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Fulltext Screening of high-risk deleterious missense variations in the CYP1B1 gene implicated in the pathogenesis of primary congenital glaucoma: A comprehensive in silico approach

Shahid M, Azfaralariff A, Tufail M, Hussain Khan N, Abdulkareem Najm A, Firasat S, et al.

PeerJ, 2022;10:e14132.
PMID: 36518267 DOI: 10.7717/peerj.14132

BACKGROUND: Primary congenital glaucoma (PCG) is the most common subtype of glaucoma caused by defects in the cytochrome P450 1B1 (CYP1B1) gene. It is developing among infants in more than 80% of cases who exhibit impairments in the anterior chamber angle and the trabecular meshwork. Thus, a comprehensive in silico approach was performed to evaluate the effect of high-risk deleterious missense variations in the CYP1B1 gene.
MATERIAL AND METHODS: All the information for CYP1B1 missense variants was retrieved from the dbSNP database. Seven different tools, namely: SIFT, PolyPhen-2, PROVEAN, SNAP2, PANTHER, PhD-SNP, and Predict-SNP, were used for functional annotation, and two packages, which were I-Mutant 2.0 and MUpro, were used to predict the effect of the variants on protein stability. A phylogenetic conservation analysis using deleterious variants was performed by the ConSurf server. The 3D structures of the wild-type and mutants were generated using the I-TASSER tool, and a 50 ns molecular dynamic simulation (MDS) was executed using the GROMACS webserver to determine the stability of mutants compared to the native protein. Co-expression, protein-protein interaction (PPI), gene ontology (GO), and pathway analyses were additionally performed for the CYP1B1 in-depth study.
RESULTS: All the retrieved data from the dbSNP database was subjected to functional, structural, and phylogenetic analysis. From the conducted analyses, a total of 19 high-risk variants (P52L, G61E, G90R, P118L, E173K, D291G, Y349D, G365W, G365R, R368H, R368C, D374N, N423Y, D430E, P442A, R444Q, F445L, R469W, and C470Y) were screened out that were considered to be deleterious to the CYP1B1 gene. The phylogenetic analysis revealed that the majority of the variants occurred in highly conserved regions. The MD simulation analysis exhibited that all mutants' average root mean square deviation (RMSD) values were higher compared to the wild-type protein, which could potentially cause CYP1B1 protein dysfunction, leading to the severity of the disease. Moreover, it has been discovered that CYP1A1, VCAN, HSD17B1, HSD17B2, and AKR1C3 are highly co-expressed and interact with CYP1B1. Besides, the CYP1B1 protein is primarily involved in the metabolism of xenobiotics, chemical carcinogenesis, the retinal metabolic process, and steroid hormone biosynthesis pathways, demonstrating its multifaceted and important roles.
DISCUSSION: This is the first comprehensive study that adds essential information to the ongoing efforts to understand the crucial role of genetic signatures in the development of PCG and will be useful for more targeted gene-disease association studies.
Fulltext Norfloxacin Loaded Lipid Polymer Hybrid Nanoparticles for Oral Administration: Fabrication, Characterization, In Silico Modelling and Toxicity Evaluation

Khan MA, Khan S, Kazi M, Alshehri SM, Shahid M, Khan SU, et al.

Pharmaceutics, 2021 Oct 06;13(10).
PMID: 34683925 DOI: 10.3390/pharmaceutics13101632

