Cullin 4A and 4B ubiquitin ligases interact with γ-tubulin and induce its polyubiquitination.

Regulated polyubiquitination is a key step for controlling protein degradation and maintaining proper balance between the proliferation of normal and uncontrolled cells. Addition of ubiquitin to the proteins by E3 ubiquitin ligases targets them for degradation by the 26S proteosome machinery. Discrepancies in ubiquitination and/or proteosome degradation might lead to multiple genetic disorders in humans. It is reported that CUL1 and BRCA1 ubiquitin ligases localize on centrosome region and regulate the centrosome duplication cycle for genomic stability. In the current study, we predicted the possible interaction of E3 ubiquitin ligase CUL4A complex with γ-tubulin, a centrosome-specific protein, using bioinformatic protein-protein docking analysis. We also confirmed their interaction by performing co-immunoprecipitation studies using endogenous CUL4A/B and stable cell lines that overexpress Flag-CUL4A or Flag-CUL4B. We additionally noted that the γ-tubulin was polyubiquitinated by CUL4A or 4B immune complex indicating that CUL4A or CUL4B may regulate the stability of γ-tubulin. Furthermore, the inhibition of proteosomal degradation pathway using MG132 or LLNV drugs resulted in accumulation and co-localization of CUL4A with γ-tubulin in the centrosome region. Overall, our observation has identified γ-tubulin as a novel target for E3 ubiquitin ligase CUL4 complex, and might lead to the establishment of a unique mechanism for controlling centrosome stability.

Evaluation of lupeol-chitosan nanoparticles infused cellulose acetate membranes for enhanced in-vitro anticancer and antidiabetic activities.

This study utilizes the abundance of pharmacologically active compounds found in natural products and concentrates on the promising anticancer agent lupeol (LUP). The limited water solubility and bioavailability of lupeol have limited its therapeutic utility. To test their potential for treating diabetes and cancer, we synthesized lupeol@chitosan (LUP@CS) nanoparticles encapsulated in cellulose acetate (CA) membranes (LUP@CS/CA). Extensive characterization, including Scanning electron microscopy, Thermogravimetric analysis, X-ray photoelectron spectroscopy, and mechanical strength analysis, confirmed the membrane's structural integrity and drug release capacity. Notably, in vitro experiments utilizing A431 human skin cancer cells revealed remarkable anticancer activity, positioning the membrane as a potential novel therapeutic agent for the treatment of skin cancer. Inhibiting carbohydrate-digesting enzymes effectively, as evidenced by IC50 values as low as 54.56 mg/mL, the membrane also exhibited significant antidiabetic potential. These results demonstrate the multifarious potential of the membrane, which offers promise for both the treatment of skin cancer and the management of diabetes, and has significant implications for nano biological applications.

Inhibition of the TIRAP-c-Jun interaction as a therapeutic strategy for AP1-mediated inflammatory responses.

Bacterial endotoxin-induced sepsis causes 30-40% of the deaths in the intensive care unit (ICU) globally, for which there is no pharmacotherapy. Lipopolysaccharide (LPS), a bacterial endotoxin, stimulates the Toll-like receptor (TLR)-4 signalling pathways to upregulate the expression of various inflammatory mediators. Here, we show that the TIRAP and c-Jun protein signalling complex forms in macrophages in response to LPS stimulation, which increases the AP1 transcriptional activity, thereby amplifying the expression of inflammatory mediators. Using a computer-aided molecular docking platform, we identified gefitinib as a putative inhibitor of the TIRAP-c-Jun signalling complex. Further, we demonstrated the ability of gefitinib to inhibit the interaction of TIRAP-c-Jun with in vitro experiments and with a mouse model of sepsis. Importantly, pre-treatment with gefitinib increased the survival of the mice that received a lethal dose of LPS compared to that of the controls. These findings verify the ability of gefitinib to directly disrupt the interaction of TIRAP and c-Jun, thereby inhibiting a major inflammatory response that is often observed in patients experiencing sepsis.

Heterotrimeric complex of p38 MAPK, PKCδ, and TIRAP is required for AP1 mediated inflammatory response.

