Displaying publications 1 - 20 of 354 in total

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  1. Fulltext Mutation-specific pathophysiological mechanisms define different neurodevelopmental disorders associated with SATB1 dysfunction
    den Hoed J, de Boer E, Voisin N, Dingemans AJM, Guex N, Wiel L, et al.
    Am J Hum Genet, 2021 02 04;108(2):346-356.
    PMID: 33513338 DOI: 10.1016/j.ajhg.2021.01.007
    Whereas large-scale statistical analyses can robustly identify disease-gene relationships, they do not accurately capture genotype-phenotype correlations or disease mechanisms. We use multiple lines of independent evidence to show that different variant types in a single gene, SATB1, cause clinically overlapping but distinct neurodevelopmental disorders. Clinical evaluation of 42 individuals carrying SATB1 variants identified overt genotype-phenotype relationships, associated with different pathophysiological mechanisms, established by functional assays. Missense variants in the CUT1 and CUT2 DNA-binding domains result in stronger chromatin binding, increased transcriptional repression, and a severe phenotype. In contrast, variants predicted to result in haploinsufficiency are associated with a milder clinical presentation. A similarly mild phenotype is observed for individuals with premature protein truncating variants that escape nonsense-mediated decay, which are transcriptionally active but mislocalized in the cell. Our results suggest that in-depth mutation-specific genotype-phenotype studies are essential to capture full disease complexity and to explain phenotypic variability.
    Matched MeSH terms: Models, Molecular
  2. Fulltext Large-scale 3D chromatin reconstruction from chromosomal contacts
    Zhang Y, Liu W, Lin Y, Ng YK, Li S
    BMC Genomics, 2019 Apr 04;20(Suppl 2):186.
    PMID: 30967119 DOI: 10.1186/s12864-019-5470-2
    BACKGROUND: Recent advances in genome analysis have established that chromatin has preferred 3D conformations, which bring distant loci into contact. Identifying these contacts is important for us to understand possible interactions between these loci. This has motivated the creation of the Hi-C technology, which detects long-range chromosomal interactions. Distance geometry-based algorithms, such as ChromSDE and ShRec3D, have been able to utilize Hi-C data to infer 3D chromosomal structures. However, these algorithms, being matrix-based, are space- and time-consuming on very large datasets. A human genome of 100 kilobase resolution would involve ∼30,000 loci, requiring gigabytes just in storing the matrices.

    RESULTS: We propose a succinct representation of the distance matrices which tremendously reduces the space requirement. We give a complete solution, called SuperRec, for the inference of chromosomal structures from Hi-C data, through iterative solving the large-scale weighted multidimensional scaling problem.

    CONCLUSIONS: SuperRec runs faster than earlier systems without compromising on result accuracy. The SuperRec package can be obtained from http://www.cs.cityu.edu.hk/~shuaicli/SuperRec .

    Matched MeSH terms: Models, Molecular
  3. Phenolic components and assessment of biological properties of Tchihatchewia isatidea Boiss. extracts: Docking and functional approaches for designing novel products
    Zengin G, Abdallah HH, Dogan A, Mollica A, Aumeeruddy-Elalfi Z, Mahomoodally MF
    Food Chem Toxicol, 2018 Jan;111:423-431.
    PMID: 29198858 DOI: 10.1016/j.fct.2017.11.055
    The potentiality of bioactive phenolic compounds may result in plant extracts having multiple biological activities. The aim of this study was to investigate into the biological activities of the methanolic, ethyl acetate, and water extracts of Tchihatchewia isatidea Boiss, an endemic medicinal plant of Turkey. The phenolic compositions of the extracts were confirmed using RP-HPLC. Extracts were screened for their potential antioxidant through a panoply of assays; their anti-diabetic potential, and plausible inhibitory activity against tyrosinase and acetylcholinesterase. Molecular modelling methods were also used to assess the docking properties of phenolic compounds on tyrosinase. The major and most abundant compounds were rosmarinic acid (570 ± 14 μg/g extract in the methanolic extract), ferrulic acid (336 ± 6 μg/g extract in the methanolic extract), (+)-catechin (340 ± 4 μg/g extract in the water extract), apigenin (182 ± 4 μg/g extract in the methanolic extract), and epicatechin (188 ± 12 μg/g extract in the water extract). Radical scavenging, reducing capacity, and metal chelating activities were detected in the extracts, with preponderance activity observed in the methanolic extract. In conclusion, the potential clinical applications observed during this study may provide new insights into the molecular aspect particularly for neuroprotective and anti-diabetic mechanisms involving oxidative stress.
