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Designing hypothesis of substituted benzoxazinones as HIV-1 reverse transcriptase inhibitors: QSAR approach

Veerasamy R, Subramaniam DK, Chean OC, Ying NM

J Enzyme Inhib Med Chem, 2012 Oct;27(5):693-707.
PMID: 21961709 DOI: 10.3109/14756366.2011.608664

A linear quantitative structure activity relationship (QSAR) model is presented for predicting human immunodeficiency virus-1 (HIV-1) reverse transcriptase enzyme inhibition. The 2D QSAR and 3D-QSAR models were developed by stepwise multiple linear regression, partial least square (PLS) regression and k-nearest neighbor-molecular field analysis, PLS regression, respectively using a database consisting of 33 recently discovered benzoxazinones. The primary findings of this study is that the number of hydrogen atoms, number of (-NH2) group connected with solitary single bond alters the inhibition of HIV-1 reverse transcriptase. Further, presence of electrostatic, hydrophobic and steric field descriptors significantly affects the ability of benzoxazinone derivatives to inhibit HIV-1 reverse transcriptase. The selected descriptors could serve as a primer for the design of novel and potent antagonists of HIV-1 reverse transcriptase.

Matched MeSH terms: RNA-Directed DNA Polymerase/pharmacology*; RNA-Directed DNA Polymerase/chemistry*
Fulltext Genome Sequence of Complex HIV-1 Unique Recombinant Forms Sharing a Common Recombination Breakpoint Identified in Malaysia

Cheong HT, Ng KT, Ong LY, Takebe Y, Chan KG, Koh C, et al.

Genome Announc, 2015;3(6).
PMID: 26543107 DOI: 10.1128/genomeA.01220-15

Three strains of HIV-1 unique recombinant forms (URFs) descended from subtypes B, B', and CRF01_AE were identified among people who inject drugs in Kuala Lumpur, Malaysia. These three URFs shared a common recombination breakpoint in the reverse transcriptase region, indicating frequent linkage within the drug-injecting networks in Malaysia.

Matched MeSH terms: RNA-Directed DNA Polymerase
Fulltext Expression analysis of ribosomal protein genes, el13 and el14 in nasopharyngeal carcinoma cell lines

Phei-Lian, Wang, Edmund Sim, Ui Hang

Trends in Undergraduate Research, 2020;3(1):5-12.
MyJurnal

Increasing evidence of the association between ribosomal protein (RP) genes with nasopharyngeal carcinoma (NPC) have been derived from findings of their differential expression patterns in NPC cell lines. Nevertheless, expression data from a comprehensive list of RP gene family members is still lacking. This paper reports the assessment of two RP genes, eL13 and eL14, with regards to their expression patterns in several NPC cell lines (TW04, TW01, HK1, HONE1 and SUNE-1) relative to a non-malignant control (NP69). A conventional Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) assay was employed. Analysis of eL13 has never been explored before this, whereas investigation of eL14 represents an extended study. We found a general over-expression trend of eL14 in 40% (2 of 5; TW01 and HONE-1) of the NPC cell lines studied, with higher upregulated level in only one (TW01) of them. However, this pattern of expression level is not statistically significant. Expression of eL13 was not detected in any of the cell lines used. The inconsistency of these expression patterns demonstrates an elusive nature of RP activities in the malignancy of the nasopharynx.

Matched MeSH terms: RNA-Directed DNA Polymerase
Fulltext Assessment of Noroviruses in selected Ulam from local market

Tuan Zainazor, T. C., Afsah-Hejri, L., Noor Hidayah, M. S., Noor Eliza, M. R., Naziehah, M. D., Tang, J. Y. H., et al.

International Food Research Journal, 2012;19(3):877-881.
MyJurnal

Presence of Norovirus in food can cause viral gasteroenteritis. Recently, lots of reports relating to Norovirus in food have been published. Special attention must be paid to the raw foods as they are not subjected to further heat treatment. In this study, pegaga, kesum, tauge and ulam raja (popular salad vegetables in Malaysia) were investigated for Norovirus. A total of 32 samples from each type of salad vegetables were purchased from local market and analyzed using One-step RT-PCR (Reverse Transcriptase-Polymerase Chain Reaction) for both genogroups namely Norovirus Genogroup I and Genogroup II. Results showed that tauge had the highest contamination with Norovirus Genogroup I (15.6%) comparing to pegaga (9.4%), kesum (12.5%)
and ulam raja (0%). Samples were free from Norovirus Genogroup II. The study showed that raw vegetables are high-risk foods and can be contaminated with Norovirus.

Matched MeSH terms: RNA-Directed DNA Polymerase
Fulltext Elevated expression of CD151 gene in estrogen receptor and progesterone receptor positive breast carcinoma

Ivyna Bong, P.N., Zubaidah, Z., Rohaizak, M., Naqiyah, I., Noor Hisham, A., Sharifah, N.A., et al.

