February 13, 2020

On Compound Salt Forms

In order to dissolve a compound to make a solution of a specified concentration, you need to know its molecular weight. Most compounds are sold in a pure (non-salt) free form and it is clear what the molecular weight is: but a number of compounds are sold in a salt form, which means that you need to calculate the effective molecular weight that takes into account the compound to salt weight ratio. We therefore strongly prefer the salt information to be included in the structure diagram of the product, as in this example:

tert-butyl 4-(3-aminopyrrolidin-1-yl)piperidine-1-carboxylate

sesquioxalate

tert-butyl 4-(3-aminopyrrolidin-1-yl)piperidine-1-carboxylate has molecular formula C14H27N302 and molecular weight 269.39 g mol-1.

The effective molecular weight can then be normalized to one molecule of the compound and used to calculate the weight of compound needed for a particular concentration. For the example above dot-disconnected is formula C14H27N302.1:1.5C2H2O4 and effective molecular weight 404.44 g mol-1.


Suppliers don’t always include salt data in the chemical structure diagram of the compound. A common approach is to include a field called Salt or Salt Data where the salt identity and stoichiometric ratio can be provided.

There are over 1600 unique salt comments in the MolPort database. This means that a given salt may be described in text in multiple ways.

Here are some examples we see for representing the chloride salt of a compound:

Representing the chloride salt of a compound

When stoichiometry and salt and solvate combinations are included, there are even more variations.



Here are the 100 most commonly encountered salt field comments:



While it is feasible to manually calculate the correct effective molecular weight for one or a few compounds, it is nevertheless inconvenient. For large library acquisitions, manual interpretation and calculation are simply not practical. At MolPort we have been working on a process that interprets supplier-provided salt data comments and adds this information to the chemical structure of a product.

Currently we are successfully processing approximately 99% of the salt comments. When we update supplier catalogs, this information is transformed and added to the chemical structure. The free form and the salt form are saved as different structures and are assigned different MolPort IDs. As we process more and more supplier catalogs with the new process, you will notice that some of the previously available free-form compounds become unavailable and new MolPort IDs become available (for the salt forms of the structures).

We are planning to add new fields to the MolPort database export files and API. We will post more details in the near future.

Imants Zudāns
CEO
molport.com

November 12, 2019

Announcing Screening Compound Solubility Crowdsourcing

Today MolPort is launching a new initiative with the goal of crowdsourcing screening compound solubility. This blog post explains why. You are welcome to use one of these quick links for navigation to the right resource.

Quick links:




About the initiative


One of the issues that screening compound buyers bring up most frequently is compound solubility. It used to be discussed at compound management conferences. Scientists and compound managers estimate that 1-5% of the compounds they purchase for their screening projects or compound libraries can not be dissolved. For large library acquisitions this is sort of an annoying fact of life. You spend time to carefully build your library – perform diversity analysis and choose compounds carefully to represent as broad a chemical space as possible. And then when you procure the compounds you get out-of-stock cancellations, QC failures and insoluble compounds. The chemical space puzzle you labored so carefully to cover in full ends up having blank spots. While you do not pay for cancelled compounds and get a refund for QC-failed compounds, there are usually no guarantees that a compound is soluble and therefore you end up paying for samples that you can not use. Therefore, this category is a real budget-waster.

Large compound libraries typically have multiple similar compounds. Cancellation of any single compound may not affect screening results significantly. As in-silico modeling algorithms improve and are augmented by machine learning algorithms, the typical size of a screening library is shrinking. The loss of data points for any reason is therefore more important. Losing a few data points because of compound insolubility may mean that you need to buy another set of compounds, wait for their delivery and screening results.

We are working to increase screening compound sourcing ease and efficiency: reducing lead times, minimizing cancellations with more up-to-date inventory data, reformatting of samples. However, compound insolubility is still a common concern. Software tools predicting compound solubility are constantly improving. We have seen how their use makes a real improvement. Yet, they do not yet have a perfect prediction capability. Why can't solubility be measured? It is a complex test and it would be expensive and time consuming to run it on 7 million commercially available compounds.

Most often, screening compounds are dissolved in DMSO. Currently 10mM concentration seems to be the industry standard. A precise solubility value is not needed. All one needs to know when buying compounds for screening is whether it is possible to create their 10mM DMSO solution.

