scholarly journals Nanomechanics combined with HDX reveal allosteric drug binding sites of CFTR NBD1

2021 ◽  
Author(s):  
Rita Padanyi ◽  
Bianka Farkas ◽  
Hedvig Tordai ◽  
Balint Kiss ◽  
Helmut Grubmuller ◽  
...  
Keyword(s):  
Binding Sites ◽  
Thermal Stabilization ◽  
Drug Efficacy ◽  
Md Simulations ◽  
Drug Binding ◽  
Structural Defects ◽  
Mechanical Resistance ◽  
Atomic Force ◽  
Δf508 Cftr ◽  
Hydrogen Deuterium

Cystic fibrosis is most frequently caused by the deletion of F508 (ΔF508) in CFTR's nucleotide binding domain 1 (NBD1), thereby compromising CFTR folding, stability and domain assembly. Limitation to develop a successful therapy has been attributed to the lack of molecules that synergistically facilitate folding by targeting distinct structural defects of ΔF508-CFTR. To improve drug efficacy by targeting the ΔF508-NBD1 folding and stability, and to study potential ΔF508-NBD1 allosteric corrector binding sites at the atomic level, we combined molecular dynamics (MD) simulations, atomic force spectroscopy (AFM) and hydrogen-deuterium exchange (HDX) experiments to elucidate the mechanical and thermal stabilization mechanisms of ΔF508-NBD1 by 5-bromoindole-3-acetic acid (BIA). MD and AFM allowed us to describe unfolding intermediates and forces acting during NBD1 mechanical unfolding. Application of the low-potency corrector BIA increased the mechanical resistance of the ΔF508-NBD1 α-subdomain, which was confirmed as a binding site by computational modeling and HDX experiments. Our results underline the complementarity of MD and AFM despite their different pulling speeds and provide a possible strategy to improve folding correctors.

scholarly journals Interaction betweenPlectranthus barbatusherbal tea components and human serum albumin and lysozyme: Binding and activity studies

2011 ◽  
Vol 26 (2) ◽  
pp. 79-92 ◽  
Author(s):  
Pedro L. V. Falé ◽  
Lia Ascensão ◽  
Maria L. M. Serralheiro ◽  
Parvez I. Haris
Keyword(s):  
Plant Extract ◽  
Binding Sites ◽  
Rosmarinic Acid ◽  
Tertiary Structure ◽  
Lysozyme Activity ◽  
Deuterium Exchange ◽  
Drug Binding ◽  
Hydrogen Deuterium Exchange ◽  
Fatty Acid Binding ◽  
Hydrogen Deuterium

Anti-cholinesterase and antioxidant active constituents ofPlectranthus barbatusaqueous extract were found in plasma of rats after its administration – rosmarinic acid, luteolin and apigenin. The aim of the present work is to determine if the extract components can interact with human plasma proteins, namely albumin and lysozyme. Protein intrinsic fluorescence analysis showed that the plant phenolic compounds may bind to albumin, the main transport protein in plasma, and to lysozyme. The estimated thermodynamic parameters suggest that the main intermolecular interaction is hydrophobic association. FTIR analysis of the protein amide bands showed that the plant extract components do not alter the secondary structure of either albumin or lysozyme, however the rate of hydrogen–deuterium exchange suggests that tertiary structure changes might have occurred. An increase of hydrogen deuterium exchange suggests that rosmarinic acid may bind to the fatty acid binding sites in albumin, while luteolin and apigenin may bind to the drug binding sites. The plant extract components also inhibit lysozyme activity with IC50values around 100 μM. ThereforeP. barbatusherbal tea, rosmarinic acid, luteolin and apigenin interact and may be transported by albumin and lysozyme. The inhibition of lysozyme activity may be an additional mechanism for its anti-inflammatory activity.

scholarly journals How does a small molecule bind at a cryptic binding site?

