Campylobacter jejuni is an important cause of human foodborne gastroenteritis; strategies to prev... more Campylobacter jejuni is an important cause of human foodborne gastroenteritis; strategies to prevent infection are hampered by a poor understanding of the complex interactions between host and pathogen. Previous work showed that C. jejuni could bind human histo-blood group antigens (BgAgs) in vitro and that BgAgs could inhibit the binding of C. jejuni to human intestinal mucosa ex vivo. Here, the major flagella subunit protein (FlaA) and the major outer membrane protein (MOMP) were identified as BgAg-binding adhesins in C. jejuni NCTC11168. Significantly, the MOMP was shown to be O-glycosylated at Thr(268); previously only flagellin proteins were known to be O-glycosylated in C. jejuni. Substitution of MOMP Thr(268) led to significantly reduced binding to BgAgs. The O-glycan moiety was characterized as Gal(β1-3)-GalNAc(β1-4)-GalNAc(β1-4)-GalNAcα1-Thr(268); modelling suggested that O-glycosylation has a notable effect on the conformation of MOMP and this modulates BgAg-binding capaci...
The activation barriers for internal rotation around the C-N bond in p-substituted nitrosobenzene... more The activation barriers for internal rotation around the C-N bond in p-substituted nitrosobenzenes were calculated using the density functional theory (DFT) and second-order Moller-Plesset (MP2) methods with the 6-31+g(d) basis set. The polarisable continuum model (PCM) was used to model the solvent effect. An explicit water molecule was also introduced to form a hydrogen bond with the nitrosogroup and its effect on the barrier was studied by DFT. The barriers were well-correlated with Hammett sigma+ rather than sigma values, meaning a strong resonance effect. The MP2 method produces better and comparable results with the few available experimental values.
The emerged Coronavirus disease (COVID-19) causes severe or even fatal respiratory tract infectio... more The emerged Coronavirus disease (COVID-19) causes severe or even fatal respiratory tract infection, and to date there is no FDA-approved therapeutics or effective treatment available to effectively combat this viral infection. This urgent situation is an attractive research area in the field of drug design and development. One of the most important targets of SARS-coronavirus-2 (SARS Cov-2) is the main protease (3CLpro). Actinomycetes are important resources for drug discovery. The angucylines that are mainly produced by Streptomyces genus of actinomycetes exhibit a broad range of biological activities such as anticancer, antibacterial and antiviral. This study aims to investigate the binding affinity and molecular interactions of 157 available angucycline compounds with 3CLpro using docking and molecular dynamics simulations. MM-PBSA calculations showed that moromycin A has a better binding energy (− 30.42 kcal mol−1) compared with other ligands (in a range of − 18.66 to − 22.89 kc...
A rhizosphere isolate Streptomyces sp. CAH29 was found to possess potent antibacterial and antifu... more A rhizosphere isolate Streptomyces sp. CAH29 was found to possess potent antibacterial and antifungal activity against a variety of test organisms. Based on 16S ribosomal ribonucleic acid sequence homology studies, this strain was found to be similar to Streptomyces stramineus (gene sequence similarity 99 %). The major bioactive metabolite produced by Streptomyces sp. CAH29 isolate was extracted, purified andidentified by nuclear magnetic resonance as tetrangomycin. This known anthraquinone-exhibited antimicrobial activity against Staphylococcus aureus, Streptococcus pyogenes, methicillin resistant Staphylococcus aureus and Candida albicans with inhibition zones of 14, 10, 12 and 8 mm, respectively. Docking results demonstrate that tetrangomycin has a similar mode of action and a comparable docking score to bind to the dehydrosqualene synthase (CrtM) enzyme of methicillin resistant Staphylococcus aureus compared to the current inhibitor. Hence, this suggests that tetrangomycin has a potential to be used as an anti-methicillin resistant Staphylococcus aureus agent. Tetrangomycin also showed moderate free radical scavenging activity with 1,1-diphenyl-2-picryl-hydrazil. Tetrangomycin apparently decreased all of the studied cytokine (pro-inflammatory: interleukin 1B, interleukin 2, tumor necrosis factor and interleukin L6 and anti-inflammatory: interleukin 10) expression levels at IC50 concentrations in A459 (adenocarcinomic human alveolar basal epithelial) and LNCAP (human prostate adenocarcinoma) cell lines. In addition, it reduced Caspase 8 and 3 mRNA levels in LNCAP and A549 cells. This study describes for the first time novel in vitro immunosuppressive function of tetrangomycin by reducing the transcription of cytokine genes.
