ABSTRACT
The interaction between nucleotide molecules and lipid molecules plays important roles in cell activities, but the molecular mechanism is very elusive. In the present study, a small but noticeable interaction between the negatively charged phosphatidylethanolamine (PE) and Guanosine monophosphate (GMP) molecules was observed from the PE monolayer at the air/water interface. As shown by the sum frequency generation (SFG) spectra and Pi-A isotherm of the PE monolayer, the interaction between the PE and GMP molecules imposes very small changes to the PE molecules. However, the Brewster angle microscopy (BAM) technique revealed that the assembly conformations of PE molecules are significantly changed by the adsorption of GMP molecules. By comparing the SFG spectra of PE monolayers after the adsorption of GMP, guanosine and guanine, it is also shown that the hydrogen bonding effect plays an important role in the nucleotide-PE interactions. These results provide fundamental insight into the structure changes during the nucleotide-lipid interaction, which may shed light on the molecular mechanism of viral infection, DNA drug delivery, and cell membrane curvature control in the brain or neurons.
Subject(s)
Guanosine Monophosphate , Phosphatidylethanolamines , Phosphatidylethanolamines/chemistry , Guanosine Monophosphate/chemistry , Guanosine Monophosphate/metabolism , Adsorption , Surface Properties , Microscopy , Hydrogen Bonding , Water/chemistryABSTRACT
Several compounds with taste-modulating properties have been investigated, improving the taste impression without having a pronounced intrinsic taste. The best-known representatives of umami taste-modulating compounds are ribonucleotides and their derivatives. Especially the thio derivatives showed high taste-modulating potential in structure-activity relationship investigations. Therefore, this study focuses on the formation of guanosine 5'-monophosphate derivatives consisting of Maillard-type generated compounds like the aroma-active thiols (2-methyl-3-furanthiol, 3-mercapto-2-pentanone, 2-furfurylthiol) and formaldehyde to gain insights into the potential of combinations of taste and aroma-active compounds. One literature-known (N2-(furfurylthiomethyl)-guanosine 5'-monophosphate) and three new derivatives (N2-(2-methyl-1-furylthiomethyl)-guanosine 5'-monophosphate, N2-((5-hydroxymethyl)-2-methyl-1-furylthiomethyl)-guanosine 5'-monophosphate, N2-((2-pentanon-1-yl)thiomethyl)-guanosine 5'-monophosphate) were successfully produced using green natural deep eutectic solvents and isolated, and their structures were completely elucidated. Besides the intrinsic taste properties, the kokumi and umami taste-modulating effects of the four derivatives were evaluated via psychophysical investigations, ranging from 19 to 22 µmol/L.
Subject(s)
Flavoring Agents , Guanosine Monophosphate , Maillard Reaction , Taste , Guanosine Monophosphate/chemistry , Humans , Flavoring Agents/chemistry , Male , Female , Molecular Structure , Adult , Young AdultABSTRACT
This aimed to develop a comprehensive theoretical protocol for examining substitution reaction processes. The researchers used a theoretical quantum-mechanical protocol based on the QM-ORSA approach, which estimates the kinetic parameters of thermodynamically favourable reaction pathways. This theoretical protocol was validated by experimentally investigating substitution mechanisms in two previously synthesised Pd(II) complexes: chlorido-[(3-(1-(2-hydroxypropylamino)ethylidene)chroman-2,4-dione)]palladium(II) (C1) and chlorido-[(3-(1-(2-mercaptoethylamino)-ethylidene)-chroman-2,4dione)]palladium(II) (C2), along with biologically relevant nucleophiles, namely L-cysteine (l-Cys), L-methionine (l-Met), and guanosine-5'-monophosphate (5'-GMP). Reactions were investigated under pseudo-first-order conditions, monitoring nucleophile concentration and temperature changes using stopped-flow UV-vis spectrophotometry. All reactions were conducted under physiological conditions (pH = 7.2) at 37 °C. The reactivity of the studied nucleophiles follows the order: l-Cys > l-Met > 5'-GMP, and the reaction mechanism is associative based on the activation parameters. The experimental and theoretical data showed that C2 is more reactive than C1, confirming that the complexes' structural and electronic properties greatly affect their reactivity with selected nucleophiles. The study's findings have confirmed that the primary interaction occurs with the acid-base species L-Cys, mostly through the involvement of the partially negative sulfur atom (87.2%). On the other hand, C2 has a higher propensity for reacting with L-Cys-, primarily through the partially negative oxygen atom (92.6%). The implementation of this theoretical framework will significantly restrict the utilization of chemical substances, hence facilitating cost reduction and environmental protection.
