Browse publications by year: 2025

  1. Lim SJ, Muhd Noor ND, Sabri S, Mohamad Ali MS, Salleh AB, Oslan SN
    J Biomol Struct Dyn, 2025 Apr;43(7):3728-3748.
    PMID: 38189364 DOI: 10.1080/07391102.2023.2300757
    Meyerozyma guilliermondii is a rare yeast pathogen contributing to the deadly invasive candidiasis. M. guilliermondii strain SO, as a promising protein expression host, showed 99% proteome similarity with the clinically isolated ATCC 6260 (type strain) in a recent comparative genomic analysis. However, their in vitro virulence features and in vivo pathogenicity were uncharacterized. This study aimed to characterize the in vitro and in vivo pathogenicity of M. guilliermondii strain SO and analyze its Als proteins (MgAls) via comprehensive bioinformatics approaches. M. guilliermondii strain SO showed lower and higher sensitivity towards β-mercaptoethanol and lithium, respectively than the avirulent S. cerevisiae but exhibited the same tolerance towards cell wall-perturbing Congo Red with C. albicans. With 7.5× higher biofilm mass, M. guilliermondii strain SO also demonstrated 75% higher mortality rate in the zebrafish embryos with a thicker biofilm layer on the chorion compared to the avirulent S. cerevisiae. Being one of the most important Candida adhesins, sequence and structural analyses of four statistically identified MgAls showed that MgAls1056 was predicted to exhibit the most conserved amyloid-forming regions, tandem repeat domain and peptide binding cavity (PBC) compared to C. albicans Als3. Favoured from the predicted largest ligand binding site and druggable pockets, it showed the highest affinity towards hepta-threonine. Non-PBC druggable pockets in the most potent virulence contributing MgAls1056 provide new insights into developing antifungal drugs targeting non-albicans Candida spp. Virtual screening of available synthetic or natural bioactive compounds and MgAls1056 deletion from the fungal genome should be further performed and validated experimentally.
    MeSH terms: Agglutinins/metabolism; Agglutinins/chemistry; Animals; Candida albicans/genetics; Candida albicans/pathogenicity; Computer Simulation; Fungal Proteins/genetics; Fungal Proteins/metabolism; Fungal Proteins/chemistry; Mucorales/metabolism; Mucorales/pathogenicity; Virulence; Zebrafish*; Biofilms/drug effects
  2. Zakaria NH, Mohamed Tap F, Aljohani GF, Abdul Majid FA
    J Biomol Struct Dyn, 2025 Apr;43(7):3429-3448.
    PMID: 38165434 DOI: 10.1080/07391102.2023.2298726
    Honey-iQfood is an herbal supplement made of a mixture of polyherbal extracts and wild honey. The mixture is traditionally claimed to improve various conditions related to brain cells and functions including dementia and Alzheimer's disease. Glycogen synthase kinase-3 beta (GSK-3β) and cyclin-dependent kinase 5 (CDK5) have been identified as being involved in the pathological hyperphosphorylation of tau proteins, which leads to the formation of neurofibrillary tangles and causes Alzheimer's disease. Therefore, this study was conducted to confirm the traditional claims by detection of active compounds, namely curcumin, gallic acid, catechin, rosmarinic acid, and andrographolide in the raw materials of Honey-iQfood through HPLC analysis, molecular docking, and dynamic simulations. Two potential compounds, andrographolide, and rosmarinic acid, produced the best binding affinities following the molecular docking of the active compounds against the GSK-3β and CDK5 targets. Andrographolide binds with GSK-3β at -8.2 kcal/mol, whereas rosmarinic acid binds to CDK5 targets at -8.6 kcal/mol. Molecular dynamics was further carried out to confirm the docking results and clarify their dynamic properties such as RMSD, RMSF, rGyr, SASA, PSA, and binding free energy. CDK5-andrographolide complexes had the best MM-GBSA score (-83.63 kcal/mol) compared to other complexes, indicating the better interaction profile and stability of the complex. These findings warrant further research into andrographolide and rosmarinic acid as efficient inhibitors of tau protein hyperphosphorylation to verify their therapeutic potential in brain-related illnesses.
    MeSH terms: Binding Sites; Brain/drug effects; Brain/metabolism; Catechin/analogs & derivatives; Catechin/pharmacology; Catechin/chemistry; Cinnamates/metabolism; Cinnamates/pharmacology; Cinnamates/chemistry; Curcumin/pharmacology; Curcumin/chemistry; Diterpenes/pharmacology; Diterpenes/chemistry; Gallic Acid/metabolism; Gallic Acid/pharmacology; Gallic Acid/chemistry; Honey*; Humans; Protein Binding; Molecular Dynamics Simulation*; Molecular Docking Simulation*
  3. Ismail NZ, Khairuddean M, Abubakar S, Arsad H
