In-silico Results Research Articles

Downregulation of miR-372 in non-proliferating human pluripotent stem cell derived cardiomyocytes

Introduction: The cell cycle arrest of the mammalian adult cardiomyocytes is the main reason for limited cardiac regeneration. A complex network of intracellular molecules facilitates cell cycle progression, from which regulatory proteins are well studied. However, the non-protein compartments such as regulatory microRNAs (miRNAs) are underrepresented. Here, we explored the miRNAs with differential expression in proliferating and non-proliferating cardiomyocytes. Methods: Candidate miRNAs with significant differential expression between 14-day and 45-day human embryonic stem cell-derived cardiomyocytes (hESC-CM) were identified using reanalysis of data set GSE35672. Human embryonic stem cells (hPSCs) were expanded and differentiated into cardiomyocytes by a cocktail of small molecules targeting Wnt/β-catenin and TGF-β signaling, and samples were collected for expression analysis of in silico-identified candidate miRNAs at days 10, 20, and 30 of differentiation. Findings: miR-302d, miR-371-5p, and miR-372 were selected as candidate differentially expressed miRNAs (DEmiRNAs). While miR-302d and miR-371-5p expression did not repeat the in-silico results in cTNT+hESC-CM, miR-372 showed a significant downregulation from day 10 to day 30. Conclusion: This finding suggests a possible regulatory effect of miRNA-372 in cell cycle arrest of mature cardiomyocytes.

Evaluasi Toksisitas Akut Kulit Batang Manihot esculenta Crantz. : Pendekatan In Silico dan In Vitro

Manihot esculenta Crantz has been used in research focused on drug discovery and development. Although the compound content and pharmacological effects of this plant have been widely reported, it is necessary to conduct a toxicity evaluation when developing it as a potential drug candidate to determine its effectiveness and therapeutic potential. This study aims to evaluate the acute toxicity of stem bark of M. esculenta both in silico and in vitro. In-silico toxicology was conducted on 13 compounds using ProTox-II. The indicators assessed were LC50 and organ toxicity such hepatotoxic, carcinogenic, immunotoxicity, mutagenic, nephrotoxic, neurotoxic. The in vitro assay used BSLT with Artemia salina. The mortality percentage of A. salina was calculated to determine the LC50 value. The in-silico results showed five compounds Hydrocyanic acid, beta stigmasterol, 6'-Apiosyllotaustralin, Yucalexin B22, and Yucalexin B14 with a toxicity category of < 5. The in vitro results showed LC50 values for the ethanol and n-hexane fractions of 548.774 and 375.787 µg/mL, respectively. Further in vivo toxicity testing is needed to provide additional evidence of the toxicity of M. esculenta stem bark. The stem bark of M. esculenta is toxic depending on the concentration, with compounds such as hydrocyanic acid, beta stigmasterol, 6'-Apiosyllotaustralin, Yucalexin B22, and Yucalexin B14 suspected to play an important role in the toxic effects.

Novel dibenzoylmethane derivative 2-allyl-1,3-diphenyl-1,3-propanedione: a safe and effective topical treatment for melanoma.

