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Network pharmacology, molecular docking and molecular dynamics simulation of chalcone scaffold-based compounds targeting breast cancer receptors

Ismail NZ, Khairuddean M, Abubakar S, Arsad H

J Biomol Struct Dyn, 2023 Dec 27.
PMID: 38149857 DOI: 10.1080/07391102.2023.2296606

Compounds with a chalcone scaffold-based structure have demonstrated promising anticancer biological activity. However, the molecular interactions between chalcone scaffold-based compounds and breast cancer-associated proteins remain unclear. Through network pharmacology, molecular docking, and molecular dynamics (MD) simulation analyses, compounds with a chalcone scaffold-based structure were evaluated for their interaction with potential breast cancer targets. The compounds were retrieved from the ASINEX database, resulting in 575,302 compounds. A total of 342 compounds with chalcone scaffold-based structures were discovered. From the 342 compounds that was analysed, ten were chosen due to their adherence to Lipinski's rule, having an appropriate range of lipophilicity (LOGP), and topological polar surface area (TPSA), and absence of any toxicity. Based on target intersection, 50 target genes were found and subjected to protein-protein interaction (PPI), gene ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Four target genes were found to be involved in the breast cancer pathway. Consequently, molecular docking was utilised to analyse the molecular interactions between the compounds and four target protein receptors. Compound 211 exhibited the highest binding affinities for the epidermal growth factor receptor (EGFR), fibroblast growth factor receptor 1 (FGFR1), oestrogen receptor (ESR1), and cyclin dependent kinase 6 (CDK6) with values of -8.95 kcal/mol, -8.60 kcal/mol, -10.33 kcal/mol, and -9.90 kcal/mol, respectively. During MD simulation, compound 211 and its respective proteins were stable, compact, and had minimal flexibility. The findings provide foundations for future studies into the interaction underlying the anti-breast cancer potential of compounds with chalcone-based scaffold structures.Communicated by Ramaswamy H. Sarma.
Nipah virus RNA synthesis in cultured pig and human cells

Chang LY, Ali AR, Hassan SS, AbuBakar S

J Med Virol, 2006 Aug;78(8):1105-12.
PMID: 16789019

Nipah virus infection of porcine stable kidney cells (PS), human neuronal cells (SK-N-MC), human lung fibroblasts cells (MRC-5), and human monocytes (THP-1) were examined. Rapid progression of cytopathic effects (CPE) and cell death were noted in PS cell cultures treated with Nipah virus, followed by MRC-5, SK-N-MC, and THP-1 cell cultures, in descending order of rapidity. Significant increase in the intracellular Nipah virus RNA occurred beginning at 24 hr PI in all the infected cells. Whereas, the extracellular release of Nipah virus RNA increased significantly beginning at 48 and 72 hr PI for the infected MRC-5 cells and PS cells, respectively. No significant release of extracellular Nipah virus RNA was detected from the Nipah virus-infected SK-N-MC and THP-1 cells. At its peak, approximately 6.6 log PFU/microl of extracellular Nipah virus RNA was released from the Nipah virus-infected PS cells, with at least a 100-fold less virus RNA was recorded in the Nipah virus-infected SK-N-MC and THP-1. Approximately 15.2% (+/-0.1%) of the released virus from the infected PS cell cultures was infectious in contrast to approximately 5.5% (+/-0.7%) from the infected SK-N-MC cells. The findings suggest that there are no differences in the capacity to support Nipah virus replication between pigs and humans in fully susceptible PS and MRC-5 cells. However, there are differences between these cells and human neuronal cells and monocytes in the ability to support Nipah virus replication and virus release.
Association of total and dengue-specific IgE levels in the sera with dengue virus inhibition and antibody-dependent enhancement

