Protein Inhibitor Research Articles

Computational Study of Designed Peptide Analogs against Pseudomonas aeruginosa as a Possible Inhibitor of LptD Membrane Protein

Background: Pseudomonas aeruginosa is a common cause of nosocomial infection worldwide and is responsible for 18-61% of deaths alone. The organism has gained resistance to many known antibiotics and evolved into a multidrug-resistant strain. The LptD outer membrane protein of P. aeruginosa is a special target of interest due to its role in outer membrane biogenesis. Objective: The study aimed to gain an insight into how mutations affect the overall properties of antimicrobial peptides and to identify novel peptide analogs against P. aeruginosa. Methods: The peptide analogs were designed and shortlisted based on physicochemical parameters and estimated free energy change in the current study. The docking studies for wild type and shortlisted peptides were performed against LptD protein of P. aeruginosa. The toxicity, allergenicity, and solubility analyses of peptide analogs with high binding affinity to LptD were also conducted. Results: The molecular docking results indicated that peptide analogs 523M26, 523M29, 523M34, and 523M35 for AP00523 (wild type); 608M12, 608M13, 608M19, 608M31, 608M32, 608M39, and 608M43 for AP00608 (wild type); and 2858M25 for AP02858 (wild type) bound effectively with LptD membrane than their wild types. The toxicity, allergenicity, and solubility analyses revealed all these peptide analogs to be nontoxic, non-allergen, and have good water solubility. Conclusion: The binding energies predicted 523M26, 608M39, and 2858M25 bind effectively to LptD proteins than their wild type. Based on docking analysis, it was further predicted that 608M39 has an estimated binding affinity greater than L27-11, which is a known peptidomimetic inhibitor of the LptD protein.

Cardiac Surgery-Associated Acute Kidney Injury.

AKI is a common and serious complication of cardiac surgery that has a significant impact on patient morbidity and mortality. The Kidney Disease Improving Global Outcomes definition of AKI is widely used to classify and identify AKI associated with cardiac surgery (cardiac surgery-associated AKI [CSA-AKI]) on the basis of changes in serum creatinine and/or urine output. There are various preoperative, intraoperative, and postoperative risk factors for the development of CSA-AKI which should be recognized and addressed as early as possible to expedite its diagnosis, reduce its occurrence, and prevent or ameliorate its devastating complications. Crucial issues are the inaccuracy of serum creatinine as a surrogate parameter of kidney function in the perioperative setting of cardiothoracic surgery and the necessity to discover more representative markers of the pathophysiology of AKI. However, except for the tissue inhibitor of metalloproteinase-2 and insulin-like growth factor binding protein 7 ratio, other diagnostic biomarkers with an acceptable sensitivity and specificity are still lacking. This article provides a comprehensive review of various aspects of CSA-AKI, including pathogenesis, risk factors, diagnosis, biomarkers, classification, prevention, and treatment management.

Abstract 3132: Examining The Role Of The Lung Endothelial Cell Anti-apoptotic Protein C-iap2 In Schistosomiasis-associated Pulmonary Hypertension

Introduction: Schistosomiasis-associated Pulmonary Hypertension (Sch-PH) is the most common form of group I PH worldwide and remains with no targeted therapy. Previously, we observed that the loss of the anti-inflammatory protein caveolin-1 (Cav-1) in lung endothelial cells (EC) contributed to the survival of the abnormal EC phenotype in Sch-PH. Abnormal cell survival has been associated with some members of the inhibitor of apoptosis protein (IAP) family, but their role in Sch-PH is unknown. Hypothesis: The major etiological agent of Sch-PH, i.e., S. mansoni , may contribute to the abnormal lung EC phenotype via altered IAP family expression, specifically the inducible member c-IAP2. Methods/Methods: To test this hypothesis, we first quantified constitutive c-IAP1 and inducible c-IAP2 expression on lung samples from male and female control and pre-clinical S. mansoni egg-exposed mice (240 eggs/gram body weight intraperitoneally followed by intravenous injection of 175 eggs/gram body weight). Then, the specific contribution of EC-c-IAP2 expression to the progression of the disease was evaluated in our new mouse model ( Cdh5.CreERT2;cIAP1 -/- ,cIAP2 fl/fl - Cdh5.CreERT2;cIAP1 +/- ,cIAP2 +/fl ). EC- Cav1 -/- mice were also evaluated to test the contribution of EC-Cav-1 to lung c-IAP2 expression. Results/Discussion: Western blot and immunohistochemistry analysis revealed a reduction in c-IAP2 expression in the whole lung tissue of S. mansoni egg-exposed mice compared to controls (1.21 ± 0.12; 0.88 ± 0.06, control and egg-exposed mice respectively; p<0.05; n=6). No difference was observed in c-IAP1 expression. Preliminary data indicate that genetic ablation of c-IAP2 in EC heterozygous mice promoted a mild increase in microvascular thickness and area in Masson’s Trichrome -stained lung sections. Consistent with our previous findings, c-IAP2 expression was also significantly impaired when Cav-1 expression was absent in lung ECs, suggesting that EC-Cav-1 may contribute to reduced lung c-IAP2 expression, leading to the severe vascular remodeling that underlies the development of Sch-PH. Conclusion: Our data is uncovering whether c-IAP2 expression is a novel and specific molecular target for future therapeutic approaches against chronic Sch-PH.