This study investigated 2-allyl-1,3-diphenyl-1,3-propanedione (DPAP), a dibenzoylmethane derivative, as a potentially more effective and safer alternative to dacarbazine for melanoma treatment. The antitumor activity of DPAP was assessed through comprehensive in-vitro, in-silico, and in-vivo experiments. In-vitro assays evaluated DPAP's IC50 values against melanoma cells, benchmarking its efficacy against dacarbazine. Molecular analyses explored apoptosis mechanisms, emphasizing the roles of FAS receptors and caspase pathways. In-silico absorption, distribution, metabolism, excretion, and toxicity analysis provided insights into DPAP's pharmacokinetic profile, including absorption, distribution, metabolism, and toxicity. In-vivo studies examined its effects on tumor volume, vascular endothelial growth factor (VEGF) levels, and the histopathology of the liver, kidney, and lymph nodes. DPAP demonstrated significantly enhanced antitumor activity, reflected by markedly lower IC50 values compared with dacarbazine, underscoring its superior efficacy and specificity toward tumor cells. Molecular assays confirmed that DPAP induces apoptosis through modulation of FAS receptors and activation of caspase pathways. In-silico results revealed favorable pharmacokinetic properties, including high intestinal absorption and good tissue distribution, with no evidence of carcinogenic potential. Notably, in-vivo experiments showed that DPAP effectively reduced tumor volume and VEGF levels, while also preventing hepatotoxicity and nephrotoxicity. In addition, it inhibited the migration of tumor cells to lymph nodes. These findings position DPAP as a promising candidate for melanoma treatment, particularly as a topical therapeutic, offering enhanced efficacy and safety compared with existing treatments. DPAP is a promising candidate for melanoma treatment, particularly through topical application, offering a safer and more effective alternative to current treatments.

Hypoglycemic and Hypolipidemic Potentials of Ananas comosus (Linn.) Merr. Fruit Peel: An In Silico Modelling and In Vivo Analysis

Introduction: Diabetes mellitus (DM) is a non-communicable, complex disorder that affects all groups of people, whether young, old, short, tall, black, white, male, or female, and it is still without a cure. Medicinal plants, functional foods, and their waste products are known veritable sources of antidiabetic drugs. This study investigated the blood glucose-lowering (hypoglycemic) and lipid-lowering (hypolipidemic) effects of Ananas comosus aqueous-ethanol fruit peel extract (ACAPE) using in-silico and in vivo methodologies. Methods: The in-silico (site-specific and blind) molecular docking assessed the interaction of ACAPE bioactive compounds with diabetic-related protein targets, specifically human α-amylase and aldose reductase, using PyRx, AutoDock Vina, and Biovia Discovery Studio. Animals were made diabetic using 60 mg/kg body weight streptozotocin (STZ) and later treated for 28 days, sacrificed, and blood collected for biochemical parameter evaluation using standard procedures and kits: glucose and protein concentrations; lipid profile levels; and hepatic antioxidant enzymes (superoxide dismutase (SOD) and catalase (CAT) and he-patic function (alanine (ALT) and aspartate (AST) transaminases) activities. Results: The results indicated that ACAPE had abundant polyphenolics. Treatment of dia-betic animals with ACAPE restored the dysfunction in glucose and lipid concentrations and significantly (p<0.05) increased the hepatic function and antioxidant enzyme activities in diabetic animals. 2-Chloro-4-(4-methoxyphenyl)-6-(4-nitrophenyl) pyrimidine (-10.5 kcal/mol) and α-muurolene (-8.9 kcal/mol) showed overall good binding energy and affinity against aldose reductase and α-amylase in silico. Discussion: This study highlights the antidiabetic potential of Ananas comosus peel extract, which significantly improved blood glucose, lipid profile, liver enzymes, and antioxidant activities in diabetic rats. The in-silico results also showed strong interactions between key phytochemicals and diabetic-related enzymes, supporting the observed biological effects. However, this study is limited by the absence of mechanistic studies such as gene/protein expression, a lack of histopathological evaluation, dose optimization, and a lack of clinical human studies to confirm these findings. Conclusion: It can be concluded from the findings of this study that ACAPE is rich in phy-tochemical constituents, especially polyphenolics, that can be explored for the treatment of diabetes and its related complications.

EGFR Kinase Inhibiting Amino-enones for Breast Cancer; CADD Approach.

