13 research outputs found
5‑Substituted Pyrimidine and 7‑Substituted 7‑Deazapurine dNTPs as Substrates for DNA Polymerases in Competitive Primer Extension in the Presence of Natural dNTPs
A complete
series of 5-substituted uracil or cytosine, as well
as 7-substituted 7-deazaadenine and 7-deazaguanine 2′-deoxyribonucleoside
triphosphates (dNTPs) bearing substituents of increasing bulkiness
(H, Me, vinyl, ethynyl, and phenyl) were systematically studied in
competitive primer extension in the presence of their natural counterparts
(nonmodified dNTPs), and their kinetic data were determined. The results
show that modified dNTPs bearing π-electron-containing substituents
(vinyl, ethynyl, Ph) are typically excellent substrates for DNA polymerases
comparable to or better than natural dNTPs. The kinetic studies revealed
that these modified dNTPs have higher affinity to the active site
of the enzyme–primer–template complex, and the calculations
(semiempirical quantum mechanical scoring function) suggest that it
is due to the cation−π interaction of the modified dNTP
with Arg629 in the active site of Bst DNA polymerase
Chalcogen and Pnicogen Bonds in Complexes of Neutral Icosahedral and Bicapped Square-Antiprismatic Heteroboranes
A systematic quantum mechanical study
of σ-hole (chalcogen,
pnicogen, and halogen) bonding in neutral experimentally known <i>closo</i>-heteroboranes is performed. Chalcogens and pnicogens
are incorporated in the borane cage, whereas halogens are considered
as <i>exo</i>-substituents of dicarbaboranes. The chalcogen
and pnicogen atoms in the heteroborane cages have partial positive
charge and thus more positive σ-holes. Consequently, these heteroboranes
form very strong chalcogen and pnicogen bonds. Halogen atoms in dicarbaboranes
also have a highly positive σ-hole, but only in the case of
C-bonded halogen atoms. In such cases, the halogen bond of heteroboranes
is also strong and comparable to halogen bonds in organic compounds
with several electron-withdrawing groups being close to the halogen
atom involved in the halogen bond
Assessing the Accuracy and Performance of Implicit Solvent Models for Drug Molecules: Conformational Ensemble Approaches
The accuracy and performance of implicit
solvent methods for solvation
free energy calculations were assessed on a set of 20 neutral drug
molecules. Molecular dynamics (MD) provided ensembles of conformations
in water and water-saturated octanol. The solvation free energies
were calculated by popular implicit solvent models based on quantum
mechanical (QM) electronic densities (COSMO-RS, MST, SMD) as well
as on molecular mechanical (MM) point-charge models (GB, PB). The
performance of the implicit models was tested by a comparison with
experimental water–octanol transfer free energies (Δ<i>G</i><sub>ow</sub>) by using single- and multiconformation approaches.
MD simulations revealed difficulties in a priori estimation of the
flexibility features of the solutes from simple structural descriptors,
such as the number of rotatable bonds. An increasing accuracy of the
calculated Δ<i>G</i><sub>ow</sub> was observed in
the following order: GB1 ∼ PB < GB7 ≪ MST < SMD
∼ COSMO-RS with a clear distinction identified between MM-
and QM-based models, although for the set excluding three largest
molecules, the differences among COSMO-RS, MST, and SMD were negligible.
It was shown that the single-conformation approach applied to crystal
geometries provides a rather accurate estimate of Δ<i>G</i><sub>ow</sub> for rigid molecules yet fails completely for the flexible
ones. The multiconformation approaches improved the performance, but
only when the deformation contribution was ignored. It was revealed
that for large-scale calculations on small molecules a recent GB model,
GB7, provided a reasonable accuracy/speed ratio. In conclusion, the
study contributes to the understanding of solvation free energy calculations
for physical and medicinal chemistry applications
Assessing the Accuracy and Performance of Implicit Solvent Models for Drug Molecules: Conformational Ensemble Approaches
The accuracy and performance of implicit
solvent methods for solvation
free energy calculations were assessed on a set of 20 neutral drug
molecules. Molecular dynamics (MD) provided ensembles of conformations
in water and water-saturated octanol. The solvation free energies
were calculated by popular implicit solvent models based on quantum
mechanical (QM) electronic densities (COSMO-RS, MST, SMD) as well
as on molecular mechanical (MM) point-charge models (GB, PB). The
performance of the implicit models was tested by a comparison with
experimental water–octanol transfer free energies (Δ<i>G</i><sub>ow</sub>) by using single- and multiconformation approaches.
