Displaying publications 41 - 60 of 245 in total

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  1. Fulltext Insight into Improved Thermostability of Cold-Adapted Staphylococcal Lipase by Glycine to Cysteine Mutation
    Veno J, Rahman RNZRA, Masomian M, Ali MSM, Kamarudin NHA
    Molecules, 2019 Aug 30;24(17).
    PMID: 31480403 DOI: 10.3390/molecules24173169
    Thermostability remains one of the most desirable traits in many lipases. Numerous studies have revealed promising strategies to improve thermostability and random mutagenesis often leads to unexpected yet interesting findings in engineering stability. Previously, the thermostability of C-terminal truncated cold-adapted lipase from Staphylococcus epidermidis AT2 (rT-M386) was markedly enhanced by directed evolution. The newly evolved mutant, G210C, demonstrated an optimal temperature shift from 25 to 45 °C and stability up to 50 °C. Interestingly, a cysteine residue was randomly introduced on the loop connecting the two lids and accounted for the only cysteine found in the lipase. We further investigated the structural and mechanistic insights that could possibly cause the significant temperature shift. Both rT-M386 and G210C were modeled and simulated at 25 °C and 50 °C. The results clearly portrayed the effect of cysteine substitution primarily on the lid stability. Comparative molecular dynamics simulation analysis revealed that G210C exhibited greater stability than the wild-type at high temperature simulation. The compactness of the G210C lipase structure increased at 50 °C and resulted in enhanced rigidity hence stability. This observation is supported by the improved and stronger non-covalent interactions formed in the protein structure. Our findings suggest that the introduction of a single cysteine residue at the lid region of cold-adapted lipase may result in unexpected increased in thermostability, thus this approach could serve as one of the thermostabilization strategies in engineering lipase stability.
    Matched MeSH terms: Hydrogen Bonding
  2. Fulltext Dielectrophoresis of Amyloid-Beta Proteins as a Microfluidic Template for Alzheimer's Research
    Al-Ahdal SA, Ahmad Kayani AB, Md Ali MA, Chan JY, Ali T, Adnan N, et al.
    Int J Mol Sci, 2019 Jul 23;20(14).
    PMID: 31340481 DOI: 10.3390/ijms20143595
    We employed dielectrophoresis to a yeast cell suspension containing amyloid-beta proteins (Aβ) in a microfluidic environment. The Aβ was separated from the cells and characterized using the gradual dissolution of Aβ as a function of the applied dielectrophoretic parameters. We established the gradual dissolution of Aβ under specific dielectrophoretic parameters. Further, Aβ in the fibril form at the tip of the electrode dissolved at high frequency. This was perhaps due to the conductivity of the suspending medium changing according to the frequency, which resulted in a higher temperature at the tips of the electrodes, and consequently in the breakdown of the hydrogen bonds. However, those shaped as spheroidal monomers experienced a delay in the Aβ fibril transformation process. Yeast cells exposed to relatively low temperatures at the base of the electrode did not experience a positive or negative change in viability. The DEP microfluidic platform incorporating the integrated microtip electrode array was able to selectively manipulate the yeast cells and dissolve the Aβ to a controlled extent. We demonstrate suitable dielectrophoretic parameters to induce such manipulation, which is highly relevant for Aβ-related colloidal microfluidic research and could be applied to Alzheimer's research in the future.
    Matched MeSH terms: Hydrogen Bonding
  3. Self-assembly of a robust hydrogen-bonded octylphosphonate network on cesium lead bromide perovskite nanocrystals for light-emitting diodes
    Brown AAM, Hooper TJN, Veldhuis SA, Chin XY, Bruno A, Vashishtha P, et al.
    Nanoscale, 2019 Jul 07;11(25):12370-12380.