Abstract The enantioselective reduction of prochiral ketones with borane in the presence of a chi... more Abstract The enantioselective reduction of prochiral ketones with borane in the presence of a chiral ligand has received considerable attention. Hydroxylamine-based chiral ligands with amide and hydroxyl functions in the presence of other co-ordinating groups are highly effective in these asymmetric reductions. The current work presents a simple one step synthesis of a series of β-hydroxyamide-based ligands from the reaction between 3-hydroxy-2-naphthoic acid and chiral amino alcohols and their applications as catalysts in asymmetric borane-mediated reductions of aromatic prochiral ketones in THF. The reductions provided the corresponding secondary alcohols with up to 96% ee and in good to excellent yields (89–99%). DFT calculations at B3LYP/6-31+g(d) level offered theoretical models to account for the enantioselectivity imposed by the chiral ligands in the reductions of the ketones.
The work involves an experimental ((1)H NMR) and theoretical (MD, MM-PBSA and DFT) investigation ... more The work involves an experimental ((1)H NMR) and theoretical (MD, MM-PBSA and DFT) investigation of the molecular recognition and discrimination properties of a chiral aza-15-crown-5 against methyl esters of alanine, phenylalanine and valine hydrochloride salts. The results indicate that the receptor binds enantiomers with moderate binding constants (88-1,389 M(-1)), with phenylalanine being more discriminated. The difference in experimental binding free energies (ΔG (R) - ΔG (S)) for alanine, phenylalanine and valine enantiomers were calculated as -0.36, -1.58 and 0.80 kcal mol(-1), respectively. The differences in theoretical binding energies were calculated by MM-PBSA (ΔE (R) PB - ΔE (S) PB=) as -0.30, -1.45 and 0.88, by B3LYP/6-31+G(d) as -1.17, -0.84 and 0.74 and by M06-2X/6-31+G(d) as -1.40, -3.26 and 1.66 kcal mol(-1). The data obtained give valuable information regarding the molecular recognition mode of the organoammonium complexes of chiral aza-crown ether with C 1 symmetry, which may be relevant to biological systems.
The non-integrin laminin receptor (LAMR1/RPSA) and galectin-3 (Gal-3) are multi-functional host m... more The non-integrin laminin receptor (LAMR1/RPSA) and galectin-3 (Gal-3) are multi-functional host molecules with roles in diverse pathological processes, particularly of infectious or oncogenic origins. Using bimolecular fluorescence complementation and confocal imaging, we demonstrate that the two proteins homo- and heterodimerize, and that each isotype forms a distinct cell surface population. We present evidence that the 37 kDa form of LAMR1 (37LRP) is the precursor of the previously described 67 kDa laminin receptor (67LR), whereas the heterodimer represents an entity that is distinct from this molecule. Site-directed mutagenesis confirmed that the single cysteine (C 173 ) of Gal-3 or lysine (K 166 ) of LAMR1 are critical for heterodimerization. Recombinant Gal-3, expressed in normally Gal-3-deficient N2a cells, dimerized with endogenous LAMR1 and led to a significantly increased number of internalized bacteria ( Neisseria meningitidis ), confirming the role of Gal-3 in bacterial ...
Abstract Four novel C 2 -symmetric macrocyclic compounds with a pyridine function and possessing ... more Abstract Four novel C 2 -symmetric macrocyclic compounds with a pyridine function and possessing amide and ester lingeages were prepared. The enantiomeric discrimination abilities of these macrocycles against α-phenylethylammonium and α-(1-naphthyl)ethylammonium perchlorate salts were measured by standard 1 H NMR titration techniques in DMSO- d 6 . A binding constant ratio of 31 (Kbind(S)/Kbind(R)) for two enantiomers of α-(1-naphthyl)ethylammonium salt with the macrocyclic host ( S , S )- 4 bearing phenyl arms was observed, which corresponds to an enantiomeric discrimination of approximately 94%. Molecular dynamic calculations were performed for some of the supramolecular complexes to in order to gain insight into the mode of molecular recognition between the macrocyclic compounds and ammonium salts; these results were consistent with experimental observations, which may be relevant to those in biochemical processes occurring in organisms.
