IMU University Learning Resources Repository
IMU University Learning Resources Repository (LRR) Database is a digital collection of the university’s intellectual output, which aims to provide a single place to access and view the breadth and scope of the intellectual work of IMU University. It comprises works of IMU University faculty members and students. This includes theses, research projects, community project reports, portfolios, papers written by faculties, etc.
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Thesis
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COMPUTATIONAL PHARMACOKINETICS AND MOLECULAR DOCKING OF ALPINIA LABDANE DITERPENOIDS AS BUTYRYLCHOLINESTERASE INHIBITORS FOR ALZHEIMER’S DISEASE
(IMU University, 2025)
LEONG HOW WAN
Labdane diterpenoids are phytochemicals which have been reported effectively against acetylcholinesterase inhibition. Butyrylcholinesterase is another enzyme involved in hydrolysis of acetylcholine in the brain. Both enzymes are regarded as important therapeutic target for Alzheimer’s disease. Nonetheless, study on the effect of labdane diterpenoids towards butyrylcholinesterase inhibition is scarce. This project aimed to study the pharmacokinetic profiles of labdane diterpenoids of Alpinia genus via in silico methods and to evaluate their binding interactions in the active site of butyrylcholinesterase through molecular docking.
A series of thirty labdane diterpenoids from Alpinia genus were investigated for their physicochemical properties using Molinspiration server and the pharmacokinetics profiles using pkCSM. Docking systems consisting of butyrylcholinesterase protein (PDB ID: 4BDS) and labdane diterpenoids were subjected to docking studies using AutoDockTools. Protein-Ligand Interaction Profiler was used to analyse the docking outputs; LigPlot Plus was used to illustrate the binding interactions between butyrylcholinesterase protein and labdane diterpenoids.
A total of twenty labdane diterpenoids met the requirement of Lipinski’s rule and complied to Veber rule. Several labdane diterpenoids in the present study have exhibited drug likeness, good oral bioavailability as well as considerable drug distribution and blood-brain-barrier penetration based on in silico prediction. All compounds were shown to have relatively good binding within the binding site of butyrylcholinesterase from the docking studies in comparison to the co-crystallised ligand, tacrine based on the binding energy; their binding energies ranged from -17.70 kcal/mol to -7.3 kcal/mol versus that of tacrine with binding energy of -7.71 kcal/mol. Hydrogen bonding and hydrophobic interactions were found as the main binding interactions between the binding site residues and labdane diterpenoids. Amongst the compounds, ligand no. 1 showed the highest binding energy of -16.00 kcal/mol and the lowest estimated Ki of 1.86 pM. In conclusion, several labdane diterpenoids in the present study have demonstrated good pharmacokinetic profiles based on the in silico prediction. These compounds were also shown to have relatively good binding within the binding site of butyrylcholinesterase based on the molecular docking studies.
Keywords: Labdane diterpenoids, butyrylcholinesterase, Alzheimer’s disease, pharmacokinetics, molecular docking
Thesis
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ANTIMICROBIAL DRUG DISCOVERY OF A NOVEL QUATERNARY AMMONIUM SILANE: EFFECT ON BACTERIAL BIOFILMS, MACROPHAGES AND PERIODONTAL STEM CELLS
(IMU University, 2025)
RANJEET AJIT BAPAT
Background:
Bacterial biofilms within the root canal system are a major contributor in the failure of endodontic treatment, primarily attributed to the presence of significant pathogens such as Enterococcus faecalis (E. faecalis), Fusobacterium nucleatum (F. nucleatum), and Porphyromonas gingivalis (P. gingivalis), which demonstrate considerable virulence, antimicrobial resistance, and the capacity to penetrate dentinal tubules. Conventional irrigants such sodium hypochlorite (NaOCl) and chlorhexidine gluconate (CHX) have limitations including cytotoxicity, inadequate biofilm eradication, and adverse responses including tissue irritation and precipitate formation. Quaternary ammonium silane (codename- K21), a functionalised organosilicon compound with antibacterial and anti-inflammatory properties, not only disrupts microbial biofilms but also preserves compatibility with host tissue components, including macrophages. Comprehensive research is warranted to confirm K21's therapeutic benefits since it has potential to block Sortase Av(SrtA) and matrix metalloproteinases (MMPs), enzymes engaged in bacterial adherence and tissue breakdown.
