the strategy for drug development which remarkably reduces the cost and development time. Research suggests that breast cancer development in women have been associated with cholesterol and its transporters. Cholesterol lowering drugs can be repurposed as potential therapeutic agents to prevent high cholesterol in estrogen receptor positive- breast cancer. The objective of this study was to carryout in-silico molecular docking of HMG-CoA reductase inhibitors (statins) with estrogen α receptor (3ERT) to repurpose the statins as breast cancer inhibitors. Molecular docking studies were performed to explore the mechanism of interactions between the statins and human estrogen α receptor. Docking results revealed that statins bind to the hydrophobic pocket of the estrogen α receptor with high binding affinity. The docking scores were compared with the standard drug 4- hydroxy tamoxifen. The study helped to compare the interactions amongst different statins with the receptor and the energy values produced were ranging from -8.5 to -5.5 kcal/mol. Molinspiration web servers was used to calculate the physiochemical properties and ADMET of the statins. Simvastatin showed better interaction amongst the docked statins with best protein ligand interactions, it was found to exhibit higher docking score of -8.5 kcal/mol. Therefore, we conclude that statins can be employed as an alternative drug for treatment of breast cancer.

Identification of 35 C-Type Lectins in the Oriental Armyworm, Mythimna separata (Walker)

Insect C-type lectins (CTLs) play vital roles in modulating humoral and cellular immune responses. The oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae) is a migratory pest that causes significant economic loss in agriculture. CTLs have not yet been systematically identified in M. separata. In this study, we first constructed a transcriptome of M. separata larvae, generating a total of 45,888 unigenes with an average length of 910 bp. Unigenes were functionally annotated in six databases: NR, GO, KEGG, Pfam, eggNOG, and Swiss-Prot. Unigenes were enriched in functional pathways, such as those of signal transduction, endocrine system, cellular community, and immune system. Thirty-five unigenes encoding C-type lectins were identified, including CTL-S1~CTL-S6 (single CRD) and IML-1~IML-29 (dual CRD). Phylogenetic analyses showed dramatic lineage-specific expansions of IMLs. Sequence alignment and structural modeling identified potential ligand-interacting residues. Real-time qPCR revealed that CTL-Ss mainly express in eggs and early stage larvae, while IMLs mainly express in mid-late-stage larvae, pupae, and adults. In naïve larvae, hemocytes, fat body, and epidermis are the major tissues that express CTLs. In larvae challenged by Escherichia coli, Staphylococcus aureus, or Beauveria bassiana, the expression of different CTLs was stimulated in hemocytes, fat body and midgut. The present study will help further explore functions of M. separata CTLs.