ABSTRACT The synthesis of four diaza-18-crown-6 ethers with C2-symmetry derived from trans-(R,R)-... more ABSTRACT The synthesis of four diaza-18-crown-6 ethers with C2-symmetry derived from trans-(R,R)-1,2-diaminocyclohexane bearing methyl, phenyl and phenoxymethyl moeities attached to a stereogenic centre on the crown ring were achieved. Enantiomeric discrimination of these macrocycles against amino acid methyl ester salts was examined by 1H NMR titration method. They exhibit strong binding ability and some of them show a very high enantioselectivity towards amino acid esters, corresponding to 5.37 kJ/mol of binding energy difference in CDCl3 at 25 °C. Computational modelling showed parallel results with experimental calculations, thus providing a detailed understanding of molecular recognition mode and binding sites between the hosts and the guests.
A full-length model of integrase (IN) of the human immunodeficiency virus type 1 (HIV-1) was cons... more A full-length model of integrase (IN) of the human immunodeficiency virus type 1 (HIV-1) was constructed based on the distinctly resolved X-ray crystal structures of its three domains, named N-terminal, catalytic core and C-terminal. Thirty-one already known inhibitors with varieties of structural differences as well as nine newly tested ones were docked into the catalytic core. The molecular dynamic (MD) and binding properties of these complexes were obtained by MD calculations. The binding energies calculated by molecular mechanic/Poisson Boltzmann solvation area were significantly correlationed with available IC50. Four inhibitors including two newly designed were also docked into the full-length model and their MD behaviors and binding properties were calculated. It was found that one of the newly designed compounds forms a better complex with HIV-1 IN compared to the rest including raltegravir. MD calculations were performed with AMBER suite of programs using ff99SB force field for the proteins and the general Amber force field for the ligands. In conclusion, the results have produced a promising standpoint not only in the construction of the full-length model but also in development of new drugs against it. However, the role of multimer formation and the involvement of DNAs, and their subsequent effect on the complexation and inhibition, are required to arrive at a conclusive decision.
The acid-catalysed solvolysis reaction of 9-methoxy-9-methyl-9, 10-dihydroanthracene (2-OMe) in 5... more The acid-catalysed solvolysis reaction of 9-methoxy-9-methyl-9, 10-dihydroanthracene (2-OMe) in 50 vol% acetonitrile in water at 25 C provides the substitution product 9-hydroxy-9-methyl-9, 10-dihydroanthracene (2-OH) and the elimination product 9-methylanthracene ( ...
The kinetics of hydrolysis of substituted monobenzoate esters of 4-tert-butylcalix [4] arene in 5... more The kinetics of hydrolysis of substituted monobenzoate esters of 4-tert-butylcalix [4] arene in 50%(v/v) ethanolwater solvent (at 25 C) obey pseudo-first-order kinetics which fit the rate law, k obs=(k 1 K w/K′ a+ k 2 [OH])[OH]/(K w/K′ a+[OH]) where k 1 and k 2 correspond ...
Page 1. Received: 8 October 2007, Revised: 3 March 2008, Accepted: 5 March 2008, Published online... more Page 1. Received: 8 October 2007, Revised: 3 March 2008, Accepted: 5 March 2008, Published online in Wiley InterScience: 2008 A study on a primitive artificial esterase model: reactivity of a calix[4]resorcinarene bearing carboxyl groups ...
Org. Biomol. Chem., 2007, 5, 4001-4009 DOI:10.1039/B711538E (Paper). Experimental and computation... more Org. Biomol. Chem., 2007, 5, 4001-4009 DOI:10.1039/B711538E (Paper). Experimental and computational evidence for α-lactone intermediates in the addition of aqueous bromine to disodium dimethyl-maleate and -fumarate. ...
The bimolecular rate constants for reaction of imidazole with phenyl acetates complexed with sodi... more The bimolecular rate constants for reaction of imidazole with phenyl acetates complexed with sodium dodecyl sulfate (SDS) or cetyltrimethylammonium bromide (CTAB) micelles obey Brønsted equations with βlg similar to that of the reaction in aqueous solution. The ...