Subject(s)
Coordination Complexes , Coumarins , Cysteine , Palladium , Palladium/chemistry , Kinetics , Coordination Complexes/chemistry , Coordination Complexes/chemical synthesis , Coumarins/chemistry , Cysteine/chemistry , Methionine/chemistry , Guanosine Monophosphate/chemistry , Thermodynamics , Quantum Theory , Hydrogen-Ion Concentration , Molecular StructureABSTRACT
Retinitis pigmentosa (RP) is a form of retinal degeneration affecting a young population with an unmet medical need. Photoreceptor degeneration has been associated with increased guanosine 3',5'-cyclic monophosphate (cGMP), which reaches toxic levels for photoreceptors. Therefore, inhibitory cGMP analogues attract interest for RP treatments. Here we present the synthesis of dithio-CN03, a phosphorodithioate analogue of cGMP, prepared using the H-phosphonothioate route. Two crystal modifications were identified as a trihydrate and a tetrahydrofuran monosolvates. Dithio-CN03 featured a lower aqueous solubility than its RP-phosphorothioate counterpart CN03, a drug candidate, and this characteristic might be favorable for sustained-release formulations aimed at retinal delivery. Dithio-CN03 was tested in vitro for its neuroprotective effects in photoreceptor models of RP. The comparison of dithio-CN03 to CN03 and its diastereomer SP-CN03, and to their phosphate derivative oxo-CN03 identifies dithio-CN03 as the compound with the highest efficacy in neuroprotection and thus as a promising new candidate for the treatment of RP.
Subject(s)
Cyclic GMP , Neuroprotective Agents , Retinal Rod Photoreceptor Cells , Cyclic GMP/metabolism , Cyclic Nucleotide Phosphodiesterases, Type 6/antagonists & inhibitors , Cyclic Nucleotide Phosphodiesterases, Type 6/metabolism , Guanosine Monophosphate/chemistry , Guanosine Monophosphate/metabolism , Neuroprotective Agents/pharmacology , Neuroprotective Agents/chemical synthesis , Neuroprotective Agents/chemistry , Neuroprotective Agents/therapeutic use , Retinal Degeneration/drug therapy , Retinal Rod Photoreceptor Cells/drug effects , Retinal Rod Photoreceptor Cells/pathology , Retinal Rod Photoreceptor Cells/metabolism , Retinitis Pigmentosa/drug therapy , Retinitis Pigmentosa/metabolism , Structure-Activity RelationshipABSTRACT
Guanosine monophosphate (GMP) is a nucleotide that can self-assemble in aqueous solution under certain conditions. An understanding of the process at the molecular level is an essential step to comprehend the involvement of DNA substructures in transcription and replication, as well as their relationship to genetic diseases such as cancer. We present the temperature-dependent terahertz (1.5-12 THz, 50-400 cm-1) absorptivity spectra of aqueous Na2 GMP solution in comparison with the aqueous solutions of other RNA nucleotides. Distinct absorption features were observed in the spectrum of GMP, which we attribute to the intramolecular modes of the self-assemblies (i.e., G-complexes) that, at 1 M, start to form at 313 K and below. Changes in broad-band features of the terahertz spectrum were also observed, which we associate with the release of hydration water in the temperature-dependent formation of guanine quadruplexes. Using a state-of-the-art THz calorimetry approach correlating spectroscopic to thermodynamic changes, we propose a molecular mechanism of hydrophilic hydration driving GMP self-assembly as a function of temperature. The free energy contribution of hydrophilic hydration is shown as a decisive factor in guanine-quadruplex formation. Our findings spotlight the role of hydration in the formation of macromolecular structures and suggest the potential of hydration tuning for regulating DNA transcription and replication.
