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- Volume 21, Issue 15, 2024
Letters in Drug Design & Discovery - Volume 21, Issue 15, 2024
Volume 21, Issue 15, 2024
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Prediction and Validation of Proline-containing Tripeptides with Angiotensin I-converting Enzyme Inhibitory Activity Using Machine Learning Models
Authors: Toshiya Hatakenaka, Yuki Fujimoto, Kouji Okamoto and Tamaki KatoBackgroundNumerous inhibitory peptides against angiotensin I-converting enzyme, a target for hypertension treatment, have been found in previous studies. Recently, machine learning screening has been employed to predict unidentified inhibitory peptides using a database of known inhibitory peptides and descriptor data from docking simulations.
ObjectiveThe aim of this study is to focus on angiotensin I-converting enzyme inhibitory tripeptides containing proline, to predict novel inhibitory peptides using the machine learning algorithm PyCaret based on their IC50 and descriptors from docking simulations, and to validate the screening method by machine learning by comparing the results with in vitro inhibitory activity studies.
MethodsIC50 of known inhibitory peptides were collected from an online database, and descriptor data were summarized by docking simulations. Candidate inhibitory peptides were predicted from these data using the PyCaret. Candidate tripeptides were synthesized by solid-phase synthesis and their inhibitory activity was measured in vitro.
ResultsSeven novel tripeptides were found from the peptides predicted to have high inhibitory activity by machine learning, and these peptides were synthesized and evaluated for inhibitory activity in vitro. As a result, the proline-containing tripeptide MPA showed high inhibitory activity, with an IC50 value of 8.6 μM.
ConclusionIn this study, we identified a proline-containing tripeptide with high ACE inhibitory activity among the candidates predicted by machine learning. This finding indicates that the method of predicting by machine learning is promising for future inhibitory peptide screening efforts.
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Computational and In vitro Elucidation of Indolenine-barbituric Acid Zwitterions as Potential Chemotherapeutical Agents
Authors: Kang Kit Ong, Abdul Qaiyum Ramle, Min Phin Ng, Siew Huah Lim, Kae Shin Sim and Chun Hoe TanIntroductionThe continuous pursuit of novel chemotherapeutical agents with improved efficacy and reduced adverse effects remains a critical area of research despite advancements in chemotherapy. We have previously synthesized indolenine and barbituric acid zwitterion scaffolds 1–10 sustainably; however, their precise chemotherapeutical properties are still lacking.
MethodsIn this present work, we conducted in silico ADMET analyses, molecular docking calculations, DNA binding studies, and cytotoxicity assays on these zwitterions.
Results and DiscussionAmong the 10 zwitterions, zwitterion 3 bearing a methoxy group demonstrated the highest drug-likeness score, low toxicity, as well as no violation of Lipinski’s rule of five and Veber’s rule. Both molecular docking calculations and DNA binding studies suggested that the minor groove of DNA is the most probable molecular target of 3 among the others (i.e., topoisomerase and tubulin). In addition, zwitterion 3 exhibited selective cytotoxicity against a wide array of human cancer cell lines without noticeable effect against the normal human colon fibroblast CCD-18Co.
ConclusionOverall, these preliminary findings from our combined computational and experimental strategy suggested that 3 remains promising for further elaboration as a chemotherapeutic agent.
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Efficacy of Ginger, Cardamom, Purslane, Saffron and Cinnamon Consumption on Lipid Profile, Glycemic Control, Blood Pressure and Markers of Anthropometric and Inflammation in Metabolic Syndrome Patients: A Systematic Review and Network Meta-Analysis
BackgroundMetabolic syndrome (MetS), also known as syndrome X or insulin resistance, is a complex disorder characterized by multiple risk factors. It is caused by insulin resistance, which is accompanied by abnormal accumulation and dysfunction of adipose tissue.
IntroductionRecently, several studies have evaluated the efficacy of herbs on MetS. The purpose of this meta-analysis is the comprehensive assessment of the impact of cardamom, cinnamon, saffron, purslane and ginger on the parameters of MetS in patients with MetS.
MethodsA systematic search was performed based on the English language reports of literature from databases including PubMed, Scopus, Cochrane, and Web of Science and 29 RCT (randomized clinical trial) studies were included in the meta-analysis. This meta-analysis was registered in PROSPERO.
ResultsThe results showed significant beneficial effects of cardamom on Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) and waist circumference (WC), cinnamon on diastolic blood pressure (DBP) and weight, ginger on fasting blood sugar (FBS), Hemoglobin A1c HbA1c and HOMA-IR and purslane on triglyceride (TG), total cholesterol (TC), body mass index (BMI) and FBS compared to the placebo; thus, they can be useful in the management of patients with MetS.
