scholarly journals Discovery of Aminoglycosides as First in Class, Nanomolar Inhibitors of Heptosyltransferase I

2021 ◽  
Author(s):  
Jozafina A. Milicaj ◽  
Bakar A. Hassan ◽  
Joy M. Cote ◽  
Carlos A Ramirez-Mondragon ◽  
Nadiya A. Jaunbocus ◽  
...  
Keyword(s):  
Mixed Model ◽  
Tryptophan Fluorescence ◽  
Md Simulations ◽  
Inhibitory Effect ◽  
Inhibition Mechanism ◽  
Valuable Insight ◽  
Dynamic Simulations ◽  
Enzyme Active Site ◽  
Cell Membrane Stability ◽  
Experimental Findings

A clinically relevant inhibitor for Heptosyltransferase I (HepI) has been sought after for many years and while many have designed novel small-molecule inhibitors, these compounds lack the bioavailability and potency necessary for therapeutic use. Extensive characterization of the HepI protein has provided valuable insight into the dynamic motions necessary for catalysis that could be targeted for inhibition. With the help of molecular dynamic simulations, aminoglycoside antibiotics were shown to be putative inhibitors for HepI and in this study, they were experimentally determined to be the first in-class nanomolar inhibitors of HepI with the best inhibitor demonstrating a Ki of 600 +/- 90 nM. Detailed kinetic analyses were performed to determine the mechanism of inhibition while circular dichroism spectroscopy, intrinsic tryptophan fluorescence, docking, and MD simulations were used to corroborate kinetic experimental findings. Kinetic analysis methods include Lineweaver-Burk, Dixon, Cornish-Bowden and Mixed-Model of Inhibition which allowed for unambiguous assignment of inhibition mechanism for each inhibitor. In this study, we show that neomycin and kanamycin b are competitive inhibitors against the sugar acceptor substrate while tobramycin exhibits a mixed inhibitory effect and streptomycin is non-competitive. MD simulations also allowed us to suggest that the inhibitors bind tightly and inhibit catalytic dynamics due to a major desolvation penalty of the enzyme active site. While aminoglycosides have long been known as a class of potent antibiotics, they also have been scientifically shown to impact cell membrane stability, and we propose that inhibition of HepI contributes to this effect by disrupting lipopolysaccharide biosynthesis.

scholarly journals Zinc ions bind to and inhibit activated protein C

2010 ◽  
Vol 104 (09) ◽  
pp. 544-553 ◽  
Author(s):  
Tianqing Zhu ◽  
Wimal Ubhayasekera ◽  
Noëlle Nickolaus ◽  
Wei Sun ◽  
Susanne Tingsborg ◽  
...  
Keyword(s):  
Conformational Change ◽  
Protein C ◽  
Anticoagulant Activity ◽  
Activated Protein C ◽  
Physiological Role ◽  
Tryptophan Fluorescence ◽  
Inhibitory Effect ◽  
Regulatory Function ◽  
Inhibition Mechanism ◽  
D Values

SummaryZn2+ ions were found to efficiently inhibit activated protein C (APC), suggesting a potential regulatory function for such inhibition. APC activity assays employing a chromogenic peptide substrate demonstrated that the inhibition was reversible and the apparent K I was 13 ± 2 μM. k cat was seven fold decreased whereas K M was unaffected in the presence of 10 μM Zn2+. The inhibitory effect of Zn2+ on APC activity was also observed when factor Va was used as a substrate in an assay coupled to a prothrombinase assay. The interaction of Zn2+ with APC was accompanied by a reversible ~40% decrease in tryptophan fluorescence, consistent with the ion inducing a conformational change in the protein. The apparent K D was 7.4 ± 1.5 μM and thus correlated well with the apparent K I. In the presence of physiological Ca2+ concentration the K I and K D values were three to four fold enhanced, presum-ably due to the Ca2+-induced conformational change affecting the conformation of the Zn2+-binding site. The inhibition mechanism was non-competitive both in the absence and presence of Ca2+. Comparisons of sequences and structures suggested several possible sites for zinc binding. The magnitude of the apparent KI in relation to the blood and platelet concentrations of Zn2+ supports a physiological role for this ion in the regulation of anticoagulant activity of APC. These findings broaden the understanding of this versatile serine protease and enable the future development of potentially more efficient anticoagulant APC variants for treatments of thrombotic diseases.