Downregulation of miR-4284 can Inhibit the Apoptosis of Human Arterial Smooth Muscle Cells (HASMCs) in Arteriosclerosis Obliterans (ASO).

The disease arteriosclerosis obliterans (ASO) affects the lower extremities. ASO's mechanism involves the proliferation and migration of vascular smooth muscle cells (VSMCs). The miR-4284 is involved in several biological processes of the cardiovascular system, including VSMC proliferation, migration, and death. However, it is unknown if the miR-4284 gene is involved in the control of ASO. Furthermore, the molecular processes behind the contribution of human arterial smooth muscle cells (HASMCs), one of the most significant components of the arterial wall, to arteriosclerosis obliterans (ASO) pathogenesis remain unknown. Previously, we explored the alterations of miRNAs in the blood of ASO patients, and now we wanted to test further whether these changes also take place in the HASMCs that are responsible for the pathogenesis of ASO. The expression levels of miR-29a in arterial walls were analyzed via a real-time polymerase chain reaction. An ASO cell model was established to investigate the expression of miR- 4284 on HASMCs. The Transwell system and CCK-8 detection were used to assess the migration and proliferation of HASMCs. The proportion of apoptotic cells as well as the concentrations of apoptotic signal protein production were assessed using flow cytometry. A Western blot technique was used to identify B cell lymphoma-2 (Bcl2), Bcl2-associated X protein (BAX), as well as Xlinked inhibitors of apoptosis protein (XIAP). The results showed that PCR confirmed that the qualified production or expression of miR-4284 was significantly reduced in HASMCs after they were cultured without FBS and in an atmosphere of 1% O2 + 5% CO2 + 94% N2 and that glucose had no effect on its expression. MiR- 4284 has no effect on migration and proliferation, but downregulation of miR-4284 can decrease the apoptotic rate of HASMCs, as revealed by flow cytometry. Furthermore, western blot experiments showed that the expression of BAX was low, while the expression of the other two proteins, viz., Bcl2 and XIAP, was over-expressed. We found that miR-4284 downregulation enhanced Bcl2, as well as XIAP, and decreased Bax. This shows that downregulated miR-4284 regulates apoptosis-related protein expression in HASMCs. The mechanism is not clear, and we need further study to confirm it.

An in silico study of the effects of chemical compounds in Petiveria alliacea leaf extract on inflammatory mediators

Background: Petiveria alliacea (P. alliacea) is a botanical species renowned for its bioactive compounds and is utilised for medicinal purposes worldwide. In Southwestern Nigeria, P. alliacea finds common application in herbal medicine to address diverse ailments, including diabetes due to chronic inflammation. Objective: This study investigates the drug-like molecular properties of chemical compounds in P. alliacea, targeting the interleukin one receptor (IL1R) and Tumor Necrosis Factor-alpha receptor (TNFAR). Method: The target binding of the P. alliacea chemical compounds was evaluated through drug-likeness tests on the SCFBIO server. All compounds found in P. alliacea adhere to Lipinski’s Rule of Five, classifying them as drug-like molecules. Employing molecular docking simulations on PyRx v9.9.0, the interaction dynamics between P. alliacea ligands and IL1R and TNFAR were simulated. Result: Among the compounds found in P. alliacea, namely astilbin and isoarborinol, emerge as potential candidates for IL1R and TNFAR protein inhibitors due to their notably elevated negative binding affinity values and involve Van der Waals, hydrogen and alkyl bond interactions. Then, a response was elicited that was marked by diminished oxidative stress and anti-inflammatory activity. Conclusion: P. alliacea has the potential to inhibit proinflammatory proteins, such as IL1R and TNFAR, due to its content, namely astilbin and isoarborinol.