The Computer-Aided Drug Discovery (CADD) approach was used to develop a few Epidermal Growth Factor Receptor (EGFR) kinase inhibitors. EGFR kinase expression is highly associated with genomic instability, higher proliferation, lower hormone receptor levels, and HER2 over-expression. It is more common in breast cancer. Thus, EGFR Kinase is one of the main targets in discovering new cancer medicine. To computationally validate some amides substituted β-amino enones as EGFR inhibitors and to carry out associated in vitro anticancer agents. We used tools such as molecular docking, MD simulations, DFT calculations, and ADMET predictions in silico to establish a preliminary SAR. In vitro, we used BT474 (ER+HER2+) and MCF-7 (ER-HER2) cell lines along with normal breast cell epithelial cells (MFC-10a) for anticancer studies and EGFR kinase inhibition assay studies. As the Reactive Oxygen Species (ROS) plays the main role in cancer development, we also analyzed the antioxidant potentials of these compounds. Among the family of eleven amides substituted (Z)-β-amino enones (5a-k), compounds 5b, 5c, 5g, and 5h showed valuable in silico and in vitro bio-activity. Remarkably, the in-silico results almost coincided with in vitro study results. We recommend compounds 5b, 5c, 5g, and 5h for pre-clinical and clinical evaluation to establish them as future cancer therapeutics.

Increased Expression of RCN1P2, TPM3P9, and HSP90AB3P as Non-Coding RNA in Gastric Cancer Linked to Proliferative, Inflammatory and Metastatic Pathways through a Competing Endogenous RNAs Network

Background: This study aimed to find pseudogenes with significant expression alterations in gastric cancer (GC) that could be implicated in the disease's development via the competing endogenous RNAs (ceRNAs) network. Methods: Pseudogenes, mRNAs, and microRNAs, whose expression changes considerably in GC specimens, were identified using the Cancer Genome Atlas (TCGA) data from 2006 to 2017 (USA). The ceRNAs network was constructed using the miRWalk, miRTarBase, and DIANA-LncBase. The cox regression test was performed to assess the correlation between candidate genes and patient prognosis. Finally, using the RT-qPCR method, the in-silico results were evaluated using GC samples and adjacent normal. Samples were collected from Imam Khomeini Hospital in Tehran (Iran) between 2020 and 2021. Results: In the cancer samples compared to the normal ones, there were 86 miRNAs, 1985 mRNAs, and 33 pseudogenes showing expression alterations, either more than or less than a twofold difference. Constructed ceRNA network demonstrated that pseudogenes such as RCN1P2, TPM3P9, and HSP90AB3P were most connected to changed mRNAs and microRNAs in GC. The analysis of the ceRNA network for each of the mentioned pseudogenes indicated that the associated mRNAs play roles in cell proliferation, inflammation, and metastatic pathways. Furthermore, elevated expression of several mRNAs linked to potential pseudogenes was linked to a poor prognosis. RT-qPCR revealed a significant increase in the expression levels of RCN1P2, TPM3P9, and HSP90AB3P in GC samples. Conclusion: The expression of RCN1P2, TPM3P9, and HSP90AB3P is dramatically enhanced in GC. They can also influence the survival rate of GC patients by regulating pathways involved in cell proliferation, inflammation, and metastasis via the ceRNAs network.

Designing a multi-epitope vaccine against African swine fever virus using immunoinformatics approach

African swine fever (ASF) is a highly contagious and fatal haemorrhagic disease affecting domestic and wild pigs, with no effective vaccine currently available. The lack of an effective vaccine has hindered global ASF control efforts, leading to devastating economic losses in the swine industry. Traditional vaccine development approaches have faced challenges due to ASFV’s genetic complexity and immune evasion strategies. Therefore, this study aims to leverage immunoinformatic approaches to facilitate acceleration of the early stages of vaccine development, optimizing resource utilization and time efficiency while providing a rational design for a potent multi-epitope vaccine against ASFV. In this study, a multi-epitope vaccine against ASFV was designed using an in-silico approach incorporating epitopes from conserved ASFV genes - B646L (p72), CP204L (p30), E183L (p54) and EP402R (CD2v). Promising epitopes that were antigenic and non-allergenic were used for the vaccine construct along with suitable adjuvant and linkers. Further analyses of the construct interpreted the physico-chemical properties, secondary and tertiary structure prediction and validation. The docking and molecular dynamics analysis of the docked complex (vaccine construct and SLA-1 0401) were performed. The docking analysis demonstrated that the vaccine construct binds well with SLA-1 0401 and the molecular dynamics analysis confirmed its strong binding affinity. The vaccine construct was confirmed as stable through normal mode analysis (NMA). Immune simulations demonstrated that this multi-epitope vaccine construct generates a strong adaptive immune response including both humoral and cell-mediated immunity. The sequence of the vaccine construct was further codon optimized with better CAI and GC content, for enhanced expression in the host Sus scrofa. Finally, the optimized sequence of vaccine construct was cloned into the plasmid pVAX1-eGFP. These in-silico results prove that the designed multi-epitope vaccine is potentially effective and warrants for further in vitro and in vivo studies to confirm the efficiency of the vaccine against ASFV.