    PMID: 31215940 DOI: 10.1039/c9nr02566a
    We report the self-assembly of an extensive inter-ligand hydrogen-bonding network of octylphosphonates on the surface of cesium lead bromide nanocrystals (CsPbBr3 NCs). The post-synthetic addition of octylphosphonic acid to oleic acid/oleylamine-capped CsPbBr3 NCs promoted the attachment of octylphosphonate to the NC surface, while the remaining oleylammonium ligands maintained the high dispersability of the NCs in non-polar solvent. Through powerful 2D solid-state 31P-1H NMR, we demonstrated that an ethyl acetate/acetonitrile purification regime was crucial for initiating the self-assembly of extensive octylphosphonate chains. Octylphosphonate ligands were found to preferentially bind in a monodentate mode through P-O-, leaving polar P[double bond, length as m-dash]O and P-OH groups free to form inter-ligand hydrogen bonds. The octylphosphonate ligand network strongly passivated the nanocrystal surface, yielding a fully-purified CsPbBr3 NC ink with PLQY of 62%, over 3 times higher than untreated NCs. We translated this to LED devices, achieving maximum external quantum efficiency and luminance of 7.74% and 1022 cd m-2 with OPA treatment, as opposed to 3.59% and 229 cd m-2 for untreated CsPbBr3 NCs. This represents one of the highest efficiency LEDs obtained for all-inorganic CsPbBr3 NCs, accomplished through simple, effective passivation and purification processes. The robust binding of octylphosphonates to the perovskite lattice, and specifically their ability to interlink through hydrogen bonding, offers a promising passivation approach which could potentially be beneficial across a breadth of halide perovskite optoelectronic applications.
    Matched MeSH terms: Hydrogen Bonding
  4. The mechanistic role of active site residues in non-stereo haloacid dehalogenase E (DehE)
    Zainal Abidin MH, Abd Halim KB, Huyop F, Tengku Abdul Hamid TH, Abdul Wahab R, Abdul Hamid AA
    J Mol Graph Model, 2019 07;90:219-225.
    PMID: 31103914 DOI: 10.1016/j.jmgm.2019.05.003
    Dehalogenase E (DehE) is a non-stereospecific enzyme produced by the soil bacterium, Rhizobium sp. RC1. Till now, the catalytic mechanism of DehE remains unclear although several literature concerning its structure and function are available. Since DehE is non-stereospecific, the enzyme was hypothesized to follow a 'direct attack mechanism' for the catalytic breakdown of a haloacid. For a molecular insight, the DehE modelled structure was docked in silico with the substrate 2-chloropropionic acid (2CP) in the active site. The ideal position of DehE residues that allowed a direct attack mechanism was then assessed via molecular dynamics (MD) simulation. It was revealed that the essential catalytic water was hydrogen bonded to the 'water-bearer', Asn114, at a relatively constant distance of ∼2.0 Å after 50 ns. The same water molecule was also closely sited to the catalytic Asp189 at an average distance of ∼2.0 Å, signifying the imperative role of the latter to initiate proton abstraction for water activation. This reaction was crucial to promote a direct attack on the α-carbon of 2CP to eject the halide ion. The water molecule was oriented favourably towards the α-carbon of 2CP at an angle of ∼75°, mirrored by the formation of stable enzyme-substrate orientations throughout the simulation. The data therefore substantiated that the degradation of a haloacid by DehE followed a 'direct attack mechanism'. Hence, this study offers valuable information into future advancements in the engineering of haloacid dehalogenases with improved activity and selectivity, as well as functionality in solvents other than water.
    Matched MeSH terms: Hydrogen Bonding
  5. Fulltext Adsorption and in vitro release study of curcumin form polyethyleneglycol functionalized multi walled carbon nanotube: kinetic and isotherm study
    Koupaei Malek S, Gabris MA, Hadi Jume B, Baradaran R, Aziz M, Karim KJBA, et al.
    Daru, 2019 Jun;27(1):9-20.
    PMID: 30554368 DOI: 10.1007/s40199-018-0232-2
    Polyethylene glycol functionalized with oxygenated multi-walled carbon nanotubes (O-PEG-MWCNTs) as an efficient nanomaterial for the in vitro adsorption/release of curcumin (CUR) anticancer agent. The synthesized material was morphologically characterized using scanning electron microscopy, Fourier transform infrared spectroscopy and transmission electron microscopy. In addition, the CUR adsorption process was assessed with kinetic and isotherm models fitting well with pseudo-second order and Langmuir isotherms. The results showed that the proposed O-PEG-MWCNTs has a high adsorption capacity for CUR (2.0 × 103 mg/g) based on the Langmuir model. The in vitro release of CUR from O-PEG-MWCNTs was studied in simulating human body fluids with different pHs (ABS pH 5, intestinal fluid pH 6.6 and body fluid pH 7.4). Lastly, to confirm the success compliance of the O-PEG-MWCNT nanocomposite as a drug delivery system, the parameters affecting the CUR release such as temperature and PEG content were investigated. As a result, the proposed nanocomposite could be used as an efficient carrier for CUR delivery with an enhanced prolonged release property. Graphical Abstract ᅟ.