Inhibition of microtubule function prevents hypoxia-induced glycolysis

In normoxic conditions where oxygen supply exceeds demand, mammalian cells produce 38 molecules of adenosine triphosphate (ATP) per molecule of glucose through cellular respiration which is primarily oxygen-dependent. In hypoxia where oxygen demand exceeds supply, the cell enters a bioenergetic crisis due to the decrease in oxygen-dependent ATP synthesis. The cell relies on overcoming this deficiency in ATP through upregulation of glycolytic gene expression via the hypoxia inducible factor 1-a (HIF-1a). However, it is highly unlikely, if not impossible, that the bioenergetic requirements of the hypoxic cell depend solely on the increased expression of glycolytic enzymes distributed randomly in the cytoplasm. We have recently shown that in response to hypoxia, glycolytic enzymes coalesce to form a glycolytic metabolon to effciently increase ATP production in response to this metabolic challenge (Kierans SJ, et al., 2023). While the function of this metabolon has been characterised, the mechanisms underpinning formation, scaffolding, and intracellular distribution remains poorly understood. Here we investigate the possible role of the cytoskeleton as a scaffold or transport system. Microtubules are a primary method of intracellular transport and may alter the energy distribution strategies of cells in bioenergetic crisis. It is hypothesized that the microtubular network transports glycolytic enzymes and/or facilitates increased glycolytic ATP production by promoting metabolon formation to induce glycolysis in hypoxia. Through western blots, it was successfully shown that upon exposure to 1% oxygen, caco2 intestinal epithelial cells induce a robust hypoxic response by stabilising HIF-1a. To investigate the role of the microtubules, two microtubule inhibitors were used: nocodazole, a microtubule assembly and disassembly inhibitor and dynarrestin, a dynein-1 motor transport protein inhibitor. Non-toxic concentrations of nocodazole and dynarrestin were determined using cell viability assays (trypan blue and resazurin assays). Upon exposure to 24 hours of hypoxia, caco2 cells elicit a statistically significant increase in intracellular lactate (185.9% ± 7.5% SEM, n = 3), which was then supressed when treated with nocodazole or dynarrestin (20.6% ± 10.2% SEM and 74.9% ± 8.87 SEM respectively, n = 3). These results thus implicate a role for the transport and structural capabilities of the microtubules in hypoxia-induced glycolysis. Kierans, S. J., Fagundes, R. R., Malkov, M. I., Sparkes, R., Dillon, E. T., Smolenski, A.,... & Taylor, C. T. (2023). Hypoxia induces a glycolytic complex in intestinal epithelial cells independent of HIF-1-driven glycolytic gene expression. Proceedings of the National Academy of Sciences, 120(35), e2208117120. University College Dublin, School of Medicine. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Precision Vaccine Development: Unraveling the Immunoinformatics Code Against Epstein-Barr Virus's T41 Glycoprotein 350/220

Epstein-Barr Virus (EBV) poses a substantial global health threat, with a 90% morbidity rate in adults worldwide. Linked to infectious mononucleosis, autoimmune diseases, and cancers, there is an imperative for effective preventive measures, given the absence of current vaccines or medications. This study employs a bioinformatics strategy to design an epitope vaccine targeting EBV. The primary target for immunity is the EBV glycoprotein 350/220 (gp350), which mediates attachment to B cells through complement receptor 2 (CR2/CD21). The selected protein, EBV glycoprotein 350/220 was chosen based on its role in pathogenicity. In the post-therapeutic approach, three-dimensional structure prediction, validation, and verification processes were conducted, followed by molecular docking studies to identify potential drug-binding sites and suitable therapeutic inhibitors for the target protein. The protein's ability to stimulate humoral and cell-mediated immunity was assessed, leading to the identification of a peptide segment ATNLFLLEL from positions 342 to 356 as the predominant T cell epitope. This epitope demonstrated compatibility with various HLA profiles, enhanced by its interaction with eight HLA-A and HLA-B alleles. Population coverage analysis revealed broad responsiveness across geographies, suggesting its potential as a widely applicable vaccine component. Its non-allergic classification further supports its potential efficacy for diverse individuals. Docking studies with HLA-B*3501 confirmed its significant affinity for MHC-I molecules, establishing it as a promising vaccination candidate. Additionally, a region from amino acid positions 253 to 310 was identified as containing potential B-cell epitopes, with the sequence "LGAGELALTMRSKKLP" showing promise due to its antigenic potential. This computational approach to epitope-based peptide vaccine design and target site prediction against EBV represents a pioneering advancement in EBV virus research, emphasizing the need for validation through <i>in vitro</i> and <i>in vivo</i> trials.