Norfloxacin (NOR), widely employed as an anti-bacterial drug, has poor oral bioavailability. Nano based drug delivery systems are widely used to overcome the existing oral bioavailability challenges. Lipid-Polymer Hybrid Nanoparticles (LPHNs) exhibit the distinctive advantages of both polymeric and liposomes nanoparticles, while excluding some of their disadvantages. In the current study, NOR loaded LPHNs were prepared, and were solid amorphous in nature, followed by in vitro and in vivo evaluation. The optimized process conditions resulted in LPHNs with the acceptable particle size 121.27 nm, Polydispersity Index (PDI) of 0.214 and zeta potential of -32 mv. The addition of a helper lipid, oleic acid, and polymers, ethyl cellulose, substantially increased the encapsulation efficiency (EE%) (65% to 97%). In vitro study showed a sustained drug release profile (75% within 12 h) for NOR LPHNs. The optimized NOR LPHNs showed a significant increase (p < 0.05) in bioavailability compared to the commercial product. From the acute toxicity study, the LD50 value was found to be greater than 1600 mg/kg. The molecular modelling studies substantiated the experimental results with the best combination of polymers and surfactants that produced highly stable LPHNs. Therefore, LPHNs proved to be a promising system for the delivery of NOR, as well as for other antibiotics and hydrophobic drugs.
Uncovering Potentially Therapeutic Phytochemicals, In silico Analysis, and Biological Assessment of South-Chinese Red Dragon Fruit (Hylocereus polyrhizus)

Asghar A, Huichun L, Fang Q, Khan NA, Shahid M, Rui W, et al.

Plant Foods Hum Nutr, 2024 Feb 16.
PMID: 38363439 DOI: 10.1007/s11130-024-01151-4

Red dragon fruit is gaining popularity globally due to its nutritional value and bioactive components. The study aimed to assess the phytochemical, nutritional composition, antioxidant, antibacterial, and cytotoxic properties of extracts from the South Chinese red dragon fruit peel, flesh, and seeds. Extract fractions with increasing polarity (ethyl acetate
Fulltext Improved accuracy and less fault prediction errors via modified sequential minimal optimization algorithm

Asim Shahid M, Alam MM, Mohd Su'ud M

PLoS One, 2023;18(4):e0284209.
PMID: 37053173 DOI: 10.1371/journal.pone.0284209

The benefits and opportunities offered by cloud computing are among the fastest-growing technologies in the computer industry. Additionally, it addresses the difficulties and issues that make more users more likely to accept and use the technology. The proposed research comprised of machine learning (ML) algorithms is Naïve Bayes (NB), Library Support Vector Machine (LibSVM), Multinomial Logistic Regression (MLR), Sequential Minimal Optimization (SMO), K Nearest Neighbor (KNN), and Random Forest (RF) to compare the classifier gives better results in accuracy and less fault prediction. In this research, the secondary data results (CPU-Mem Mono) give the highest percentage of accuracy and less fault prediction on the NB classifier in terms of 80/20 (77.01%), 70/30 (76.05%), and 5 folds cross-validation (74.88%), and (CPU-Mem Multi) in terms of 80/20 (89.72%), 70/30 (90.28%), and 5 folds cross-validation (92.83%). Furthermore, on (HDD Mono) the SMO classifier gives the highest percentage of accuracy and less fault prediction fault in terms of 80/20 (87.72%), 70/30 (89.41%), and 5 folds cross-validation (88.38%), and (HDD-Multi) in terms of 80/20 (93.64%), 70/30 (90.91%), and 5 folds cross-validation (88.20%). Whereas, primary data results found RF classifier gives the highest percentage of accuracy and less fault prediction in terms of 80/20 (97.14%), 70/30 (96.19%), and 5 folds cross-validation (95.85%) in the primary data results, but the algorithm complexity (0.17 seconds) is not good. In terms of 80/20 (95.71%), 70/30 (95.71%), and 5 folds cross-validation (95.71%), SMO has the second highest accuracy and less fault prediction, but the algorithm complexity is good (0.3 seconds). The difference in accuracy and less fault prediction between RF and SMO is only (.13%), and the difference in time complexity is (14 seconds). We have decided that we will modify SMO. Finally, the Modified Sequential Minimal Optimization (MSMO) Algorithm method has been proposed to get the highest accuracy & less fault prediction errors in terms of 80/20 (96.42%), 70/30 (96.42%), & 5 fold cross validation (96.50%).
Fulltext Convergent synthesis, kinetics insight and allosteric computational ascriptions of thiazole-(5-aryl)oxadiazole hybrids embraced with propanamides as alkaline phosphatase inhibitors

Butt ARS, Abbasi MA, Aziz-Ur-Rehman, Siddiqui SZ, Muhammad S, Raza H, et al.

