7 research outputs found
Ensemble-Based Docking Using Biased Molecular Dynamics
Proteins are dynamic molecules, and
understanding their movements,
especially as they relate to molecular recognition and proteinâligand
interactions, poses a significant challenge to structure-based drug
discovery. In most instances, protein flexibility is underrepresented
in computer-aided drug design due to uncertainties on how it should
be accurately modeled as well as the computational cost associated
with attempting to incorporate flexibility in the calculations. One
approach that aims to address these issues is ensemble-based docking.
With this technique, ligands are docked to an ensemble of rigid protein
conformations. Molecular dynamics (MD) simulations can be used to
generate the ensemble of protein conformations for the subsequent
docking. Here we present a novel approach that uses biased-MD simulations
to generate the docking ensemble. The MD simulations are biased toward
an initial proteinâligand X-ray complex structure. The biasing
maintains some of the original crystallographic pocket-ligand information
and thereby enhances sampling of the more relevant conformational
space of the protein. Resulting trajectories are clustered to select
a representative set of protein conformations, and ligands are docked
to that reduced set of conformations. Cross-docking to this ensemble
and then selecting the lowest scoring pose enables reliable identification
of the correct binding mode. Various levels of biasing are investigated,
and the method is validated for cyclin-dependent kinase 2 and factor
Xa
Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP
The
SZMAP method computes binding free energies and the corresponding
thermodynamic components for water molecules in the binding site of
a protein structure [SZMAP, 1.0.0; OpenEye Scientific Software
Inc.: Santa Fe, NM, USA, 2011]. In this work, the ability of SZMAP
to predict water structure and thermodynamic stability is examined
for the X-ray crystal structures of a series of proteinâligand
complexes. SZMAP results correlate with higher-level replica exchange
thermodynamic integration double decoupling calculations of the absolute
free energy of bound waters in the test set complexes. In addition,
SZMAP calculations show good agreement with experimental data in terms
of water conservation (across multiple crystal structures) and B-factors
over a subset of the test set. In particular, the SZMAP neutral entropy
difference term calculated at crystallographic water positions within
each of the complex structures correlates well with whether that crystallographic
water is conserved or displaceable. Furthermore, the calculated entropy
of the water probe relative to the continuum shows a significant degree
of correlation with the B-factors associated with the oxygen atoms
of the water molecules. Taken together, these results indicate that
SZMAP is capable of quantitatively predicting water positions and
their energetics and is potentially a useful tool for determining
which waters to attempt to displace, maintain, or build in through
water-mediated interactions when evolving a lead series during a drug
discovery program
Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites
The
knowledge of ligand binding hot spots and of the important
interactions within such hot spots is crucial for the design of lead
compounds in the early stages of structure-based drug discovery. The
computational solvent mapping server FTMap can reliably identify binding
hot spots as consensus clusters, free energy minima that bind a variety
of organic probe molecules. However, in its current implementation,
FTMap provides limited information on regions within the hot spots
that tend to interact with specific pharmacophoric features of potential
ligands. E-FTMap is a new server that expands on the original FTMap
protocol. E-FTMap uses 119 organic probes, rather than the 16 in the
original FTMap, to exhaustively map binding sites, and identifies
pharmacophore features as atomic consensus sites where similar chemical
groups bind. We validate E-FTMap against a set of 109 experimentally
derived structures of fragmentâlead pairs, finding that highly
ranked pharmacophore features overlap with the corresponding atoms
in both fragments and lead compounds. Additionally, comparisons of
mapping results to ensembles of bound ligands reveal that pharmacophores
generated with E-FTMap tend to sample highly conserved proteinâligand
interactions. E-FTMap is available as a web server at https://eftmap.bu.edu
Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites
The
knowledge of ligand binding hot spots and of the important
interactions within such hot spots is crucial for the design of lead
compounds in the early stages of structure-based drug discovery. The
computational solvent mapping server FTMap can reliably identify binding
hot spots as consensus clusters, free energy minima that bind a variety