Identification of active main metabolites of anti-infective inhibitors of the macrophage infectivity potentiator protein by liquid chromatography using mass detection.

Due to increasing antibiotic resistance, the development of anti-infectives with new mechanisms of action is crucial. Virulence factors such as the "macrophage infectivity potentiator" (Mip) protein, which catalyzes the folding of proline-containing proteins by means of their cis-trans isomerase (PPIase) activity, have come into focus as a potential new target. Since the inhibition of Mip by small molecules has been shown to lead to reduced virulence and survival in vitro, especially of Gram-negative bacteria such as Burkholderia pseudomallei (Bp), Neisseria meningitidis (Nm), and Neisseria gonorrhoeae (Ng), or Coxiella burnetii (Cb), among many others, a library of Mip inhibitors was developed. As drug metabolism has a significant impact on the overall therapeutic outcome, this report describes the biotransformation of the most potent Mip inhibitors. Therefore, the anti-infectives were treated using human liver microsomes in vitro. Liquid chromatography with tandem mass spectrometry (LC/MS-MS) methods were applied to identify the metabolites and quantify the metabolic degradation of the hit compounds. Active metabolites, N-oxides, were found, leading to new opportunities for further drug development.

Small-Molecule Inhibitors of TIPE3 Protein Identified through Deep Learning Suppress Cancer Cell Growth In Vitro.

Tumor necrosis factor-α-induced protein 8-like 3 (TNFAIP8L3 or TIPE3) functions as a transfer protein for lipid second messengers. TIPE3 is highly upregulated in several human cancers and has been established to significantly promote tumor cell proliferation, migration, and invasion and inhibit the apoptosis of cancer cells. Thus, inhibiting the function of TIPE3 is expected to be an effective strategy against cancer. The advancement of artificial intelligence (AI)-driven drug development has recently invigorated research in anti-cancer drug development. In this work, we incorporated DFCNN, Autodock Vina docking, DeepBindBC, MD, and metadynamics to efficiently identify inhibitors of TIPE3 from a ZINC compound dataset. Six potential candidates were selected for further experimental study to validate their anti-tumor activity. Among these, three small-molecule compounds (K784-8160, E745-0011, and 7238-1516) showed significant anti-tumor activity in vitro, leading to reduced tumor cell viability, proliferation, and migration and enhanced apoptotic tumor cell death. Notably, E745-0011 and 7238-1516 exhibited selective cytotoxicity toward tumor cells with high TIPE3 expression while having little or no effect on normal human cells or tumor cells with low TIPE3 expression. A molecular docking analysis further supported their interactions with TIPE3, highlighting hydrophobic interactions and their shared interaction residues and offering insights for designing more effective inhibitors. Taken together, this work demonstrates the feasibility of incorporating deep learning and MD simulations in virtual drug screening and provides inhibitors with significant potential for anti-cancer drug development against TIPE3-.

SBFI-26 enhances apoptosis in docetaxel-treated triple-negative breast cancer cells by increasing ROS levels