2021 ◽  
Author(s):  
Yibing Shan ◽  
Venkatesh P. Mysore ◽  
Abba E. Leffler ◽  
Eric T. Kim ◽  
Shiori Sagawa ◽  
...  
Keyword(s):  
Small Molecules ◽  
Binding Site ◽  
Small Molecule ◽  
Protein Interactions ◽  
Binding Sites ◽  
Rational Design ◽  
Structural Information ◽  
Interleukin 2 ◽  
Md Simulations ◽  
Drug Binding

Protein-protein interactions (PPIs) are ubiquitous biomolecular processes that are central to virtually all aspects of cellular function. Identifying small molecules that modulate specific disease-related PPIs is a strategy with enormous promise for drug discovery. The design of drugs to disrupt PPIs is challenging, however, because many potential drug-binding sites at PPI interfaces are "cryptic": When unoccupied by a ligand, cryptic sites are often flat and featureless, and thus not readily recognizable in crystal structures, with the geometric and chemical characteristics of typical small-molecule binding sites only emerging upon ligand binding. The rational design of small molecules to inhibit specific PPIs would benefit from a better understanding of how such molecules bind at PPI interfaces. To this end, we have conducted unbiased, all-atom MD simulations of the binding of four small-molecule inhibitors (SP4206 and three SP4206 analogs) to interleukin 2 (IL2)—which performs its function by forming a PPI with its receptor—without incorporating any prior structural information about the ligands' binding. In multiple binding events, a small molecule settled into a stable binding pose at the PPI interface of IL2, resulting in a protein–small-molecule binding site and pose virtually identical to that observed in an existing crystal structure of the IL2-SP4206 complex. Binding of the small molecule stabilized the IL2 binding groove, which when the small molecule was not bound emerged only transiently and incompletely. Moreover, free energy perturbation (FEP) calculations successfully distinguished between the native and non-native IL2–small-molecule binding poses found in the simulations, suggesting that binding simulations in combination with FEP may provide an effective tool for identifying cryptic binding sites and determining the binding poses of small molecules designed to disrupt PPI interfaces by binding to such sites.

Study of Biomolecules Imaging Using Molecular Dynamics Simulations

NANO ◽  
2015 ◽  
Vol 10 (07) ◽  
pp. 1550096 ◽  
Author(s):  
Mohsen Kheirodin ◽  
Hossein Nejat Pishkenari ◽  
Ali Moosavi ◽  
Ali Meghdari
Keyword(s):  
Molecular Dynamics ◽  
Small Diameter ◽  
Operating Mode ◽  
Md Simulations ◽  
Mechanical Resistance ◽  
Atomic Force ◽  
Number Of Layers ◽  
Sample Structure ◽  
Afm Probe ◽  
Dynamics Simulations

The process of imaging a biomolecule by atomic force microscope (AFM) is modeled using molecular dynamics (MD) simulations. Since the large normal force exerted by the tip on the biosample in contact and tapping modes may damage the sample structure and produce irreversible deformation, the noncontact mode of AFM (NC-AFM) is employed as the operating mode. The biosample is scanned using a carbon nanotube (CNT) as the AFM probe. CNTs because of their small diameter, high aspect ratio and high mechanical resistance attract many attentions for imaging purposes. The tip–sample interaction is simulated by the MD method. The protein, which has been considered as the biomolecule, is ubiquitin and a graphene sheet is used as the substrate. The effects of CNT's geometric parameters such as the CNT height, the diameter, the tilt angle, the flexibility and the number of layers on the image quality have been evaluated.

Identification of Drug Binding Sites and Action Mechanisms with Molecular Dynamics Simulations

2019 ◽  
Vol 18 (27) ◽  
pp. 2268-2277 ◽  
Author(s):  
Yang Wang ◽  
Cecylia Severin Lupala ◽  
Haiguang Liu ◽  
Xubo Lin
Keyword(s):  
Molecular Dynamics ◽  
Drug Discovery ◽  
Binding Sites ◽  
Lipid Membrane ◽  
Md Simulations ◽  
Drug Action ◽  
Drug Binding ◽  
Action Mechanisms ◽  
Drug Binding Sites ◽  
Dynamics Simulations

Identifying drug binding sites and elucidating drug action mechanisms are important components in a drug discovery process. In this review, we briefly compared three different approaches (sequence- based methods, structure-based methods and probe-based molecular dynamics (MD) methods) to identifying drug binding sites, and concluded that probe-based MD methods are much more advantageous in dealing with flexible target macromolecules and digging out druggable macromolecule conformations for subsequent drug screening. The applications of MD simulation to studying drug-target interactions were demonstrated with different types of target molecules, including lipid membrane, protein and DNA. The results indicate that MD simulations with enhanced sampling methods provide a powerful tool to determine free energy profiles/surfaces and identify important intermediate states, which are essential for the elucidation of drug action mechanisms. The future development of methods in MD simulations will benefit and speed up the drug discovery processes.

