Displaying publications 1 - 20 of 265 in total

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  1. Muniyandi RC, Zin AM
    Pak J Biol Sci, 2011 Dec 15;14(24):1100-8.
    PMID: 22335049
    Ligand-Receptor Networks of TGF-beta plays essential role in transmitting a wide range of extracellular signals that affect many cellular processes such as cell growth. However, the modeling of these networks with conventional approach such as ordinary differential equations has not taken into account, the spatial structure and stochastic behavior of processes involve in these networks. Membrane computing as the alternatives approach provides spatial structure for molecular computation in which processes are evaluated in a non-deterministic and maximally parallel way. This study is carried out to evaluate the membrane computing model of Ligand-Receptor Networks of TGF-beta with model checking approach. The results show that membrane computing model has sustained the behaviors and properties of Ligand-Receptor Networks of TGF-beta. This reinforce that membrane computing is capable in analyzing processes and behaviors in hierarchical structure of cell such as Ligand-Receptor Networks of TGF-beta better than the deterministic approach of conventional mathematical models.
    Matched MeSH terms: Ligands*
  2. Nokhala A, Siddiqui MJ, Ahmed QU, Ahamad Bustamam MS, Zakaria AZA
    Biomolecules, 2020 02 12;10(2).
    PMID: 32059529 DOI: 10.3390/biom10020287
    Stone leaf (Tetracera scandens) is a Southeast Asian medicinal plant that has been traditionally used for the management of diabetes mellitus. The underlying mechanisms of the antidiabetic activity have not been fully explored yet. Hence, this study aimed to evaluate the α-glucosidase inhibitory potential of the hydromethanolic extracts of T. scandens leaves and to characterize the metabolites responsible for such activity through gas chromatography-mass spectrometry (GC-MS) metabolomics. Crude hydromethanolic extracts of different strengths were prepared and in vitro assayed for α-glucosidase inhibition. GC-MS analysis was further carried out and the mass spectral data were correlated to the corresponding α-glucosidase inhibitory IC50 values via an orthogonal partial least squares (OPLS) model. The 100%, 80%, 60% and 40% methanol extracts displayed potent α-glucosidase inhibitory potentials. Moreover, the established model identified 16 metabolites to be responsible for the α-glucosidase inhibitory activity of T. scandens. The putative α-glucosidase inhibitory metabolites showed moderate to high affinities (binding energies of -5.9 to -9.8 kcal/mol) upon docking into the active site of Saccharomyces cerevisiae isomaltase. To sum up, an OPLS model was developed as a rapid method to characterize the α-glucosidase inhibitory metabolites existing in the hydromethanolic extracts of T. scandens leaves based on GC-MS metabolite profiling.
    Matched MeSH terms: Ligands
  3. Ramanujam P, Tan WS, Nathan S, Yusoff K
    Arch Virol, 2002 May;147(5):981-93.
    PMID: 12021868
    A disulfide constrained random heptapeptide library displayed on filamentous bacteriophage M13 was applied to select specific ligands that interact with Newcastle disease virus (NDV). A fusion phage carrying the amino acid sequence TLTTKLY was selected from the panning procedure. An antibody competition assay showed that the selected phage was capable of competing with the polyclonal antibodies raised against NDV for binding sites on the virus. Determination of the binding affinity of this phage with NDV by an equilibrium binding assay in solution revealed two different dissociation constants, suggesting that there could be two distinct binding sites for the phage on NDV. Synthetic peptides with the sequence CTLTTKLYC, either in linear or cyclic conformations inhibited the binding of phage bearing the same sequence to NDV. These peptides also inhibited the hemolytic activity of the virus as well as its propagation in embryonated chicken eggs.
    Matched MeSH terms: Ligands
  4. Wang H, Chen M, Sang X, You X, Wang Y, Paterson IC, et al.
    Eur J Med Chem, 2020 Apr 01;191:112154.