ConclusionIt is suggested that more RCT studies should be performed on the factors affecting the efficacy of these plants on the parameters of the MetS.
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Bioactivity-guided Separation of Antinociceptive and Antioxidant Subfractions from Alkaline Chloroform Fraction of Fenugreek Seeds (Trigonella foenum-graecum L.) in an Animal Model
Authors: Amir Asadi, Ali Mandegary, Mostafa Pournamdari, Mahboobe Abbasi, Neda Mohamadi and Fariba SharififarBackgroundAntinociceptive effect of fenugreek seeds (Trigonella foenum-graecum L.) has been reported in different animal models in response to various chemical or thermal stimuli. In a recent study, alkaline chloroform fraction (AKC) of this plant has exhibited the greatest analgesic effect.
ObjectiveIn the present study, to isolate the active component(s) from the plant, the subfractions resulting from AKC column chromatography were evaluated in an animal model for anti-nociception effect.
MethodsFrom the 17 separated fractions, 5 major fractions (F4, F6, F14, F15 and F16) were used for the formalin test at three different doses (2.5, 5 10 mg/kg). Antioxidant activity of the most active subfractions was studied too.
ResultsSubfractions F16 and F14 (5, 10 mg/kg) showed the greatest analgesic effect and reduced the pain score which was similar to morphine and even stronger than morphine in some doses. The greatest antioxidant activity was observed by F14 (radical inhibition percentage of 17.34 ± 0.14 in DPPH assay, reduction power percentage of 74.05 ± 4.23 in RPA versus green tea (91.68 ± 3.04 and 97.59 ± 6.24 in DPPH assay and RPA test respectively). The absorbance of F14 was 0.25 ± 0.11 in the FTC method in comparison to ascorbic acid 10 µg/ml and 100 µg/ml (0.72 ± 0.33 and 0.05 ± 0.41 respectively).
ConclusionSeparated subfractions exhibited more antinociceptive effect than AKC fraction, so further separation can lead to the acquisition of antinociceptive compound (s), while AKC fraction was found to be more potent antioxidant than separated sub-fractions in all three experiments. So, most likely, the anti-nociception effect of subfractions might be achieved via other mechanisms than antioxidant activity. Based on phytochemical screening, AKC and all sub-fractions especially F14, F15 and F16 were positive for the presence of alkaloids and only F14 was positive for flavonoids.
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Essential Structural Profile of Novel Adenosine Derivatives as Antiplatelet Aggregation Inhibitors based on 3D-QSAR Analysis
Authors: Shunlai Li, Pengyu Zheng, Yajing Ren and Hongguang DuAimsIn this research, 3D-QSAR evaluation on a set of fresh purinoid compounds that we produced was conducted. This analysis aims to illustrate the correlation between the structure of purine and its ability to prevent platelet aggregation. Our findings could pave the way to discovering novel antithrombotic medications.
BackgroundThe incidence of cardiovascular disease triggered by the clumping of platelets poses a significant danger to human health. Purine derivatives are important molecules with antiplatelet aggregation activity.
ObjectiveThe objectives of this research are to establish the correlation between the structure of purine and its ability to prevent platelet aggregation. Such a correlation could aid in the development of innovative antithrombotic medications.
MethodsIn this study, 3D-QSAR investigation on a collection of 75 new purine derivatives, which we synthesized, was conducted, utilizing Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA).
ResultsSignificant correlation coefficients (CoMFA, q2= 0.843, r2= 0.930, F value= 266.755, SEE= 0.165; CoMSIA, q2= 0.869, r2= 0.918, F value= 222.571, SEE= 0.179) were obtained, and assessed the model's predictive capabilities by validating it with the test set.
ConclusionOur findings indicate that the introduction of an appropriately sized structure at position 2 of the compound yields significant benefits. Conversely, the attachment of an excessively large group is detrimental. Direct attachment of a bulky substituent at C-6 of the compound is not feasible, and its activity increases when the structure with low electron cloud density is added. Moreover, the presence of a voluminous functional group at the 5' position of the compound is advantageous, and its activity will be further increased by the presence of hydrogen bond receptors in this region. These discoveries furnish significant comprehension for the formation of innovative structures with heightened efficacy.
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Highly Efficient and One-pot New Betti Bases: PEG-400 and Al2O3 Mediated Synthesis, Optimizations, and Cytotoxic Studies
Authors: Reshmabanu Piludiya and Khushal M. KapadiyaBackgroundMulticomponent reactions (MCRs) have proven as one of the best alternatives to minimize several environmental consequences, mainly the use of hazardous chemicals, by-products, and severe production processes. Literature reveals that MCRs with PEG-400 and metal oxide-based greener media provide a new and useful strategy for the construction of biologically potent organic systems.