Medicine & Health, 2011;6(1):33-40.
MyJurnal

The tetraspanin gene, CD151 is involved in various tumour cell progression and metastasis. Its expression is increased in high grade, estrogen receptor negative and c-erbB-2 positive breast cancer. However, the biological function and expression phenotype among different tumour status, estrogen receptor (ER) status, progesterone receptor (PR) status and c-erbB-2 expression in multi-ethnic Malaysian breast cancer patients has not been well investigated. We used quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) to measure the CD151 gene expression in 45 breast cancers. Our preliminary results revealed that CD151 expression is significantly higher in ER positive and PR positive breast cancers at 95% and 99% confidence intervals, respectively. In contrast, there is no significant correlation between CD151 expression and tumour grades or c-erbB-2 status at 95% confidence interval level. Our preliminary findings suggested that CD151 may be involved in the estrogen responsive pathways. CD151 could be a potential prognostic marker and therapeutic target in the treatment of estrogen dependent breast cancer patients.

Matched MeSH terms: RNA-Directed DNA Polymerase
Identification of a molecular marker for the Y chromosome of Brugia malayi

Underwood AP, Bianco AE

Mol Biochem Parasitol, 1999 Mar 15;99(1):1-10.
PMID: 10215019

Random amplification of polymorphic DNA (RAPD) was used to analyse genomic DNA from virgin females and males of Brugia malayi, with a view to identifying sex-specific differences predicted by an XX/XY system of chromosomal sex determination. A product of 2338 bp, amplified with the arbitrary primer 5' GTTGCGATCC 3', was obtained exclusively from males. Primers based on the sequence of this product amplified a DNA fragment of the expected size from each of two independent isolates of B. malayi (from Malaysia and Indonesia) by PCR. No reaction product was obtained from the closely related species Brugia pahangi. In a genetic cross between B. malayi males and B. pahangi females, F1 hybrid microfilariae were PCR-positive, indicating that the locus is paternally-inherited. Southern blotting demonstrated that the target sequence resides in the high molecular weight fraction of genomic DNA, confirming that it is of chromosomal, rather than mitochondrial, origin. Sequencing of the locus revealed significant similarity with members of a family of reverse transcriptase-like genes in Caenorhabditis elegans. In-frame stops indicate that the gene is non-functional, but multiple bands of hybridisation in Southern blots suggest that the RT sequence may be the relic of a transposable element. Multiple repeats of the dinucleotide AT occurred in another region of the sequence. These varied in number between the two isolates of B. malayi in the manner of a microsatellite, surprisingly the first to be described from the B. malayi genome. Because of its association with the Y chromosome, we have given the locus the acronym TOY (Tag On Y). Identification of this chromosome-specific marker confirms the XX/XY heterogametic karyotype in B. malayi and opens the way to elucidation of the role of Y in sex determination.

Matched MeSH terms: RNA-Directed DNA Polymerase/genetics
Fulltext Influenza and Respiratory Syncytial viral infections in Malaysia: Demographic and Clinical perspective

Rahman MM, Wong KK, Hanafiah A, Isahak I

Pak J Med Sci, 2014 Jan;30(1):161-5.
PMID: 24639853 DOI: 10.12669/pjms.301.4272

Respiratory infections represent a major public health problem worldwide. The study aimed to determine the prevalence of respiratory syncytial and influenza virus infections and analyzed in respect to demography and clinical perspective. Methods : The specimens were processed by cell culture and immunofluorescent assay (IFA) and real-time reverse transcriptase-PCR (rRT-PCR) for detection of respiratory viruses. Results : Out of 505 specimens 189 (37.8%) were positive, in which RSV was positive in 124(24.8%) cases and influenza A was positive in 65(13%) cases. Positive cases for influenza virus A and RSV were analyzed based on demography: age, gender, ethnicity and clinical symptoms. There were no significant differences among gender, ethnicity and clinical symptoms in both RSV and influenza A virus infections. It was observed that children below 3 years of ages were more prone to RSV infections. On the contrary, influenza virus A infected all age groups of humans.