Objectives:
The aim of this research was to assess K21's antibacterial and anti-inflammatory performance as an endodontic irrigant. Among specific objectives were comparing 1.00% K21 with 0.5% K21, 2.00% CHX, 6.00% NaOCl, and saline on single-species (E. faecalis, F. nucleatum and P. gingivalis respectively) and dual-species (F. nucleatum and P. gingivalis) biofilms at 200 μm and 400 μm dentinal tubule depths. Additionally evaluated in the study were K21's effects on hPDLSCs survival as well as RAW 264.7 macrophage viability and anti-inflammatory (M2) polarization. Moreover, molecular simulations were performed to assess the interaction of K21 with SrtA and MMP-9 molecular structures. While the null hypothesis predicted no significant differences, the hypotheses postulated that 1.00% K21 would show better biofilm reduction, higher macrophage and hPDLSCs viability, and greater anti-inflammatory benefits than conventional irrigants.
Methods:
This multimodal investigation utilized a combination of in vitro assays and imaging techniques. Biofilms of E. faecalis, F. nucleatum, and P. gingivalis were cultured on dentin specimens and exposed to different irrigants: saline, 6.00% NaOCl, 2.00% CHX, 0.5%K21, and 1.00% K21. Colony-forming unit (CFU) counts were used to assess bacterial viability, while structural changes were analyzed via scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Raman spectroscopy was employed to identify chemical alterations in post-treatment biofilm components. Cell viability was evaluated using the MTT assay and mitochondrial staining in RAW264.7 macrophages, while the alamar blue assay was utilised for hPDLSCs. Additionally, the expression of cytokines (TNF-α, IL-1β, TGF-β, VEGF-A) associated with macrophage polarization was evaluated using Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) and gene expression analysis to determine the immunomodulatory impact of all the irrigants. Molecular simulations were carried out inside the Schrödinger Drug Discovery Suite using the Desmond package. Molecular simulations analyzed K21’s binding to MMP-9 and SrtA molecular structures with stability assessed via root mean square deviation (RMSD) and binding free energy (MM-GBSA). Statistical analysis used ANOVA with Tukey’s post hoc test (p < 0.05) and Pearson’s correlation for depth-dependent efficacy.
Results:
The CFU analysis revealed that K21, especially at a 1.00% concentration, consistently showed enhanced antibacterial efficacy relative to 6.00% NaOCl and was frequently comparable to or more effective than 2.00% CHX against E. faecalis, F. nucleatum, P. gingivalis, and dual-species biofilms. For CFU findings of E. faecalis, at a depth of 200 μm and a duration of 1-minute, 1.00% K21 exhibited the lowest CFU at 1.358 ± 0.193, in contrast to 0.5% K21 (3.453 ± 0.205), 2.00% CHX (4.65 ± 0.093), 6.00% NaOCl (5.64 ± 0.108), and saline (9.63 ± 0.031), with statistically significant differences (p < 0.001). At 400 μm and 1-minute, similar trends were observed. In 5-minute exposures, 1.00% K21 consistently exhibited the lowest CFUs (0.9687–0.9924), significantly surpassing 2.00% CHX and 6.00% NaOCl at both 200 μm and 400 μm (p < 0.001). For F. nucleatum biofilm, 1.00% K21 exhibited the lowest CFUs (2.1199 ± 0.20274 at 200 μm/5 min and 2.1782 ± 0.55736 at 400 μm/5 min), demonstrating significant reductions compared to 6.00% NaOCl (p < 0.001) and comparable efficacy to 2.00% CHX. At 1-minute application, CFU counts were markedly diminished by K21 group compared to 6.00% NaOCl. For P. gingivalis, at 200 μm/1 min, 1.00% K21 (3.9831 ± 0.10972) and 0.5%K21 were significantly better than 6.00% NaOCl (5.1798 ± 0.39327) and were comparable to 2.00% CHX (4.0792 ± 0.10074). At 400 μm/1 min and 5 min, all test irrigants demonstrated effectiveness relative to saline; nevertheless, 1.00% K21 consistently exhibited the lowest CFU counts with no statistically significant difference from 2.00% CHX. In dual-species biofilm, 1.00% K21 demonstrated significant reductions compared to saline at both 200 μm and 400 μm for 1 and 5-minute treatments. At 200 μm/5 min, 1.00% K21 (4.6173 ± 0.37708) and 0.5%K21 (4.7104 ± 0.34656) demonstrated superior efficacy compared to 6.00% NaOCl (5.1432 ± 0.48289). 1.00% K21 was comparable to 2.00% CHX (p > 0.05) and significantly better than saline (p < 0.001) and 6.00% NaOCl (p = 0.046).