In silico screening and molecular dynamic simulations of FDA-approved drugs as an inhibitor of trypanothione reductase of Leishmania donovani.

In silico screening and molecular dynamic simulations of FDA-approved drugs as an inhibitor of trypanothione reductase of Leishmania donovani.

Network pharmacology, molecular docking, and molecular dynamics analyses to explore the molecular mechanism of paclitaxel in atherosclerosis therapy

Atherosclerosis is a chronic arterial disease and the leading cause of vascular death. Paclitaxel has long been recognized as an anticancer agent, but recent studies have shown that paclitaxel can also potentially reduce the progression of atherosclerosis. The aim of this study was to explore the molecular mechanism of paclitaxel as an atherosclerosis therapy using in silico study. Pharmacokinetic and pharmacodynamic analyses of paclitaxel were conducted using SwissADME, ProTox v3.0, and SCFbio websites. Cytoscape software was used to construct a network of protein-protein interactions, and the key proteins involved in paclitaxel-related atherosclerosis were identified, including AKT serine/threonine kinase 1 (AKT1), Jun N-terminal kinase (JNK), and Endothelin 1 (ET1). These key proteins were then subjected to molecular docking and molecular dynamic simulation using MOE and Yasara applications. Pharmacokinetic and pharmacodynamic analyses revealed that paclitaxel has good distribution, metabolism, and excretion properties. However, paclitaxel has shortcomings in absorption, toxicity, and water solubility. According to the results of molecular docking, paclitaxel showed consistent results as the most potential inhibitor of AKT1 (-9.59 kcal/mol), ET1 (-9.16 kcal/mol), JNK (-8.72 kcal/mol) when compared to the control ligands. Molecular dynamics simulations also confirmed the interaction stability between paclitaxel with AKT1, ET1, and JNK, with paclitaxel-AKT1 demonstrating the highest conformational stability (Carbon-α Root Mean Square Deviation <3.0 Å). Even though our in-silico results are promising, more experimental studies are required to confirm the efficacy of paclitaxel as an atherosclerosis therapy.

The In Vitro and In Silico Assessment of the Cytotoxic Effect of Daidzein Alone or in Combination with 5-Fluorouracil on Human Colorectal Adenocarcinoma Cell Line Caco-2.

We aimed to evaluate the cytotoxic effect of daidzein alone and in combination with 5-fluorouracil (5-FU) on Caco-2 cells and investigate potential interactions between daidzein and 5-FU with apoptosis-related tumor necrosis factor-related apoptosis-inducing ligand receptor-2, tumor necrosis factor -alpha receptor-1 and Interferon gamma receptor-1. In this study, we used trypan blue and MTT assays to evaluate the cytotoxic effect of daidzein and the effect of daidzein on the amount of substance P released from the cells using the ELISA method. We utilized the ligand-protein molecular docking method for our in-silico assessments. According to our cytotoxicity experiment results, daidzein decreased the proliferation of Caco-2 cells. It should be pointed out that our ELISA test results daidzein and 5-FU increase the level of Substance-P (SP), a proinflammatory cytokine released by Caco-2 cells. Based on our in-silico results, daidzein interacted with all three apoptosis-related receptors on the membrane of Caco-2 cells to a better extent than 5-FU. In sum, although daidzein increases the amount of SP, it is a compound that has significant cytotoxic effect on colon cancer cells and promise as a potential therapeutic agent for the treatment of colon cancer.