Subject(s)
G-Quadruplexes , Guanosine Monophosphate , Guanosine Monophosphate/chemistry , Water/chemistry , Nucleotides , DNA/chemistryABSTRACT
The guanosine analog AT-527 represents a promising candidate against Severe Acute Respiratory Syndrome coronavirus type 2 (SARS-CoV-2). AT-527 recently entered phase III clinical trials for the treatment of COVID-19. Once in cells, AT-527 is converted into its triphosphate form, AT-9010, that presumably targets the viral RNA-dependent RNA polymerase (RdRp, nsp12), for incorporation into viral RNA. Here we report a 2.98 Å cryo-EM structure of the SARS-CoV-2 nsp12-nsp7-nsp82-RNA complex, showing AT-9010 bound at three sites of nsp12. In the RdRp active-site, one AT-9010 is incorporated at the 3' end of the RNA product strand. Its modified ribose group (2'-fluoro, 2'-methyl) prevents correct alignment of the incoming NTP, in this case a second AT-9010, causing immediate termination of RNA synthesis. The third AT-9010 is bound to the N-terminal domain of nsp12 - known as the NiRAN. In contrast to native NTPs, AT-9010 is in a flipped orientation in the active-site, with its guanine base unexpectedly occupying a previously unnoticed cavity. AT-9010 outcompetes all native nucleotides for NiRAN binding, inhibiting its nucleotidyltransferase activity. The dual mechanism of action of AT-527 at both RdRp and NiRAN active sites represents a promising research avenue against COVID-19.
Subject(s)
Antiviral Agents/chemistry , Antiviral Agents/pharmacology , Guanosine Monophosphate/analogs & derivatives , Phosphoramides/chemistry , Phosphoramides/pharmacology , RNA-Dependent RNA Polymerase/antagonists & inhibitors , SARS-CoV-2/enzymology , Viral Proteins/antagonists & inhibitors , Viral Proteins/metabolism , COVID-19/virology , Cryoelectron Microscopy , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Guanosine Monophosphate/chemistry , Guanosine Monophosphate/pharmacology , Humans , RNA-Dependent RNA Polymerase/chemistry , RNA-Dependent RNA Polymerase/genetics , RNA-Dependent RNA Polymerase/metabolism , SARS-CoV-2/chemistry , SARS-CoV-2/drug effects , SARS-CoV-2/genetics , Viral Proteins/geneticsABSTRACT
Human GMP reductase (hGMPR) enzyme is involved in a cellular metabolic pathway, converting GMP into IMP, and also it is an important target for anti-leukemic agents. Present computational investigations explain dynamical behavior of water molecules during the conformational transition process from GMP to IMP using molecular dynamics simulations. Residues at substrate-binding site of cancerous protein (PDB Id. 2C6Q) are mostly more dynamic in nature than the normal protein (PDB Id. 2BLE). Nineteen conserved water molecules are identified at the GMP/IMP binding site and are classified as (i) conserved stable dynamic and (ii) infrequent dynamic. Water molecules W11, W14, and W16 are classified as conserved stable dynamic due to their immobile character, whereas remaining water molecules (W1, W2, W3, W4, W5, W7, W8, W9, W10, W12, W13, W15, W17, W18, and W19) are infrequent with dynamic nature. Entrance or displacement of these infrequent water molecules at GMP/IMP sites may occur due to forward and backward movement of reference residues involving ligands. Four water molecules of hGMPR-I and nine water molecules of hGMPR-II are observed in repetitive transitions from GMP to IMP pathway, which indicates discrimination between two isoforms of hGMPRs. Water molecules in cancerous protein are more dynamic and unstable compared to normal protein. These water molecules execute rare dynamical events at GMP binding site and could assist in detailed understanding of conformational transitions that influence the hGMPR's biological functionality. The present study should be of interest to the experimental community engaged in leukemia research and drug discovery for CML cancer.
Subject(s)
GMP Reductase , Guanosine Monophosphate , Water , Humans , GMP Reductase/chemistry , GMP Reductase/metabolism , Guanosine Monophosphate/chemistry , Guanosine Monophosphate/metabolism , Molecular Dynamics Simulation , Protein Conformation , Thermodynamics , Water/chemistryABSTRACT
Nuclease P1 (NP1) can hydrolyze nucleic acids into four 5'-mononucleotides, which are widely used in the pharmaceutical and food industries. In this paper, an aqueous two-phase system (ATPS) was developed to purify NP1 from Penicillium citrinum. Polyethylene glycol (PEG) and nucleotides salts were studied to form ATPSs, among which PEG3000/disodium guanosine monophosphate (GMPNa2) was researched, including the phase composition and pH. Using 14% (w/w) PEG3000 and 20% (w/w) GMPNa2 ATPS at pH 5.0, the best recovery and purification factor, 82.4% and 3.59, were obtained. The recovery of NP1 was 98.3% by the separation of ultrafiltration from the PEG-rich phase. The recycling use of GMPNa2 was also studied, and 95.1% of GMPNa2 in the salt-rich phase was obtained with the addition of ethanol as the solvent. These results showed that the ATPS was effective for purification of NP1.
