Assaying Compound Activity - Revision history

Sbarelier: /* Testing Compounds with CRO */

2014-10-24T21:37:59Z

Testing Compounds with CRO

← Older revision		Revision as of 21:37, 24 October 2014
Line 48:		Line 48:

	==Testing Compounds with CRO==		==Testing Compounds with CRO==

			Here is a list of CROs [http://wiki.bkslab.org/index.php?title=Contract_Research_Organizations].
	*Quote administration		*Quote administration
	** If the vendor is not in the BearBuy system, they will need to fill out a form that Yvonne can provide		** If the vendor is not in the BearBuy system, they will need to fill out a form that Yvonne can provide

Matthew O'Meara: Reorganize testing compounds with CRO

2014-09-02T15:23:13Z

Reorganize testing compounds with CRO

← Older revision		Revision as of 15:23, 2 September 2014
Line 48:		Line 48:

	==Testing Compounds with CRO==		==Testing Compounds with CRO==
	* If the vendor is not in the BearBuy system, they will need to fill out a form that Yvonne can provide		*Quote administration
	* Get a quote from the company and give it to ~~Yvonne or whoever is doing~~ the ~~ordering~~		** If the vendor is not in the BearBuy system, they will need to fill out a form that Yvonne can provide
	** ~~Make sure to include a phone~~ number ~~contact~~		** Get a quote from the company and
	** ~~indicate~~ if the order should be rushed (unless necessary, rushed orders should be avoided as they are generally much more expensive)		** With the quote, get a PO number
	* ~~When sending out the compounds you'll need to provide the courier, the address and full name and telephone number of the person who will receive it.~~		** Give the PO number to the vendor when placing the order
	* If the supply of compound is limited, often less is required if it is sent in solution, but it is easier and more stable to send powder, so check with the assay vendor		** The vendor will then give an Invoice that can go directly to the UCSF Accounts Payable department (COapmail@ucsf.edu) and they will pay the vendor.
	* ~~Testing concentrations~~		*Sending compounds
			** Provide the courier (e.g. FedEx) with the address and full name and telephone number of the person who will receive it.
			** Indicate with the vendor if the order should be rushed (unless necessary, rushed orders should be avoided as they are generally much more expensive)
			** If the supply of the compound is limited, often less is required if it is sent in solution, but it is easier and more stable to send powder, so check with the assay vendor
			* Compound testing
	** For the given receptor/ligand pair check the known activities to help guide where to start testing.		** For the given receptor/ligand pair check the known activities to help guide where to start testing.
	** If possible, start with a few high concentration (e.g. 2 replicates @ 20 uM) "primary" points to see if there is any activity		** If possible, start with a few high concentration (e.g. 2 replicates @ 20 uM) "primary" points to see if there is any activity

Matthew O'Meara: /* Testing Compounds with CRO */

2014-09-02T14:13:13Z

Testing Compounds with CRO

← Older revision		Revision as of 14:13, 2 September 2014
Line 53:		Line 53:
	** indicate if the order should be rushed (unless necessary, rushed orders should be avoided as they are generally much more expensive)		** indicate if the order should be rushed (unless necessary, rushed orders should be avoided as they are generally much more expensive)
	* When sending out the compounds you'll need to provide the courier, the address and full name and telephone number of the person who will receive it.		* When sending out the compounds you'll need to provide the courier, the address and full name and telephone number of the person who will receive it.
			* If the supply of compound is limited, often less is required if it is sent in solution, but it is easier and more stable to send powder, so check with the assay vendor
	* Testing concentrations		* Testing concentrations
	** If the ~~supply of compound is limited, often less is required if it is sent in solution, but it is easier and more stable to send powder, so~~ check ~~with~~ the ~~assay vendor~~		** For the given receptor/ligand pair check the known activities to help guide where to start testing.
	** If ~~it is subtantially cheaper~~, ~~and nothing else is known see if the CRO can~~ start with a ~~single dose at 30uM and~~ if there is activity ~~then reduce~~ by half log or (1/3) ~~for 5-10 to generate data for dose response curves~~		** If possible, start with a few high concentration (e.g. 2 replicates @ 20 uM) "primary" points to see if there is any activity
			** If there is some activity follow up with a 5-10 point dose response curve reducing by half log or 1/3 at each step (where the highest concentrations will depend on the activity of the primary assay).

