Blagotvorno djelovanje ekstrakta lovorova lista na hepatotoksičnost u štakora uzrokovanu 2,3,7,8-tetraklordibenzo-p-dioksinom in Vitro

2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a very toxic environmental pollutant that raises great public concern about its impact on human health. Recent studies indicate that laurel leaf extract exhibits antioxidant properties that can counter the toxic effects of certain compounds in the liver. The aim of this study was to assess how effective LE is against the toxicity of TCDD in a primary culture of rat hepatocytes. The extract (50 mg L-1, 100 mg L-1, and 200 mg L-1) was added to cultures alone or with TCDD (1.61 mg L-1 and 3.22 mg L-1) for 48 hours. Cell viability was measured using the [3-(4,5-dimethyl-thiazol-2-yl) 2,5-diphenyltetrazolium bromide] (MTT) assay and the lactate dehydrogenase (LDH) cytotoxicity assay, while oxidative damage was assessed by measuring total antioxidant capacity (TAC) and total oxidative stress (TOS). DNA damage was also analysed using the micronucleus (MN) assay of the cultured hepatocytes. TCDD alone lowered, and laurel extract had no effect on cell viability. TCDD also increased TOS and signifi cantly decreased TAC. It signifi cantly increased the frequency of micronucleated hepatocytes in a dose-dependent manner. In cultures exposed to LE alone, TOS did not change and TAC signifi cantly increased in a dose-dependent manner. Added to TCDD, laurel countered its toxic effects and showed protective effects against TCDD-mediated DNA damage. This points to the therapeutic potential of laurel against TCDD toxicity in the liver.2,3,7,8-tetraklordibenzo-p-dioksin (TCDD) vrlo je toksičan onečišćivač okoliša koji izaziva veliku zabrinutost zbog mogućih posljedica za zdravlje ljudi. Nedavna su ispitivanja pokazala da ekstrakt lovorova lista (Laurus nobilis L.) ima antioksidacijska svojstva koja ublažavaju hepatotoksičnost. Cilj je ovog ispitivanja bio istražiti djelotvornost ekstrakta lovorova lista protiv toksičnoga djelovanja TCDD-a na primarnoj kulturi hepatocita. Kulturama je ekstrakt dodan u dozama od 50 mg L-1, 100 mg L-1 odnosno 200 mg L-1 sam ili zajedno s TCDD-om u dozama od 1,61 mg L-1 odnosno 3,22 mg L-1. Izloženost je u oba slučaja trajala 48 h. Zatim je ispitana vijabilnost hepatocita s pomoću MTT-testa i testa na laktat dehidrogenazu (LDH). Oksidativno oštećenje mjerili smo s pomoću ukupnog antioksidativnoga kapaciteta i ukupnoga oksidativnog stresa. Oštećenje DNA hepatocita procijenjeno je s pomoću mikronukleus testa. MTT i LDH pokazali su da TCDD smanjuje vijabilnost hepatocita, ali ne i ekstrakt lovorova lista. TCDD je također povisio razinu ukupnoga oksidativnog stresa te smanjio ukupni antioksidativni kapacitet. Broj mikronukleusa rastao je s dozom TCDD-a. Nasuprot tomu, u hepatocitima izloženim samo ekstraktu lovorova lista nisu izmijenjene razine ukupnoga oksidativnog stresa, dok je ukupni antioksidativni kapacitet značajno rastao s dozom. Ekstrakt lovorova lista usto je ublažio toksično djelovanje TCDD-a na hepatocite u primarnoj kulturi. Stoga lovorov list štiti protiv oštećenja DNA uzrokovanoga TCDD-om. To ukazuje na mogućnost terapijske primjene ekstrakta lovorova lista protiv toksičnoga djelovanja TCDD-a u jetri

Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning

Simple Summary Drug repurposing is an accelerated route for drug development and a promising approach for finding medications for orphan and common diseases. Here, we compiled databases that comprise both computationally- or experimentally-derived data, and categorized them based on quiddity and origin of data, further focusing on those that present high throughput omic data or drug screens. These databases were then contextualized with genome-wide screening methods such as CRISPR/Cas9 and RNA interference, as well as state of art systems biology approaches that enable systematic characterizations of multi-omic data to find new indications for approved drugs or those that reached the latest phases of clinical trials. Modern drug discovery through de novo drug discovery entails high financial costs, low success rates, and lengthy trial periods. Drug repositioning presents a suitable approach for overcoming these issues by re-evaluating biological targets and modes of action of approved drugs. Coupling high-throughput technologies with genome-wide essentiality screens, network analysis, genome-scale metabolic modeling, and machine learning techniques enables the proposal of new drug-target signatures and uncovers unanticipated modes of action for available drugs. Here, we discuss the current issues associated with drug repositioning in light of curated high-throughput multi-omic databases, genome-wide screening technologies, and their application in systems biology/medicine approaches

Addressing the heterogeneity in liver diseases using biological networks

The abnormalities in human metabolism have been implicated in the progression of several complex human diseases, including certain cancers. Hence, deciphering the underlying molecular mechanisms associated with metabolic reprogramming in a disease state can greatly assist in elucidating the disease aetiology. An invaluable tool for establishing connections between global metabolic reprogramming and disease development is the genome-scale metabolic model (GEM). Here, we review recent work on the reconstruction of cell/tissue-type and cancer-specific GEMs and their use in identifying metabolic changes occurring in response to liver disease development, stratification of the heterogeneous disease population and discovery of novel drug targets and biomarkers. We also discuss how GEMs can be integrated with other biological networks for generating more comprehensive cell/tissue models. In addition, we review the various biological network analyses that have been employed for the development of efficient treatment strategies. Finally, we present three case studies in which independent studies converged on conclusions underlying liver disease

A Gene Co-Expression Network-Based Drug Repositioning Approach Identifies Candidates for Treatment of Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is a malignant liver cancer that continues to increase deaths worldwide owing to limited therapies and treatments. Computational drug repurposing is a promising strategy to discover potential indications of existing drugs. In this study, we present a systematic drug repositioning method based on comprehensive integration of molecular signatures in liver cancer tissue and cell lines. First, we identify robust prognostic genes and two gene co-expression modules enriched in unfavorable prognostic genes based on two independent HCC cohorts, which showed great consistency in functional and network topology. Then, we screen 10 genes as potential target genes for HCC on the bias of network topology analysis in these two modules. Further, we perform a drug repositioning method by integrating the shRNA and drug perturbation of liver cancer cell lines and identifying potential drugs for every target gene. Finally, we evaluate the effects of the candidate drugs through an in vitro model and observe that two identified drugs inhibited the protein levels of their corresponding target genes and cell migration, also showing great binding affinity in protein docking analysis. Our study demonstrates the usefulness and efficiency of network-based drug repositioning approach to discover potential drugs for cancer treatment and precision medicine approach

Longitudinal metabolomics analysis reveals the acute effect of cysteine and NAC included in the combined metabolic activators

Growing evidence suggests that the depletion of plasma NAD+ and glutathione (GSH) may play an important role in the development of metabolic disorders. The administration of Combined Metabolic Activators (CMA), consisting of GSH and NAD+ precursors, has been explored as a promising therapeutic strategy to target multiple altered pathways associated with the pathogenesis of the diseases. Although studies have examined the therapeutic effect of CMA that contains N-acetyl-L-cysteine (NAC) as a metabolic activator, a system-wide comparison of the metabolic response to the administration of CMA with NAC and cysteine remains lacking. In this placebo-controlled study, we studied the acute effect of the CMA administration with different metabolic activators, including NAC or cysteine with/without nicotinamide or flush free niacin, and performed longitudinal untargeted-metabolomics profiling of plasma obtained from 70 well-characterized healthy volunteers. The time-series metabolomics data revealed the metabolic pathways affected after the administration of CMAs showed high similarity between CMA containing nicotinamide and NAC or cysteine as metabolic activators. Our analysis also showed that CMA with cysteine is well-tolerated and safe in healthy individuals throughout the study. Last, our study systematically provided insights into a complex and dynamics landscape involved in amino acid, lipid and nicotinamide metabolism, reflecting the metabolic responses to CMA administration containing different metabolic activators