    Matched MeSH terms: Hydrogen Bonding
  6. Molecular interaction study of an anticancer drug, ponatinib with human serum albumin using spectroscopic and molecular docking methods
    Tayyab S, Sam SE, Kabir MZ, Ridzwan NFW, Mohamad SB
    Spectrochim Acta A Mol Biomol Spectrosc, 2019 May 05;214:199-206.
    PMID: 30780089 DOI: 10.1016/j.saa.2019.02.028
    Binding of a potent anticancer agent, ponatinib (PTB) to human serum albumin (HSA), main ligand transporter in blood plasma was analyzed with several spectral techniques such as fluorescence, absorption and circular dichroism along with molecular docking studies. Decrease in the KSV value with increasing temperature pointed towards PTB-induced quenching as the static quenching, thus affirming complexation between PTB and HSA. An intermediate binding affinity was found to stabilize the PTB-HSA complex, as suggested by the Ka value. Thermodynamic analysis of the binding phenomenon revealed participation of hydrophobic and van der Waals interactions along with hydrogen bonds, which was also supported by molecular docking analysis. Changes in both secondary and tertiary structures as well as in the microenvironment around Trp and Tyr residues of HSA were anticipated upon PTB binding to the protein, as manifested from circular dichroism and three-dimensional fluorescence spectra, respectively. Binding of PTB to HSA led to protein's thermal stabilization. Competitive ligand displacement experiments using different site markers such as warfarin, indomethacin and ketoprofen disclosed the binding site of PTB as Sudlow's site I in HSA, which was further confirmed by molecular docking analysis.
    Matched MeSH terms: Hydrogen Bonding
  7. Co-crystallization of a neutral mol-ecule and its zwitterionic tautomer: structure and Hirshfeld surface analysis of 5-methyl-4-(5-methyl-1H-pyrazol-3-yl)-2-phenyl-2,3-di-hydro-1H-pyrazol-3-one 5-methyl-4-(5-methyl-1H-pyrazol-2-ium-3-yl)-3-oxo-2-phenyl-2,3-di-hydro-1H-pyrazol-1-ide monohydrate
    Asiri AM, Alzahrani KAH, Faidallah HM, Alamry KA, Jotani MM, Tiekink ERT
    Acta Crystallogr E Crystallogr Commun, 2019 May 01;75(Pt 5):565-570.
    PMID: 31110787 DOI: 10.1107/S2056989019004389
    The title compound, 2C14H14N4O·H2O, comprises a neutral mol-ecule containing a central pyrazol-3-one ring flanked by an N-bound phenyl group and a C-bound 5-methyl-1H-pyrazol-3-yl group (at positions adjacent to the carbonyl substituent), its zwitterionic tautomer, whereby the N-bound proton of the central ring is now resident on the pendant ring, and a water mol-ecule of crystallization. Besides systematic variations in geometric parameters, the two independent organic mol-ecules have broadly similar conformations, as seen in the dihedral angle between the five-membered rings [9.72 (9)° for the neutral mol-ecule and 3.32 (9)° for the zwitterionic tautomer] and in the dihedral angles between the central and pendant five-membered rings [28.19 (8) and 20.96 (8)° (neutral mol-ecule); 11.33 (9) and 11.81 (9)°]. In the crystal, pyrazolyl-N-H⋯O(carbon-yl) and pyrazolium-N-H⋯N(pyrazol-yl) hydrogen bonds between the independent organic mol-ecules give rise to non-symmetric nine-membered {⋯HNNH⋯NC3O} and {⋯HNN⋯HNC3O} synthons, which differ in the positions of the N-bound H atoms. These aggregates are connected into a supra-molecular layer in the bc plane by water-O-H⋯N(pyrazolide), water-O-H⋯O(carbon-yl) and pyrazolyl-N-H⋯O(water) hydrogen bonding. The layers are linked into a three-dimensional architecture by methyl-C-H⋯π(phen-yl) inter-actions. The different inter-actions, in particular the weaker contacts, formed by the organic mol-ecules are clearly evident in the calculated Hirshfeld surfaces, and the calculated electrostatic potentials differentiate the tautomers.