	[[Category:Tutorials]]		[[Category:Tutorials]]

Frodo at 15:40, 13 August 2014

2014-08-13T15:40:15Z

← Older revision		Revision as of 15:40, 13 August 2014
Line 56:		Line 56:
	** If the supply of compound is limited, often less is required if it is sent in solution, but it is easier and more stable to send powder, so check with the assay vendor		** If the supply of compound is limited, often less is required if it is sent in solution, but it is easier and more stable to send powder, so check with the assay vendor
	** If it is subtantially cheaper, and nothing else is known see if the CRO can start with a single dose at 30uM and if there is activity then reduce by half log or (1/3) for 5-10 to generate data for dose response curves		** If it is subtantially cheaper, and nothing else is known see if the CRO can start with a single dose at 30uM and if there is activity then reduce by half log or (1/3) for 5-10 to generate data for dose response curves

			[[Category:Tutorials]]

Matthew O'Meara: /* Identifying Compounds to Buy */

2014-08-06T17:13:02Z

Identifying Compounds to Buy

← Older revision		Revision as of 17:13, 6 August 2014
Line 6:		Line 6:
	==Identifying Compounds to Buy==		==Identifying Compounds to Buy==
	Depending on the project, compounds may have different requirements		Depending on the project, compounds may have different requirements
	*In vitro testing		*Requirements for in vitro testing
	** Purity: If possible get the compounds at 95% or greater purity even if it costs 100$ or 200$ more. If it's tested to be active but has low purity, it will likely need to be re-purified and then tested.		** Purity: If possible get the compounds at 95% or greater purity even if it costs 100$ or 200$ more. If it's tested to be active but has low purity, it will likely need to be re-purified and then tested.
	** Aggregation: Check the compound with the aggregator advisor (advisor.bkslab.org) and if it's close to or known to be an aggregator (indications include uM nonspecific activity, logP great than 3 or actually shown to be an aggregator through appropriate controls) then either skip the compound or plan on doing aggregation controls, e.g. testing for detergent sensitive nonspecific activity, determine particle formation using DLS, or perform the assay with/without detergent (and just detergent controls).		** Aggregation: Check the compound with the aggregator advisor (advisor.bkslab.org) and if it's close to or known to be an aggregator (indications include uM nonspecific activity, logP great than 3 or actually shown to be an aggregator through appropriate controls) then either skip the compound or plan on doing aggregation controls, e.g. testing for detergent sensitive nonspecific activity, determine particle formation using DLS, or perform the assay with/without detergent (and just detergent controls).
	** Amount: try to get 10mg if possible, but if it's very expensive you can get less. If you're sending it to a CRO sending it in solution usually requires less compound. If you're planning on further controls (e.g. for purity, aggregation), make sure to get enough.		** Amount: try to get 10mg if possible, but if it's very expensive you can get less. If you're sending it to a CRO sending it in solution usually requires less compound. If you're planning on further controls (e.g. for purity, aggregation), make sure to get enough.
			** Note the solubility (e.g. water, DMSO, etc.)

	*In vivo testing		*Requirements for in vivo testing
	** Check pharmacokinetics ~~(ask an expert)~~		** Check pharmacokinetics

	==Finding Vendors==		==Finding Vendors==

Matthew O'Meara: /* Testing Compounds with CRO */

2014-07-17T13:14:21Z

Testing Compounds with CRO

← Older revision		Revision as of 13:14, 17 July 2014
Line 51:		Line 51:
	** Make sure to include a phone number contact		** Make sure to include a phone number contact
	** indicate if the order should be rushed (unless necessary, rushed orders should be avoided as they are generally much more expensive)		** indicate if the order should be rushed (unless necessary, rushed orders should be avoided as they are generally much more expensive)
			* When sending out the compounds you'll need to provide the courier, the address and full name and telephone number of the person who will receive it.
	* Testing concentrations		* Testing concentrations
	** If the supply of compound is limited, often less is required if it is sent in solution, but it is easier and more stable to send powder, so check with the assay vendor		** If the supply of compound is limited, often less is required if it is sent in solution, but it is easier and more stable to send powder, so check with the assay vendor
	** If it is subtantially cheaper, and nothing else is known see if the CRO can start with a single dose at 30uM and if there is activity then reduce by half log or (1/3) for 5-10 to generate data for dose response curves		** If it is subtantially cheaper, and nothing else is known see if the CRO can start with a single dose at 30uM and if there is activity then reduce by half log or (1/3) for 5-10 to generate data for dose response curves

