scholarly journals Attractive and repulsive residue fragments at the interface of SARS-CoV-2 and hACE2

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jorge H. Rodriguez
Keyword(s):  
Covalent Binding ◽  
Protein Conformations ◽  
X Ray ◽  
X Ray Crystallography ◽  
Binding Domains ◽  
Viral Binding ◽  
Contact Residues ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Intermolecular Recognition

AbstractThe initial stages of SARS-CoV-2 coronavirus attachment to human cells are mediated by non-covalent interactions of viral spike (S) protein receptor binding domains (S-RBD) with human ACE2 receptors (hACE2). Structural characterization techniques, such as X-ray crystallography (XRC) and cryoelectron microscopy (cryo-EM), previously identified SARS-CoV-2 spike protein conformations and their surface residues in contact with hACE2. However, recent quantum-biochemical calculations on the structurally related S-RBD of SARS-CoV-1 identified some contact-residue fragments as intrinsically attractive and others as repulsive. This indicates that not all surface residues are equally important for hACE2 attachment. Here, using similar quantum-biochemical methods, we report some four-residue fragments (i.e quartets) of the SARS-CoV-2 S-RBD as intrinsically attractive towards hACE2 and, therefore, directly promoting host–virus non-covalent binding. Other fragments are found to be repulsive although involved in intermolecular recognition. By evaluation of their respective intermolecular interaction energies we found two hACE2 fragments that include contact residues (ASP30, LYS31, HIS34) and (ASP38, TYR41, GLN42), respectively, behaving as important SARS-CoV-2 attractors. LYS353 also promotes viral binding via several mechanisms including dispersion van der Waals forces. Similarly, among others, three SARS-CoV-2 S-RBD fragments that include residues (GLN498, THR500, ASN501), (GLU484, PHE486, ASN487) and (LYS417), respectively, were identified as hACE2 attractors. In addition, key hACE2 quartets identified as weakly-repulsive towards the S-RBD of SARS-CoV-1 were found strongly attractive towards SARS-CoV-2 explaining, in part, the stronger binding affinity of hACE2 towards the latter coronavirus. These findings may guide the development of synthetic antibodies or identify potential viral epitopes.

Probing non-covalent interactions driving molecular assembly in organo-electronic building blocks

CrystEngComm ◽  
2019 ◽  
Vol 21 (20) ◽  
pp. 3151-3157 ◽  
Author(s):  
Sarah N. Johnson ◽  
Thomas L. Ellington ◽  
Duong T. Ngo ◽  
Jorge L. Nevarez ◽  
Nicholas Sparks ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Density Functional ◽  
Building Blocks ◽  
Molecular Assembly ◽  
Functional Theory ◽  
X Ray ◽  
X Ray Crystallography ◽  
Non Covalent Interactions ◽  
Density Functional Theory Computations ◽  
Covalent Interactions

One co-crystal structure characterized to identify and quantify various non-covalent interactions with spectroscopy, X-ray crystallography and density functional theory computations.

Organometallic pyrene-containing porphyrins: Synthesis, characterization, and non-covalent interactions with C60 fullerenes

2016 ◽  
Vol 20 (08n11) ◽  
pp. 1098-1113 ◽  
Author(s):  
Yang Li ◽  
Hannah M. Rhoda ◽  
Anthony M. Wertish ◽  
Victor N. Nemykin
Keyword(s):  
Excited States ◽  
Electronic Structures ◽  
Density Functional ◽  
Functional Theory ◽  
X Ray ◽  
X Ray Crystallography ◽  
H Nmr ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
C60 Fullerenes