Stratification of patients with clear cell renal cell carcinoma to facilitate drug repositioning

Clear cell renal cell carcinoma (ccRCC) is the most common histological type of kidney cancer and has high heterogeneity. Stratification of ccRCC is important since distinct subtypes differ in prognosis and treatment. Here, we applied a systems biology approach to stratify ccRCC into three molecular subtypes with different mRNA expression patterns and prognosis of patients. Further, we developed a set of biomarkers that could robustly classify the patients into each of the three subtypes and predict the prognosis of patients. Then, we reconstructed subtype-specific metabolic models and performed essential gene analysis to identify the potential drug targets. We identified four drug targets, including SOAT1, CRLS1, and ACACB, essential in all the three subtypes and GPD2, exclusively essential to subtype 1. Finally, we repositioned mitotane, an FDA-approved SOAT1 inhibitor, to treat ccRCC and showed that it decreased tumor cell viability and inhibited tumor cell growth based on in vitro experiments

Klorheksidin diglukonatın insan periferal kan kültürlerinde antioksidan enzim seviyeleri üzerine etkilerinin incelenmesi

Objectives: In the present study, it was aimed to investigate the biochemical effects of chlorhexidine digluconate (CHX) on the antioxidant enzyme levels in human peripheral blood cell cultures. Materials and Methods: The blood cultures were prepared using the blood samples obtained from 10 individuals (5 male and 5 female) who were systemically healthy and were not exposed to any toxic agent before. The cultures were exposed to different concentrations of CHX (0.05, 0.1, 0.2 ve 0.4 mmol/L). Glutation peroxidase (GPx), superoxide dismutase (SOD) and Catalase (CAT) enzyme activities were analyzed in order to evaluate the biochemical effects. Results: A dose-dependent statistically significant reduction was seen in the GPx, SOD and CAT enzyme activities in the blood cultures treated with 0.1, 0.2 ve 0.4 mmol/L concentrations of CHX. Conclusion: This is the first in vitro study investigating the effects of CHX on antioxidant enzyme levels in the human peripheral blood cultures. In conclusion, it was revealed that CHX had dose-depended cytotoxic effects by influencing the antioxidant enzyme activities in blood cells. ÖZET Amaç: Bu çalışmada, klorheksidin diglukonatın (KHG) insan periferal kan kültürlerinde antioksidan enzim seviyeleri üzerine olan biyokimyasal etkilerinin araştırılması amaçlandı. Gereç ve Yöntem: Daha önce herhangi bir toksik ajana maruz kalmamış ve sistemik olarak sağlıklı 10 bireyden (5 erkek, 5 kadın) elde edilen kan örnekleri ile kan kültürleri hazırlandı. Elde edilen kültürler farklı konsantrasyonlarda KHG (0.05, 0.1, 0.2 ve 0.4 mmol/L) ile muamele edildi. Biyokimyasal etkilerin değerlendirilmesi amacıyla glutatyon peroksidaz (GPx), süperoksit dismutaz (SOD) ve katalaz (KAT) enzim aktiviteleri incelendi. Bulgular: KHG'nin 0.1, 0.2 ve 0.4 mmol/L'luk konsantrasyonları ile muamele edilen kan kültürlerinde GPx, SOD ve CAT enzim aktivitelerinde doza bağlı istatistiksel olarak anlamlı derecede azalma izlendi (p<0.05). Sonuç: Bu çalışma, KHG'nin insan periferal kan kültürlerinde antioksidan enzim seviyeleri üzerindeki etkilerini araştıran ilk in vitro çalışmadır. Sonuç olarak, bu bileşiğin kan hücrelerindeki antioksidan enzim aktivitelerini etkilemek suretiyle doza bağlı sitotoksik etkilere sahip olduğu da ortaya konulmuştur