Matthew O'Meara: /* Finding Vendors */

2014-07-14T18:31:14Z

Finding Vendors

← Older revision		Revision as of 18:31, 14 July 2014
Line 30:		Line 30:
	* Sometimes compounds are available from special catalogs		* Sometimes compounds are available from special catalogs
	** NCI Platted: 1) Here is a description of the NCI Platted process from there end [[NCI_Platted]]. Look up the NCS identifier in PubChem. 2) submit a request form through their webpage. Contact the industry contacts officer at ucsf (Esteban.Mendoza@ucsf.edu \| t: 415-502-1599) to have him sign the "Simple Letter of Agreement". He'll will give you a materials transfer form that you need to fill out.		** NCI Platted: 1) Here is a description of the NCI Platted process from there end [[NCI_Platted]]. Look up the NCS identifier in PubChem. 2) submit a request form through their webpage. Contact the industry contacts officer at ucsf (Esteban.Mendoza@ucsf.edu \| t: 415-502-1599) to have him sign the "Simple Letter of Agreement". He'll will give you a materials transfer form that you need to fill out.
	* Remember that our lab will continue to buy from these vendors ~~in the future~~ so be nice ~~to our contacts at these companies!~~		* Remember that our lab will continue to buy from these vendors so be nice, and inquire if we can get a lab discount
			* For each compound record
			** ZincID, supplier, supplier product code, molecular weight, purity

	==Ordering Compounds==		==Ordering Compounds==

Matthew O'Meara at 20:54, 2 July 2014

2014-07-02T20:54:48Z

← Older revision		Revision as of 20:54, 2 July 2014
Line 1:		Line 1:
	Depending on the project, assaying compound activity typically involves acquiring the compound and then getting it tested either in house or sending it out somewhere to be tested. This page details some of the common tasks and considerations in this process.		Depending on the project, assaying compound activity typically involves acquiring the compound and then getting it tested either in house or sending it out somewhere to be tested. This page details some of the common tasks and considerations in this process. Note, this information is somewhat specific to the Shoichet lab at UCSF.


Line 49:		Line 49:
	** Make sure to include a phone number contact		** Make sure to include a phone number contact
	** indicate if the order should be rushed (unless necessary, rushed orders should be avoided as they are generally much more expensive)		** indicate if the order should be rushed (unless necessary, rushed orders should be avoided as they are generally much more expensive)
			* Testing concentrations
			** If the supply of compound is limited, often less is required if it is sent in solution, but it is easier and more stable to send powder, so check with the assay vendor
			** If it is subtantially cheaper, and nothing else is known see if the CRO can start with a single dose at 30uM and if there is activity then reduce by half log or (1/3) for 5-10 to generate data for dose response curves

Matthew O'Meara at 17:55, 2 July 2014

2014-07-02T17:55:37Z

← Older revision		Revision as of 17:55, 2 July 2014
Line 34:		Line 34:
	==Ordering Compounds==		==Ordering Compounds==
	* Get quotes either through the webpage or through vendor contacts		* Get quotes either through the webpage or through vendor contacts
	* Get Brian to approve the ~~order~~		* Get Brian to approve the orders costing more than 500USD.
	* Forward quotes to Yvonne or whoever is doing the ordering		* Forward quotes to Yvonne or whoever is doing the ordering
	*** Be cognizant of the hours the orderer works, sometimes they share time with other labs		*** Be cognizant of the hours the orderer works, sometimes they share time with other labs
	*** the quote should including the zincid, vendor, vendor id, amount, and price		*** the quote should including the zincid, vendor, vendor id, amount, and price
	*** the grant number (ask Brian),		*** lookup the project [[grant number]] (or ask Brian),
	*** a shipping address		*** a shipping address
	*** whose project this is for		*** whose project this is for
	*** who should receive the compounds		*** who should receive the compounds
			*** indicate if the order should be rushed (unless necessary, rushed orders should be avoided as they are generally much more expensive)

