4 research outputs found
<i>In Silico</i> Categorization of <i>in Vivo</i> Intrinsic Clearance Using Machine Learning
Machine
learning has recently become popular and much used within
the life science research domain, e.g., for finding quantitative structure鈥揳ctivity
relationships (QSARs) between molecular structures and different biological
end points. In the work presented here, we have applied orthogonal
partial least-squares (OPLS), principal component analysis (PCA),
and random forests (RF) methods for classification as well as regression
analysis to a publicly available <i>in vivo</i> data set
in order to assess the intrinsic metabolic clearance (CL<sub>int</sub>) in humans. The derived classification models are able to identify
compounds with CL<sub>int</sub> lower and higher than 1500 mL/min,
respectively, with nearly 80% accuracy. The most relevant descriptors
are of lipophilicity and charge/polarizability types. Furthermore,
the accuracy from a classification model based on regression analysis,
using the 1500 mL/min cutoff, is also around 80%. These results suggest
the usefulness of machine learning techniques to derive robust and
predictive models in the area of <i>in vivo</i> ADMET (absorption,
distribution, metabolism, elimination, and toxicity) modeling
The Central Role of Gln63 for the Hydrogen Bonding Network and UV鈥揤isible Spectrum of the AppA BLUF Domain
In blue-light sensing using flavin (BLUF) domains, the
side-chain
orientation of key residues close to the flavin chromophore is still
under debate. We report quantum refinements of the wild-type AppA
BLUF protein from Rhodobacter sphaeroides starting from two published X-ray structures (1YRX and 2IYG) with
different arrangements of the residues around the chromophore. Quantum
refinement uses the same experimental X-ray raw data as conventional
refinement, but includes data from quantum mechanics/molecular mechanics
(QM/MM) calculations as restraints, which is expected to be more reliable
than the normally employed MM data. In addition to quantum refinement,
pure QM/MM geometry optimizations are performed for the 1YRX and 2IYG
structures and for five models derived therefrom. Vertical excitation
energies are computed at the QM颅(DFT/MRCI)/MM level to assess the resulting
structures. The experimental absorption maximum of the dark state
of wild-type AppA is well reproduced for structures that contain the
Gln63 residue in 1YRX-type orientation. The computed excitation energies
are red-shifted for structures with a flipped Gln63 residue in 2IYG-type
orientation. The calculated 1YRX- and 2IYG-type hydrogen-bonding networks
are discussed in detail, particularly with regard to the orientation
of the chromophore and the Gln63, Trp104, and Met106 residues
A Pragmatic Approach Using First-Principle Methods to Address Site of Metabolism with Implications for Reactive Metabolite Formation
A majority of xenobiotics are metabolized by cytochrome
P450 (CYP)
enzymes. The discovery of drug candidates with low propensity to form
reactive metabolites and low clearance can be facilitated by understanding
CYP-mediated xenobiotic metabolism. Being able to predict the sites
where reactive metabolites form is beneficial in drug design to produce
drug candidates free of reactive metabolite issues. Herein, we report
a pragmatic protocol using first-principle density functional theory
(DFT) calculations for predicting sites of epoxidation and hydroxylation
of aromatic substrates mediated by CYP. The method is based on the
relative stabilities of the CYP-substrate intermediates or the substrate
epoxides. Consequently, it concerns mainly the electronic reactivity
of the substrates. Comparing to the experimental findings, the presented
protocol gave excellent first-ranked epoxidation site predictions
of 83%, and when the test was extended to CYP-mediated sites of aromatic
hydroxylation, satisfactory results were also obtained (73%). This
indicates that our assumptions are valid and also implies that the
intrinsic reactivities of the substrates are in general more important
than their binding poses in proteins, although the protocol may benefit
from the addition of docking information
Cooperative Modes of Action of Antimicrobial Peptides Characterized with Atomistic Simulations: A Study on Cecropin B
Antimicrobial peptides
(AMPs) are widely occurring host defense
agents of interest as one route for addressing the growing problem
of multidrug-resistant pathogens. Understanding the mechanisms behind
their antipathogen activity is instrumental in designing new AMPs.
Herein, we present an all-atom molecular dynamics and free energy
study on cecropin B (CB) and its constituent domains. We find a cooperative
mechanism in which CB inserts into an anionic model membrane with
its amphipathic N-terminal segment, supported by the hydrophobic C-terminal
segment of a second peptide. The two peptides interact via a Glu路路路Lys
salt bridge and together sustain a pore in the membrane. Using a modified
membrane composition, we demonstrate that when the lower leaflet is
overall neutral, insertion of the cationic segment is retarded and
thus this mode of action is membrane specific. The observed mode of
action utilizes a flexible hinge, a common structural motif among
AMPs, which allows CB to insert into the membrane using either or
both termini. Data from both unbiased trajectories and enhanced sampling
simulations indicate that a requirement for CB to be an effective
AMP is the interaction of its hydrophobic C-terminal segment with
the membrane. Simulations of these segments in isolation reveal their
aggregation in the membrane and a different mechanism of supporting
pore formation. Together, our results show the complex interaction
of different structural motifs of AMPs and, in particular, a potential
role for electronegative side chains in an overall cationic AMP