Research Title: Synthesis, anti-inflammatory evaluation, and docking studies of some new thiazole derivatives

Author: Balakumar Chandrasekarn, Published Year: 2014

Medicinal Chemistry Research, 23

Faculty: Pharmacy

Abstract: A series of new 2-substituted-N-(1,3-thiazole-2-yl)acetamide 3–7 and N-(benzo[d]thiazol-2-yl)-2-(substituted)acetamide 10–13 derivatives have been synthesized and evaluated in vivo (rat paw edema) for their anti-inflammatory activities and in silico(docking studies) to recognize the hypothetical binding motif of the title compounds with the cyclooxygenase isoenzyme (COX-2) employing GLIDE software (Schrodinger Inc.). The compounds, 10–13 were found to have good anti-inflammatory activities [around 84–93 % of the standard: indomethacin]. The binding mode of the title compounds has been proposed based on the docking studies. Further, the predicted ADME properties of all the tested compounds were found to be in the ranges as predicted by QikProp for 95 % of known oral drugs and also satisfy the Lipinski’s rule of five.

Keywords: anti-inflammatory evaluation, docking studies

Research Title: Development and Validation of a Specific RP-HPLC Method for the Estimation of γ-Aminobutyric Acid in Rat Brain Tissue Samples Using Benzoyl Chloride Derivatization and PDA Detection

Author: Balakumar Chandrasekarn, Published Year: 2015

Acta Chromatographica, 27

Faculty: Pharmacy

Abstract: A new, rapid, and specific reversed phase high-performance liquid chromatographic (RP-HPLC) method involving precolumn derivatization with benzoyl chloride was developed and validated for the estimation of γ-aminobutyric acid (GABA) in rat brain tissue preparations. The derivatization product of GABA was identified by melting point, infrared, and proton nuclear magnetic resonance (1H NMR) spectroscopy to be n-benzoyl GABA. Various parameters which influenced derivatization and elusion were optimized. The chromatographic system consisted of C-18 column with ultraviolet (UV)—photodiode array detection ranging from 210 to 400 nm. Elution with an isocratic mobile phase consisting of 0.025 M disodium hydrogen phosphate buffer—methanol (65:35, v/v; pH 6) at a flow rate of 1 mL min−1 yielded sharp and specific peak of n-benzoyl GABA within 7 min. The method was validated with respect to the linearity, accuracy, precision, sensitivity, selectivity, and stability, wherein the benzoyl derivative of GABA showed stability for 2 months. The lower limit of detection was 0.5 nmol L−1. This novel derivatization procedure for the estimation of GABA with benzoyl chloride was also applied for rat brain tissue preparations that gave highly specific peak and good component recovery. The results show that the method for the determination of GABA by benzoylation using RP-HPLC has good linearity, accuracy, precision, sensitivity, and specificity and is simple and economical to perform.

Keywords: GABA, benzoyl chloride, RP-HPLC, PDA, brain tissues, validation

Research Title: Dehydrozingerone Inspired Styryl Hydrazine Thiazole Hybrids as Promising Class of Antimycobacterial Agents

Author: Balakumar Chandrasekarn, Published Year: 2016

ACS Medicinal Chemistry Letters, 7

Faculty: Pharmacy

Abstract: Series of styryl hydrazine thiazole hybrids inspired from dehydrozingerone (DZG) scaffold were designed and synthesized by molecular hybridization approach. In vitro antimycobacterial activity of synthesized compounds was evaluated against Mycobacterium tuberculosis H37Rv strain. Among the series, compound 6o exhibited significant activity (MIC = 1.5 μM; IC50 = 0.48 μM) along with bactericidal (MBC = 12 μM) and intracellular antimycobacterial activities (IC50 = <0.098 μM). Furthermore, 6o displayed prominent antimycobacterial activity under hypoxic (MIC = 46 μM) and normal oxygen (MIC = 0.28 μM) conditions along with antimycobacterial efficiency against isoniazid (MIC = 3.2 μM for INH-R1; 1.5 μM for INH-R2) and rifampicin (MIC = 2.2 μM for RIF-R1; 6.3 μM for RIF-R2) resistant strains of Mtb. Presence of electron donating groups on the phenyl ring of thiazole moiety had positive correlation for biological activity, suggesting the importance of molecular hybridization approach for the development of newer DZG clubbed hydrazine thiazole hybrids as potential antimycobacterial agents.