	==Testing Compounds with CRO==		==Testing Compounds with CRO==
Line 47:		Line 48:
	* Get a quote from the company and give it to Yvonne or whoever is doing the ordering		* Get a quote from the company and give it to Yvonne or whoever is doing the ordering
	** Make sure to include a phone number contact		** Make sure to include a phone number contact
			** indicate if the order should be rushed (unless necessary, rushed orders should be avoided as they are generally much more expensive)

Matthew O'Meara: Created page with "Depending on the project, assaying compound activity typically involves acquiring the compound and then getting it tested either in house or sending it out somewhere to be tes..."

2014-07-02T16:35:01Z

Created page with "Depending on the project, assaying compound activity typically involves acquiring the compound and then getting it tested either in house or sending it out somewhere to be tes..."

New page

Depending on the project, assaying compound activity typically involves acquiring the compound and then getting it tested either in house or sending it out somewhere to be tested. This page details some of the common tasks and considerations in this process.

=Buying Compounds=

==Identifying Compounds to Buy==
Depending on the project, compounds may have different requirements
*In vitro testing
** Purity: If possible get the compounds at 95% or greater purity even if it costs 100$ or 200$ more. If it's tested to be active but has low purity, it will likely need to be re-purified and then tested.
** Aggregation: Check the compound with the aggregator advisor (advisor.bkslab.org) and if it's close to or known to be an aggregator (indications include uM nonspecific activity, logP great than 3 or actually shown to be an aggregator through appropriate controls) then either skip the compound or plan on doing aggregation controls, e.g. testing for detergent sensitive nonspecific activity, determine particle formation using DLS, or perform the assay with/without detergent (and just detergent controls).
** Amount: try to get 10mg if possible, but if it's very expensive you can get less. If you're sending it to a CRO sending it in solution usually requires less compound. If you're planning on further controls (e.g. for purity, aggregation), make sure to get enough.

*In vivo testing
** Check pharmacokinetics (ask an expert)

==Finding Vendors==
The easiest way to find vendors is through the ZINC portal. Once you login, go to Manage Carts in the upper right and then create new cart, where you put in a list of smiles or zinc ids. Once you've verified these are the right compounds, click purchasability report where it lists which compounds are available from which vendors. In selecting vendors keep the following in mind
* Here are some reliable vendors
** AK Sientific (in SF)
** Toronto Research Chemicals
** Sigma Aldrich (sometimes higher prices but reliable)
** Enamine (has a large catalog, in europe)
** ChemBridge (in SF)
** Santa Cruz Biotech (in CA)
* Some vendors are just resellers, which makes them have larger catalogs, but can increase the price and take longer. Though often this is offset by the ease of use and not having to pay multiple shipping and handling costs.
** MolPort (ieva.kluga@molport.com has been the contact as of July 2014)
** EMolecules
** Ambinter
* If possible try to group multiple compounds per vendor to reduce shipping and handling costs
* Sometimes compounds are available from special catalogs
** NCI Platted: 1) Here is a description of the NCI Platted process from there end [[NCI_Platted]]. Look up the NCS identifier in PubChem. 2) submit a request form through their webpage. Contact the industry contacts officer at ucsf (Esteban.Mendoza@ucsf.edu | t: 415-502-1599) to have him sign the "Simple Letter of Agreement". He'll will give you a materials transfer form that you need to fill out.
* Remember that our lab will continue to buy from these vendors in the future so be nice to our contacts at these companies!

==Ordering Compounds==
* Get quotes either through the webpage or through vendor contacts
* Get Brian to approve the order
* Forward quotes to Yvonne or whoever is doing the ordering
*** Be cognizant of the hours the orderer works, sometimes they share time with other labs
*** the quote should including the zincid, vendor, vendor id, amount, and price
*** the grant number (ask Brian),
*** a shipping address
*** whose project this is for
*** who should receive the compounds

==Testing Compounds with CRO==
* If the vendor is not in the BearBuy system, they will need to fill out a form that Yvonne can provide
* Get a quote from the company and give it to Yvonne or whoever is doing the ordering
** Make sure to include a phone number contact