Development of an Anatomy-Mimicking, Wave Transport-Preserving Mock Circulation Loop for Evaluating Pulsatile Hemodynamics as Supported by Cardiovascular Assist Devices.

Assessing circulatory hemodynamics in-vitro is crucial for cardiovascular device design before in-vivo testing. Current mock circulation loops (MCLs) rely on simplified, lumped-parameter hydraulic representations of human circulation. There is a need for a more sophisticated MCL that can accurately represent the human circulatory physiology and allow for critical assessment of device-supported hemodynamics. An anatomy-mimicking MCL design guided by one-dimensional flow models has been developed, using tree-like arterial casts to create a complex system. The MCL comprises cardiac simulators, systemic circulatory subsystems consisting of 46 connected arterial casts, and lumped venous and pulmonary components. A parameter tuning process was also developed to ensure that the simulated MCL baselines are consistent with targeted healthy or heart failure scenarios. Blood pressure and flow waveforms in the thoracic aorta, upper and lower limb arteries and abdominal organs (kidney, liver, spleen, etc.) were reproduced and validated against published data. Complex afferent and efferent flows in cerebral circulation and phasic coronary flow subjected to myocardial compression effect were replicated with precision. Pulse wave behavior was authentically generated and compared favorably to the published in-vivo and in-silico results. This wave transport-preserving MCL is able to simulate pulsatile human circulatory hemodynamics with sufficient detail and accuracy. Complex cardiovascular device-intervened hemodynamics in large arteries and end organs can be systematically assessed using this new MCL, potentially contributing to a rapid and accurate in-vitro simulation to help advance device design and functional optimization.

Investigation of hemodynamic bulk flow patterns caused by aortic stenosis using a combined 4D Flow MRI-CFD framework.

Aortic stenosis (AS) leads to alterations of supra-valvular flow patterns which can cause increased damage of red blood cell (RBC) membranes. We investigated these patient specific patterns of a severe AS patient and their reversal in healthy flow through a 4D Flow MRI-based CFD methodology. Computational models of subject-specific aortic geometries were created using in-vivo medical imaging data. Temporally and spatially resolved boundary conditions derived from 4D Flow MRI were implemented for an AS patient and a healthy subject. After validation of the in-silico results with in-vivo data, a healthy inflow profile was set for the AS patient in the CFD model. Pathological versus healthy flow fields were compared regarding their blood flow characteristics, i.e., shear stresses on RBCs and helicity. The accuracy of the 4D Flow MRI-based CFD model was proven with excellent agreement between in-vivo and in-silico velocity fields and R² = 0.9. A pathological high shear stress region in the bulk flow was present during late systole with an increase of 125% compared to both healthy flow. The physiological bihelical structure with predominantly right-handed helices vanished for the pathological state. Instead, a left-handed helix appeared, accompanied by an overall increase in turbulent kinetic energy in areas of accumulated left-handed helicity. The validated 4D Flow MRI-based CFD model identified marked differences between AS and healthy flow. It suggests that altered turbulent and helical structures in the bulk flow are the cause for increased, potentially damaging forces acting upon RBCs in AS.

In vivo and in silico analysis of anti inflammatory, antipyretic and analgesic activity of methanolic extract of Nigella sativa.