Annsley DS, Chin KL, Tan KK, AbuBakar S, Zainal N

Trop Biomed, 2024 Dec 01;41(4):481-490.
PMID: 39876506 DOI: 10.47665/tb.41.4.009

Dengue, caused by the dengue virus (DENV), poses a significant global health challenge. Effective vaccines and treatments for dengue are lacking due to gaps in understanding its pathogenesis and mechanisms in severe cases. This study investigates the role of immunoglobulin E (IgE) in dengue, focusing on its potential association with virus neutralization and antibody-dependent enhancement (ADE) in DENV replication. Serum samples were obtained from dengue-positive (dengue-IgG positive), SLE (dengue-IgG negative), and control (dengue-IgG and SLE-negative) individuals. SLE sera were included as a control for their high total IgE levels. Total IgE and dengue-specific IgE levels were measured using ELISA. Neutralization assays in Vero and KU812 cells were conducted to assess virus neutralization and ADE, respectively. Dengue-positive and SLE sera showed higher total IgE levels than control sera, although there was no significance seen. Dengue-positive sera showed the presence of dengue-specific IgE, whereas SLE and control sera exhibited negligible levels. Neutralization assay in dengue-positive sera revealed no correlation between IgE levels and virus inhibition. SLE sera, however, demonstrated an inverse correlation between total IgE levels and DENV neutralization, suggesting a potential involvement of total IgE in DENV replication in the context of SLE. Seventy-eight percent of SLE sera, 65% of denguepositive and 54% of control sera exhibited enhanced virus replication in KU812 cells with serum compared to virus alone, indicating the highest occurrence of ADE in SLE, followed by dengue-positive and control sera. DENV expression in KU812 cells was notably higher in SLE sera, indicating increased ADE risk. However, no association was found between IgE levels and virus expression in KU812 cells across all groups. The inverse correlation between total IgE levels and DENV neutralization in SLE sera suggests that IgE may facilitate virus replication. Further comprehensive exploration is needed to fully understand the role of IgE in dengue pathogenesis.
Fulltext Knowledge assessment of anti-snake venom among healthcare practitioners in northern Nigeria

Bala AA, Jatau AI, Yunusa I, Mohammed M, Mohammed AH, Isa AM, et al.

Ther Adv Infect Dis, 2021 08 19;8:20499361211039379.
PMID: 34434552 DOI: 10.1177/20499361211039379

Introduction: Anti-snake venom (ASV) is the standard therapy for the management of snakebite envenoming (SBE). Therefore, the knowledge of ASV among healthcare practitioners (HCPs) is essential for achieving optimal clinical outcomes in snakebite management. This study aimed to assess knowledge of ASV among the HCPs in northern Nigeria.
Methods: We conducted a cross-sectional study involving eligible HCPs from different healthcare settings in northern Nigeria. The participants were recruited into the study using a combination of online (via Google Form) and face-to-face paper-based survey methods. The ASV knowledge of the respondents was measured using a validated anti-snake venom knowledge assessment tool (AKAT). Inadequate overall knowledge of ASV was defined as scores of 0-69.9%, and 70-100% were considered adequate overall knowledge scores. The predictors of ASV knowledge were determined using multiple logistic regression.
Results: Three hundred and thirty-one (331) eligible HCPs were included in the study analysis (310 from online and 21 from paper-based survey). Overall, an estimated 12.7% of the participants had adequate knowledge of ASV. Adequate ASV knowledge was higher among physicians compared with other HCPs (21.7%; χ2 = 8.1; p = 0.04). Those without previous training on ASV (adjusted odds ratio [aOR], 0.37; 95% confidence interval [CI], 0.18-0.73; p = 0.004) and who have not previously administered/dispensed ASV (aOR, 0.31; 95% CI, 0.15-0.63; p
Fulltext The Use of NS1 Rapid Diagnostic Test and qRT-PCR to Complement IgM ELISA for Improved Dengue Diagnosis from Single Specimen

Teoh BT, Sam SS, Tan KK, Johari J, Abd-Jamil J, Hooi PS, et al.