Subject(s)
Fungal Proteins , Guanosine Monophosphate/chemistry , Penicillium/enzymology , Polyethylene Glycols/chemistry , Single-Strand Specific DNA and RNA Endonucleases , Fungal Proteins/chemistry , Fungal Proteins/isolation & purification , Single-Strand Specific DNA and RNA Endonucleases/chemistry , Single-Strand Specific DNA and RNA Endonucleases/isolation & purificationABSTRACT
We synthesized and characterized the ruthenium(iii) pincer-type complex [RuCl3(H2Lt-Bu] (H2Lt-Bu = 2,6-bis(5-tert-butyl-1H-pyrazol-3-yl)pyridine, 1) by elemental analysis, IR and UV-Vis spectroscopy, and the mass spectrometry (MS) method ESI Q-TOF. For comparison reasons, we also studied ruthenium(iii) terpyridine complexes of the general formula [Ru(N-N-N)Cl3], where N-N-N = 4'-chloro-terpyridine (Cl-tpy; 2) or 4'-chlorophenyl-terpyridine (Cl-Ph-tpy; 3). A kinetic study of the substitution reactions of 1-3 with biomolecules showed that the rate constants depend on the properties of the spectator ligand and the nature of the entering nucleophile. The DNA/HSA binding study showed that in comparison to complex 1 (bis-pyrazolylpyridine), the other two (2 and 3) terpyridine complexes had a slightly better binding affinity to calf thymus DNA (CT DNA), while in the case of human serum albumin (HSA), complex 1 exhibited the strongest quenching ability. We demonstrated that 1 possesses significant in vitro cytotoxic activity against mouse colon carcinoma CT26 cells and in vivo antitumor activity in murine heterotopic colon carcinoma. Complex 1 induced G0/G1 cell cycle arrest and apoptotic death in CT26 cells. Additionally, 1 showed antiproliferative activity, as evaluated by the detection of the expression levels of the Ki67 protein. Furthermore, the in vivo results showed that 1 reduced primary tumour growth and the number and growth of lung and liver metastases, significantly prolonging the treated mice's survival rate. This study highlighted that 1 does not show hepato- and nephrotoxicity. Our data demonstrated the considerable antitumor activity of the ruthenium(iii) pincer complex against CT26 tumour cells and implicated further investigations of its role as a potential chemotherapeutic agent for colon carcinoma.
Subject(s)
Antineoplastic Agents , Colonic Neoplasms/drug therapy , Coordination Complexes , Pyrazoles , Pyridines , Ruthenium , Animals , Antineoplastic Agents/chemistry , Antineoplastic Agents/pharmacology , Antineoplastic Agents/therapeutic use , Cell Line, Tumor , Cell Survival/drug effects , Colonic Neoplasms/pathology , Coordination Complexes/chemistry , Coordination Complexes/pharmacology , Coordination Complexes/therapeutic use , DNA/chemistry , Guanosine Monophosphate/chemistry , Histidine/chemistry , Male , Methionine/chemistry , Mice, Inbred BALB C , Molecular Docking Simulation , Pyrazoles/chemistry , Pyrazoles/pharmacology , Pyrazoles/therapeutic use , Pyridines/chemistry , Pyridines/pharmacology , Pyridines/therapeutic use , Ruthenium/chemistry , Ruthenium/pharmacology , Ruthenium/therapeutic use , Serum Albumin, Human/chemistry , Tumor Burden/drug effectsABSTRACT
Minor structural modifications to the DNA and RNA nucleobases have a significant effect on their excited state dynamics and electronic relaxation pathways. In this study, the excited state dynamics of 7-deazaguanosine and guanosine 5'-monophosphate are investigated in aqueous solution and in a mixture of methanol and water using femtosecond broadband transient absorption spectroscopy following excitation at 267 nm. The transient spectra are collected using photon densities that ensure no parasitic multiphoton-induced signal from solvated electrons. The data can be fit satisfactorily using a two- or three-component kinetic model. By analyzing the results from steady-state, time-resolved, computational calculations, and the methanol-water mixture, the following general relaxation mechanism is proposed for both molecules, Lb â La â 1πσ*(ICT) â S0, where the 1πσ*(ICT) stands for an intramolecular charge transfer excited singlet state with significant πσ* character. In general, longer lifetimes for internal conversion are obtained for 7-deazaguanosine compared to guanosine 5'-monophosphate. Internal conversion of the 1πσ*(ICT) state to the ground state occurs on a similar time scale of a few picoseconds in both molecules. Collectively, the results demonstrate that substitution of a single nitrogen atom for a methine (C-H) group at position seven of the guanine moiety stabilizes the 1ππ* Lb and La states and alters the topology of their potential energy surfaces in such a way that the relaxation dynamics in 7-deazaguanosine are slowed down compared to those in guanosine 5'-monophosphate but not for the internal conversion of 1πσ*(ICT) state to the ground state.