ObjectiveThe present study aimed to synthesize newer Betti bases by a modified Betti reaction employing a highly efficient catalyst for the direct synthesis of a novel class of non-racemic amino benzyl naphthol ligands under green solvent media. The involvement of the articulated framework (4a-4j) was studied against nine cancer panels (NCI-60 cell lines) in terms of inhibiting/killing cancer cells.
MethodsFor the modification of the Betti reaction, we used 2-aminopyridin-3-ol, aromatic aldehydes, and a naphthol system using greener media employing PEG-400 and alumina as a prime active and highly selective catalyst. Furthermore, the antiproliferative activity against NCI-60 human cancer cell lines (GI50) was used for the development of pharmacologically active compounds and exhibited the single dose (10-5 M) study.
ResultsBased on greener media synthesis, recompenses of ease of workup, less reaction time, higher yield, and higher atom economy, as well as environmentally friendly, were reported. Betti bases were obtained at a yield of 87-98% and characterized by spectroscopic techniques. Among the synthesized scaffolds, compound 4b was found to be extra potent in melanoma cancer [MDA-MB-435], while compound 4h showed promising inhibition in leukemic cancer cell lines [HL-60(TB) and MOLT-4].
ConclusionA straightforward way for an efficient synthesis of Betti bases was developed via the reaction of naphthol and aldehydes with amines in PEG-400 media. An Al2O3 was effectively catalyzed in the Betti reaction in excellent yields without the formation of any other by-product in atom economy and environmentally benign way. The newly synthesized hybrids were tested in vitro against a panel of cancer cell lines, and some of the compounds exhibited significant inhibitory anti-proliferative effects. The most potent compounds (4b and 4h) showed interesting results, and compound 4b was found extra potent in melanoma cancer cell lines with -62% GI values.
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Hepatoprotective Effects of Rheum turkestanicum Janisch on High-fat Diet-induced Non-alcoholic Fatty Liver Disease in Mice
BackgroundConsumption of a high-fat diet (HFD) is one of the main causes of non-alcoholic fatty liver disease (NAFLD), which is increasing due to lifestyle changes and is still an important global health issue. Despite the efforts, there is still no common treatment for this disease. Studies have shown that the root of Rheum turkestanicum Janisch has a hypolipidemic effect and a significant antioxidant effect on liver tissue in diabetic rats. However, no experimental study has been performed on the hepatoprotective effects of this herb on HFD-induced NAFLD have been proven.
ObjectiveThis study aimed to evaluate the effect of Rheum turkestanicum Janisch extract (RTE) on HFD-induced NAFLD in BALB/c mice.
Materials and MethodsThe study was performed with two models of prevention and therapeutic effect of RTE. Serum biochemical markers, histopathology, oxidative stress indicators, and qRT-PCR were measured to evaluate the effects of RTE on lipid metabolism disorders in mice feeding with HFD.
ResultsIn the prevention model, compared to the HFD group, RTE treatment decreased the levels of glucose, triglyceride, and cholesterol and improved liver profile markers, oxidative stress, and expression of genes involved in lipid metabolism.
ConclusionThe results of this study suggest that RTE has hepatoprotective effects against HFD-induced liver damage by reducing oxidative stress, lipogenesis, and increasing beta-oxidation of free fatty acids.
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The Synergistic Effect of Curcumin and Piperine Nanoparticles on Methamphetamine-induced Neurotoxicity, Oxidative Stress, and Memory Impairments in Mice Brain
BackgroundMethamphetamine (METH) is a highly addictive neural stimulant that severely affects the CNS and can induce oxidative damage. Piperine and curcumin are active constituents that have numerous properties, including antioxidant, anti-inflammatory, and neuroprotective.
ObjectiveIn this study, the synergistic effect of piperine and curcumin nanoparticles was investigated on the acute doses of METH-induced neurotoxicity in mice brains.
MethodsMETH (6 mg/kg, i.p) was administered to 14 groups of mice and piperine-curcumin nanoparticles at different doses (10, 20, 40 mg/kg and 20, 40 and 60 mg/kg, respectively) were administered. Open field test (OFT) and conditioned place preference (CPP) were used to investigate locomotor activity, anxiety-like behavior, and addictive behavior in mice. Oxidative stress biomarkers (reactive oxygen species (ROS), protein carbonyl content, lipid peroxidation, glutathione content, and mitochondrial function were evaluated in isolated brain mitochondria.