Sci Rep, 2016 06 09;6:27663.
PMID: 27278716 DOI: 10.1038/srep27663

Timely and accurate dengue diagnosis is important for differential diagnosis and immediate implementation of appropriate disease control measures. In this study, we compared the usefulness and applicability of NS1 RDT (NS1 Ag Strip) and qRT-PCR tests in complementing the IgM ELISA for dengue diagnosis on single serum specimen (n = 375). The NS1 Ag Strip and qRT-PCR showed a fair concordance (κ = 0.207, p = 0.001). While the NS1 Ag Strip showed higher positivity than qRT-PCR for acute (97.8% vs. 84.8%) and post-acute samples (94.8% vs. 71.8%) of primary infection, qRT-PCR showed higher positivity for acute (58.1% vs. 48.4%) and post-acute (50.0% vs.41.4%) samples in secondary infection. IgM ELISA showed higher positivity in samples from secondary dengue (74.2-94.8%) than in those from primary dengue (21.7-64.1%). More primary dengue samples showed positive with combined NS1 Ag Strip/IgM ELISA (99.0% vs. 92.8%) whereas more secondary samples showed positive with combined qRT-PCR/IgM ELISA (99.4% vs. 96.2%). Combined NS1 Ag Strip/IgM ELISA is a suitable combination tests for timely and accurate dengue diagnosis on single serum specimen. If complemented with qRT-PCR, combined NS1 Ag Strip/IgM ELISA would improve detection of secondary dengue samples.
Fulltext Avoid haste in defining human muscular sarcocystosis

Italiano CM, Wong KT, AbuBakar S, Lau YL, Ramli N, Syed Omar SF, et al.

Clin Infect Dis, 2015 Apr 1;60(7):1134.
PMID: 25537869 DOI: 10.1093/cid/ciu1163
Tick-borne viruses: a review from the perspective of therapeutic approaches

Lani R, Moghaddam E, Haghani A, Chang LY, AbuBakar S, Zandi K

Ticks Tick Borne Dis, 2014 Sep;5(5):457-65.
PMID: 24907187 DOI: 10.1016/j.ttbdis.2014.04.001

Several important human diseases worldwide are caused by tick-borne viruses. These diseases have become important public health concerns in recent years. The tick-borne viruses that cause diseases in humans mainly belong to 3 families: Bunyaviridae, Flaviviridae, and Reoviridae. In this review, we focus on therapeutic approaches for several of the more important tick-borne viruses from these 3 families. These viruses are Crimean-Congo hemorrhagic fever virus (CCHF) and the newly discovered tick-borne phleboviruses, known as thrombocytopenia syndromevirus (SFTSV), Heartland virus and Bhanja virus from the family Bunyaviridae, tick-borne encephalitis virus (TBEV), Powassan virus (POWV), Louping-ill virus (LIV), Omsk hemorrhagic fever virus (OHFV), Kyasanur Forest disease virus (KFDV), and Alkhurma hemorrhagic fever virus (AHFV) from the Flaviviridae family. To date, there is no effective antiviral drug available against most of these tick-borne viruses. Although there is common usage of antiviral drugs such as ribavirin for CCHF treatment in some countries, there are concerns that ribavirin may not be as effective as once thought against CCHF. Herein, we discuss also the availability of vaccines for the control of these viral infections. The lack of treatment and prevention approaches for these viruses is highlighted, and we hope that this review may increase public health awareness with regard to the threat posed by this group of viruses.
Fulltext A novel rare copy number variant of the ABCF1 gene identified among dengue fever patients from Peninsular Malaysia

Hoh BP, Sam SS, Umi SH, Mahiran M, Nik Khairudin NY, Rafidah Hanim S, et al.

Genet. Mol. Res., 2014;13(1):980-5.
PMID: 24634119 DOI: 10.4238/2014.February.19.9

Copy number variation (CNV) is a form of genetic variation in addition to single nucleotide polymorphisms. The significance of CNV in the manifestation of a number of diseases is only recently receiving considerable attention. We genotyped 163 dengue patients from Peninsular Malaysia for genes possibly linked to dengue infection using quantitative real-time PCR. Here, we report a serendipitous discovery of a novel rare CNV of the ABCF1 gene among the dengue patients. Among these patients, two had a gain of 1 copy (CN = 3) and one had lost 1 copy (CN = 1), indicating that a rare CNV of the ABCF1 gene was detected among dengue patients from Peninsular Malaysia. Although the gene is suspected to regulate inflammatory responses and pathogen-induced cytokine storm, its relevance to dengue requires further investigation.
Fulltext A review on antibacterial, antiviral, and antifungal activity of curcumin

