Investigation of non-hydroxamate scaffolds against HDAC6 inhibition: A pharmacophore modeling, molecular docking, and molecular dynamics simulation approach

Zeb, A.,Park, C.,Son, M.,Rampogu, S.,Alam, S. I.,Park, S. J.,Lee, K. W. Imperial College Press 2018 JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOG Vol.16 No.3

<P>Proteins deacetylation by Histone deacetylase 6 (HDAC6) has been shown in various human chronic diseases like neurodegenerative diseases and cancer, and hence is an important therapeutic target. Since, the existing inhibitors have hydroxamate group, and are not HDAC6-selective, therefore, this study has designed to investigate non-hydroxamate HDAC6 inhibitors. Ligand-based pharmacophore was generated from 26 training set compounds of HDAC6 inhibitors. The statistical parameters of pharmacophore (Hypo1) included lowest total cost of 115.63, highest cost difference of 135.00, lowest RMSD of 0.70 and the highest correlation of 0.98. The pharmacophore was validated by Fischer's Randomization and Test Set validation, and used as screening tool for chemical databases. The screened compounds were filtered by fit value (> 10.00), estimated Inhibitory Concentration (IC50) (<0.459), Lipinski's Rule of Five and Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) Descriptors to identify drug-like compounds. Furthermore, the drug-like compounds were docked into the active site of HDAC6. The best docked compounds were selected having gold fitness score > 66.46 and chemscore < -28.31, and hydrogen bond interaction with catalytic active residues. Finally, three inhibitors having sulfamoyl group were selected by Molecular Dynamic (MD) simulation, which showed stable root mean square deviation (RMSD) (1.6-1.9 angstrom), lowest potential energy (< -6.3 x 10(5) kJ/mol), and hydrogen bonding with catalytic active residues of HDAC6.</P>

Heat-inducible C3HC4 type RING zinc finger protein gene from Capsicum annuum enhances growth of transgenic tobacco

Zeba, Naheed,Isbat, Mohammad,Kwon, Nak-Jung,Lee, Mi Ok,Kim, Seong Ryong,Hong, Choo Bong Springer-Verlag 2009 Planta Vol.229 No.4

Molecular Characterization of the Capsicum annuum RING Zinc Finger Protein 1 (CaRZFP1) Gene Induced by Abiotic Stresses

( N. Zeba ),( M. Ashrafuzzaman ),( Choo Bong Hong ) 한국식물학회 2006 Journal of Plant Biology Vol.49 No.6

Novelty seeking as driving factor for fashion apparel innovators: A qualitative investigation

Farrah Zeba,Chuanlan Liu 한국마케팅과학회 2019 Journal of Global Fashion Marketing Vol.10 No.3

The objective of the paper is to comprehend the parsimoniously explored phenomenon of novelty seeking in the fashion apparel consumption through the lived experiences of fashion apparel innovators in the context of adult career women of emergingmarket. Interpretive phenomenological analysis is used to explicate consumers’ everyday lived experiences of fashion apparel consumption. Based on the interpretation of the findings of the qualitative data, we endeavored to conceptualize novelty seeking as a multidimensional second-order construct comprising of four main dimensions of themes with three subdimensions viz. sensory appeal (Fairy tale experience, Stress anecdote, Self-confidence booster), finding the niche (Idiosyncratic attire, Self-expressing through clothing, Red carpet dress), clothes-aholic (Hoarding of the clothes, Ever lacking wardrobe, Impulse clothes purchase), and socially bound (Varied persona, First impression, Balancing effect). The conceptualization encapsulates how novelty seeking is driving innovative behavior in fashion apparel context. Novelty seeking is an interdisciplinary concept. Apart from psychology domain, several studies have been conducted across various industries in the consumer behavior domain, especially in tourism, hi-tech products, and telecom. However, in-depth research on novelty seeking in fashion industry is limited. Value of this article lies in developing a theoretical base of novelty seeking in fashion industry through lived experiences of consumers in emerging market.

A Security Framework for Cluster-Based Wireless Sensor Networks against the Selfishness Problem

Ishaq, Zeba,Park, Seongjin,Yoo, Younghwan WILEY INTERSCIENCE 2018 WIRELESS COMMUNICATIONS AND MOBILE COMPUTING Vol.2018 No.-

<P>Over the last few decades, Cluster-Based Wireless Sensor Networks (CBWSNs) have played a crucial role in handling various challenges (load balancing, routing, network lifetime, etc.) of large scale Wireless Sensor Networks (WSNs). However, the security becomes a big problem for CBWSNs, especially when nodes in the cluster selfishly behave, e.g., not forwarding other nodes’ data, to save their limited resources. This may make the cluster obsolete, even destroying the network. Thus, a way to guarantee the secure and consistent clusters is needed for proper working of CBWSNs. We showed that the selfishness attack, i.e., passive attack or insider attack, in CBWSNs can cause severe performance disaster, when particularly a cluster head node becomes selfish. In order to prevent this situation, this paper proposes a security framework that involves a novel clustering technique as well as a reputation system at nodes for controlling selfishness, making them cooperative and honest. The novelty of the clustering comes from the existence of inspector node (IN) to monitor the cluster head (CH) and its special working style. The experimental results showed that the proposed security framework can control the selfishness and improve the security of the clusters.</P>

M Protein from Dengue virus oligomerizes to pentameric channel protein: in silico analysis study

Ayesha Zeba,Kanagaraj Sekar,Anjali Ganjiwale Korea Genome Organization 2023 Genomics & informatics Vol.21 No.3

The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.