Nigella Sativa (N. sativa) belongs to the family of Ranunculaceae and is an annual herb which is also known as black cumin or black seed. Since ancient times N. sativa has been used because of its widespread therapeutic properties which has been proven effective in respiratory, cardiovascular, gastrointestinal, inflammatory conditions and in inflammation. This study investigates the antiinflammatory, antipyretic, and analgesic properties of Nigella sativa (N. sativa) methanol extract using albino rats (n = 36). Diclofenac and paracetamol were used as standard medications in the trial, and the four concentrations of the methanolic extract (250, 500, 1000, and 2000mg/kg) were tested for their effects on inflammation, pain, and fever. The methanolic extract of N. sativa seeds showed significant inhibition of fever (96%), inflammation (89%), and pain (85%). In addition, bioactive compounds in the seeds, including thymol, p-cymene, and limonene, were examined through in-silico studies. Ligand molecules and proteins associated with anti-inflammatory, analgesic, and antipyretic effects were 1DFN, 1A06, and 3LN0, respectively. The molecular docking results indicated significant binding interactions, with effective binding energy values corresponding to analgesic, antipyretic, and anti-inflammatory properties. Both in-silico and in-vivo results demonstrate the efficacy of N. sativa methanol extract in alleviating pain, inflammation, and fever.

DESIGNING A MULTI-EPITOPE VACCINE AGAINST SARS-COV2: AN IMMUNOINFORMATIC APPROACH

Background: An outbreak of SARS-CoV-2 in 2019 has brought a great challenge to public health and rapid identification of immune epitopes for designing an effective vaccine for different variants of SARS-CoV-2 is necessary at the time of the pandemic. Rational, rapid, and precise vaccine design, especially vaccine antigen identification and optimization by in silico methods of bioinformatics, structural biology, and immunoinformatic is critical to efficient vaccine development against the SARS-CoV-2 virus. The aim of this study was to develop a particular novel and effective vaccines vaccine using bioinformatics approaches and resources that can target B- and T-cell epitopes to combat SARS-CoV-2 infection. Methods: The variants of SARS-CoV2 (Alpha, Beta, Delta, and Omicron strains) spike protein were selected for designing the vaccine. The B-cell, T-cell, and interferon-gamma-inducing epitopes were predicted. The beta-defensin-3 protein was selected as adjuvant and predicted epitopes were connected using suitable linkers. The vaccine's allergenicity, antigenicity, physicochemical characteristics, 2D and 3D structure modeling, and molecular docking were evaluated for the final construct. Results: The in-silico results showed that the multi-epitope vaccine has a stable structure and can induce humoral and cellular immune responses against SARS-CoV2. Conclusions: B-cell and T-cell epitopes on spike protein were identified and recommended for design and confirmation of in vivo evaluation for multi-epitope peptides as vaccines against SARS-CoV-2.

60 In-Silico Modelling in the Development of Novel Devices in Thoracic and Abdominal Surgery: A Systematic Review

Abstract Background Surgical innovation has made significant leaps in recent years, but the adoption of novel devices has lagged due to prolonged efficacy and safety assessment through randomised controlled trials. In-silico modelling may provide a solution, utilising computational simulations to develop and improve surgical devices. This systematic review aimed to evaluate the current use of in-silico modelling for devices utilised in thoracic and abdominal surgery. Methods Studies in the last five years were searched in PubMed databases (Jan 2019 - Aug 2024). Specified inclusion criteria included original studies using mathematical/computational modelling to investigate thoracic/abdominal surgical devices which are invasive in nature. Results Of 2968 studies derived from the search strategy, 42 were included in the final analysis and categorised by surgical specialty: general surgery (n=4); hepato-pancreato-biliary (n=2); vascular (n=5); paediatric (n=9); and cardiothoracic (n=22). Three core themes were identified: proof of concept (n=19), device improvement (n=22), and in-silico clinical trials (ISCTs) with simulated human patients (n=1). Most studies were at IDEAL stage 0 (pre-clinical) and 19 studies validated in-silico results with in-vitro/ in-vivo data. Discussion In future, in-silico modelling could replace components of pre-clinical in-vitro and in-vivo testing of surgical devices. Applications include generating efficacy data for novel devices in the pre-clinical stage, modelling minority patient demographics or rare diseases, and developing/repurposing existing devices to reduce complications. Standardised core outcomes and credibility frameworks will minimise inter-study heterogeneity in methodologies and reporting of results. Global collaboration will help bring in-silico modelling to the forefront of surgical device research.

