10 research outputs found
Computational Screening and Selection of Cyclic Peptide Hairpin Mimetics by Molecular Simulation and Kinetic Network Models
Designing peptidomimetic compounds
to have a preorganized structure
in solution is highly nontrivial. To show how simulation-based approaches
can help speed this process, we performed an extensive simulation
study of designed cyclic peptide mimics of a β-hairpin from
bacterial protein LapD involved in a proteinâprotein interaction
(PPI) pertinent to bacterial biofilm formation. We used replica exchange
molecular dynamics (REMD) simulation to screen 20 covalently cross-linked
designs with varying stereochemistry and selected the most favorable
of these for massively parallel simulation on Folding@home in explicit
solvent. Markov state models (MSMs) built from the trajectory data
reveal how subtle chemical modifications can have a significant effect
on conformational populations, leading to the overall stabilization
of the target structure. In particular, we identify a key steric interaction
between a methyl substituent and a valine side chain that acts to
allosterically shift population between native and near-native states,
which could be exploited in future designs. Visualization of this
mechanism is aided considerably by the tICA method, which identifies
degrees of freedom most important in slow conformational transitions.
The combination of quantitative detail and human comprehension provided
by MSMs suggests such approaches will be increasingly useful for design
Molecular Simulation of Conformational Pre-Organization in Cyclic RGD Peptides
To test the ability of molecular
simulations to accurately predict
the solution-state conformational properties of peptidomimetics, we
examined a test set of 18 cyclic RGD peptides selected from the literature,
including the anticancer drug candidate cilengitide, whose favorable
binding affinity to integrin has been ascribed to its pre-organization
in solution. For each design, we performed all-atom replica-exchange
molecular dynamics simulations over several microseconds and compared
the results to extensive published NMR data. We find excellent agreement
with experimental NOE distance restraints, suggesting that molecular
simulation can be a useful tool for the computational design of pre-organized
solution-state structure. Moreover, our analysis of conformational
populations estimates that, despite the potential for increased flexibility
due to backbone amide isomerizaton, N-methylation provides about 0.5
kcal/mol of reduced conformational entropy to cyclic RGD peptides.
The combination of pre-organization and binding-site compatibility
explains the strong binding affinity of cilengitide to integrin
Diverted Total Synthesis of the Baulamycins and Analogues Reveals an Alternate Mechanism of Action
The
baulamycins were identified as in vitro siderophore biosynthesis
inhibitors. Diverted total synthesis was used to construct the natural
products and eight strategic analogues, three of which had improved
inhibitory activity. Biological testing then revealed that membrane
damage is the predominant mode of action in <i>Staphylococcus
aureus</i> cells
A Concise Synthesis of Carolacton
A synthesis
of carolacton, a myxobacterial natural product that
has profound effects on Streptococcus mutans biofilms, is reported. The synthesis proceeds via a longest linear
sequence of 14 steps from an Evans β-ketoimide and enabled preliminary
evaluations of the effects of late-stage intermediates on S. mutans biofilms. These studies suggest that further
investigations into carolactonâs structureâfunction
relationships are warranted
Honokiol-Inspired Analogs as Inhibitors of Oral Bacteria
The oral microbiome
is a complex ecological niche where both commensal
and pathogenic bacteria coexist. Previous reports have cited that
the plant isolate honokiol is a potent inhibitor of <i>S. mutans</i> biofilms. Herein we report a cross-coupling method that provides
access to a concise library of honokiol-inspired analogs. Through
this work we determined that the inhibitory activity of honokiol is
highly dependent on the growth conditions. Further, we identify a
series of analogs that display significant potency against oral bacteria
leading to the discovery of a potent antimicrobial
Diverted Total Synthesis of Promysalin Analogs Demonstrates That an Iron-Binding Motif Is Responsible for Its Narrow-Spectrum Antibacterial Activity
Promysalin
is a species-specific <i>Pseudomonad</i> metabolite
with unique bioactivity. To better understand the mode of action of
this natural product, we synthesized 16 analogs utilizing diverted
total synthesis (DTS). Our analog studies revealed that the bioactivity
of promysalin is sensitive to changes within its hydrogen bond network
whereby alteration has drastic biological consequences. The DTS library
not only yielded three analogs that retained potency but also provided
insights that resulted in the identification of a previously unknown
ability of promysalin to bind iron. These findings coupled with previous
observations hint at a complex multifaceted role of the natural product
within the rhizosphere
Dual Inhibitor of Staphylococcus aureus Virulence and Biofilm Attenuates Expression of Major Toxins and Adhesins
Staphylococcus
aureus is a major
bacterial pathogen that invades and damages host tissue by the expression
of devastating toxins. We here performed a phenotypic screen of 35
molecules that were structurally inspired by previous hydroxyamide-based S. aureus virulence inhibitors compiled from commercial
sources or designed and synthesized de novo. One of the most potent
compounds, <b>AV73</b>, not only reduced hemolytic alpha-hemolysin
production in S. aureus but also impeded
in vitro biofilm formation. The effect of <b>AV73</b> on bacterial
proteomes and extracellular protein levels was analyzed by quantitative
proteomics and revealed a significant down-regulation of major virulence
and biofilm promoting proteins. To elucidate the mode of action of <b>AV73</b>, target identification was performed using affinity-based
protein profiling (AfBPP), where among others YidC was identified
as a target
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Promysalin Elicits Species-Selective Inhibition of <i>Pseudomonas aeruginosa</i> by Targeting Succinate Dehydrogenase
Natural products
have served as an inspiration to scientists both
for their complex three-dimensional architecture and exquisite biological
activity. Promysalin is one such <i>Pseudomonad</i> secondary
metabolite that exhibits narrow-spectrum antibacterial activity, originally
isolated from the rhizosphere. We herein utilize affinity-based protein
profiling (AfBPP) to identify succinate dehydrogenase (Sdh) as the
biological target of the natural product. The target was further validated
in silico, in vitro, in vivo, and through the selection, and sequencing,
of a resistant mutant. Succinate dehydrogenase plays an essential
role in primary metabolism of <i>Pseudomonas aeruginosa</i> as the only enzyme that is involved both in the tricarboxylic acid
cycle (TCA) and in respiration via the electron transport chain. These
findings add credence to other studies that suggest that the TCA cycle
is an understudied target in the development of novel therapeutics
to combat <i>P. aeruginosa</i>, a significant pathogen in
clinical settings