Mohd Basyaruddin Abdul Rahman

Putra University, Malaysia, Putrajaya, Putrajaya, Malaysia

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Publications (92)142.58 Total impact

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    Erma Fatiha Muhammad · Rohana Adnan · Muhammad Alif Mohammad Latif · Mohd Basyaruddin Abdul Rahman ·

    Journal of inclusion phenomena and macrocyclic chemistry 10/2015; DOI:10.1007/s10847-015-0576-x · 1.43 Impact Factor
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  • Samira Yousefi · Saadi Bayat · Mohd Basyaruddin Abdul Rahman · Intan Safinar Ismail · Elnaz Saki · Sze Wei Leong · Emilia Abdulmalek ·
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    ABSTRACT: Some new oleic acid, linoleic acid, lauric acid derivatives of 5-aminosalicylic acid were produced in order to enhance bioactivity properties of 5-aminosalicylic acid. All new compounds' structures were confirmed by spectroscopic methods. Moreover, in vitro antibacterial, anticancer, and anti-inflammatory activities of new synthesized compounds were investigated. Antibacterial activity was studied against pathogenic Gram-negative bacteria, Escherichia coli and Gram-positive bacteria, Staphylococcus aureus via disc diffusion method. Additionally, all derivatives' anti-inflammatory activity were evaluated through NO suppression assay using interferon gamma (IFN-γ)/lipopolysaccharide (LPS)-stimulated RAW264.7 macrophages. Furthermore, in vitro cytotoxicity assay was probed using MTT test against 3T3 and HT-29 cell lines. In another effort, docking studies were performed to predict the possible interactions and binding energy of new compounds against cyclooxygenase (COX-1/COX-2) and lipoxygenase (5-LOX) proteins. In conclusion, all new compounds exhibited moderate to better bioactivity improvements in comparison with parent drug. Also study of interactions between the new derivatives with active sites of proteins presented greater binding affinities than 5-aminosalicylic acid. Graphical abstract: [Figure not available: see fulltext.]
    Monatshefte fuer Chemie/Chemical Monthly 08/2015; 146(12). DOI:10.1007/s00706-015-1538-0 · 1.22 Impact Factor
  • Saadi Bayat · Abu Bakar Salleh · Emilia Abd Malek · Samira Yousefi · Mohd Basyaruddin Abdul Rahman ·

    Catalysis Letters 07/2015; DOI:10.1007/s10562-015-1583-7 · 2.31 Impact Factor
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    Azira Muhamad · Kok Lian Ho · Mohd Basyaruddin Abdul Rahman · Bimo A Tejo · Dusan Uhrin · Wen Siang Tan ·
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    ABSTRACT: Hepatitis B virus (HBV) infection remains a health problem globally despite the availability of effective vaccines. In the assembly of the infectious virion, both the preS and S regions of the HBV large surface antigen (L-HBsAg) interact synergistically with the viral core antigen (HBcAg). Peptides preS and S based on the L-HBsAg were demonstrated as potential inhibitors to block the viral assembly. Therefore, the objectives of this study were to determine the solution structures of these peptides and study their interactions with HBcAg. The solution structures of these peptides were solved using (1)H, (13)C, and (15)N NMR spectroscopy. Peptide preS has several structured regions of β-turns at Ser7-Pro8-Pro9, Arg11-Thr12-Thr13 and Ser22-Thr23-Thr24 sequences whereas peptide S has only one structured region observed at Ser3-Asn4-His5. Both peptides contain bend-like structures surrounding the turn structures. Docking studies revealed that both peptides interacted with the immunodominant region of HBcAg located at the tip of the viral capsid spikes. Saturation Transfer Difference (STD) NMR experiments identified several aromatic residues in peptides preS and S that interact with HBcAg. This study provides insights into the contact regions of L-HBsAg and HBcAg at atomic resolution which can be used to design antiviral agents that inhibit HBV morphogenesis.