Campylobacter jejuni is an important cause of human foodborne gastroenteritis; strategies to prev... more Campylobacter jejuni is an important cause of human foodborne gastroenteritis; strategies to prevent infection are hampered by a poor understanding of the complex interactions between host and pathogen. Previous work showed that C. jejuni could bind human histo-blood group antigens (BgAgs) in vitro and that BgAgs could inhibit the binding of C. jejuni to human intestinal mucosa ex vivo. Here, the major flagella subunit protein (FlaA) and the major outer membrane protein (MOMP) were identified as BgAg-binding adhesins in C. jejuni NCTC11168. Significantly, the MOMP was shown to be O-glycosylated at Thr(268); previously only flagellin proteins were known to be O-glycosylated in C. jejuni. Substitution of MOMP Thr(268) led to significantly reduced binding to BgAgs. The O-glycan moiety was characterized as Gal(β1-3)-GalNAc(β1-4)-GalNAc(β1-4)-GalNAcα1-Thr(268); modelling suggested that O-glycosylation has a notable effect on the conformation of MOMP and this modulates BgAg-binding capaci...
The activation barriers for internal rotation around the C-N bond in p-substituted nitrosobenzene... more The activation barriers for internal rotation around the C-N bond in p-substituted nitrosobenzenes were calculated using the density functional theory (DFT) and second-order Moller-Plesset (MP2) methods with the 6-31+g(d) basis set. The polarisable continuum model (PCM) was used to model the solvent effect. An explicit water molecule was also introduced to form a hydrogen bond with the nitrosogroup and its effect on the barrier was studied by DFT. The barriers were well-correlated with Hammett sigma+ rather than sigma values, meaning a strong resonance effect. The MP2 method produces better and comparable results with the few available experimental values.
The emerged Coronavirus disease (COVID-19) causes severe or even fatal respiratory tract infectio... more The emerged Coronavirus disease (COVID-19) causes severe or even fatal respiratory tract infection, and to date there is no FDA-approved therapeutics or effective treatment available to effectively combat this viral infection. This urgent situation is an attractive research area in the field of drug design and development. One of the most important targets of SARS-coronavirus-2 (SARS Cov-2) is the main protease (3CLpro). Actinomycetes are important resources for drug discovery. The angucylines that are mainly produced by Streptomyces genus of actinomycetes exhibit a broad range of biological activities such as anticancer, antibacterial and antiviral. This study aims to investigate the binding affinity and molecular interactions of 157 available angucycline compounds with 3CLpro using docking and molecular dynamics simulations. MM-PBSA calculations showed that moromycin A has a better binding energy (− 30.42 kcal mol−1) compared with other ligands (in a range of − 18.66 to − 22.89 kc...
A rhizosphere isolate Streptomyces sp. CAH29 was found to possess potent antibacterial and antifu... more A rhizosphere isolate Streptomyces sp. CAH29 was found to possess potent antibacterial and antifungal activity against a variety of test organisms. Based on 16S ribosomal ribonucleic acid sequence homology studies, this strain was found to be similar to Streptomyces stramineus (gene sequence similarity 99 %). The major bioactive metabolite produced by Streptomyces sp. CAH29 isolate was extracted, purified andidentified by nuclear magnetic resonance as tetrangomycin. This known anthraquinone-exhibited antimicrobial activity against Staphylococcus aureus, Streptococcus pyogenes, methicillin resistant Staphylococcus aureus and Candida albicans with inhibition zones of 14, 10, 12 and 8 mm, respectively. Docking results demonstrate that tetrangomycin has a similar mode of action and a comparable docking score to bind to the dehydrosqualene synthase (CrtM) enzyme of methicillin resistant Staphylococcus aureus compared to the current inhibitor. Hence, this suggests that tetrangomycin has a potential to be used as an anti-methicillin resistant Staphylococcus aureus agent. Tetrangomycin also showed moderate free radical scavenging activity with 1,1-diphenyl-2-picryl-hydrazil. Tetrangomycin apparently decreased all of the studied cytokine (pro-inflammatory: interleukin 1B, interleukin 2, tumor necrosis factor and interleukin L6 and anti-inflammatory: interleukin 10) expression levels at IC50 concentrations in A459 (adenocarcinomic human alveolar basal epithelial) and LNCAP (human prostate adenocarcinoma) cell lines. In addition, it reduced Caspase 8 and 3 mRNA levels in LNCAP and A549 cells. This study describes for the first time novel in vitro immunosuppressive function of tetrangomycin by reducing the transcription of cytokine genes.