A novel immunoinformatic approach for design and evaluation of heptavalent multiepitope foot-and-mouth disease virus vaccine

BackgroundFoot-and-mouth disease virus (FMDV) vaccine development can be a laborious task due to the existence of various serotypes and lineages and its quasi-species nature. Immunoinformatics provide effective and promising avenue for the development of multiepitope vaccines against such complex pathogens. In this study, we developed an immunoinformatic pipeline to design a heptavalent multi-epitope vaccine targeting circulating FMDV isolates in Egypt.ResultB and T-cell epitopes were predicted and selected epitopes were proved to be non-allergenic, non-toxic, with high antigenicity, and able to induce interferon-gamma response. The epitopes were used to construct a vaccine by adding suitable linkers and adjuvant. Prediction, refinement, and validation of the final construct proved its stability and solubility, having a theoretical isoelectric point (PI) of 9.4 and a molecular weight of 75.49 kDa. The final construct was evaluated for its interaction with bovine toll-like receptor (TLR) 2 and 4 using molecular docking analysis and molecular dynamic simulation showed high binding affinity, especially toward TLR4. MM/GBSA energy calculation supported these findings, confirming favorable energetics of the interaction. Finally, the DNA sequence of the vaccine was cloned in pET-30a (+) for efficient expression in Escherichia coli.ConclusionThe inclusion of computational and immunoinformatic approaches will ensure cost-effectiveness and rapid design of FMDV vaccine, decrease wet lab experimentation, and aid the selection of novel FMDV vaccines. While the vaccine demonstrates promising in-silico results, experimental assessment of vaccine efficiency is required.

MCP-1 promotes ILK phosphorylation at Ser246 during endometriosis development and affects the pregnancy outcome.

In women with endometriosis, monocyte chemoattractant protein 1 (MCP-1) or chemokine (C-C motif) ligand 2 (CCL2) is elevated in serum, peritoneal fluid, and endometriotic lesions, though its exact role in endometriosis is still unknown. The MCP-1 downstream molecule integrin-linked kinase (ILK) is involved in several cellular events. Our recent findings suggest that MCP-1 promotes an inflammatory response via ILK in a mouse endometriosis model. MCP-1 also favors human endometriotic cell aggregation, colonization, migration, and invasion, which are reversed by the ILK inhibitor compound (CPD) 22 (600 nM). Furthermore, the inflammatory response to MCP-1 is reduced by ILK inhibition (CPD22, 20 mg/kg body weight) in a mouse model. We studied MCP-1/chemokine (C-C motif) receptor type (CCR)2-mediated ILK signaling in endometriosis and observed a positive association of ILK and CCR2 with endometriosis in patients. Our immunoprecipitation and molecular docking studies confirmed ILK interaction with CCR2 under a high MCP-1 level in Hs832(C).TCs (human endometriotic cells). MCP-1 promotes ILK-Ser246 phosphorylation in endometriotic cells in human and mouse models. The mouse model shows the same inflammatory markers as seen in human endometriosis and mimics some of the aspects of the inflammatory reaction. Targeting ILK by CDP22 (20 mg/kg) suppresses endometriosis progression in the mouse model. Altered MCP-1-ILK signaling leads to poor pregnancy outcomes in the mouse model. Further, our in silico results suggest that CPD22 stabilizes the interaction with Asp234 and His318 residues of ILK and inhibits the Ser246 phosphorylation. In conclusion, MCP-1 activates ILK at the Ser246 residue and leads to lesion development/progression, reflecting the therapeutic importance of ILK for endometriosis management through the mouse model.

Designing lysyl hydroxylase inhibitors for oral submucous fibrosis - Insights from molecular dynamics.

Designing lysyl hydroxylase inhibitors for oral submucous fibrosis - Insights from molecular dynamics.