Subject(s)
Guanosine Monophosphate/chemistry , Guanosine/analogs & derivatives , Quantum Theory , Electrons , Guanosine/chemistry , Kinetics , Models, Molecular , Molecular Conformation , Thermodynamics , Water/chemistryABSTRACT
Adsorption kinetic studies are conducted to investigate the potential to use chiral mesoporous materials nanoporous guanosine monophosphate material-1 (NGM-1) and nanoporous folic acid material-1 (NFM-1) for the enantiomeric separation of l- and d-valine. A pseudo-second-order (PSO) kinetic model is applied to test the experimental adsorption equilibrium isotherms, according to both the Langmuir and Freundlich models and the characteristic parameters for each model are determined. The calcined versions of both NGM-1 and NFM-1 fit the Langmuir model with maximum sorption capacities of 0.36 and 0.26 g/g for the preferred adsorption enantiomers, d-valine and l-valine, respectively. Experimental results and the analysis of adsorption models suggest a strong adsorbate-adsorbent interaction, and the formation of a monolayer of tightly packed amino acid on the internal mesopore surface for the preferred enantiomers.
Subject(s)
Folic Acid/chemistry , Guanosine Monophosphate/chemistry , Nanostructures/chemistry , Silicon Dioxide/chemistry , Valine/isolation & purification , Adsorption , Kinetics , Nanopores/ultrastructure , Nanostructures/ultrastructure , Porosity , Stereoisomerism , Valine/analysisABSTRACT
A novel innovative viscoelastic gelling agent (novel gel, NG) has been developed by combining citric acid (CA) and disodium 5-guanylate (DG). NG has the potential to replace other gelling agents such as gelatine, which has been commonly used in foods, dietary supplements, pharmaceutical and cosmetic products including ointments and sprays. NG has unique physico-chemical properties, including a wide range of concentration-dependent, temperature-sensitive gel strengths. Based on the rheological measurement results, NG depicted similar shear thinning behaviour to gelatine, within shear rates ranging from 25.8 to 129 (s-1). NG also significantly increased the shelf-life (by 21 days) of minced beef, as well as inhibited the growth of major spoilage pathogens, such as E. coli, S. aureus, Salmonella sp., Listeria sp., yeast and moulds, making it an ideal candidate for gelatine replacement.
Subject(s)
Anti-Bacterial Agents/chemistry , Chemical Phenomena , Elasticity , Animals , Anti-Bacterial Agents/pharmacology , Cattle , Citric Acid/chemistry , Food Microbiology , Food Storage , Gelatin/chemistry , Gels , Guanosine Monophosphate/chemistry , Red Meat/microbiology , Rheology , Temperature , ViscosityABSTRACT
Platinum-based antineoplastic agents play a major role in the treatment of numerous types of cancer. A new bulky, lipophilic, and chiral ligand based on 1,2-diaminodiamantane in both of its enantiomeric forms was employed for the preparation of new platinum(ii) complexes with chloride and oxalate ligands. The dichloride complexes have a higher solubility and were evaluated as anti-proliferation agents for human ovarian cancer cell lines A2780 and cisplatin-resistant A2780cis. Its R,R-enantiomer showed increased efficacy compared to cisplatin for both cancer cell lines. A chromatographic approach was used to estimate the solvent partition coefficient of the dichloride complex. The binding of diamondoid-based platinum complexes to nucleotides was tested for both enantiomers with guanosine monophosphate (GMP) and deoxyguanosine monophosphate (dGMP) and occurs at a similar or faster rate for both isomers compared to cisplatin despite greatly increased steric demand. These findings highlight the potential in 1,2-diaminodiamantane as a viable pharmacophore.