A BAX inhibitor-1 gene in <i>Capsicum annuum</i> is induced under various abiotic stresses and endows multi-tolerance in transgenic tobacco

Isbat, Mohammad,Zeba, Naheed,Kim, Seong Ryong,Hong, Choo Bong Elsevier 2009 Journal of plant physiology Vol.166 No.15

<P><B>Summary</B></P><P>Programmed cell death (PCD) is a highly conserved cellular suicide process important in developmental processes and elimination of damaged cells upon environmental stresses. Among the important regulators of PCD, much interest has been centered on BCL2-associated x protein (BAX) as the pro-PCD factor. On the other hand, BAX inhibitor-1 (BI-1) has been implicated as an anti-PCD factor that balances out the activity of BAX in the developmental processes and responses to environment. A cDNA clone coding a BI-1 gene was isolated from a cDNA library of heat-stressed hot pepper (<I>Capsicum annuum</I>) and named as <I>CaBI-1</I>. This gene contains an open reading frame (ORF) of 248 amino acids encoding a BI-1 protein. Genomic DNA-blot analysis for <I>CaBI-1</I> suggested one or two loci in the <I>C. annuum</I> genome. Transcription of <I>CaBI-1</I> was induced in response to high or low temperatures, drought, high salinity, flooding and heavy metal stresses, and ABA. We introduced the ORF of <I>CaBI-1</I> under the control of the CaMV 35S promoter (P<SUB>35S</SUB>) into tobacco (<I>Nicotiana tabacum</I> cv. Wisconsin 38) genome by <I>Agrobacterium</I>-mediated transformation. The P<SUB>35S</SUB>:<I>CaBI-1</I> transgenic plants displayed markedly improved tolerance to high temperature, water deficit, and high salinity in comparison to the control plants. The results indicate that <I>CaBI-1</I> is a BI-1 gene of which expression induced under various abiotic stresses and endows tolerance to several types of environmental stresses.</P>

Exploring the neural mechanisms of aversion to bitter gourd phytochemicals in insects using Drosophila

Chakraborty Rusha,Thakur Tamanna Singh,Chauhan Riti,Manzar Zeba,Das Gaurav,Mitra Aniruddha 한국응용곤충학회 2021 Journal of Asia-Pacific Entomology Vol.24 No.3

Bitter gourd (Momordica charantia L.) has compounds that repel insect pests. Unlike conventional pesticides, these compounds are eco-friendly and beneficial for human health. However the mechanisms by which these compounds repel insects and affect their physiology remains poorly known. Here we used Drosophila melanogaster (Meigen) to address these issues. We tested a wild strain, and a laboratory bred Canton S strain. Bitter gourd extract reduced the viability of developing flies, but did not affect survival in adults. Flies avoided bitter gourd extract in a food choice assay, and consumed a significantly low amount of food mixed with bitter gourd – indicating that it acts as an antifeedant. Transgenic flies with impaired aversive taste sensitive neurons showed a reduced aversion towards bitter gourd extract showing that these compounds act through the bitter sensitive gustatory neurons. Finally, flies also retained the memory of consuming bitter gourd extract for at least 24 hours, suggesting an additional cognitive mechanism for long term aversion. Our study provides the first evidence of bitter gourd compounds acting as antifeedants and also as potent reinforcers of aversive memory in drosophilids. We suggest that flies can be used to understand the physiological and neural mechanisms underlying the mode of action of other such phyto-extracts with the goal of developing potent but less harmful pest control formulations.

Symposium: “Oncology Leadership in Asia”

노동영,노재경,김열홍,Kazuhiro Yoshida,Hideo Baba,Marie Cherry Lynn Samson-Fernando,Sanjeev Misra,Zeba Aziz,Rainy Umbas,Yogendra P. Singh,Tony Shu Kam Mok,양한광,Hideyuki Akaza 대한암학회 2017 Cancer Research and Treatment Vol.49 No.2

The symposium on “Oncology Leadership in Asia” was held as part of the official program of the 42nd Annual Meeting of the Korean Cancer Association with International Cancer Conference. Given the increasing incidence of cancer in all countries and regions of Asia, regardless of developmental stage, and also in light of the recognized need for Asian countries to enhance collaboration in cancer prevention, research, treatment and follow-up, the symposium was held with the aim of bringing together oncology specialists from eight countries and regions in Asia to present the status in their own national context and discuss the key challenges and requirements in order to establish a greater Asian presence in the area of cancer control and research. The task of bringing together diverse countries and regions is made all the more urgent in that while Asia now accounts for more than half of all new cancer cases globally, clinical guidelines are based predominantly on practices adopted in Western countries, which may not be optimized for unique ethnic, pharmacogenomic and cultural characteristics in Asia. Recognizing the need for Asia to better gather information and data for the compilation of Asia-specific clinical guidelines, the participants discussed the current status in Asia in the national and regional contexts and identified future steps towards integrated and collaborative initiatives in Asia. A key outcome of the symposium was a proposal to combine and integrate the activities of existing pan-Asian societies, including the Asian Pacific Federation of Organizations for Cancer Research and Control (APFOCC) and Asian Clinical Oncology Society (ACOS). Further proposals included the expansion of pan-Asian society membership to include individuals and the essential need to encourage the participation of young researchers in order to ensure self-sustainability of cancer control efforts in the future.