Abstract The enantioselective reduction of prochiral ketones with borane in the presence of a chi... more Abstract The enantioselective reduction of prochiral ketones with borane in the presence of a chiral ligand has received considerable attention. Hydroxylamine-based chiral ligands with amide and hydroxyl functions in the presence of other co-ordinating groups are highly effective in these asymmetric reductions. The current work presents a simple one step synthesis of a series of β-hydroxyamide-based ligands from the reaction between 3-hydroxy-2-naphthoic acid and chiral amino alcohols and their applications as catalysts in asymmetric borane-mediated reductions of aromatic prochiral ketones in THF. The reductions provided the corresponding secondary alcohols with up to 96% ee and in good to excellent yields (89–99%). DFT calculations at B3LYP/6-31+g(d) level offered theoretical models to account for the enantioselectivity imposed by the chiral ligands in the reductions of the ketones.
The work involves an experimental ((1)H NMR) and theoretical (MD, MM-PBSA and DFT) investigation ... more The work involves an experimental ((1)H NMR) and theoretical (MD, MM-PBSA and DFT) investigation of the molecular recognition and discrimination properties of a chiral aza-15-crown-5 against methyl esters of alanine, phenylalanine and valine hydrochloride salts. The results indicate that the receptor binds enantiomers with moderate binding constants (88-1,389 M(-1)), with phenylalanine being more discriminated. The difference in experimental binding free energies (ΔG (R) - ΔG (S)) for alanine, phenylalanine and valine enantiomers were calculated as -0.36, -1.58 and 0.80 kcal mol(-1), respectively. The differences in theoretical binding energies were calculated by MM-PBSA (ΔE (R) PB - ΔE (S) PB=) as -0.30, -1.45 and 0.88, by B3LYP/6-31+G(d) as -1.17, -0.84 and 0.74 and by M06-2X/6-31+G(d) as -1.40, -3.26 and 1.66 kcal mol(-1). The data obtained give valuable information regarding the molecular recognition mode of the organoammonium complexes of chiral aza-crown ether with C 1 symmetry, which may be relevant to biological systems.
The non-integrin laminin receptor (LAMR1/RPSA) and galectin-3 (Gal-3) are multi-functional host m... more The non-integrin laminin receptor (LAMR1/RPSA) and galectin-3 (Gal-3) are multi-functional host molecules with roles in diverse pathological processes, particularly of infectious or oncogenic origins. Using bimolecular fluorescence complementation and confocal imaging, we demonstrate that the two proteins homo- and heterodimerize, and that each isotype forms a distinct cell surface population. We present evidence that the 37 kDa form of LAMR1 (37LRP) is the precursor of the previously described 67 kDa laminin receptor (67LR), whereas the heterodimer represents an entity that is distinct from this molecule. Site-directed mutagenesis confirmed that the single cysteine (C 173 ) of Gal-3 or lysine (K 166 ) of LAMR1 are critical for heterodimerization. Recombinant Gal-3, expressed in normally Gal-3-deficient N2a cells, dimerized with endogenous LAMR1 and led to a significantly increased number of internalized bacteria ( Neisseria meningitidis ), confirming the role of Gal-3 in bacterial ...
Abstract Four novel C 2 -symmetric macrocyclic compounds with a pyridine function and possessing ... more Abstract Four novel C 2 -symmetric macrocyclic compounds with a pyridine function and possessing amide and ester lingeages were prepared. The enantiomeric discrimination abilities of these macrocycles against α-phenylethylammonium and α-(1-naphthyl)ethylammonium perchlorate salts were measured by standard 1 H NMR titration techniques in DMSO- d 6 . A binding constant ratio of 31 (Kbind(S)/Kbind(R)) for two enantiomers of α-(1-naphthyl)ethylammonium salt with the macrocyclic host ( S , S )- 4 bearing phenyl arms was observed, which corresponds to an enantiomeric discrimination of approximately 94%. Molecular dynamic calculations were performed for some of the supramolecular complexes to in order to gain insight into the mode of molecular recognition between the macrocyclic compounds and ammonium salts; these results were consistent with experimental observations, which may be relevant to those in biochemical processes occurring in organisms.