    J Biomol Struct Dyn, 2025 Apr;43(7):3242-3257.
    PMID: 38149857 DOI: 10.1080/07391102.2023.2296606
    Compounds with a chalcone scaffold-based structure have demonstrated promising anticancer biological activity. However, the molecular interactions between chalcone scaffold-based compounds and breast cancer-associated proteins remain unclear. Through network pharmacology, molecular docking, and molecular dynamics (MD) simulation analyses, compounds with a chalcone scaffold-based structure were evaluated for their interaction with potential breast cancer targets. The compounds were retrieved from the ASINEX database, resulting in 575,302 compounds. A total of 342 compounds with chalcone scaffold-based structures were discovered. From the 342 compounds that was analysed, ten were chosen due to their adherence to Lipinski's rule, having an appropriate range of lipophilicity (LOGP), and topological polar surface area (TPSA), and absence of any toxicity. Based on target intersection, 50 target genes were found and subjected to protein-protein interaction (PPI), gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Four target genes were found to be involved in the breast cancer pathway. Consequently, molecular docking was utilised to analyse the molecular interactions between the compounds and four target protein receptors. Compound 211 exhibited the highest binding affinities for the epidermal growth factor receptor (EGFR), fibroblast growth factor receptor 1 (FGFR1), oestrogen receptor (ESR1), and cyclin dependent kinase 6 (CDK6) with values of -8.95 kcal/mol, -8.60 kcal/mol, -10.33 kcal/mol, and -9.90 kcal/mol, respectively. During MD simulation, compound 211 and its respective proteins were stable, compact, and had minimal flexibility. The findings provide foundations for future studies into the interaction underlying the anti-breast cancer potential of compounds with chalcone-based scaffold structures.
    MeSH terms: Chalcone/pharmacology; Chalcone/chemistry; Female; Humans; Ligands; Protein Binding; Chalcones/pharmacology; Chalcones/chemistry; Molecular Dynamics Simulation*; Protein Interaction Maps/drug effects; Molecular Docking Simulation*
  4. Ishaq A, Said MIM, Azman SB, Abdulwahab MF, Houmsi MR, Jagun ZT
    Environ Sci Pollut Res Int, 2025 Feb;32(6):3114-3129.
    PMID: 38151563 DOI: 10.1007/s11356-023-31472-x
    Microbial fuel cells (MFCs) have garnered attention in bio-electrochemical leachate treatment systems. The most common forms of inorganic ammonia nitrogen are ammonium ( NH 4 + ) and free ammonia. Anaerobic digestion can be inhibited in both direct (changes in environmental conditions, such as fluctuations in temperature or pH, can indirectly hinder microbial activity and the efficiency of the digestion process) and indirect (inadequate nutrient levels, or other conditions that indirectly compromise the microbial community's ability to carry out anaerobic digestion effectively) ways by both kinds. The performance of a double-chamber MFC system-composed of an anodic chamber, a cathode chamber with fixed biofilm carriers (carbon felt material), and a Nafion 117 exchange membrane is examined in this work to determine the impact of ammonium nitrogen ( NH 4 - N ) inhibition. MFCs may hold up to 100 mL of fluid. Therefore, the bacteria involved were analysed using 16S rRNA. At room temperature, with a concentration of 800 mg L-1 of ammonium nitrogen and 13,225 mg L-1 of chemical oxygen demand (COD), the study produced a considerable power density of 234 mWm-3. It was found that NH 4 - N concentrations above 800 mg L-1 have an inhibitory influence on power output and treatment effectiveness. Multiple routes removed the most nitrogen ( NH 4 + -N: 87.11 ± 0.7%, NO2 -N: 93.17 ± 0.2% and TN: 75.24 ± 0.3%). Results from sequencing indicate that the anode is home to a rich microbial community, with anammox (6%), denitrifying (6.4%), and electrogenic bacteria (18.2%) making up the bulk of the population. Microbial fuel cells can efficiently and cost-effectively execute anammox, a green nitrogen removal process, in landfill leachate.
    MeSH terms: Bioelectric Energy Sources*; Waste Disposal, Fluid/methods; Water Pollutants, Chemical
  5. Bhaskar V, Kumar S, Sujathan Nair A, Gokul S, Rajappan Krishnendu P, Benny S, et al.
    J Biomol Struct Dyn, 2025 Feb;43(3):1329-1351.
    PMID: 38064315 DOI: 10.1080/07391102.2023.2291549