Matched MeSH terms: RNA-Directed DNA Polymerase
Fulltext Milestone of polio Environmental Surveillance in Malaysia conjoining with the Polio Global Eradication Initiative

Kamal Haikal Mat Rabi, Amry Khursany Ismail, Mohd Samsul Samsuddin, Manisha Zauri Abdul Wahid, Zarina Mohd Zamawi, Ravindran Thayan

Malaysian Journal of Medicine and Health Sciences, 2019;15(106):78-78.
MyJurnal

Introduction: Poliomyelitis is an incapacitating and highly infectious disease which effect mostly young children. It is caused by one of the three serotypes of polioviruses (PV) and transmitted through faecal-oral route hence making the disease quite pertinent to the lower and middle class society or under-immunized population. This surveillance is one of the strategy included by WHO in the “Eradication, Integration and Certification: The Endgame Strategy 2019-2023” as a supplement to AFP surveillance by which it could be more sensitive to detect low circulation of WPV and circulating vaccine derived poliovirus (cVDPV). Methods: Routine collection and testing of representative environmental surveillance are carried out in the National Polio Laboratory. The specimens are collected from designated locations draining target populations at increased risk of poliovirus transmission using the grab method once a month and processed according to WHO standard protocol. Polioviruses were identified by real time reverse transcriptase polymerase chain reaction (rRT-PCR) for intratypic differentiation (ITD) and vaccine derived poliovirus (VDPV) whereas non-polio enteroviruses (NPEVs) were identified by PCR and sequencing. Results: From 2012 to 2019, results showed various isolation of PVs and NPEVs. A total of 12 sewage disposal plants located in urban highly populated areas in Kuala Lumpur (3), Selangor (5), Sabah (3 ) and Negeri Sembilan (1) were investigated. A total of 22 Sabin-like PVs were isolated consisting of 3 PV1, 8 PV2 and 11 PV3 thus indicated that in Malaysia even though PVs were existed in environment, but all of them were Sabin-Like viruses and no evidence of imported WPV or VDPV in the sampling sites. Conclusion: Even though Malaysia has been declared as WPV free country in 2000, Environmental Surveillance is very important and crucial in detecting the introduction and silent circulation of WPV and cVDPV before the virus reaches the community.

Matched MeSH terms: RNA-Directed DNA Polymerase
Fulltext Comparative evaluation of osteogenic differentiation potential of stem cells derived from dental pulp and exfoliated deciduous teeth cultured over granular hydroxyapatite based scaffold

Hagar MN, Yazid F, Luchman NA, Ariffin SHZ, Wahab RMA

BMC Oral Health, 2021 May 15;21(1):263.
PMID: 33992115 DOI: 10.1186/s12903-021-01621-0

BACKGROUND: Mesenchymal stem cells isolated from the dental pulp of primary and permanent teeth can be differentiated into different cell types including osteoblasts. This study was conducted to compare the morphology and osteogenic potential of stem cells from exfoliated deciduous teeth (SHED) and dental pulp stem cells (DPSC) in granular hydroxyapatite scaffold (gHA). Preosteoblast cells (MC3T3-E1) were used as a control group.
METHODOLOGY: The expression of stemness markers for DPSC and SHED was evaluated using reverse transcriptase-polymerase chain reaction (RT-PCR). Alkaline phosphatase assay was used to compare the osteoblastic differentiation of these cells (2D culture). Then, cells were seeded on the scaffold and incubated for 21 days. Morphology assessment using field emission scanning electron microscopy (FESEM) was done while osteogenic differentiation was detected using ALP assay (3D culture).
RESULTS: The morphology of cells was mononucleated, fibroblast-like shaped cells with extended cytoplasmic projection. In RT-PCR study, DPSC and SHED expressed GAPDH, CD73, CD105, and CD146 while negatively expressed CD11b, CD34 and CD45. FESEM results showed that by day 21, dental stem cells have a round like morphology which is the morphology of osteoblast as compared to day 7. The osteogenic potential using ALP assay was significantly increased (p

Matched MeSH terms: RNA-Directed DNA Polymerase
Fulltext Biodynamics of hepatitis C virus in haemodialysis patients in Pahang

Mohammed Saad, A.M., Mohammed Imad, A.M., Aini, H.H., Seman, M.R.

International Medical Journal Malaysia, 2012;11(1):23-30.
MyJurnal

Introduction: HCV infection is frequent in patients undergoing maintenance haemodialysis, with prevalence between 8 and 10%. Hepatitis C has an adverse effect on both patient and graft survival in those who get renal transplants. There are relatively scarce reports on the natural fluctuation in viral load level in patients on chronic haemodialysis. Materials and Methods: This is a longitudinal short-term three months study, where 27 chronic haemodialysis patients infected with known HCV genotypes were recruited from seven haemodialysis centres in Pahang. Serum samples were collected monthly, both pre- and post-haemodialysis sessions, over a period of three months. Viral RNA was extracted from serum using QIAamp Viral RNA Extraction kit (Qiagen). The HCV viral load was measured using one-step reverse transcriptase qPCR (Applied Biosystems) targeting the 5`HCV non-coding region (5’UTR). The serum α-IFN level was measured using commercial ELISA kit (Amersham, UK). Six biochemical liver function tests (AST, ALP, TP, albumin, ALT and TB) were also done for all pre-haemodialysis samples. Results: All patients showed persistent low level viral load that varied significantly over the study period (p = 0.001). HCV genotype 1 viral load was significantly higher than that of genotype 3. Conclusion: No apparent correlation could be recognized between the viral loads and the corresponding interferon-alpha levels which were detectable in only a few patients during the period of study.