    Matched MeSH terms: Models, Molecular
  4. Fulltext Angiotensin Converting Enzyme (ACE)-Peptide Interactions: Inhibition Kinetics, In Silico Molecular Docking and Stability Study of Three Novel Peptides Generated from Palm Kernel Cake Proteins
    Zarei M, Abidin NBZ, Auwal SM, Chay SY, Haiyee ZA, Sikin AM, et al.
    Biomolecules, 2019 10 04;9(10).
    PMID: 31590308 DOI: 10.3390/biom9100569
    Three novel peptide sequences identified from palm kernel cake (PKC) generated protein hydrolysate including YLLLK, WAFS and GVQEGAGHYALL were used for stability study against angiotensin-converting enzyme (ACE), ACE-inhibition kinetics and molecular docking studies. Results showed that the peptides were degraded at different cleavage degrees of 94%, 67% and 97% for YLLLK, WAFS and GVQEGAGHYALL, respectively, after 3 h of incubation with ACE. YLLLK was found to be the least stable (decreased ACE-inhibitory activity) compared to WAFS and GVQEGAGHYALL (increased ACE-inhibitory activity). YLLLK showed the lowest Ki (1.51 mM) in inhibition kinetics study when compared to WAFS and GVQEGAGHYALL with Ki of 2 mM and 3.18 mM, respectively. In addition, ACE revealed the lowest Kmapp and Vmaxapp and higher catalytic efficiency (CE) in the presence of YLLLK at different concentrations, implying that the enzyme catalysis decreased and hence the inhibition mode increased. Furthermore, YLLLK showed the lowest docking score of -8.224 and seven interactions with tACE, while peptide GVQEGAGHYALL showed the higher docking score of -7.006 and five interactions with tACE.
    Matched MeSH terms: Models, Molecular
  5. Fulltext Nucleoside Analogs with Selective Antiviral Activity against Dengue Fever and Japanese Encephalitis Viruses
    Zandi K, Bassit L, Amblard F, Cox BD, Hassandarvish P, Moghaddam E, et al.
    Antimicrob Agents Chemother, 2019 Jul;63(7).
    PMID: 31061163 DOI: 10.1128/AAC.00397-19
    Dengue virus (DENV) and Japanese encephalitis virus (JEV) are important arthropod-borne viruses from the Flaviviridae family. DENV is a global public health problem with significant social and economic impacts, especially in tropical and subtropical areas. JEV is a neurotropic arbovirus endemic to east and southeast Asia. There are no U.S. FDA-approved antiviral drugs available to treat or to prevent DENV and JEV infections, leaving nearly one-third of the world's population at risk for infection. Therefore, it is crucial to discover potent antiviral agents against these viruses. Nucleoside analogs, as a class, are widely used for the treatment of viral infections. In this study, we discovered nucleoside analogs that possess potent and selective anti-JEV and anti-DENV activities across all serotypes in cell-based assay systems. Both viruses were susceptible to sugar-substituted 2'-C-methyl analogs with either cytosine or 7-deaza-7-fluoro-adenine nucleobases. Mouse studies confirmed the anti-DENV activity of these nucleoside analogs. Molecular models were assembled for DENV serotype 2 (DENV-2) and JEV RNA-dependent RNA polymerase replication complexes bound to nucleotide inhibitors. These models show similarities between JEV and DENV-2, which recognize the same nucleotide inhibitors. Collectively, our findings provide promising compounds and a structural rationale for the development of direct-acting antiviral agents with dual activity against JEV and DENV infections.
    Matched MeSH terms: Models, Molecular
  6. Fulltext The effect of laser repetition rate on the LASiS synthesis of biocompatible silver nanoparticles in aqueous starch solution
    Zamiri R, Zakaria A, Ahangar HA, Darroudi M, Zamiri G, Rizwan Z, et al.