    Tuberculosis is one of the most ancient infectious diseases known to mankind predating upper Paleolithic era. In the current scenario, treatment of drug resistance tuberculosis is the major challenge as the treatment options are limited, less efficient and more toxic. In our study we have developed an atom based 3D QSAR model, statistically validated sound with R2 > 0.90 and Q2 > 0.72 using reported direct inhibitors of InhA (2018-2022), validated by enzyme inhibition assay. The model was used to screen a library of 3958 molecules taken from Binding DB and candidates molecules with promising predicted activity value (pIC50) > 5) were selected for further analyzed screening by using molecular docking, ADME profiling and molecular dynamic simulations. The lead molecule, ZINC11536150 exhibited good docking score (glideXP = -11.634 kcal/mol) compared to standard triclosan (glideXP =  -7.129 kcal/mol kcal/mol) and through molecular dynamics study it was observed that the 2nv6-complex of ZINC11536150 with Mycobacterium tuberculosis InhA (PDB entry: 2NV6) complex remained stable throughout the entire simulation time of 100 ns.Communicated by Ramaswamy H. Sarma.
    MeSH terms: Binding Sites; Enzyme Inhibitors/pharmacology; Enzyme Inhibitors/chemistry; Humans; Ligands; Protein Binding; Quantitative Structure-Activity Relationship*; Molecular Dynamics Simulation*; Molecular Docking Simulation*
  6. Gao P, Md Shaarani S, Mohd Noor NQI
    Crit Rev Food Sci Nutr, 2025;65(6):1109-1125.
    PMID: 38059602 DOI: 10.1080/10408398.2023.2289077
    The development of reliable and sensitive detection methods is essential for addressing the escalating concerns surrounding fish and fish products, driven by increasing market demands. This comprehensive review presents recent advances in detection approaches, specifically focusing on microplastic, biological, and chemical hazards associated with these products. The overview encompasses 21 distinct detection methods, categorized based on the type of hazard they target. For microplastic hazards, six methods are visual, spectroscopic, and thermal analyses. Biological hazard identification relies on six approaches employing nucleic-acid sequence, immunological, and biosensor technologies. The investigation of chemical hazards encompasses ten methods, including chromatography, spectroscopy, mass spectrometry, immunological, biosensor, and electrochemical techniques. The review provides in-depth insights into the basic principles, general characteristics, and the recognized advantages and disadvantages of each method. Moreover, it elaborates on recent advancements within these methodologies. The concluding section of the review discusses current challenges and outlines future perspectives for these detection methods. Overall, this comprehensive summary not only serves as a guide for researchers involved in fish safety and quality control but also emphasizes the significance of staying abreast of evolving detection technologies to ensure the continued safety of fish and fish products in response to emerging food safety hazards.
    MeSH terms: Animals; Fishes*; Food Inspection/methods; Humans; Biosensing Techniques/methods; Seafood/analysis
  7. Zaini MS, Liew JYC, Paiman S, Tee TS, Kamarudin MA
    J Fluoresc, 2025 Jan;35(1):245-256.
    PMID: 38038875 DOI: 10.1007/s10895-023-03528-1
    Waste peels are considered an environmental burden and typically disposed in landfills. The aim of this study was to investigate the effects of various solvents on the luminescence properties of carbon quantum dots (CQDs). Watermelon peels were recycled and reuse as precursors for the synthesis of biomass CQDs via a green carbonization method. The colloidal stability, surface charge, and particle size were characterized using zeta potential and dynamic light scattering (DLS). DLS revealed that the size of the CQDs was approximately 5.80 ± 0.4 nm to 9.74 ± 0.8 nm. The high-resolution transmission electron microscopy (HRTEM) results demonstrated a correlation with the DLS results. The optical properties were characterized by photoluminescence (PL) and UV-Visible (UV-Vis) spectroscopy. PL measurements at different excitation wavelengths revealed that the CQDs emissions were influenced by the polarity of the solvents. Meanwhile, the Fourier transform infra-red (FTIR) results showed the presence of oxygen-containing groups on the surface of the CQDs. These results deepen our understanding of the solvent-dependent behavior and colloidal stability of the CQDs.
  8. Tan SH, King TL, Tan SSN, Lai WH, Bujang MA, Voon PJ
    Asia Pac J Clin Oncol, 2025 Feb;21(1):95-101.
    PMID: 37943536 DOI: 10.1111/ajco.14034
    AIM: Participant recruitment has always been a major challenge in clinical trials. This study aimed to develop and validate the Join Clinical Trial Questionnaire (JoinCT), exploring the willingness to join a clinical trial and associated factors in patients.

