January 2010 Webinar: Database usage in ChemDraw and...

January 2010 Webinar: Database usage in g

ChemDraw and ChemOffice

Jesse GordonJesse GordonCambridgeSoft Director

of Software Marketingjgordon@cambridgesoft.comOffi 617 588 9306

Office: 617-588-9306Cell: 617-320-6989Skype: jessegordon

Database Usage: Webinar OverviewWebinar Overview

•1. Content in Context1a. Interface to ChemDraw (ChemACX input)1b. Interface to ChemBioFinder (ChemACX export)1c. ChemBioFinder HotLink (ChemDraw lookup)1c. ChemBioFinder HotLink (ChemDraw lookup)1d. Chem3D PDB lookup (Future interfaces)

•2 Database Portfolio•2. Database Portfolio

2a. Drugs and Reference Works (what is it?)2b h i l i f2b. Chemical Sourcing & Safety (where to get it?)2c. Synthetic Methodology (how to make it?)

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•3. New Research Databases

Database Usage: ChemBioFinder com 2010ChemBioFinder.com 2010

• Substantial re-indexing of ChemBioFinder.com based on logical intersections ofbased on logical intersections of names, structures, and CAS Registry Numbers

• Re-indexing includes:Re indexing includes:- mixtures of stereoisomers- isotopically labeled compounds- acids and salts

• Newly indexed structures in new databases- Off-Label- MartindaleMartindale- EROS

• ChemBioFinder.com index now contains >900K i t t

>900K unique structures.

Content in ContextGlobal Search

Data Visualization

Proprietary DatabasesInstrument Systems

Reference Content

Application Content

Experiment Management Registration Management

Biology Management Materials Management

Query and Decision

Biology Management Materials Management

Third Party ContentLIMS, SAP, Data Mgmt.

Query and Reporting

Decision Support

Webinar Overview: Interfacing with DatabasesInterfacing with Databases

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1a. Interface to ChemBioDraw:ChemDraw panel in ChemACXChemDraw panel in ChemACX

Simple structures can be drawn in the ChemDraw pane directly in ChemACX:in the ChemDraw pane directly in ChemACX:

1a. Interface to ChemBioDraw:Paste into ChemACXPaste into ChemACX

More complicated structures can be drawn in ChemDraw and pasted into ChemACX:in ChemDraw and pasted into ChemACX:

1a. Interface to ChemBioDraw:Structure-plus-formula searchStructure-plus-formula search

You can paste in variable structures,f fand then add further refinements:

1a. Interface to ChemBioDraw:Peptide name search in ChemACXPeptide name search in ChemACX

Can skip chemical structure and search by name, including wildcarding:

Webinar Overview: Export from DatabasesExport from Databases

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1b. Interface to ChemBioFinder:Export from ChemACXExport from ChemACX

Most databasest t SDfilexport to SDfile.

ChemACX willexport any list up to 500 at a time.

1b. Interface to ChemBioFinder:Import SDfilesImport SDfiles

SDfiles can be imported intoimported into…

• ChemFinder• ChemDraw• CD/Excel• Chem3D

1b. Interface to ChemBioFinder:Merge SDfilesMerge SDfiles

ChemBioFinder can merge SDfiles even without structures (for example by CASwithout structures (for example by CAS number)

Webinar Overview: ChemBioFinder HotLinkChemBioFinder HotLink

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1c. ChemBioFinder HotLink:ChemBioDraw interfaceChemBioDraw interface

Automatic links while drawing structures:

1c. ChemBioFinder HotLink:Ashgate DrugsAshgate Drugs

• 8K drugs marketed worldwide• Check names/synonyms biological activity therapeuticCheck names/synonyms, biological activity, therapeutic

indications, properties

Ashgate Drugs:Synonyms and PropertiesSynonyms and Properties

Online, fully searchable version of the popular book, “Drugs: Synonyms and Properties.” g y y p

Each entry is accompanied by:

1. CAS Number2. EINECS number (European Inventory of Existing commercial

Chemical Substances))3. Chemical name & Molecular weight4. Molecular formula & Structure 5. Synonyms, including tradenames 6. Medical application 7. Manufacturer 8. Physical Properties 9 R l t d t t i f ti

9. Regulatory and patent information

1c. ChemBioFinder HotLink:Off-Label DatabaseOff-Label Database

• Unique, literature-derived database of novel off label clinical uses of drugsnovel, off-label, clinical uses of drugs

• In tune with trends in translational medicine and drug repositioning and repurposing

• Offers novel therapeutic opportunities for p ppout-of-patent or underperforming drugs

• Mirrors the serendipity of drug discoveryMirrors the serendipity of drug discovery (Wellbutrin, Viagra….)

Off-Label Database• Who is it for?

– Medicinal chemists, business development, i di ti diindications discovery …..

• Why do they need it?– They need to refill pipelines and extend patent life– They need to refill pipelines and extend patent life,

with a diminishing R&D budget– Off-Label is unique in providing up-to-date, curated,

searchable information on reported off-label clinical uses of drugs and clinical candidates

• Typical question• Typical question– Does this compound/series show any off-label

therapeutic benefit against this condition?

Off-Label Database interface• Text-searchable database at:

http://offlabel.cambridgesoft.comUpdated daily– Updated daily

– 400 new entries per month• Structure-searchable database (8000 records)Structure searchable database (8000 records)

– Search by drug, structure, indication, off-label use

Sample Off-Label record

1c. ChemBioFinder HotLink:The Merck Index 14th EditionThe Merck Index 14th Edition

– Monographs on chemicals drugs and biologicals– Monographs on chemicals, drugs and biologicals– Structure, name and synonym searchable

• What’s known about this molecule & others like it?– 18,000 compounds + 50,000 synonyms– > 15,000 trademarks and associated companies – CAS Registry Numbers for over 12,000 compounds – > 8,500 chemical structures – 450 Named reactions– Updated twice per year

1c. The Merck Index• Detailed descriptions, properties

1c. ChemBioFinder HotLink:ChemINDEXChemINDEX

ChemINDEX linksData for over 100,000 compounds: •Physical Properties•Physical Properties•Chem3D structure•ChemACX, NCI, Merck Index•Additional Chemical Information, e.g.:, g- Medications: Drug Data Base with UV data - Physical Properties: NIST Chemistry WebBook - LogP & pKa: Environmental Science Center

databaseR l t OSHA Ch i l S li d

- Regulatory: OSHA Chemical Sampling and Methods

1c. ChemBioFinder HotLink:Martindale’s for ScientistsMartindale s for Scientists

•Based on the authoritative reference work Martindale’s: The Complete Drug Reference

f•Martindale’s is a world-renowned brand signifying trusted information of the highest quality and builds on 125 years’ experience•Essential facts about drugs, chemicals, and biologicals of interest in medicine and the pharmaceutical sciences •International coverage•International coverage•Content is regularly reviewed and re-evaluated•Reliable unbiased and based on published sourcesReliable, unbiased, and based on published sources•Complements The Merck Index and R&D Insight with undivided focus on drugs (Phase III and marketed) and in depth coverage

in-depth coverage.

Martindale’s - What’s in it?•Drug names, systematic names, international trade names, ‘street’ names, CAS Registry Numbers, synonyms, and codes

•Molecular formulas and weights

•Molecular structures

•Salts and derivatives

•Summary of clinical properties

•Summary of physical properties

•Summary of pharmacokinetics

•Uses and administration

Martindale – sample text record

• Over 6600 substances including human and veterinary d g di g ti i h b l di i d g f drugs, diagnostics, vaccines, herbal medicines, drugs of abuse, excipients, pesticides, and nutritional agents

• 180,000 proprietary and non-proprietary medicines• 17 700 manufacturers and trade names from 40 countries

• 17,700 manufacturers and trade names from 40 countries

1c. ChemBioFinder HotLink:NCI/AIDSNCI/AIDS

• > 200K compounds tested by US National Cancer Institute• Structures and bioassay results:

diverse test sets for SAR studiesdiverse test sets for SAR studies

1c. ChemBioFinder HotLink:NetPro Molecular ConnectionsNetPro Molecular Connections

NetPro™, developed at Molecular Connections, offers solutions for the pharmaceutical and life sciencessolutions for the pharmaceutical and life sciences industries/researchers to streamline and speed up the drug discovery process.

