Browsing by Author "Muhamad Arif Mohamad Jamali"
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Publication Impact of Rapid Vaccination on Sars-Cov-2 Genomic Diversity: An Intervention to Minimise the Public Burden of the Pandemic(Malaysian Journal of Public Health Medicine, 2023) ;Amirah Azzeri ;Shuhaila Mat-Sharani ;Danish A/L Kumareahsan ;Ismatul Nurul Asyikin Ismail ;Muhamad Arif Mohamad JamaliLiyana AzmiGlobal sharing of SARS-CoV-2 sequences enabled comprehensive analyses of COVID-19 genomic diversity and demographics. Yet, regional genomic surveillance is often neglected, leading to the possible oversight of novel mutations by public health authorities. Our study used the Global Initiative on Sharing Avian Influenza Data (GISAID) database to analyse infection patterns in the state of Negeri Sembilan, and compare infection patterns to the state of Selangor, in Malaysia. We discuss the impact of rapid vaccination on resulting single nucleotide variants (SNVs) and identified novel sporadic mutations may affect viral fitness and pathogenicity. Four hundred and seventeen SARS-CoV-2 sequences extracted from Negeri Sembilan from July 2021 until June 2022. Infection patterns based on pangolin lineages from Negeri Sembilan was compared to infections of the same period from Selangor. SNVs from the spike protein were sorted by frequency, with the lowest frequency variant submitted for functional prediction using PredictSNP. Negeri Sembilan exhibited a comparable infection pattern to Selangor, but with fewer Omicron sequences which was postulated to occur due to the rapid vaccination strategies by Negeri Sembilan. Omicron outbreaks were associated with eased lockdowns and policy changes in December 2021. From our extracted data, seventy novel SNVs in the spike protein of SARS-CoV-2 were extracted from this study. In silico predictions indicated five of the SNVs (S221L, L226S, V826L, C1240F and C1243F) to may cause functional defects to the spike protein. Rapid sequencing and analysis will aid policymaking for public health controls by detecting potential outbreaks within transient variants. - Some of the metrics are blocked by yourconsent settings
Publication Molecular Dynamic Simulations Of Mlac Inhibition By Antibiotic In Escherichia Coli(Malaysian Society for Biochemistry and Molecular Biology, 2023) ;Umairah Ramli ;Muhamad Arif Mohamad Jamali ;Ismatul Nurul Asyikin Ismail ;Fatin Hilyani MohamadLiyana AzmiAntimicrobial resistance has emerged as a global public health concern. Gram-negative bacteria such as Escherichia coli (E. coli) pose a significant threat to human health due to their increasing antibiotic resistance. For instance, Shiga toxin-producing E. coli (STEC) is a strain that produces toxins that cause damage to the lining of the intestines and kidneys. Antibiotic exposures to STEC would induce the hemolytic uraemic syndrome and bloody diarrhea, a potentially fatal-condition to the patient. The outer membrane architecture in Gram-negatives, specifically the OmpC–Mla complex, maintains the outer membrane lipid asymmetry. The MlaC protein transfers phospholipids from outer membranes to inner membranes and ensures the integrity of the membrane. Inactivation of MlaC protein increases the penetrability of OM and increases the antibiotic’s sensitivity. Therefore, screening for inhibitor compounds that can bind and inhibit the function of MlaC is a viable strategy for antibiotic development.This study aims to understand the interactions of four types of inhibitors in MlaC protein from E. coli via docking and molecular dynamic (MD) simulation. The four types of inhibitors namely albacarcin V, clorobiocin, 1-N,4-N-bis(3- phenylphenyl)piperazine-1,4-dicarboxamide (piperazine dicarboxamide) and -2-[2-[(6- oxobenzo[c]chromen-2-yl)carbamoyl]phenyl]benzoic acid (salicylanilide benzoate). The docking showed that the inhibitors fit into the lipid pocket of MlaC. MD for each system run at 100 ns showed that the system has stable Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and reasonable Radius of Gyration (Rg) value. The RMSD, RMSF and Rg were comparable to the native phospholipid binding in the crystal structure, which suggests the potential use of these four types of inhibitors. Salicylanilide benzoate was revealed to be the most stable in complex with MlaC, with the least deviation, least fluctuation, and most compact throughout the simulation