10 research outputs found
Molecular Mechanisms in the Selectivity of Nonsteroidal Anti-Inflammatory Drugs
Nonsteroidal
anti-inflammatory drugs (NSAIDs) inhibit cyclooxygenase (COX) 1 and
2 with varying degrees of selectivity. A group of COX-2 selective
inhibitorscoxibsbinds in a time-dependent manner through
a three-step mechanism, utilizing a side pocket in the binding site.
Coxibs have been extensively probed to identify the structural features
regulating the slow tight-binding mechanism responsible for COX-2
selectivity. In this study, we further probe a structurally and kinetically
diverse data set of COX inhibitors in COX-2 by molecular dynamics
and free energy simulations. We find that the features regulating
the high affinities associated with time-dependency in COX depend
on the inhibitor kinetics. In particular, most time-dependent inhibitors
share a common structural binding mechanism, involving an induced-fit
rotation of the side-chain of Leu531 in the main binding pocket. The
high affinities of two-step slow tight-binding inhibitors and some
slow reversible inhibitors can thus be explained by the increased
space in the main binding pocket after this rotation. Coxibs that
belong to a separate class of slow tight-binding inhibitors benefit
more from the displacement of the neighboring side-chain of Arg513,
exclusive to the COX-2 side-pocket. This displacement further stabilizes
the aforementioned rotation of Leu531 and can explain the selectivity
of coxibs for COX-2
Probing the Time Dependency of Cyclooxygenase‑1 Inhibitors by Computer Simulations
Time-dependent
inhibition of the cyclooxygenases (COX) by a range
of nonsteroidal anti-inflammatory drugs has been described since the
first experimental assays of COX were performed. Slow tight-binding
inhibitors of COX-1 bind in a two-step mechanism in which the EI →
EI* transition is slow and practically irreversible. Since then, various
properties of the inhibitors have been proposed to cause or affect
the time dependency. Conformational changes in the enzyme have also
been proposed to cause the time dependency, but no particular structural
feature has been identified. Here, we investigated a series of inhibitors
of COX-1 that are either time-independent or time-dependent using
a combination of molecular dynamics simulations, binding free energy
calculations, and potential of mean force calculations. We find that
the time-dependent inhibitors stabilize a conformational change in
the enzyme mainly identified by the rotation of a leucine side chain
adjacent to the binding pocket. The induced conformation has been
previously shown to be essential for the high binding affinities of
tight-binding inhibitors in COX-1. The results of this work show that
the structural features of the enzyme involved in both time-dependent
and tight-binding inhibition are identical and further identify a
structural mechanism responsible for the transition between the two
enzyme–inhibitor complexes characteristic of slow tight-binding
COX-1 inhibitors
Origin of the Enigmatic Stepwise Tight-Binding Inhibition of Cyclooxygenase‑1
Nonsteroidal
anti-inflammatory drugs (NSAIDs) are widely used for
the treatment of pain, fever, inflammation, and some types of cancers.
Their mechanism of action is the inhibition of isoforms 1 and 2 of
the enzyme cyclooxygenase (COX-1 and COX-2, respectively). However,
both nonselective and selective NSAIDs may have side effects that
include gastric intestinal bleeding, peptic ulcer formation, kidney
problems, and occurrences of myocardial infarction. The search for
selective high-affinity COX inhibitors resulted in a number of compounds
characterized by a slow, tight-binding inhibition that occurs in a
two-step manner. It has been suggested that the final, only very slowly
reversible, tight-binding event is the result of conformational changes
in the enzyme. However, the nature of these conformational changes
has remained elusive. Here we explore the structural determinants
of the tight-binding phenomenon in COX-1 with molecular dynamics and
free energy simulations. The calculations reveal how different classes
of inhibitors affect the equilibrium between two conformational substates
of the enzyme in distinctly different ways. The class of tight-binding
inhibitors is found to exclusively stabilize an otherwise unfavorable
enzyme conformation and bind significantly stronger to this state
than to that normally observed in crystal structures. By also computing
free energies of binding to the two enzyme conformations for 16 different
NSAIDs, we identify an induced-fit mechanism and the key structural
features associated with high-affinity tight binding. These results
may facilitate the rational development of new COX inhibitors with
improved selectivity profiles
Toward an Optimal Docking and Free Energy Calculation Scheme in Ligand Design with Application to COX‑1 Inhibitors
Cyclooxygenase-1
(COX-1) is one of the main targets of most pain-relieving
pharmaceuticals. Although the enzyme is well characterized, it is
known to be a difficult target for automated molecular docking and
scoring. We collected from the literature a structurally diverse set
of 45 nonsteroidal anti-inflammatory drugs (NSAIDs) and COX-2-selective
inhibitors (coxibs) with a wide range of binding affinities for COX-1.