Targeting RECQL4 in hepatocellular carcinoma: from prognosis to therapeutic potential

ObjectiveThe aim of this study is to assess the clinical utility of RecQ Like Helicase 4 (RECQL4) as a prognostic marker in hepatocellular carcinoma (HCC) and investigate its associations with various biological processes, angiogenesis-related factors, immune cell infiltration, immune checkpoints, and drug sensitivity.MethodsRECQL4 expression was analyzed across a range of cancer types utilizing data from the TCGA database. Disparities in RECQL4 expression levels between normal and malignant tissues were evaluated, alongside an analysis of progression-free interval (PFI), disease-specific survival (DSS), and overall survival (OS) curves. Exploration of pertinent pathways, immune cell infiltration, single-cell RNA-seq data, and drug sensitivity was conducted employing The Cancer Genome Atlas (TCGA) and Tumor Immune Single-Cell Hub (TISCH) databases. Furthermore, validation of in-silico results was validated through qPCR, Western blotting, CCK-8 assay, EdU assay, clonogenic assay, wound-healing assay, and transwell assay.ResultsIn HCC, RECQL4 was highly expressed and associated with poorer prognosis (p < 0.05). It positively correlated with pathways related to MYC targets, DNA replication, PI3K/AKT/mTOR signaling, DNA repair mechanisms, and the G2/M checkpoint (R > 0.24, p < 0.001). RECQL4 also showed significant correlations with angiogenesis-related genes, including PTK2 (R > 0.4, p < 0.05), suggesting a potential role in angiogenesis regulation. Immune analysis indicated that RECQL4 was associated with immune cell types such as T helper 2 cells, NK CD56bright cells, and follicular helper T cells, suggesting a positive relationship with their infiltration. High RECQL4 expression was also linked to increased sensitivity to drugs including Sorafenib, 5-Fluorouracil, Cisplatin, and Doxorubicin. Cellular experiments showed that RECQL4 expression at the mRNA and protein levels were significantly higher in HCC cell lines Hep3B and Huh7 compared to the normal liver cell line MHA. Moreover, RECQL4 knockdown resulted in reduced proliferation and migration in HCC cell lines (p < 0.05).ConclusionsRECQL4 shows promise as a biomarker for predicting recurrence and survival in HCC and may affect angiogenesis regulation. Its expression also appears to impact sensitivity to drugs such as Sorafenib, 5-Fluorouracil, Cisplatin, and Doxorubicin. Furthermore, silencing RECQL4 significantly inhibits HCC cell line proliferation and migration.

A Performance-Based Adaptation Index for Automated Insulin Delivery Systems.

Automated insulin delivery (AID) algorithms can benefit from tuning of their aggressiveness to meet individual needs, as insulin requirements vary among and within users. We introduce the Performance-Based Adaptation Index (PAI), a tool designed to enable automatic adjustment of an AID system aggressiveness based on continuous glucose monitoring (CGM) metrics. PAI integrates two CGM-based metrics-one for hypoglycemia and another for hyperglycemia exposure-over a previous time window into a single index (). We propose two methods to compute : one based on time in range (TIR, 70-180 mg/dL), and the other on glycemic risk indices. Using , we developed a multiplicative strategy to adjust the AID system's aggressiveness, accounting for situations where cannot be reliably calculated. The feasibility of this method was assessed in-silico using the UVA/Padova Type 1 Diabetes Simulator and our full closed-loop algorithm (UVA-model predictive control (MPC)) across five scenarios: optimal tuning (baseline), conservative and aggressive tunings, and temporary and permanent changes in insulin needs. Glycemic outcomes were evaluated from the simulated glucose traces. Negligible performance variations were observed in the baseline scenario. For the conservative scenario, adjusting improved TIR (35.1% vs 71.8%) and increased total daily insulin (32.1 U vs 41.2 U). Conversely, for the aggressive scenario, it reduced hypoglycemia exposure (TBR: 2.6% vs 1.4%) and overall insulin usage (45.6 U vs 43.0 U). In-silico results demonstrated the safety and efficacy of using PAI to automatically tune the UVA-MPC controller, achieving TIR values above 70% under fully closed-loop conditions and across various physiological states. Clinical validation of these results is warranted.