An in silico tool to aid identification of degradants from forced degradation studies

Senior Research Scientist

rachel.hemingway@lhasalimited.org

Dr Rachel Hemingway

Aim of the talk

➢ To provide an overview of the current Zeneth

program

➢ To outline how the knowledge base is developed

➢ To detail the new scientific features being added

into the re-developed software

Contents

• Introduction to Lhasa Limited

• The Zeneth program

• Developing the knowledge base in Zeneth

• New scientific developments

• Future aspirations

• Concluding remarks

INTRODUCTION

Lhasa Limited

➢ Established 1983, headquarters in Leeds, UK

➢ Not-for-profit organisation and educational charity

▪ “Shared Knowledge, Shared Progress”

➢ It is controlled by its members (more than 350 organisations worldwide)

▪ Pharmaceutical companies▪ Chemical and agrochemical companies▪ Personal product and cosmetic companies▪ Food/Flavour companies▪ Tobacco companies▪ Universities▪ Contract research organisations▪ Government (including regulatory) bodies▪ Consultants

Lhasa: about us

Expert system

Database

Purge Factor

calculation tool

Statistical/

machine

learning

Vitic

Toxicity

Sarah Nexus

Mutagenicity Mirabilis

Purge Factors

Derek Nexus

Toxicity

Meteor Nexus

Xenobiotic metabolism

Zeneth

Chemical degradation

https://www.lhasalimited.org

THE ZENETH PROGRAM

Degradation workflow

Forced Degradation

Stability-Indicating Method

Stability Modelling

Final Formulation

Formulation Development

Packaging

Degradant Identification

Degradation Mechanism

In silico approach

Forced Degradation

Stability-Indicating

Method

Stability Modelling

Final Formulation

Formulation Development

Packaging

Degradant Identification

Degradation Mechanism

API

In silico assumption

RealSpace

PotentialSpace

HypotheticalSpace

A

B

C

D

E

F

GH

I

API

Hypothetical degradation products as in stress testing conditions and in silico

methods

BC

D

E

H

API

Potential degradation products as in accelerated and stability studies

BC H

API

Real degradation products in final packaging and storage conditions

Zeneth: an in silico tool

Z is for……….

• Expert knowledge based system for the prediction of forced degradation1, 2

• The program uses its knowledge base to:➢ find ‘matching’ transformations,

➢ predict chemical degradation,

➢ assess the likelihood of a given degradant

Transformation

Knowledge base

• Zeneth contains a ‘library’ of chemical transformations

1. An Expert System To Predict the Forced Degradation of Organic Molecules, Parenty DC, Button WG, Ott MA, Mol.

Pharmaceutics, 2013, 10, 292-2974, 10.1021/mp400083h.

2. Chapter 3: In silico drug degradation prediction, Ali MA, Hemingway R, Ott MA, in: Methods for Stability Testing of

Pharmaceuticals. Editors: Sanjay Bajaj, Saranjit Singh, pp 53-73.

Chemical patterns

Chemical degradation reactions are represented as patterns in the knowledge base

1. Degradation reaction

2. Determine the ‘degradophore’

3. Define the scope of the transformation, masking any proprietary nature

Excipients

• Potential API-excipient interactions can be predicted by Zeneth

• Important use case for many members

• Database of 188 structures (excipients, counterions and their associated

degradants and impurities)

Esterification with primary

aliphatic alcohol

Methodology

Query

Likelihood Threshold

Knowledge base Transformation Library

Environmental conditions

Reasoning

Degradant

Relative

Compares the likelihood of competing transformations

Absolute

Evaluates the likelihood that a degradation will

occur

Inp

ut

Tran

sfo

rmat

ion

En

gin

eAPI (+ excipients)

Environmental conditions

*Information from Q3B guideline

Methodology

Query

Likelihood Threshold

Knowledge base Transformation Library

Environmental conditions

Reasoning

Degradant

Relative

Compares the likelihood of competing transformations

Absolute

Evaluates the likelihood that a degradation will

occur

Inp

ut

Tran

sfo

rmat

ion

En

gin

eAPI (+ excipients)

Worked example

Query

Likelihood Threshold

Knowledge base Transformation Library

Environmental conditions

Reasoning

Degradant

Relative Absolute

Inp

ut

Tran

sfo

rmat

ion

En

gin

e

Conditions:Water, pH 4

Very Likely

N

R2

R1

R3

O

R2

R1 NH2

R3

H2O+

R1, R2 = Carbon or HydrogenR3 = Aliphatic or aromatic carbonC=N bond cannot be in a ring

Transformation 009

DEVELOPING THE KNOWLEDGE BASE

Knowledge base status

Knowledge base growth

Year No. of

transformations

Increase

2013 300 -

2014 367 +67

2015 400 +33

2016 446 +46

2017 492 +46

Knowledge base Transformation Library

Oxidation (152)

Hydrolysis(110)

Condensation (93)

Elimination (59)

Isomerisation(36)

Photolysis(42)

Total = 492

Industry influence

➢ Run brainstorming sessions with a group of Zeneth users

➢ We put forward proposals for inclusion in the knowledge base

➢ Industry can (and do) suggest proposals

➢ These decisions directly influence the chemistry that goes into the

knowledge base

Pfizer

Industry proposals

Norrish-Yang cyclisationBoron chemistry

+ hydrolysis of borinic, boronic and boric esters

Knowledge base Transformation LibraryRecent additions to the

NEW SCIENTIFIC DEVELOPMENTS FOR ZENETH 8

Re-development

What’s new?