Morphological analyses utilising SEM and TEM corroborated the CFU findings, demonstrating that 1.00% K21 induced significant membrane rupture, cytoplasmic leakage, and biofilm matrix disintegration across all the three species. The 1.00% K21 treated groups exhibited the most pronounced intensity deterioration, and Raman spectroscopy examination indicated notable spectrum shifts in the 480–490 cm⁻¹ range, so corroborating the hypothesis of heightened structural disruption of bacterial components.
For macrophage viability, all groups showed cell viability above 80%. While 0.5% and 1.00% K21 showed higher viability (87.17% and 87.4%), viability reduced for 6.00% NaOCl (82.42%) and 2.00% CHX (86.08%). K21 groups were noticeably better than 6.00% NaOCl, although all test groups had lowered viability relative to saline (p<0.05). Fluorescence imaging depicted strong, homogeneous mitochondrial signals maintained by saline and 0.5% K21 that indicated healthy, viable cells. The 1.00% K21 group maintained general function while only modestly altered mitochondrial structure. While 6.00% NaOCl produced severe cytotoxicity, low cell density, and weak fluorescence, 2.00% CHX exhibited variable effects with some mitochondrial fragmentation. At a concentration of 0.5%, K21 demonstrated superior mitochondrial preservation compared to 2.00% CHX and 6.00% NaOCl. SEM and TEM analysis indicated that macrophages treated with saline exhibited normal integrity and morphology. K21 exhibited electron-dense inclusions at elevated concentrations, signifying stress, but preserving cell morphology with slight surface alterations. The 6.00% NaOCl treatment caused severe structural damage, membrane fragmentation, and cytoplasmic debris; 2.00% CHX treated cells showed surface shrinkage and internal aggregates. K21 group displayed generally better cellular preservation than CHX and NaOCl groups.
Gene expression analysis demonstrated that K21 induced modest upregulation of pro-inflammatory cytokines (TNF-α: ~4.24–4.26; IL-1β: ~1.43–1.89), whereas 2.00% CHX and 6.00% NaOCl strongly upregulated both TNF-α (~19.38 and 19.30) and IL-1β (~2.30 and 1.89). Conversely, K21-treated groups exhibited significantly higher anti-inflammatory markers, with VEGF-A reaching 58.93 ± 0.16 for 1.00% K21 and TGF-β at 6.51 ± 0.11, substantially exceeding levels observed with CHX (TGF-β: 6.31 ± 0.66) and NaOCl. Overall, K21 demonstrated a balanced immunomodulatory profile characterized by reduced inflammatory activation and enhanced pro-healing capacity compared to conventional irrigants. At 30 minutes of exposure, the viability of human periodontal ligament stem cells (hPDLSCs) remained approximately close to 80% for all tested irrigating agents. Specifically, 1.00% K21 demonstrated a viability of 81.13%, 0.5% K21 at 80.13%, CHX at 80.16%, and NaOCl at 79.34%. Saline showed the highest cell viability at 98.48%. High viability was indicated by SEM and TEM studies of hPDLSCs showing intact morphology and membrane integrity from saline-treated cells. Severe structural damage, membrane lysis, and cytoplasmic disintegration were produced by 6.00% NaOCl. Moderate membrane distortion and vacuolation caused by 2.00% CHX indicated cytotoxic effects. Although 1.00% K21 showed some structural changes while 0.5%K21 maintained better integrity. TEM verified that although K21 caused subcellular changes, it maintained membrane continuity, hence indicating better biocompatibility than 2.00% CHX and 6.00% NaOCl. The K21 group shows a specific pocket binding on several MMPs and specific SrtA structures, according to molecular simulation, which generates a classic clouting effect. This can prevent SrtA enzymes and MMPs from acting catalytically, avoiding structural changes in dentin.