ResultsWe found that piperine and curcumin nanoparticles significantly decreased hyperlocomotion and anxiety-like behavior in METH-treated mice. Also, METH enhanced CPP whilst piperine and curcumin nanoparticles suppressed the effect of METH-induced CPP. METH administration significantly increased ROS, protein carbonyl content, and lipid peroxidation and decreased glutathione content and mitochondrial function in the isolated brain mitochondria. Piperine and curcumin nanoparticles (at all doses) showed synergistic effects on reducing oxidative damages in a dose-dependent manner compared to the METH group.
ConclusionIn conclusion, combined piperine and curcumin nanoparticles showed greater neuroprotective effects against METH-induced neurotoxicity due to their greater permeability and better antioxidant properties than piperine and curcumin alone.
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Crocin Potentiates Anti-tumor Properties of 5-FU by Regulating Cell Proliferation and Tumor Necrosis in Breast Cancer
IntroductionBreast cancer is one of the most prevalent malignancies among women around the world. Crocus sativus, a natural food coloring and flavoring, has potent anti-tumor properties. The aim of the current study was to investigate the therapeutic potential of crocin, the main pharmacological active component of saffron, either alone or in combination with the standard chemotherapeutic treatment, 5-FU, in Breast cancer (BC) progression in both cellular and animal models.
Material and MethodsMTT, Real-Time PCR, Western Blotting, Hematoxylin and eosin (H&E) tissue staining were applied to determine the anti-tumor properties of crocin in in vitro and in vivo samples.
ResultsOur findings showed that crocin decreased breast cancer cell proliferation by suppressing cyclin D1 expression and Wnt/β-catenin signaling activation. Moreover, this molecule improved 5-FU anti-cancer activities by decreasing the tumor volume and weight, increasing tumor necrosis, and suppressing tumor inflammation in an animal model. Inflammation-associated anti-cancer activity of crocin is mediated by the down-regulation of pro-inflammatory genes, including IFN-γ and IL-1β, as well as inhibition of oxidative stress responses within the tumor environment.
ConclusionThis is the first study demonstrating the potent anti-tumor properties of crocin against BC progression. Our results suggest that this effective and low-toxic molecule could be a promising agent for reducing BC tumor progression when administered either alone or in combination with standard treatment in breast cancer patients.
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Bioinformatics-based Analysis of the Variability of MPOX Virus Proteins
BackgroundPreviously restricted to remote areas of Central and Western Africa, the MPOX virus-based disease, also known as monkeypox, has now spread to more than 90 countries and has become endemic. As a consequence, the MPOX virus has become a global public health concern.
ObjectiveThe objective of this study was to conduct a computational-multiparametric study (at the genomic and proteomic levels) of the biological sequences that express the MPOX virus envelopes in order to fathom the physicochemical regularities of these proteins.
MethodsUsing computer programs, we determined the polarity index method (PIM) profile and protein intrinsic disorder predisposition (PIDP) for each studied protein.
ResultsThe UniProt database was able to identify sequences similar to those of the MPOX virus expressed thanks to the computational regularities found in the virus' envelope sequences.
ConclusionThe polarity index method and protein intrinsic disorder predisposition profiles could aid in elucidating the sequence-level structural regularities of the MPOX virus envelopes.
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Synthesis of Some Novel 4-bromobenzoic Acid Clubbed Hydrazone Schiff Base Derivatives as Potent α-amylase Inhibitors: In vitro and In silico Studies
AimsSynthesis of novel 4-bromobenzoic acid-based hydrazone-Schiff base derivatives and to screen them for their α-amylase inhibitory activity.
BackgroundThe most often employed organic compounds are derivatives of the hydrazone-Schiff base. Numerous biological actions, such as antipyretic, antiviral, anti-inflammatory, anti-proliferative, anti-malarial, antibacterial, and anti-fungal ones, have been linked to them.
ObjectiveThe biological activities of hydrazone-Schiff base compounds encouraged us to evaluate the synthesized derivatives (4-32) for in-vitro inhibition activity against the α-amylase enzyme.
MethodsIn current research work twenty-nine Schiff base derivatives (4-32) of 4-bromobenzoic acid were synthesized in worthy yields by treating various replaced aldehydes with 4-bromobenzohydrazide using methanol solvent in catalytic quantity of acetic acid. The products were structurally described through the support of several spectroscopic methods (EI-MS and 1H-NMR) and finally evaluated against α-amylase enzyme.