scholarly journals How Different Substitution Positions of F, Cl Atoms in Benzene Ring of 5-Methylpyrimidine Pyridine Derivatives Affect the Inhibition Ability of EGFRL858R/T790M/C797S Inhibitors: A Molecular Dynamics Simulation Study

Molecules ◽  
2020 ◽  
Vol 25 (4) ◽  
pp. 895
Author(s):  
Jingwen E ◽  
Ye Liu ◽  
Shanshan Guan ◽  
Zhijian Luo ◽  
Fei Han ◽  
...  
Keyword(s):  
Growth Factor Receptor ◽  
Inhibitory Effect ◽  
Kinase Domain ◽  
Free Energy Calculations ◽  
Dynamics Simulation ◽  
Inhibition Mechanism ◽  
Dynamic Simulations ◽  
Lung Cancers ◽  
Two Factors ◽  
Epidermal Growth

Lung cancer is the most frequent cause of cancer-related deaths worldwide, and mutations in the kinase domain of the epidermal growth factor receptor (EGFR) are a common cause of non-small-cell lung cancers, which is a major subtype of lung cancers. Recently, a series of 5-methylpyrimidine-pyridinone derivatives have been designed and synthesized as novel selective inhibitors of EGFR and EGFR mutants. However, the binding-based inhibition mechanism has not yet been determined. In this study, we carried out molecular dynamic simulations and free-energy calculations for EGFR derivatives to fill this gap. Based on the investigation, the three factors that influence the inhibitory effect of inhibitors are as follows: (1) The substitution site of the Cl atom is the main factor influencing the activity through steric effect; (2) The secondary factors are repulsion between the F atom (present in the inhibitor) and Glu762, and the blocking effect of Lys745 on the phenyl ring of the inhibitor. (3) The two factors function synergistically to influence the inhibitory capacity of the inhibitor. The theoretical results of this study can provide further insights that will aid the design of oncogenic EGFR inhibitors with high selectivity.

Spotting Differences in Molecular Dynamic Simulations of Influenza A M2 Protein-Ligand Complexes by Varying M2 construct, Lipid Bilayer and Force Field

2019 ◽  
Author(s):  
Dimitrios Kolokouris ◽  
Iris Kalenderoglou ◽  
Panagiotis Lagarias ◽  
Antonios Kolocouris
Keyword(s):  
Molecular Dynamic ◽  
Lipid Bilayer ◽  
Influenza A ◽  
Md Simulations ◽  
Membrane Curvature ◽  
Buffer Size ◽  
M2 Protein ◽  
Dynamic Simulations ◽  
Amphipathic Helices ◽  
Drug Protein Binding