A reaction between 5,10,15,20-tetra(4-hydroxyphenyl)porphyrin and 1-bromopyrene resulted in the formation of 5,10,15,20-tetra[4-(4-(pyrenyl-1)butoxy)phenyl]porphyrin (1), while cross-condensation between 4-(4-(pyrenyl-1)butoxy)benzaldehyde, ferrocenecaboxaldehyde, and pyrrole resulted in the formation of 5-ferrocenyl-10,15,20-tri[4-(4-(pyrenyl-1)butoxy)phenyl]porphyrin (2), 5,10-diferrocenyl-15,20-di[4-(4-(pyrenyl-1)butoxy)phenyl]porphyrin (3), and 5,15-diferrocenyl-10,20-di[4-(4-(pyrenyl-1)butoxy)phenyl]porphyrin (4). All pyrene-containing porphyrins were characterized by 1H NMR, UV-vis, MCD, and high-resolution ESI methods, while their electronic structures and the nature of the excited states were elucidated using density functional theory (DFT) and time-dependent DFT (TDDFT) calculations. The molecular structure of 1 and its fluorescence quenching upon the addition of C[Formula: see text] fullerene was also investigated using X-ray crystallography and steady-state fluorescence approaches.

scholarly journals Organotrifluoroborates as attractive self-assembling systems: the case of bifunctional dipotassium phenylene-1,4-bis(trifluoroborate)

2015 ◽  
Vol 44 (45) ◽  
pp. 19447-19450 ◽  
Author(s):  
Aurelia Falcicchio ◽  
Sten O. Nilsson Lill ◽  
Filippo M. Perna ◽  
Antonio Salomone ◽  
Donato I. Coppi ◽  
...  
Keyword(s):  
Computational Chemistry ◽  
Self Assembly ◽  
X Ray ◽  
Dipotassium Salt ◽  
X Ray Crystallography ◽  
Self Assembling ◽  
Non Covalent Interactions ◽  
Covalent Interactions

A multitude of non-covalent interactions, investigated by X-ray crystallography and computational chemistry techniques, proved to be responsible of the spontaneous self-assembly of a bis(trifluoroborate) dipotassium salt.

scholarly journals Chiral Self-Sorting in Truxene-Based Metallacages

Inorganics ◽  
2019 ◽  
Vol 8 (1) ◽  
pp. 1 ◽  
Author(s):  
Simon Séjourné ◽  
Antoine Labrunie ◽  
Clément Dalinot ◽  
Amina Benchohra ◽  
Vincent Carré ◽  
...  
Keyword(s):  
Solid State ◽  
The Self ◽  
X Ray ◽  
X Ray Crystallography ◽  
Self Assembling ◽  
Sorting Process ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Two chiral face-rotating metalla-assembled polyhedra were constructed upon self-assembling achiral components, i.e., a tritopic ligand based on a truxene core (10,15-dihydro-5H-diindeno[1,2-a;1′,2′-c]fluorene) and two different hydroxyquinonato–bridged diruthenium complexes. Both polyhedra were characterized in solution as well as in the solid state by X-ray crystallography. In both cases, the self-sorting process leading to only two homo-chiral enantiomers was governed by non-covalent interactions between both truxene units that faced each other.

scholarly journals Investigation of the synthesis of water-soluble 1,3,5-trihydroxy-2,4,6- trimethylsulfonic acid benzene, its complexes with lanthanide cations and sulfonato-resorcin[4]arenes, and the study of gas storage in iodine doped p-tert-butylcalix[4]arenes

2014 ◽  
Author(s):  
◽  
Makabodee Ruaysap
Keyword(s):  
Metal Ions ◽  
Single Crystal ◽  
13C Nmr ◽  
Gas Storage ◽  
Hydrogen Gas ◽  
Water Soluble ◽  
X Ray ◽  
X Ray Crystallography ◽  
Non Covalent Interactions ◽  
Covalent Interactions