    Int J Nanomedicine, 2013;8:233-44.
    PMID: 23345971 DOI: 10.2147/IJN.S36036
    Laser ablation-based nanoparticle synthesis in solution is rapidly becoming popular, particularly for potential biomedical and life science applications. This method promises one pot synthesis and concomitant bio-functionalization, is devoid of toxic chemicals, does not require complicated apparatus, can be combined with natural stabilizers, is directly biocompatible, and has high particle size uniformity. Size control and reduction is generally determined by the laser settings; that the size and size distribution scales with laser fluence is well described. Conversely, the effect of the laser repetition rate on the final nanoparticle product in laser ablation is less well-documented, especially in the presence of stabilizers. Here, the influence of the laser repetition rate during laser ablation synthesis of silver nanoparticles in the presence of starch as a stabilizer was investigated. The increment of the repetition rate does not negatively influence the ablation efficiency, but rather shows increased productivity, causes a red-shift in the plasmon resonance peak of the silver-starch nanoparticles, an increase in mean particle size and size distribution, and a distinct lack of agglomerate formation. Optimal results were achieved at 10 Hz repetition rate, with a mean particle size of ~10 nm and a bandwidth of ~6 nm 'full width at half maximum' (FWHM). Stability measurements showed no significant changes in mean particle size or agglomeration or even flocculation. However, zeta potential measurements showed that optimal double layer charge is achieved at 30 Hz. Consequently, Ag-NP synthesis via the laser ablation synthesis in solution (LASiS) method in starch solution seems to be a trade-off between small size and narrow size distributions and inherent and long-term stability.
    Matched MeSH terms: Models, Molecular
  7. Fulltext Formulation optimization of a palm-based nanoemulsion system containing levodopa
    Zainol S, Basri M, Basri HB, Shamsuddin AF, Abdul-Gani SS, Karjiban RA, et al.
    Int J Mol Sci, 2012;13(10):13049-64.
    PMID: 23202937 DOI: 10.3390/ijms131013049
    Response surface methodology (RSM) was utilized to investigate the influence of the main emulsion composition; mixture of palm and medium-chain triglyceride (MCT) oil (6%-12% w/w), lecithin (1%-3% w/w), and Cremophor EL (0.5%-1.5% w/w) as well as the preparation method; addition rate (2-20 mL/min), on the physicochemical properties of palm-based nanoemulsions. The response variables were the three main emulsion properties; particle size, zeta potential and polydispersity index. Optimization of the four independent variables was carried out to obtain an optimum level palm-based nanoemulsion with desirable characteristics. The response surface analysis showed that the variation in the three responses could be depicted as a quadratic function of the main composition of the emulsion and the preparation method. The experimental data could be fitted sufficiently well into a second-order polynomial model. The optimized formulation was stable for six months at 4 °C.
    Matched MeSH terms: Models, Molecular
  8. Structurally conserved binding sites of hemagglutinin as targets for influenza drug and vaccine development
    Yusuf M, Konc J, Sy Bing C, Trykowska Konc J, Ahmad Khairudin NB, Janezic D, et al.
    J Chem Inf Model, 2013 Sep 23;53(9):2423-36.
    PMID: 23980878 DOI: 10.1021/ci400421e
    ProBiS is a new method to identify the binding site of protein through local structural alignment against the nonredundant Protein Data Bank (PDB), which may result in unique findings compared to the energy-based, geometry-based, and sequence-based predictors. In this work, binding sites of Hemagglutinin (HA), which is an important target for drugs and vaccines in influenza treatment, have been revisited by ProBiS. For the first time, the identification of conserved binding sites by local structural alignment across all subtypes and strains of HA available in PDB is presented. ProBiS finds three distinctive conserved sites on HA's structure (named Site 1, Site 2, and Site 3). Compared to other predictors, ProBiS is the only one that accurately defines the receptor binding site (Site 1). Apart from that, Site 2, which is located slightly above the TBHQ binding site, is proposed as a potential novel conserved target for membrane fusion inhibitor. Lastly, Site 3, located around Helix A at the stem domain and recently targeted by cross-reactive antibodies, is predicted to be conserved in the latest H7N9 China 2013 strain as well. The further exploration of these three sites provides valuable insight in optimizing the influenza drug and vaccine development.