The binding of this data set to a homology model of human COX-1 was
analyzed with different combinations of molecular docking algorithms,
scoring functions, and the linear interaction energy (LIE) method
for estimating binding affinities. It is found that the computational
protocols for estimation of binding affinities are extremely sensitive
to the initial orientations of the ligands in the binding pocket.
To overcome this limitation, we propose a systematic exploration of
docking poses using the LIE calculations as a postscoring function.
This scheme yields predictions in excellent agreement with experiment,
with a mean unsigned error of 0.9 kcal/mol for binding free energies
and structures of high quality. A significant improvement of the results
is also seen when averaging over experimental data from several independent
measurements
Discovery of Potent and Highly Selective A<sub>2B</sub> Adenosine Receptor Antagonist Chemotypes
Three novel families of A<sub>2B</sub> adenosine receptor antagonists
were identified in the context of the structural exploration of the
3,4-dihydropyrimidin-2(1<i>H</i>)-one chemotype. The most
appealing series contain imidazole, 1,2,4-triazole, or benzimidazole
rings fused to the 2,3-positions of the parent diazinone core. The
optimization process enabled identification of a highly potent (3.49
nM) A<sub>2B</sub> ligand that exhibits complete selectivity toward
A<sub>1</sub>, A<sub>2A</sub>, and A<sub>3</sub> receptors. The results
of functional cAMP experiments confirmed the antagonistic behavior
of representative ligands. The main SAR trends identified within the
series were substantiated by a molecular modeling study based on a
receptor-driven docking model constructed on the basis of the crystal
structure of the human A<sub>2A</sub> receptor
Enantiospecific Recognition at the A<sub>2B</sub> Adenosine Receptor by Alkyl 2‑Cyanoimino-4-substituted-6-methyl-1,2,3,4-tetrahydropyrimidine-5-carboxylates
A novel
family of structurally simple, potent, and selective nonxanthine
A<sub>2B</sub>AR ligands was identified, and its antagonistic behavior
confirmed through functional experiments. The reported alkyl 2-cyanoimino-4-substituted-6-methyl-1,2,3,4-tetrahy-dropyrimidine-5-carboxylates
(<b>16</b>) were designed by bioisosteric replacement of the
carbonyl group at position 2 in a series of 3,4-dihydropyrimidin-2-ones.