    PMID: 32092587 DOI: 10.1016/j.ejmech.2020.112154
    Transforming growth factor-β (TGF-β) is a member of a superfamily of pleiotropic proteins that regulate multiple cellular processes such as growth, development and differentiation. Following binding to type I and II TGF-β serine/threonine kinase receptors, TGF-β activates downstream signaling cascades involving both SMAD-dependent and -independent pathways. Aberrant TGF-β signaling is associated with a variety of diseases, such as fibrosis, cardiovascular disease and cancer. Hence, the TGF-β signaling pathway is recognized as a potential drug target. Various organic molecules have been designed and developed as TGF-β signaling pathway inhibitors and they function by either down-regulating the expression of TGF-β or by inhibiting the kinase activities of the TGF-β receptors. In this review, we discuss the current status of research regarding organic molecules as TGF-β inhibitors, focusing on the biological functions and the binding poses of compounds that are in the market or in the clinical or pre-clinical phases of development.
    Matched MeSH terms: Ligands
  5. Han H, Sabani NB, Nobusawa K, Takei F, Nakatani K, Yamashita I
    Anal Chem, 2023 Jul 04;95(26):9729-9733.
    PMID: 37341999 DOI: 10.1021/acs.analchem.3c01126
    We have developed a DNA sensor that can be finalized to detect a specific target on demand. The electrode surface was modified with 2,7-diamino-1,8-naphthyridine (DANP), a small molecule with nanomolar affinity for the cytosine bulge structure. The electrode was immersed in a solution of synthetic probe-DNA that had a cytosine bulge structure at one end and a complementary sequence to the target DNA at the other end. The strong binding between the cytosine bulge and DANP anchored the probe DNAs to the electrode surface, and the electrode became ready for target DNA sensing. The complementary sequence portion of the probe DNA can be changed as requested, allowing for the detection of a wide variety of targets. Electrochemical impedance spectroscopy (EIS) with the modified electrode detected target DNAs with a high sensitivity. The charge transfer resistance (Rct) extracted from EIS showed a logarithmic relationship with the concentration of target DNA. The limit of detection (LoD) was less than 0.01 μM. By this method, highly sensitive DNA sensors for various target sequences could be easily produced.
    Matched MeSH terms: Ligands
  6. Farhan N, Al-Maleki AR, Sarih NM, Yahya R
    Bioorg Chem, 2023 Nov;140:106786.
    PMID: 37586131 DOI: 10.1016/j.bioorg.2023.106786
    Recent studies show that some metal ions, injure microbial cells in various ways due to membrane breakdown, protein malfunction, and oxidative stress. Metal complexes are suited for creating novel antibacterial medications due to their distinct mechanisms of action and the variety of three-dimensional geometries they can acquire. In this Perspective, the present study focused on new antibacterial strategies based on metal oleoyl amide complexes. Thus, oleoyl amides ligand (fatty hydroxamic acid and fatty hydrazide hydrate) with the transition metal ions named Ag (I), Co (II), Cu (II), Ni (II) and Sn (II) complexes were successfully synthesized in this study. The metals- oleoyl amide were characterized using elemental analysis, and fourier transforms infrared (FTIR) spectroscopy. The antibacterial effect of metals- oleoyl amide complexes was investigated for Gram-negative bacteria (Escherichia coli) and Gram-positive bacteria (Staphylococcus aureus) by analysing minimum inhibitory concentration (MIC), minimal bactericidal concentration (MBC), and scanning electron microscopy (SEM). The results showed that metal-oleoyl amide complexes have high antibacterial activity at low concentrations. This study inferred that metal oleoyl amide complexes could be utilised as a promising therapeutic antibacterial agent.
    Matched MeSH terms: Ligands
  7. Zulkifli MH, Viswenaden P, Jasamai M, Azmi N, Yaakob NS
    Biomed Pharmacother, 2019 Feb 20;112:108630.
    PMID: 30797147 DOI: 10.1016/j.biopha.2019.108630
    5-HT3R antagonists such as ondansetron, granisetron and tropisetron have been clinically used to treat nausea and vomiting in chemotherapy patients. However, current study and research revealed novel potentials of these ligands in other diseases like inflammation, Alzheimer's, and drug abuse. Towards utilising these drugs as anti-smoking agents to treat nicotine dependence problem, there are conflicting reports regarding the potential of these ligands in modulating the effects of nicotine in both human and animal behavioural studies. This is complicated by the heterogeneity of 5-HT3R itself, cross regulation between nicotinic acetylcholinergic receptor (nAChR) and distinct pharmacological profiles of 5-HT3R antagonists. This review gathered existing studies conducted investigating the potential of "-setron" class of 5-HT3R antagonists in modulating nicotine effects. We proposed that the mechanism where 5-HT3R antagonists mediate the effects of nicotine could be attributed by both direct at 5-HT3R and indirect mechanism in nicotine addiction downstream regulation. The indirect mechanism mediated by the 5-HT3R antagonist could be through α7 nAChR, 5-HT1B receptor (5-HT1BR), 5-HT1C receptor (5-HT1CR), calcineurin activity, p38 MAPK level, PPAR-γ and NF-κβ. Our review suggested that future studies should focus on newer 5-HT3R antagonist with superior pharmacological profile or the one with multitarget action rather than high selectivity at single receptor.
