Computational analysis of target genes in monkeypox virus infection and potential therapeutic precursors.

BACKGROUND: Monkeypox is an orthopoxvirus that is responsible for zoonotic infections in humans. The virus has recently spread rapidly and the WHO has listed it as an international public health emergency of concern. RESEARCH DESIGN AND METHODS: Here, we used network analysis and gene enrichment protocols and analyzed datasets of MPXV infection that induced host cell gene expression list and subsequently mapped them against two herbal target gene lists which highlighted considerable coherence in pharmacological attributes with COVID-19. Molecular docking and simulation were performed for the screened compounds. RESULTS: Our results identified ß-carotene and kaempferol possessing tremendous ability against the MPXV PLD protein. Both compounds were subjected to each of 100 ns molecular dynamics simulation and were found native to the PLD pocket. MM-PB (GB) SA analyses indicated -25.4, -40.1 kcal/mol and -17.2, -26.4kcal/mol of ΔGbind to the active pocket of PLD. Our data suggest the adaptive nature of the MPXV PLD active pocket toward hydrophobic inhibitors. CONCLUSION: These results will be of high importance for the viral researchers to be tested in wet lab settings in designing potential inhibitors.

Androgen receptor, a possible anti-infective therapy target and a potent immune respondent in SARS-CoV-2 spike binding: a computational approach.

BACKGROUND: Although androgen in gender disparity of COVID-19 has been implied, no direct link has been provided. RESEARCH DESIGN AND METHODS: Here, we applied AlphaFold multimer, network and single cells database analyses to highlight specificity of Androgen receptor (AR) against spike receptor binding protein (RBD) of SARS-CoV-2. RESULTS: LXXL motifs in spike RBD are essential for AR binding. RBD LXXA mutation complex with the AR depicting slightly reduced binding energy, as LXXLL motif usually mediates nuclear receptor binding to coregulators. Moreover, AR preferred to bind a LYRL motif in specificity and interaction interface, and showed reduced affinity against Omicron compared to other variants (alpha, beta, gamma, and delta). Importantly, RBD LYRL motif is a conserved antigenic epitope (9 residues) for T-cell response. Network analysis of AR-related genes against COVID-19 database showed T-cell signaling regulation, and CD8+ T-cell spatial location in AR+ single cells, which is consistent with the AR binding motif LYRL in epitope function. CONCLUSIONS: We provided the potent mechanisms of AR binding to RBD linking to immune response and vaccination shift. AR could be an anti-infective therapy target for anti-Omicron new lineages.

Andrographolide prevents bone loss via targeting estrogen-related receptor-α-regulated metabolic adaption of osteoclastogenesis.

BACKGROUND AND PURPOSE: Metabolic adaptation driven by oestrogen-related receptor-α (ERRα/NR3B1) is required to meet the increased energy demand during osteoclast differentiation. Here, we hypothesize that natural product, andrographolide, acts as an ERRα inverse agonist to inhibit osteoclastogenesis. EXPERIMENTAL APPROACH: Virtual docking and site-directed mutagenesis analysis were employed to study the binding mode of andrographolide to ERRα. Co-immunoprecipitation, luciferase reporter assay, real-time polymerase chain reaction (PCR) and immunoblot analyses were performed to identify andrographolide as an ERRα inverse agonist. The pharmacological effects of andrographolide in vivo were assessed in mice models of osteopenia induced by either a high-fat diet in male or ovariectomy in female mice. KEY RESULTS: ERRα-dependent expression of glutaminase, a rate-limiting enzyme of mitochondrial glutamine anaplerosis, is required for ex vivo bone marrow osteoclast differentiation. Andrographolide inhibited glutaminase expression induced by ERRα and co-activator peroxisome proliferator-activated receptor γ co-activator-1ß (PGC-1ß), leading to reduction in osteoclastogenesis. Andrographolide acted as an inverse agonist of ERRα by disrupting its interaction with co-activator PGC-1ß. Phenylalanine 232, valine 395 and phenylalanine 399 of ERRα ligand-binding domain were confirmed to be essential for this effect. In contrast, glutaminase overexpression restored the impairment triggered by andrographolide. Accordingly, andrographolide suppressed osteoclastic bone resorption and attenuated bone loss in vivo. CONCLUSIONS AND IMPLICATIONS: These findings demonstrate that andrographolide acts as an ERRα inverse agonist for perturbation of ERRα/PGC-1ß/glutaminase axis-driven metabolic adaption during osteoclast differentiation, implying that andrographolide may be a promising natural compound for preventing physiological and pathological bone loss.

Dynamics and conformational propensities of staphylococcal CntA.

Enzymes use transition metals as co-factors for catalytic roles in biological processes. Notably, manganese, iron, cobalt, nickel, copper and zinc are abundantly used. Staphylococcus aureus, a commensal bacterium asymptomatically, lies on the human body causing variety of infections. S. aureus is equipped by advanced virulence-regulatory circuits of metal acquisition like Cnt that acquires metals at infection sites by utilizing a nicotianamine-like metallophore staphylopine. Despite significant growth in structural studies, how CntA of Cnt system transmits conformational signal upon staphylopine recognition remains elusive. Here, we analyzed the structural changes adopted by CntA during close-to-open transition by computational approaches. CntA uses a bi-domain architectural form of domain II which performed 37° rigid body rotation and 1.1 Å translation assisted by inter-domain hinge cluster residues. Important clustered communities were found regulating the conformational changes in CntA where communities 4 and 5 are found crucial. Besides open and close states, the fluctuating regions sampled two additional intermediate states which were considered close or open previously. CntA prefers fluctuating the non-conserved regions rather than conserved where domain II turned out to be rigid and maintains a stable fold. Overall, the CntA system is a potential target for structural biologist to hamper such conformational behaviors at family level.Communicated by Ramaswamy H. Sarma.