Keywords: Antimycobacterial activity bactericidal dehydrozingerone NIAID thiazole

Research Title: Whole exome sequencing highlights variants in association with Keratoconus in Jordanian families

Author: Tawfiq Froukh, Published Year: 2019

BMC Medical Genetics,

Faculty: Science

Abstract: Background Keratoconus (KC) is usually bilateral, noninflammatory progressive corneal ectasia in which the cornea becomes progressively thin and conical, resulting in myopia, irregular astigmatism, and corneal scarring. Methods eight families characterized by multiple keratoconic individuals and consanguineous marriages were examined genetically. Whole exome sequencing was done as trio or quadro per family. The filtration procedure based on minor allele frequency (MAF) less than 0.01 for homozygous variants and MAF=0 for heterozygous variants identified twenty-two missense variants. Candidate variants were prioritized based on the protein function and six variants were highlighted in five families. Results Two variants were highlighted in one family within the genes MYOF and STX2, and one variant is highlighted in each of the other four families within the genes: MLLT4, COL6A5, ZNF676 and ZNF765. Conclusion This study is one of the very rare that highlights genetic variants in association with KC.

Keywords: NGS, Genome, Ocular, Epithelial, Dry-eye

Research Title: Genetic study in a family with novel mutation in the gene sepiapterin reductase (SPR)

Author: Tawfiq Froukh, Published Year: 2019

European Human Genetics Conference 2019, Gothenburg, Sweden

Faculty: Science

Abstract: Dopa-responsive dystonia due to sepiapterin reductase deficiency (OMIM#612716) is caused by recessive mutations in the gene encoding sepiapterin reductase (SPR), which plays an important role in the biosynthesis of tetrahydrobiopterin (BH4). One Jordanian patient to first cousin parents is reported in this study. The parents of the proband have recognized the symptoms of their daughter at six months old with motor developmental delay. The symptoms were progressed after-then to include speech delay, seizure, ataxia, oculomotor apraxia, dysarthia and choreoathetosis. Despite of these symptoms, the clinicians in Jordan were unable to diagnose the case. In August 2018, the proband (8 years old) was presented to the department of biotechnology and genetic engineering at Philadelphia University in Jordan for the purposes of performing whole exome sequencing (WES). Analysis of WES data has revealed novel homozygous frameshift variant in the gene SPR (NM_003124.4:c.40delG,p.Ala15Profs*100). The variant is heterozygous in the parents and in the healthy male siblings. Therefore, the studied case was diagnosed with sepiapterin reductase deficiency. Because this disease is likely to be treated recommendations were given to the family immediately to start treatments trials. The case in this study illustrates the difficulties of diagnosing sepiapterin reductase deficiency based on clinical symptoms only and thus renders the possibilities of early management. Also, this study reinforces the importance of running WES to undiagnosed neurodevelopmental cases.

Keywords: Intellectual disability, Serotonin, Dopamine, Autosomal recessive, Genome.

Research Title: Autosomal recessive non-syndromic Keratoconus: homozygous frameshift variant in the candidate novel gene GALNT14

Author: Tawfiq Froukh, Published Year: 2018

68th Annual Meeting of the American Society of Human Genetics, San Diego, California, USA

Faculty: Science

Abstract: Background: Keratoconus (KC) is usually bilateral, noninflammatory progressive corneal ectasia in which the cornea becomes progressively thin and conical. Despite the strong evidence of genetic contribution in KC, the etiology of KC is not understood in most cases. Methods: In this study, we used whole-exome sequencing to identify the genetic cause of KC in two sibs in a consanguineous family. The Homozygous frameshift variant NM_001253826.1:c.60delC;p.Leu21Cysfs*6 was identified in the gene Nacetylgalactosaminyltransferase 14 (GALNT14). The variant does not exist in all public databases neither in our internal exome database. Moreover, no database harbours homozygous loss of function variants in the candidate gene. GALNT14 catalyses the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-Dgalactosamine residue to a serine or threonine residue on target proteins especially Mucins. Conclusion: As alterations of mucin’s glycosylation are linked to a number of eye diseases, we demonstrate in this study an association between the truncated protein GALNT14 and KC.

Keywords: NGS, genome, ocular, epithelial, dry-eye, keratoconus.

Research Title: Genetic causes of intellectual disability in 102 consanguineous families from Jordan

Author: Tawfiq Froukh, Published Year: 2017

67th Annual Meeting of the American Society of Human Genetics, Orlando, USA

Faculty: Science

Abstract: We recruited 103 families from Jordan with neurodevelopmental disorders (NDD) and patterns of inheritance mostly suggestive of autosomal recessive inheritance. In each family, we investigated at least one affected individual using exome sequencing and an in-house diagnostic variant interpretation pipeline including a search for copy number variation. This approach led us to identify the likely molecular defect in established disease genes in 37 families. We could identify 25 pathogenic nonsense and 11 missense variants as well as 3 pathogenic CNVs and one repeat expansion. Notably, 11 of the disease-causal variants occurred de novo. In addition, we prioritized a homozygous frameshift variant in PUS3 in two sisters with intellectual disability. To our knowledge, PUS3 has been postulated only recently as a candidate disease gene for intellectual disability in a single family with three affected siblings. Our findings provide additional evidence to establish loss of PUS3 function as a cause of intellectual disability.

