Small Molecules

In contrast to high-throughput screening, which relies on vast libraries of small molecules, fragment-based drug discovery takes a different approach to identify potential starting molecules for drug development. Using libraries typically comprising just a few thousand molecules, each of <20 heavy (non‑hydrogen) atoms, fragment-based drug discovery identifies hits with varying affinity for the drug target. The hit‑molecules can subsequently be merged, linked, or expanded to transform weak binders and fragments with moderate binding affinity into high‑affinity small molecules. A major advantage of this method is that it promises higher hit rates compared to traditional small molecule screening, since the lower molecular complexity of fragments corresponds to fewer unfavorable interactions with the drug target.

Despite being driven by recent developments in screening technologies, fragment‑based drug discovery remains challenging. This is mainly due to the small size of the fragment molecules, the limited quantities of material available, and the molecular stability.

Traditional approaches to fragment‑based drug discovery rank molecules by affinity rather than kinetics. This is because fragment libraries often contain a high proportion of weak binders with very fast off‑rates that cannot be resolved by standard instrumentation. Since affinity describes the relationship between the on‑rate and the off‑rate, it does not discriminate between a hit and a non‑specific binding event. Moreover, due to the weak binding and often low purities, the signal obtained from fragments may be mistaken for affinity when no actual binding has occurred. Measuring affinity can therefore extend workflows by generating large numbers of false positive results.

Kinetic trajectory as lead matter progresses from hits to drugs, adapted from "Application of label‑free biosensing in drug discovery: The past, present and future", CHI Drug Discovery Chemistry, April 22nd 2016" by John Quinn.


 

REINVENTING FRAGMENT‑BASED DRUG DISCOVERY WITH THE CREOPTIX™ WAVEsystem

Using the Creoptix™ WAVEsystem, researchers can reliably determine off‑rates of up to 10s-1, starting with just a crude reaction mixture. By adopting this approach, the occurrence of false positives is minimized. Moreover, since the off‑rate is not concentration dependent, only very small amounts of material are required to generate a comprehensive data set, making the Creoptix™ WAVEsystem ideal for fragment‑based screening. A further advantage of the Creoptix™ WAVEsystem is that it provides high sensitivity at even very low immobilization levels, significantly reducing the costs associated with obtaining purified target protein.

FULL KINETIC CHARACTERIZATION FOR IMPROVED ANALYSIS OF SMALL MOLECULE BINDING KINETICS

Exceptional sensitivity
Work with low immobilization levels and experience signal resolution to ≤ 1pg/mm2 (equivalent to <1RU)

Small molecules can’t hide any more
Analyze interactions between small molecules and large drug targets with confidence (target‑to‑analyte molecular weight ratios up to >1000:1)

Extend studies
Prevent evaporation to maintain sample integrity, perform kinetic analysis for extended periods of time (up to 120h of unattended operation)


 

ANALYSIS OF SMALL MOLECULE BINDING KINETICS COMPLEMENTS FRAGMENT-BASED DRUG DISCOVERY

Historically, hit compounds have been identified from libraries of small molecules by high throughput screening. This usually involves running the libraries through an assay designed to analyze the impact of each molecule on one or more downstream readouts, an approach that can be extremely costly and time-consuming and that can generate false positive results. A further drawback of many high throughput screens is that they frequently offer only limited sensitivity, especially at large target‑to‑analyte molecular weight ratios, meaning that low-potency small molecules are frequently overlooked.

By using the Creoptix™ WAVEsystem to perform real-time kinetic analysis of small molecule binding to drug targets, researchers can gain valuable insight to more effectively guide the optimization and progression of promising drug candidates. Employing our proprietary Grating-Coupled Interferometry (GCI) technology to deliver superior sensitivity over traditional Surface Plasmon Resonance (SPR) technologies, the Creoptix™ WAVEsystem pushes the limits of what is possible to overcome mass-transport limitations. This is achievable within a broad range of immobilization levels, meaning that it is no longer necessary to saturate the surface with the drug target.

Used in combination with fragment‑based screening approaches, kinetic analysis of small molecule binding to drug targets has considerable potential to expedite drug discovery programs. Chemical engineering based on structural insights from the fragment‑based screen allows researchers to develop small molecules that are more likely to deliver the specificity and potency necessary to achieve the desired therapeutic outcome.

RAPID OFF-RATE KINETIC ANALYSIS OF FRAGMENT LIBRARIES WITH THE CREOPTIX™ WAVEsystem

Compatible with crude reaction mixtures
Save time by removing the need for fragment purification

Eliminate false positives
Measure off‑rates rather than affinity for accurate identification of hits, resolve off‑rates of up to 10 s‑1

Standardized results
Avoid drift through stringent temperature control (± 0.2°C) and constant flow rate (1-400ul/min)

More than buffer
Experiment with non-traditional solvents, including high percentages of acetonitrile and DMSO, thanks to our robust microfluidic technology

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