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A critical view on the analysis of fluorescence quenching data for determining ligand-protein binding affinity

Bakar KA, Feroz SR

Spectrochim Acta A Mol Biomol Spectrosc, 2019 Dec 05;223:117337.
PMID: 31302564 DOI: 10.1016/j.saa.2019.117337

The past decade has seen an increase in the number of research papers on ligand binding to proteins based on fluorescence spectroscopy. In most cases, determination of the binding affinity is made by analyzing the quenching of protein fluorescence induced by the ligand. However, many such articles, even those published in reputed journals, suffer from several mistakes with regard to analysis of fluorescence quenching data. Using the binding of phenylbutazone to human serum albumin as a model, we consider some of these mistakes and show how they affect the values of the association constant. In particular, the failure to correct for the inner filter effect and the use of unsuitable equations are discussed. Ligand binding data presented in these articles should be treated with caution, especially in the absence of data from complementary techniques.
Fulltext Exploiting Layered Multi-Path Routing Protocols to Avoid Void Hole Regions for Reliable Data Delivery and Efficient Energy Management for IoT-Enabled Underwater WSNs

Butt SA, Bakar KA, Javaid N, Gharaei N, Ishmanov F, Afzal MK, et al.

Sensors (Basel), 2019 Jan 26;19(3).
PMID: 30691141 DOI: 10.3390/s19030510

The key concerns to enhance the lifetime of IoT-enabled Underwater Wireless Sensor Networks (IoT-UWSNs) are energy-efficiency and reliable data delivery under constrained resource. Traditional transmission approaches increase the communication overhead, which results in congestion and affect the reliable data delivery. Currently, many routing protocols have been proposed for UWSNs to ensure reliable data delivery and to conserve the node's battery with minimum communication overhead (by avoiding void holes in the network). In this paper, adaptive energy-efficient routing protocols are proposed to tackle the aforementioned problems using the Shortest Path First (SPF) with least number of active nodes strategy. These novel protocols have been developed by integrating the prominent features of Forward Layered Multi-path Power Control One (FLMPC-One) routing protocol, which uses 2-hop neighbor information, Forward Layered Multi-path Power Control Two (FLMPC-Two) routing protocol, which uses 3-hop neighbor information and 'Dijkstra' algorithm (for shortest path selection). Different Packet Sizes (PSs) with different Data Rates (DRs) are also taken into consideration to check the dynamicity of the proposed protocols. The achieved outcomes clearly validate the proposed protocols, namely: Shortest Path First using 3-hop neighbors information (SPF-Three) and Breadth First Search with Shortest Path First using 3-hop neighbors information (BFS-SPF-Three). Simulation results show the effectiveness of the proposed protocols in terms of minimum Energy Consumption (EC) and Required Packet Error Rate (RPER) with a minimum number of active nodes at the cost of affordable delay.
Fulltext Fischer Linear Discrimination and Quadratic Discrimination Analysis-Based Data Mining Technique for Internet of Things Framework for Healthcare

Hasan MK, Ghazal TM, Alkhalifah A, Abu Bakar KA, Omidvar A, Nafi NS, et al.

Front Public Health, 2021;9:737149.
PMID: 34712639 DOI: 10.3389/fpubh.2021.737149

The internet of reality or augmented reality has been considered a breakthrough and an outstanding critical mutation with an emphasis on data mining leading to dismantling of some of its assumptions among several of its stakeholders. In this work, we study the pillars of these technologies connected to web usage as the Internet of things (IoT) system's healthcare infrastructure. We used several data mining techniques to evaluate the online advertisement data set, which can be categorized as high dimensional with 1,553 attributes, and the imbalanced data set, which automatically simulates an IoT discrimination problem. The proposed methodology applies Fischer linear discrimination analysis (FLDA) and quadratic discrimination analysis (QDA) within random projection (RP) filters to compare our runtime and accuracy with support vector machine (SVM), K-nearest neighbor (KNN), and Multilayer perceptron (MLP) in IoT-based systems. Finally, the impact on number of projections was practically experimented, and the sensitivity of both FLDA and QDA with regard to precision and runtime was found to be challenging. The modeling results show not only improved accuracy, but also runtime improvements. When compared with SVM, KNN, and MLP in QDA and FLDA, runtime shortens by 20 times in our chosen data set simulated for a healthcare framework. The RP filtering in the preprocessing stage of the attribute selection, fulfilling the model's runtime, is a standpoint in the IoT industry. Index Terms: Data Mining, Random Projection, Fischer Linear Discriminant Analysis, Online Advertisement Dataset, Quadratic Discriminant Analysis, Feature Selection, Internet of Things.
Interaction mechanism of a cysteine protease inhibitor, odanacatib, with human serum albumin: In vitro and bioinformatics studies

