33 research outputs found
Tower 1978
1978 yearbook of Westbrook College in Portland, Maine.https://dune.une.edu/wchc_yearbooks/1007/thumbnail.jp
Integrated Covalent Drug Design Workflow Using Site Identification by Ligand Competitive Saturation
Covalent drug design is an important component in drug
discovery.
Traditional drugs interact with their target in a reversible equilibrium,
while irreversible covalent drugs increase the drugātarget
interaction duration by forming a covalent bond with targeted residues
and thus may offer a more effective therapeutic approach. To facilitate
the design of this class of ligands, computational methods can be
used to help identify reactive nucleophilic residues, frequently cysteines,
on a target protein for covalent binding, to test various warhead
groups for their potential reactivities, and to predict noncovalent
contributions to binding that can facilitate drugātarget interactions
that are important for binding specificity. To further aid covalent
drug design, we extended a functional group mapping approach based
on explicit solvent all-atom molecular simulations (SILCS: site identification
by ligand competitive saturation) that intrinsically considers protein
flexibility, functional group, and protein desolvation along with
functional groupāprotein interactions. Through docking of a
library of representative warhead fragments using SILCS-Monte Carlo
(SILCS-MC), reactive cysteines can be correctly identified for proteins
being tested. Furthermore, a machine learning model was trained to
quantify the effectiveness of various warhead groups for proteins
using metrics from SILCS-MC as well as experimental model compound
warhead reactivity data. The ability to rank covalent molecular binders
with similar warheads using SILCS ligand grid free energy (LGFE) ranking
was also tested for several proteins. Based on these tools, an integrated
SILCS-based workflow was developed, named SILCS-Covalent, which can
both qualitatively and quantitatively inform covalent drug discovery
Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations
Solute
sampling of explicit bulk-phase aqueous environments in
grand canonical (GC) ensemble simulations suffer from poor convergence
due to low insertion probabilities of the solutes. To address this,
we developed an iterative procedure involving Grand Canonical-like
Monte Carlo (GCMC) and molecular dynamics (MD) simulations. Each iteration
involves GCMC of both the solutes and water followed by MD, with the
excess chemical potential (Ī¼<sub>ex</sub>) of both the solute
and the water oscillated to attain their target concentrations in
the simulation system. By periodically varying the Ī¼<sub>ex</sub> of the water and solutes over the GCMC-MD iterations, solute exchange
probabilities and the spatial distributions of the solutes improved.
The utility of the oscillating-Ī¼<sub>ex</sub> GCMC-MD method
is indicated by its ability to approximate the hydration free energy
(HFE) of the individual solutes in aqueous solution as well as in
dilute aqueous mixtures of multiple solutes. For seven organic solutes:
benzene, propane, acetaldehyde, methanol, formamide, acetate, and
methylammonium, the average Ī¼<sub>ex</sub> of the solutes and
the water converged close to their respective HFEs in both 1 M standard
state and dilute aqueous mixture systems. The oscillating-Ī¼<sub>ex</sub> GCMC methodology is also able to drive solute sampling in
proteins in aqueous environments as shown using the occluded binding
pocket of the T4 lysozyme L99A mutant as a model system. The approach
was shown to satisfactorily reproduce the free energy of binding of
benzene as well as sample the functional group requirements of the
occluded pocket consistent with the crystal structures of known ligands
bound to the L99A mutant as well as their relative binding affinities
Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules
Receptor-based pharmacophore modeling
is an efficient computer-aided
drug design technique that uses the structure of the target protein
to identify novel leads. However, most methods consider protein flexibility
and desolvation effects in a very approximate way, which may limit
their use in practice. The Site-Identification by Ligand Competitive
Saturation (SILCS) assisted pharmacophore modeling protocol (SILCS-Pharm)
was introduced recently to address these issues, as SILCS naturally
takes both protein flexibility and desolvation effects into account
by using full molecular dynamics simulations to determine 3D maps
of the functional group-affinity patterns on a target receptor. In
the present work, the SILCS-Pharm protocol is extended to use a wider
range of probe molecules including benzene, propane, methanol, formamide,
acetaldehyde, methylammonium, acetate and water. This approach removes
the previous ambiguity brought by using water as both the hydrogen-bond
donor and acceptor probe molecule. The new SILCS-Pharm protocol is
shown to yield improved screening results, as compared to the previous
approach based on three target proteins. Further validation of the
new protocol using five additional protein targets showed improved
screening compared to those using common docking methods, further
indicating improvements brought by the explicit inclusion of additional
feature types associated with the wider collection of probe molecules
in the SILCS simulations. The advantage of using complementary features
and volume constraints, based on exclusion maps of the protein defined
from the SILCS simulations, is presented. In addition, reranking using
SILCS-based ligand grid free energies is shown to enhance the diversity
of identified ligands for the majority of targets. These results suggest
that the SILCS-Pharm protocol will be of utility in rational drug
design
Comprehensive Conformational Studies of Five Tripeptides and a Deduced Method for Efficient Determinations of Peptide Structures
Thorough searches on the potential energy surfaces of
five tripeptides, GGG, GYG, GWG, TGG, and MGG, were performed by considering
all possible combinations of the bond rotational degrees of freedom
with a semiempirical and ab initio combined computational approach.