    Matched MeSH terms: Hydrogen Bonding
  8. Fulltext Electrospun Combination of Peppermint Oil and Copper Sulphate with Conducive Physico-Chemical properties for Wound Dressing Applications
    Jaganathan SK, Mani MP, Khudzari AZM
    Polymers (Basel), 2019 Apr 01;11(4).
    PMID: 30960571 DOI: 10.3390/polym11040586
    The ultimate goal in tissue engineering is to fabricate a scaffold which could mimic the native tissue structure. In this work, the physicochemical and biocompatibility properties of electrospun composites based on polyurethane (PU) with added pepper mint (PM) oil and copper sulphate (CuSO₄) were investigated. Field Emission Electron microscope (FESEM) study depicted the increase in mean fiber diameter for PU/PM and decrease in fiber diameter for PU/PM/CuSO₄ compared to the pristine PU. Fourier transform infrared spectroscopy (FTIR) analysis revealed the formation of a hydrogen bond for the fabricated composites as identified by an alteration in PU peak intensity. Contact angle analysis presented the hydrophobic nature of pristine PU and PU/PM while the PU/PM/CuSO₄ showed hydrophilic behavior. Atomic force microscopy (AFM) analysis revealed the increase in the surface roughness for the PU/PM while PU/PM/CuSO₄ showed a decrease in surface roughness compared to the pristine PU. Blood compatibility studies showed improved blood clotting time and less toxic behavior for the developed composites than the pristine PU. Finally, the cell viability of the fabricated composite was higher than the pristine PU as indicated in the MTS assay. Hence, the fabricated wound dressing composite based on PU with added PM and CuSO₄ rendered a better physicochemical and biocompatible nature, making it suitable for wound healing applications.
    Matched MeSH terms: Hydrogen Bonding
  9. Fulltext A 1:1:1 co-crystal solvate comprising 2,2'-di-thiodi-benzoic acid, 2-chloro-benzoic acid and N,N-di-methyl-formamide: crystal structure, Hirshfeld surface analysis and computational study
    Tan SL, Tiekink ERT
    Acta Crystallogr E Crystallogr Commun, 2019 Apr 01;75(Pt 4):475-481.
    PMID: 31161060 DOI: 10.1107/S205698901900375X
    The asymmetric unit of the three-component title compound, 2,2'-di-thiodi-benzoic acid-2-chloro-benzoic acid-N,N-di-methyl-formamide (1/1/1), C14H10O4S2·C7H5ClO2·C3H7NO, contains a mol-ecule each of 2,2'-di-thiodi-benzoic acid (DTBA), 2-chloro-benzoic acid (2CBA) and di-methyl-formamide (DMF). The DTBA mol-ecule is twisted [the C-S-S-C torsion angle is 88.37 (17)°] and each carb-oxy-lic group is slightly twisted from the benzene ring to which it is connected [CO2/C6 dihedral angles = 7.6 (3) and 12.5 (3)°]. A small twist is evident in the mol-ecule of 2CBA [CO2/C6 dihedral angle = 4.4 (4)°]. In the crystal, the three mol-ecules are connected by hydrogen bonds with the two carb-oxy-lic acid residues derived from DTBA and 2CBA forming a non-symmetric eight-membered {⋯HOCO}2 synthon, and the second carb-oxy-lic acid of DTBA linked to the DMF mol-ecule via a seven-membered {⋯HOCO⋯HCO} heterosynthon. The three-mol-ecule aggregates are connected into a supra-molecular chain along the a axis via DTBA-C-H⋯O(hydroxyl-2CBA), 2CBA-C-H⋯O(hydroxyl-DTBA) and DTBA-C-H⋯S(DTBA) inter-actions. Supra-molecular layers in the ab plane are formed as the chains are linked via DMF-C-H⋯S(DTBA) contacts, and these inter-digitate along the c-axis direction without specific points of contact between them. A Hirshfeld surface analysis points to additional but, weak contacts to stabilize the three-dimensional architecture: DTBA-C=O⋯H(phenyl-DTBA), 2CBA-Cl⋯H(phenyl-DTBA), as well as a π-π contact between the delocalized eight-membered {⋯HOC=O}2 carb-oxy-lic dimer and the phenyl ring of 2CBA. The latter was confirmed by electrostatic potential (ESP) mapping.