    Organic & Biomolecular Chemistry 06/2015; 13:7780-7789. DOI:10.1039/C5OB00449G · 3.56 Impact Factor
  • Swi See Ang · Abu Bakar Salleh · Adam Leow Thean Chor · Yahaya M. Normi · Bimo Ario Tejo · Mohd Basyaruddin Abdul Rahman ·
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    ABSTRACT: Cytochrome P450s are a superfamily of heme monooxygenases which catalyze a wide range of biochemical reactions. The reactions involve the introduction of an oxygen atom into an inactivated carbon of a compound which is essential to produce an intermediate of a hydroxylated product. The diversity of chemical reactions catalyzed by cytochrome P450s has led to their increased demand in numerous industrial and biotechnology applications. A recent study showed that a gene sequence encoding a CYP was found in the genome of Bacillus lehensis G1, and this gene shared structural similarity with the bacterial vitamin D hydroxylase (Vdh) from Pseudonocardia autotrophica. The objectives of present study was to mine, for a novel CYP from a new isolate B. lehensis G1 alkaliphile and determine the biological properties and functionalities of CYP in this bacterium. Our study employed the usage of computational methods to search for the novel CYP from CYP structural databases to identify the conserved pattern, functional domain and sequence properties of the uncharacterized CYP from B. lehensis G1. A computational homology model of the protein's structure was generated and a docking analysis was performed to provide useful structural knowledge on the enzyme's possible substrate and their interaction. Sequence analysis indicated that the newly identified CYP, termed CYP107CB2, contained the fingerprint heme binding sequence motif FxxGxxxCxG at position 336-345 as well as other highly conserved motifs characteristic of cytochrome P450 proteins. Using docking studies, we identified Ser-79, Leu-81, Val-231, Val-279, Val-383, Ala-232, Thr-236 and Thr-283 as important active site residues capable of stabilizing interactions with several potential substrates, including vitamin D3, 25-hydroxyvitamin D3 and 1α-hydroxyvitamin D3, in which all substrates docked proximally to the enzyme's heme center. Biochemical analysis indicated that CYP107CB2 is a biologically active protein to produce 1α,25-dihydroxyvitamin D3 from 1α-hydroxyvitamin D3. Based on these results, we conclude that the novel CYP107CB2 identified from B. lehensis G1 is a putative vitamin D hydroxylase which is possibly capable of catalyzing the bioconversion of parental vitamin D3 to calcitriol, or related metabolic products. Copyright © 2015 Elsevier Ltd. All rights reserved.
    Computational Biology and Chemistry 02/2015; 56. DOI:10.1016/j.compbiolchem.2015.02.015 · 1.12 Impact Factor
  • Samira Yousefi · Saadi Bayat · Mohd Basyaruddin Abdul Rahman · Intan Safinar Ismail · Elnaz Saki · Emilia Abdulmalek ·

    RSC Advances 01/2015; 5(118):97295-97307. DOI:10.1039/C5RA19623J · 3.84 Impact Factor
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    ABSTRACT: Most substrate for esterification has the inherent problem of low miscibility which requires addition of solvents into the reaction media. In this contribution, we would like to present an alternative and feasible option for an efficient solvent-free synthesis of menthyl butyrate using a novel thermostable crude T1 lipase. We investigated the effects of incubation time,temperature, enzyme loading and substrate molar ratio and determined the optimum conditions. The high conversion of menthyl butyrate catalyzed by crude T1 lipase in a solvent-free system is greatly affected by temperature and time of the reaction media. The highest yield of menthyl butyrate was 99.3% under optimized conditions of 60 C, incubation time of 13.15 h, 2.53 mg, 0.43% (w/w) enzyme to substrate ratio and at molar ratio of butyric anhydride/menthol 2.7:1. Hence, the investigation revealed that the thermostable crude T1 lipase successfully catalyzed the high-yield production of menthyl butyrate in a solvent-free system. The finding suggests that the crude T1 lipase was a promising alternative to overcome shortcomings associated with solvent-assisted enzymatic reactions.
    Biotechnology & Biotechnological Equipment 12/2014; 28(6):1065-1072. DOI:10.1080/13102818.2014.978220 · 0.30 Impact Factor
  • Saadi Bayat · Emilia Abd Malek · Normi M. Yahaya · Abu Bakar Salleh · Bimo Ario Tejo · Mohd Basyaruddin Abdul Rahman ·
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    ABSTRACT: The promiscuous aldo–ketoreductase (AKR) enzyme is used as a sustainable biocatalyst for the first time to catalyze asymmetric aldol reactions in aqueous medium. The reactions between aromatic aldehydes and cyclic/acyclic ketones give the corresponding products in moderate yields and enantioselectivities in the presence of water. The influence of solvents, the mole ratio of substrates, and enzyme concentration are investigated. The mechanism of the AKR1A1-catalyzed aldol reaction is also discussed.