Introduction: Fatty acid binding protein 5 (FABP5) exhibits heightened expression levels in triple-negative breast cancer. The inhibitor of FABP5, Stony Brook fatty acid‐binding protein inhibitor 26 (SBFI-26), has demonstrated the capacity to suppress cell proliferation, migration, and invasion. This study delves into the functional mechanism and impact of combining SBFI-26 with docetaxel in treating MDA-MB-231 cells of triple-negative breast cancer. Methods: Various concentrations of docetaxel and SBFI-26 were chosen for individual or combined treatments. The effects of SBFI-26, docetaxel, or their combination on cell cycle arrest and apoptosis were assessed using flow cytometry. Western blotting was utilised to detect the expression of apoptosis-related proteins, namely cysteinyl aspartate-specific proteases 3 (Caspase3), B cell leukemia/lymphoma 2 (Bcl-2), and Bcl-2 associated X (Bax), while intracellular reactive oxygen species (ROS) levels were determined using a fluorescence spectrophotometer. Results: The IC50 values for SBFI-26 and docetaxel in inhibiting MDA-MB-231 cells were determined to be 106.1 μM and 86.14 nM, respectively. Significantly, the combination treatment augmented the proportion of G1 phase (apoptotic) cells by 3.67-fold compared to the control group (P < 0.0001). Furthermore, the apoptosis rate in the combination group was 2.59-fold higher than that in the docetaxel group (P < 0.0001) and demonstrated a significant increase of 1.82-fold compared with the SBFI-26 group (P < 0.001). Analyses revealed a decrease in the protein expression of Bcl-2, while Bax and Caspase3 exhibited an increase in the combination group for MDA-MB-231 cells. Moreover, the combined treatment group demonstrated a 2.97-fold increase (P < 0.0001) in ROS fluorescence intensity compared to the control group, a noteworthy 1.39-fold increase (P < 0.01) compared to the SBFI-26 treatment group, and a substantial 1.70-fold increase (P < 0.0001) compared to the docetaxel treatment group. Conclusion: These findings suggest that the co-administration of SBFI-26 with docetaxel effectively enhances apoptosis in triple-negative breast cancer MDA-MB-231 cells by elevating intracellular ROS levels.

The virtual antivenom prediction of tamarind compounds as inhibitor against Ophiophagus hannah phospholipase A2

Ophiophagus hannah has significant medical important among snakebite cases. The enzyme Phospholipase A2 (PLA2) is crucial for venom impacts in life-threatening symptoms. However, specific antivenom against this species remains under explored. This study aimed to analyze the potential of secondary metabolites from tamarind as PLA2 protein inhibitor specifically from Ophiophagus hannah venom using in-silico approaches. The sequences and three-dimensional structure of the PLA2 protein from O. hannah were physicochemicaly predicted using ProtParam. Virtual screening, drug-likeness, pharmacokinetic, and toxicity profiles of metabolite compound from Tamarind was performed using SwissADME. All ligands were downloaded from PubChem database. Molecular docking was carried out using PyRx and visualized using Discovery Studio 2016 software. All tamarind’s compounds are safe for long term administration because they displayed minimum risk for hepatotoxicity and AMES. The best interaction of secondary metabolites with PLA2 is owned by quercetin. Future in-vitro and in-vivo studies are needed to evaluate the use of secondary metabolite compounds as specific alternatives of antivenoms.

Impact of non‐thermal processing on the nutritional quality and bioactive properties of industrial hempseed flours and protein isolate

AbstractThere is an unmet demand for plant‐based ingredients with desirable nutritional, techno‐functional properties, and health benefits. In this study, the composition, nutritional quality, and bioactives in industrial hempseed flours and protein isolate generated by milling, germination, isoelectric precipitation (IEP), and enzyme‐assisted extraction (EAE) were evaluated. Moisture, ash, fat, protein, phytic acid, tannin, and trypsin inhibitor content of the hempseed flours and protein isolate were 2.80%–6.46%, 5.07%–28.89%, 0.00%–31.44%, 22.71%–89.94%, 0.55%–1.05%, 274.24–1300.76 μg/g, and 0.00–42.66 U/g, respectively. IEP resulted in the highest protein content (89.94%), indicative of its effective to isolate hempseed protein. Germination and IEP significantly reduced phytic acid and tannin contents by 1.53‐ and 3.63‐fold, respectively. All processing methods improved in vitro protein digestibility (IVPD). SDS‐PAGE analysis revealed comparable band patterns in milled and protein isolate, with a strong 50 kDa band attributed as edestin. Amino acid analysis showed that EAE augmented total essential amino acids, particularly protease. Milling and pronase treatment yielded the highest and lowest IVPD‐corrected amino acid score (IVPDCAAS) of 76% and 47%, respectively. Milled and germinated flours contained varying amounts of γ‐tocopherol, lutein, zeaxanthin, α‐carotene, and β‐carotene. Germinated flour exhibited elevated levels of total phenolic (14.36 mg/g), and flavonoid (1.76 mg/g) contents, FRAP, TEAC, and DPPH compared to the other flours suggesting superior antioxidant capacity. Strong positive correlations (r >0.70) were found between IVPD and phytic acid for the protein isolate, total phenolic content, and FRAP for IEP and germinated flours. Overall, hempseed flours with diverse properties could be produced using non‐thermal processing.