Subject(s)
Antineoplastic Agents/chemical synthesis , Coordination Complexes/chemical synthesis , Organoplatinum Compounds/chemical synthesis , Ovarian Neoplasms/drug therapy , Platinum/chemistry , Antineoplastic Agents/pharmacology , Apoptosis/drug effects , Cell Line, Tumor , Cell Proliferation/drug effects , Cisplatin/pharmacology , Coordination Complexes/pharmacology , Drug Design , Drug Resistance, Neoplasm , Female , Guanosine Monophosphate/chemistry , Humans , Isomerism , Ligands , Molecular Conformation , Organoplatinum Compounds/pharmacology , Structure-Activity RelationshipABSTRACT
1H/31P NMR techniques were applied to analyze the binding mode of guanosine 2'-monophosphate (2'-GMP) to histone. To date, no structures of the complex comprising 2'-GMP and histone have been deposited in Protein Data Bank. Because the 31P nucleus can be a selective marker of phosphorylated compounds, the combined use of 1H and 31P NMR spectroscopy has been applied to investigate these molecular interactions. The complex formation was initially confirmed by 31P-diffusion ordered spectroscopy and 31P-T1 measurements. In 1H{1H} saturation transfer difference experiments, H2' and H3' signals of 2'-GMP were significantly attenuated, while the rest of the unexchangeable protons were observed, indicating that the contribution of H2' and H3' to the binding epitopes was low. The WaterLOGSY-type experiment with 31P detection also indicated that a phosphorylated group located close to H2' and H3' had little access to histone.
Subject(s)
Guanosine Monophosphate/chemistry , Guanosine Monophosphate/metabolism , Histones/metabolism , Magnetic Resonance Spectroscopy , Models, Molecular , Molecular Conformation , Protein BindingABSTRACT
The remarkable power and specificity of enzyme catalysis rely on the dynamic alignment of the enzyme, substrates, and cofactors, yet the role of dynamics has usually been approached from the perspective of the protein. We have been using an underappreciated NMR technique, subtesla high-resolution field cycling 31P NMR relaxometry, to investigate the dynamics of the enzyme-bound substrates and cofactor on guanosine-5'-monophosphate reductase (GMPR). GMPR forms two dead end, yet catalytically competent, complexes that mimic distinct steps in the catalytic cycle: E·IMP·NADP+ undergoes a partial hydride transfer reaction, while E·GMP·NADP+ undergoes a partial deamination reaction. A different cofactor conformation is required for each partial reaction. Here we report the effects of mutations designed to perturb cofactor conformation and ammonia binding with the goal of identifying the structural features that contribute to the distinct dynamic signatures of the hydride transfer and deamination complexes. These experiments suggest that Asp129 is a central cog in a dynamic network required for both hydride transfer and deamination. In contrast, Lys77 modulates the conformation and mobility of substrates and cofactors in a reaction-specific manner. Thr105 and Tyr318 are part of a deamination-specific dynamic network that includes the 2'-OH of GMP. These residues have comparatively little effect on the dynamic properties of the hydride transfer complex. These results further illustrate the potential of high-resolution field cycling NMR relaxometry for the investigation of ligand dynamics. In addition, exchange experiments indicate that NH3/NH4+ has a high affinity for the deamination complex but a low affinity for the hydride transfer complex, suggesting that the movement of ammonia may gate the cofactor conformational change. Collectively, these experiments reinforce the view that the enzyme, substrates, and cofactor are linked in intricate, reaction-specific, dynamic networks and demonstrate that distal portions of the substrates and cofactors are critical features in these networks.