    Tetrahedron Letters 11/2014; 55(46):6303–6306. DOI:10.1016/j.tetlet.2014.09.012 · 2.38 Impact Factor
  • Ruzanna Yahya · Roghayeh Abedi Karjiban · Mahiran Basri · Mohd Basyaruddin Abdul Rahman · Mauricio Girardi ·
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    ABSTRACT: Nonionic surfactants such as the Brij® series are important in the preparation of transdermal drug nanodelivery products using nanoemulsions because of their low toxicity and low irritancy. Here, Monte Carlo (MC) simulation was used to examine the physical behavior of the model deterministic system by using sampling procedures. Metropolis MC simulations were run on three mixtures of two different nonionic surfactants, Brij92 and Brij96, with different compositions in aqueous solution. The system was simulated in the canonical ensemble with constant temperature, volume and number of molecules. Hence, the acceptance ratio for single atom moves of the mixed surfactants increased as the concentration of surfactants increased from 0.494 to 0.591. The lowest total energy for the mixed surfactant systems was -99,039 kcal mol(-1) due to the interaction between all molecules in the system simulated. The physicochemical properties of models such as the radius of gyration and radial distribution function, were also determined. These observations indicate that the behavior and physicochemical of mixed surfactant and PKOEs nanoemulsion systems were described adequately during the simulation.
    Journal of Molecular Modeling 11/2014; 20(11):2512. DOI:10.1007/s00894-014-2512-1 · 1.74 Impact Factor
  • Muhammad Alif Mohammad Latif · Nuno Micaêlo · Mohd Basyaruddin Abdul Rahman ·
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    ABSTRACT: Stochastic molecular dynamics simulations were performed to investigate the solvation free energy of 15 neutral amino acid side chain analogues in aqueous and five, 1-buty1-3-methylimidazolium ([BMIM])-based ionic liquids. The results in aqueous were found highly correlated with previous experimental and simulation data. Meanwhile, [BMIM]-based RTILs showed better solvation thermodynamics than water to an extent that they were capable of solvating molecules immiscible in water. Non-polar analogues showed stronger solvation in hydrophobic RTIL anions such as [PF6](-) and [Tf2N](-) while polar analogues showed stronger solvation in the more hydrophilic RTIL anions such as [Cl](-), [TfO](-) and [BF4](-).
    Chemical Physics Letters 11/2014; 615:69–74. DOI:10.1016/j.cplett.2014.08.073 · 1.90 Impact Factor
  • Pik Mun Foong · Roghayeh Abedi Karjiban · Normi Mohd Yahaya · Abu Bakar Salleh · Mohd Basyaruddin Abdul Rahman ·
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    ABSTRACT: Metal ions are one of the essential elements which are extensively involved in many cellular activities. With rapid advancements in genome sequencing techniques, bioinformatics approaches have provided a promising way to extract functional information of a protein directly from its primary structure. Recent findings have suggested that the metal content of an organism can be predicted from its complete genome sequences. Characterizing the biological metal usage of cold-adapted organism may help to outline a comprehensive understanding of the metal-partnerships between the psychrophile and its adjacent environment. The focus of this study is targeted towards the analysis of the metal composition of a psychrophilic yeast Glaciozyma antarctica PI12 isolated from sea ice of Antarctica. Since the cellular metal content of an organism is usually reflected in the expressed metal-binding proteins, the putative metal-binding sequences from G. antarctica PI12 were identified in respect to their sequence homologies, domain compositions, protein families and cellular distribution. Most of the analyses revealed that the proteome was enriched with zinc, and the content of metal decreased in the order of Zn > Fe > Mg > Mn, Ca > Cu. Upon comparison, it was found that the metal compositions among yeasts were almost identical. These observations suggested that G. antarctica PI12 could have inherited a conserved trend of metal usage similar to modern eukaryotes, despite its geographically isolated habitat.
