Hit Identification Services

WuXi Biology provides a one-stop Target-to-Hit services that enable companies in pharmaceuticals, biotechs and academics worldwide to seek premium drug discovery. As an innovation-driven and customer-focused unit, we help our partners improve the productivity of advancing hit discovery through high-quality and cost-effective solutions. With industry-leading capabilities such as protein science, biophysics, DNA-encoded library technology, high-throughput screening, ASMS and structure-based drug design. We are committed to drive toward the realization of the vision that every drug can be made and every disease can be treated.

Empowered by our platform, our partners can start with an idea in mind and be provided with a high quality, one-stop solution that gives a validated hit with clear MOA for the following hit-to-lead research.


Protein Production

The comprehensive evaluation of the target protein and their down-stream applications would be set as the starting point. The construct is then designed and precisely tailored towards the following screening or biophysical assay. Target proteins are produced with our highly parallelized expression and purification platform. Taking advantage of our proprietary tools and expression vectors, we are able to produce complexes and even virus-like particles with one single vector. With the help of our in house state-of-the-art biophysics platform, comprehensive protein QC can be performed on aspects including stability, folding, aggregation and post-translational modifications.

  • All target classes
  • High level protein engineering
  • Tailored tagging strategies
  • Customized conjugation (e.g., biotinylation)
  • Isotope labeling (15N, 13C)
  • Antibody and Nanobody
  • Comprehensive Protein QC

Screening

DNA-Encoded Library Technology

HitS provides customers with a cutting-edge hit identification and optimization platform using an affinity-based selection method against DNA-encoded small molecule libraries.

  • More than 80 billion synthetic compounds
  • Custom library synthesis with proprietary self-designed scaffolds
  • Bioinformatics system to collect, process and analyze data; facilitate involvement of the client to make collective decisions
  • Flexible business models to accommodate different needs

Fragment Based Screening (FBDD)

HitS offers fast and cost-efficient hit identification by fragment screening. We have several well-tended fragment libraries totaling more than 3,100 compounds. In addition, client libraries can easily be integrated in our workflow.

  • Automated screening (MST, SPR, DSF/nanoDSF)
  • Fragment screening via X-ray or NMR
  • DEL screening
  • Flexible business models to accommodate different needs

High Throughput Screening

WuXi Biology provides in vitro efficacy & MOA services to identify New Chemical Matter via High Throughput Screening (HTS)

  • Major Target Classes Enzyme
  • Immuno-oncology Checkpoint enzyme
  • GPCR
  • Nuclear Hormone Receptor
  • Transporter
  • Ion Channel
  • Protein-protein Interaction
  • Infectious disease targets
  • Major Assay platforms
    • Fluorescence: FI, FP, HTRF, FRET, FLIPR
    • Luminescence/Absorbance
    • HCS
    • Radiometric assays
    • LC/MS
    • Label free technology
    • MSD, Luminex, ELISA
  • Major Phenotypic Assays
    • Proliferation/Anti-proliferation
    • Viability/Cytotoxicity
    • Apoptosis
    • Translocation
    • Internalization/Recycling
    • Cytokine Profiling
    • Cellular Uptake

ASMS Screening

Our dedicated ASMS (Affinity selection mass spectrometry) screening team offers clients this unique platform for the identification of small molecules capable of binding to the active sites of target proteins. These active small molecules will be the perfect starting point for your drug discovery programs. Our high quality service supports both established and newly emerging targets and is backed up by access to small molecule libraries, automated operational systems, sensitive high resolution mass spectrometry devices and efficient data processing software. 

  • WuXi designed library (available for sale)
  • Biotech derived (exclusive)
  • Purified natural products or extracts
  • Library of Pharmacologically Active Compounds
  • LOPAC, Prestwick, etc..

Virtual screening

WuXi Biology offers Virtual screening (VS) to identify hits from extensive chemical space. This computational technique is used to search real or virtual libraries of small molecules in order to identify potential hit candidates.


Hit Confirmation & Validation

Biophysical & Biochemical Platform

WuXi Biology has established a number of biophysical and biochemical assays and methods which can be combined according to the needs of a specific project.