MD simulations revealed difficulties in a priori estimation of the
flexibility features of the solutes from simple structural descriptors,
such as the number of rotatable bonds. An increasing accuracy of the
calculated Δ<i>G</i><sub>ow</sub> was observed in
the following order: GB1 ∼ PB < GB7 ≪ MST < SMD
∼ COSMO-RS with a clear distinction identified between MM-
and QM-based models, although for the set excluding three largest
molecules, the differences among COSMO-RS, MST, and SMD were negligible.
It was shown that the single-conformation approach applied to crystal
geometries provides a rather accurate estimate of Δ<i>G</i><sub>ow</sub> for rigid molecules yet fails completely for the flexible
ones. The multiconformation approaches improved the performance, but
only when the deformation contribution was ignored. It was revealed
that for large-scale calculations on small molecules a recent GB model,
GB7, provided a reasonable accuracy/speed ratio. In conclusion, the
study contributes to the understanding of solvation free energy calculations
for physical and medicinal chemistry applications
SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein–Ligand Poses
We
have recently introduced the “SQM/COSMO” scoring
function which combines a semiempirical quantum mechanical description
of noncovalent interactions at the PM6-D3H4X level and the COSMO implicit
model of solvation. This approach outperformed standard scoring functions
but faced challenges with a metalloprotein featuring a Zn<sup>2+</sup>···S<sup>–</sup> interaction. Here, we invoke
SCC-DFTB3-D3H4, a higher-level SQM method, and observe improved behavior
for the metalloprotein and high-quality results for the other systems.
This method holds promise for diverse protein–ligand complexes
including metalloproteins
Superior Performance of the SQM/COSMO Scoring Functions in Native Pose Recognition of Diverse Protein–Ligand Complexes in Cognate Docking
General and reliable description of structures and energetics in protein–ligand
(PL) binding using the docking/scoring methodology has until now been
elusive. We address this urgent deficiency of scoring functions (SFs)
by the systematic development of corrected semiempirical quantum mechanical
(SQM) methods, which correctly describe all types of noncovalent interactions
and are fast enough to treat systems of thousands of atoms. Two most
accurate SQM methods, PM6-D3H4X and SCC-DFTB3-D3H4X, are coupled with
the conductor-like screening model (COSMO) implicit solvation model
in so-called “SQM/COSMO” SFs and have shown unique recognition
of native ligand poses in cognate docking in four challenging PL systems,
including metalloprotein. Here, we apply the two SQM/COSMO SFs to
17 diverse PL complexes and compare their performance with four widely
used classical SFs (Glide XP, AutoDock4, AutoDock Vina, and UCSF Dock).
We observe superior performance of the SQM/COSMO SFs and identify
challenging systems. This method, due to its generality, comparability
across the chemical space, and lack of need for any system-specific
parameters, gives promise of becoming, after comprehensive large-scale
testing in the near future, a useful computational tool in structure-based
drug design and serving as a reference method for the development
of other SFs
QM/MM Calculations Reveal the Different Nature of the Interaction of Two Carborane-Based Sulfamide Inhibitors of Human Carbonic Anhydrase II
The crystal structures of two novel
carborane-sulfamide inhibitors
in the complex with human carbonic anhydrase II (hCAII) have been
studied using QM/MM calculations. Even though both complexes possess
the strongly interacting sulfamide···zinc ion motif,
the calculations have revealed the different nature of binding of
the carborane parts of the inhibitors. The neutral <i>closo</i>-carborane cage was bound to hCAII mainly via dispersion interactions
and formed only very weak dihydrogen bonds. On the contrary, the monoanionic <i>nido</i> cage interacted with the protein mainly via electrostatic
interactions. It formed short and strong dihydrogen bonds (stabilization
of up to 4.2 kcal/mol; H···H distances of 1.7 Å)
with the polar hydrogen of protein NH<sub>2</sub> groups. This type
of binding is unique among all of the classical organic and inorganic
inhibitors of hCAII. Virtual glycine scanning allowed us to identify
the amino-acid side chains, which made important contributions to
ligand-binding energies. In summary, using QM/MM calculations, we
have provided a detailed understanding of the differences between
the interactions of two carborane sulfamides, identified the amino
acids of hCAII with which they interact, and thus paved the way for
the computer-aided rational design of selective boron-cluster-containing
hCAII inhibitors
Quantum Mechanics-Based Scoring Rationalizes the Irreversible Inactivation of Parasitic <i>Schistosoma mansoni</i> Cysteine Peptidase by Vinyl Sulfone Inhibitors
The
quantum mechanics (QM)-based scoring function that we previously
developed for the description of noncovalent binding in protein–ligand
complexes has been modified and extended to treat covalent binding
of inhibitory ligands. The enhancements are (i) the description of
the covalent bond breakage and formation using hybrid QM/semiempirical
QM (QM/SQM) restrained optimizations and (ii) the addition of the
new Δ<i>G</i><sub>cov</sub>′ term to the noncovalent
score, describing the “free” energy difference between
the covalent and noncovalent complexes. This enhanced QM-based scoring
function is applied to a series of 20 vinyl sulfone-based inhibitory
compounds inactivating the cysteine peptidase cathepsin B1 of the Schistosoma mansoni parasite (SmCB1). The available
X-ray structure of the SmCB1 in complex with a potent vinyl sulfone
inhibitor K11017 is used as a template to build the other covalently
bound complexes and to model the derived noncovalent complexes. We
present the correlation of the covalent score and its constituents
with the experimental binding data. Four outliers are identified.