    Matched MeSH terms: Models, Molecular
  9. Fulltext Structural and functional insights into TRiC chaperonin from a psychrophilic yeast, Glaciozyma antarctica
    Yusof NA, Kamaruddin S, Abu Bakar FD, Mahadi NM, Abdul Murad AM
    Cell Stress Chaperones, 2019 Mar;24(2):351-368.
    PMID: 30649671 DOI: 10.1007/s12192-019-00969-1
    Studies on TCP1-1 ring complex (TRiC) chaperonin have shown its indispensable role in folding cytosolic proteins in eukaryotes. In a psychrophilic organism, extreme cold temperature creates a low-energy environment that potentially causes protein denaturation with loss of activity. We hypothesized that TRiC may undergo evolution in terms of its structural molecular adaptation in order to facilitate protein folding in low-energy environment. To test this hypothesis, we isolated G. antarctica TRiC (GaTRiC) and found that the expression of GaTRiC mRNA in G. antarctica was consistently expressed at all temperatures indicating their importance in cell regulation. Moreover, we showed GaTRiC has the ability of a chaperonin whereby denatured luciferase can be folded to the functional stage in its presence. Structurally, three categories of residue substitutions were found in α, β, and δ subunits: (i) bulky/polar side chains to alanine or valine, (ii) charged residues to alanine, and (iii) isoleucine to valine that would be expected to increase intramolecular flexibility within the GaTRiC. The residue substitutions observed in the built structures possibly affect the hydrophobic, hydrogen bonds, and ionic and aromatic interactions which lead to an increase in structural flexibility. Our structural and functional analysis explains some possible structural features which may contribute to cold adaptation of the psychrophilic TRiC folding chamber.
    Matched MeSH terms: Models, Molecular
  10. Fulltext Thermotolerance and molecular chaperone function of an SGT1-like protein from the psychrophilic yeast, Glaciozyma antarctica
    Yusof NA, Hashim NH, Beddoe T, Mahadi NM, Illias RM, Bakar FD, et al.
    Cell Stress Chaperones, 2016 Jul;21(4):707-15.
    PMID: 27154490 DOI: 10.1007/s12192-016-0696-2
    The ability of eukaryotes to adapt to an extreme range of temperatures is critically important for survival. Although adaptation to extreme high temperatures is well understood, reflecting the action of molecular chaperones, it is unclear whether these molecules play a role in survival at extremely low temperatures. The recent genome sequencing of the yeast Glaciozyma antarctica, isolated from Antarctic sea ice near Casey Station, provides an opportunity to investigate the role of molecular chaperones in adaptation to cold temperatures. We isolated a G. antarctica homologue of small heat shock protein 20 (HSP20), GaSGT1, and observed that the GaSGT1 mRNA expression in G. antarctica was markedly increased following culture exposure at low temperatures. Additionally, we demonstrated that GaSGT1 overexpression in Escherichia coli protected these bacteria from exposure to both high and low temperatures, which are lethal for growth. The recombinant GaSGT1 retained up to 60 % of its native luciferase activity after exposure to luciferase-denaturing temperatures. These results suggest that GaSGT1 promotes cell thermotolerance and employs molecular chaperone-like activity toward temperature assaults.
    Matched MeSH terms: Models, Molecular
  11. A 35 kDa antigenic protein from Shigella flexneri: in silico structural and functional studies
    Yung-Hung RL, Ismail A, Lim TS, Choong YS
    Biochem Biophys Res Commun, 2011 Nov 18;415(2):229-34.