Keywords: exome sequencing, neurodevelopmental disorder, PUS3, Jordan

Research Title: Chromosomal translocation, cnv deletion and missense mutations associated with intellectual disability in consanguineous families from Jordan

Author: Tawfiq Froukh, Published Year: 2016

66th Annual Meeting of the American Society of Human Genetics, Vancouver, Canada

Faculty: Science

Abstract: Intellectual disability (ID), occurs in approximately 1 to 3% of the population and tends to be higher in low-income countries and in inbred communities. Despite the high rates of consanguineous marriages and the likely enrichment for recessive forms of ID, the genetic bases of ID in Jordan are largely unstudied. In this study, whole exome sequencing (WES) and homozygosity mapping were used to identify the genetic causes of ID in ten families from Jordan. The studied families are characterized by consanguineous marriage and having one or more progeny with ID. Likely disease-causing missense mutations were identified in eight families; four families are due to mutations in genes previously implicated with ID and the other four families are due to mutations in genes that are not previously implicated with ID. The novel genes include: BSN (Protein Basson), PTCHD2 (Protein dispatched homolog 3), DHRS3 (Short-chain dehydrogenase/reductase 3), and LGI3 (Leucine-rich repeat LGI family member 3). In addition, copy number variant (CNV) deletion and/or duplication were identified in 2 families; one family with 3.5 mega base (Mb) deletion on chromosome17 previously implicated with Smith Magenis Syndrome, and the other family with a novel combination of deletion and duplication in chromosomes 5 and 11. In this pilot study, four genes and one CNV deletion/duplication are identified for the first time in association with ID. The finding of this study further demonstrates the power of WES and homozygosity mapping for clinical diagnostics of ID in consanguineous families in small populations.

Keywords: epilepsy; heterozygous; IQ; mental retardation; next generation sequencing

Research Title: A dynamic rule-induction method for classification in data mining

Author: Issa Qabaja, Published Year: 2015

Journal of Management Analytics, Volume 2

Faculty: Information Technology

Abstract: Rule induction (RI) produces classifiers containing simple yet effective ‘If–Then' rules for decision makers. RI algorithms normally based on PRISM suffer from a few drawbacks mainly related to rule pruning and rule-sharing items (attribute values) in the training data instances. In response to the above two issues, a new dynamic rule induction (DRI) method is proposed. Whenever a rule is produced and its related training data instances are discarded, DRI updates the frequency of attribute values that are used to make the next in-line rule to reflect the data deletion. Therefore, the attribute value frequencies are dynamically adjusted each time a rule is generated rather statically as in PRISM. This enables DRI to generate near perfect rules and realistic classifiers. Experimental results using different University of California Irvine data sets show competitive performance in regards to error rate and classifier size of DRI when compared to other RI algorithms.

Keywords: data mining, classification rules, rule induction, expected accuracy.

Research Title: Constrained dynamic rule induction learning

Author: Issa Qabaja, Published Year: 2016

Expert Systems with Applications, Volume 63

Faculty: Information Technology

Abstract: One of the known classification approaches in data mining is rule induction (RI). RI algorithms such as PRISM usually produce If-Then classifiers, which have a comparable predictive performance to other traditional classification approaches such as decision trees and associative classification. Hence, these classifiers are favourable for carrying out decisions by users and therefore they can be utilised as decision making tools. Nevertheless, RI methods, including PRISM and its successors, suffer from a number of drawbacks primarily the large number of rules derived. This can be a burden especially when the input data is largely dimensional. Therefore, pruning unnecessary rules becomes essential for the success of this type of classifiers. This article proposes a new RI algorithm that reduces the search space for candidate rules by early pruning any irrelevant items during the process of building the classifier. Whenever a rule is generated, our algorithm updates the candidate items frequency to reflect the discarded data examples associated with the rules derived. This makes items frequency dynamic rather static and ensures that irrelevant rules are deleted in preliminary stages when they don't hold enough data representation. The major benefit will be a concise set of decision making rules that are easy to understand and controlled by the decision maker. The proposed algorithm has been implemented in WEKA (Waikato Environment for Knowledge Analysis) environment and hence it can now be utilised by different types of users such as managers, researchers, students and others. Experimental results using real data from the security domain as well as sixteen classification datasets from University of California Irvine (UCI) repository reveal that the proposed algorithm is competitive in regards to classification accuracy when compared to known RI algorithms. Moreover, the classifiers produced by our algorithm are smaller in size which increase their possible use in practical applications.

Keywords: ClassificationData mfiningPredictionPRISMRule inductionOnline security.