    Metallomics 10/2014; 7(1). DOI:10.1039/C4MT00163J · 3.59 Impact Factor
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    Mohd Basyaruddin Abdul Rahman · Ahmad Jaafar · Mahiran Basri · Raja Noor Abdul Rahman · Abu Bakar Salleh ·

  • Muhammad Alif Mohammad Latif · Nuno M Micaelo · Mohd Basyaruddin Abdul Rahman ·
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    ABSTRACT: In this report, molecular dynamics simulations were applied in order to investigate the effect of Room Temperature Ionic Liquid (RTIL) anions toward the structure and dynamic properties of lipases. Two lipases were studied; Candida antarctica lipase B and Candida rugosa lipase were solvated by five RTILs that contained the same cation, with increasing hydration levels. Several properties were investigated: structural deviations and flexibility of the protein conformation, the behaviour of RTILs at the protein surface, and the interactions between RTILs and water molecules in the systems. Both lipases' conformations showed an increased structural stability in RTILs when compared to an aqueous solution. The lowest structural deviation was observed around 15 to 20 percent of water content (w/w protein). The RTIL with chloride anion was shown to be the exception however: inducing the least structural stability at low water percentages. The flexibility of both lipases was clearly affected when transferred from aqueous into RTILs. The flexible regions found for both lipases in water were significantly more rigid in RTILs. Around the protein surface, the behaviour of RTIL anions and the water molecules was similar to other conventional organic solvents. The water retention ability for all RTIL anions was consistent for both lipases accept for the bis(trifluoromethylsulfonyl)imide anion, which showed distinctive behaviour toward different protein surface properties. The effect of water content was more profound compared to the difference between the RTILs anions studied. However, it was found that the structural and dynamic properties of the lipases were affected by the behaviour of anions toward the hydration layer of the enzymes.
    RSC Advances 09/2014; 4(89). DOI:10.1039/C4RA07460B · 3.84 Impact Factor
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    Saadi Bayat · Bimo A. Tejo · Emilia Abdulmalek · Abu Bakar Salleh · Yahaya M. Normi · Mohd Basyaruddin Abdul Rahman ·
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    ABSTRACT: Peptides as a kind of important chiral scaffold are broadly identified for their obvious advantages, diverse structures and accessibility. Based on promiscuous aldo-keto-reductase enzymes, several mimetic peptides were designed which were synthesized and tested as multifunctional organocatalysts in direct asymmetric aldol reactions. The corresponding aldol products were produced with high yields (up to 97%) and excellent diastereoselectivities (up to 99/1) and enantioselectivities (>98%) under mild reaction selectivity and enantioselectivity. The secondary structures of peptide catalysts provide an understanding of their mechanism.
    RSC Advances 08/2014; 4(73). DOI:10.1039/C4RA04866K · 3.84 Impact Factor
  • Mahiran Basri · Mohammad Abu Alrub · Emilia Abd Malek · Shahrul Ainliah · Abu Bakar Salleh · Mohd Basyaruddin Abdul Rahman ·
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    ABSTRACT: Enzymatic synthesis of N-trans-feruloyltyramine amide was optimized by response surface methodology (RSM) using 4-hydroxy-3-methoxycinnamic acid and tyramine hydrochloride in a one-step lipase catalyzed reaction using Lipozyme TL IM. Response surface methodology (RSM) based on five-level, four-variable central composite rotatable design (CCRD) was used to evaluate the interaction of synthesis, reaction time (24–96 h), temperature (30°–50°C), amount of enzyme (50–500 mg, 12.5–125.0 IUN), and substrate molar ratio (cinnamic acid:tyramine HCl) 1:1–8:1 mmol on the percentage yield of N-trans-feruloyltyramine amide. The optimum conditions derived via RSM were: reaction time 52 h, temperature 43°C, amount of enzyme 260 mg (65.0 IUN), and substrate molar ratio (cinnamic acid:tyramine HCl) 6.2:1. The actual experimental yield was 96.3% under optimum conditions, which compared well to the maximum predicted value of 97.2%.
    Chemical Engineering Communications 06/2014; 201(12). DOI:10.1080/00986445.2013.821060 · 1.10 Impact Factor
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    Rizana Yusof · Emilia Abdulmalek · Kamaliah Sirat · Mohd Basyaruddin Abdul Rahman ·
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    ABSTRACT: Density, viscosity and ionic conductivity data sets of deep eutectic solvents (DESs) formed by tetrabutylammonium bromide (TBABr) paired with ethlyene glycol, 1,3-propanediol, 1,5-pentanediol and glycerol hydrogen bond donors (HBDs) are reported. The properties of DES were measured at temperatures between 303 K and 333 K for HBD percentages of 66.7% to 90%. The effects of HBDs under different temperature and percentages are systematically analyzed. As expected, the measured density and viscosity of the studied DESs decreased with an increase in temperature, while ionic conductivity increases with temperature. In general, DESs made of TBABr and glycerol showed the highest density and viscosity and the lowest ionic conductivity when compared to other DESs. The presence of an extra hydroxyl group on glycerol in a DES affected the properties of the DES.