    Matched MeSH terms: Hydrogen Bonding
  10. Fulltext Redetermination of the crystal structure of 2-oxo-1,3-thia-zolidin-4-iminium chloride
    Muthukkumar M, Karthikeyan A, Poovarasan M, Ruckmani V, Rajaram D, Jegan Jennifer S, et al.
    Acta Crystallogr E Crystallogr Commun, 2019 Apr 01;75(Pt 4):443-446.
    PMID: 31161053 DOI: 10.1107/S2056989019003189
    In the redetermination of the title compound, C3H5N2OS+·CI-, the asymmetric unit consists of one independent 2-oxo-1,3-thia-zolidin-4-iminium cation and one independent chloride anion. The cation inter-acts with a chloride anion via N-H⋯Cl hydrogen bonds forming a supra-molecular chain along [010]. These supra-molecular chains are further extended by weak C-H⋯Cl and C-H⋯O inter-actions, forming a two-dimensional network parallel to (001). The crystal structure is further stabilized by weak C-O⋯π inter-actions, supporting a three-dimensional architecture. The structure was previously determined by Ananthamurthy & Murthy [Z. Kristallogr. (1975). 8, 356-367] but has been redetermined with higher precision to allow the hydrogen-bonding patterns and supra-molecular inter-actions to be investigated.
    Matched MeSH terms: Hydrogen Bonding
  11. Fulltext Microwave-Assisted Synthesis of Mono- and Disubstituted 4-Hydroxyacetophenone Derivatives via Mannich Reaction: Synthesis, XRD and HS-Analysis
    Aljohani G, Said MA, Lentz D, Basar N, Albar A, Alraqa SY, et al.
    Molecules, 2019 Feb 07;24(3).
    PMID: 30736403 DOI: 10.3390/molecules24030590
    An efficient microwave-assisted one-step synthetic route toward Mannich bases is developed from 4-hydroxyacetophenone and different secondary amines in quantitative yields, via a regioselective substitution reaction. The reaction takes a short time and is non-catalyzed and reproducible on a gram scale. The environmentally benign methodology provides a novel alternative, to the conventional methodologies, for the synthesis of mono- and disubstituted Mannich bases of 4-hydroxyacetophenone. All compounds were well-characterized by FT-IR, ¹H NMR, 13C NMR, and mass spectrometry. The structures of 1-{4-hydroxy-3-[(morpholin-4-yl)methyl]phenyl}ethan-1-one (2a) and 1-{4-hydroxy-3-[(pyrrolidin-1-yl)methyl]phenyl}ethan-1-one (3a) were determined by single crystal X-ray crystallography. Compound 2a and 3a crystallize in monoclinic, P2₁/n, and orthorhombic, Pbca, respectively. The most characteristic features of the molecular structure of 2a is that the morpholine fragment adopts a chair conformation with strong intramolecular hydrogen bonding. Compound 3a exhibits intermolecular hydrogen bonding, too. Furthermore, the computed Hirshfeld surface analysis confirms H-bonds and π⁻π stack interactions obtained by XRD packing analyses.
    Matched MeSH terms: Hydrogen Bonding
  12. PHA synthase (PhaC): interpreting the functions of bioplastic-producing enzyme from a structural perspective
    Chek MF, Hiroe A, Hakoshima T, Sudesh K, Taguchi S
    Appl Microbiol Biotechnol, 2019 Feb;103(3):1131-1141.
    PMID: 30511262 DOI: 10.1007/s00253-018-9538-8
    Polyhydroxyalkanoates (PHAs) are biopolymers synthesized by a wide range of bacteria, which serve as a promising candidate in replacing some conventional petrochemical-based plastics. PHA synthase (PhaC) is the key enzyme in the polymerization of PHA, and the crystal structures were successfully determined using the catalytic domain of PhaC from Cupriavidus necator (PhaCCn-CAT) and Chromobacterium sp. USM2 (PhaCCs-CAT). Here, we review the beneficial mutations discovered in PhaCs from a structural perspective. The structural comparison of the residues involved in beneficial mutation reveals that the residues are near to the catalytic triad, but not inside the catalytic pocket. For instance, Ala510 of PhaCCn is near catalytic His508 and may be involved in the open-close regulation, which presumably play an important role in substrate specificity and activity. In the class II PhaC1 from Pseudomonas sp. 61-3 (PhaC1Ps), Ser325 stabilizes the catalytic cysteine through hydrogen bonding. Another residue, Gln508 of PhaC1Ps is located in a conserved hydrophobic pocket which is next to the catalytic Asp and His. A class I, II-conserved Phe420 of PhaCCn is one of the residues involved in dimerization and its mutation to serine greatly reduced the lag phase. The current structural analysis shows that the Phe362 and Phe518 of PhaC from Aeromonas caviae (PhaCAc) are assisting the dimer formation and maintaining the integrity of the core beta-sheet, respectively. The structure-function relationship of PhaCs discussed in this review will serve as valuable reference for future protein engineering works to enhance the performance of PhaCs and to produce novel biopolymers.