They contain bulky R<sub>1</sub>′ substituents structurally
divergent from the template, which might induce larger protein rearrangements
than could be accurately modeled. In summary, we propose a new computational
approach and an optimal protocol for the rapid evaluation and prospective
design of covalent inhibitors with a conserved binding mode
IDD388 Polyhalogenated Derivatives as Probes for an Improved Structure-Based Selectivity of AKR1B10 Inhibitors
Human
enzyme aldo-keto reductase family member 1B10 (AKR1B10) has
evolved as a tumor marker and promising antineoplastic target. It
shares high structural similarity with the diabetes target enzyme
aldose reductase (AR). Starting from the potent AR inhibitor IDD388,
we have synthesized a series of derivatives bearing the same halophenoxyacetic
acid moiety with an increasing number of bromine (Br) atoms on its
aryl moiety. Next, by means of IC<sub>50</sub> measurements, X-ray
crystallography, WaterMap analysis, and advanced binding free energy
calculations with a quantum-mechanical (QM) approach, we have studied
their structure–activity relationship (SAR) against both enzymes.
The introduction of Br substituents decreases AR inhibition potency
but improves it in the case of AKR1B10. Indeed, the Br atoms in <i>ortho</i> position may impede these drugs to fit into the AR
prototypical specificity pocket. For AKR1B10, the smaller aryl moieties
of MK181 and IDD388 can bind into the external loop A subpocket. Instead,
the bulkier MK184, MK319, and MK204 open an inner specificity pocket
in AKR1B10 characterized by a π–π stacking interaction
of their aryl moieties and Trp112 side chain in the native conformation
(not possible in AR). Among the three compounds, only MK204 can make
a strong halogen bond with the protein (−4.4 kcal/mol, using
QM calculations), while presenting the lowest desolvation cost among
all the series, translated into the most selective and inhibitory
potency AKR1B10 (IC<sub>50</sub> = 80 nM). Overall, SAR of these IDD388
polyhalogenated derivatives have unveiled several distinctive AKR1B10
features (shape, flexibility, hydration) that can be exploited to
design novel types of AKR1B10 selective drugs
IDD388 Polyhalogenated Derivatives as Probes for an Improved Structure-Based Selectivity of AKR1B10 Inhibitors
Human
enzyme aldo-keto reductase family member 1B10 (AKR1B10) has
evolved as a tumor marker and promising antineoplastic target. It
shares high structural similarity with the diabetes target enzyme
aldose reductase (AR). Starting from the potent AR inhibitor IDD388,
we have synthesized a series of derivatives bearing the same halophenoxyacetic
acid moiety with an increasing number of bromine (Br) atoms on its
aryl moiety. Next, by means of IC<sub>50</sub> measurements, X-ray
crystallography, WaterMap analysis, and advanced binding free energy
calculations with a quantum-mechanical (QM) approach, we have studied
their structure–activity relationship (SAR) against both enzymes.
The introduction of Br substituents decreases AR inhibition potency
but improves it in the case of AKR1B10. Indeed, the Br atoms in <i>ortho</i> position may impede these drugs to fit into the AR
prototypical specificity pocket. For AKR1B10, the smaller aryl moieties
of MK181 and IDD388 can bind into the external loop A subpocket. Instead,
the bulkier MK184, MK319, and MK204 open an inner specificity pocket
in AKR1B10 characterized by a π–π stacking interaction
of their aryl moieties and Trp112 side chain in the native conformation
(not possible in AR). Among the three compounds, only MK204 can make
a strong halogen bond with the protein (−4.4 kcal/mol, using
QM calculations), while presenting the lowest desolvation cost among
all the series, translated into the most selective and inhibitory
potency AKR1B10 (IC<sub>50</sub> = 80 nM). Overall, SAR of these IDD388
polyhalogenated derivatives have unveiled several distinctive AKR1B10
features (shape, flexibility, hydration) that can be exploited to
design novel types of AKR1B10 selective drugs