    Matched MeSH terms: Ligands
  8. Nasaruddin RR, Yao Q, Chen T, Hülsey MJ, Yan N, Xie J
    Nanoscale, 2018 Dec 04.
    PMID: 30512030 DOI: 10.1039/c8nr07197g
    Quasi-homogeneous ligand-protected gold nanoclusters (Au NCs) with atomic precision and well-defined structure offer great opportunity for exploring the catalytic nature of nanogold catalysts at a molecular level. Herein, using real-time electrospray ionization mass spectrometry (ESI-MS), we have successfully identified the desorption and re-adsorption of p-mercaptobenzoic acid (p-MBA) ligands from Au25(p-MBA)18 NC catalysts during the hydrogenation of 4-nitrophenol in solution. This ligand dynamic (desorption and re-adsorption) would initiate structural transformation of Au25(p-MBA)18 NC catalysts during the reaction, forming a mixture of smaller Au NCs (Au23(p-MBA)16 as the major species) at the beginning of catalytic reaction, which could further be transformed into larger Au NCs (Au26(p-MBA)19 as the major species). The adsorption of hydrides (from NaBH4) is identified as the determining factor that could induce the ligand dynamic and structural transformation of NC catalysts. This study provides fundamental insights into the catalytic nature of Au NCs, including catalytic mechanism, active species and stability of Au NC catalysts during a catalytic reaction.
    Matched MeSH terms: Ligands
  9. Zafar MN, Masood S, Chaudhry GE, Muhammad TST, Dalebrook AF, Nazar MF, et al.
    Dalton Trans, 2019 Aug 08.
    PMID: 31393494 DOI: 10.1039/c9dt01923e
    The two cationic palladium(ii) complexes, [Pd(Len)2][OTf]2 (4) and [Pd(Lphen)2][OTf]2 (5), were synthesized by treatment of bis(benzonitrile)dichloropalladium(ii) with [H2Len][OTf]2 (2) or [H2Lphen][OTf]2 (3), respectively, in the presence of a weak base. The pro-ligands 2 and 3 were synthesized by melt reactions between N-methyl-4-chloropyridinium triflate (1) and the amines ethylenediamine or phenylenediamine, respectively. The water-soluble compounds 2-5 were fully characterized, including by single-crystal X-ray crystal structure determinations for 2-4. UV-Vis and fluorescence spectroscopy were used to study the binding interactions of 2-5 with CT-DNA. The spectroscopic data suggested the presence of intercalative and groove binding modes and this was supported by molecular docking studies. The in vitro cytotoxicity studies (IC50 values) showed that the human breast cancer cell lines MCF-7 and T47D were more sensitive towards 3, 4 and 5 than cisplatin. The cytotoxicity of the new compounds decreased in the order 5 > 4 > 3 > 2. Furthermore, the annexin V-FITC staining method strongly suggested the presence of phosphatidylserine (PS) on the outer membrane of the treated cells, which is a hallmark of apoptosis.
    Matched MeSH terms: Ligands
  10. Zafar MN, Butt AM, Chaudhry GE, Perveen F, Nazar MF, Masood S, et al.
    J Inorg Biochem, 2021 11;224:111590.