Two-component systems regulate ABC transporters in antimicrobial peptide production, immunity and resistance.

Bacteria offer resistance to a broad range of antibiotics by activating their export channels of ATP-binding cassette transporters. These transporters perform a central role in vital processes of self-immunity, antibiotic transport and resistance. The majority of ATP-binding cassette transporters are capable of detecting the presence of antibiotics in an external vicinity and are tightly regulated by two-component systems. The presence of an extracellular loop and an adjacent location of both the transporter and two-component system offers serious assistance to induce a quick and specific response against antibiotics. Both systems have demonstrated their ability of sensing such agents, however, the exact mechanism is not yet fully established. This review highlighted the three key functions of antibiotic resistance, transport and self-immunity of ATP-binding cassette transporters and an adjacent two-component regulatory system.

Histone acetyl transferase GCN5 promotes human hepatocellular carcinoma progression by enhancing AIB1 expression.

BACKGROUND: General control non-depressible 5 (GCN5) is a crucial catalytic component of a transcriptional regulatory complex that plays important roles in cellular functions from cell cycle regulation to DNA damage repair. Although GCN5 has recently been implicated in certain oncogenic roles, its role in liver cancer progression remains vague. RESULTS: In this study, we report that GCN5 was overexpressed in 17 (54.8 %) of 31 human hepatocellular carcinoma (HCC) specimens. Down-regulation of GCN5 inhibited HCC cell proliferation and xenograft tumor formation. GCN5 knockdown decreased the protein levels of the proliferation marker proliferating cell nuclear antigen (PCNA) and amplified in breast cancer 1 (AIB1), but increased the protein levels of cell cycle inhibitor p21(Cip1/Waf1) in HepG2 cells. GCN5 regulated AIB1 expression, at least in part, by cooperating with E2F1 to enhance AIB1 transcription. Consistently, GCN5 expression was positively correlated with AIB1 expression in human HCC specimens in two GEO profile datasets. CONCLUSION: Since AIB1 plays a promoting role in HCC progression, our results propose that GCN5 promotes HCC progression at least partially by regulating AIB1 expression. This study implicates that GCN5 might be a potential molecular target for HCC diagnosis and treatment.

Amplified in breast cancer 1 promotes colorectal cancer progression through enhancing notch signaling.

Aberrant activation of Notch signaling has an essential role in colorectal cancer (CRC) progression. Amplified in breast cancer 1 (AIB1), also known as steroid receptor coactivator 3 or NCOA3, is a transcriptional coactivator that promotes cancer cell proliferation and invasiveness. However, AIB1 implication in CRC progression through enhancing Notch signaling is unknown. In this study, we found that several CRC cell lines expressed high levels of AIB1, and knockdown of AIB1 decreased cell proliferation, colony formation and tumorigenesis of these CRC cells. Specifically, knockdown of AIB1 inhibited cell cycle progression at G1 phase by decreasing the mRNA levels of cyclin A2, cyclin B1, cyclin E2 and hairy and enhancer of split (Hes) 1. Furthermore, AIB1 interacted with Notch intracellular domain and Mastermind-like 1 and was recruited to the Hes1 promoter to enhance Notch signaling. Downregulation of AIB1 also decreased CRC cell invasiveness in vitro and lung metastasis in vivo. Besides that, knockout of AIB1 in mice inhibited colon carcinogenesis induced by azoxymethane/dextran sodium sulfate treatment. The mRNA levels of cyclin B1 and Hes5 were downregulated, but p27, ATOH1 and MUC2 were upregulated in the colon tumors from AIB1-deficient mice compared with those from wild-type mice. Thus, our results signify the importance of AIB1 in CRC and demonstrate that AIB1 promotes CRC progression at least in part through enhancing Notch signaling, suggesting that AIB1 is a potential molecular target for CRC treatment.

Deficiency in steroid receptor coactivator 3 enhances cytokine production in IgE-stimulated mast cells and passive systemic anaphylaxis in mice.

BACKGROUND: Steroid receptor coactivator 3 (SRC-3) is a multifunctional protein that plays an important role in malignancy of several cancers and in regulation of bacterial LPS-induced inflammation. However, the involvement of SRC-3 in allergic response remains unclear. Herein we used passive systemic anaphylaxis (PSA) and passive cutaneous anaphylaxis (PCA) mouse models to assess the role of SRC-3 in allergic response. RESULTS: SRC-3-deficient mice exhibited more severe allergic response as demonstrated by a significant drop in body temperature and a delayed recovery period compared to wild-type mice in PSA mouse model, whereas no significant difference was observed between two kinds of mice in PCA mouse models. Mast cells play a pivotal role in IgE-mediated allergic response. Antigen-induced aggregation of IgE receptor (FcϵRI) on the surface of mast cell activates a cascade of signaling events leading to the degranulation and cytokine production in mast cells. SRC-3-deficient bone marrow derived mast cells (BMMCs) developed normally but secreted more proinflammatory cytokines such as TNF-α and IL-6 than wild-type cells after antigen stimulation, whereas there was no significant difference in degranulation between two kinds of mast cells. Further studies showed that SRC-3 inhibited the activation of nuclear factor NF-κB pathway and MAPKs including extracellular signal-regulated kinase (ERK), c-jun N-terminal kinase (JNK), and p38 in antigen-stimulated mast cells. CONCLUSIONS: Our data demonstrate that SRC-3 suppresses cytokine production in antigen-stimulated mast cells as well as PSA in mice at least in part through inhibiting NF-κB and MAPK signaling pathways. Therefore, SRC-3 plays a protective role in PSA and it may become a drug target for anaphylactic diseases.