Moghadamtousi SZ, Kadir HA, Hassandarvish P, Tajik H, Abubakar S, Zandi K

Biomed Res Int, 2014;2014:186864.
PMID: 24877064 DOI: 10.1155/2014/186864

Curcuma longa L. (Zingiberaceae family) and its polyphenolic compound curcumin have been subjected to a variety of antimicrobial investigations due to extensive traditional uses and low side effects. Antimicrobial activities for curcumin and rhizome extract of C. longa against different bacteria, viruses, fungi, and parasites have been reported. The promising results for antimicrobial activity of curcumin made it a good candidate to enhance the inhibitory effect of existing antimicrobial agents through synergism. Indeed, different investigations have been done to increase the antimicrobial activity of curcumin, including synthesis of different chemical derivatives to increase its water solubility as well ass cell up take of curcumin. This review aims to summarize previous antimicrobial studies of curcumin towards its application in the future studies as a natural antimicrobial agent.
Fulltext Review of Dengue hemorrhagic fever fatal cases seen among adults: a retrospective study

Sam SS, Omar SF, Teoh BT, Abd-Jamil J, AbuBakar S

PLoS Negl Trop Dis, 2013;7(5):e2194.
PMID: 23658849 DOI: 10.1371/journal.pntd.0002194

Dengue is a mosquito-borne viral disease endemic in many countries in the tropics and sub-tropics. The disease affects mainly children, but in recent years it is becoming more of an adult disease. Malaysia experienced a large dengue outbreak in 2006 to 2007, involving mostly adults, with a high number of deaths.
Fulltext Flavone enhances dengue virus type-2 (NGC strain) infectivity and replication in vero cells

Zandi K, Lani R, Wong PF, Teoh BT, Sam SS, Johari J, et al.

Molecules, 2012;17(3):2437-45.
PMID: 22374315 DOI: 10.3390/molecules17032437

This study investigates the effects of 2-phenyl-1-benzopyran-4-one (flavone) on DENV-2 infectivity in Vero cells. Virus adsorption and attachment and intracellular virus replication were investigated using a foci forming unit assay (FFUA) and quantitative RT-PCR, respectively. Addition of flavone (100 μg/mL) significantly increased the number of DENV-2 foci by 35.66% ± 1.52 and 49.66% ± 2.51 when added during and after virus adsorption to the Vero cells, respectively. The average foci size after 4 days of infection increased by 33% ± 2.11 and 89% ± 2.13. The DENV-2 specific RNA copy number in the flavone-treated infected cells increased by 6.41- and 23.1-fold when compared to the mock-treated infected cells. Flavone (100 μg/mL) did not promote or inhibit Vero cell proliferation. The CC₅₀ value of flavone against Vero cells was 446 µg/mL. These results suggest that flavone might enhance dengue virus replication by acting antagonistically towards flavonoids known to inhibit dengue virus replication.
Fulltext Novel antiviral activity of baicalein against dengue virus

Zandi K, Teoh BT, Sam SS, Wong PF, Mustafa MR, Abubakar S

BMC Complement Altern Med, 2012;12:214.
PMID: 23140177 DOI: 10.1186/1472-6882-12-214

Dengue is a serious arboviral disease currently with no effective antiviral therapy or approved vaccine available. Therefore, finding the effective compound against dengue virus (DENV) replication is very important. Among the natural compounds, bioflavonoids derived mainly from plants are of interest because of their biological and medicinal benefits.
Isolation of Aggregatibacter aphrophilus from a patient with acute appendicitis

Aye AM, Law CW, Sabet NS, Karunakaran R, Hanifah YA, Jafar FL, et al.