ABSTRACT The synthesis of four diaza-18-crown-6 ethers with C2-symmetry derived from trans-(R,R)-... more ABSTRACT The synthesis of four diaza-18-crown-6 ethers with C2-symmetry derived from trans-(R,R)-1,2-diaminocyclohexane bearing methyl, phenyl and phenoxymethyl moeities attached to a stereogenic centre on the crown ring were achieved. Enantiomeric discrimination of these macrocycles against amino acid methyl ester salts was examined by 1H NMR titration method. They exhibit strong binding ability and some of them show a very high enantioselectivity towards amino acid esters, corresponding to 5.37 kJ/mol of binding energy difference in CDCl3 at 25 °C. Computational modelling showed parallel results with experimental calculations, thus providing a detailed understanding of molecular recognition mode and binding sites between the hosts and the guests.
A full-length model of integrase (IN) of the human immunodeficiency virus type 1 (HIV-1) was cons... more A full-length model of integrase (IN) of the human immunodeficiency virus type 1 (HIV-1) was constructed based on the distinctly resolved X-ray crystal structures of its three domains, named N-terminal, catalytic core and C-terminal. Thirty-one already known inhibitors with varieties of structural differences as well as nine newly tested ones were docked into the catalytic core. The molecular dynamic (MD) and binding properties of these complexes were obtained by MD calculations. The binding energies calculated by molecular mechanic/Poisson Boltzmann solvation area were significantly correlationed with available IC50. Four inhibitors including two newly designed were also docked into the full-length model and their MD behaviors and binding properties were calculated. It was found that one of the newly designed compounds forms a better complex with HIV-1 IN compared to the rest including raltegravir. MD calculations were performed with AMBER suite of programs using ff99SB force field for the proteins and the general Amber force field for the ligands. In conclusion, the results have produced a promising standpoint not only in the construction of the full-length model but also in development of new drugs against it. However, the role of multimer formation and the involvement of DNAs, and their subsequent effect on the complexation and inhibition, are required to arrive at a conclusive decision.
The acid-catalysed solvolysis reaction of 9-methoxy-9-methyl-9, 10-dihydroanthracene (2-OMe) in 5... more The acid-catalysed solvolysis reaction of 9-methoxy-9-methyl-9, 10-dihydroanthracene (2-OMe) in 50 vol% acetonitrile in water at 25 C provides the substitution product 9-hydroxy-9-methyl-9, 10-dihydroanthracene (2-OH) and the elimination product 9-methylanthracene ( ...
The kinetics of hydrolysis of substituted monobenzoate esters of 4-tert-butylcalix [4] arene in 5... more The kinetics of hydrolysis of substituted monobenzoate esters of 4-tert-butylcalix [4] arene in 50%(v/v) ethanolwater solvent (at 25 C) obey pseudo-first-order kinetics which fit the rate law, k obs=(k 1 K w/K′ a+ k 2 [OH])[OH]/(K w/K′ a+[OH]) where k 1 and k 2 correspond ...
Page 1. Received: 8 October 2007, Revised: 3 March 2008, Accepted: 5 March 2008, Published online... more Page 1. Received: 8 October 2007, Revised: 3 March 2008, Accepted: 5 March 2008, Published online in Wiley InterScience: 2008 A study on a primitive artificial esterase model: reactivity of a calix[4]resorcinarene bearing carboxyl groups ...
Org. Biomol. Chem., 2007, 5, 4001-4009 DOI:10.1039/B711538E (Paper). Experimental and computation... more Org. Biomol. Chem., 2007, 5, 4001-4009 DOI:10.1039/B711538E (Paper). Experimental and computational evidence for α-lactone intermediates in the addition of aqueous bromine to disodium dimethyl-maleate and -fumarate. ...
The bimolecular rate constants for reaction of imidazole with phenyl acetates complexed with sodi... more The bimolecular rate constants for reaction of imidazole with phenyl acetates complexed with sodium dodecyl sulfate (SDS) or cetyltrimethylammonium bromide (CTAB) micelles obey Brønsted equations with βlg similar to that of the reaction in aqueous solution. The ...
Uploads