RSC Adv, 2023 May 02;13(20):13798-13808.
PMID: 37197574 DOI: 10.1039/d3ra01348k

Considering the varied pharmacological prominence of thiazole and oxadiazole heterocyclic moieties, a unique series of bi-heterocyclic hybrids, 8a-h, was synthesized in a convergent manner. The structures of newly synthesized compounds were characterized by 1H-NMR, 13C-NMR, and IR spectral studies. The structure-activity relationship of these compounds was predicted by examining their inhibitory effects against alkaline phosphatase, whereby all these molecules exhibited superb inhibitory potentials relative to the standard used. The kinetics mechanism was determined by Lineweaver-Burk plots which revealed that 8g inhibited the studied enzyme non-competitively by forming an enzyme-inhibitor complex. The inhibition constant Ki calculated from Dixon plots for this compound was 0.42 μM. The allosteric computational study was coherent with the experimental records and these ligands exhibited good binding energy values (kcal mol-1). The hemolytic analysis revealed their mild cytotoxicity towards red blood cell membranes and hence, these molecules have potential to be nontoxic medicinal scaffolds for the treatment of alkaline phosphate-associated ailments.
Fulltext Author Correction: The Plasmodium falciparum male gametocyte protein P230p, a paralog of P230, is vital for ookinete formation and mosquito transmission

Marin-Mogollon C, van de Vegte-Bolmer M, van Gemert GJ, van Pul FJA, Ramesar J, Othman AS, et al.

Sci Rep, 2019 May 03;9(1):7061.
PMID: 31053746 DOI: 10.1038/s41598-019-43505-y

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
Fulltext Comprehensive computational target fishing approach to identify Xanthorrhizol putative targets

Shahid M, Azfaralariff A, Law D, Najm AA, Sanusi SA, Lim SJ, et al.

Sci Rep, 2021 01 15;11(1):1594.
PMID: 33452398 DOI: 10.1038/s41598-021-81026-9

Xanthorrhizol (XNT), is a bioactive compound found in Curcuma xanthorrhiza Roxb. This study aimed to determine the potential targets of the XNT via computational target fishing method. This compound obeyed Lipinski's and Veber's rules where it has a molecular weight (MW) of 218.37 gmol-1, TPSA of 20.23, rotatable bonds (RBN) of 4, hydrogen acceptor and donor ability is 1 respectively. Besides, it also has half-life (HL) values 3.5 h, drug-likeness (DL) value of 0.07, oral bioavailability (OB) of 32.10, and blood-brain barrier permeability (BBB) value of 1.64 indicating its potential as therapeutic drug. Further, 20 potential targets were screened out through PharmMapper and DRAR-CPI servers. Co-expression results derived from GeneMANIA revealed that these targets made connection with a total of 40 genes and have 744 different links. Four genes which were RXRA, RBP4, HSD11B1 and AKR1C1 showed remarkable co-expression and predominantly involved in steroid metabolic process. Furthermore, among these 20 genes, 13 highly expressed genes associated with xenobiotics by cytochrome P450, chemical carcinogenesis and steroid metabolic pathways were identified through gene ontology (GO) and KEGG pathway analysis. In conclusion, XNT is targeting multiple proteins and pathways which may be exploited to shape a network that exerts systematic pharmacological effects.
Fulltext The Plasmodium falciparum male gametocyte protein P230p, a paralog of P230, is vital for ookinete formation and mosquito transmission

Marin-Mogollon C, van de Vegte-Bolmer M, van Gemert GJ, van Pul FJA, Ramesar J, Othman AS, et al.

