CHEMAXON PORTFOLIO – WALK THROUGH from Toolkits to End-User Applications to Deliver Solutions WHO WE ARE

Aurora Costache, PhD

CHEMAXON PORTFOLIO – WALK THROUGH From toolkits to end-user applications to deliver solutions WHO WE ARE

Hungarians Czechs Romanians Hawaiian Nigerian Canadian Ukrainians Serbians Polish French Americans Indians Iranians Locations Budapest, Hungary – Prague, Czech Republic - Cambridge, MA USA How we work… How we do meetings… How we are listening to our clients… How we have fun… Cheminformatics leaders, since 1998, solution providers General Pharmaceutical and Chemistry Biotech Industry – Polymer Drug Discovery Chemistry • Small molecules • Biological entities Petrochemistry Academia

Agrochemistry Flavors and Fragrances Two faces of one world Committed to quality

• Tests – improved and evolving • Feedback • Weekly releases CHEMAXON PORTFOLIO Fate of a compound Create Analyse

Store Publish

Sketch/Convert /Import Query/Display Knowledge, Synthesize, Purchase, Assay data, Experience Comprehend Outcome Vision Collect accumulation Register/Index Reports Fate of a compound Create

Design/Sketchers Naming/Annotating Marvin/Marvin JS ChemCurator BioEddie ChemLocator Sketch/Convert Property Calculations Chemicalize /Import Reactor/Plexus Design Knowledge, Vision MarvinSketch Marvin JS Creating chemical content with Best drawing tools on the market! MarvinSketch

- Advanced chemical editor

- Publication quality drawing Marvin JS Chemistry Education

Concept Mastery Reaction Explorer End of Chapter/Testbank

Homework and test preparation Marvin JS Industry Standard BioEddie Drawing and viewing complex molecules in your browser

• Fully characterized to fully unknown

• Exact chemical descriptions to heterogeneous products

• Biological sequences to exotic bioconjugates Property calculators High-quality predictions

An analysis of the attrition of drug candidates from four major pharmaceutical companies (AstraZeneca, GlaxoSmithKline, Pfizer, Eli Lilly) „A set of physicochemical descriptors was independently calculated for these compounds by each company using ChemAxon 5.9 (see Further information) to provide a consistent set of descriptors.”

Nature Reviews Drug Discovery 14, 475–486 (2015) Property calculators Powerful lead generation and lead optimization engine Baeyer-Villiger ketone oxidation Baylis-Hillman vinyl alkylation Reactor Beckmann rearrangement Bischler-Napieralski isoquinoline synthesis Friedel-Crafts reaction Products Friedlander quinoline synthesis Reactants Gabriel synthesis Grignard reaction Hell-Volhardt-Zelinski halogenation

REACTOR Reactor In Instant JChem Reactor In JChem for Excel Reactor In Plexus Suite – Plexus Design Naming Suite A reliable chemical name conversion and mining engine text (2-butyl-4-chloro-1- Trivial names {[2'-(2H-1,2,3,4- CAS Numbers tetrazol-5-yl)-[1,1'- Internal ID-s biphenyl]-4- yl]methyl}-1H- pdf imidazol-5- IUPAC names yl)methanol Simple structures xls losartan Tautomeric forms docx hyzaar cozaar lortaan Generic structures Lozartan html Salt forms OLE objects clopidogrel pptx 114798-26-4 Chemical strings Naming Suite Document annotation ChemCurator Computer-Assisted Document Curation and Analysis – Compound Extraction View

Compound list

Project explorer Annotated document

Selected structures ChemCurator Computer-Assisted Document Curation and Analysis – Compound Extraction View Annotated document Markush editor

Structure checker

Selected structures Example structures Markush Editor Toolkit for the analysis of virtual combinatorial library and patent Markush structures

- Handling complex Markush structures - Markush drawing and visualization - Enumeration - Automatic Markush generation (composer) - Real time interactive analysis against stucture lists (hit and non-hit visualization) ChemLocator Chemical Search in Unstructured Data JChem

Shared Directories

C:\\ Fate of a compound Store

Compound/Project Management Marvin Live Compliance Checker Instant JChem Register/Index Compound Registration Synthesize, Purchase, Assay data, Experience Biomolecule Toolkit Collect accumulation Marvin Live Molecule Design and Idea Management - Flexible interface - Harmonized CADD and design capabilities - Predictive models - Databases - CXN Calculated properties - 3D alignment - Protein surface visualization - Reaxys - KNIME - Pipeline Pilot… 70 + plugins (ChemAxon + 3D party) Create, collect, challenge ideas in a project Rigid alignment Compliance Checker Stay out of jail!