    METHODS: This questionnaire development study involved four phases: (i) exploring and understanding the subject matter, (ii) questionnaire development, (iii) content validity testing, and lastly, (iv) field-testing of the questionnaire. For the field-testing phase, a cross-sectional self-administered survey of JoinCT was conducted among cancer patients with various socio-demographic backgrounds and medical conditions. Besides content validity, Cronbach's alpha was used to evaluate the internal consistency of domains, and confirmatory factor analysis was used to evaluate the model fit of the JoinCT framework.

    RESULTS: A total of 389 respondents participated in the survey. Based on the results obtained from a field data collection phase, JoinCT consisted of four independent variables domains, namely "knowledge", "perception of benefits", "perception of risks", and "confidence". The only dependent variable was the willingness to participate in a clinical trial. The minimum Cronbach's alpha was 0.937, and the model fit for the overall framework of JoinCT is also excellent with Comparative Fit Index (> 0.90), root mean square error approximation (

    MeSH terms: Adult; Aged; Cross-Sectional Studies; Female; Humans; Male; Middle Aged; Neoplasms/psychology; Psychometrics/methods; Surveys and Questionnaires; Reproducibility of Results
  9. Tanjung M, Tjahjandarie TS, Aldin MF, Mardhiyyah S, Saputri RD, Syah YM, et al.
    Nat Prod Res, 2025 Feb;39(3):498-505.
    PMID: 37874007 DOI: 10.1080/14786419.2023.2272783
    Four isoprenylated flavonols, including two new compounds, macainermisins A-B (1-2), and two known compounds, sinoflavonoid P (3), broussoflavonol F (4), were isolated from the leaves of Macaranga inermis. A combination of HRESIMS, UV, 1D, and 2D NMR spectra elucidated the structures of 1-2. Flavonols (1-4) were evaluated against three cancer cells. Compound 1 showed high cytotoxicity against WiDR with an IC50 value of 0.93 µM, and compound 2 was active towards HeLa and WiDR (IC50 values of 0.90 and 0.94 µM), and compound 3 showed high activity towards 4T1 and HeLa (IC50 values of 0.83 and 0.98 µM).
    MeSH terms: Drug Screening Assays, Antitumor; HeLa Cells; Humans; Magnetic Resonance Spectroscopy; Molecular Structure; Euphorbiaceae/chemistry; Cell Line, Tumor
  10. Xin YH, Ying TJ, Syeed MS, Veettil SK, Menon RK
    J Prosthet Dent, 2025 Jan;133(1):108-123.
    PMID: 36863936 DOI: 10.1016/j.prosdent.2023.01.007
    STATEMENT OF PROBLEM: Symptomatic denture stomatitis (DS) is a painful oral mucosal disorder that can impair quality of life in denture wearers. A complete cure of DS is difficult to achieve, and the most efficacious regimen to treat DS has not yet been conclusively established.

    PURPOSE: The purpose of this network meta-analysis was to assess the comparative efficacy of interventions used for the treatment of DS.

    MATERIAL AND METHODS: A search was conducted for trials published in Medline, Scopus, PubMed, and Cochrane Central Register of Controlled Trials from inception until February 2022 (PROSPERO Reg no: CRD42021271366). Network meta-analysis was performed on data from randomized controlled trials that assessed the comparative efficacy of any form of intervention for the treatment of DS in denture wearers. Agents were ranked according to their effectiveness in the treatment of DS based on outcomes using surface under the cumulative ranking (SUCRA).

