27 research outputs found
Tower 1978
1978 yearbook of Westbrook College in Portland, Maine.https://dune.une.edu/wchc_yearbooks/1007/thumbnail.jp
Inhibition of CDC25B Phosphatase Through Disruption of Protein–Protein Interaction
CDC25
phosphatases are key cell cycle regulators and represent
very attractive but challenging targets for anticancer drug discovery.
Here, we explored whether fragment-based screening represents a valid
approach to identify inhibitors of CDC25B. This resulted in identification
of 2-fluoro-4-hydroxybenzonitrile, which directly binds to the catalytic
domain of CDC25B. Interestingly, NMR data and the crystal structure
demonstrate that this compound binds to the pocket distant from the
active site and adjacent to the protein–protein interaction
interface with CDK2/Cyclin A substrate. Furthermore, we developed
a more potent analogue that disrupts CDC25B interaction with CDK2/Cyclin
A and inhibits dephosphorylation of CDK2. Based on these studies,
we provide a proof of concept that targeting CDC25 phosphatases by
inhibiting their protein–protein interactions with CDK2/Cyclin
A substrate represents a novel, viable opportunity to target this
important class of enzymes
Two Loops Undergoing Concerted Dynamics Regulate the Activity of the ASH1L Histone Methyltransferase
ASH1L
(absent, small, or homeotic-like 1) is a histone methyltransferase
(HMTase) involved in gene activation that is overexpressed in multiple
forms of cancer. Previous studies of ASH1L’s catalytic SET
domain identified an autoinhibitory loop that blocks access of histone
substrate to the enzyme active site. Here, we used both nuclear magnetic
resonance and X-ray crystallography to identify conformational dynamics
in the ASH1L autoinhibitory loop. Using site-directed mutagenesis,
we found that point mutations in the autoinhibitory loop that perturb
the structure of the SET domain result in decreased enzyme activity,
indicating that the autoinhibitory loop is not a simple gate to the
active site but is rather a key feature critical to ASH1L function.
We also identified a second loop in the SET-I subdomain of ASH1L that
experiences conformational dynamics, and we trapped two different
conformations of this loop using crystallographic studies. Mutation
of the SET-I loop led to a large decrease in ASH1L enzymatic activity
in addition to a significant conformational change in the SET-I loop,
demonstrating the importance of the structure and dynamics of the
SET-I loop to ASH1L function. Furthermore, we found that three C-terminal
chromatin-interacting domains greatly enhance ASH1L enzymatic activity
and that ASH1L requires native nucleosome substrate for robust activity.
Our study illuminates the role of concerted conformational dynamics
in ASH1L function and identifies structural features important for
ASH1L enzymatic activity
Profiling the Dynamic Interfaces of Fluorinated Transcription Complexes for Ligand Discovery and Characterization
The conformationally dynamic binding surfaces of transcription
complexes present a particular challenge for ligand discovery and
characterization. In the case of the KIX domain of the master coactivator
CBP/p300, few small molecules have been reported that target its two
allosterically regulated binding sites despite the important roles
that KIX plays in processes ranging from memory formation to hematopoiesis.
Taking advantage of the enrichment of aromatic amino acids at protein
interfaces, here we show that the incorporation of six <sup>19</sup>F-labeled aromatic side chains within the KIX domain enables recapitulation
of the differential binding footprints of three natural activator
peptides (MLL, c-Myb, and pKID) in complex with KIX and effectively
reports on allosteric changes upon binding using 1D NMR spectroscopy.
Additionally, the examination of both the previously described KIX
protein–protein interaction inhibitor Napthol-ASE-phosphate
and newly discovered ligand 1-10 rapidly revealed both the binding
sites and the affinities of these small molecules. Significantly,
the utility of using fluorinated transcription factors for ligand
discovery was demonstrated through a fragment screen leading to a
new low molecular weight fragment ligand for CBP/p300, 1G7. Aromatic
amino acids are enriched at protein–biomolecule interfaces;
therefore, this quantitative and facile approach will be broadly useful
for studying dynamic transcription complexes and screening campaigns
complementing existing biophysical methods for studying these dynamic
interfaces
Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein–Ligand Complexes
Multipolar interactions involving
fluorine and the protein backbone
have been frequently observed in protein–ligand complexes.
Such fluorine–backbone interactions may substantially contribute
to the high affinity of small molecule inhibitors. Here we found that
introduction of trifluoromethyl groups into two different sites in
the thienopyrimidine class of menin–MLL inhibitors considerably
improved their inhibitory activity. In both cases, trifluoromethyl
groups are engaged in short interactions with the backbone of menin.