  • Over 10 biophysical methods available
  • Affinity, thermodynamics, stoichiometry, kinetics, thermal and chemical stability, aggregation
  • Flexible business models to accommodate different needs
  • Various technologies (incl. HTRF, AlphaScreen)
  • Various luminescent, fluorescent, colorimetric assays
Physicochemical Characterization

Drug leads should have sufficient target specificity and efficacy but these properties alone are not enough. To be a druggable candidate for preclinical development, the compound should also have sufficient biocompatibility in terms of dissolution and absorption and favorable pharmacokinetics. Many pharmacologically active compounds fail even at this stage due to poor bioavailability, unacceptable pharmacokinetics, or unexpected safety problems, some of which can be predicted based on the measured physicochemical properties. As a result, physicochemical parameters have been incorporated into drug discovery programs to rank the lead compounds and filter out unsuitable compounds. Properties such as pKa, solubility (KS, TS), and lipophilicity are among the most fundamental physicochemical traits of a drug candidate and their measurements are essential for both in silico and in vitro evaluation of drug-like properties.[1] WuXi AppTec’s physicochemical property platform utilizes some widely used methods for measuring these three parameters (Table 1).

Physicochemical property

Measurable

Method

Lipophilicity

logP

Scaled down shake flask method

Potentiometric method

logD

Shake flask method

pKa

pKa

Potentiometric method

Spectrophotometric method

Solubility

Kinetic solubility (K.S.)

Shake flask method

Thermodynamic solubility (T.S.)

Shake flask method

Table 1. A summary list of WuXi AppTec’s methods for measuring common physicochemical properties.

Solubility Assays – Kinetic Solubility and Thermodynamic solubility

The aqueous solubility of a drug substance is an important physicochemical parameter that has a significant role in various physical and biological processes including absorption, clearance and formulation. In rating the solubility of compounds for discovery project teams, compounds below 10 μg/mL are classified as poorly soluble, 10-60 μg/mL are moderately soluble and above 60 μg/mL are considered soluble. These solubility classification ranges can be suggested for medicinal chemists. [2] And it is important to distinguish between “kinetic” and “thermodynamic” solubility.

Items

Kinetic solubility

Thermodynamic solubility

Starting material

Initially fully dissolved in an organic solvent (e.g., DMSO) then added to the aqueous buffer

Solid crystalline material added into aqueous buffer

Equilibrium

Not reached

Reached

Effect of crystal form

Not related as it begins fully dissolved

The crystal form dictates solubility and dissolution rate

Application

Early discovery stage to mimic the protocols for discovery assays that begin with DMSO stock solutions

Late discovery and early development where a large batch of API has been synthesized and its crystal form been characterized

Table 2. Differences between kinetic and thermodynamic solubility.

Discovery and development scientists have different needs when considering solubility. [2,3,4] The goal of discovery scientists is to ensure they can obtain sufficient assay concentrations when they dilute a stock solution of drug into a working buffer. In this case, amorphous and metastable crystal forms are not necessary to consider. During the development phase, the goal is to develop a viable drug formulation and perform the detailed technical studies required for regulatory approval, thus full characterization of the API is necessary. WuXi AppTec’s solubility platform provides both kinetic solubility and thermodynamic solubility assays though which one is necessary for a given study will depend on the stage of development.

pKa assay

Knowing and understanding the pKa of a compound is very important in drug discovery and development as it influences how a drug will behave in various bodily fluids thus making it easier to foresee absorption and pharmacokinetic issues. WuXi AppTec’s pKa platform utilizes both potentiometric and spectrophotometric methods using a Sirius T3 instrument. The choice of whether to run a potentiometric or spectrophotometric assay depends on a number of factors including: the expected solubility of the compound, the amount of compound available, the expected pKa values and the UV absorbance characteristics of the drug.

Method

Description

TAT (working days)

vPotentiometric method (pH-metric method)

• The standard working pH range is 3.0 to 11.0
• ≥ 10 mg sample powder is required

5

Spectrophotometric method (UV absorbance method)

• The standard working pH range is 2.0 to 12.0.