Sci Rep, 2018 10 08;8(1):14902.
PMID: 30297725 DOI: 10.1038/s41598-018-33236-x

Two members of 6-cysteine (6-cys) protein family, P48/45 and P230, are important for gamete fertility in rodent and human malaria parasites and are leading transmission blocking vaccine antigens. Rodent and human parasites encode a paralog of P230, called P230p. While P230 is expressed in male and female parasites, P230p is expressed only in male gametocytes and gametes. In rodent malaria parasites this protein is dispensable throughout the complete life-cycle; however, its function in P. falciparum is unknown. Using CRISPR/Cas9 methodology we disrupted the gene encoding Pfp230p resulting in P. falciparum mutants (PfΔp230p) lacking P230p expression. The PfΔp230p mutants produced normal numbers of male and female gametocytes, which retained expression of P48/45 and P230. Upon activation male PfΔp230p gametocytes undergo exflagellation and form male gametes. However, male gametes are unable to attach to red blood cells resulting in the absence of characteristic exflagellation centres in vitro. In the absence of P230p, zygote formation as well as oocyst and sporozoite development were strongly reduced (>98%) in mosquitoes. These observations demonstrate that P230p, like P230 and P48/45, has a vital role in P. falciparum male fertility and zygote formation and warrants further investigation as a potential transmission blocking vaccine candidate.
Fulltext Anti-breast cancer synthetic peptides derived from the Anabas testudineus skin mucus fractions

Najm AAK, Azfaralariff A, Dyari HRE, Othman BA, Shahid M, Khalili N, et al.

Sci Rep, 2021 11 30;11(1):23182.
PMID: 34848729 DOI: 10.1038/s41598-021-02007-6

Previous study has shown the antimicrobial activities of mucus protein extracted from Anabas testudineus. In this study, we are interested in characterizing the anticancer activity of the A. testudineus antimicrobial peptides (AMPs). The mucus was extracted, fractioned, and subjected to antibacterial activity testing to confirm the fish's AMPs production. The cytotoxic activity of each fraction was also identified. Fraction 2 (F2), which shows toxicity against MCF7 and MDA-MB-231 were sent for peptide sequencing to identify the bioactive peptide. The two peptides were then synthetically produced and subjected to cytotoxic assay to prove their efficacy against cancer cell lines. The IC50 for AtMP1 against MCF7 and MDA-MB-231 were 8.25 ± 0.14 μg/ml and 9.35 ± 0.25 μg/ml respectively, while for AtMP2 it is 5.89 ± 0.14 μg/ml and 6.97 ± 0.24 μg/ml respectively. AtMP1 and AtMP2 treatment for 48 h induced breast cancer cell cycle arrest and apoptosis by upregulating the p53, which lead to upregulate pro-apoptotic BAX gene and downregulate the anti-apoptotic BCL-2 gene, consequently, trigger the activation of the caspase-3. This interaction was supported by docking analysis (QuickDBD, HPEPDOCK, and ZDOCK) and immunoprecipitation. This study provided new prospects in the development of highly effective and selective cancer therapeutics based on antimicrobial peptides.
Facile synthesis of graphene oxide-silver nanocomposite and its modified electrode for enhanced electrochemical detection of nitrite ions

Ikhsan NI, Rameshkumar P, Pandikumar A, Mehmood Shahid M, Huang NM, Vijay Kumar S, et al.

Talanta, 2015 Nov 1;144:908-14.
PMID: 26452907 DOI: 10.1016/j.talanta.2015.07.050

In this report, silver nanoparticles (Ag NPs) were successfully deposited on graphene oxide (GO) sheets to form GO-Ag nanocomposite using garlic extract and sunlight and the nanocomposite modified glassy carbon (GC) electrode was applied as an electrochemical sensor for the detection of nitrite ions. The formation of GO-Ag nanocomposite was confirmed by using UV-visible absorption spectroscopy, TEM, XRD and FTIR spectroscopy analyses. Further, TEM pictures showed a uniform distribution Ag on GO sheets with an average size of 19 nm. The nanocomposite modified electrode produced synergistic catalytic current in nitrite oxidation with a negative shift in overpotential. The limit of detection (LOD) values were found as 2.1 µM and 37 nM, respectively using linear sweep voltammetry (LSV) and amperometric i-t curve techniques. The proposed sensor was stable, reproducible, sensitive and selective toward the detection nitrite and could be applied for the detection of nitrite in real water sample.
Global differences in lung function by region (PURE): an international, community-based prospective study

Duong M, Islam S, Rangarajan S, Teo K, O'Byrne PM, Schünemann HJ, et al.