Prediction of drug candidates for clear cell renal cell carcinoma using a systems biology-based drug repositioning approach

Background: The response rates of the clinical chemotherapies are still low in clear cell renal cell carcinoma (ccRCC). Computational drug repositioning is a promising strategy to discover new uses for existing drugs to treat patients who cannot get benefits from clinical drugs. Methods: We proposed a systematic approach which included the target prediction based on the co-expression network analysis of transcriptomics profiles of ccRCC patients and drug repositioning for cancer treatment based on the analysis of shRNA- and drug-perturbed signature profiles of human kidney cell line. Findings: First, based on the gene co-expression network analysis, we identified two types of gene modules in ccRCC, which significantly enriched with unfavorable and favorable signatures indicating poor and good survival outcomes of patients, respectively. Then, we selected four genes, BUB1B, RRM2, ASF1B and CCNB2, as the potential drug targets based on the topology analysis of modules. Further, we repurposed three most effective drugs for each target by applying the proposed drug repositioning approach. Finally, we evaluated the effects of repurposed drugs using an in vitro model and observed that these drugs inhibited the protein levels of their corresponding target genes and cell viability. Interpretation: These findings proved the usefulness and efficiency of our approach to improve the drug repositioning researches for cancer treatment and precision medicine. Funding: This study was funded by Knut and Alice Wallenberg Foundation and Bash Biotech Inc., San Diego, CA, USA

Antidepressant Flavonoids and Their Relationship with Oxidative Stress

Depression is a serious disorder that affects hundreds of millions of people around the world and causes poor quality of life, problem behaviors, and limitations in activities of daily living. Therefore, the search for new therapeutic options is of high interest and growth. Research on the relationship between depression and oxidative stress has shown important biochemical aspects in the development of this disease. Flavonoids are a class of natural products that exhibit several pharmacological properties, including antidepressant-like activity, and affects various physiological and biochemical functions in the body. Studies show the clinical potential of antioxidant flavonoids in treating depressive disorders and strongly suggest that these natural products are interesting prototype compounds in the study of new antidepressant drugs. So, this review will summarize the chemical and pharmacological perspectives related to the discovery of flavonoids with antidepressant activity. The mechanisms of action of these compounds are also discussed, including their actions on oxidative stress relating to depression

Discovery of therapeutic agents targeting PKLR for NAFLD using drug repositioning

Background: Non-alcoholic fatty liver disease (NAFLD) encompasses a wide spectrum of liver pathologies. However, no medical treatment has been approved for the treatment of NAFLD. In our previous study, we found that PKLR could be a potential target for treatment of NALFD. Here, we investigated the effect of PKLR in in vivo model and performed drug repositioning to identify a drug candidate for treatment of NAFLD. Methods: Tissue samples from liver, muscle, white adipose and heart were obtained from control and PKLR knockout mice fed with chow and high sucrose diets. Lipidomics as well as transcriptomics analyses were conducted using these tissue samples. In addition, a computational drug repositioning analysis was performed and drug candidates were identified. The drug candidates were both tested in in vitro and in vivo models to evaluate their toxicity and efficacy. Findings: The Pklr KO reversed the increased hepatic triglyceride level in mice fed with high sucrose diet and partly recovered the transcriptomic changes in the liver as well as in other three tissues. Both liver and white adipose tissues exhibited dysregulated circadian transcriptomic profiles, and these dysregulations were reversed by hepatic knockout of Pklr. In addition, 10 small molecule drug candidates were identified as potential inhibitor of PKLR using our drug repositioning pipeline, and two of them significantly inhibited both the PKLR expression and triglyceride level in in vitro model. Finally, the two selected small molecule drugs were evaluated in in vivo rat models and we found that these drugs attenuate the hepatic steatosis without side effect on other tissues. Interpretation: In conclusion, our study provided biological insights about the critical role of PKLR in NAFLD progression and proposed a treatment strategy for NAFLD patients, which has been validated in preclinical studies. Funding: ScandiEdge Therapeutics and Knut and Alice Wallenberg Foundation