Inflammation could be described as a physiological response of the body to tissue injury, pathogen invasion, and irritants. During the inflammatory phase, cells of both the innate as well as adaptive immune system are activated and recruited to the site of inflammation. These mediators are downstream targets for the transcription factors; activator protein-1 (AP1), nuclear factor kappa-light-chain-enhancer (NF-κB), signal transducers and activators of transcription factors (STAT1), as well as interferon regulatory factors (IRFs), which control the expression of most immunomodulatory genes. There is a significant increase in active p38 mitogen-activated protein kinase (p38MAK) immediately after lipopolysaccharide (LPS) stimulation, which results in the activation of AP-1 transcription factor and expression of proinflammatory cytokines, IL-12 and IL-23. We studied the novel mechanism of p38 MAPK activation through the formation of a heterotrimeric complex of Protein kinase C delta type (PKCδ), Toll-Interleukin 1 Receptor (TIR) Domain Containing Adaptor Protein (TIRAP), and p38 proteins. TIRAP serves as an adaptor molecule which brings PKCδ and p38 in close proximity. The complex facilitates the activation of p38MAPK by PKCδ. Therefore, we propose that disruption of the heterotrimeric complex may be a good strategy to dampen the inflammatory response. Structure-based design of small molecules or peptides targetting PKCδ-TIRAP or TIRAP-p38 interfaces would be beneficial for therapy in AP1 mediated inflammatory diseases.

Structural insights into tumor-specific chaperoning activity of gamma synuclein in protecting estrogen receptor alpha 36 and its role in tamoxifen resistance in breast cancer.

Gamma synuclein (γSyn), a tumor-specific molecular chaperone, protects Hsp90 client proteins like ERα36 and stimulates rapid membrane-initiated estrogen signalling in breast cancer cells. However, the structural perspectives of this tumor-specific chaperone function of γSyn remains unclear. Hence, in this present work, we studied the conformational dynamics of ERα36 in the absence and presence of Hsp90 and γSyn. Results indicate that in a chaperone-free state, ERα36 undergoes an inter-domain movement and exposes the hydrophobic patch of residues that are responsible for binding with ubiquitin. However, independent of Hsp90, γSyn, by establishing transient interactions, prevents interdomain movement, unveils the co-activator binding groove, masks the ubiquitin-binding residues and maintains 'open' pocket conformation of LBD. By doing so, γSyn effectively protects ERα36 from degradation and maintains its functional state like Hsp90 based chaperoning machinery but independent of ATP. Our studies also show that the γSyn protected conformation of ERα36 can effectively bind with both estradiol (E2) and 4-hydroxy tamoxifen (4-OHT). Although they exhibit unique binding modes, they maintained the functionally active conformation of ERα36. Interestingly, the molecular dynamics simulation studies showed that 4-OHT, like γSyn, prevented the interdomain movements, primes the co-activator binding groove of ERα36 for complexation with downstream signalling proteins and this mechanism explains its agonist activity and associated anti-estrogen resistance observed in the presence of ERα36. The observed differences in the chaperoning mechanism of γSyn sheds light on its selectivity over Hsp90 in cancer cells, for promoting rapid protection of crucial oncogenic proteins. Based on our findings, we speculate that the compounds, which can hamper association of γSyn with ERα36 and/or can arrest ERα36 in an ubiquitin binding state, would be promising alternatives for treating ERα36 expressed breast carcinomas.

Structural perspective of ARHI mediated inhibition of STAT3 signaling: an insight into the inactive to active transition of ARHI and its interaction with STAT3 and importinß.

ARHI, a putative tumor suppressor protein with unique 32 amino acid extension in the N-terminal region, differs from oncogenes Ras and Rap, negatively regulates STAT3 signaling and inhibits the migration of ovarian cancer cells. ARHI associates directly with STAT3, also forms complex with importinß, and prevents formation of RanGTPase-importinß complex, which is essential for transporting STAT3 into the nucleus. Hence, the structural aspects pertaining to ARHI mediated inhibition of STAT3 translocation can provide hints on the regulation of STAT3 signaling mechanism. Accordingly, in the present study, the structure of ARHI was predicted and its transition from inactive to active state studied using MD simulations and free energy landscape analysis. The transition of ARHI is marked by the movement of switch I region towards γ-phosphate of GTP, in addition, the hydrophobic interaction between N-terminal helix and switch II region of ARHI accounts for its low intrinsic GTPase activity. Further, the protein-protein interaction studies reveal that the residues of N-terminal helix, effector domain, P-loop and G box motif of ARHI actively form polar and non-polar interaction with NTD of STAT3 and make them compact thereby rendering STAT3 inaccessible for Ran-importinß mediated translocation. On the other hand, ARHI competes with RanGTPase and interacts with importinß via basic-acidic patch interaction, which leads to inhibition of STAT3 translocation. The interacting residues involved for this structural mechanism would be instrumental in designing inhibitors for STAT3, which mimics ARHI thereby leading to the suppression of cancer cell growth.