ResultsAll the made derivatives exhibited worthy inhibition potential from IC50 = 0.21 ± 0.01 to 5.50 ± 0.01 µM when equated to the usual acarbose drug having IC50 = 1.34 ± 0.01 µM. Compound 21 (IC50 = 0.21 ± 0.01 µM) was established as the most active inhibitor among the series better than standard. The structure-activity relationship study showed that the alteration in the activity of the produced products might be due to the attached position and nature of the substituents. Furthermore, in-silico study supported the effects of groups attached on the binding interaction with α-amylase enzyme.
ConclusionA series of substituted hydrazone Schiff bases based on 4-bromobenzoic acid were produced, confirmed the structures by EI-MS and 1H-NMR spectroscopic methods and lastly tested for their in-vitro α-amylase inhibitory potential. Among the series, twenty-four products indicated brilliant inhibition potential having IC50 values from 0.21 ± 0.01 to 1.30 ± 0.01 µM. The structure-activity relationship study showed that the alteration in the activity of the synthesized products might be due to the attached position and nature of the substituents. On the other hand, in silico studies advocated that the synthesized Schiff base derivatives have prevalent interactions of binding within the active site of the α-amylase enzyme, and because of their various attached substituent, their conformation is altered in the active site of the enzyme. The current study recognized a number of lead candidates derived from 4-bromobenzoic acid. Additional investigation of the synthesized derivatives for coming research to get novel α-amylase inhibitors.
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In-silico Docking and Dynamics Simulation Analysis of Peroxisome Proliferator-Activated Receptor-Gamma and β-Carotene
BackgroundPeroxisome proliferator-activated receptor-gamma (PPAR-γ) plays a crucial role in regulating lipid and glucose metabolism, cancer, and inflammation, making it an attractive target for drug development. Meanwhile, β-Carotene, known for its antioxidant, anticancer and anti-inflammatory properties, holds promise for modulating PPAR-γ activity. Understanding their interaction is crucial.
ObjectiveThis study aims to explore the therapeutic potential of β-carotene in modulating PPAR-γ activity by investigating their binding interactions.
MethodsScreening of bioactive compounds from PubChem was conducted using GlideXP to identify potential PPAR-γ (PDB: 2PRG) ligands. During this screening, both protein and bioactive compounds were prepared following established protocols. Subsequently, the compounds were docked into the ligand binding domain (LBD) of the protein using XP docking. Rosiglitazone was used as an internal control. β-Carotene emerged as a lead based on Lipinski’s rule, docking score, free energy, and LBD interactions. Molinspiration analysis assessed its drug likeness. Molecular dynamics (MD) simulations utilizing Desmond with OPLS 2005 force field were employed to examine the dynamics and stability of the PPAR-γ/β-carotene complex.
Resultsβ-carotene had strong hydrophobic interactions with specific residues within the ligand-binding domain of PPAR-γ. The calculated binding affinity (-9.07 kcal/mol) indicated a strong interaction between β-carotene and PPAR-γ, suggesting that β-carotene may modulate the activity of PPAR-γ. On a time scale of 100 ns, the MD simulations provided insights into the conformational changes, flexibility, and intermolecular interactions within the complex.
ConclusionIn silico docking and dynamics simulation analyses show that PPAR-γ and β-carotene can form a stable complex, suggesting potential implications for metabolic modulation.
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Integrating Network Pharmacology and Transcriptomic Strategies to Explore the Pharmacological Mechanism of Paeoniflorin Exerts Antidepressant Effects
Authors: Lili Su, Zixian Wang, Pengli Guo, Zhongmei He, Jianming Li, Yan Zhao, Ying Zong, Weijia Chen and Rui DuBackgroundPaeoniflorin has been proven to have neuroprotective and antidepressant effects in several studies. However, there is currently no comprehensive elaboration of its antidepressant effects through network pharmacology combined with transcriptomics analysis. The purpose of this study is to explore the potential mechanisms by which paeoniflorin exerts its antidepressant effects using network pharmacology and transcriptomics sequencing approaches.
MethodsWe utilized metascape to enrich the intersecting targets for paeoniflorin and depression for enrichment analyses. Additionally, we employed Cytoscape software to construct target pathway networks. For the screening of differentially expressed genes (DEGs) altered by paeoniflorin, we sequenced mRNA from the hippocampal tissue of CUMS model mice using the BMKCloud platform. We further enriched their biological functions and signaling pathways by using the Omishare database. The study utilized a combination of network pharmacology and transcriptomics analysis to evaluate the interactions between paeoniflorin and key targets. The results were then verified through a molecular docking process and a subsequent Western blot experiment.
