Author: Ibrahim Mahmood Mahdi
In Vitro and In Silico Antidiabetic Efficacy of Solanum lasiocarpum Dunal Fruit Extract
Exploring the possibility of familiar dietary sources as additional diabetes treatments is crucial, especially considering the financial difficulties related to diabetes mellitus. Using both in vitro and in silico techniques, this work aims to assess the antidiabetic benefits of extract from Solanum lasiocarpum Dunal. The evaluations encompass the ability to scavenge DPPH radicals, inhibition of α-amylase, α-glucosidase, inhibition of DPP-4, cytotoxicity, and glucose absorption kinetics. With an IC50 value of 0.69 ± 0.14 mg/ml, S. lasiocarpum showed encouraging DPPH inhibition. IC50 values of 2.123 ± 0.14 mg/ml inhibited the enzymes α-amylase, α-glucosidase, and DPP-4. Furthermore, a notable increase (P < 0.05) in glucose uptake by L6 myoblasts was observed with the administration of various combinations. In silico analysis, including XP docking and MM-GBSA, revealed that 10 and 21 compounds within the combination exhibited substantial interactions and stable binding capabilities with α-amylase and DPP-4 proteins, indicating their potential as enzyme inhibitors. Therefore, it can be inferred that S. lasiocarpum represents a promising therapeutic approach for diabetes management.
In vitro evaluation of antidiabetic potential of Coix lacryma-jobi fruit extract
This study systematically explored the antidiabetic potential of Coix lacryma-jobi (Job’s tears) fruit extract through various in vitro assays. The extract demonstrated potent inhibition of key glucose-metabolising enzymes: α-glucosidase (50% inhibitory concentration [IC50] = 4.31 ± 0.19 mg/ml), α-amylase (IC50 = 11.02 ± 0.11 mg/ml), and dipeptidyl peptidase-4 (DPP-4) surpassing the effects of insulin and sitagliptin at optimal concentrations. Glucose uptake assays in L6 myoblasts showed enhanced absorption (122.89% at 62.5 μg/ml), akin to insulin’s activity, likely via GLUT4 modulation. The extract’s antioxidant capacity (IC50 = 7.18 ± 0.12 mg/ml 2,2-diphenyl-1-picrylhydrazyl scavenging) was attributed to its phenolic (5.3 ± 0.62 mg gallic acid equivalent per gram) and flavonoid content (1.219 ± 0.15 mg quercetin equivalent per gram), aiding in oxidative stress mitigation. Polymerase chain reaction (PCR) array analysis indicated upregulation of insulin signalling genes (GLUT4, IRS1, and PIK3R1) and downregulation of inflammatory markers (TNF and IL6). Minimal cytotoxicity (IC50 > 6 mg/ml) in L6 and 3T3-L1 cells highlighted its safety. Coix lacryma-jobi shows promise as both a therapeutic agent and a functional food ingredient, offering new insights into DPP-4 inhibition and multifaceted antidiabetic mechanisms.
From Zebrafish To Humans: In Silico Comparative Study of RAD50 Sequences
DNA damage, particularly the occurrence of DNA double-strand breaks (DSBs), presents a significant hazard to the integrity and viability of cells. Improper repair of DSBs can result in chromosomal alterations, oncogenic changes, or cell demise. The MRE11-RAD50-NBS1 (MRN) complex plays a crucial role in DNA repair and signaling under the Ataxia Telangiectasia Mutated (ATM) kinase regulation. In this study, we employed comprehensive computational techniques to analyze the structure of RAD50 in Danio rerio (Zebrafish), utilized as a model organism. Additionally, we conducted in silico assessments of RAD50 from both Zebrafish and humans, comparing their characteristics. The substantial sequence resemblance between DrRAD50 and HsRAD50 suggests that DrRAD50 could potentially serve as a valuable model for HsRAD50. However, it is important to acknowledge that sequence similarity alone does not necessarily imply functional equivalence. Further functional studies are needed to confirm the extent of their functional similarities. By examining the secondary and tertiary protein structures of RAD50, we observed a notable likeness between Zebrafish and Human RAD50 proteins. In silico analysis demonstrated that the sequence of RAD50 in zebrafish shares 70% similarity with the human RAD50 protein.