In order to understand the effect of fluorine, we synthesized a series
of analogues by systematically changing the number of fluorine atoms,
and we determined high-resolution crystal structures of the complexes
with menin. We found that introduction of fluorine at favorable geometry
for interactions with backbone carbonyls may improve the activity
of menin–MLL inhibitors as much as 5- to 10-fold. In order
to facilitate the design of multipolar fluorine–backbone interactions
in protein–ligand complexes, we developed a computational algorithm
named FMAP, which calculates fluorophilic sites in proximity to the
protein backbone. We demonstrated that FMAP could be used to rationalize
improvement in the activity of known protein inhibitors upon introduction
of fluorine. Furthermore, FMAP may also represent a valuable tool
for designing new fluorine substitutions and support ligand optimization
in drug discovery projects. Analysis of the menin–MLL inhibitor
complexes revealed that the backbone in secondary structures is particularly
accessible to the interactions with fluorine. Considering that secondary
structure elements are frequently exposed at protein interfaces, we
postulate that multipolar fluorine–backbone interactions may
represent a particularly attractive approach to improve inhibitors
of protein–protein interactions
Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein–Ligand Complexes
Multipolar interactions involving
fluorine and the protein backbone
have been frequently observed in protein–ligand complexes.
Such fluorine–backbone interactions may substantially contribute
to the high affinity of small molecule inhibitors. Here we found that
introduction of trifluoromethyl groups into two different sites in
the thienopyrimidine class of menin–MLL inhibitors considerably
improved their inhibitory activity. In both cases, trifluoromethyl
groups are engaged in short interactions with the backbone of menin.
In order to understand the effect of fluorine, we synthesized a series
of analogues by systematically changing the number of fluorine atoms,
and we determined high-resolution crystal structures of the complexes
with menin. We found that introduction of fluorine at favorable geometry
for interactions with backbone carbonyls may improve the activity
of menin–MLL inhibitors as much as 5- to 10-fold. In order
to facilitate the design of multipolar fluorine–backbone interactions
in protein–ligand complexes, we developed a computational algorithm
named FMAP, which calculates fluorophilic sites in proximity to the
protein backbone. We demonstrated that FMAP could be used to rationalize
improvement in the activity of known protein inhibitors upon introduction
of fluorine. Furthermore, FMAP may also represent a valuable tool
for designing new fluorine substitutions and support ligand optimization
in drug discovery projects. Analysis of the menin–MLL inhibitor
complexes revealed that the backbone in secondary structures is particularly
accessible to the interactions with fluorine. Considering that secondary
structure elements are frequently exposed at protein interfaces, we
postulate that multipolar fluorine–backbone interactions may
represent a particularly attractive approach to improve inhibitors
of protein–protein interactions
An Evolution-Based Approach to <i>De Novo</i> Protein Design and Case Study on <i>Mycobacterium tuberculosis</i>
<div><p>Computational protein design is a reverse procedure of protein folding and structure prediction, where constructing structures from evolutionarily related proteins has been demonstrated to be the most reliable method for protein 3-dimensional structure prediction. Following this spirit, we developed a novel method to design new protein sequences based on evolutionarily related protein families. For a given target structure, a set of proteins having similar fold are identified from the PDB library by structural alignments. A structural profile is then constructed from the protein templates and used to guide the conformational search of amino acid sequence space, where physicochemical packing is accommodated by single-sequence based solvation, torsion angle, and secondary structure predictions. The method was tested on a computational folding experiment based on a large set of 87 protein structures covering different fold classes, which showed that the evolution-based design significantly enhances the foldability and biological functionality of the designed sequences compared to the traditional physics-based force field methods. Without using homologous proteins, the designed sequences can be folded with an average root-mean-square-deviation of 2.1 Ă… to the target. As a case study, the method is extended to redesign all 243 structurally resolved proteins in the pathogenic bacteria <i>Mycobacterium tuberculosis</i>, which is the second leading cause of death from infectious disease. On a smaller scale, five sequences were randomly selected from the design pool and subjected to experimental validation. The results showed that all the designed proteins are soluble with distinct secondary structure and three have well ordered tertiary structure, as demonstrated by circular dichroism and NMR spectroscopy. Together, these results demonstrate a new avenue in computational protein design that uses knowledge of evolutionary conservation from protein structural families to engineer new protein molecules of improved fold stability and biological functionality.</p></div
Evaluation of designed sequences.
<p>Data is averaged over 87 test proteins. The details on each protein can be found at <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003298#pcbi.1003298.s007" target="_blank">Table S2</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003298#pcbi.1003298.s008" target="_blank">S3</a>, <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003298#pcbi.1003298.s009" target="_blank">S4</a>.</p>a<p>TM-score between the first I-TASSER model and the target scaffold.</p>b<p>RMSD between the first I-TASSER model and the target scaffold.</p>c<p>SS: Secondary structure.</p>d<p>SA: Solvent accessibility.</p>e<p>PBM: Physics-based method using FoldX.</p>f<p>EvBM: Evolution-based method using only evolutionary terms in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003298#pcbi.1003298.e004" target="_blank">Eq. (1)</a>.</p>g<p>EBM: Evolutionary based method using both evolutionary and physics-based terms in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003298#pcbi.1003298.e006" target="_blank">Eq. (3)</a>.</p
Average RMSD between the scaffold structures and I-TASSER models on the proteins designed by PBM and EBM.
<p>The dataset is divided by the TM-score cutoff of the template proteins that were used for constructing the sequence profiles.</p
Average fractional difference in amino acid composition between the target and designed sequences.
<p>(A) EBM; (B) PBM.</p