Eur Rev Med Pharmacol Sci, 2011 Jul;15(7):845-7.
PMID: 21780555

Acute appendicitis is a common surgical emergency. The etiology and pathophysiology of appendicitis have been well investigated. Aggregatibacter aphrophilus is a fastidious gram-negative coccobacilli. Detection of this organism in clinical samples and its differentiation from Haemophilus aphrophilus or from Aggregatibacter actinomycetemcomitans in routine microbiology settings could be difficult.
Fulltext Tsukamurella tyrosinosolvens intravascular catheter-related bacteremia in a haematology patient: a case report

Karunakaran R, Halim HA, Ng KP, Hanifah YA, Chin E, Jaafar FL, et al.

Eur Rev Med Pharmacol Sci, 2011 Nov;15(11):1343-6.
PMID: 22195371

Tsukamurella spp. are a rare but important cause of intravascular catheter-related bacteremia in immunocompromised patients. The organism is an aerobic, Gram-positive, weakly acid-fast bacillus that is difficult to differentiate using standard laboratory methods from other aerobic actinomycetales such as Nocardia spp., Rhododoccus spp., Gordonia spp., and the rapid growing Mycobacterium spp. We report a case of Tsukamurella tyrosinosolvens catheter-related bacteremia in a 51-year-old haematology patient who responded to treatment with imipenem and subsequent line removal. 16srRNA sequencing allowed for the prompt identification of this organism.
Fulltext Antiviral activity of four types of bioflavonoid against dengue virus type-2

Zandi K, Teoh BT, Sam SS, Wong PF, Mustafa MR, Abubakar S

Virol J, 2011;8:560.
PMID: 22201648 DOI: 10.1186/1743-422X-8-560

Dengue is a major mosquito-borne disease currently with no effective antiviral or vaccine available. Effort to find antivirals for it has focused on bioflavonoids, a plant-derived polyphenolic compounds with many potential health benefits. In the present study, antiviral activity of four types of bioflavonoid against dengue virus type -2 (DENV-2) in Vero cell was evaluated. Anti-dengue activity of these compounds was determined at different stages of DENV-2 infection and replication cycle. DENV replication was measured by Foci Forming Unit Reduction Assay (FFURA) and quantitative RT-PCR. Selectivity Index value (SI) was determined as the ratio of cytotoxic concentration 50 (CC50) to inhibitory concentration 50 (IC50) for each compound.
Eurycomanone suppresses expression of lung cancer cell tumor markers, prohibitin, annexin 1 and endoplasmic reticulum protein 28

Wong PF, Cheong WF, Shu MH, Teh CH, Chan KL, AbuBakar S

Phytomedicine, 2012 Jan 15;19(2):138-44.
PMID: 21903368 DOI: 10.1016/j.phymed.2011.07.001

Bioactive compounds from the medicinal plant, Eurycoma longifolia Jack have been shown to promote anti-proliferative effects on various cancer cell lines. Here we examined the effects of purified eurycomanone, a quassinoid found in Eurycoma longifolia Jack extract, on the expression of selected genes of the A549 lung cancer cells. Eurycomanone inhibited A549 lung cancer cell proliferation in a dose-dependent manner at concentrations ranging from 5 to 20 μg/ml. The concentration that inhibited 50% of cell growth (GI(50)) was 5.1 μg/ml. The anti-proliferative effects were not fully reversible following the removal of eurycomanone, in which 30% of cell inhibition still remained (p<0.0001, T-test). At 8 μg/ml (GI(70)), eurycomanone suppressed anchorage-independent growth of A549 cells by >25% (p<0.05, T-test, n=8) as determined using soft agar colony formation assay. Cisplatin, a chemotherapy drug used for the treatment of non small cell lung cancer on the other hand, inhibited A549 cells proliferation at concentrations ranging from 0.2 μg/ml to 15 μg/ml with a GI(50) of 0.58 μg/ml. The treatment with eurycomanone reduced the abundance expression of the lung cancer markers, heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1, p53 tumor suppressor protein and other cancer-associated genes including prohibitin (PHB), annexin 1 (ANX1) and endoplasmic reticulum protein 28 (ERp28) but not the house keeping genes. The mRNA expressions of all genes with the exception of PHB were significantly downregulated, 72 h after treatment (p<0.05, T-test, n=9). These findings suggest that eurycomanone at viable therapeutic concentrations of 5-20 μg/ml exhibited significant anti-proliferative and anti-clonogenic cell growth effects on A549 lung cancer cells. The treatment also resulted in suppression of the lung cancer cell tumor markers and several known cancer cell growth-associated genes.
Fulltext Molecular identification of adenovirus causing respiratory tract infection in pediatric patients at the University of Malaya Medical Center

