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Use of computational and wet lab techniques to examine the molecular association between a potent hepatitis C virus inhibitor, PSI-6206 and human serum albumin

Abubakar M, Mohamed SB, Abd Halim AA, Tayyab S

Spectrochim Acta A Mol Biomol Spectrosc, 2023 Jun 05;294:122543.
PMID: 36868020 DOI: 10.1016/j.saa.2023.122543

This study explores the plausible molecular interaction between a potent hepatitis C virus inhibitor, PSI-6206 (PSI), and human serum albumin (HSA), a primary transporter in blood plasma. Results obtained from both computational viz. molecular docking and molecular dynamics (MD) simulation and wet lab techniques such as UV absorption, fluorescence, circular dichroism (CD), and atomic force microscopy (AFM) complemented each other. While docking results identified PSI binding to subdomain IIA (Site I) of HSA by forming six hydrogen bonds, MD simulations signified the complex stability throughout the 50,000 ps. A consistent cutback in the Stern-Volmer quenching constant (Ksv) along with rising temperatures supported the static mode of fluorescence quenching in response to PSI addition and implied the development of the PSI-HSA complex. This discovery was backed by the alteration of the HSA UV absorption spectrum, a larger value (>1010 M-1.s-1) of the bimolecular quenching rate constant (kq) and the AFM-guided swelling of the HSA molecule, in the presence of PSI. Moreover, the fluorescence titration results revealed a modest binding affinity (4.27-6.25×103 M-1) in the PSI-HSA system, involving hydrogen bonds, van der Waals and hydrophobic interactions, as inferred from ΔS = + 22.77 J mol-1 K-1 and ΔH = - 11.02 KJ mol-1values. CD and 3D fluorescence spectra reminded significant adjustment in the 2° and 3° structures and modification in the Tyr/Trp microenvironment of the protein in the PSI-bound state. The results obtained from drug competing experiments also advocated the binding location of PSI in HSA as Site I.
Fulltext Associations Between Suicidal Behaviour, Attitudes Towards Suicide, and Psychological Distress Among Students in a University in East Malaysia

Kamaruddin MNSB, Hashim NAB, Mohamed SB, Azhari ZIB

East Asian Arch Psychiatry, 2023 Dec;33(4):114-119.
PMID: 38955783 DOI: 10.12809/eaap2342

BACKGROUND: Suicidal behaviour can be influenced by attitudes towards suicide and psychological distress. This study aimed to investigate the associations between psychological distress, attitudes towards suicide, and suicidal behaviour and to determine the prevalence of suicidal behaviour among students of a public university in East Malaysia.
METHODS: A total of 521 students from a public university in East Malaysia were asked to complete the Malay versions of the Suicidal Behaviour Questionnaire-Revised (SBQ-R), the Attitudes Towards Suicide Scale, and the Depression Anxiety Stress Scale.
RESULTS: 197 women and 290 men (mean age, 19.13 years) completed the questionnaires, giving a response rate of 93.4%. The prevalence of high-risk suicidal behaviour (SBQ-R score ≥7) was 23.8%. Suicidal behaviour was positively associated with psychological distress and favourable attitudes towards suicide, and negatively associated with unfavourable attitudes towards suicide. Predictors for suicidal behaviour were psychological distress and favourable attitudes towards suicide ('the ability to understand and accept suicide').
CONCLUSION: The prevalence of suicidal behaviour is high among students in a public university in East Malaysia. Services and education for mental health awareness and screening for early detection and intervention of psychological distress should be provided to university students. Implementation of suicide awareness policies and suicide prevention training is crucial.
Isoledene from Mesua ferrea Oleo-gum resin induces apoptosis in HCT 116 cells through ROS-mediated modulation of multiple proteins in the apoptotic pathways: a mechanistic study

Asif M, Shafaei A, Jafari SF, Mohamed SB, Ezzat MO, Majid AS, et al.

Toxicol Lett, 2016 Jun 3.
PMID: 27268964 DOI: 10.1016/j.toxlet.2016.05.027

Colorectal cancer (CRC) is one of the most common human malignant tumors worldwide. Arising from the transformation of epithelial cells in the colon and/or rectum into malignant cells, the foundation of CRC pathogenesis lies in the progressive accumulation of mutations in oncogenes and tumor-suppressor genes, such as APC and KRAS. Resistance to apoptosis is one of the key mechanisms in the development of CRC as it is for any other kind of cancer. Natural products have been shown to induce the expression of apoptosis regulators that are blocked in cancer cells. In the present study, a series of in vitro assays were employed to study the apoptosis inducing attributes of Isoledene rich sub-fraction (IR-SF) collected from the oleo-gum resin of M. ferrea. Data obtained, shows that IR-SF inhibited cell proliferation and induced typical apoptotic changes in the overall morphology of all the CRC cell lines tested. Fluorescent staining assays revealed characteristic nuclear condensation, and marked decrease in mitochondrial outer membrane potential in treated cells. In addition, an increment in the levels of ROS, caspase-8,-9 and -3 was observed. Proteomic analysis revealed that IR-SF up-regulated the expression of pro-apoptotic proteins, i.e., Bid, Bid and cytochrome c. Cytochrome c in turn activated caspases cascade resulting in the induction of apoptosis. Moreover, IR-SF significantly down-regulated Bcl-2, Bcl-w, survivin, xIAP and HSPs pro-proteins and induced DNA fragmentation and G0/G1-phase arrest in HCT 116 cells. Chemical characterization of IR-SF by GC-MS and HPLC methods identified Isoledene as one of the major compounds. Altogether, the results of the present study demonstrate that IR-SF may induce apoptosis in human colorectal carcinoma cells through activation of ROS-mediated apoptotic pathways.
Support vector machines for oil classification link with polyaromatic hydrocarbon contamination in the environment