Molecular dynamic simulations of the tubulin-human gamma synuclein complex: structural insight into the regulatory mechanism involved in inducing resistance against Taxol.

Members of the synuclein family (α, ß and γ synucleins) are intrinsically disordered in nature and play a crucial role in the progression of various neurodegenerative disorders and cancers. The association of γSyn with both BubR1 as well as microtubule subunits renders resistance against various anti-cancer drugs. However, the structural aspects underlying drug resistance have not been explored. In this study, the mechanism involved in the association between γSyn and microtubule subunits (αßTub) was investigated and the results reveal a strong interaction between γSyn and the tail regions of αßTub. Complexation of γSyn induces conformational rearrangements in the nucleotide binding loops (NBL), interdomain and tail regions of both α and ßTub. Moreover, in ßTub, the massive displacement observed in M and S loops significantly alters the binding site of microtubule targeting drugs like Taxol. The resulting weak association between Taxol and ßTub of the γSyn-αßTub complex was confirmed by molecular dynamic simulation studies. In addition, the effect of Taxol on NBL, M and S loops of αßTub, is reversed in the presence of γSyn. These results clearly indicate that the presence of γSyn annulled the allosteric regulation imposed by Taxol on the αßTub complex as well as preventing the binding of microtubule targeting drugs, which eventually leads to the development of resistance against these drugs in cancer cells.

Structural insights into interacting mechanism of ID1 protein with an antagonist ID1/3-PA7 and agonist ETS-1 in treatment of ovarian cancer: molecular docking and dynamics studies.

Among the many abnormally expressed proteins in ovarian cancer, the prominent cancer in women, ID1 (inhibitors of DNA binding protein 1) is a potential one among other several targets. Interaction of ID1 with ETS-1 (transcriptional activator of p16(INK4a)) suppresses the transcription of p16(INK4a) and causes abnormal cell proliferation. A peptide aptamer (ID1/3-PA7) has been designed to prevent this interaction and thereby leading to the transcription of p16(INK4a). However, the structural basis behind the molecular interaction of ID1 with ETS-1 (agonist) and ID1/3-PA7 (antagonist) is poorly understood. In order to understand this structural recognition and their interaction mechanism, in silico methods were used. From this interaction analysis, the residues of ETS-1 involved in interaction with the p16(INK4a) promoter were found to be targeted by ID1. Subsequently, ETS-1 binding residues of ID1 were found to be targeted by its aptamer- ID1/3-PA7. These results suggest that both ETS-1 and ID1/3-PA7 binds at the same region harbored by the residues-H97, D100, R103, D104, L107, A144, C145, D149, D150 and C154 of ID1. All these observations correlate with the experimental reports, suggesting that the identified residues might play a crucial role in promulgating the oncogenic effects of ID1. In silico alanine scanning mutagenesis also confirms the role of identified hot spot residues in p16(INK4a) regulation. Finally, the molecular dynamic simulation studies reveal the prolonged stability of the aforementioned interacting complexes. The obtained results throw light on the structure and residues of ID1 involved in transcriptional regulation of p16(INK4a).

Molecular dynamics simulation of the Staphylococcus aureus YsxC protein: molecular insights into ribosome assembly and allosteric inhibition of the protein.

YsxC from Staphylococcus aureus is a member of the GTPase protein family, and is involved in the ribosomal assembly and stability of this microorganism through its interactions with the L17, S2 and S10 ribosomal proteins. Inhibition of its interactions with L17, S2, S10 and the ß' subunit of RNA polymerase influences ribosomal assembly, which may affect the growth of the microorganism. This makes YsxC a novel target for the design of inhibitors to treat the disease caused by S. aureus. Understanding the interaction mechanism between YsxC and its partners would aid in the identification of potential catalytic residues, which could then be targeted to inhibit its function. Accordingly, in the present study, an in silico analysis of the interactions between YsxC and L17, S2 and S10 was performed, and the potential residues involved in these interactions were identified. Based on the simulation results, a possible mechanism for the interactions between these proteins was also proposed. Finally, six ligands from among a library of 81,000 chemical molecules were found to interact with parts of the G2 and switch II regions of the YsxC protein. Moreover, their interactions with the YsxC protein were observed to provoke changes at its GTP-binding site, which suggests that the binding of these ligands leads to a reduction in GTPase activity, and they were also found to affect the interactions of YsxC with its partners. This observation indicates that the proposed interacting site of YsxC may act as an allosteric site, and disrupting interactions at this site might lead to novel allosteric inhibition of the YsxC protein.