Structural characteristics of the obtained stable tripeptide conformers
were carefully analyzed. Conformers of the five tripeptides were found
to be closely connected with conformers of their constituting dipeptides
and amino acids. A method for finding all important tripeptide conformers
by optimizing a small number of trial structures generated by suitable
superposition of the parent amino acid and dipeptide conformers is
thus proposed. Applying the method to another five tripeptides, YGG,
FGG, WGG, GFA, and GGF, studied before shows that the new approach
is both efficient and reliable by providing the most complete ensembles
of tripeptide conformers. The method is further generalized for application
to larger peptides by introducing the breeding and mutation concepts
in a genetic algorithm way. The generalized method is verified to
be capable of finding tetrapeptide conformers with secondary structures
of strands, helices, and turns, which are highly populated in larger
peptides. This show some promise for the proposed method to be applied
for the structural determination of larger peptides
Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and GāProtein Coupled Receptors
Occluded ligand-binding pockets (LBP)
such as those found in nuclear
receptors (NR) and G-protein coupled receptors (GPCR) represent a
significant opportunity and challenge for computer-aided drug design.
To determine free energies maps of functional groups of these LBPs,
a Grand-Canonical Monte Carlo/Molecular Dynamics (GCMC/MD) strategy
is combined with the Site Identification by Ligand Competitive Saturation
(SILCS) methodology. SILCS-GCMC/MD is shown to map functional group
affinity patterns that recapitulate locations of functional groups
across diverse classes of ligands in the LBPs of the androgen (AR)
and peroxisome proliferator-activated-Ī³ (PPARĪ³) NRs and
the metabotropic glutamate (mGluR) and Ī²<sub>2</sub>-adreneric
(Ī²<sub>2</sub>AR) GPCRs. Inclusion of protein flexibility identifies
regions of the binding pockets not accessible in crystal conformations
and allows for better quantitative estimates of relative ligand binding
affinities in all the proteins tested. Differences in functional group
requirements of the active and inactive states of the Ī²<sub>2</sub>AR LBP were used in virtual screening to identify high efficacy
agonists targeting Ī²<sub>2</sub>AR in Airway Smooth Muscle (ASM)
cells. Seven of the 15 selected ligands were found to effect ASM relaxation
representing a 46% hit rate. Hence, the method will be of use for
the rational design of ligands in the context of chemical biology
and the development of therapeutic agents
The influence of peripheral immune on mice with chronic i.n. LPS.
<p>At the 5th month after LPS inoculation, mice were sacrificed and splenic mononuclear cells and the serum were isolated. The viability of T cells, oxidation products and inflammatory cytokines from spleens were detected in the presence and/or absence of Ī±-synuclein stimulation by MTT, Nitrite and ELISA assays, respectively. Inflammatory cytokines from the serum were detected by ELISA assays. a) The viability of T cells; b) NO production, c) The secretion of inflammatory cytokines IL-1Ī², IL-6 and TNF-Ī±; d) the secretion of Th1 IFN-Ī³, Th2 IL-10 and Th17 IL-17 and e) The secretion of inflammatory cytokines IL-1Ī², IL-6, IL-10 and TNF-Ī± from the serum of the mice. There was no statistical significance between and within two groups. Determinations were performed in duplicate and results were expressed as meanĀ±S.E.M. from at least six mice.</p
Pathological changes in mice subjected to chronic i.n. LPS administration.
<p>a) Loss of dopaminergic neurons in the SN of mice challenged with right intranasal LPS administration of 10 Āµg/ every other day for 5 months; b) DA neurons in the VTA region on both sides; c) Representative photomicrographs illustrating TH immunoreactivity in the striatum; d) Neurons in the hippocampus and cortex were immunostained with anti-NeuN antibodies. Bars indicate SD for 7-10 mice. **<i>P</i><0.01 compared with contralateral side and saline control, respectively; scale bar is 2 mm. </p
Behavioral alteration in mice with chronic i.n. LPS administration.
<p>a) The ambulatory motility (VM=voluntary movement), Motor behavior was analyzed in an open-field test at the 1st, 3rd and 5th months after LPS instillation. b) Adhesive removal test, the asymmetry of left and right movement was detected by the adhesive removal test at the 5th month after LPS instillation. c) Latency to find platforms (from day 1 to day 5), the cognition was measured by Morris water maze at the 5th month after LPS instillation. Left=time to remove adhesive dots from left forelimb; Right= time to remove adhesive dots from right forelimb. Bars indicate SD for 7-10 mice at each point. *<i>P</i><0.05 compared with the contralateral side and/or saline control, respectively. </p
The changes of the striatal biogenic amines following chronic i.n.
<div><p><b>LPS in mice</b>. </p>
<p>The levels of DA and its major metabolites DOPAC and HVA, as well as NE, Iso, 5-HT and 5-HIAA in SN were determined by specific HPLC assay at the 5th month after LPS inoculation. a) DA; b) DOPAC; c) HVA and d) the ration of HVA/DA; e) NE; f) Iso; g) 5-HT; h) 5-HIAA. Quantitative results were obtained from among at least six mice. *<i>P</i><0.05 and **<i>P</i><0.01 compared with the contralateral striatum and saline control, respectively.</p></div