Facilities: Library

Diversity Oriented Synthesis Collections

Important information about BCB DOS libraries:
The structure of the compound in each well must be decoded before cherry pick requests for DOS compounds can be filled.

• Cherry pick requests for DOS compounds should be submitted to Nicky Tolliday

Links to Libraries:

• Chemical Technology Libraries
• Screening Libraries

Submitting Discrete Compound Collections

1. Compounds should be submitted in one of two ways.
   • Vials - Fisher, 03-391-7B - National Scientific Glass Screw Thread Sample Vials with Teflon-Fluorocarbon-Resin-Lined Caps 1 dram (4 ml) 15x45mm NSC no. B7800 2.
     
   • Microliter Plate - In a 96-well plate, compounds should be shipped dry.
     • Please leave the last column of the plate (column 12) empty, allowing for a maximum of 88 compounds per plate.
     • In addition, please provide an extra, unused plate for calibration purposes.
2. Please submit at least 1 mg of compound.
3. Compound Submissions should be sent via Fed-Ex* to:
   

   John P McGrath
   The Broad Institute of Harvard & MIT
   Chemical Biology Program
   7 Cambridge Center
   Cambridge, MA 02142

   *Fed-Ex has proven reliable for the shipment of small chemical samples, but any comparable shipping service is acceptable. Ground service is sufficient
4. Fill out the Data and Protocol Sharing Agreement (PDF)
5. Fill out the SubmissionTemplate.xls

Submission Template Instructions

The submission template document (SubmissionTemplate.xls), is a Microsoft Excel worksheet that was created with, and is designed to be modified using the ChemDraw plug-in for Excel (CFXL).

The submission template contains two worksheets, one provideing examples and the other providing a template for you to input your own information. Within the examples worksheet are four examples that cover the cases of submission in vials versus microliter plates and of submissing discrete compounds versus those with regular relationships between the structures (e.g., libraries resulting from combinatorial chemistry or diversity-oriented synthesis). If presenting your submission in one of these four formats creates a significant problem, please contact the compound curator directly to discuss other options (xli@broad.harvard.edu).

What follows is a field-by-field breakdown of the contents of the submission template.

STRUCTURE
This column holds structures created in ChemDraw and imported into the spreadsheet with the ChemDraw for Excel "Paste Molecule" function (for more information, see the "Using Chemdraw for Excel" section below).

Library
If this is your first submission, the name of your institution should be fine as a library name. Otherwise, please use a unique name ot distinguish current submissions from compounds that you may have submitted before. Furthermore, if you are simultaneously submitting compounds from multiple, different, building block-based synthesis schemes, the products from these schemes should have different library names.

Source
The name of the scientist who synthesized the compound.

CompoundName
A unique identifies must be provided for each compound. Combining the Library or Source field with a number is usually a fairly good procedure (e.g., SmithOO1). If submitting in vials, this name should match the label on the vial.

BB_A, BB_B
If using a building block based synthesis scheme, use these fields to enumerate the building blocks used for each compound. If necessary, you may add additional fields (i.e., BB_C, BB_D, etc.) using the same logic. This field is not required for all submissions.

Box
If submitting more than one or rack of vials, each box or rack must also bear a unique identifier. If submitting only one box or rack of vials, or if submitting in plates, this is not a required field.

Vial
If submitting in vials, please label the vial with the compound name or number each vial and put the number here; this is not a required field.

Plate
If submitting multiple plates of compounds, please label the plates with a unique identifier and list it here. If submitting only one plate, or if submitting in vials, this is not a required field.

Well
If submitting in plates, please identify the well containing each compound, using leading zeroes in columns 1 through 9 (i.e., use "A01" rather than "A1"). If submitting in vials, this is not a required field.

Amount
Mass (in mg) of your submitted compound to the nearest 0.1 mg.

Using ChemDraw for Excel (CFXL)

ChemDraw for Excel (CFXL) is an Excel plug-in that allows one or more SDFs to be handled in a tabular ( i.e. , spreadsheet) format, making their annotation straightforward. This section provides detailed information about setting up a computer to use CFXL, and using CFXL to accept structures from your pre-existing ChemDraw files.

NOTE: If using ChemDraw for Excel (CFXL) is not an option for you, please submit your structures either in one or more ChemDraw files or using SMILES strings. SMILES strings can be submitted by adding a field (i.e., "SMILES") to the submission template. If ChemDraw files are used, each structure in the ChemDraw file should be annotated with the CompoundName that also appears in the submission template.

Part One: Preparing a computer.

Find a Windows machine and launch Microsoft Excel directly. From the "Tools" menu, select "Macro > Security...". On the "Security Level" tab, set the radio button to "Low". On the "Trusted Sources" tab, make sure "CambridgeSoft Corporation" is listed. Also on the "Trusted Sources" tab, check both "Trust..." checkboxes. From the "Tools" menu, select "Add-Ins...". Check the checkbox next to "ChemDraw for Excel". Exit Microsoft Excel.

Part Two: Adding structures and annotations.

Launch Microsoft Excel indirectly by opening the Excel template to be used ( e.g. , “SubmissionTemplate.xls”). Open your pre-existing ChemDraw (.CDX) file, and position the two windows to see both applications simultaneously. Select a single structure from your .CDX file and put it in the Windows copy buffer (CTRL-C). Activate the Excel window and place the cursor in the appropriate blank cell in Column A (the "STRUCTURE" field) of the CFXL worksheet. From the "ChemDraw" menu in Excel, select "Paste Molecule". This action should result in the display of "Structure1" in the destination cell of the "STRUCTURE" field. If you wish to view the structure, use the "Show Picture" command in the "ChemDraw" menu. Repeat the "Copy" (from ChemDraw) > "Paste Molecule" (in Excel) sequence for each structure you wish to insert. Note that there is a toolbar button for "Paste Molecule" on the ChemDraw toolbar; the button looks like a clipboard superimposed with a white blob.

Record any additional information about each molecule, using normal Excel commands, in the other fields of the table. Use the field definitions above to guide your entries.

Save the file with a filename reflecting its new contents.

Please direct any questions regarding template construction to xli@broad.harvard.edu