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Zeneth 8: A faster, more intuitive, degradation predictive system Dr Martin Ott (Head of Chemistry) [email protected] Dr Ash Ali (Senior Scientist) [email protected]

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Page 1: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Zeneth 8: A faster, more intuitive,

degradation predictive system

Dr Martin Ott (Head of Chemistry)

[email protected]

Dr Ash Ali (Senior Scientist)

[email protected]

Page 2: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Contents

• Zeneth 8 overview

Knowledge manager

Predictor

• Transformations and patterns

• Degradant scoring

• Excipient functionality

• New scientific developments

Stereochemistry

pKa calculator

• Demonstration

Page 3: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Expert knowledge-based system for the prediction of forced degradation

Zeneth 8

Query

compound

Environmental

conditions“Predictor”

• H2O (hydrolysis)

• O2, H2O2, AIBN (oxidation)

• Light (photochemistry)

• pH

• Temperature

Potential degradants

Other

constraints

• Transformations [507]

• Excipients [189]

• References [546]

Knowledge

base

Page 4: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Knowledge manager

Page 5: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Knowledge manager

Page 6: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Knowledge manager

Page 7: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Knowledge manager

Page 8: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Transformation patterns

z457:

Photodecarboxylation

of aryloxyacetic acid

Atom 13: requiredBondType(AROMATIC)

Atoms 16, 17: (heteroCount == 0 and allowedBondType(SINGLE))

or requiredBondType(AROMATIC)

Explora pattern language

Pattern 1

Prediction

breakBond(10, 15);

hideStructure(15);

breakBond(8, 9);

setBondType(9, 10, DOUBLE);

hideStructure(9);

setCharge(8, -1);

captureIntermediate("");

setIntermediateTypeMechanistic();

setIntermediateAsPresumed();

unsetCharge(8);

setScore(0.7); LTL

2 Script

Page 9: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Zeneth prediction

QQuery Compound

Environmental

Conditions

• Water

• pH 3

Structure perception:

valences, rings, aromaticity

Match pattern

and conditions

No

Prediction

Generate

potential degradants

“Predictor”Knowledge

Base

pH profile

“Hydrolysis of acetal”

• requires water

• catalysed by acid

Prediction score = 700

Page 10: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Degradant likelihood/scoring

Many transformations have a pH profile:

pH

Pre

dic

ted

lik

elih

ood

Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score

800

700

600

pH 3.9 likely

pH 3 likely

pH 2 likely

pH 1.9 very likely

Page 11: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Scoring and multiplied step likelihood

Child degradant can never have a higher score than the parent

300 (Unl)

Individual step likelihoods

Q

500 (Eq)

D1

D2

D3

700 (Lik)

2nd Gen.

1st Gen.

3rd Gen.

“Lowest step”pathway

likelihoods

Q

500D1

D3

500

300

D2

Q

D1

D2

D3

350 [0.50 x 0.70 = 0.35]

105 [0.35 x 0.30]

500

“Multiplied step”pathway

likelihoods

Page 12: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Excipients

Page 13: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Building the knowledge base

Knowledge base

• External requests (members)

- provide data for a reaction

- proprietary data via data sharing initiatives

• Group discussion with members

- discuss proposals for new reactions

- provide feedback on new & existing chemistry

• Internal requests, updates to existing knowledge

- general maintenance

- investigation of primary literature

- specialised degradation chemistry books

• Strategic decision (e.g. cover a new reaction type)

0

100

200

300

400

500

600

2008 2010 2012 2014 2016 2018 2020

New knowledge added & existing

knowledge continuously maintained

Oxidation [148]

Hydrolysis [118]

Condensation [109]

Elimination [60]

Isomerisation [28]

Photolysis [44]

Page 14: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

New developments

• Stereochemistry

• Three-component reactions

• Intramolecular reactions

• Chemical descriptors / calculators

Page 15: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Stereochemistry

• Take into account stereodefinition

This transformation now operates only on carbon centres that have a defined stereocentre:

z045

No prediction

• Nucleophilic substitutions

SN2-type reactions exhibit inversion of configuration at a stereocentre:

z138

Page 16: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Three-component reactions

• Three-component reactions can now be expressed and handled:

2 bidentate oxygen boric acid spiroborate anion

nucleophiles

z505

Page 17: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Intramolecular reactions

More intramolecular transformations can now be written

• Cyclisations

• Cycloadditionsillustrated with the photochemical [2+2] addition of two alkenes

h

h

intermolecular

intramolecular

Page 18: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Intramolecular reactions

Page 19: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Chemical descriptors / calculators

• pKa

• Bond Dissociation Energy (BDE)

• Electrophilicity/Nucleophilicity

• Photochemical Reactivity

• Aromaticity

• Steric Hindrance

Reasoning Engine

Page 20: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

C1

C4

pKa Calculator implemented

z045: Epimerisation alpha to electron-withdrawing group

Epimerisation is more likely at C1 than C4

if (!isDefinedStereocentre(1)) { abort(); }if (isBridgehead(1)) { abort(); }

substitutionWithInversion(4, 1, 3);hideStructure(3);

real pH = getpH();real pKa = getpKa(1);real raw_score = (max(pH, 14 - pH) + 6 - pKa) / 10;if (raw_score < 0.1) { abort(); }

setScore(min(raw_score, 0.9));

