scholarly journals Molecular modelling of the interaction of carbocyclic analogues of netropsin and distamycin with d(CGCGAATTCGCG)2.

2000 ◽  
Vol 47 (3) ◽  
pp. 855-866 ◽  
Author(s):  
K Bielawski ◽  
A Bielawska ◽  
D Bartulewicz ◽  
A Rózański
Keyword(s):  
Molecular Structure ◽  
Molecular Dynamics ◽  
Complex Formation ◽  
Hydrogen Bonds ◽  
Electrostatic Interactions ◽  
Minor Groove ◽  
Model Complexes ◽  
Dna Minor Groove ◽  
Energetic Analysis ◽  
Effective Penetration

A molecular mechanics and molecular dynamics approach was used to examine the structure of complexes formed between the d(CGCGAATTCGCG)2 duplex and netropsin, distamycin, and four carbocyclic analogues of netropsin and distamycin (1-4). The resulting structures of the ligand-DNA model complexes and their energetics were examined. It is predicted that the compounds 1-4 should have a decreased affinity for the minor groove of AT-rich regions in comparison to netropsin and distamycin. From the energetic analysis it appears that van der Waals and electrostatic interactions are more important than specific hydrogen bonds in stabilizing the ligand-duplex complexes. We predict that compounds 1 and 2 are effectively isohelical with the DNA minor groove. The superior DNA-binding afforded by 1 and 2 in comparison to 3 and 4 results from their more effective penetration into the minor groove and smaller perturbation of molecular structure upon complex formation.

scholarly journals Cooperation/Competition between Halogen Bonds and Hydrogen Bonds in Complexes of 2,6-Diaminopyridines and X-CY3 (X = Cl, Br; Y = H, F)

Symmetry ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 766
Author(s):  
Barbara Bankiewicz ◽  
Marcin Palusiak
Keyword(s):  
Complex Formation ◽  
Hydrogen Bonds ◽  
Dft Calculations ◽  
Electrostatic Interactions ◽  
Dipole Moments ◽  
Main Role ◽  
Halogen Bonds ◽  
Topological Parameters ◽  
Leading Role ◽  
The Impact

The DFT calculations have been performed on a series of two-element complexes formed by substituted 2,6-diaminopyridine (R−PDA) and pyridine (R−Pyr) with X−CY3 molecules (where X = Cl, Br and Y = H, F). The primary aim of this study was to examine the intermolecular hydrogen and halogen bonds in the condition of their mutual coexistence. Symmetry/antisymmetry of the interrelation between three individual interactions is addressed. It appears that halogen bonds play the main role in the stabilization of the structures of the selected systems. However, the occurrence of one or two hydrogen bonds was associated with the favourable geometry of the complexes. Moreover, the impact of different substituent groups attached in the para position to the aromatic ring of the 2,6-diaminopyridine and pyridine on the character of the intermolecular hydrogen and halogen bonds was examined. The results indicate that the presence of electron-donating substituents strengthens the bonds. In turn, the presence of electron-withdrawing substituents reduces the strength of halogen bonds. Additionally, when hydrogen and halogen bonds lose their leading role in the complex formation, the nonspecific electrostatic interactions between dipole moments take their place. Analysis was based on geometric, energetic, and topological parameters of the studied systems.

Molecular dynamics simulations and binding free energy analysis of DNA minor groove complexes of curcumin

2011 ◽  
Vol 17 (11) ◽  
pp. 2805-2816 ◽  
Author(s):  
Mathew Varghese Koonammackal ◽  
Unnikrishnan Viswambharan Nair Nellipparambil ◽  
Chellappanpillai Sudarsanakumar
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulations ◽  
Energy Analysis ◽  
Binding Free Energy ◽  
Minor Groove ◽  
Dna Minor Groove ◽  
Dynamics Simulations ◽  
Free Energy Analysis

Three-centre C—H...O hydrogen bonds in the DNA minor groove: analysis of oligonucleotide crystal structures

1999 ◽  
Vol 55 (12) ◽  
pp. 2005-2012 ◽  
Author(s):  
Anirban Ghosh ◽  
Manju Bansal
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Base Pair ◽  
Minor Groove ◽  
Local Geometry ◽  
Data Sets ◽  
Base Pairs ◽  
Dna Minor Groove ◽  
Close Proximity ◽  
Using Data

AA·TT and GA·TC dinucleotide steps in B-DNA-type oligomeric crystal structures and in protein-bound DNA fragments (solved using data with resolution <2.6 Å) show very small variations in their local dinucleotide geometries. A detailed analysis of these crystal structures reveals that in AA·TT and GA·TC steps the electropositive C2—H2 group of adenine is in very close proximity to the keto O atoms of both the pyrimidine bases in the antiparallel strand of the duplex structure, suggesting the possibility of intra-base pair as well as cross-strand inter-base pair C—H...O hydrogen bonds in the DNA minor groove. The C2—H2...O2 hydrogen bonds in the A·T base pairs could be a natural consequence of Watson–Crick pairing. However, the cross-strand interactions between the bases at the 3′-end of the AA·TT and GA·TC steps obviously arise owing to specific local geometry of these steps, since a majority of the H2...O2 distances in both data sets are considerably shorter than their values in the uniform fibre model (3.3 Å) and many are even smaller than the sum of the van der Waals radii. The analysis suggests that in addition to already documented features such as the large propeller twist of A·T base pairs and the hydration of the minor groove, these C2—H2...O2 cross-strand interactions may also play a role in the narrowing of the minor groove in A-tract regions of DNA and help explain the high structural rigidity and stability observed for poly(dA)·poly(dT).