    RESULTS: A total of 25 articles were included in the quantitative analysis. Topical antifungal agents (risk ratio [RR]=4.37[95% confidence interval [CI]: 2.15,8.90), topical antimicrobial agents used along with systemic antifungal agents (RR=4.25[95% CI: 1.79,10.33]), systemic antifungal agents (RR=4.25[95% CI: 1.79,10.10]), photodynamic therapy (RR=4.25[95% CI: 1.75,8.98]), and topical plant products (RR=3.40[95% CI: 1.59,7.26]) were found to effectively improve DS. Microwave disinfection concurrently administered with topical antifungal agents (RR=7.38(95% CI: 2.75,19.81), microwave disinfection 7.38[95% CI: 2.75,19.81]), topical antifungal agents (RR=4.88[95% CI: 1.92,12.42]), topical plant products (RR=4.49[95% CI: 1.70,11.82]), systemic antifungal agents together with topical antimicrobial agents (RR=3.85[95% CI: 1.33,11.10]), topical antimicrobial agents (RR=3.39[95% CI: 1.17,9.81]), systemic antifungal agents (RR=3.37[95% CI: 1.21,9.34]), and photodynamic therapy or photochemotherapy (PDT) (RR=2.93[95% CI: 1.01,8.47]) were found to effectively resolve mycological DS. Topical antifungals ranked highest in the SUCRA ranking for clinical improvement, whereas microwave disinfection concurrently administered with topical antifungal agents ranked highest for mycological resolution. None of the agents demonstrated significant side effects except for topical antimicrobial agents which demonstrated altered taste and staining of oral structures.

    CONCLUSIONS: Available evidence suggests that topical antifungals, microwave, and systemic antifungals are effective in the treatment of DS, but confidence in these findings is low because of the limited number of studies and a high risk of bias. Additional clinical trials are needed on photodynamic therapy, topical plant products, and topical antimicrobials.

    MeSH terms: Anti-Infective Agents/therapeutic use; Humans; Quality of Life; Randomized Controlled Trials as Topic; Treatment Outcome; Network Meta-Analysis*
  11. Eturajulu RC, Tan MP, Zakaria MI, Chinna K, Ng KH
    Singapore Med J, 2025 Jan 01;66(1):33-40.
    PMID: 36751846 DOI: 10.4103/singaporemedj.SMJ-2021-254
    INTRODUCTION: Medical errors commonly occur in medical imaging departments. These errors are frequently influenced by patient safety culture. This study aimed to develop a suitable patient safety culture assessment tool for medical imaging departments.

    METHODS: Staff members of a teaching hospital medical imaging department were invited to complete the generic short version of the Safety Attitude Questionnaire (SAQ). Internal consistency and reliability were evaluated using Cronbach's α. Confirmatory factor analysis (CFA) was conducted to examine model fit. A cut-off of 60% was used to define the percentage positive responses (PPR). PPR values were compared between occupational groups.

    RESULTS: A total of 300 complete responses were received and the response rate was 75.4%. In reliability analysis, the Cronbach's α for the original 32-item SAQ was 0.941. Six subscales did not demonstrate good fit with CFA. A modified five-subscale, 22-item model (SAQ-MI) showed better fit (goodness-to-fit index ≥0.9, comparative fit index ≥ 0.9, Tucker-Lewis index ≥0.9 and root mean square error of approximation ≤0.08). The Cronbach's α for the 22 items was 0.921. The final five subscales were safety and teamwork climate, job satisfaction, stress recognition, perception of management and working condition, with PPR of 62%, 68%, 57%, 61% and 60%, respectively. Statistically significant differences in PPR were observed between radiographers, doctors and others occupational groups.

    CONCLUSION: The modified five-factor, 22-item SAQ-MI is a suitable tool for the evaluation of patient safety culture in a medical imaging department. Differences in patient safety culture exist between occupation groups, which will inform future intervention studies.

    MeSH terms: Adult; Attitude of Health Personnel*; Diagnostic Imaging/methods; Factor Analysis, Statistical; Female; Hospitals, Teaching; Humans; Job Satisfaction; Male; Middle Aged; Surveys and Questionnaires; Reproducibility of Results; Organizational Culture; Safety Management; Medical Errors/prevention & control; Patient Safety*
  12. Ismail SI, Nunome H, Lysdal FG, Kersting UG, Tamura Y
    Sports Biomech, 2025 Jan;24(1):41-52.
    PMID: 36342420 DOI: 10.1080/14763141.2022.2143415
    We aimed to clarify the effect of different futsal playing surface structural properties on the resultant change of direction (COD) performance, perceived traction and frictional properties. Twenty experienced male university soccer players performed a COD slalom-course test and perceived traction evaluation on three different types of playing surfaces (area-elastic: AE, point-elastic no.1: PE1 and point-elastic no.2: PE2). Frictional properties of these surfaces were mechanically evaluated against a futsal shoe, using a hydraulic moving force platform, and expressed as available friction coefficient (AFC). In the COD performance test, the participants performed significantly better on the point-elastic surfaces (PE1 and PE2) when compared to the area-elastic surface (AE) (p 
    MeSH terms: Biomechanical Phenomena; Humans; Male; Perception/physiology; Shoes; Surface Properties*; Friction*; Sports Equipment; Young Adult
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