NetPro™ is a comprehensive manually curated knowledgebase of Molecular Interactions and differs from other interaction databases in providing all experimental details of anexperimental details of an interaction along with relevant references.

NetPro Molecular ConnectionsHighlightsHighlights

• Comprehensive data on varied molecule types:viz. Proteins, Small molecules, DNA and RNA.

• 100% manually curated knowledgebase y gof molecular interactions

• Captures Quantitative/Qualitative variationsCaptures Quantitative/Qualitative variations

• Accurate experimental details of an interaction

• 250 Unique interaction terms grouped under 10 categories

1c. ChemBioFinder HotLink:Sigma Aldrich MSDSSigma Aldrich MSDS

SAMSDS is a collection of 130,000 MSDS’s for compounds in ChemACX which are available under one of the Sigma Aldrich family of brands:

• AldrichFl k Ch i l C• Fluka Chemical Corp.

• Riedel-de Haen• Sigma Chemical Company• Supelco

SAMSDS: Material Safety Data SheetsMaterial Safety Data Sheets

1c. ChemBioFinder HotLink: ChemACXChemACX

• Availability information at your fingertips

1c. ChemBioFinder HotLink: CAS# and Name lookupCAS# and Name lookup

ChemDraw’s ChemBioFinder HotLinkreads data from databases as well as linking to themas well as linking to them.

CAS# Common nameKey in naphthalene 91-20-3 MothballsReplace 1-carbon with nitrogen 91-22-5 chinoline, leucolineReplace 4 carbon with nitrogen 91 19 0 quinoxaline phenpiazineReplace 4-carbon with nitrogen 91-19-0 quinoxaline, phenpiazineAdd methyl to 2-carbon 7251-61-8 2-methylquinoxaline

1c. ChemBioFinder.com: Online versionOnline version

Same onlineas in ChemDraw

- Links- SynonymsSynonyms- CAS#- PropertiesProperties- SMILES- InChI

1c. ChemBioFinder HotLink: ChemSpiderChemSpider

• Link from InChI string on ChemBioFinder.com

Webinar Overview: Chem3D PDB lookupChem3D PDB lookup

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1d. Chem3D PDB lookup:Online database interfaceOnline database interface

• Import PDB’s from online databases:(retrieved from Brookhaven Natl. Lab)For example PDB ID = “1tag”For example PDB ID = 1tag (GTP-Binding Protein)

• Import structures by ACX numberp y(ChemDraw includes Online function:“Find ACX numbers from Structure”)e.g. X1001488-9 for benzene g

• Import from ChemACX(by name or structure)

• Links to our website

Webinar Overview: Database PortfolioDatabase Portfolio

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2. Current Portfolio• Databases to help researchers make better decisions,

providing info on chemical properties, uses, safety, how to make or buy and literature & patent citationshow to make or buy, and literature & patent citations

• Delivery options (online in house desktop)(online, in-house, desktop)

• Access applications (Ch Bi Fi d d W b h f(ChemBioFinder and Web search forms; ChemBioDraw Database Hotlink; application links)pp )

• http://www.cambridgesoft.com/databases/for more information

2. Major content groups to address common questionsto address common questions

• Drugs and Reference Works– What is this stuff?– What is this stuff?– What else is like it?

Can I make something better?– Can I make something better?• Chemical Sourcing and Safety

Where can I buy stuff?– Where can I buy stuff?– How do I handle it safely?

S th ti M th d l• Synthetic Methodology– OK, it’s not for sale: how do I make it?

– How do I make stuff like it?