    Molecules 06/2014; 19(6):8011-8026. DOI:10.3390/molecules19068011 · 2.42 Impact Factor
  • Roghayeh Abedi Karjiban · Wui Zhuan Lim · Mahiran Basri · Mohd Basyaruddin Abdul Rahman ·
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    ABSTRACT: Lipases are known for their versatility in addition to their ability to digest fat. They can be used for the formulation of detergents, as food ingredients and as biocatalysts in many industrial processes. Because conventional enzymes are frangible at high temperatures, the replacement of conventional chemical routes with biochemical processes that utilize thermostable lipases is vital in the industrial setting. Recent theoretical studies on enzymes have provided numerous fundamental insights into the structures, folding mechanisms and stabilities of these proteins. The studies corroborate the experimental results and provide additional information regarding the structures that were determined experimentally. In this paper, we review the computational studies that have described how temperature affects the structure and dynamics of thermoenzymes, including the thermoalkalophilic L1 lipase derived from Bacillus stearothermophilus. We will also discuss the potential of using pressure for the analysis of the stability of thermoenzymes because high pressure is also important for the processing and preservation of foods.
    The Protein Journal 05/2014; 33(4). DOI:10.1007/s10930-014-9568-8 · 0.91 Impact Factor
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    ABSTRACT: At least a quarter of any complete genome encodes for hypothetical proteins (HPs) which are largely non-similar to other known, well-characterized proteins. Predicting and solving their structures and functions is imperative to aid understanding of any given organism as a complete biological system. The present study highlights the primary effort to classify and cluster 1202 HPs of Bacillus lehensis G1 alkaliphile to serve as a platform to mine and select specific HP(s) to be studied further in greater detail. All HPs of B. lehensis G1 were grouped according to their predicted functions based on the presence of functional domains in their sequences. From the metal-binding group of HPs of the cluster, an HP termed Bleg1_2507 was discovered to contain a thioredoxin (Trx) domain and highly-conserved metal-binding ligands represented by Cys69, Cys73 and His159, similar to all prokaryotic and eukaryotic Sco proteins. The built 3D structure of Bleg1_2507 showed that it shared the betaalphabetaalphabetabeta core structure of Trx-like proteins as well as three flanking beta-sheets, a 310 -helix at the N-terminus and a hairpin structure unique to Sco proteins. Docking simulations provided an interesting view of Bleg1_2507 in association with its putative cytochrome c oxidase subunit II (COXII) redox partner, Bleg1_2337, where the latter can be seen to hold its partner in an embrace, facilitated by hydrophobic and ionic interactions between the proteins. Although Bleg1_2507 shares relatively low sequence identity (47%) to BsSco, interestingly, the predicted metal-binding residues of Bleg1_2507 i.e. Cys-69, Cys-73 and His-159 were located at flexible active loops similar to other Sco proteins across biological taxa. This highlights structural conservation of Sco despite their various functions in prokaryotes and eukaryotes. We propose that HP Bleg1_2507 is a Sco protein which is able to interact with COXII, its redox partner and therefore, may possess metallochaperone and redox functions similar to other documented bacterial Sco proteins. It is hoped that this scientific effort will help to spur the search for other physiologically relevant proteins among the so-called "orphan" proteins of any given organism.
    BMC Structural Biology 03/2014; 14(1):11. DOI:10.1186/1472-6807-14-11 · 1.18 Impact Factor
  • Saadi Bayat · Emilia Abdulmalek · Bimo Ario Tejo · Abu Bakar Salleh · Yahaya M. Normi · Mohd Basyaruddin Abdul Rahman ·
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    ABSTRACT: In this work, three forms of a novel octapeptide have been evaluated as asymmetric catalysts for the Michael reaction. Low quantity catalyst loading, ecofriendly solvents, and reusability of organocatalyst successfully applied to attain excellent yields and moderate enantioselectivities in the Michael reaction.[Supplementary materials are available for this article. Go to the publisher's online edition of Synthetic Communications® for the following free supplemental resources: Full experimental and spectral details.]
    ChemInform 02/2014; 45(8). DOI:10.1002/chin.201408028