Conclusions
The 1.00% K21 group demonstrated superior antibacterial efficacy against E. faecalis, F. nucleatum, and P. gingivalis in dentinal tubules at 200 μm and 400 μm depths compared to 6.00% NaOCl and saline, with performance comparable to 0.5% K21 and 2.00% CHX. In dual-species biofilms, 1.00% K21 outperformed NaOCl and saline while showing equivalent results to CHX and 0.5% K21. It exhibited significantly enhanced biocompatibility and anti-inflammatory properties in RAW 264.7 macrophages and hPDLSCs compared to NaOCl, with results comparable to 0.5% K21 and CHX. K21 promoted M2 macrophage polarization and a balanced immune response. Molecular docking revealed specific binding affinity to MMPs and Sortase A, indicating a unique "clouting effect" that enhances antibacterial and regenerative capabilities. Overall, 1.00% K21 represents a promising biocompatible, multifunctional endodontic irrigant with superior antibacterial and anti-inflammatory potential.
Keywords: antibacterial, human periodontal ligament stem cells, K21, macrophages, molecular simulation, quaternary ammonium silane.
Thesis
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INFLUENCE OF MICRO- AND NANOPLASTIC (POLYETHYLENE MICRO- AND NANOSPHERE) ON THE COMBINED TOXICITY OF COPPER AND CADMIUM IN MICROALGAE
(IMU University, 2025)
LUKMAN HAKIM BIN ABDULLAH
Heavy metals and plastics pollutions in the environment are becoming more common due to their extensive usage in our everyday lives and improper waste management. Interaction between heavy metals with plastics has been shown to have negative effects to the ecosystem. The aim of this study was to investigate the influence of polyethylene (PE) microplastic (MP) and nanoplastic (NP) on the combined toxicity of copper (Cu) and cadmium (Cd) in microalgae. The effects of PEMP and NP on the toxicity of Cu and Cd were assessed based on the algal physiological responses such as photosynthetic pigment contents and oxidative stress response. Our results showed that after 10 days of exposure, Cu and Cd caused more growth inhibition to Raphidocelis subcapitata (CuIC50=32.32 mg/L, Cd IC50=23.25 mg/L) compared to Chlorella sp. TJ6-5 (CuIC50=34.77 mg/L, Cd IC50=36.45 mg/L). Combinations of Cu and Cd at various IC concentrations (IC10, IC25, IC50, IC90) displayed synergistic effects and caused higher observed toxicity to both algal species compared to the expected level of toxicity. Although PE MP and NP did not cause significant growth inhibition to both algae species at concentrations up to 2 g/L. However, presence of PE MP and NP did enhance the growth inhibition effect of Cu and Cd (at IC50) on both algal strains with higher lipid peroxidation and reactive oxygen species (ROS) production. In addition, our results showed the combined exposure to mixture of PE MP and NP and Cu and Cd can compromise the cellular antioxidant defence capacity, potentially leading to increased susceptibility to oxidative damage and cellular death. In conclusion, the presence of PE MP/NP enhance the toxicity of Cu and Cd to freshwater microalgae particularly in R. subcapitata and Chlorella sp., with species-specific responses and varying degrees of synergistic effects.