The design of new calixarene derivatives based on supramolecular principles -- the formation of molecules, ions, or complex ions with the weak non-covalent interactions to form a larger moiety with applicable properties compositioned by the starting material's attributes -- has attracted attention in many scientific fields. Herein, the new synthesis method of 1,3,5-trihydroxy-2,4,6-trimethylenesulfonic acid benzene, 1 was studied. As a result, the new synthetic method was less complicated and required fewer steps than that of the previous work. This compound also presents a novel tautomeric conformational change using NMR spectroscopy. Furthermore, the lanthanide (Sm, Eu, La, Ho, and Nd) complexes of 1 are isostructural and the packing of the complexes is a bilayer structure arrangement with ?-stacking between the benzene rings. In addition, the study investigated the formation of tetramethylsulfonatoresorcin[4]arenes, a diaza-18-crown-6, and LN(III) metal ions such as europium (Eu) holmium (Ho), and samarium (Sm) and their crystalline structures using single crystal X-ray crystallography. The results show the various ways that these molecules can assemble into different supramolecular frameworks. Different solvents result in drastically the different packing of these molecules resulting in the diverse range of packing motifs. Hydrogen gas-storage properties of modified p-tert-butylcalix[4]arenes with doping by iodine molecules (I2 doped TBC4) was studied. The iodine-doped p-tert-butylcalix[4]arenes are structurally studied by using the 1H-NMR, 13C-NMR in liquid and solid-state 13C-NMR, and single crystal X-ray crystallography. The decomposition temperature was studied by thermogravimetric analysis. Iodine doped p-tertbutylcalix[4]arenes show an evidence of hydrogen gas-sorption which is a good sign that the new material, Iodine-doped - p-tert-butylcalix[4]arenes can possibly be developed for hydrogen gas storage in the future. Notably, the weak non-covalent interactions that are often responsible for the formation of supramolecules are also responsible for reversible adsorption/desorption properties found in host-guest systems. Examples of guest species include gases, organic molecules, inorganic complexes, and metal ions. Therefore, this research is dedicated to exploring and designing new materials for sorption/desorption purposes, as they may be useful in storage of fuel gases, for carrying/releasing drugs to the target parts of the body, or used as biological mimics.

scholarly journals Phosphorus Kβ X-Ray emission spectroscopy detects non-covalent interactions of phosphate biomolecules in situ

2021 ◽  
Author(s):  
Zachary Mathe ◽  
Olivia McCubbin Stepanic ◽  
Sergey Peredkov ◽  
Serena DeBeer
Keyword(s):  
Nucleic Acids ◽  
Emission Spectroscopy ◽  
Adenine Nucleotides ◽  
X Ray ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Phosphate Groups

Phosphorus is ubiquitous in biochemistry, found in the phosphate groups of nucleic acids and the energy-transferring system of adenine nucleotides (e.g. ATP). Kβ X-ray emission spectroscopy (XES) at phosphorus has...

scholarly journals Weak Interactions in Cocrystals of Isoniazid with Glycolic and Mandelic Acids

Crystals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 328
Author(s):  
Raquel Álvarez-Vidaurre ◽  
Alfonso Castiñeiras ◽  
Antonio Frontera ◽  
Isabel García-Santos ◽  
Diego M. Gil ◽  
...  
Keyword(s):  
Density Functional ◽  
Glycolic Acid ◽  
Weak Interactions ◽  
Three Dimensional ◽  
Functional Theory ◽  
Molecular Systems ◽  
X Ray Crystallography ◽  
Hydroxycarboxylic Acids ◽  
Non Covalent Interactions ◽  
Covalent Interactions

This work deals with the preparation of pyridine-3-carbohydrazide (isoniazid, inh) cocrystals with two α-hydroxycarboxylic acids. The interaction of glycolic acid (H2ga) or d,l-mandelic acid (H2ma) resulted in the formation of cocrystals or salts of composition (inh)·(H2ga) (1) and [Hinh]+[Hma]–·(H2ma) (2) when reacted with isoniazid. An N′-(propan-2-ylidene)isonicotinic hydrazide hemihydrate, (pinh)·1/2(H2O) (3), was also prepared by condensation of isoniazid with acetone in the presence of glycolic acid. These prepared compounds were well characterized by elemental analysis, and spectroscopic methods, and their three-dimensional molecular structure was determined by single crystal X-ray crystallography. Hydrogen bonds involving the carboxylic acid occur consistently with the pyridine ring N atom of the isoniazid and its derivatives. The remaining hydrogen-bonding sites on the isoniazid backbone vary based on the steric influences of the derivative group. These are contrasted in each of the molecular systems. Finally, Hirshfeld surface analysis and Density-functional theory (DFT) calculations (including NCIplot and QTAIM analyses) have been performed to further characterize and rationalize the non-covalent interactions.

Sign in / Sign up

Export Citation Format

Share Document