A Systematic Review of Aquatic Organism Antimicrobial Peptides.
Antimicrobial peptides (AMPs), sourced from various organisms, including aquatic life, are promising alternatives to combat antibiotic resistance. Their investigation is essential amid global antibiotic resistance concerns. The invaluable impact of antibiotics on human health, having saved numerous lives, is currently at risk. The growing global incidence of antibiotic-resistant bacteria poses a serious challenge to their ability to effectively treat various illnesses. This situation demands immediate attention and the exploration of alternative medical solutions. One of the most promising alternatives to antibiotics is antimicrobial peptides (AMPs), which can treat bacterial infections, particularly those brought by multi-drug-resistant pathogens. With a particular focus on their antimicrobial properties, this systematic review aims to evaluate and classify recent AMPs isolated from aquatic organisms. This review advances knowledge of these aquatic life-derived AMPs’ potential as alternatives to conventional antibiotics by examining their unique antibacterial characteristics and modes of action. A systematic review of articles published in English between 2014 and 2024 was carried out in the Science Direct, PubMed NCBI and Google Scholar
Ibrahim Mahmood Mahdi [HTML] from peerj.com In silico directed evolution of Anabas testudineus AtMP1 antimicrobial peptide to improve in vitro anticancer activity
Various studies have demonstrated that directed evolution is a powerful tool in enhancing protein properties. In this study, directed evolution was used to enhance the efficacy of synthesised Anabas testudineus AtMP1 antimicrobial peptides (AMPs) in inhibiting the proliferation of cancer cells. The modification of antimicrobial peptides (AMPs) and prediction of peptide properties using bioinformatic tools were carried out using four databases, including ADP3, CAMP-R3, AMPfun, and ANTICP. One modified antimicrobial peptide (AMP), ATMP6 (THPPTTTTTTTTTTTTTAAPARTT), was chosen based on its projected potent anticancer effect, taking into account factors such as amino acid length, net charge, anticancer activity score, and hydrophobicity. The selected AMPs were subjected to study in deep-learning databases, namely ToxIBTL and ToxinPred2, to predict their toxicity. Furthermore, the allergic properties of these antimicrobial peptides (AMPs) were verified by utilising AllerTOP and AllergenFP. Based on the results obtained from the database study, it was projected that antimicrobial peptides (AMPs) demonstrate a lack of toxicity towards human cells that is indicative of the broader population. After 48 hours of incubation, the IC50 values of ATMP6 against the HS27 and MDA-MB-231 cell lines were found to be 48.03 ± 0.013 µg/ml and 7.52 ± 0.027 µg/ml, respectively. The IC50 values of the original peptide ATMP1 against the MDA-MB-231 and HS27 cell lines were determined to be 59.6 ± 0.14 µg/ml and 8.25 ± 0.14 µg/ml, respectively, when compared. Furthermore, the results indicated that the injection of ATMP6 induced apoptosis in the MDA-MB-231 cell lines. The present investigation has revealed new opportunities for advancing novel targeted peptide therapeutics to tackle cancer.