Asngari NJM, Bakar KA, Feroz SR, Razak FA, Halim AAA

Biophys Chem, 2024 Feb;305:107140.
PMID: 38118338 DOI: 10.1016/j.bpc.2023.107140

Odanacatib (ODN) is a selective cathepsin K inhibitor that acts as an anti-resorptive agent to treat osteoporosis. ODN is also found effective in reducing the effect of severe periodontitis. The interaction between ODN and human serum albumin (HSA) was investigated using spectroscopic, microscopic, and in silico approaches to characterize their binding. The fluorescence intensity of HSA increased upon the addition of increasing concentrations of ODN accompanied by blueshift in the fluorescence spectrum, which suggested hydrophobic formation around the microenvironment of the fluorophores upon ODN binding. A moderate binding affinity was obtained for ODN-HSA binding, with binding constant (Ka) values of ∼104 M-1. Circular dichroism results suggested that the overall secondary and tertiary structures of HSA were both only slightly altered upon ODN binding. The surface morphology of HSA was also affected upon ODN binding, showing aggregate formation. Drug displacement and molecular docking results revealed that ODN preferably binds to site III in subdomain IB of HSA, while molecular dynamics simulations indicated formation of a stable protein complex when site III was occupied by ODN. The ODN-HSA complex was mainly stabilized by a combination of hydrogen bonding, hydrophobic interactions, and van der Waals forces. These findings provide additional information to understand the interaction mechanism of ODN in blood circulation and may help in future improvements on the adverse effects of ODN.
Health-related quality of life amongst children with chronic kidney disease in Malaysia: performance of the Bahasa Melayu version of the PedsQL 3.0 ESRD Module : (PedsQL 3.0 VerBATIM: version in Bahasa Melayu. Translated for use in Malaysia)

Bakar KA, Muhamad NA, Sarpin MA, Shaharudin S, Sidhu S, Yap SL, et al.

Pediatr Nephrol, 2023 Jun;38(6):1897-1905.
PMID: 36272027 DOI: 10.1007/s00467-022-05774-0

BACKGROUND: The PedsQL 3.0 End Stage Renal Disease (ESRD) Module is a well-accepted instrument internationally but it is not available in the local language. We aimed to validate the Bahasa Melayu (Malay language) version and determine the health-related quality of life (HRQoL) scores amongst children with CKD in Malaysia.
METHODS: The source questionnaire in English was translated into Bahasa Melayu. Linguistic validation guidelines by the MAPI Research Institute were followed. The already validated Bahasa Melayu PedsQL 4.0 Generic Core Scales was used for comparison. Sociodemographic data were collected during the interview. Statistical analyses were performed using SPSS version 25.0.
RESULTS: Sixty-nine children aged 8 to 18 with CKD stages 4 and 5, with or without dialysis, and their caregivers were recruited. Mean age was 12.62 ± 2.77 (SD). Evaluation of the PedsQL 3.0 ESRD Module Bahasa Melayu version demonstrated good internal consistency (Cronbach alpha 0.82). There was good agreement between child self-report and parent proxy report in all domains; average intraclass correlation coefficients (ICC) were 0.78, 95% CI (0.71, 0.84). Scores obtained from Generic 4.0 scales correlated with the disease-specific ESRD 3.0 scale, Spearman's rho = 0.32, p = 0.007. The Kruskal-Wallis H test indicated that there were no significant differences between stages of CKD and their respective mean HRQoL score, χ2(2) = 2.88, p = 0.236.
CONCLUSIONS: The PedsQL 3.0 ESRD Module Bahasa Melayu version is a reliable and feasible tool for cross-cultural adaptation. A longer prospective study may help better illustrate the quality of life in this group of children.