    Matched MeSH terms: Hydrogen Bonding
  13. The two mutations of actin-myosin interface and their effect on the dynamics, structures, and functions of skeletal muscle actin
    Sadat Mohajer F, Parvizpour S, Razmara J, Shahir Shamsir M
    J Biomol Struct Dyn, 2019 Feb;37(2):372-382.
    PMID: 29338614 DOI: 10.1080/07391102.2018.1427630
    Congenital myopathy is a broad category of muscular diseases with symptoms appearing at the time of birth. One type of congenital myopathy is Congenital Fiber Type Disproportion (CFTD), a severely debilitating disease. The G48D and G48C mutations in the D-loop and the actin-myosin interface are the two causes of CFTD. These mutations have been shown to significantly affect the structure and function of muscle fibers. To the author's knowledge, the effects of these mutations have not yet been studied. In this work, the power stroke structure of the head domain of myosin and the wild and mutated types of actin were modeled. Then, a MD simulation was run for the modeled structures to study the effects of these mutations on the structure, function, and molecular dynamics of actin. The wild and mutated actins docked with myosin showed differences in hydrogen bonding patterns, free binding energies, and hydrogen bond occupation frequencies. The G48D and G48C mutations significantly impacted the conformation of D-loops because of their larger size compared to Glycine and their ability to interfere with the polarity or hydrophobicity of this neutralized and hydrophobic loop. Therefore, the mutated loops were unable to fit properly into the hydrophobic groove of the adjacent G-actin. The abnormal structure of D-loops seems to result in the abnormal assembly of F-actins, giving rise to the symptoms of CFTD. It was also noted that G48C and G48D did not form hydrogen bonds with myosin in the residue 48 location. Nevertheless, in this case, muscles are unable to contract properly due to muscle atrophy.
    Matched MeSH terms: Hydrogen Bonding
  14. Probing the interaction of 2,4-dichlorophenoxyacetic acid with human serum albumin as studied by experimental and computational approaches
    Tayyab S, Francis JA, Kabir MZ, Ghani H, Mohamad SB
    Spectrochim Acta A Mol Biomol Spectrosc, 2019 Jan 15;207:284-293.
    PMID: 30267976 DOI: 10.1016/j.saa.2018.09.033
    To characterize the binding of a widely used herbicide, 2,4-dichlorophenoxyacetic acid (2,4-D) to the major transporter in human circulation, human serum albumin (HSA), multi-spectroscopic approaches such as fluorescence, absorption and circular dichroism along with computational methods were employed. Analysis of the fluorescence and absorption spectroscopic data confirmed the 2,4-D-HSA complex formation. A static quenching mechanism was evident from the inverse temperature dependence of the KSV values. The complex was stabilized by a weak binding affinity (Ka = 5.08 × 103 M-1 at 298 K). Quantitative analysis of thermodynamic data revealed participation of hydrophobic and van der Waals interactions as well as hydrogen bonds in the binding process. Circular dichroism and three-dimensional fluorescence spectral results showed structural (secondary and tertiary) changes in HSA as well as microenvironmental perturbation around protein fluorophores (Trp and Tyr residues) upon 2,4-D binding. Addition of 2,4-D to HSA was found to improve protein's thermal stability. Competitive displacement results as well as computational analyses suggested preferred location of the 2,4-D binding site as Sudlow's site I (subdomain IIA) in HSA.
    Matched MeSH terms: Hydrogen Bonding
  15. Fulltext Crystal structure of a second monoclinic polymorph of 3-meth-oxy-benzoic acid with Z' = 1
    Chia TS, Kwong HC, Wong QA, Quah CK, Arafath MA
    Acta Crystallogr E Crystallogr Commun, 2019 Jan 01;75(Pt 1):8-11.