Matched MeSH terms: RNA-Directed DNA Polymerase
Fulltext Measles: a disease often forgotten but not gone

Leung AK, Hon KL, Leong KF, Sergi CM

Hong Kong Med J, 2018 Oct;24(5):512-520.
PMID: 30245481 DOI: 10.12809/hkmj187470

Measles (rubeola) is a highly contagious vaccine-preventable disease caused by the measles virus-a virus of the Paramyxoviridae family. The illness typically begins with fever, runny nose, cough, and pathognomonic enanthem (Koplik spots) followed by a characteristic erythematous, maculopapular rash. The rash classically begins on the face and becomes more confluent as it spreads cephalocaudally. Laboratory confirmation of measles virus infection can be based on a positive serological test for measles-specific immunoglobulin M antibody, a four-fold or greater increase in measles-specific immunoglobulin G between acute and convalescent sera, isolation of measles virus in culture, or detection of measles virus ribonucleic acid by reverse transcriptase-polymerase chain reaction. Complications occur in 10% to 40% of patients, and treatment is mainly symptomatic. Bacterial superinfections, if present, should be properly treated with antibiotics. To eradicate measles, universal childhood immunisation and vaccination of all susceptible individuals with measles vaccine would be ideal. In developed countries, routine immunisation with measles-containing vaccine is recommended, with the first and second doses at ages 12 to 15 months and 4 to 6 years, respectively. The World Health Organization recommends that the first and second doses of measles-containing vaccine be given at ages 9 months and 15 to 18 months, respectively, in countries with high rates of measles transmission.

Matched MeSH terms: RNA-Directed DNA Polymerase
Phylogenetic analysis of respiratory syncytial virus identified at Universiti Kebangsaan Malaysia Medical Centre

Rahman M, Wong K, Ishak I, Rashid Z, Alfizah H

Sains Malaysiana, 2014;43:739-744.

Human respiratory syncytial virus (RSV) is an important cause of acute respiratory tract infection in infants and young children. Phylogenetic analysis for RSV in Malaysia has not been reported before. We investigated the genetic features of RSV in respiratory specimens from March to August 2011 with molecular methods. From a total of 130 throat swab and nasopharyngeal aspirate specimens, 54 (41.5%) were positive with RSV, identified by in-house real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assay. Thirty-four out of 54 (63.0%) RSV positive patients were children below two years old and two (1.4%) were adults. Phylogenetic analysis showed 39 isolates were genotype GA5, 13 genotypes GA2, one genotype GA1 and one genotype GA7. The findings indicated four genotypes of RSV circulating in the country and the predominant genotype is GA5.

Matched MeSH terms: RNA-Directed DNA Polymerase
Fulltext Identifications of drug resistance mutations among antiretroviral treatment naive HIV-1 patients in Peninsular Malaysia

Zain RM, Ibrahim N, Ismail S, Suppiah J, Mat Rahim NA, Thayan R

Asian Pac J Trop Med, 2017 Jan;10(1):75-78.
PMID: 28107870 DOI: 10.1016/j.apjtm.2016.12.005

OBJECTIVE: To determine drug resistance mutations and the HIV-1 subtypes among antiretroviral treatment naive HIV-1 patients in Peninsular Malaysia.
METHODS: A total of 45 samples from four hospitals that provide HIV viral load services were subjected to the amplification of the protease and two third of reverse transcriptase regions of the pol gene by RT-PCR and Sanger sequencing. Drug resistance mutation (DRM) interpretation reports the presence of mutations related to protease inhibitors (PIs), Nucleoside reverse-transcriptase inhibitors (NRTI) and Non-nucleoside reverse-transcriptase inhibitors (NNRTI) based on analysis using Stanford HIV database program.
RESULTS: DRMs were identified in 35% of patients, among which 46.7% of them showed minor resistance to protease inhibitor with A71V and L10l were the commonest DRMs detected. About 21.4% and 50.0% of patients had mutations to NRTIs and NNRTIs, respectively. CRF01_AE was found to be the predominant HIV-1 subtype.
CONCLUSIONS: These findings have served as an initial crucial data in determining the prevalence of transmitted HIV-1 drug resistance for the country. However, more samples from various parts of the country need to be accumulated and analyzed to provide overall HIV-1 drug resistance in the country.

Matched MeSH terms: RNA-Directed DNA Polymerase

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