Pharmaceutical companies, academic and non-profit screening institutes and other R&D centers have been buying screening compounds for over a decade. It is reasonable to assume that nearly every compound suppliers’ list in their catalogs has been purchased and attempted to dissolve. Information systems of organizations are full of data: what is soluble and what is not. Yet, apart from a few mentions in publications, this information is locked up and inaccessible. Organizations continue to waste their resources on compounds that someone already tried and failed to solubilize.

We at MolPort have discussed compound solubilization issues with our clients. What can we do to help scientists around the world to avoid buying not fit for purpose compounds? One way to do that is to create a compound solubility data bank. Several of our clients agreed to share their data with us. We already know which compounds they ordered, so confidentiality is not an issue. We combined data from multiple sources and incorporated this information on our website and downloadable data. You can read more about it on a documentation page. These data are available free of charge to anyone interested. Currently we have data on about 1/7 of the stock compounds listed in the MolPort database. These data may not be perfect. Use it as a guide. We internally at MolPort do not say a compound is insoluble, we say that solubilization problems were reported by a client. So don't use this data as a training set for solubility software. It is not meant for that. But the label name aside, it may be safer to choose a soluble analogue of a compound with reported solubilization problems, when that is possible.


How to contribute

And now the important part. We know that not every organization will be able to share their data. But everyone can benefit from knowing compound solubility. We lack data for 6 million compounds. Please, contribute your data to this pre-competitive initiative. If you can't share data, talk about this project to someone who can share. It does not matter that you have few data – you may have data on compounds that no one else has covered. Help us spread the message. The more organizations that participate, the quicker we will cover all commercially available compounds.

Do you have suggestions for improvements or questions? If so, please, use the blog comments below this post or contact MolPort privately.

A data template, to share solubility data for addition to the online MolPort database, together with more details about database is available on MolPort Solubility Center.

We will use hashtag #CompoundSolubility to share news about this project.

Subscibe to MolPort bi-monthly Newsletter to receive updates on this project and other MolPort developements.


Imants Zudāns
CEO
molport.com

October 24, 2019

MolPort 2019 Christmas & New Year's Holiday Schedule

MolPort offices will be closed on December 24th, 25th and 26th for Christmas, as well as December 31st and January 1st for New Year's Day.

Please note: Holiday schedules vary by supplier. Please, review these shipment cutoffs for our major suppliers.


August 6, 2019

MolPort Inc. – now open for faster, more efficient chemical sourcing in the USA

MolPort is pleased to announce the opening of US-based MolPort Inc. to streamline compound ordering and payment for its many US customers.

By placing orders and processing payments via MolPort Inc., US-based customers will benefit from faster and more efficient chemical sourcing.

No More Customs Headaches

For US customers, understanding the various international customs rules and procedures is daunting, navigating chemical orders through the custom mazes can be frustrating and time consuming, and the smallest error can potentially hold up shipments or incur additional charges.
Orders placed through MolPort Inc. will have all the required international customs formalities taken care of, and so packages will sail through customs without delay or additional costs, saving time in preparing customs documentation and speeding the arrival of needed compounds.

Seamless Payment Options

As anyone who has tried to transfer money internationally from the USA knows, the process is complicated and more expensive than making a local payment.
With MolPort Inc., customers can pay for orders by cheque from a US bank, or they can get a quote online, provide a Purchase Order, and have it processed via MolPort Inc. – saving time and costs by avoiding an international funds transfer.

I’m a US customer: how do I interact with MolPort Inc.?

For optimal experience in placing your first order via MolPort Inc., we suggest that your procurement specialist gets in contact with us to open a new supplier account.

They will need to complete and provide the following documents/information so that we can add you to our procurement system:

o W-9 form
o Employee Identification Number (EIN)
o Tax-exempt status, if relevant

The MolPort Inc. W-9 form can be requested by email.

With MolPort Inc. open for business, our US customers can now enjoy faster and more time- and cost-efficient chemical ordering to better support their research.

For more information on MolPort Inc., please contact us 

June 11, 2019

MolPort real time order tracking and documentation

MolPort order tracking system allows the customer to gain insight into where their order is at any given point in time. From the time an order is placed until it is delivered. Be up to date with your order!