2a. The Merck Index• Detailed descriptions, properties

2a. R&D Insight for Chemists24K d i th d l t i li• 24K compounds in the development pipeline

• Monitor stage of development, competitor activities, licensing dealslicensing deals

• Updated weekly

2a. Ashgate Drugs: Synonyms and PropertiesSynonyms and Properties

• 8K drugs marketed worldwide• Check names/synonyms biological activity therapeuticCheck names/synonyms, biological activity, therapeutic

indications, properties

2a. Nanogen Index• >1000 pesticides, environmental contaminants• Check names/synonyms, activity, properties

2a. NCI/AIDS• > 200K compounds tested by US National Cancer Institute• Structures and bioassay results:

diverse test sets for SAR studiesdiverse test sets for SAR studies

Webinar Overview: Chemical Sourcing & SafetyChemical Sourcing & Safety

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2b. ChemACX: Available ChemicalsAvailable Chemicals

• ChemACX– ~ 525 Suppliers’ catalogs, including Sigma-Aldrich, pp g , g g ,

Fisher, Acros, Alfa Aesar, Lancaster, VWR– Structure, name and synonym searchable

• Can I buy this stuff, or things like it?– ~ 500,000 unique chemical substances

> 1 500 000 products– > 1,500,000 products– Updated quarterly– Integrated with E-Notebook and InventoryIntegrated with E Notebook and Inventory – Can be linked to ERP and purchasing systems

2b. ChemACX search within Inventory UltraSearch via ChemDraw structuresSearch via ChemDraw structures,substructures, or Tanimoto similarity:

2b. Chemical Safety• Sigma-Aldrich MSDS

– 130K MSDS integrated into ChemACX30 S S eg a ed o C e C

Webinar Overview: Synthetic MethodologySynthetic Methodology

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2c. Synthetic MethodologyPlan syntheses, search for reaction transformations, starting materials, catalysts, products

Ch RXN• ChemRXN– 28K important reactions from

ISI (ChemPrep) and InfoChem (ChemSelect)ISI (ChemPrep) and InfoChem (ChemSelect)• ChemReact500

– 500K synthetically useful reactions from 1974 - 2001• ChemSynth (subset of ChemReact500)

– 180K reactions with >50% yield and cited > 1 time• ChemReact68 (subset of ChemSynth)

– 68K reactions with >50% yield and cited > 5 times

2c. ChemSynth Example

Webinar Overview: Synthetic MethodologySynthetic Methodology

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3. Delivering Content in Context• One Global Search function across all CS applications

• Provides data in a consistent, unified wayProvides data in a consistent, unified way

• Provides data in the context of a workflow or activity – not as a separate, disjointed activityp , j y

• Removes the boundaries between separate data silos

• Delivers data to scientists when & as they need it• Delivers data to scientists when & as they need it

– E.g. ELN access to ChemACX and reaction databases as reactions are planned and sourceddatabases as reactions are planned and sourced

• Database Hotlink in ChemDraw & Database Gateway on Internet

& Database Gateway on Internet

3. New Content: New opportunities• Extending our portfolio

3 D d R f D t ( h t i it?)• 3a. Drugs and Reference Data (what is it?)– Off-Label Database– Royal Pharmaceutical Society databases:

• Martindale’s: The Complete Drug Reference• Martindale s: The Complete Drug Reference• Clarke’s Analysis of Drugs and Poisons• Handbook of Pharmaceutical Excipients

• 3b. ChemACX is constantly extended! (where to get it?)

• 3c Synthetic Methodology (how to make it?)• 3c. Synthetic Methodology (how to make it?)– Wiley content– Rich family with “household names”

• Fieser & Fieser EROS Organic Reactions

Fieser & Fieser, EROS, Organic Reactions …..

3a. Off-Label Database

• Unique, literature-derived database of novel off label clinical uses of drugsnovel, off-label, clinical uses of drugs

• In tune with trends in translational medicine and drug repositioning and repurposing

• Offers novel therapeutic opportunities for p ppout-of-patent or underperforming drugs

• Mirrors the serendipity of drug discoveryMirrors the serendipity of drug discovery (Wellbutrin, Viagra….)