    PMID: 34507110 DOI: 10.1016/j.jinorgbio.2021.111590
    The bidentate N-(1-Alkylpyridin-4(1H)-ylidene)amide (PYA) pro-ligands [H2LBn][Cl]2 (2), and [H2LMe][TfO]2 (3) were prepared by simple alkylation reactions of the known compound, N,N-di(pyridin-4-yl)oxalamide (H2L, 1). The Pd(II) complexes, [Pd(LBn)2][Cl]2 (4), [Pd(LMe)2][Cl][TfO] (5), Pd(LBn)Cl2 (6) and Pd(LMe)Cl2 (7) were synthesized through reactions between these pro-ligands and suitable Pd(II) substrates in the presence of base. The molecular structures of 3 and 6 were obtained by single crystal X-ray structure determinations. Studies of the experimental and computational DNA binding interactions of the compounds 1-7 revealed that overall 4 and 6 have the largest values for the binding parameters Kb and ΔGbo. The results showed a good correlation with the steric and electronic parameters obtained by quantitative structure activity relationship (QSAR) studies. In-vitro cytotoxicity studies against four different cell lines showed that the human breast cancer cell lines MCF-7, T47D and cervical cancer cell line HeLa had either higher or similar sensitivities towards 4, 6 and 2, respectively, compared to cisplatin. In general, the cytotoxicity of the compounds, represented by IC50 values, decreased in the order 4 > 6 > 2 > 5 > 3 > 1 > 7 in cancer cell lines. Apoptosis contributed significantly to the cytotoxic effects of these anticancer agents as evaluated by apoptosis studies.
    Matched MeSH terms: Ligands
  11. Sun RW, Zhang M, Li D, Zhang ZF, Cai H, Li M, et al.
    Chemistry, 2015 Dec 14;21(51):18534-8.
    PMID: 26459298 DOI: 10.1002/chem.201503656
    A dinuclear gold(I) pyrrolidinedithiocarbamato complex (1) with a bidentate carbene ligand has been constructed and shows potent in vitro cytotoxic activities towards cisplatin-resistant ovarian cancer cells A2780cis. Its rigid scaffold enables a zinc(II)-based metal-organic framework (Zn-MOF) to be used as a carrier in facilitating the uptake and release of 1 in solutions. Instead of using a conventional dialysis approach for the drug-release testing, in this study, a set of transwell assay-based experiments have been designed and employed to examine the cytotoxic and antimigratory activities of 1@Zn-MOF towards A2780cis.
    Matched MeSH terms: Ligands
  12. Abdo A, Chen B, Mueller C, Salim N, Willett P
    J Chem Inf Model, 2010 Jun 28;50(6):1012-20.
    PMID: 20504032 DOI: 10.1021/ci100090p
    A Bayesian inference network (BIN) provides an interesting alternative to existing tools for similarity-based virtual screening. The BIN is particularly effective when the active molecules being sought have a high degree of structural homogeneity but has been found to perform less well with structurally heterogeneous sets of actives. In this paper, we introduce an alternative network model, called a Bayesian belief network (BBN), that seeks to overcome this limitation of the BIN approach. Simulated virtual screening experiments with the MDDR, WOMBAT and MUV data sets show that the BIN and BBN methods allow effective screening searches to be carried out. However, the results obtained are not obviously superior to those obtained using a much simpler approach that is based on the use of the Tanimoto coefficient and of the square roots of fragment occurrence frequencies.
    Matched MeSH terms: Ligands
  13. Ahmad SN, Zaharim WN, Sulaiman S, Hasan Baseri DF, Mohd Rosli NA, Ang LS, et al.
    ACS Omega, 2020 Dec 29;5(51):33253-33261.
    PMID: 33403287 DOI: 10.1021/acsomega.0c04937
    Density functional theory computational investigation was performed to study the electronic structures, muon sites, and the associated hyperfine interactions in [Au25(SR)18]0 and [Au25(SeR)18]0 where R is phenylethane. The calculated electronic structures show inhomogeneous spin density distribution and are also affected by different ligands. The two most stable muon sites near Au atoms in the thiolated system are MAu11 and MAu6. When the thiolate ligands were replaced by selenolate ligands, the lowest energy positions of muons moved to MAu6 and MAu5. Muons prefer to stop inside the Au12 icosahedral shell, away from the central Au and the staple motifs region. Muonium states at phenyl ring and S/Se atoms in the ligand were found to be stable and the Fermi contact fields are much larger as compared to the field experienced by muons near Au atoms.
    Matched MeSH terms: Ligands
  14. Gan Z, Roslan MAM, Abd Shukor MY, Halim M, Yasid NA, Abdullah J, et al.
    Biosensors (Basel), 2022 Oct 25;12(11).