Order tracking service is available to everyone placing orders with us.

Registered users at molport.com have access to their complete order history and associated documentation.

Non-registered users are given access to their current order only.



Report sections:

 

No.1 Order tracking

An overview of the order, including the Billing and Shipping addresses and the download link of a spreadsheet with the detailed status for all ordered products.
































No.2 Order status


As order transitions from one phase to the next, completed order process stages are marked green. Order may transition through following stages (actual order stages vary by order):

Order received
order has been received, registered and processed by MolPort
Compounds processing
compounds are being processed by suppliers (QC, packaging, shipment preparation)
Packaged
package has been prepared and is waiting for the shipment
In transit
compounds are in transit from supplier to MolPort warehouse
In MolPort Warehouse
compounds have been received at MolPort warehouse and are waiting for the shipment or additional services
Reweighing/
Reformatting
compounds have been received at MolPort warehouse and are being re-formatted in customer’s preferred format – re-weighing, sample splitting, DMSO solutions
Shipped
compounds are shipped out to customer address
Cancelled
number of ordered compounds that cannot be delivered and have been cancelled from the order


No.3 Shipment summary


A shipment summary becomes available after a package is sent out to customer address. This includes:
  • Shipping courier name;
  • Shipment type (direct shipments from suppliers or single shipment from MolPort warehouse);
  • Tracking number (including a link to real time tracking at the courier’s website);
  • Packing list (packing data as Excel and SDF files).

No.4 Detailed delivery progress


The delivery progress report section list status of each ordered product. You can filter the product list by:
  • Supplier name;
  • Status (In transit, Shipped, Cancelled, Processing, in MolPort WH);
  • Ordered amount;
  • Ship out date.


We are able to follow and provide insight into the status of the order through its entire journey to the customer.

October 23, 2018

MolPort 2018 Christmas & New Year's Holiday Shedule

MolPort offices will be closed on December 24th, 25th and 26th for Christmas, as well as December 31st and January 1st for New Year's Day.

Please note: Holiday schedules vary by supplier. Please, review these shipment cutoffs for our major suppliers.





We look forward to assisting you with all your compound ordering needs this year and in 2019!

April 10, 2018

KNIME workflows for downloading of MolPort data for offline usage

MolPort provides a number of ways to access data and catalog information on commercially available compounds: the MolPort website, the MolPort downloadable database, MolPort web services (API). With web services you can instantly check the current stock level information for MolPort compounds from your software application, Microsoft Excel, Optibrium StarDrop, Pipeline Pilot or KNIME nodes.

A certain type of data analysis, like filtering by specific parameters, diversity selection, virtual screening or docking, require you to have full data locally. Full data download and its preparation for use require a certain amount of effort on the user’s side. Following MolPort user requests, we created two examples of workflows that automate this process using KNIME. Now you can get to MolPort data in KNIME easier.

The first workflow named “LoadAllMolPortMolecules” does not require data access credentials. With this workflow you get chemical structures of all available compounds, their MolPort IDs and website links to acquire further information. You can easily share this example with colleagues to provide them with a fast and easy way to access MolPort data. The process of downloading the complete data set (100 MB) and loading it to KNIME may take less than 5 minutes and requires 2 GB of space on your hard drive. All you must do is set up a folder for local file storage.



The second workflow, named “LoadMolPortExtendedData”, allows you to acquire extended information version of data. In this case there are multiple downloadable files.. For each compound additional data includes the largest available  stock amount, the fastest shipping time, price ranges for 1mg/5mg/50mg, whether it is available as a Screening Compound or a Building Block, the QC type, the InChI and the InChIKey. Access to such data is also free, however requires use of credentials. To get yours, simply send a message from your corporate email address to customerservice@molport.com. Then set up the second workflow example to get full data version.




Some companies have a restriction for FTP access. You may need to work with your system administrator to add MolPort FTP location to allowed list. Alternatively, contact us to get access to files through HTTPS.

Both workflows contain descriptions and are compatible with KNIME version 3.3 or later.