ResultsAccording to a comprehensive analysis, paeoniflorin has 19 key targets that are closely related to its therapeutic effect. Molecular docking revealed that paeoniflorin has a high affinity for HIF-1α, VEGFA, and other targets. Furthermore, protein expression and immunofluorescence staining analysis showed that paeoniflorin significantly increased the expression level of HIF-1α and VEGFA in the hippocampus of depression model mice.
ConclusionThese findings suggest that paeoniflorin may have therapeutic potential in depression through the activation of the HIF-1α-VEGFA pathway.
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Short-term Administration of Naringin Improves Renal Function in Renal Ischemia-reperfusion by Increasing Aquaporin-1 and Aquaporin-2 Levels
Authors: Zübeyde Demir, Gozde Acar, Dervis Dasdelen, Rasim Mogulkoc and Abdulkerim Kasim BaltaciBackgroundSince renal ischemia-reperfusion (I/R) can lead to a serious health problem, aquaporins have important roles in preventing negative changes in electrolyte-water balance. This study aimed to determine the effect of naringin treatment on renal function and AQP1 and AQP2 levels in the kidney cortex and medulla tissues in experimental renal I/R in rats.
Materials and MethodsThe study was carried out on 40 male Wistar-type rats, 8-12 weeks old. Experimental groups were formed as follows: 1) Control, 2) Sham+vehicle, 3) Renal (I/R)+vehicle, 4) Renal I/R+ Naringin (50 mg/kg/day) (3 days of administration), and 5) Renal I/R+ Naringin (100 mg/kg/day) (3 days supplementation) group. First, the left kidney was removed by nephrectomy under general anesthesia, and then the right kidney was subjected to 45 minutes of ischemia and then 72 hours of reperfusion. Naringin was given to the experimental animals by an intraperitoneal route at the beginning of the reperfusion, after 24 and 48 hours. At the end of the experiments, first of all, blood samples were taken from the heart in animals under general anesthesia, and then the animals were killed by cervical dislocation, and kidney tissue samples were taken. Osmolarity in plasma and urine and plasma creatinine levels were evaluated. AQP1 and AQP2 levels were analyzed in the kidney cortex and medulla tissues by ELISA and PCR methods.
ResultsIn kidney tissues, I/R led to a decrease in plasma and urinary osmolarity, AQP1 and AQP2 levels in the cortex and medulla, and an increase in urea and creatinine levels (p < 0.001). However, naringin supplementation corrected the deterioration to a certain extent.
ConclusionThe results of the study show that naringin supplementation at different doses, such as 50 or 100 mg/kg, may have protective effects on the deterioration of renal function caused by unilateral nephrectomy and I/R in rats.
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- Drug Design, Discovery and Therapy, Drug Design & Discovery, Medicinal Chemistry, Pharmacology
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Identification of Novel CDK 4/6 Inhibitors by High-throughput Virtual Screening
Authors: Abhijit Debnath and Rupa MazumderBackgroundCDK4/6 plays a crucial role in regulating cell proliferation, and inhibiting this kinase can effectively prevent the initiation of cell growth and division. However, current FDA-approved CDK4/6 inhibitors have limitations such as poor bioavailability, adverse effects, high cost, and limited accessibility. Thus, this research aimed to discover novel CDK4/6 inhibitors to overcome the challenges associated with FDA-approved inhibitors.
MethodsTo identify potential CDK4/6 inhibitors, we have performed structure-based virtual screening. Chem-space and Mcule databases have been screened, followed by a series of filtering steps. These steps included assessing drug-likeness, PAINS alert, synthetic accessibility scores, ADMET properties, consensus molecular docking, and performing molecular dynamics simulations.
ResultsFour new compounds (CSC089414133, CSC091186116, CSC096023304, CSC101755872) have been identified as potential CDK4/6 inhibitors. These compounds exhibited strong binding affinity with CDK4/6, possessed drug-like features, showed no PAINS alert, had a low synthetic accessibility score, demonstrated effective ADMET properties, were non-toxic, and exhibited high stability.
ConclusionInhibiting CDK4/6 with the identified compounds may lead to reduced cell proliferation and the promotion of cancer cell death.
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3D and 2D-QSAR Studies on Natural Flavonoids for Nitric Oxide Production Inhibitory Activity
Authors: Chunqiang Wang, Yuzhu Fan, Minfan Pei, Chaoqun Yan and Taigang LiangBackgroundNitric oxide (NO), an important second messenger molecule, regulates numerous physiological responses, while excessive NO generates negative effects on the circulatory, nervous and immune systems. Recently, some natural flavonoids were reported to possess the capability of inhibiting LPS-induced NO production. To fully understand the nature of their own NO inhibitory activity, it is necessary to address the structural requirements of flavonoids as NO inhibitors.