(2,6-Dimethylphenyl)arsonic Acid Induces Apoptosis through the Mitochondrial Pathway, Downregulates XIAP, and Overcomes Multidrug Resistance to Cytostatic Drugs in Leukemia and Lymphoma Cells In Vitro.

Cancer treatment is greatly challenged by drug resistance, highlighting the need for novel drug discoveries. Here, we investigated novel organoarsenic compounds regarding their resistance-breaking and apoptosis-inducing properties in leukemia and lymphoma. Notably, the compound (2,6-dimethylphenyl)arsonic acid (As2) demonstrated significant inhibition of cell proliferation and induction of apoptosis in leukemia and lymphoma cells while sparing healthy leukocytes. As2 reached half of its maximum activity (AC50) against leukemia cells at around 6.3 µM. Further experiments showed that As2 overcomes multidrug resistance and sensitizes drug-resistant leukemia and lymphoma cell lines to treatments with the common cytostatic drugs vincristine, daunorubicin, and cytarabine at low micromolar concentrations. Mechanistic investigations of As2-mediated apoptosis involving FADD (FAS-associated death domain)-deficient or Smac (second mitochondria-derived activator of caspases)/DIABLO (direct IAP binding protein with low pI)-overexpressing cell lines, western blot analysis of caspase-9 cleavage, and measurements of mitochondrial membrane integrity identified the mitochondrial apoptosis pathway as the main mode of action. Downregulation of XIAP (x-linked inhibitor of apoptosis protein) and apoptosis induction independent of Bcl-2 (B-cell lymphoma 2) and caspase-3 expression levels suggest the activation of additional apoptosis-promoting mechanisms. Due to the selective apoptosis induction, the synergistic effects with common anti-cancer drugs, and the ability to overcome multidrug resistance in vitro, As2 represents a promising candidate for further preclinical investigations with respect to refractory malignancies.

Circ-METTL15 stimulates the aggressive behaviors of papillary thyroid cancer cells by coordinating the miR-200c-3p/XIAP axis.

Papillary thyroid carcinoma (PTC) is the most common form of thyroid cancer. The critical importance of circular RNA (circRNA) in a range of cancer types has been lately recognized. However, research on the functions of circRNAs in PTC has been limited thus far. Therefore, this research aimed at exploring the function and mechanism of circ-methyltransferase-like 15 (METTL15) in PTC cells. Quantitative measurements of circ-METTL15, miR-200c-3p, and X-linked inhibitor of apoptosis protein (XIAP) in PTC cells were conducted using reverse transcription-quantitative polymerase chain reaction or Western blot analysis. To investigate cell growth, cell counting kit-8 and colony formation tests were employed, apoptosis was analyzed using flow cytometry, and migration and invasion were studied through Transwell assays. The targeted binding sites between miR-200c-3p and circ-METTL15 or XIAP were predicted by starBase and then verified by dual luciferase reporter assay. circ-METTL15 and XIAP were upregulated in the PTC cells, while miR-200c-3p was downregulated. Downregulating circ-METTL15 or upregulating miR-200c-3p resulted in inhibited proliferation, migration, and invasion of PTC cells, while promoting apoptosis. miR-200c-3p was the downstream molecule of circ-METTL15, and XIAP was the direct target of miR-200c-3p. Forcing XIAP expression obstructed circ-METTL15 silencing to inhibit PTC cell activity. By coopting miR-200c-3p/XIAP, Circ-METTL15 stimulates aggressive behavior in PTC cells.

Cheminformatics and QSAR‐Based Identification of Natural Bioactive Compounds as Potent Inhibitors of SARS‐CoV‐2 N‐7 Methyltransferases

AbstractEver since the emergence of the COVID‐19 pandemic, to date, no specific and efficient therapeutic cure is available for the SARS‐CoV‐2 viral infection. Few reports have been observed with the late cardiovascular or neurodegenerative disorders that are associated with altered immunity. The nsp14 protein of SARS‐CoV‐2 is a key target for antiviral drug development as it controls replication of virus and evasion of host immune system. In this study, a consensus of cheminformatics approaches involving virtual screening, molecular docking, ADMET profiling, molecular dynamics simulations, free‐energy landscape, MM‐GBSA, DFT and 2D‐QSAR analysis is employed to discover the inhibitor of nsp14 protein. Our investigation reveals four natural bioactive compounds, i. e. ZINC2132169, ZINC8791872, ZINC8952607 and ZINC6624334 that possess enhanced binding affinity towards nsp14 protein with no predicted toxicity. Molecular docking, MD simulations and MM‐GBSA analysis established that all hit compounds strongly bind at the same pocket through hydrophobic interactions and hydrogen bonding. DFT analysis revealed greater reactivity of hit compounds and their stable complex formation with nsp14 protein, while the 2D‐QSAR (R2=0.92) predicted their pIC50 value in the range of 5.30–6.71 nM. These findings imply that hit compounds would be potent drug candidates in controlling the SARS‐CoV‐2 by inhibiting nsp14 protein.