Files for download:


LoadAllMolPortMolecules.knwf
LoadMolPortExtendedData.knwf

December 18, 2017

MolPort 2017 Christmas & New Year's Holiday Shedule

MolPort offices will be closed on December 25th and 26th for Christmas, as well as January 1st January for New Year's Day.

Please note: Holiday schedules vary by supplier. Please, review these shipment cutoffs for our major suppliers.





We look forward to assisting you with all your compound ordering needs in 2018! Happy Holidays!

May 3, 2017

Drawing Tricks for More Effective Substance Online Ordering - Webinar presentation

On April 27th MolPort and ChemAxon held a joint webinar, aimed at helping scientists master the MolPort chemical structure search interface. ChemAxon's Marvin JS is a state of the art chemical structure editor that is integrated into MolPort’s web interface to query the commercially available compound space. In the course of this webinar, you will be walked through the basic structure search editor interface on www.molport.com, will pick up productivity tips and advanced structure query capabilities.

 View the recorded webinar video presentation:


Visit  Marvin JS user guide and query strategies for additional documentation.

April 26, 2017

Structure Search User Interface Gets a Number of Small but Important Improvements

We Part with the Marvin Sketch Applet Editor


We removed the Java Applet structure editor from our website. Browsers have poorly supported Applets in corporate environments; they were slow to load and the IT industry, as a whole, has moved on to JavaSript and HTML5 technologies for a number of reasons. The newer and quicker ChemAxon's Marvin JS editor has been available on our website for some time already and our users overwhelmingly favored it over the applet version of the editor. You can still use the ChemAxon Marvin Sketch applet installed on your PC, if that is your preferred editor, and copy-and-paste the structure to the editor on the MolPort structure search website.

Building Structure Queries


We made several changes to the page, where you start your structure search. This is it’s current version:




You may notice that the editor is now larger in comparison. We moved search filters and options to the lower part of the page. Recent and saved queries will be listed below the filters and options.
Notice that there are now 3 tabs above the editor:

  • Draw Structure
  • Convert to Structure 
  • Load from File

Draw the Structure


It is the first tab shown, when you load the page. Here you can graphically compile the structure query.

Convert to Structure


This is the tab, where we introduce you to some nice new functionality. Your searches by chemical names now result in exact compounds you are looking for. However, not only does this compound has to be in our database, we also need to have the particular version of the name you used stored in it. That is how text search engines work. And since chemical names can be complex, chances are you may miss the compound. Structure search is a much more powerfull and robust way to find the needed compound. And it offers other noteworthy benefits: you can search for close analogues of the compound, for example. Drawing the structure may be tedious for larger compounds, however.

Now you can start with a compound name, convert it to a structure, modify the structure, if needed, and proceed to run a structure search in the MolPort database. Currently we support the following data input types for conversion:

  • IUPAC name
  • Synonyms and traditional names
  • InChI
  • SMILES
  • SMARTS

We use a combination of database lookup and name-to-structure conversion strategies to convert the text input to a chemical structure. While it works for most valid chemical names, it is not always successful.

Example


Here is an example compound and various names, i.e. identifiers, that can be successfully parsed to chemical structure:
2,3,6,9-tetrahydro-1H-purine-2,6-dione structure
  • 2,3,6,9-tetrahydro-1H-purine-2,6-dione
  • 1,3-dihydropurine-2,6-dione
  • 1H-Purine-2,6(3H,7H)-dione
  • 2,3,6,9-tetrahydro-1H-purine-2,6-dione
  • 3,9-dihydro-1H-purine-2,6-dione
  • 3,9-Dihydro-purine-2,6-dione
  • Xanthine
  • O=c1[nH]c2[nH]cnc2c(=O)[nH]1
  • 1S/C5H4N4O2/c10-4-2-3(7-1-6-2)8-5(11)9-4/h1H,(H3,6,7,8,9,10,11)

Load from File


As the name implies, in this tab you can upload a saved structure or query to the tool.

Better navigation


We improved search-related navigation as well. First of all, when you go back from search results to the structure editor and query building, the last searched structure will be automatically loaded in the editor. That way you can adjust the query to make it more specific or broaden it.