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EXPLORING THE PERCEPTIONS OF ASSESSMENT PRACTICES ON LEARNER AGENCY AMONG UNDERGRADUATE MEDICAL STUDENTS IN THE MBBS PROGRAMME AT IMU UNIVERSITY: A QUALITATIVE STUDY.
(IMU University, 2025)
SUNIL PAZHAYANUR VENKATESWARAN
Background: Learner agency is recognised as a critical attribute in health professions education, influencing students’ motivation, engagement, and capacity for self-regulated learning. However, the relationship between assessment practices and learner agency in medical education remains underexplored.
Objective: This study explored the perceptions and experiences of undergraduate medical students regarding assessment practices and their influence on the development of learner agency within the MBBS programme at IMU University.
Methods: A qualitative phenomenological design using focus group discussions (FGDs) was employed to examine the experiences of 27 medical students across Years 1 to 4. A purposive sample of 21 females and 6 males from diverse backgrounds participated in seven online FGDs conducted via Microsoft Teams©. Each session included 3–5 students. Data was analysed using iterative transcript review, inductive coding, and thematic analysis.
Results: Three main dimensions of learner agency—environmental, behavioural, and intrapersonal—emerged as central to students’ experiences. Continuous assessments and timely, constructive feedback supported engagement and self-regulation. However, variability in feedback quality, limited student voice in assessment design, and lack of clarity in expectations hindered students’ sense of control and ownership of learning.
Conclusion: Assessment practices significantly influence the development of learner agency among medical students. Enhancing the quality of feedback, promoting opportunities for co-agency, and designing student-inclusive assessment systems may strengthen learner empowerment and self-directed learning within medical education.
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AN EXPLORATORY STUDY ON THE MENTORSHIP EXPERIENCES AND NEEDS OF UNDERGRADUATE MEDICAL STUDENTS AT IMU UNIVERSITY, MALAYSIA
(IMU University, 2026)
SHAHNAJ PERVIN
Medical students frequently experience inconsistent and inadequately structured mentorship. Moreover, research shows that mentorship programmes tend to focus narrowly on academic monitoring without addressing the underlying factors contributing to students' holistic developmental needs. Recognising this gap, the present study seeks to explore the experiences and needs of undergraduate medical students regarding mentorship during their medical training. This study was guided by three theories: Kram's Mentoring Functions Theory, Social Support Theory, and Developmental Network Theory. Nine participants were purposely sampled based on their enrolment in Semesters 4-8. A descriptive qualitative research design with semi-structured individual interviews conducted via Microsoft Teams was employed for data gathering. The interviews were transcribed, and the data were analysed using Braun and Clarke's six steps of thematic analysis. The themes for the mentorship experiences and needs were constructed. The experience themes include "Mentorship as Multifaceted Support System," "Quality of Mentor-Mentee Relationship and Communication," "Mentorship as Catalyst for Growth," "Mentor Attributes and Credibility," and "Structure of Systems." Meanwhile the themes for need of mentorship include "Academic Support," "Trusting Relationship," "Driver of Growth," "Systems that Enable Support," and "Credible, Well-Prepared Mentors." Students provided insights on their mentorship experiences and needs as well as its effects on their personal, academic, and professional development. Several significant trends were found related to academic guidance, emotional support, career preparation, networking, and research engagement. However, students frequently expressed concerns about poor mentor responsiveness, inadequate career guidance, dysfunctional communication infrastructure, and strong emotional impact from a lack of proactive support and unclear expectations. The results supported the need for comprehensive mentorship programmes focusing on career planning, time management, stress management, networking, and research competencies, whilst creating supportive environments characterised by psychological safety, genuine engagement, and structured meeting frequencies rather than perfunctory monitoring. The study's findings add to the literature on mentorship programmes aimed at addressing students' multidimensional needs and promoting holistic wellbeing during medical training. The insights from the undergraduate medical students' viewpoint are helpful for institutions in designing evidence-based mentorship programmes.


