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Ian Gordon

CHEM 2P21 SciFinder Reaxys SciFinder, Espacenet & ChemDraw ExerciseHappyPearl Jacobson, Science Librarian, Carleton University

The objective of this exercise is to:

• access, explore and evaluate the chemistry literature• understand the use of chemistry databases including Reaxys,

SciFinder, Espacenet, PubChem, ChemSpider, etc. • use chemical drawing software e.g. ChemDraw• incorporate ACS Style conventions• explore chemical naming conventions, reaction sequences, and, • be better informed of biochemical research on antibiotics /

antibacterial drug development, their chemical properties, reactions, regulatory and scholarly information.

Select one of the following antibiotics / antibacterial drugs from the following list of chemical, common or trade names, from Drugs.com compounds listed on Medications for Bacterial Infection or pick a different drug / chemical. Remember that you need to pick a chemical/drug that allows you to complete all the elements of this assignment:

Amoxicillin, Ampicillin, Azithromycin, Cefaclor, Cefzil, Cefoxitin, Cefprozil, Ceftin, Cefuroxime, Cephalexin, Chloramphenicol, Ciprofloxacin, Clarithromycin, Doxycycline, Erythromycin, Flagyl, Invanz, Merrem, Nitrofurantoin, Free penicillin G, Rifampin, Streptomycin, Tetracycline, Tigecycline, Trimethoprim, Tyrothricin, Zymar

Drug Information Handbook (APA)

Compendium of Pharmaceuticals and Specialties (CPA)

current - fast indexingexhaustive – comprehensive coveragestructure searching1907+

New Reaxys – suggest using older version until May 2017

current in-depth indexingexhaustive physical propertiesorganic synthesis planning1771+

older version https://www.reaxys.com/reaxys/secured/search.do

1. Go to the Library Chemistry Research Guide under Chemicals / Drugs.

Name your drug to be used for this exercise:

Common, Generic or Trade Name(s):

IUPAC or Systematic Name:

CAS Registry Number:

PubChem CID Number:

Molecular Formula (using Hill Notation System):

2. Go to the Library Chemistry Research Guide using Chemical, Drug

& Pharmaceutical databases and find additional information on your drug:

Chemical Classification / Taxonomy or Family:

Drug Classification / Pharmacologic Category:

3. Browse through individual databases including: ChEBI, ChEMBL, ChemSpider, DrugBank, Compendium of Pharmaceuticals and Specialties (Canadian), FDA Drugs (American), Drug Information Handbook, drugs.com Online and PubChem databases and in one or two sentences summarize this drug’s bioactivity, pharmacologic action, chemical uniqueness, target indicator or mode of chemical action.

In essence, how does this small molecule work as a drug?

4. Go to SciFinder entering your drug by exploring using Substance Identifier to complete the following:

a) How many retrieved reactions did you find searching your drug as a product? _____b) How many references did you find when limited to Preparation? _____c) How many references when limited to Preparation, then analyzed by Database are found in

MEDLINE / PubMed _____ and CAPLUS / SciFinder _____. d) How many references when limited to Preparation, then analyzed by Document Type are

Patents? _____e) Select a single SciFinder reaction preparation that looks the easiest to reproduce at Brock

and comment why, cite this article/patent below using ACS Style:f) Select one patent, please provide Patent Number _________________g) Use this patent number / title to search the Espacenet database and pull up the “original

document” Read the patent’s abstract, claims, description, drawings, etc. In your own words, what is unique about this patent and cite below using ACS Style?

h) Download ChemDraw, or use a similar structure drawing program, copy this reaction sequence or a single structure diagram to include the ACS Style citation and drug name.

Searched reactions analyzed byDocument Type - Patent

5. Exploring the Reaxys database, searching by Reactions, search using your drug’s chemical structure as Product answering these questions:

Number of citations for structure as drawn, for products _____Filter by number of citations with yields greater than 50% _____Filter by number of steps being 1 or 2 _____Filter by document type equals patents _____Filter by bioactivity equals pharmacological _____Sort all reactions by Publication Year and cite the oldest citation in ACS Style

6. Exploring the Reaxys database, searching by Substances, search

by chemical structure or since you know your drug identifiers,

enter a number identifier e.g. CAS Registry Number. Click on the

box for the most obvious and usually the first entry. Click on

bioactivity, then pharmacological data, limit by the Document

Type filter, limit to article, find an interesting citation, click on

Show Details to find the citation and cite in ACS Style:

7. Reaxys is a relational database that allows searchers to find

experimental or predicted property data. Exploring the Reaxys database,

searching by Substances, search by chemical structure or since you know

your drug identifiers, enter a number identifier e.g. CAS Registry Number.

This time filter by Spectroscopic Data, click on More, click on NMR

Spectroscopy available or an equivalent, entering a number for Frequency

greater than > (you pick a number e.g. 25, click Limit to, click on

References, selecting the most relevant, and cite in ACS Style:

8. Reaxys is a relational database that assists with synthesis plans. Click on

Query or start over, click on the Literature icon, Click on Create Structure

Template from Name, enter name/number of drug, select appropriate

drug choices, click on Document Type = ‘article’ and include the term(s)

green chemistry or green synthesis or just green and click on Search

Literature. Click on citations, select a citation of interest to better

understand why the term “green” was used, and cite in ACS Style:

9. In one or two sentences use your own words to comment on

whether this paper’s reactions are indicative of “green chemistry.”

10. Comment: One thing you learned about Reaxys through this exercise?

Williams, J. M.; Brands, K. M. J.; Skerlj, R. T.; Jobson, R. B.; P. G.; et al. Practical Synthesis of the New Carbapenem Antibiotic Ertapenem Sodium. J. Org. Chem. 2005, 44, 7479–7487.

Junker, T.; Alexy, R.; Knacker, T.; Kümmerer, K. Environ. Sci. Technol. 2006, 40, 318–324.

Select one of the following antibiotics / antibacterial drugs from the following list of chemical, common or trade names, from Drugs.com compounds listed on Medications for Bacterial Infection or pick a different drug / chemical. Remember that you need to pick a chemical/drug that allows you to complete all the elements of this assignment:

Amoxicillin, Ampicillin, Azithromycin, Cefaclor, Cefzil, Cefoxitin, Cefprozil, Ceftin, Cefuroxime, Cephalexin, Chloramphenicol, Ciprofloxacin, Clarithromycin, Doxycycline, Erythromycin, Flagyl, Invanz, Merrem, Nitrofurantoin, Free penicillin G, Rifampin, Streptomycin, Tetracycline, Tigecycline, Trimethoprim, Tyrothricin, Zymar

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Ian Gordon

CHEM 2P21 SciFinder Reaxys SciFinder, Espacenet & ChemDraw ExerciseHappyPearl Jacobson, Science Librarian, Carleton University