Subject(s)
Coenzymes , GMP Reductase , NADP , Humans , Ammonia/metabolism , Biocatalysis , Coenzymes/chemistry , Coenzymes/metabolism , GMP Reductase/genetics , GMP Reductase/metabolism , Guanosine Monophosphate/chemistry , Kinetics , Molecular Conformation , Mutation , NADP/chemistry , NADP/metabolism , Protein BindingABSTRACT
AIMS: A newly emerged Human Coronavirus (HCoV) is reported two months ago in Wuhan, China (COVID-19). Until today >2700 deaths from the 80,000 confirmed cases reported mainly in China and 40 other countries. Human to human transmission is confirmed for COVID-19 by China a month ago. Based on the World Health Organization (WHO) reports, SARS HCoV is responsible for >8000 cases with confirmed 774 deaths. Additionally, MERS HCoV is responsible for 858 deaths out of about 2500 reported cases. The current study aims to test anti-HCV drugs against COVID-19 RNA dependent RNA polymerase (RdRp). MATERIALS AND METHODS: In this study, sequence analysis, modeling, and docking are used to build a model for Wuhan COVID-19 RdRp. Additionally, the newly emerged Wuhan HCoV RdRp model is targeted by anti-polymerase drugs, including the approved drugs Sofosbuvir and Ribavirin. KEY FINDINGS: The results suggest the effectiveness of Sofosbuvir, IDX-184, Ribavirin, and Remidisvir as potent drugs against the newly emerged HCoV disease. SIGNIFICANCE: The present study presents a perfect model for COVID-19 RdRp enabling its testing in silico against anti-polymerase drugs. Besides, the study presents some drugs that previously proved its efficiency against the newly emerged viral infection.
Subject(s)
Adenosine Monophosphate/analogs & derivatives , Alanine/analogs & derivatives , Antiviral Agents/chemistry , Betacoronavirus/enzymology , Coronavirus Infections/drug therapy , Guanosine Monophosphate/analogs & derivatives , Pneumonia, Viral/drug therapy , RNA-Dependent RNA Polymerase/antagonists & inhibitors , Ribavirin/chemistry , Sofosbuvir/chemistry , Viral Proteins/antagonists & inhibitors , Adenosine Monophosphate/chemistry , Adenosine Monophosphate/metabolism , Alanine/chemistry , Alanine/metabolism , Alphacoronavirus/enzymology , Alphacoronavirus/genetics , Amino Acid Sequence , Antiviral Agents/metabolism , Betacoronavirus/genetics , COVID-19 , Catalytic Domain , Computational Biology/methods , Coronavirus Infections/virology , Drug Repositioning/methods , Guanosine Monophosphate/chemistry , Guanosine Monophosphate/metabolism , Guanosine Triphosphate/chemistry , Guanosine Triphosphate/metabolism , Humans , Molecular Docking Simulation , Pneumonia, Viral/virology , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , RNA-Dependent RNA Polymerase/chemistry , RNA-Dependent RNA Polymerase/metabolism , Ribavirin/metabolism , SARS-CoV-2 , Sequence Alignment , Sequence Homology, Amino Acid , Sofosbuvir/metabolism , Thermodynamics , Uridine Triphosphate/chemistry , Uridine Triphosphate/metabolism , Viral Proteins/chemistry , Viral Proteins/metabolism , COVID-19 Drug TreatmentABSTRACT
Expanding the catalytic repertoire of ribozymes to include vitamin synthesis requires efficient labelling of RNA with the substrate of interest, prior to in vitro selection. For this purpose, we rationally designed and synthesized six GMP-conjugates carrying a synthetic pre-thiamine or biotin precursor and investigated their transcription incorporation properties by T7 RNA polymerase.
Subject(s)
DNA-Directed RNA Polymerases/metabolism , Guanosine Monophosphate/biosynthesis , Viral Proteins/metabolism , Vitamins/biosynthesis , Biocatalysis , Biotin/chemistry , Biotin/metabolism , Guanosine Monophosphate/chemistry , Molecular Structure , Thiamine/chemistry , Thiamine/metabolism , Vitamins/chemistryABSTRACT
The motile-sessile transition is critical for bacterial survival and growth. Cyclic-di-GMP (c-di-GMP) plays a central role in controlling this transition and regulating biofilm formation via various effectors. As an effector of c-di-GMP in Escherichia coli and related species, the PilZ domain-containing protein YcgR responds to elevated c-di-GMP concentrations and acts on the flagellar motor to suppress bacterial motility in a brakelike fashion, which promotes bacterial surface attachment. To date, several target proteins within the motor, MotA, FliG, and FliM, along with different regulatory mechanisms have been reported. However, how YcgR acts on these components remains unclear. Here, we report that activated YcgR stably binds to MotA at the MotA-FliG interface and thereby regulates bacterial swimming. Biochemical and structural analyses revealed that c-di-GMP rearranges the PilZ domain configuration, resulting in the formation of a MotA-binding patch consisting of an RXXXR motif and the C-tail helix α3. Moreover, we noted that a conserved region in the YcgR-N domain, which is independent of MotA interaction, is necessary for motility regulation. On the basis of these findings, we infer that the YcgR-N domain is required for activity on other motor proteins. We propose that activated YcgR appends to MotA via its PilZ domain and thereby interrupts the MotA-FliG interaction and simultaneously interacts with other motor proteins via its YcgR-N domain to inhibit flagellar motility. Our findings suggest that the mode of interaction between YcgR and motor proteins may be shared by other PilZ family proteins.