Abd-Jamil J, Teoh BT, Hassan EH, Roslan N, Abubakar S

BMC Pediatr, 2010;10:46.
PMID: 20594359 DOI: 10.1186/1471-2431-10-46

There are at least 51 adenovirus serotypes (AdV) known to cause human infections. The prevalence of the different human AdV (HAdV) serotypes varies among different regions. Presently, there are no reports of the prevalent HAdV types found in Malaysia. The present study was undertaken to identify the HAdV types associated primarily with respiratory tract infections (RTI) of young children in Malaysia.
Chikungunya infection in Malaysia: comparison with dengue infection in adults and predictors of persistent arthralgia

Mohd Zim MA, Sam IC, Omar SF, Chan YF, AbuBakar S, Kamarulzaman A

J Clin Virol, 2013 Feb;56(2):141-5.
PMID: 23201456 DOI: 10.1016/j.jcv.2012.10.019

Chikungunya virus (CHIKV) and dengue virus (DENV) co-circulate in areas endemic with the Aedes mosquito vectors. Both viruses cause similar illnesses which may be difficult to distinguish clinically. CHIKV is also associated with persistent arthralgia.
Fulltext An Inactivated Antibiotic-Exposed Whole-Cell Vaccine Enhances Bactericidal Activities Against Multidrug-Resistant Acinetobacter baumannii

Shu MH, MatRahim N, NorAmdan N, Pang SP, Hashim SH, Phoon WH, et al.

Sci Rep, 2016;6:22332.
PMID: 26923424 DOI: 10.1038/srep22332

Vaccination may be an alternative treatment for infection with multidrug-resistance (MDR) Acinetobacter baumannii. The study reported here evaluated the bactericidal antibody responses following immunization of mice using an inactivated whole-cell vaccine derived from antibiotic-exposed MDR A. baumannii (I-M28-47-114). Mice inoculated with I-M28-47 (non-antibiotic-exposed control) and I-M28-47-114 showed a high IgG antibody response by day 5 post-inoculation. Sera from mice inoculated with I-M28-47-114 collected on day 30 resulted in 80.7 ± 12.0% complement-mediated bacteriolysis in vitro of the test MDR A. baumannii treated with imipenem, which was a higher level of bacteriolysis over sera from mice inoculated with I-M28-47. Macrophage-like U937 cells eliminated 49.3 ± 11.6% of the test MDR A. baumannii treated with imipenem when opsonized with sera from mice inoculated with I-M28-47-114, which was a higher level of elimination than observed for test MDR A. baumannii opsonized with sera from mice inoculated with I-M28-47. These results suggest that vaccination with I-M28-47-114 stimulated antibody responses capable of mounting high bactericidal killing of MDR A. baumannii. Therefore, the inactivated antibiotic-exposed whole-cell vaccine (I-M28-47-114) has potential for development as a candidate vaccine for broad clearance and protection against MDR A. baumannii infections.
Oral vaccine of Lactococcus lactis harbouring pandemic H1N1 2009 haemagglutinin1 and nisP anchor fusion protein elevates anti-HA1 sIgA levels in mice

Joan SS, Pui-Fong J, Song AA, Chang LY, Yusoff K, AbuBakar S, et al.

Biotechnol Lett, 2016 May;38(5):793-9.
PMID: 26758876 DOI: 10.1007/s10529-016-2034-2

An oral lactococcal-based vaccine which haboured the haemagglutinin1 (HA1) antigen fused to nisP anchor protein for the purpose of surface displaying the HA1 antigen was developed against H1N1 virus.

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