A thermodynamic and structural analysis of DNA minor-groove complex formation 1 1Edited by I. Tinoco

2000 ◽  
Vol 300 (2) ◽  
pp. 321-337 ◽  
Author(s):  
Suzann Mazur ◽  
Farial A. Tanious ◽  
Daoyuan Ding ◽  
Arvind Kumar ◽  
David W. Boykin ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Complex Formation ◽  
Minor Groove ◽  
Dna Minor Groove

scholarly journals Four pyrrole derivatives used as building blocks in the synthesis of minor-groove binders

2017 ◽  
Vol 73 (2) ◽  
pp. 254-259 ◽  
Author(s):  
Alan R. Kennedy ◽  
Abedawn I. Khalaf ◽  
Fraser J. Scott ◽  
Colin J. Suckling
Keyword(s):  
Hydrogen Bonds ◽  
Pyrrole Ring ◽  
Building Blocks ◽  
Minor Groove ◽  
The Other ◽  
Pyrrole Derivatives ◽  
Dna Minor Groove ◽  
Minor Groove Binders ◽  
Modified Dna ◽  
Groove Binders

The title nitropyrrole-based compounds, C7H8N2O4, (I) (ethyl 4-nitro-1H-pyrrole-2-carboxylate), its derivative C12H14N2O4, (II) [ethyl 4-nitro-1-(4-pentynyl)-1H-pyrrole-2-carboxylate], C15H26N4O3, (III) {N-[3-(dimethyamino)propyl]-1-isopentyl-4-nitro-1H-pyrrole-2-carboxamide}, and C20H27N9O5, (IV) {1-(3-azidopropyl)-4-(1-methyl-4-nitro-1H-pyrrole-2-carboxamido)-N-[2-(morpholin-4-yl)ethyl]-1H-pyrrole-2-carboxamide}, are intermediates used in the synthesis of modified DNA minor-groove binders. In all four compounds, the nitro groups lie in the plane of the pyrrole ring. In compounds (I) and (II), the ester groups also lie in the plane of the pyrrole ring. In compound (III), both of the other substituents lie out of the plane of the pyrrole ring. In the case of compound (IV), the coplanarity extends to the second pyrrole ring and through both amide groups. In the crystals of all four compounds, layer-like structures are formed,viaa combination of N—H...O and C—H...O hydrogen bonds for (I), (III) and (IV), but by only C—H...O hydrogen bonds for (II).

scholarly journals Intra- and Interpolyelectrolyte Complexes of Polyampholytes

2018 ◽  
Author(s):  
Sarkyt Kudaibergenov ◽  
Nurxat Nuraje
Keyword(s):  
Complex Formation ◽  
Hydrogen Bonds ◽  
Electrostatic Interactions ◽  
Water Soluble ◽  
Polymer Complex ◽  
Dye Molecules ◽  
Interpolymer Complexes ◽  
Interpolyelectrolyte Complexes ◽  
Points Of View

At present, a large amount of research works from experimental and theoretical points of view have been done on interpolyelectrolyte complexes formed by electrostatic interactions and/or interpolymer complexes stabilized by hydrogen bonds. On the contrary, relatively less attention has been given to polymer-polymer complex formation with synthetic polyampholytes. In this review the complexation of polyampholytes with polyelectrolytes is considered from theoretical and application points of view. Formation of intra- and interpolyelectrolyte complexes of random, regular, block, dendritic polyampholytes are outlined. The separate subchapter is devoted to amphoteric behavior of interpolyelectrolyte complexes. The realization of so-called &ldquo;isoelectric effect&rdquo; for interpolyelectrolyte complexes of water-soluble polyampholytes, amphoteric hydrogels and cryogels with respect to surfactants, dye molecules, polyelectrolytes and proteins is demonstrated.

scholarly journals SARS-Cov-2 Spike binding to ACE2 is stronger and longer ranged with glycans

2021 ◽  
Author(s):  
Yihan Huang ◽  
Bradley S Harris ◽  
Shiaki A Minami ◽  
Seongwon Jung ◽  
Priya Shah ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Electrostatic Interactions ◽  
Spike Protein ◽  
Binding Strength ◽  
Lennard Jones ◽  
Binding Domains ◽  
Interaction Mode ◽  
Dynamics Simulations ◽  
New Interactions

Highly detailed steered Molecular Dynamics simulations are performed on differently glycosylated receptor binding domains of the SARS-CoV-2 spike protein. The binding strength and the binding range increases with glycosylation. The interaction energy rises very quickly with pulling the proteins apart and only slowly drops at larger distances. We see a catch slip type behavior where interactions during pulling break and are taken over by new interactions forming. The dominant interaction mode are hydrogen bonds but Lennard-Jones and electrostatic interactions are relevant as well.

Sign in / Sign up

Export Citation Format

Share Document