<p>We studied by molecular dynamic (MD) simulations systems including the inward<sub>closed</sub> state of influenza A M2 protein in complex with aminoadamantane drugs in membrane bilayers. We varied the M2 construct and performed MD simulations in M2TM or M2TM with amphipathic helices (M2AH). We also varied the lipid bilayer by changing either the lipid, DMPC or POPC, POPE or POPC/cholesterol (chol), or the lipids buffer size, 10x10 Å<sup>2 </sup>or 20x20 Å<sup>2</sup>. We aimed to suggest optimal system conditions for the computational description of this ion channel and related systems. Measures performed include quantities that are available experimentally and include: (a) the position of ligand, waters and chlorine anion inside the M2 pore, (b) the passage of waters from the outward Val27 gate of M2 S31N in complex with an aminoadamantane-aryl head blocker, (c) M2 orientation, (d) the AHs conformation and structure which is affected from interactions with lipids and chol and is important for membrane curvature and virus budding. In several cases we tested OPLS2005, which is routinely applied to describe drug-protein binding, and CHARMM36 which describes reliably protein conformation. We found that for the description of the ligands position inside the M2 pore, a 10x10 Å<sup>2</sup> lipids buffer in DMPC is needed when M2TM is used but 20x20 Å<sup>2</sup> lipids buffer of the softer POPC; when M2AH is used all 10x10 Å<sup>2</sup> lipid buffers with any of the tested lipids can be used. For the passage of waters at least M2AH with a 10x10 Å<sup>2</sup> lipid buffer is needed. The folding conformation of AHs which is defined from hydrogen bonding interactions with the bilayer and the complex with chol is described well with a 10x10 Å<sup>2</sup> lipids buffer and CHARMM36. </p>

Effects of viscosity and osmotic stress on the reaction of human butyrylcholinesterase with cresyl saligenin phosphate, a toxicant related to aerotoxic syndrome: kinetic and molecular dynamics studies

2013 ◽  
Vol 454 (3) ◽  
pp. 387-399 ◽  
Author(s):  
Patrick Masson ◽  
Sofya Lushchekina ◽  
Lawrence M. Schopfer ◽  
Oksana Lockridge
Keyword(s):  
Osmotic Stress ◽  
Osmotic Pressure ◽  
Active Site ◽  
Md Simulations ◽  
Catalytic Triad ◽  
Wild Type ◽  
Irreversible Inhibitor ◽  
Enzyme Active Site ◽  
Diffusion Controlled ◽  
Peripheral Site

CSP (cresyl saligenin phosphate) is an irreversible inhibitor of human BChE (butyrylcholinesterase) that has been involved in the aerotoxic syndrome. Inhibition under pseudo-first-order conditions is biphasic, reflecting a slow equilibrium between two enzyme states E and E′. The elementary constants for CSP inhibition of wild-type BChE and D70G mutant were determined by studying the dependence of inhibition kinetics on viscosity and osmotic pressure. Glycerol and sucrose were used as viscosogens. Phosphorylation by CSP is sensitive to viscosity and is thus strongly diffusion-controlled (kon≈108 M−1·min−1). Bimolecular rate constants (ki) are about equal to kon values, making CSP one of the fastest inhibitors of BChE. Sucrose caused osmotic stress because it is excluded from the active-site gorge. This depleted the active-site gorge of water. Osmotic activation volumes, determined from the dependence of ki on osmotic pressure, showed that water in the gorge of the D70G mutant is more easily depleted than that in wild-type BChE. This demonstrates the importance of the peripheral site residue Asp70 in controlling the active-site gorge hydration. MD simulations provided new evidence for differences in the motion of water within the gorge of wild-type and D70G enzymes. The effect of viscosogens/osmolytes provided information on the slow equilibrium E⇌E′, indicating that alteration in hydration of a key catalytic residue shifts the equilibrium towards E′. MD simulations showed that glycerol molecules that substitute for water molecules in the enzyme active-site gorge induce a conformational change in the catalytic triad residue His438, leading to the less reactive form E′.

scholarly journals An Analysis Based on Molecular Docking and Molecular Dynamics Simulation Study of Bromelain as Anti-SARS-CoV-2 Variants

2021 ◽  
Vol 12 ◽  
Author(s):  
Trina Ekawati Tallei ◽  
Fatimawali ◽  
Afriza Yelnetty ◽  
Rinaldi Idroes ◽  
Diah Kusumawaty ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Three Dimensional ◽  
Md Simulations ◽  
Inhibitory Effect ◽  
Dynamics Simulation ◽  
Novel Coronavirus