    PMID: 30713724 DOI: 10.1107/S2056989018016900
    A new polymorphic form of the title compound, C8H8O3, is described in the centrosymmetric monoclinic space group P21/c with Z' = 1 as compared to the first polymorph, which crystallizes with two conformers (Z' = 2) in the asymmetric unit in the same space group. In the crystal of the second polymorph, inversion dimers linked by O-H⋯O hydrogen bonds occur and these are linked into zigzag chains, propagating along the b-axis direction by C-H⋯O links. The crystal structure also features a weak π-π inter-action, with a centroid-to-centroid distance of 3.8018 (6) Å. The second polymorph of the title compound is less stable than the reported first polymorph, as indicated by its smaller calculated lattice energy.
    Matched MeSH terms: Hydrogen Bonding
  16. Fulltext A 1:2 co-crystal of 2,2'-di-thiodi-benzoic acid and benzoic acid: crystal structure, Hirshfeld surface analysis and computational study
    Tan SL, Tiekink ERT
    Acta Crystallogr E Crystallogr Commun, 2019 Jan 01;75(Pt 1):1-7.
    PMID: 30713723 DOI: 10.1107/S2056989018017097
    The asymmetric unit of the title 1:2 co-crystal, C14H10O4S2·2C7H6O2, comprises half a mol-ecule of di-thiodi-benzoic acid [systematic name: 2-[(2-carb-oxy-phen-yl)disulfan-yl]benzoic acid, DTBA], as the mol-ecule is located about a twofold axis of symmetry, and a mol-ecule of benzoic acid (BA). The DTBA mol-ecule is twisted about the di-sulfide bond [the C-S-S-C torsion angle is -83.19 (8)°] resulting in a near perpendicular relationship between the benzene rings [dihedral angle = 71.19 (4)°]. The carb-oxy-lic acid group is almost co-planar with the benzene ring to which it is bonded [dihedral angle = 4.82 (12)°]. A similar near co-planar relationship pertains for the BA mol-ecule [dihedral angle = 3.65 (15)°]. Three-mol-ecule aggregates are formed in the crystal whereby two BA mol-ecules are connected to a DTBA mol-ecule via hy-droxy-O-H⋯O(hydroxy) hydrogen bonds and eight-membered {⋯HOC=O}2 synthons. These are connected into a supra-molecular layer in the ab plane through C-H⋯O inter-actions. The inter-actions between layers to consolidate the three-dimensional architecture are π-π stacking inter-actions between DTBA and BA rings [inter-centroid separation = 3.8093 (10) Å] and parallel DTBA-hy-droxy-O⋯π(BA) contacts [O⋯ring centroid separation = 3.9049 (14) Å]. The importance of the specified inter-actions as well as other weaker contacts, e.g. π-π and C-H⋯S, are indicated in the analysis of the calculated Hirshfeld surface and inter-action energies.
    Matched MeSH terms: Hydrogen Bonding
  17. Fulltext Crystal structure and Hirshfeld surface analysis of a chalcone derivative: (E)-3-(4-fluoro-phen-yl)-1-(4-nitro-phen-yl)prop-2-en-1-one
    Wong QA, Chia TS, Kwong HC, Chidan Kumar CS, Quah CK, Arafath MA
    Acta Crystallogr E Crystallogr Commun, 2019 Jan 01;75(Pt 1):53-57.
    PMID: 30713733 DOI: 10.1107/S2056989018017450
    The mol-ecular structure of the title chalcone derivative, C15H10FNO3, is nearly planar and the mol-ecule adopts a trans configuration with respect to the C=C double bond. The nitro group is nearly coplanar with the attached benzene ring, which is nearly parallel to the second benzene ring. In the crystal, mol-ecules are connected by pairs of weak inter-molecular C-H⋯O hydrogen bonds into inversion dimers. The dimers are further linked by another C-H⋯O hydrogen bond and a C-H⋯F hydrogen bond into sheets parallel to (104). π-π inter-actions occur between the sheets, with a centroid-centroid distance of 3.8860 (11) Å. Hirshfeld surface analysis was used to investigate and qu-antify the inter-molecular inter-actions.
    Matched MeSH terms: Hydrogen Bonding
  18. Fulltext In Silico Screening of Aptamers Configuration against Hepatitis B Surface Antigen
    Sabri MZ, Abdul Hamid AA, Sayed Hitam SM, Abdul Rahim MZ
    Adv Bioinformatics, 2019;2019:6912914.