Targeting Breast Cancer Cells with G4 PAMAM Dendrimers and Valproic Acid Derivative Complexes

2020 ◽  
Vol 20 (15) ◽  
pp. 1857-1872
Author(s):  
Alberto M. Muñoz ◽  
Manuel J. Fragoso-Vázquez ◽  
Berenice P. Martel ◽  
Alma Chávez-Blanco ◽  
Alfonso Dueñas-González ◽  
...  
Keyword(s):  
Valproic Acid ◽  
Cell Lines ◽  
Water Solubility ◽  
Md Simulations ◽  
Pamam Dendrimer ◽  
Pamam Dendrimers ◽  
Force Microscopy ◽  
Micromolar Concentration ◽  
Atomic Force

Background: Our research group has developed some Valproic Acid (VPA) derivatives employed as anti-proliferative compounds targeting the HDAC8 enzyme. However, some of these compounds are poorly soluble in water. Objective: Employed the four generations of Polyamidoamine (G4 PAMAM) dendrimers as drug carriers of these compounds to increase their water solubility for further in vitro evaluation. Methods: VPA derivatives were subjected to Docking and Molecular Dynamics (MD) simulations to evaluate their affinity on G4 PAMAM. Then, HPLC-UV/VIS, 1H NMR, MALDI-TOF and atomic force microscopy were employed to establish the formation of the drug-G4 PAMAM complexes. Results: The docking results showed that the amide groups of VPA derivatives make polar interactions with G4 PAMAM, whereas MD simulations corroborated the stability of the complexes. HPLC UV/VIS experiments showed an increase in the drug water solubility which was found to be directly proportional to the amount of G4 PAMAM. 1H NMR showed a disappearance of the proton amine group signals, correlating with docking results. MALDI-TOF and atomic force microscopy suggested the drug-G4 PAMAM dendrimer complexes formation. Discussion: In vitro studies showed that G4 PAMAM has toxicity in the micromolar concentration in MDAMB- 231, MCF7, and 3T3-L1 cell lines. VPA CF-G4 PAMAM dendrimer complex showed anti-proliferative properties in the micromolar concentration in MCF-7 and 3T3-L1, and in the milimolar concentration in MDAMB- 231, whereas VPA MF-G4 PAMAM dendrimer complex didn’t show effects on the three cell lines employed. Conclusion: These results demonstrate that G4 PAMAM dendrimers are capableof transporting poorly watersoluble aryl-VPA derivate compounds to increase its cytotoxic activity against neoplastic cell lines.

Visualization of molecular binding sites at the nanoscale in the lift-up mode by amplitude-modulation atomic force microscopy

Nanoscale ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 4213-4220
Author(s):  
Tatsuhiro Maekawa ◽  
Takashi Nyu ◽  
Evan Angelo Quimada Mondarte ◽  
Hiroyuki Tahara ◽  
Kasinan Suthiwanich ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Molecular Recognition ◽  
Amplitude Modulation ◽  
Binding Sites ◽  
Local Distribution ◽  
New Approach ◽  
Molecular Binding ◽  
Force Microscopy ◽  
Atomic Force ◽  
Recognition Sites

We report a new approach to visualize the local distribution of molecular recognition sites with nanoscale resolution by amplitude-modulation atomic force microscopy.

Structuring of Silicon Wafer Surfaces on the Sub-100 nm Scale by Hydrogen Plasma Treatments

2003 ◽  
Vol 788 ◽  
Author(s):  
R. Job ◽  
Y. Ma ◽  
A. G. Ulyashin
Keyword(s):  
Hydrogen Plasma ◽  
Structural Defects ◽  
Process Conditions ◽  
Force Microscopy ◽  
Czochralski Silicon ◽  
Atomic Force ◽  
Nano Structures ◽  
Plasma Treatments ◽  
The Impact ◽  
Wafer Surfaces

ABSTRACTHydrogen plasma treatments applied on standard Czochralski silicon (Cz Si) wafers cause a structuring of the surface regions on the sub-100 nm scale, i.e. a thin ‘nano-structured’ Si layer is created up to a depth of ∼ 150 nm. The formation of the ‘nano-structures’ and their evolution in dependence on the process conditions was studied. The impact of post-hydrogenation annealing on the morphology of the structural defects was studied up to 1200 °C. The H-plasma treated and annealed samples were analyzed at surface and sub-surface regions by scanning electron microscopy (SEM), atomic force microscopy (AFM), and μ-Raman spectroscopy.

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