    PMID: 36354431 DOI: 10.3390/bios12110922
    Aptamers are a group of synthetic single-stranded nucleic acids. They are generated from a random library of single-stranded DNA or RNA by a technology named systematic evolution of ligands by exponential enrichment (SELEX). SELEX is a repetitive process to select and identify suitable aptamers that show high affinity and specificity towards target cells. Great strides have been achieved in the design, construction, and use of aptamers up to this point. However, only a small number of aptamer-based applications have achieved widespread commercial and clinical acceptance. Additionally, finding more effective ways to acquire aptamers with high affinity remains a challenge. Therefore, it is crucial to thoroughly examine the existing dearth and advancement in aptamer-related technologies. This review focuses on aptamers that are generated by SELEX to detect pathogenic microorganisms and mammalian cells, as well as in cell-internalizing SELEX for diagnostic and therapeutic purposes. The development of novel aptamer-based biosensors using optical and electrical methods for microbial detection is reported. The applications and limitations of aptamers are also discussed.
    Matched MeSH terms: Ligands
  15. Usman A, Fun HK, Chantrapromma S, Zhu HL, Wang XJ
    Acta Crystallogr C, 2003 Mar;59(Pt 3):m97-9.
    PMID: 12711770
    In the ternary title compound, catena-poly[[silver(I)-mu-ethylenediamine-kappa(2)N:N'] 3-nitrobenzoate monohydrate], [[Ag(C(2)H(8)N(2))](C(7)H(4)NO(4)) x H(2)O](n), the Ag atom is bicoordinated in a linear configuration by two different N atoms from two symmetry-related ethylenediamine ligands, thus giving linear polymeric chains with an [-Ag-N-C-C-N-](n) backbone running parallel to the a axis. In the crystal packing, these linear chains are interconnected by N-H...O and O-H...O hydrogen bonds to form layers parallel to the ab plane.
    Matched MeSH terms: Ligands
  16. Shanmuga Sundara Raj S, Razak IA, Fun HK, Zhao PS, Jian F, Yang X, et al.
    Acta Crystallogr C, 2000 Apr 15;56(Pt 4):E130-1.
    PMID: 15263175
    In the crystal of the title complex, [Co(C(9)H(6)NO)(3)].C(2)H(5)OH, the central Co atom has a distorted octahedral coordination comprised of three N atoms and three O atoms from the three 8-quinolinolato ligands. The three Co-O bond distances are in the range 1.887 (2)-1.910 (2) A, while the three Co-N bond distances range from 1.919 (2) to 1.934 (2) A. The solvent ethanol molecule forms an intermolecular O-H.O hydrogen bonding with a quinolinolato ligand.
    Matched MeSH terms: Ligands
  17. Hong W, Li J, Laughton CA, Yap LF, Paterson IC, Wang H
    J Mol Graph Model, 2014 Jun;51:193-202.
    PMID: 24937176 DOI: 10.1016/j.jmgm.2014.05.010
    Protein arginine methyltransferases (PRMTs) catalyse the methylation of arginine residues of target proteins. PRMTs utilise S-adenosyl methionine (SAM) as the methyl group donor, leading to S-adenosyl homocysteine (SAH) and monomethylarginine (mMA). A combination of homology modelling, molecular docking, Active Site Pressurisation, molecular dynamic simulations and MM-PBSA free energy calculations is used to investigate the binding poses of three PRMT1 inhibitors (ligands 1-3), which target both SAM and substrate arginine binding sites by containing a guanidine group joined by short linkers with the SAM derivative. It was assumed initially that the adenine moieties of the inhibitors would bind in sub-site 1 (PHE44, GLU137, VAL136 and GLU108), the guanidine side chain would occupy sub-site 2 (GLU 161, TYR160, TYR156 and TRP302), with the amino acid side chain occupying sub-site 3 (GLU152, ARG62, GLY86 and ASP84; pose 1). However, the SAH homocysteine moiety does not fully occupy sub-site 3, suggesting another binding pose may exist (pose 2), whereby the adenine moiety binds in sub-site 1, the guanidine side chain occupies sub-site 3, and the amino acid side chain occupies sub-site 2. Our results indicate that ligand 1 (pose 1 or 2), ligand 2 (pose 2) and ligand 3 (pose 1) are the predominant binding poses and we demonstrate for the first time that sub-site 3 contains a large space that could be exploited in the future to develop novel inhibitors with higher binding affinities.