of organic probe molecules. However, in its current implementation,
FTMap provides limited information on regions within the hot spots
that tend to interact with specific pharmacophoric features of potential
ligands. E-FTMap is a new server that expands on the original FTMap
protocol. E-FTMap uses 119 organic probes, rather than the 16 in the
original FTMap, to exhaustively map binding sites, and identifies
pharmacophore features as atomic consensus sites where similar chemical
groups bind. We validate E-FTMap against a set of 109 experimentally
derived structures of fragmentâlead pairs, finding that highly
ranked pharmacophore features overlap with the corresponding atoms
in both fragments and lead compounds. Additionally, comparisons of
mapping results to ensembles of bound ligands reveal that pharmacophores
generated with E-FTMap tend to sample highly conserved proteinâligand
interactions. E-FTMap is available as a web server at https://eftmap.bu.edu
Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites
The
knowledge of ligand binding hot spots and of the important
interactions within such hot spots is crucial for the design of lead
compounds in the early stages of structure-based drug discovery. The
computational solvent mapping server FTMap can reliably identify binding
hot spots as consensus clusters, free energy minima that bind a variety
of organic probe molecules. However, in its current implementation,
FTMap provides limited information on regions within the hot spots
that tend to interact with specific pharmacophoric features of potential
ligands. E-FTMap is a new server that expands on the original FTMap
protocol. E-FTMap uses 119 organic probes, rather than the 16 in the
original FTMap, to exhaustively map binding sites, and identifies
pharmacophore features as atomic consensus sites where similar chemical
groups bind. We validate E-FTMap against a set of 109 experimentally
derived structures of fragmentâlead pairs, finding that highly
ranked pharmacophore features overlap with the corresponding atoms
in both fragments and lead compounds. Additionally, comparisons of
mapping results to ensembles of bound ligands reveal that pharmacophores
generated with E-FTMap tend to sample highly conserved proteinâligand
interactions. E-FTMap is available as a web server at https://eftmap.bu.edu
Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites
The
knowledge of ligand binding hot spots and of the important
interactions within such hot spots is crucial for the design of lead
compounds in the early stages of structure-based drug discovery. The
computational solvent mapping server FTMap can reliably identify binding
hot spots as consensus clusters, free energy minima that bind a variety
of organic probe molecules. However, in its current implementation,
FTMap provides limited information on regions within the hot spots
that tend to interact with specific pharmacophoric features of potential
ligands. E-FTMap is a new server that expands on the original FTMap
protocol. E-FTMap uses 119 organic probes, rather than the 16 in the
original FTMap, to exhaustively map binding sites, and identifies
pharmacophore features as atomic consensus sites where similar chemical
groups bind. We validate E-FTMap against a set of 109 experimentally
derived structures of fragmentâlead pairs, finding that highly
ranked pharmacophore features overlap with the corresponding atoms
in both fragments and lead compounds. Additionally, comparisons of
mapping results to ensembles of bound ligands reveal that pharmacophores
generated with E-FTMap tend to sample highly conserved proteinâligand
interactions. E-FTMap is available as a web server at https://eftmap.bu.edu
<i>In Vivo</i> Validation of Thymidylate Kinase (TMK) with a Rationally Designed, Selective Antibacterial Compound
There is an urgent need for new antibacterials that pinpoint
novel targets and thereby avoid existing resistance mechanisms. We
have created novel synthetic antibacterials through structure-based
drug design that specifically target bacterial thymidylate kinase
(TMK), a nucleotide kinase essential in the DNA synthesis pathway.
A high-resolution structure shows compound TK-666 binding partly in
the thymidine monophosphate substrate site, but also forming new induced-fit
interactions that give picomolar affinity. TK-666 has potent, broad-spectrum
Gram-positive microbiological activity (including activity against
methicillin-resistant <i>Staphylococcus aureus</i> and vancomycin-resistant <i>Enterococcus</i>), bactericidal action with rapid killing kinetics,
excellent target selectivity over the human ortholog, and low resistance
rates. We demonstrate <i>in vivo</i> efficacy against <i>S. aureus</i> in a murine infected-thigh model. This work presents
the first validation of TMK as a compelling antibacterial target and
provides a rationale for pursuing novel clinical candidates for treating
Gram-positive infections through TMK