We also improved the breadcrumb navigation from Search to Molecule. A typical navigation path when searching is:


Home > Draw Structure > Search Results > Molecule



Now you can navigate from the Molecule back to the Search Results, to see other search results, or to Draw Structure, to edit the query structure.

April 18, 2017

Launching an Automatic Update Site for MolPort KNIME Nodes

MolPort provides a number of ways to access data on commercially available compounds and their catalog data: the MolPort web portal, a downloadable database, web services (API). With web services you can instantly check the latest stock level information for MolPort compounds from your software application, Microsoft Excel, Optibrium StarDrop, PipelinePilot or KNIME.

Starting today, MolPort KNIME Nodes are available from the traditional KNIME install/update website. This will not only make the installation process much easier, but will also keep them up-to-date automatically. Just add https://www.molport.com/knime/ to the list of update websites.

Here is how you do it:

 

Open KNIME, then click Help menu, select Install New Software.
Paste https://www.molport.com/knime/ into the Work with field.
Press the Add... button and then save the update resource with a name of your choice. We have used MolPort nodes as an example (see figure below).



Check the box for MolPort KNIME Nodes or just use Select All below to install or update the existing version of MolPort Nodes.




Press Next > or Finish and follow the next installation steps.

The download size does not exceed 10Mb for the current version, but the installation process usually takes up to 5 min. When the installation is complete, KNIME will prompt you to restart the application.




 After the restart, you can find MolPort Nodes in your local Node Repository.




 Please find here more information about MolPort KNIME nodes here.

We would appreciate your feedback and suggestions regarding this feature very much. In case of any question regarding the installation process or the MolPort nodes themselves, you are welcome to get in touch with us, using the contact form.

April 12, 2017

Specify Sample Amount Individually for Each Item in List Search

MolPort List Search is a tool, available on the MolPort homepage, which aims to simplify the sourcing of a list of reagents or HTS samples. If you have compound structures in form of an SD file, a SMILES string list, or a list of MolPort ID references, you can do a quick search and optimize the shopping cart in real time.  See the List Search user guide. However, your specified sample amount applies to all compounds by default, which is great for HTS compounds, but may not be the optimal way to order building blocks.

On user demand, we added the feature to specify required sample amounts for individual compound in List Search. This is an example compound list:

Ref Nr
SMILES
Required amount, mg
Minimum acceptable amount, mg
LID2828
NC(C(O)=O)c1ccc2OCCOc2c1
300
100
LID1617
NC(C(O)=O)c1ccc(cc1)-c1ccccc1
300
100
LID2982
NC(C(O)=O)c1cccc(c1)[N+]([O-])=O
1000
100
LID4215
CC(C)(C)OC(=O)NC1CCCCC1N
800
100
LID3556
NC(C(O)=O)c1cccnc1
500
100
LID2377
COc1ccccc1C(N)C(O)=O
1000
100
LID4350
NC(C(O)=O)c1ccccc1F
700
100
LID2486
CC(C)(C)OC(=O)N1CCCCCC1C(O)=O
200
100
LID3074
NC(C1CCCCC1)C(O)=O
800
100
LID1893
NC(C1CC1)C(O)=O
100
100
LID2888
OC1CCCNCC1
300
100
LID2027
NC(C(O)=O)c1ccc2ccccc2c1
900
100
LID2759
CC(N)=N
200
100
LID0164
NC(C(O)=O)c1ccc(F)cc1
900
100
LID2173
NC(C(O)=O)c1ccc(cc1)C(F)(F)F
300
100
LID1590
Cl.NC(=N)C12CC3CC(CC(C3)C1)C2
800
100
LID4312
NC(C(O)=O)c1ccccc1Cl
300
100

Where:

Ref Nr
Your reference number for the compound.
SMILES
Specifies the structure of the compound.
Required amount
This is the desired sample amount of the compound in milligrams (other measurement units should be converted to milligrams to use this feature).
Minimum acceptable amount
Should the required amount of the compound is not available, you can specify the minimum amount you would be interested in. The sourced amount will be within the range of the Minimum acceptable amount and the Required amount. If the available sample amount is less than this quantity, the compound will be listed as unavailable.



Results of a List Search:



After specifying the desired amounts for separate compounds, you can either finish the ordering process online or generate a quote for creating a purchase order through your Purchasing Department.

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