Open Compound Sourcing*

Before registering to participate in this program, please confirm with your institution as to whether an agreement already exists between us and your institution, contact us to enquire about such an agreement.

If such an agreement already exists, we ask you to provide us with a standard letter signed by you and your institution, in which your participation in the said program is approved. The template for such a standard letter is part of the agreement between Merck KGaA, Darmstadt, Germany, and your institution.

If such an agreement does not yet exist, we will be happy to provide the necessary information and documents to your institution. Alternatively, please feel free to contact the responsible function/person at your institution and encourage them to get in touch with us (please send requests to open.innovation@emdgroup.com).    

If you are legally the owner of the compounds, you can participate in the program. However, if you are an employee e.g. in an academic institution, then, in many cases, your employer (e.g. the institution) is the legal owner of the compounds and therefore the correct contract partner. Because this may vary between different institutions or countries, we kindly request that you check with your institution first as to whether you or your institution would be the correct partner for the Participation & Material Transfer Agreement (P&MSA).

In the case that you wish to participate as an individual in the program, you must provide proper documentation of your legal ownership of the compounds you submit to us.

The P&MSA has been set up to accommodate the needs of both partners, including provisions for intellectual property rights and inventor rights, commercial use and financial compensation. Thus, the agreement should be acceptable to the majority of (academic as well as
commercial) institutions and potential partners.

Any request for amendments or alterations lengthens the application process and delays the submission of the compounds.

Structures of compounds (as the respective salt form, if applicable) intended for submission have to be provided in the Structure Data (SD) file format. Please ensure that the structures are submitted in the proper file format; we cannot set up SD files for you.

Submission of compound structures in formats others than the SD file format will result in rejection of the application without assessment of the content. This would mean you are not eligible for compensation.

Set-up of an SD file is provided as an export format by nearly all standard chemistry software packages (compare here). You can check whether the upload will be successful on the PubChem structure search website. In order to keep the file size to a minimum, we recommend uploading a zipped or gzipped SD file.

Many software packages for drawing (organic) chemical structures–found online and available free of charge for academic employees– allow the export of the structures in SD file format.

The US government website also lists software for working with SD files    

• Include salt forms in the structure
• Avoid overlaying structures on top of each other
• Draw only one structure per entry (plus respective salt molecules, if applicable)
• Any counter ions of salt forms should be drawn explicitly in the structure
• So called “super atoms” (abbreviations like “iPr”, “OEt”, “NMe2“, etc.) should be replaced by explicitly drawn atoms

Structures should be arranged in one SD file per submission. In order to identify compounds in any correspondence with you, a unique alphanumerical identifier (structure name or your individual compound ID) must be assigned to each structure as an SD file data field.

The compound structures provided will be subjected to an internal review process in order to determine whether the submitted compounds fulfill the requirements listed in Attachment 1 of the P&MSA (see below for a respective listing), i.e. comply with the criteria outlined below. They will also be checked against internal as well as commercial compound data bases.

Based upon the outcome of this evaluation, you will receive an email detailing the compound(s) we are interested in obtaining from you, as well as detailed information on how to proceed with physically shipping the compound(s) to us.

Structures submitted should show the following property profile:

• Small organic compound with molecular weight between 150 and 450
• No inorganic elements (except usual counter ions)
• Not part of publicly available databases or vendor catalogues
• Symmetry < C2v
• A minimum of three N or O atoms 
• Less than 50% of heavy atoms being N or O
• Log of calculated solubility in water at pH 7.4 in mol/l (LogS74 mol/l) > -6
• Obeying Lipinski's Rule-of-Five (max one violation of the following conditions: Molecular weight ≤500, LogP ≤5, number of H-bond acceptors ≤10, number of H-bond donors ≤5. For a reference, see here)
• No pharmacologically undesirable substructures contained (not disclosed here)

Furthermore, compounds intended for submission should fulfill the following conditions:

• Crystalline powder (oils will not be accepted)
• Purity should be equal to or exceeding 90 %
• No cooling required
• No biologicals, no natural compounds, no extracts
• No mixtures
• No known toxicity
• No radioactive compounds

These structures will only be used for the in-silico evaluation of these compounds. At this stage, the compound structures are kept at a server separate from our screening library and will not be used for purposes other than running our initial assessment. 

In order to ensure proper shipping and handling of the compounds, we will provide you with glass vials, which can also be used in our weighing and dissolution routing. We will cover all costs of the shipment of these vials to you and also for the transfer of the vials plus the respective amounts of the accepted compounds. The transfer will be arranged by internationally working carriers (e.g. FedEx). We will inform you ahead of time of any shipment to you or vial pick-up.

We aim to provide you with our assessment of the electronically-submitted compound structures within 14 days of your submission, provided we do not experience problems with the submitted SD file.

Physically-shipped compounds will be checked within one month of receiving them at our premises to establish whether they fulfill the requirements in terms of purity and physicochemical properties.

If compounds pass this check, they will be incorporated into our compound screening library and will be assessed in our normal high-through-put screening campaigns. At this point, you will be entitled to financial compensation as outlined in paragraph VI of the P&MSA.

We do not plan to share biological data at this time. 

Based upon the outcome of your compounds, you might be offered a collaboration and development agreement (see details in the P&MSA).

If your compounds qualify as hits, you might be entitled to additional financial compensations for up to 20.000 Euros. TheP&MSA specifies these details. 

We will only accept compounds sent in the vials we provide. Please refrain from sending any compounds directly to our Darmstadt site. 

As outlined in the P&MSA, we ask for 10 mg of the respective compound. If smaller amounts are received, we reserve the right to reduce the financial compensation accordingly.

Merck KGaA, Darmstadt, Germany, at its sole discretion, decides whether or not to return compounds that were rejected due to inadequate physicochemical properties. Financial compensation will be paid for compounds not returned to the submitter.