The scaffold (<b>16</b>) documented herein contains a chiral
center at the heterocycle. Accordingly, the most attractive ligand
of the series [(±)<b>16b</b>, <i>K</i><sub>i</sub> <b>=</b> 24.3 nM] was resolved into its two enantiomers by
chiral HPLC, and the absolute configuration was established by circular
dichroism. The biological evaluation of both enantiomers demonstrated
enantiospecific recognition at A<sub>2B</sub>AR, with the (<i>S</i>)-<b>16b</b> enantiomer retaining all the affinity
(<i>K</i><sub>i</sub> <b>=</b> 15.1 nM), as predicted
earlier by molecular modeling. This constitutes the first example
of enantiospecific recognition at the A<sub>2B</sub> adenosine receptor
and opens new possibilities in ligand design for this receptor
Discovery of Potent and Highly Selective A<sub>2B</sub> Adenosine Receptor Antagonist Chemotypes
Three novel families of A<sub>2B</sub> adenosine receptor antagonists
were identified in the context of the structural exploration of the
3,4-dihydropyrimidin-2(1<i>H</i>)-one chemotype. The most
appealing series contain imidazole, 1,2,4-triazole, or benzimidazole
rings fused to the 2,3-positions of the parent diazinone core. The
optimization process enabled identification of a highly potent (3.49
nM) A<sub>2B</sub> ligand that exhibits complete selectivity toward
A<sub>1</sub>, A<sub>2A</sub>, and A<sub>3</sub> receptors. The results
of functional cAMP experiments confirmed the antagonistic behavior
of representative ligands. The main SAR trends identified within the
series were substantiated by a molecular modeling study based on a
receptor-driven docking model constructed on the basis of the crystal
structure of the human A<sub>2A</sub> receptor
Effect of Nitrogen Atom Substitution in A<sub>3</sub> Adenosine Receptor Binding: <i>N</i>‑(4,6-Diarylpyridin-2-yl)acetamides as Potent and Selective Antagonists
We
report the first family of 2-acetamidopyridines as potent and
selective A<sub>3</sub> adenosine receptor (AR) antagonists. The computer-assisted
design was focused on the bioisosteric replacement of the N1 atom
by a CH group in a previous series of diarylpyrimidines. Some of the
generated 2-acetamidopyridines elicit an antagonistic effect with
excellent affinity (<i>K</i><sub>i</sub> < 10 nM) and
outstanding selectivity profiles, providing an alternative and simpler
chemical scaffold to the parent series of diarylpyrimidines. In addition,
using molecular dynamics and free energy perturbation simulations,
we elucidate the effect of the second nitrogen of the parent diarylpyrimidines,
which is revealed as a stabilizer of a water network in the binding
site. The discovery of 2,6-diaryl-2-acetamidopyridines represents
a step forward in the search of chemically simple, potent, and selective
antagonists for the hA<sub>3</sub>AR, and exemplifies the benefits
of a joint theoretical–experimental approach to identify novel
hA<sub>3</sub>AR antagonists through succinct and efficient synthetic
methodologies
Discovery of 3,4-Dihydropyrimidin-2(1<i>H</i>)‑ones As a Novel Class of Potent and Selective A<sub>2B</sub> Adenosine Receptor Antagonists
We
describe the discovery and optimization of 3,4-dihydropyrimidin-2(1<i>H</i>)-ones as a novel family of (nonxanthine) A<sub>2B</sub> receptor antagonists that exhibit an unusually high selectivity
profile. The Biginelli-based hit optimization process enabled a thoughtful
exploration of the structure–activity and structure–selectivity
relationships for this chemotype, enabling the identification of ligands
that combine structural simplicity with excellent hA<sub>2B</sub> AdoR
affinity and remarkable selectivity profiles
Effect of Nitrogen Atom Substitution in A<sub>3</sub> Adenosine Receptor Binding: <i>N</i>‑(4,6-Diarylpyridin-2-yl)acetamides as Potent and Selective Antagonists
We
report the first family of 2-acetamidopyridines as potent and
selective A<sub>3</sub> adenosine receptor (AR) antagonists. The computer-assisted
design was focused on the bioisosteric replacement of the N1 atom
by a CH group in a previous series of diarylpyrimidines. Some of the
generated 2-acetamidopyridines elicit an antagonistic effect with
excellent affinity (<i>K</i><sub>i</sub> < 10 nM) and
outstanding selectivity profiles, providing an alternative and simpler
chemical scaffold to the parent series of diarylpyrimidines. In addition,
using molecular dynamics and free energy perturbation simulations,
we elucidate the effect of the second nitrogen of the parent diarylpyrimidines,
which is revealed as a stabilizer of a water network in the binding
site. The discovery of 2,6-diaryl-2-acetamidopyridines represents
a step forward in the search of chemically simple, potent, and selective
antagonists for the hA<sub>3</sub>AR, and exemplifies the benefits
of a joint theoretical–experimental approach to identify novel
hA<sub>3</sub>AR antagonists through succinct and efficient synthetic
methodologies