Use of MS and NMR in Drug Discovery

Question 1

Drug discovery Goal:

Answer 1

Identification of a efficacious and safe oral drug

- Drug discovery:
Target Identification 
Hit Identification  
Lead Optimisation
Candidate Selection

• Drug development:
  Preclinical and clinical Development

Question 2

5Rs framework to drive drug discovery

Answer 2

Right target:
 Strong link between target and disease
 Differentiated efficacy
 Available and predictive biomarker

Right tissue:
 Adequate bioavailability and tissue exposure
 Definition of PD biomarkers
 Clear understanding of preclinical and clinical PK/PD
 Understanding of drug–drug interactions

Right safety:
 Differentiated and clear safety margins
 Understanding of secondary pharmacology risk
 Understanding of reactive metabolites, genotoxicity, drug–drug interactions
 Understanding of target liability

Right patients:
 Identification of the most responsive patient population
 Definition of risk–benefit for given population

Right commercial potential:
 Differentiated value proposition versus future standard of care
 Focus on market access, payer and provider
 Personalised healthcare strategy, including diagnostic and biomarkers

Question 3

What types of molecules can we study with NMR & MS

Answer 3

biomarkers
drug metabolites
fragments
proteins
antibody drug conjugates
organic molecules

Question 4

What Is Mass Spectrometry?

Answer 4

Is an analytical technique that measures the mass-to-charge ratio of charged particles

Question 5

Mass Spectrometer types

Answer 5

• Single Quadrupoles
• Triple Quadrupoles
• Ion Cyclotron Resonance (ICR)
• Traps
• Time-of-flight (Tof)
• Magnetic Sector
• Ion Mobility

Can be nominally split into two groups, high and low resolution instruments. Mass Accuracy is greater on high resolution instruments. i.e. 309.3 vs 309.31129.

Question 6

Structural Elucidation - LCMS

Answer 6

• Is the product seen in the sample?

• Use LTQ -FT with >1ppm mass error.
• Is m/z 364 present?
• What is the mass error?
• Is the Isotope pattern consistent with the structure?
• Can the empirical formula be calculated from the mass?
• Are the MSMS/MSn fragments consistent with structure?

Question 7

Structural Elucidation - GCMS

Answer 7

• Not all samples are amenable to LCMS

* Size/volatility, ionisation potential and solubility may define the most suitable technique.

Question 8

Structural Elucidation - GCMS

EI Source

Answer 8

• A gas phase ionisation process.
• The compound of interest is separated via gas chromatography, as the compound of interest enters the source it encounters high energy electrons emitted from a heated filament which have been accelerated across the source.
• For compounds which are unknown the integration of a ToF(time of Flight) analyser makes the GC significantly more powerful
• The GC EI process can give more structural information than LCMS electrospray
• The shape of a spectra can indicate whether the compound is aliphatic or aromatic in nature.

Question 9

Structural Elucidation - LCMS Advantages and disadvantages

Answer 9

 Accurate mass and generated empirical formula are consistent with structure.
 Isotope pattern is consistent

X MSMS shows only one fragment
• Try NMR for additional information

Question 10

NMR Spectroscopy

Answer 10

NMR spectroscopy exploits the magnetic properties of certain atomic nuclei, and can determine the chemical environment of atoms in the molecules in which they are contained.
Nuclei: 1H 13C …19F 31P 15N ….3H etc.

Question 11

NMR

solvents:

Answer 11

D2O, 
MeOH-d4 
DMSO-d6 
ACN-d3 
CDCl3

Question 12

Subatomic particles (electrons, protons and neutrons) can be imagined as spinning on their axes.

Answer 12

In many atoms (such as 12C) these spins are paired against each other, such that the nucleus of the atom has no overall spin. However, in some atoms (such as 1H and 13C) the nucleus does possess an overall spin.

The rules for determining the net spin of a nucleus are as follows;

• If the number of neutrons and the number of protons are both even, then the nucleus has NO spin.
• If the number of neutrons plus the number of protons is odd, then the nucleus has a half-integer spin (i.e. 1/2, 3/2, 5/2)
• If the number of neutrons and the number of protons are both odd, then the nucleus has an integer spin (i.e. 1, 2, 3)

The overall spin, I, is important. Quantum mechanics tells us that a nucleus of spin I will have 2I + 1 possible orientations.
A nucleus with spin 1/2 will have 2 possible orientations.
In the absence of an external magnetic field, these orientations are of equal energy. If a magnetic field is applied, then the energy levels split.
Each level is given a magnetic quantum number, m.