In silico identification and in vitro assessment of a potential anti-breast cancer activity of antimicrobial peptide retrieved from the ATMP1 Anabas testudineus fish peptide
A previous study has shown that synthetic antimicrobial peptides (AMPs) derived from Anabas testudineus (ATMP1) could in-vitro inhibit the progression of breast cancer cell lines. In this study, we are interested in studying altered versions of previous synthetic AMPs to gain some insight into the peptides functions. The AMPs were altered and subjected to bioinformatics prediction using four databases (ADP3, CAMP-R3, AMPfun, and ANTICP) to select the highest anticancer activity. The bioinformatics in silico analysis led to the selection of two AMPs, which are ATMP5 (THPPTTTTTTTTTTTYTAAPATTT) and ATMP6 (THPPTTTTTTTTTTTTTAAPARTT). The in silico analysis predicted that ATMP5 and ATMP6 have anticancer activity and lead to cell death. The ATMP5 and ATMP6 were submitted to deep learning databases (ToxIBTL and ToxinPred2) to predict the toxicity of the peptides and to (AllerTOP & AllergenFP) check the allergenicity. The results of databases indicated that AMPs are non-toxic to normal human cells and allergic to human immunoglobulin. The bioinformatics findings led to select the highest active peptide ATMP5, which was synthesised and applied for in-vitro experiments using cytotoxicity assay MTT Assay, apoptosis detection using the Annexin V FTIC-A assay, and gene expression using Apoptosis PCR Array to evaluate the AMP’s anticancer activity. The antimicrobial activity is approved by the disc diffusion method. The in-vitro experiments analysis showed that ATMP5 had the activity to inhibit the growth of the breast cancer cell line (MDA-MB-231) after 48 h and managed to arrest the cell cycle of the MDA-MB-231, apoptosis induction, and overexpression of the p53 by interaction with the related apoptotic genes. This research opened up new opportunities for developing potential and selective anticancer agents relying on antimicrobial peptide properties.
VARIANTS PRODUCTION OF Lentinula edodes SPORES, MONOKARYON MYCELIUM AND DIKARYON MYCELIUM BY γ-IRRADIATION
Lentinula edodes or commonly known as shiitake is a cultivated edible mushroom. This mushroom has been used in pharmaceutical, nutraceutical and cosmeceutical industries. However after years of selective inbreeding, the mushroom suffers from a small genetic pool. In this study, we attempt to produce genetic variants of shiitake via γ-irradiation. Shiitake’s spores and mycelium (both monokaryon (MM) and dikaryon (DM)) were subjected to γ-irradiation (137Cs) at series of doses ranging from 0 to 4000 Gy. Dose responses were evaluated based on mycelium growth performance and survivability. The γ-irradiation LD50 for shiitake’s spores, MM, 3rd DM subculture and 9th DM subculture were 795 Gy, 460 Gy, 735 Gy and 1330 Gy, respectively. Interestingly our result shows those higher subcultures DM are more resistant to γ-irradiation. We observed that MMs which were exposed to higher dose of γ-irradiation show lower numbers of clamp connections compared to control indicating that there are genetic compatibility changes between individual hyphal cells within the irradiated shiitake mycelia. This study revealed the potential of γ-irradiation as a tool to create diversity in shiitake genetic pool towards healthy and sustainable mushroom crops in the industries.
Potential mutant of Lentinula edodes with high yield of (1-3), (1-6-), β-D-glucan
Lentinula edodes or better known as Shiitake mushroom contains β-1,3;1,6-glucan as part of the cell wall components and studies have shown that it has the ability to enhance the immune system and work as anticancer. The aim of this study was to create potential strain of L. edodes with the high content of β-1,3;1,6-glucan, which has the potential for biotechnological purposes. L. edodes spores were irradiated with gamma ray (Ɣ-rays) and incubated, which formed monokaryon mycelium (MM). Compatible mating of mutated monokaryon formed mutant line dikaryon mycelium (MLDM) that was selected for genotypic and phenotypic comparisons with the wild-type line dikaryon mycelium (WLDM). The concentration of β-1,3;1,6-glucan was measured using a commercial β-Glucan Megazyme Assay Kit (Yeast & Mushroom). Three MLDM (A37, A26, and C07) with 38.8, 36.0 and 34.5% (w/w) of 100 mg, respectively, significantly produced higher amount of β-1,3;1,6-glucan in comparison with WLDM (20.2% (w/w) of 100 mg).
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