Ismail A, Juahir H, Mohamed SB, Toriman ME, Kassim AM, Zain SM, et al.

Water Sci Technol, 2021 Mar;83(5):1039-1054.
PMID: 33724935 DOI: 10.2166/wst.2021.038

The main focus of this study is exploring the spatial distribution of polyaromatics hydrocarbon links between oil spills in the environment via Support Vector Machines based on Kernel-Radial Basis Function (RBF) approach for high precision classification of oil spill type from its sample fingerprinting in Peninsular Malaysia. The results show the highest concentrations of Σ Alkylated PAHs and Σ EPA PAHs in ΣTAH concentration in diesel from the oil samples PP3_liquid and GP6_Jetty achieving 100% classification output, corresponding to coherent decision boundary and projective subspace estimation. The high dimensional nature of this approach has led to the existence of a perfect separability of the oil type classification from four clustered oil type components; i.e diesel, bunker C, Mixture Oil (MO), lube oil and Waste Oil (WO) with the slack variables of ξ ≠ 0. Of the four clusters, only the SVs of two are correctly predicted, namely diesel and MO. The kernel-RBF approach provides efficient and reliable oil sample classification, enabling the oil classification to be optimally performed within a relatively short period of execution and a faster dataset classification where the slack variables ξ are non-zero.
Improving oil classification quality from oil spill fingerprint beyond six sigma approach

Juahir H, Ismail A, Mohamed SB, Toriman ME, Kassim AM, Zain SM, et al.

Mar Pollut Bull, 2017 Jul 15;120(1-2):322-332.
PMID: 28535957 DOI: 10.1016/j.marpolbul.2017.04.032

This study involves the use of quality engineering in oil spill classification based on oil spill fingerprinting from GC-FID and GC-MS employing the six-sigma approach. The oil spills are recovered from various water areas of Peninsular Malaysia and Sabah (East Malaysia). The study approach used six sigma methodologies that effectively serve as the problem solving in oil classification extracted from the complex mixtures of oil spilled dataset. The analysis of six sigma link with the quality engineering improved the organizational performance to achieve its objectivity of the environmental forensics. The study reveals that oil spills are discriminated into four groups' viz. diesel, hydrocarbon fuel oil (HFO), mixture oil lubricant and fuel oil (MOLFO) and waste oil (WO) according to the similarity of the intrinsic chemical properties. Through the validation, it confirmed that four discriminant component, diesel, hydrocarbon fuel oil (HFO), mixture oil lubricant and fuel oil (MOLFO) and waste oil (WO) dominate the oil types with a total variance of 99.51% with ANOVA giving Fstat>Fcritical at 95% confidence level and a Chi Square goodness test of 74.87. Results obtained from this study reveals that by employing six-sigma approach in a data-driven problem such as in the case of oil spill classification, good decision making can be expedited.
Fulltext Genomic analysis of methicillin-resistant Staphylococcus aureus strain SO-1977 from Sudan

Ali MS, Isa NM, Abedelrhman FM, Alyas TB, Mohammed SE, Ahmed AE, et al.

BMC Microbiol, 2019 06 11;19(1):126.
PMID: 31185900 DOI: 10.1186/s12866-019-1470-2

BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is known as a leading cause of morbidity and mortality. Investigation of the MRSA's virulence and resistance mechanisms is a continuing concern toward controlling such burdens through using high throughput whole Genome Sequencing (WGS) and molecular diagnostic assays. The objective of the present study is to perform whole-genome sequencing of MRSA isolated from Sudan using Illumina Next Generation Sequencing (NGS) platform.
RESULTS: The genome of MRSA strain SO-1977 consists of 2,827,644 bp with 32.8% G + C, 59 RNAs and 2629 predicted coding sequences (CDSs). The genome has 26 systems, one of which is the major class in the disease virulence and defence. A total of 83 genes were annotated to virulence disease and defence category some of these genes coding as functional proteins. Based on genome analysis, it is speculated that the SO-1977 strain has resistant genes to Teicoplanin, Fluoroquinolones, Quinolone, Cephamycins, Tetracycline, Acriflavin and Carbapenems. The results revealed that the SO-1977, strain isolated from Sudan has a wide range of antibiotic resistance compared to related strains.
CONCLUSION: The study reports for the first time the whole genome sequence of Sudan MRSA isolates. The release of the genome sequence of the strain SO-1977 will avail MRSA in public databases for further investigations on the evolution of resistant mechanism and dissemination of the -resistant genes of MRSA.