    PMID: 31346332 DOI: 10.1155/2019/6912914
    Aptamer has been long studied as a substitute of antibodies for many purposes. However, due to the exceeded length of the aptamers obtained in vitro, difficulties arise in its manipulation during its molecular conjugation on the matrix surfaces. Current study focuses on computational improvement for aptamers screening of hepatitis B surface antigen (HBsAg) through optimization of the length sequences obtained from SELEX. Three original aptamers with affinity against HBsAg were truncated into five short hairpin structured aptamers and their affinity against HBsAg was thoroughly studied by molecular docking, molecular dynamics (MD) simulation, and Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) method. The result shows that truncated aptamers binding on HBsAg "a" determinant region are stabilized by the dynamic H-bond formation between the active binding residues and nucleotides. Amino acids residues with the highest hydrogen bonds hydrogen bond interactions with all five aptamers were determined as the active binding residues and further characterized. The computational prediction of complexes binding will include validations through experimental assays in future studies. Current study will improve the current in vitro aptamers by minimizing the aptamer length for its easy manipulation.
    Matched MeSH terms: Hydrogen Bonding
  19. Fulltext Thioguanine-based DENV-2 NS2B/NS3 protease inhibitors: Virtual screening, synthesis, biological evaluation and molecular modelling
    Hariono M, Choi SB, Roslim RF, Nawi MS, Tan ML, Kamarulzaman EE, et al.
    PLoS One, 2019;14(1):e0210869.
    PMID: 30677071 DOI: 10.1371/journal.pone.0210869
    Dengue virus Type 2 (DENV-2) is predominant serotype causing major dengue epidemics. There are a number of studies carried out to find its effective antiviral, however to date, there is still no molecule either from peptide or small molecules released as a drug. The present study aims to identify small molecules inhibitor from National Cancer Institute database through virtual screening. One of the hits, D0713 (IC50 = 62 μM) bearing thioguanine scaffold was derivatised into 21 compounds and evaluated for DENV-2 NS2B/NS3 protease inhibitory activity. Compounds 18 and 21 demonstrated the most potent activity with IC50 of 0.38 μM and 16 μM, respectively. Molecular dynamics and MM/PBSA free energy of binding calculation were conducted to study the interaction mechanism of these compounds with the protease. The free energy of binding of 18 calculated by MM/PBSA is -16.10 kcal/mol compared to the known inhibitor, panduratin A (-11.27 kcal/mol), which corroborates well with the experimental observation. Results from molecular dynamics simulations also showed that both 18 and 21 bind in the active site and stabilised by the formation of hydrogen bonds with Asn174.
    Matched MeSH terms: Hydrogen Bonding
  20. Molecular Dynamics Simulations of Glycyrrhizic Acid Aggregates as Drug-Carriers for Paclitaxel
    Hussain M
    Curr Drug Deliv, 2019;16(7):618-627.
    PMID: 30868954 DOI: 10.2174/1567201816666190313155117
    BACKGROUND: Glycyrrhizic acid (GA) is a glycoside that has shown considerable promise as a penetration enhancer and drug carrier to improve the absorption of poorly water-soluble drugs. The aggregation behavior of GA and its ability to form large micelles at higher solution concentrations are thought to contribute to these bioavailability enhancing properties. The oral absorption of Paclitaxel (PTX) for example, an anti-cancer agent which exhibits poor oral bioavailability, has been found to significantly increase in the presence of GA.

    METHODS: In an attempt to visualize the aggregation behavior of GA and its subsequent association with PTX, 100 ns molecular dynamics simulation of a 5 mM aqueous solution of GA with 10 molecules of PTX was conducted using GROMACS and an all-atom forcefield.

    RESULTS: Aggregation of GA molecules was found to occur quickly at this level of saturation leading to two stable aggregates of 13 and 17 GA molecules with an effective radius of 10.17 nm to 10.92 nm. These aggregates form not in isolation, but together with PTX molecule embedded within the structures, which reduces the number of interactions and hydrogen-bonding with water.

    CONCLUSION: GA aggregation occurs around PTX molecules in solution, forming co-joined GA-PTX cluster units at a ratio of 3:1. These clusters remain stable for the remainder of the 100ns simulation and serve to isolate and protect PTX from the aqueous environment.

    Matched MeSH terms: Hydrogen Bonding
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