    PMID: 21982766 DOI: 10.1016/j.bbrc.2011.09.116
    Shigella flexneri serotype 2a is a major public health concern in the developing and under-developed countries which contributes to shigellosis endemic and mortality. Thus, there is an urgent need for a rapid diagnostic test for effective therapy and disease management. Previous study showed that a ∼35 kDa antigenic protein from S. flexneri is a potential biomarker. We therefore modelled the three-dimensional structure of the antigen to probe its functionality which could aid in the development of an antigen-based diagnostic. Results showed that the antigen is a transmembrane protein consists of OmpA and OmpA-like domains. The OmpA domain is a beta-barrel embedded in the outer membrane with four surface-exposed extracellular loops. The OmpA-like domain is linked to the OmpA domain with a 17 amino acids linker and located in the periplasmic. Docking of peptidoglycan into the groove of OmpA-like domain might help in catalyzing the bacterial cell wall formation. Both domains are expected to be involved in the virulence, structural stability, pathogenesis and survival of Shigella thus made the 35 kDa protein a suitable shigellosis diagnostic biomarker. This structural elucidation will also enable a better identification of the epitope regions for the development of specific binders to the 35 kDa antigen.
    Matched MeSH terms: Models, Molecular
  12. Binding specificity of polypeptide substrates in NS2B/NS3pro serine protease of dengue virus type 2: A molecular dynamics Study
    Yotmanee P, Rungrotmongkol T, Wichapong K, Choi SB, Wahab HA, Kungwan N, et al.
    J Mol Graph Model, 2015 Jul;60:24-33.
    PMID: 26086900 DOI: 10.1016/j.jmgm.2015.05.008
    The pathogenic dengue virus (DV) is a growing global threat, particularly in South East Asia, for which there is no specific treatment available. The virus possesses a two-component (NS2B/NS3) serine protease that cleaves the viral precursor proteins. Here, we performed molecular dynamics simulations of the NS2B/NS3 protease complexes with six peptide substrates (capsid, intNS3, 2A/2B, 4B/5, 3/4A and 2B/3 containing the proteolytic site between P(1) and P(1)' subsites) of DV type 2 to compare the specificity of the protein-substrate binding recognition. Although all substrates were in the active conformation for cleavage reaction by NS2B/NS3 protease, their binding strength was somewhat different. The simulated results of intermolecular hydrogen bonds and decomposition energies suggested that among the ten substrate residues (P(5)-P(5)') the P(1) and P(2) subsites play a major role in the binding with the focused protease. The arginine residue at these two subsites was found to be specific preferential binding at the active site with a stabilization energy of intNS3>2A/2B>4B/5>3/4A>2B/3 in a relative correspondence with previous experimentally derived values.
    Matched MeSH terms: Models, Molecular
  13. Synthesis and evaluation of novel benzimidazole derivatives as sirtuin inhibitors with antitumor activities
    Yoon YK, Ali MA, Wei AC, Choon TS, Osman H, Parang K, et al.
    Bioorg Med Chem, 2014 Jan 15;22(2):703-10.
    PMID: 24387981 DOI: 10.1016/j.bmc.2013.12.029
    A total of 15 novel benzimidazole derivatives were designed, synthesized and evaluated for their SIRT1 and SIRT2 inhibitory activity. All compounds showed better inhibition on SIRT2 as compared to SIRT1. Among these, compound 5j displayed the best inhibitory activity for SIRT1 (IC50=58.43μM) as well as for SIRT2 (IC50=45.12μM). Cell cytotoxicity assays also showed that compound 5j possesses good antitumor activity against two different cancer cell lines derived from breast cancer (MCF-7 and MDA-MB-468). A simple structure-activity-relationship (SAR) study of the newly synthesized benzimidazole derivatives was also discussed.
    Matched MeSH terms: Models, Molecular
  14. The influence of R substituents in triphenylphosphinegold(I) carbonimidothioates, Ph3PAu[SC(OR)=NPh] (R=Me, Et and iPr), upon in vitro cytotoxicity against the HT-29 colon cancer cell line and upon apoptotic pathways
    Yeo CI, Ooi KK, Akim AM, Ang KP, Fairuz ZA, Halim SN, et al.
    J Inorg Biochem, 2013 Oct;127:24-38.
    PMID: 23850666 DOI: 10.1016/j.jinorgbio.2013.05.011
    The Ph3PAu[SC(OR)=NPh], R=Me (1), Et (2) and iPr (3), compounds are significantly cytotoxic to the HT-29 cancer cell line with 1 being the most active. Based on human apoptosis PCR-array analysis, caspase activities, DNA fragmentation, cell apoptotic assays, intracellular reactive oxygen species (ROS) measurements and human topoisomerase I inhibition, induction of apoptosis is demonstrated and both the extrinsic and intrinsic pathways of apoptosis have been shown to occur. Compound 1 activates the p73 gene, whereas each of 2 and 3 activates the p53 gene. An additional apoptotic mechanism is exhibited by 2, that is, via the JNK/MAP pathway.