The rapid spread of a novel coronavirus known as SARS-CoV-2 has compelled the entire world to seek ways to weaken this virus, prevent its spread and also eliminate it. However, no drug has been approved to treat COVID-19. Furthermore, the receptor-binding domain (RBD) on this viral spike protein, as well as several other important parts of this virus, have recently undergone mutations, resulting in new virus variants. While no treatment is currently available, a naturally derived molecule with known antiviral properties could be used as a potential treatment. Bromelain is an enzyme found in the fruit and stem of pineapples. This substance has been shown to have a broad antiviral activity. In this article, we analyse the ability of bromelain to counteract various variants of the SARS-CoV-2 by targeting bromelain binding on the side of this viral interaction with human angiotensin-converting enzyme 2 (hACE2) using molecular docking and molecular dynamics simulation approaches. We have succeeded in making three-dimensional configurations of various RBD variants using protein modelling. Bromelain exhibited good binding affinity toward various variants of RBDs and binds right at the binding site between RBDs and hACE2. This result is also presented in the modelling between Bromelain, RBD, and hACE2. The molecular dynamics (MD) simulations study revealed significant stability of the bromelain and RBD proteins separately up to 100 ns with an RMSD value of 2 Å. Furthermore, despite increases in RMSD and changes in Rog values of complexes, which are likely due to some destabilized interactions between bromelain and RBD proteins, two proteins in each complex remained bonded, and the site where the two proteins bind remained unchanged. This finding indicated that bromelain could have an inhibitory effect on different SARS-CoV-2 variants, paving the way for a new SARS-CoV-2 inhibitor drug. However, more in vitro and in vivo research on this potential mechanism of action is required.

scholarly journals Investigations on Forming Ether Coated Iron Nanoparticle Materials by First-Principle Calculations and Molecular Dynamic Simulations

Coatings ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 395 ◽  
Author(s):  
Junlei Sun ◽  
Shixuan Hui ◽  
Pingan Liu ◽  
Ruochen Sun ◽  
Mengjun Wang
Keyword(s):  
Molecular Dynamic ◽  
Md Simulations ◽  
First Principle ◽  
Sphere Model ◽  
Dynamic Simulations ◽  
First Principle Calculations ◽  
Binding Force ◽  
Adsorption Behaviors ◽  
Single Sphere ◽  
To Come

The mechanism of coating effects between ether molecules and iron (Fe) nanoparticles was generally estimated using first-principle calculations and molecular dynamic (MD) simulations coupling with Fe (110) crystal layers and sphere models. In the present work, the optimized adsorption site and its energy were confirmed. The single sphere model in MD simulations was studied for typical adsorption behaviors, and the double sphere model was built to be more focused on the gap impact between two particles. In those obtained results, it is demonstrated that ether molecules were prone to be adsorbed on the long bridge site of the Fe (110) crystal while comparing with other potential sites. Although the coating was not completely uniform at early stages, the formation of ether layer ended up being equilibrated finally. Accompanied with charge transfer, those coated ether molecules exerted much binding force on the shell Fe atoms. Additionally, when free ether molecules were close to the gap between two nanoparticles, they were found to come under double adsorption effects. Although this effect might not be sufficient to keep them adsorbed, the movement of these ether molecules were hindered to some extent.

scholarly journals Graphene Adhesion Mechanics on Iron Substrates: Insight from Molecular Dynamic Simulations

Crystals ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 579 ◽  
Author(s):  
Wang ◽  
Jin ◽  
Yang ◽  
Zong ◽  
Peng
Keyword(s):  
Molecular Dynamic ◽  
Surface Engineering ◽  
Graphene Nanosheets ◽  
Pair Potential ◽  
Md Simulations ◽  
Adhesion Energy ◽  
Dynamic Simulations ◽  
Embedded Atom ◽  
Adhesion Mechanics ◽  
Eam Potential