ObjectiveThe objective of this work was to develop efficient QSAR models for predicting the NO-inhibitory activity of new flavonoids and improving insights into the critical properties of the chemical structures that were required for the ideal NO production inhibitory activities.
MethodsTo provide insights into the structural basis of flavonoids as NO inhibitors, 3D quantitative structure-activity relationship (3D-QSAR) and 2D-QSAR models were developed on a dataset of 55 flavonoids using comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and hologram quantitative structure-activity relationship (HQSAR) approaches.
ResultsThe statistically significant models for CoMFA, CoMSIA and HQSAR resulted in cross-validated coefficient (q2) values of 0.523, 0.572 and 0.639, non-cross-validated coefficient (r2) values of 0.793, 0.828 and 0.852, respectively. The robustness of these models was further affirmed using a test set of 18 compounds, which resulted in predictive correlation coefficients (r2 pred) of 0.968, 0.954 and 0.906. Furthermore, the models-derived contour maps were appraised for activity trends for the molecules analyzed.
ConclusionThe 3D and 2D-QSAR models constructed in this paper were efficient in estimating the NO inhibitory activities of flavonoids and facilitating the design of flavonoid-derived NO production inhibitors.
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In silico Investigation of the Pro-apoptotic Potential of Syringic Acid Analog
Authors: Hossein Hosseini, Reza Rajaie Khorasani, Sepideh Ketabi and Farrokh Roya NikmaramBackgroundConformational changes in BAX are associated with the activation of its pro-apoptotic potential. Previously, small molecule BAX antagonists have been shown to bring about apoptosis by inducing conformational changes in BAX by direct binding to the serine 184 site of BAX.
MethodsIn this article, we have proposed that syringic acid analog SA14 can incur apoptosis by directly binding to and inducing conformational changes in BAX. The pro-apoptotic potential of SA14 has been investigated using an in silico structure-based approach, i.e., docking and molecular dynamics computations are employed to study the binding of SA14 to the residues of the active site of BAX.
ResultsBased on docking results, four BAX-SA14 complexes, each representative of a cluster of conformations, have been selected for molecular dynamics simulations. The root mean square deviation has indicated the formation of stable conformations for two of the complexes. Other parameters, such as root mean square fluctuation, radius of gyration, and solvent accessible surface area, have been used to confirm the results, which have indicated favorable binding between BAX and SA14.
ConclusionOverall, the results have indicated that SA14 can bring about stable conformational changes in BAX and shows merit as a potential BAX-activating pro-apoptotic agent worthy of further experimental studies.
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Unifying Theory and Experiments: Multi-Target Pharmacology of Dajihan Pill Against Hyperlipidemia
Authors: Ning Li, Canfeng Bian, Ya Gao, Lingfei Liu, Qin Hu, Lixia Xiao and Tianzhu GuanBackgroundThe increasing incidence of hyperlipidemia (HLP) is attributed to the imbalance in redox homeostasis, aberrant lipid metabolism, and the excessive intake of empty calories. Dajihan Pill (DJHP) is a Traditional Chinese Medicine (TCM) formula composed of Zingiberis Rhizoma (ZR), Piperis Longi Fructus (PLF), Alpiniae Officinarum Rhizome (AOR), and Cinnamomi Cortex (CC) in a ratio of 3:2:3:2. It exhibits a significant preventive effect on HLP. Certainly, the active components and the precise mechanism of action are not fully understood. Therefore, this study aims to elucidate the preventive and ameliorative mechanisms of DJHP against HLP by integrating network pharmacology, molecular docking, and experimental validation.
MethodsBased on the pharmacological method, active ingredients in DJHP and targets were extracted from Traditional Chinese Medicine System Pharmacology (TCMSP) and UniProt. Then core compounds and targets were obtained by constructing “compounds-targets-disease” and protein-protein interaction (PPI) network. Gene Ontology (GO) function analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) were employed to elucidate further the associated action mechanism. The molecular binding mechanisms between the core ingredients and targets were elucidated through molecular docking. Additionally, the antioxidant capacities of DJHP extracts were investigated by assessing their DPPH, hydroxyl, and ABTS radical scavenging activities.
ResultsA total of 45 active compounds and 258 targets were identified in DJHP. Network analysis indicated that quercetin, beta-sitosterol, kaempferol, and oleic acid might serve as core bioactive compounds. Seven core targets, including AKT1, INS, and TNF, were identified as potential preventive targets. GO analysis suggested the improvement of HLP by DJHP may be related to the lipid metabolic process, high-density lipoprotein particle, triglyceride binding, and inflammatory response. The KEGG analysis indicated TNF, HIF-1, and AMPK signaling pathways were involved. The observations of active compounds binding with core targets indicated an excellent combination. Additionally, antioxidant results showed that DJHP exhibited significant DPPH, hydroxyl, and ABTS radical scavenging activities.