- Combined software system and content package

- Provide ways to check whether compounds are controlled according to the relevant laws of the countries of interest Compliance Checker Coverage/Accuracy

Country Pass Rate Canada 100% France 100% USA 99% UK 99.7% Sweden 100% Switzerland 100% Instant JChem Desktop application for DB management Instant JChem to create, explore and share data

• Create, explore and share chemical and non-chemical data in local and remote databases without additional administration Instant JChem Desktop application for DB management to create, explore and share data Key features - Advanced query builder - List management, domain search - Customizable database views - form designer - Integration of library enumeration - Molecular property and descriptor predictions - Charting options - Scripting for extension and customization - Data pivoting - New Molecule Matrix - Biomolecule Toolkit integration - JChem PostgreSQL Cartridge support Compound Registration

The best registration system on the market! • Hierarchical storage o Parent structures o Salt/solvate forms o Batches/lots

• Multi-component structures • Markush structures

Batch 1 Version 1 Batch 2 Parent Version 2 Batch 3 Biomolecule Toolkit Bridge the gap between biology and chemistry

API (Java and REST-ful) for – Native HELM support (HELM, HELM2, xHELM) – Standardization – Centralized DB storage – Registration of entities and batches with custom dbusiness logic – Search by sequence/chemical structure/metadata – Conversion to/from Mol/FASTA/HELM – Property calculations Biomolecule Toolkit Bridge the gap between biology and chemistry

Integrates with –Since v16.8.1: Instant JChem, planned: Plexus Connect –Texelia BioScity, planned: IDBS E-Workbook Biomolecule Toolkit Bridge the gap between biology and chemistry in Instant JChem - Store - Index - Search

- unambiguous representation at sequence and atomic level for a diverse set of biomolecules: - peptides - oligonucleotides - proteins - antibody drug conjugates

- including those containing unnatural and chemically- modified components Fate of a compound Analyse

Store, Search and Display JChem Suite (Base + Cartridges) MadFast SS Plexus Suite Query/Display

Comprehend JChem Base Index, search and manage data: The best chemistry engine on the market! The heart of ChemAxon: Fast, invisible chemical backend you can rely on. Compliance Checker

Instant JChem JChem Web Services

Compound Registration Plexus Connect

JChem for Excel JChem for SharePoint JChem Cartridges Makes databases chemically intelligent: Oracle - PostgreSQL

Fast chemical searches Plexus Suite Plexus Connect: Instant data access for end-users on any web browser

- The discovery user interface

- Access, Display and Query scientific data

- Web-based, thin client interface

- Instant JChem for administration, form building Plexus Suite Plexus Analysis: Find the needle in the haystack

Easy and fast datasets correlations

Curve fitting

Linear regression MadFast Similarity Search Faster similarity based search, overlap analysis and clustering Multiple datasets

● Real time similarity searches

● Similarity based overlap analysis of large sets

● Similarity search on extremely large datasets

Fast similarity search and overlap analysis Fate of a compound Publish

Report JChem for Office Instant JChem Marvin Live Plexus Suite Reports

Outcome JChem for Office Microsoft Office applications (Excel, Word, PowerPoint, Outlook) with chemical intelligence

Practical and effective chemical data analysis and reporting tool

Direct data channeling from relational databases, Instant JChem or chemical data files

Easy usage, in a known milieu: optimal learning curve with minimal cost of education JChem for Office

- Property calculations - R-group decomposition - Substructure search - Reaction-based enumeration - SAR-matrix generation JChem for Office Reporting and presenting Instant JChem

and Marvin Live Plexus Suite Naming/Annotating Summary Mine Chem Curator ChemLocator Chemicalize Design/Sketchers Marvin/Marvin JS Create BioEddie Compound/Project Property Calculation Management Reactor/Plexus Design Marvin Live Register Compliance Checker Store, Search and Compound Registration Display Biomolecule Toolkit Instant JChem JChem Suite (Base + Comprehend Cartridges) Plexus Suite Report JChem for SharePoint JChem for Office MadFast SS Publish Instant JChem Marvin Live Plexus Suite CHEMAXON PORTFOLIO Future Plans ChemAxon Synergy as a platform

ChemAxon supporting rd 3rd PARTY TOOLS Integrated 3 party tools tools and POCs DISCOVERY Query, Report Compliance Checker IJC/Connect Analysis Data Analysis

Marvin Live Ontology ChemLocator Design Workflow Tools ChemAxon Modelling DATA CAPTURE Synergy SAR reports CompReg Registration

Assay (Inventory) ELN

Inventory

55 Consultancy Agenda

- Presentations of ChemAxon solutions from Product Owners and Consultancy - ChemAxon solutions from our clients - Tools and solutions from our partners

- Demo stations: - talk with Product Owners - hands-on tools and solutions THANK YOU

Aurora Costache, PhD