9 research outputs found
The Development and Applications of the HINT Scoring Function: Exploring Colchicine-Site Anticancer Agents and Tautomerism
The overall aim of this work was to apply HINT, an empirical scoring function based on the understanding of hydrophobicity, to analyze and predict the binding affinities and biological activities of colchicine-site anticancer agents. The second, concurrent aim was to improve the scoring function by incorporating tautomerism within the modeling process. Our belief is that proper evaluation of tautomeric forms for small molecules will improve performance of virtual screening. The novel pyrrole-based compounds targeting the colchicine site were docked into the receptor using HINT as a rescoring function. Two distinct binding modes dictated by the size and shape of a subpocket were predicted to differentiate the highly active compounds from the weak ones. Of the residues predicted to participate in binding for the active binding mode, Cys241β was revealed to form a weak but critical hydrogen bond with the ligand. A larger collection of colchicine-site agents, biologically tested in the same laboratory including our pyrrole-based compounds were subject to 3D quantitative structure-activity relationship (QSAR) study. Using results on docking the pyrrole compounds as a guide, relative binding poses and QSAR models were built to facilitate ligand design and optimization. A new 3D modeling approach was introduced to visually highlight the unique features of highly active compounds and the commonality of all compounds in the dataset using HINT maps and successfully tested on the colchicine-site agents. These results will provide valuable guidance in the future design and development of new colchicine-site agents. To incorporate tautomerism within HINT, we proposed and developed two workflow approaches: a general search tool using a simple and intuitive algorithm analyzing hydrogen shift patterns to identify and enumerate tautomeric structures, and a database that contains commonly observed tautomeric structures. The first approach was designed for small-scale docking studies and the second approach was designed for large-scale virtual screening. The tautomer module in HINT will give more accurate modeling results when the compound encountered is able to tautomerize
Biological Characterization of an Improved Pyrrole-Based Colchicine Site Agent Identified through Structure-Based Design s
ABSTRACT A refined model of the colchicine site on tubulin was used to design an improved analog of the pyrrole parent compound, JG-03-14. The optimized compound, NT-7-16, was evaluated in biological assays that confirm that it has potent activities as a new colchicine site microtubule depolymerizer. NT-7-16 exhibits antiproliferative and cytotoxic activities against multiple cancer cell lines, with IC 50 values of 10-16 nM, and it is able to overcome drug resistance mediated by the expression of P-glycoprotein and the bIII isotype of tubulin. NT-7-16 initiated the concentration-dependent loss of cellular microtubules and caused the formation of abnormal mitotic spindles, leading to mitotic accumulation. The direct interaction of NT-7-16 with purified tubulin was confirmed, and it was more potent than combretastatin A-4 in these assays. Binding studies verified that NT-7-16 binds to tubulin within the colchicine site. The antitumor effects of NT-7-16 were evaluated in an MDA-MB-435 xenograft model and it had excellent activity at concentrations that were not toxic. A second compound, NT-9-21, which contains dichloro moieties in place of the 3,5-dibromo substituents of NT-7-16, had a poorer fit within the colchicine site as predicted by modeling and the Hydropathic INTeractions score. Biological evaluations showed that NT-9-21 has 10-fold lower potency than NT-7-16, confirming the modeling predictions. These studies highlight the value of the refined colchicine-site model and identify a new pyrrole-based colchicine-site agent with potent in vitro activities and promising in vivo antitumor actions
How to Deal with Low-Resolution Target Structures: Using SAR, Ensemble Docking, Hydropathic Analysis, and 3D-QSAR to Definitively Map the αβ-Tubulin Colchicine Site
αβ-Tubulin
colchicine site inhibitors (CSIs) from four
scaffolds that we previously tested for antiproliferative activity
were modeled to better understand their effect on microtubules. Docking
models, constructed by exploiting the SAR of a pyrrole subset and
HINT scoring, guided ensemble docking of all 59 compounds. This conformation
set and two variants having progressively less structure knowledge
were subjected to CoMFA, CoMFA+HINT, and CoMSIA 3D-QSAR analyses.
The CoMFA+HINT model (docked alignment) showed the best statistics:
leave-one-out <i>q</i><sup>2</sup> of 0.616, <i>r</i><sup>2</sup> of 0.949, and <i>r</i><sup>2</sup><sub>pred</sub> (internal test set) of 0.755. An external (tested in other laboratories)
collection of 24 CSIs from eight scaffolds were evaluated with the
3D-QSAR models, which correctly ranked their activity trends in 7/8
scaffolds for CoMFA+HINT (8/8 for CoMFA). The combination of SAR,
ensemble docking, hydropathic analysis, and 3D-QSAR provides an atomic-scale
colchicine site model more consistent with a target structure resolution
much higher than the ∼3.6 Å available for αβ-tubulin
Pyrrole-Based Antitubulin Agents: Two Distinct Binding Modalities Are Predicted for C-2 Analogues in the Colchicine Site
3,5-Dibromo-4-(3,4-dimethoxyphenyl)-1<i>H</i>-pyrrole-2-carboxylic
acid ethyl ester is a promising antitubulin lead agent that targets
the colchicine site of tubulin. C-2 analogues were synthesized and
tested for microtubule depolymerizing and antiproliferative activity.
Molecular modeling studies using both GOLD docking and HINT (Hydropathic
INTeraction) scoring revealed two distinct binding modes that explain
the structure–activity relationships and are in accord with
the structural basis of colchicine binding to tubulin. The binding
mode of higher activity compounds is buried deeper in the site and
overlaps well with rings A and C of colchicine, while the lower activity
binding mode shows fewer critical contacts with tubulin. The model
distinguishes highly active compounds from those with weaker activities
and provides novel insights into the colchicine site and compound
design
Systematic Approach to Conformational Sampling for Assigning Absolute Configuration Using Vibrational Circular Dichroism
Systematic
methods that speed-up the assignment of absolute configuration
using vibrational circular dichrosim (VCD) and simplify its usage
will advance this technique into a robust platform technology. Applying
VCD to pharmaceutically relevant compounds has been handled in an
ad hoc fashion, relying on fragment analysis and technical shortcuts
to reduce the computational time required. We leverage a large computational
infrastructure to provide adequate conformational exploration which
enables an accurate assignment of absolute configuration. We describe
a systematic approach for rapid calculation of VCD/IR spectra and
comparison with corresponding measured spectra and apply this approach
to assign the correct stereochemistry of nine test cases. We suggest
moving away from the fragment approach when making VCD assignments.
In addition to enabling faster and more reliable VCD assignments of
absolute configuration, the ability to rapidly explore conformational
space and sample conformations of complex molecules will have applicability
in other areas of drug discovery