ConclusionTheoretical and experimental investigations indicate that DJHP can effectively modulate various signaling pathways and enhance the redox system, thus mitigating HLP. Our work provided a basis for the pharmacological study of DJHP in preventing HLP and further research.
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Discovery of the Aminated Quinoxalines as Potential Active Molecules
BackgroundIn recent years, as the biological activity of the quinoxaline skeleton has been revealed in numerous studies, interest in synthesizing new prototype molecules for the treatment of many chronic diseases, especially cancer, has increased.
MethodsThe desired alkoxy substituted aminoquinoxalines (AQNX1-9) were synthesized by the reaction of QNX and alkoxy substituted aryl amines such as 2-methoxyaniline, 4-methoxyaniline, 2-ethoxyaniline, 3-ethoxyaniline, 4-ethoxyaniline, 4-butoxyaniline, 2,4-dimethoxyaniline, 3,4-dimethoxyaniline, and 3,5-dimethoxyaniline according to the previously published procedure. QNX was aminated in DMSO at 130°C. We synthesized various alkoxy substituted aminoquinoxaline compounds (AQNX1-9) and evaluated their anticancer and antimicrobial activities in order to expand the search to related structures. In particular, two aminoquinoxaline (AQNX5 and AQNX6) compounds, coded as NSC D-835971/1 and NSC D-835972/1 by the National Cancer Institute in the USA, were screened for anticancer screening at a dose of 10-5 M on a full panel of 60 human cell lines obtained from nine human cancer cell types (leukemia, melanoma, non-small cell lung, colon, central nervous system, ovarian, kidney, prostate, and breast cancer).
ResultsFurther in silico studies were also conducted for the compound AQNX5 (NSC D-835971/1), which was found to be the most active antiproliferative agent, especially against leukemia cell lines. Molecular docking studies showed that AQNX5 interacted with Glu286 and Lys271 through hydrogen bonding and π-stacking interaction in the ATP binding region of Abl kinase, which is indicated as a potential target of leukemia. Besides, AQNX5 occupied the minor groove of the double helix of DNA via π-stacking interaction with DG-6.
ConclusionAccording to in silico pharmacokinetic determination, AQNX5 was endowed with drug-like properties as a potential anticancer drug candidate for future experiments. In the light of these findings, more research will focus on aminated quinoxalines' ability to precisely target leukemia cancer cell lines.
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Therapeutic Effects of Cortex Phellodendri, Epimedium brevicornu, and Earthworm on Chronic Prostatitis/Chronic Pelvic Pain Syndrome Mice
BackgroundThe use of traditional Chinese medicine (TCM) for the treatment of chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is widespread. The purpose of this study is to investigate the preliminary mechanism of Epimedium brevicornu Maxim., Cortex Phellodendri Chinesis (CPC), and Earthworm in the CP/CPPS model.
MethodsFifty C57BL/6 male mice were randomized into five groups: control, model, Epimedium brevicornu Maxim, Earthworm, and Cortex Phellodendri chinensis (CPC). To induce experimental autoimmune prostatitis (EAP), T2 peptide immune emulsion was subcutaneously injected into all groups except the control group on days 0 and 14 to induce experimental autoimmune prostatitis. Except for the control and model groups, all other groups were treated with Epimedium brevicornu Maxim., CPC, and earthworm after the successful induction of EAP.
ResultsOn days 1, 28, and 56, the micturition habits and pain sensitivity of rodents in each group were evaluated. Hematoxylin-eosin (H&E) staining was used to examine prostate inflammation, whereas enzyme-linked immunosorbent assay (ELISA) was used to measure the serum level of tumor necrosis factor-α (TNF). The Epimedium brevicornu Maxim. group significantly reduced the number of urine spots and frequency of pain response compared to the model group. Epimedium brevicornu Maxim. group and CPC group significantly reduced inflammatory cell infiltration and inflammatory lesions more than Earthworm groups. The serum levels of TNF-α were substantially reduced in the Epimedium brevicornu Maxim. and CPC groups compared to the model group.
ConclusionOur findings showed that Epimedium brevicornu Maxim outperformed CPC and Earthworm for EAP treatment, which relieves urinary tract symptoms, enhances pain threshold, and lowers inflammation.
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Volumes & issues
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Volume 21 (2024)
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Volume 20 (2023)
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Volume 19 (2022)
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Volume 18 (2021)
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Volume 17 (2020)
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