Molecular Imaging of Fibroblast Activation in Rabbit Atherosclerotic Plaques: a Preclinical PET/CT Study.

Atherosclerosis remains the pathological basis of myocardial infarction and ischemic stroke. Early and accurate identification of plauqes is crucial to improve clinical outcomes of atherosclerosis patients. Our study aims to evaluate the potential value of fibroblast activation protein inhibitor (FAPI)-04 PET/CT in identifying plaques via a preclinical rabbit model of atherosclerosis. New Zealand white rabbits were fed high-fat diet (HFD), and randomly divided into the model group injured by the balloon, and the sham group only with incisions. Ultrasound was performed to detect plaques, and FAPI-avid was determined through Al18F-NOTA-FAPI-04 PET/CT. Mean standardized uptake values (SUVmean) in lesions were compared, and biodistribution of Al18F-NOTA-FAPI-04 and target-to-background ratios (TBRs) were calculated. Histological staining was performed to display arterial plaques, and autoradiography (ARG) was employed to measure the in vitro intensity of Al18F-NOTA-FAPI-04. At last, the correlation among FAP levels, plaque area, SUVmean values and fibrous cap thickness was assessed. The rabbit carotid and abdominal atherosclerosis model was established. Al18F-NOTA-FAPI-04 showed a higher uptake in carotid plaques (SUVmean 1.32 ± 0.11) and abdominal plaques (SUVmean 0.73 ± 0.13) compared to corresponding controls (SUVmean 1.07 ± 0.06; 0.46 ± 0.03) (P < 0.05). Biodistribution analysis of Al18F-NOTA-FAPI-04 revealed that the bigger plaques were delineated with higher TBRs. Pathological staining showed the formation of arterial plaques, and ARG staining exhibited a higher intensity of Al18F-NOTA-FAPI-04 in the bigger plaques. Lastly, plaque area was found to be positively correlated to FAP expression and SUVmean, while FAP expression was negatively correlated to fibrous cap thickness of plaques. We successfully achieve molecular imaging of fibroblast activation in atherosclerotic lesions of rabbits, suggesting Al18F-NOTA-FAPI-04 PET/CT may be a potentially valuable tool to identify plaques.

Proteolytic system parameters in the brain of rats with hyperhomocysteinemia

Hyperhomocysteinemia (HHcy) is now being actively studied as a potential risk factor and/or biomarker for numerous pathological conditions, including brain diseases. This study aimed to analyze the proteolytic processes in the brains of rats with HHcy. Total proteolytic activity, metal-dependent, and serine proteases activities, the content of matrix metalloproteinases (MMPs), tissue inhibitor of metalloproteinases-1, cytokines, serine proteases, total protein and medium and low molecular-weight substances (MLMWS), were evaluated. HHcy was induced by DL-homocysteine thiolactone (HTL) daily intragastric administration (200 mg·kg–1 of body weight) to young and adult albino non-linear male rats for 8 weeks following rat sacrifice and brain harvesting. It was established that HHcy causes an increase in total proteolytic activity and a rise in MLMWS levels in rat brains. Serine protease activity increased to a greater extent compared to metal-dependent one, and bigger changes were observed in young rats. Rise in MMP-9 and -10 levels (in young animals), a decline in MMP-3 and -8 levels, and a decrease in the content of interleukin-1β, interferon-γ, interleukin-4 and tumor necrosis factor-α (the last two in young animals) was also detected. No significant changes were found in serine protease content. Therefore, proteolysis intensification in the brain of rats with HHcy is more likely caused by protease up-regulation through mechanisms stimulated by homocysteine, HTL, and oxidative stress, without involving pro-inflammatory signaling pathways.

NSC689857, an inhibitor of Skp2, produces antidepressant-like effects in mice.