Lancet Respir Med, 2013 Oct;1(8):599-609.
PMID: 24461663 DOI: 10.1016/S2213-2600(13)70164-4

BACKGROUND: Despite the rising burden of chronic respiratory diseases, global data for lung function are not available. We investigated global variation in lung function in healthy populations by region to establish whether regional factors contribute to lung function.
METHODS: In an international, community-based prospective study, we enrolled individuals from communities in 17 countries between Jan 1, 2005, and Dec 31, 2009 (except for in Karnataka, India, where enrolment began on Jan 1, 2003). Trained local staff obtained data from participants with interview-based questionnaires, measured weight and height, and recorded forced expiratory volume in 1 s (FEV₁) and forced vital capacity (FVC). We analysed data from participants 130-190 cm tall and aged 34-80 years who had a 5 pack-year smoking history or less, who were not affected by specified disorders and were not pregnant, and for whom we had at least two FEV₁ and FVC measurements that did not vary by more than 200 mL. We divided the countries into seven socioeconomic and geographical regions: south Asia (India, Bangladesh, and Pakistan), east Asia (China), southeast Asia (Malaysia), sub-Saharan Africa (South Africa and Zimbabwe), South America (Argentina, Brazil, Colombia, and Chile), the Middle East (Iran, United Arab Emirates, and Turkey), and North America or Europe (Canada, Sweden, and Poland). Data were analysed with non-linear regression to model height, age, sex, and region.
FINDINGS: 153,996 individuals were enrolled from 628 communities. Data from 38,517 asymptomatic, healthy non-smokers (25,614 women; 12,903 men) were analysed. For all regions, lung function increased with height non-linearly, decreased with age, and was proportionately higher in men than women. The quantitative effect of height, age, and sex on lung function differed by region. Compared with North America or Europe, FEV1 adjusted for height, age, and sex was 31·3% (95% CI 30·8-31·8%) lower in south Asia, 24·2% (23·5-24·9%) lower in southeast Asia, 12·8% (12·4-13·4%) lower in east Asia, 20·9% (19·9-22·0%) lower in sub-Saharan Africa, 5·7% (5·1-6·4%) lower in South America, and 11·2% (10·6-11·8%) lower in the Middle East. We recorded similar but larger differences in FVC. The differences were not accounted for by variation in weight, urban versus rural location, and education level between regions.
INTERPRETATION: Lung function differs substantially between regions of the world. These large differences are not explained by factors investigated in this study; the contribution of socioeconomic, genetic, and environmental factors and their interactions with lung function and lung health need further clarification.
FUNDING: Full funding sources listed at end of the paper (see Acknowledgments).
Free-living ciliates in CSF of a patient with meningoencephalitis: a contaminant?

Isa NH, Sulaiman S, Shahid MS, Rose IM, Eugene CB

Southeast Asian J. Trop. Med. Public Health, 1994 Mar;25(1):212-4.
PMID: 7825018
Fulltext Phytochemicals and Biological Activities of Garcinia atroviridis: A Critical Review

Shahid M, Law D, Azfaralariff A, Mackeen MM, Chong TF, Fazry S

Toxics, 2022 Oct 29;10(11).
PMID: 36355947 DOI: 10.3390/toxics10110656

Garcinia atriviridis Griff ex T. Anders (G. atroviridis) is one of the well-known species of the genus Garicinia that is native to Thailand, Myanmar, Peninsular Malaysia, and India. G. atroviridis is a perennial medium-sized tree that has a wide range of values, from food to medicinal use. Different parts of G. atroviridis are a great source of bioactive substances that have a positive impact on health. The extracts or bioactive constituents from G. atroviridis have demonstrated various therapeutic functions, including antioxidant, antimicrobial, anticancer, anti-inflammatory, antihyperlipidemic, and anti-diabetic. In this paper, we provide a critical review of G. atroviridis and its bioactive constituents in the prevention and treatment of different diseases, which will provide new insight to explore its putative domains of research.

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