    Matched MeSH terms: Models, Molecular
  15. Fulltext Comparative genomics of closely related Salmonella enterica serovar Typhi strains reveals genome dynamics and the acquisition of novel pathogenic elements
    Yap KP, Gan HM, Teh CS, Chai LC, Thong KL
    BMC Genomics, 2014;15:1007.
    PMID: 25412680 DOI: 10.1186/1471-2164-15-1007
    Typhoid fever is an infectious disease of global importance that is caused by Salmonella enterica subsp. enterica serovar Typhi (S. Typhi). This disease causes an estimated 200,000 deaths per year and remains a serious global health threat. S. Typhi is strictly a human pathogen, and some recovered individuals become long-term carriers who continue to shed the bacteria in their faeces, thus becoming main reservoirs of infection.
    Matched MeSH terms: Models, Molecular
  16. Homology modeling of the human 5-HT1A, 5-HT 2A, D1, and D2 receptors: model refinement with molecular dynamics simulations and docking evaluation
    Yap BK, Buckle MJ, Doughty SW
    J Mol Model, 2012 Aug;18(8):3639-55.
    PMID: 22354276 DOI: 10.1007/s00894-012-1368-5
    5-HT(1A) serotonin and D1 dopamine receptor agonists have been postulated to be able to improve negative and cognitive impairment symptoms of schizophrenia, while partial agonists and antagonists of the D2 and 5-HT(2A) receptors have been reported to be effective in reducing positive symptoms. There is therefore a need for well-defined homology models for the design of more selective antipsychotic agents, since no three-dimensional (3D) crystal structures of these receptors are currently available. In this study, homology models were built based on the high-resolution crystal structure of the β(2)-adrenergic receptor (2RH1) and further refined via molecular dynamics simulations in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer system with the GROMOS96 53A6 united atom force field. Docking evaluations with representative agonists and antagonists using AutoDock 4.2 revealed binding modes in agreement with experimentally determined site-directed mutagenesis data and significant correlations between the computed and experimental pK (i) values. The models are also able to distinguish between antipsychotic agents with different selectivities and binding affinities for the four receptors, as well as to differentiate active compounds from decoys. Hence, these human 5-HT(1A), 5-HT(2A), D1 and D2 receptor homology models are capable of predicting the activities of novel ligands, and can be used as 3D templates for antipsychotic drug design and discovery.
    Matched MeSH terms: Models, Molecular*
  17. Molecular insights into 14-membered macrolides using the MM-PBSA method
    Yam WK, Wahab HA
    J Chem Inf Model, 2009 Jun;49(6):1558-67.
    PMID: 19469526 DOI: 10.1021/ci8003495
    Erythromycin A and roxithromycin are clinically important macrolide antibiotics that selectively act on the bacterial 50S large ribosomal subunit to inhibit bacteria's protein elongation process by blocking the exit tunnel for the nascent peptide away from ribosome. The detailed molecular mechanism of macrolide binding is yet to be elucidated as it is currently known to the most general idea only. In this study, molecular dynamics (MD) simulation was employed to study their interaction at the molecular level, and the binding free energies for both systems were calculated using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. The calculated binding free energies for both systems were slightly overestimated compared to the experimental values, but individual energy terms enabled better understanding in the binding for both systems. Decomposition of results into residue basis was able to show the contribution of each residue at the binding pocket toward the binding affinity of macrolides and hence identified several key interacting residues that were in agreement with previous experimental and computational data. Results also indicated the contributions from van der Waals are more important and significant than electrostatic contribution in the binding of macrolides to the binding pocket. The findings from this study are expected to contribute to the understanding of a detailed mechanism of action in a quantitative matter and thus assisting in the development of a safer macrolide antibiotic.
    Matched MeSH terms: Models, Molecular*
  18. NCI in vitro and in silico anticancer screen, cell cycle pertubation and apoptosis-inducing potential of new acylated, benzylidene and isopropylidene derivatives of andrographolide
    Wong CC, Sagineedu SR, Sumon SH, Sidik SM, Phillips R, Lajis NH, et al.