We have previously reported that two inhibitors of an E3 ligase S-phase kinase-associated protein 2 (Skp2), SMIP004 and C1, have an antidepressant-like effect in non-stressed and chronically stressed mice. This prompted us to ask whether other Skp2 inhibitors could also have an antidepressant effect. Here, we used NSC689857, another Skp2 inhibitor, to investigate this hypothesis. The results showed that administration of NSC689857 (5 mg/kg) produced an antidepressant-like effect in a time-dependent manner in non-stressed male mice, which started 8 days after drug administration. Dose-dependent analysis showed that administration of 5 and 10 mg/kg, but not 1 mg/kg, of NSC689857 produced antidepressant-like effects in both non-stressed male and female mice. Administration of NSC689857 (5 mg/kg) also induced antidepressant-like effects in non-stressed male mice when administered three times within 24 h (24, 5, and 1 h before testing) but not when administered acutely (1 h before testing). In addition, NSC689857 and fluoxetine coadministration produced additive antidepressant-like effects in non-stressed male mice. These effects of NSC689857 were not associated with the changes in locomotor activity. Administration of NSC689857 (5 mg/kg) also attenuated depression-like behaviors in male mice induced by chronic social defeat stress, suggesting therapeutic potential of NSC689857 in depression. Overall, these results suggest that NSC689857 is capable of exerting antidepressant-like effects in both non-stressed and chronically stressed mice.

Potential Inhibitors of Lumpy Skin Disease's Viral Protein (DNA Polymerase): A Combination of Bioinformatics Approaches.

Lumpy skin disease (LSD), caused by a virus within the Poxviridae family and Capripoxvirus genus, induces nodular skin lesions in cattle. This spreads through direct contact and insect vectors, significantly affecting global cattle farming. Despite the availability of vaccines, their efficacy is limited by poor prophylaxis and adverse effects. Our study aimed to identify the potential inhibitors targeting the LSDV-encoded DNA polymerase protein (gene LSDV039) for further investigation through comprehensive analysis and computational methods. Virtual screening revealed rhein and taxifolin as being potent binders among 380 phytocompounds, with respective affinities of -8.97 and -7.20 kcal/mol. Canagliflozin and tepotinib exhibited strong affinities (-9.86 and -8.86 kcal/mol) among 718 FDA-approved antiviral drugs. Simulating the molecular dynamics of canagliflozin, tepotinib, rhein, and taxifolin highlighted taxifolin's superior stability and binding energy. Rhein displayed compactness in RMSD and RMSF, but fluctuated in Rg and SASA, while canagliflozin demonstrated stability compared to tepotinib. This study highlights the promising potential of using repurposed drugs and phytocompounds as potential LSD therapeutics. However, extensive validation through in vitro and in vivo testing and clinical trials is crucial for their practical application.

Mycosporine-Like Amino Acids as a Potential Inhibitor of Tyrosinase-Related Protein 1: Computational Screening, Pharmacokinetics, and Molecular Dynamics Simulation.

Melanin is the major pigment responsible for the coloring of mammalian skin, hair, and eyes to defend against ultraviolet radiation. However, excessive melanin production has resulted in numerous types of hyperpigmentation disorders. Tyrosinase-related protein 1 (TYRP1) is a transmembrane glycoprotein enzyme found in many organisms, including humans, that plays an important role in melanogenesis. Thus, controlling the enzyme activity of TYRP1 with tyrosinase inhibitors is a vital step in the treatment of hyperpigmentation problems in humans. In the present investigation, virtual screening, pharmacokinetics, drug docking, and molecular dynamics (MD) simulation were used to find the most potent drug as an inhibitor of TYRP1 to effectively treat hyperpigmentation disorder. The 3D structure of TYRP1 was retrieved from the Protein Data Bank (PDB) database (PDB ID: 5M8M) and validated by the Ramachandran plot. Pharmacokinetics and drug-likeness showed that mycosporine 2 glycine (M2G) and shinorine (SHI) were the best compounds over other ligands in the same (P-1) structural pose. However, MD simulations of the M2G showed the highest CDOCKER interaction energy (-45.182kcal/mol) and binding affinity (-65.0529kcal/mol) as compared to SHI and reference drugs. The molecular binding modes RMSD and RMSF plots have exhibited more relevance to the M2G ligand in comparison to other drug ligands. The bioactivity and ligand efficiency profiles revealed that M2G is the most effective compound as a TYRP1 inhibitor. Thus, M2G could be used as a most effective drug for developing valuable sunscreen products to cure hyperpigmentation-related diseases.