Subject(s)
Bacterial Proteins/chemistry , Escherichia coli Proteins/chemistry , Escherichia coli/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/ultrastructure , Escherichia coli/genetics , Escherichia coli/ultrastructure , Escherichia coli Proteins/genetics , Escherichia coli Proteins/ultrastructure , Flagella/chemistry , Flagella/genetics , Flagella/ultrastructure , Gene Expression Regulation, Bacterial , Guanosine Monophosphate/chemistry , Protein Binding/geneticsABSTRACT
Oral candidiasis as a highly prevalent and recurrent infection in medically compromised individuals is mainly caused by the opportunistic fungal pathogen Candida albicans. This epithelial infection, if not controlled effectively, can progress to life-threatening systemic conditions and complications. The efficacy of current frontline antifungals is limited due to their poor bioavailability and systemic toxicity. As such, an efficient intervention is essential for controlling disease progression and recurrence. Herein, a theranostic nanoplatform (CD-Gu+-AmB) was developed to track the penetration of antifungals and perturb the invasion of C. albicans at oral epithelial tissues, via decorating the homemade red-emissive carbon dots (CD) with positively charged guanidine groups (Gu+) followed by conjugation with antifungal polyene (amphotericin B, AmB) in a reacting site-controllable manner. The generated CD-Gu+-AmB favorably gathered within the Candida cells and exhibited potent antifungal effects in both planktonic and biofilm forms. It selectively accumulated in the nuclei of human oral keratinocytes and exhibited undetectable toxicity to the host cells. Moreover, we reported for the first time the penetration and exfoliation profiles of CD in a three-dimensional organotypic model of human oral epithelial tissues, demonstrating that the extra- and intracellular accumulation of CD-Gu+-AmB effectively resisted the invasion of C. albicans by forming a "shielding" layer throughout the entire tissue. This study establishes a multifunctional CD-based theranostic nanoplatform functioning as a traceable and topically applied antifungal to arm oral epithelia, thereby shedding light on early intervention of mucosal candidiasis for oral and general health.
Subject(s)
Amphotericin B/pharmacology , Antifungal Agents/pharmacology , Candidiasis/drug therapy , Invasive Fungal Infections/drug therapy , Amphotericin B/chemistry , Antifungal Agents/chemistry , Biofilms/drug effects , Biological Availability , Candida albicans/drug effects , Candida albicans/pathogenicity , Candidiasis/microbiology , Carbon/chemistry , Epithelial Cells/drug effects , Epithelial Cells/microbiology , Guanosine Monophosphate/chemistry , Humans , Invasive Fungal Infections/microbiology , Keratinocytes/drug effects , Microbial Sensitivity Tests , Mouth Mucosa/drug effects , Mouth Mucosa/microbiology , Polyenes/chemistry , Polyenes/pharmacology , Quantum Dots/chemistryABSTRACT
Nucleotide sugars are the activated form of monosaccharides used by glycosyltransferases during glycosylation. In eukaryotes the SLC35 family of solute carriers are responsible for their selective uptake into the Endoplasmic Reticulum or Golgi apparatus. The structure of the yeast GDP-mannose transporter, Vrg4, revealed a requirement for short chain lipids and a marked difference in transport rate between the nucleotide sugar and nucleoside monophosphate, suggesting a complex network of regulatory elements control transport into these organelles. Here we report the crystal structure of the GMP bound complex of Vrg4, revealing the molecular basis for GMP recognition and transport. Molecular dynamics, combined with biochemical analysis, reveal a lipid mediated dimer interface and mechanism for coordinating structural rearrangements during transport. Together these results provide further insight into how SLC35 family transporters function within the secretory pathway and sheds light onto the role that membrane lipids play in regulating transport across the membrane.