The adhesion feature of graphene on metal substrates is important in graphene synthesis, transfer and applications, as well as for graphene-reinforced metal matrix composites. We investigate the adhesion energy of graphene nanosheets (GNs) on iron substrate using molecular dynamic (MD) simulations. Two Fe–C potentials are examined as Lennard–Jones (LJ) pair potential and embedded-atom method (EAM) potential. For LJ potential, the adhesion energies of monolayer GN are 0.47, 0.62, 0.70 and 0.74 J/m2 on the iron {110}, {111}, {112} and {100} surfaces, respectively, compared to the values of 26.83, 24.87, 25.13 and 25.01 J/m2 from EAM potential. When the number of GN layers increases from one to three, the adhesion energy from EAM potential increases. Such a trend is not captured by LJ potential. The iron {110} surface is the most adhesive surface for monolayer, bilayer and trilayer GNs from EAM potential. The results suggest that the LJ potential describes a weak bond of Fe–C, opposed to a hybrid chemical and strong bond from EAM potential. The average vertical distances between monolayer GN and four iron surfaces are 2.0–2.2 Å from LJ potential and 1.3–1.4 Å from EAM potential. These separations are nearly unchanged with an increasing number of layers. The ABA-stacked GN is likely to form on lower-index {110} and {100} surfaces, while the ABC-stacked GN is preferred on higher-index {111} surface. Our insights of the graphene adhesion mechanics might be beneficial in graphene growing, surface engineering and enhancement of iron using graphene sheets.

Preliminary multiscale studies of the montmorillonite, amylose and fatty acids for polymer-clay nanocomposite modeling

MRS Advances ◽  
2019 ◽  
Vol 4 (20) ◽  
pp. 1155-1160
Author(s):  
Felipe A. R. Silva ◽  
Maria J. A. Sales ◽  
Mohamed Ghoul ◽  
Latifa Chebil ◽  
Elaine R. Maia
Keyword(s):  
Vegetable Oil ◽  
Dissipative Particle Dynamics ◽  
Md Simulations ◽  
Theoretical Work ◽  
Molecular Systems ◽  
Polymer Clay Nanocomposite ◽  
Starting Point ◽  
Complex Models ◽  
Experimental Findings ◽  
Materials Studio

Abstract:This work presents the mesoscale step of a theoretical study of a Polymer-Clay Nanocomposite (PCN) composed by starch, pequi vegetable oil and montmorillonite (MMT), a phyllosilicate. In the present study, amylose oligomers, oleic, palmitic and stearic acids in the proportion found in that vegetable oil and MMT were studied, as a simplified model, in order to simulate in multiscale their structural and behavioral correlations. The calculations were carried out by Dissipative Particle Dynamics (DPD), at 363 K, using Materials StudioTM suite. The DPD model had its interaction parameters calculated from previous MD simulations. It was observed that the organic material concentrated near the MMT surfaces, which correlated with the MD results, implying in the validity of the model. The new knowledge acquired about those molecular systems, works as a starting point to build more complex models and, if the theoretical work converge with the experimental findings, encourages further studies in the design of PCNs with biopolymers.

scholarly journals Solvent-induced depletion interactions in multiparticle collision dynamic simulations

2019 ◽  
Vol 30 (10) ◽  
pp. 1941008 ◽  
Author(s):  
Martin Wagner ◽  
Marisol Ripoll
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Coarse Grained ◽  
Simulation Methods ◽  
Mesoscale Simulation ◽  
Dynamic Simulations ◽  
Collision Dynamic ◽  
Versatile Tool ◽  
Depletion Interactions

Molecular-dynamics-coupled multiparticle collision dynamic (MPC-MD) simulations have emerged to be an efficient and versatile tool in the description of mesoscale colloidal dynamics. However, the compressibility of the coarse-grained fluid leads to this method being prone to spurious depletion interactions that may dominate the colloidal dynamics. In this paper, we review the existing methodology to deal with these interactions, establish and report depletion measurements, and present a method to avoid artificial depletion in mesoscale simulation methods.

Sign in / Sign up

Export Citation Format

Share Document