3a. RPS Publishing Reference Works

Major reference works for the pharmaceutical sciences – with added structures

•Martindale’s for Scientists•Handbook of Pharmaceutical Excipients•Handbook of Pharmaceutical Excipients•Clarke’s Analysis of Drugs and Poisons

3a. Martindale – sample text record

• Over 6600 substances including human and veterinary d g di g ti i h b l di i d g f drugs, diagnostics, vaccines, herbal medicines, drugs of abuse, excipients, pesticides, and nutritional agents

• 180,000 proprietary and non-proprietary medicines• 17 700 manufacturers and trade names from 40 countries

• 17,700 manufacturers and trade names from 40 countries

3a. Clarke’s Analysis of Drugs and Poisons

•Practical manual and reference source for forensic scientists and toxicologists

•Written by leading international experts and world renowned scientists

•Over 1700 monographs on individual drugs and poisons

•31 sections covering all practice areas and analytical procedures used in analytical toxicology

3a. Handbook of Pharmaceutical Excipients

•Comprehensive guide to the uses, properties, and safety of pharmaceutical excipientsand safety of pharmaceutical excipients

•Essential reference for formulators of pharmaceuticals confectionary cosmetics andpharmaceuticals, confectionary, cosmetics, and food products

J i l bli h d b Ph i l P (•Jointly published by Pharmaceutical Press (an imprint of RPS Publishing) and American Pharmacists AssociationPharmacists Association

3b. ChemACX expansion:Version 10.9.4

Number of catalogs:- 563 suppliers in 2010- 525 suppliers in 2009- 525 suppliers in 2009- 381 suppliers in 2007

Number of unique substances:Number of unique substances:- 631,262 substances in 2010- 500,000 substances in 2009

Number of products:- 1,700,000 products in 2010

1 500 000 d t i 2009- 1,500,000 products in 2009- 690,000 products in 2007

New updates quarterly

3c. Wiley Content

• New agreement to deliver Wiley’s rich family of chemistry content via CambridgeSoftof chemistry content via CambridgeSoft software and applications

• Content spans the whole gamut of synthetic chemistry and provides sources which are y phousehold names to most synthetic chemists– E.g. Fieser & Fieser; EROS; Organic g g

Reactions

3c. Wiley Content IWiley Organic Essentials

Fi & Fi R tFieser & Fieser ReagentsEncyclopedia of Reagents in Organic Synthesis (EROS)Chemistry of Heterocyclic CompoundsOrganic Chemical Drugs and their SynonymsOrganic Chemical Drugs and their SynonymsOrganic ReactionsOrganic SynthesesGreene's Protective GroupsGreene s Protective GroupsName Reactions Heterocyclic ChemistryName Reactions Functional Group TransformationsName Reactions/Reagents in Organic Synthesesg g yTopics in StereochemistryMarch's Advanced Organic ChemistryEncyclopedia of Catalysis

Organic Chemistry of Drug Synthesis Series

3c. Wiley Content II

Possible E-Notebook Delivery: additional titles

Side Reactions in Organic ChemistryAsymmetric Synthesis C t l ti A t i S th iCatalytic Asymmetric SynthesisEncyclopedia for CatalysisSpectral database productsWiley Registry of Mass spectral DataWiley CNMR dataWiley HNMR dataWiley HNMR dataWiley Hummel Polymer LibrariesBASF Industrial PolymersSynthetic Organic Chemists Companion

Synthetic Organic Chemists Companion

Summary

• CambridgeSoft offers a broad and growing portfolio of content sources covering:of content sources covering:

– Drugs and reference works

Ch i l i d f t– Chemical sourcing and safety

– Synthetic methodology

• New access methods like Global Search deliver content more effectively and usefully

N ddi i f Off l b l RPS d Wil b i• New additions from Off-label, RPS, and Wiley bring unique content to answer researchers’ questions

January 2010 Webinar: Database usage in g

ChemDraw and ChemOffice

Jesse GordonJesse GordonCambridgeSoft Director

of Software Marketingjgordon@cambridgesoft.com

Office: 617-588-9306Cell: 617-320-6989Skype: jessegordon

January 2010 Webinar: Database usage in ChemDraw and...

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