• 1 mg sample powder or 50µL of a 10 mM DMSO stock aolution is required

5

Table 5.  A comparison of the two methods used to determine pKa.

As drug-like molecules are often poorly water soluble, a water-miscible co-solvent can be used to enhance solubility. By performing titrations at several different solvent/water ratios, the pKa in a purely aqueous environment can be extrapolated for water-insoluble compounds.

Lipophilicity – log P

The lipophilicity of a compound dictates its partition coefficient (P); a measurement of the tendency to partition into a nonpolar lipid phase from an aqueous phase. It is an important determinant of most other drug properties and is a rapid and effective tool for an initial assessment of druggability. A general guide for optimal gastrointestinal absorption by passive diffusion following oral dosing is to have a moderate log P (between 0–3), as suggested in Figure 6. In this range, a good balance of permeability and solubility exists. Compounds with a lower log P are more polar and while they typically have excellent solubility, they tend to have poorer lipid bilayer permeability. Thus these compounds will need to be small enough and preferentially nonionic or cationic to absorb paracellularly, utilize natural uptake transporters in the gut lumen or be administered parenterally. Compounds with a higher log P are more nonpolar and can thus suffer from dissolution and solubility issues as well as exhibiting a depot effect in lipids making it harder to clear the compound.

Figure 6. A generalization of the relationship of log P and oral bioavailability.
Lipophilicity – log D

Since the majority of drugs (approximately 80%) are ionizable, log P is not a sufficient predictor of a compound’s behavior across the physiological pH spectrum. Instead the log D is a more useful descriptor. Since the log D is pH-dependent, the pH of the aqueous phase should always be specified when reporting a log D value. Most commonly the log D at a pH of 7.4, the physiological pH of the vasculature, is used. Table 3 shows what various log D values at pH 7.4 suggest with respect to druggability[8].

log D at pH 7.4

Typical Effect on Physiological Properties

Typical Effect on In Vivo Properties

<1

• High solubility
• Low membrane permeability, look for paracellular absorption if MW < 200 Da

• Low Vd
• Poor Fpo and poor BBB permeation
• Higher renal clearnace for small molecules

1 to 3

• Moderate solubility
• Moderate permeability

• Balanced Vd
• Favorable Fpo and BBB permeation if not a P-gp substrate

3 to 5

• Low solubility
• High permeability

• High Vd
• Fpo and BBB permeation is moderate to low

• Oral absorption variable; may see lymphatic absorption

> 5

• Poor solubility
• High permeability

• High Vd and low CL due to depot effect
• Fpo unfavorable and variable

• Dissolution limitations in GI

Table 7. General predictions on how the log D at pH 7.4 will affect the druggability of a compound. 

Quality Control (QC)

Nadolol, mexiletine, propranolol, quinidine, amitriptyline and chlorpromazine are used as assay standards for the log D assay.

Figure 11. A correlation between the observed average experimental log D value as determined by WuXi AppTec (ordinate) and the values reported in the literature (abscissa) 
Additional Validation Compounds

WuXi AppTec has screened 27 commercial drugs using our log D assay system (Figure 12). The results show the average experimental log D values correlate well with those reported in the literature.

Figure 12. A correlation between the average experimental log D values calculated by WuXi AppTec (ordinate) and the values reported in the literature (abscissa) for 27 commercial drugs.

References:

  1. Yushen Guo, pKa, Solubility, and Lipophilicity, Methods in Pharmacology and Toxicology, pp 1-17
  2. Edward H. Kerns, Li Di, (2008). drug-like properties concepts,structure design and methods, pp 56-61
  3. Venkatesh, S., & Lipper, R. A. (2000). Role of the development scientist in compound lead selection and optimization. Journal of Pharmaceutical Sciences89, 145–154.
  4. Lipper, R. A. (1999). How can we optimize selection of drug development candidates from many compounds at the discovery stage? Modern Drug Discovery2, 55–60.

Structure-Based Drug Discovery

HitS has comprehensive structural generation solutions for today´s challenging targets. We provide insights and data to support hit finding through to lead optimization.

  • X-Ray crystallography, Cryo-EM, NMR
  • Flexible business models to accommodate different needs