Degradants will

be ‘scored’

instead of being

given a defined

likelihood level

Inclusion of a

property

calculator to

calculate pKa

values

Improvements in

treatment of

stereochemistry

Ability to handle

trimolecular

reactions

Scoring methodology

Moving from likelihood levels to scores

lead to more granular predictionsVery likely

Degradant A

0 2 4 6 8 10 12 14 16

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

Formula = MIN((pH-1)/10 +0.1, 0.9)

Unlikely

Very unlikely

Equivocal

Likely

Very likely

Certain

Increasing

likelihood level

Impossible

0.90**

**scale used for illustrative purposes only, subject to change

pH profile 10 (base catalysed)

1 3 5 7 9 11 13pH

Very likely

Likely

Equivocal

Unlikely

Very unlikely

pH = 4 Equivocal

pH = 5 Equivocal

pH = 5.5 Equivocal

pH = 4 0.40

pH = 5 0.50

pH = 5.5 0.55

What are my top 20

most likely

degradants?

pKa calculator

• pKa of a molecule determines its protonation state at a given pH

• pKa tends to be governed by electronic effects that decrease with the distance from

the centre of protonation

• Generate a distance spectrum for each atom-type from the pKa centre

Dist 101101 101108 106307 106203 108103 108106 117100

1 1 1

2 0.25 0.25

3 0.22 0.11

4 0.12 0.06

Sum 1 0.34 1 0.36 0 0.25 0.06

Sybyl atom type

= distance spectrum

pKa performance

RMSE: 1.163

Preliminary results using 5-fold cross-validation

How will this calculator improve predictions?

pH = basic

Stereochemistry

• Have to define stereochemistry to garner stereochemical information

in any resulting degradants➢ No longer get individual isomers as degradants from an epimerisation reaction

unless the query had its stereochemistry defined

• SN2-type reactions will now demonstrate inversion of configuration

Transformation 134: Nucleophilic ring opening of aziridine

Trimolecular reactions

The new platform gives us the capabilities to express trimolecular reactions

FUTURE ASPIRATIONS FOR ZENETH

Other calculators

• Calculating BDEs is not trivial

• Balance between accuracy and speed of performance is a critical factor

• QM based calculation……………..a cheap one!

BDE calculator

Chromophore calculator

• Assess (the important) wavelength

• Applied as a whole-molecule property

• Modulate the prediction of photochemical reactions

Reducing false positives

• Zeneth predicts in the hypothetical chemical space

• There will always be a level of overprediction in comparison to the potential (or real) space

• Assessing how to reduce the number of false positives using a validation study

(Small) dataset of ~30 compounds with experimental data

(forced deg, accelerated and stability studies)

Are there

transformations which

fire for several APIs

which are never

actually seen?

➢ Scope amendment?

➢ Lower the score given?

What are we not

predicting that is

seen?

➢ Knowledge gaps

➢ Expand knowledge base

vs Hypothetical SpaceReal

SpacePotential

Space

Ideal in silico scenario

BC F

API

Real degradation products in final packaging and storage conditions

BC

D

E

F

API

Potential degradation products as in accelerated and stability studies

A

B

C

D

EF

API

Hypothetical degradation products as in stress testing conditions and in silico

methods

RealSpace

Hypothetical Space

PotentialSpace

RealSpace

PotentialSpace

Hypothetical Space

Concluding remarks

Zeneth is our

expert knowledge

based system for

the prediction of

forced

degradation

Helps understand

mechanistic

pathways as well

as aid degradant

identification

Zeneth generates

predictions from

its knowledge

base which

currently contains

492

transformations

Industry helps

drive the

development of

the knowledge

base and directly

influences the

content

Scientific

developments include

a granular scoring

method, improved

stereochemical

behaviour and

inclusion of a

calculator for pKa

Zeneth is

undergoing a

complete re-design

with the aim of

improving usability

as well as the quality

and speed of

predictions

Come see us!

Booth number: 10

Product Owner

for Zeneth

Lisa Leivers Maggie Coombs

US Account

Manager for Zeneth

Alison Reeves

Sales executive

Acknowledgements

Thank you all for your attention

Dr Martin Ott

Principal ScientistDr Carlos Cunha

(ex)-US Account Manager

Dr Jeff Plante

Senior Research Cheminformatician

Special thanks to:

Questions?