    Matched MeSH terms: Ligands
  18. Wu H, Sun Y, Wong WL, Cui J, Li J, You X, et al.
    Eur J Med Chem, 2020 Mar 01;189:112042.
    PMID: 31958737 DOI: 10.1016/j.ejmech.2020.112042
    Transforming growth factor-β (TGF-β) plays an important role in regulating epithelial to mesenchymal transition (EMT) and the TGF-β signaling pathway is a potential target for therapeutic intervention in the development of many diseases, such as fibrosis and cancer. Most currently available inhibitors of TGF-β signaling function as TGF-β receptor I (TβR-I) kinase inhibitors, however, such kinase inhibitors often lack specificity. In the present study, we targeted the extracellular protein binding domain of the TGF-β receptor II (TβR-II) to interfere with the protein-protein interactions (PPIs) between TGF-β and its receptors. One compound, CJJ300, inhibited TGF-β signaling by disrupting the formation of the TGF-β-TβR-I-TβR-II signaling complex. Treatment of A549 cells with CJJ300 resulted in the inhibition of downstream signaling events such as the phosphorylation of key factors along the TGF-β pathway and the induction of EMT markers. Concomitant with these effects, CJJ300 significantly inhibited cell migration. The present study describes for the first time a designed molecule that can regulate TGF-β-induced signaling and EMT by interfering with the PPIs required for the formation of the TGF-β signaling complex. Therefore, CJJ300 can be an important lead compound with which to study TGF-β signaling and to design more potent TGF-β signaling antagonists.
    Matched MeSH terms: Ligands
  19. Fazia Adyani Ahmad Fuad, Houston Douglas R, Michels Paul AM, Fothergill-gilmore Linda A, Walkinshaw Malcolm D
    Sains Malaysiana, 2016;45:1113-1120.
    Cofactor-independent phosphoglycerate mutase has been proposed as a therapeutic target for the treatment of
    trypanosomatid diseases. In this paper, we report the identification of compounds that could potentially be developed as
    selective inhibitors of cofactor-independent phosphoglycerate mutase from Leishmania mexicana (LmiPGAM). Virtual
    screening was used in this search, as well as compounds identified by high-throughput screening. A ligand-based virtual
    screen programme, ultra fast shape recognition with atom types (UFSRAT), was used to screen for compounds resembling
    the substrate/product, before a structure-based approach was applied using AutoDock 4 and AutoDock Vina in a consensus
    docking scheme. In this way eight selected compounds were identified. In addition, three compounds from the Library of
    Pharmacologically Active Compounds (LOPAC) were selected from the published results of high-throughput screening of
    this library. The inhibitory effects of these compounds were tested at a fixed concentration of 1 mM. The results showed
    that seven compounds inhibited LmiPGAM activity and of these, two compounds (one each from high-throughput and
    virtual screening) showed substantial inhibition (i.e. 14% and 49% remaining activity, respectively). Taken together, the
    findings from this study indicate that these compounds have potential as novel inhibitors that specifically target LmiPGAM.
    Matched MeSH terms: Ligands
  20. Yan MP, Wee CE, Yen KP, Stevens A, Wai LK
    Future Med Chem, 2023 Nov;15(21):1987-2009.
    PMID: 37933551 DOI: 10.4155/fmc-2023-0202
    G-quadruplexes (G4s) within the human genome have undergone extensive molecular investigation, with a strong focus on telomeres, gene promoters and repetitive regulatory sequences. G4s play central roles in regulating essential biological processes, including telomere maintenance, replication, transcription and translation. Targeting these molecular processes with G4-binding ligands holds substantial therapeutic potential in anticancer treatments and has also shown promise in treating neurological, skeletal and muscular disorders. The presence of G4s in bacterial and viral genomes also suggests that G4-binding ligands could be a critical tool in fighting infections. This review provides an overview of the progress and applications of G4-binding ligands, their proposed mechanisms of action, challenges faced and prospects for their utilization in anticancer treatments, neurological disorders and antiviral activities.
    Matched MeSH terms: Ligands
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