Score depends on pKa as well as on pH

pH = 12

Page 21: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Zeneth 8 demo

Page 22: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Zeneth 8: A faster, more intuitive,

degradation predictive system

Dr Martin Ott (Head of Chemistry)

[email protected]

Dr Ash Ali (Senior Scientist)

[email protected]

Software demonstration slides

Page 23: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Intro screen

• Projects area

Start

new project

Page 24: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Query: PU-H71

Conditions: oxygen, light, pH 11, temperature 20

°C

Pathway length: 2 steps

Minimum score: 600

Reaction types: all options off (= “no dimerisations”)

Pathway likelihood calc.: multiplied step

Page 25: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Project screen

• Empty to start with

• Click on “chalk” (edit icon) to enter query structure

Create new

query structure

Page 26: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Structure editor

• Draw a query structure or import one from file (.cdx, .mol)Use this structure

Page 27: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Project screen

• With query structure

• Click on “i” (info icon) to display details on query structure

Settings for processing

Page 28: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Settings

• Conditions

Page 29: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Settings

• Other:

Reaction types

Numerical settings

Pathway likelihood calculation

Page 30: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Project screen

• With query structure

• Click on “arrow right” icon to start processing query

Start processing

Page 31: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Project screen

• Processing completed

• Click on “View results” to view tree

Page 32: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Results

• Tree

Page 33: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Results

• Table

Page 34: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Query: Adrenaline

(epinephrine)

Conditions: oxygen, light, pH 11, temperature 20

°C

Pathway length: 3 steps

Minimum score: 600

Reaction types: all options off (= “no dimerisations”)

Pathway likelihood calc.: multiplied step

Page 35: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Project screen

• Processing completed

• Click on “View results” to view tree

Page 36: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Results

• Tree

Page 37: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Results

• Tree

Page 38: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Results

• Tree

Page 39: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Query: Boric acid

Conditions: oxygen, light, pH 11, temperature 20 °C

Pathway length: 2 steps

Minimum score: 600

Reaction types: all options off (= “no dimerisations”)

Pathway likelihood calc.: multiplied step

Excipient(s): Glycerol

Page 40: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

• Add an excipient

Project screen

Page 41: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Project screen

• Query structure with added excipient

Page 42: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Project screen

• Processing completed

• Click on “View results” to view tree

Page 43: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Results

• Tree

Page 44: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Results

• Tree with intermediates

Page 45: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Results

• Table

Page 46: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Query: Altrenogest

Conditions: oxygen, light, pH 11, temperature 20 °C

Pathway length: 2 steps

Minimum score: 600

Reaction types: all options off (= “no dimerisations”)

Pathway likelihood calc.: multiplied step

Page 47: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Project screen

• Processing completed

• Click on “View results” to view tree

Page 48: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Results

• Tree

Page 49: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Results

• Table

Page 50: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Epimerisation / pKa

Conditions: oxygen, light, pH 7 or 11, temperature 20

°C

Pathway length: 2 steps

Minimum score: 600

Reaction types: all options off (= “no dimerisations”)

Pathway likelihood calc.: multiplied step

Page 51: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Results

• Tree

Page 52: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Results

• Tree

Page 53: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Stereochemistry / SN2

Conditions: oxygen, light, pH 11, temperature 20 °C

Pathway length: 2 steps

Minimum score: 600

Reaction types: all options off (= “no dimerisations”)

Pathway likelihood calc.: multiplied step

Page 54: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Results

• Tree

Page 55: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Timing experimentComparison with Zeneth 7

Vary between

“lowest step” and

“multiplied step”

Vary between

≥ 400 (≥ equivocal)

and ≥ 600 (≥ likely)

Page 56: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Speed improvement

Zeneth 8 takes about 13%* of the time taken by Zeneth 7 for the same query

Zeneth 7 Zeneth 8

SettingsPathway

likelihood calc.Settings

Pathway

likelihood calc.

Likelihoo

d

threshold

Lowest

step

Multiplie

d

step

Score

threshold

Lowest

step

Multiplie

d step

≥

equivocal

516

degs

288

degs≥ 400

534

degs

110

degs

488 sec 455 sec 57 sec 34 sec

≥ likely116

degs7 degs ≥ 600

129

degs9 degs

208 sec 65 sec 27 sec 9 sec

*: in the absence of excipients in the query

Page 57: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Summary

➢ Zeneth is an expert knowledge-based system for the prediction of forced

degradation

➢ Helps understand mechanistic pathways as well as aid degradant

identification and structure elucidation

➢ Zeneth generates predictions from its knowledge base which currently

contains 507 transformations

➢ Our members drive the development of the Zeneth program and directly

influence the scientific content

➢ Zeneth has recently undergone a complete re-design with the result of

much improved usability as well as improvements to the quality and speed

of predictions.

➢ Efforts are underway to develop additional property

calculators and expand/improve the knowledge base,

more fully exploiting the added functionality

Page 58: Zeneth 8: A faster, more intuitive, degradation predictive system 8...Formula of yellow line = MAX (1 − pH / 10, 0.1); x 1000 score 800 700 600 pH 3.9 likely pH 3 likely pH 2 likely

Thank you for you attention!


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