    Environ Toxicol Pharmacol, 2014 Sep;38(2):489-501.
    PMID: 25168151 DOI: 10.1016/j.etap.2014.07.016
    Andrographolide (AGP) is the main bioactive constituent isolated from the traditional medicinal, Andrographis paniculata which contributes towards its various biological activities, including anticancer property. In this study, a series of new AGP derivatives were semi-synthesised and screened against the NCI in vitro 60 cell lines. From the screening results, we had identified SRS07 as the most potent AGP derivative, against breast and colon cancer cell lines. Subsequently, SRS07 was tested for its capability to induce cell cycle arrest and apoptosis in MCF-7 and HCT116 cancer cells. SRS07 effectively induced G1 cell cycle arrest in both cell lines and ultimately apoptosis by inducing DNA fragmentation in HCT116 cells. The apoptotic cell death induced by SRS07 was confirmed via FITC Annexin-V double staining. Western blot analysis of SRS07-treated HCT116 cells revealed that the compound induced apoptosis be activating caspase 8 which in turn cleaved Bid to t-Bid to initiate cell death cascade. Prediction of the possible mode of action of SRS07 by utilising NCI COMPARE analysis failed to reveal a distinct mechanism category. Hence, it is speculated that SRS07 possesses novel mechanism of action. In conclusion, SRS07 demonstrated superior in vitro anticancer profiles and emerged as a potential lead anticancer candidate.
    Matched MeSH terms: Models, Molecular
  19. Does cation break the cyano bond? A critical evaluation of nitrile-cation interaction
    Woi PM, Bakar MA, Rosli AN, Lee VS, Ahmad MR, Zain S, et al.
    J Mol Model, 2014 May;20(5):2219.
    PMID: 24770548 DOI: 10.1007/s00894-014-2219-3
    DFT and G4 results reveal that cations display the following trends in imparting its positive charge to acrylonitrile; H⁺ > Li⁺ > Na⁺ > K⁺ for group I and Be²⁺ > Mg²⁺ > Ca²⁺ for group II. Solvation by water molecules and interaction with cation make the cyano bond more polarized and exhibits ketene-imine character. Bond order in nitrile-cation complexes has been predicted based on the s character of the covalent bond orbitals. Mulliken, CHELPG, and NPA charges are in good agreement in predicting positive charge buildup and GIAO nuclear deshileding on C1. G4 enthalpies show that Mg²⁺ is more strongly bound to acrylonitrile than to acetonitrile by 3 kcal mol⁻¹, and the proton affinity of the former is higher by 0.8 kcal mol⁻¹. G4 enthalpies of reductions support prior experimental observation that metalated conjugated nitriles show enhanced reactivity toward weak nucleophiles to afford Michael addition products.
    Matched MeSH terms: Models, Molecular
  20. An antibacterial metabolite from Lasiodiplodia pseudotheobromae F2
    Wei W, Jiang N, Mei YN, Chu YL, Ge HM, Song YC, et al.
    Phytochemistry, 2014 Apr;100:103-9.
    PMID: 24529576 DOI: 10.1016/j.phytochem.2014.01.003
    In searching for symbionts derived from bioactive natural products, six sulfureous diketopiperazines designated as lasiodiplines A-F (1-6) were characterized from the culture of Lasiodiplodia pseudotheobromae F2, previously residing in the apparently normal flower of Illigera rhodantha (Hernandiaceae). Identification of structures was accomplished by a combination of spectroscopic and computational approaches, in conjunction with the low-temperature (100K) single-crystal X-ray diffraction with Cu Kα radiation. Lasiodipline E (5) was demonstrated to be antibacterial against the clinical strains Streptococcus sp., Bacteroides vulgates, Peptostreptococcus sp. and Veillonella parvula, respectively, with an minimum inhibitory concentration (MIC) range of 0.12-0.25 μg/mL. In addition, compounds 4 and 6 exemplify two unusual architectures of natural cyclodipeptides, signifying the unique biochemical characteristics of the producing fungus.
    Matched MeSH terms: Models, Molecular
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