Chemical Spaces Chemical Spaces
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Chemical Spaces

The Next Generation of Massive Molecule Collections

BioSolveIT pioneers in developing and exploring individual Chemical Spaces: Molecule collections comprising billions and trillions of entries that can be efficiently screened in a reasonable timeframe.
Chemical Spaces are created by combining building blocks with predefined chemical reaction rules. Unlike enumerated molecule libraries, entries are not explicitly listed; instead, combinatorial Chemical Spaces allow a fast and dynamic generation of compounds, enabling rapid processing — delivering only relevant results that are synthetically accessible, or simply purchasable (depending on the Chemical Space).

Combinatorial Marvel

Chemical Spaces surpass the constraints of exhaustively enumerating sets of molecules — yet cover all entries. Rocket Science!
Chemical Spaces consist of two elements: Building blocks on the one hand side, and chemistry rules on how to combine them on the other. When they both come together, a combinatorial explosion occurs, resulting in an astronomical number of compounds. This, in turn, broadens the exploration scope by generating a dataset that encompasses every synthetically accessible possibility.

Our BioSolveIT technology will dive into the molecular zillions and retrieve only those molecule that are relevant to your drug discovery project, without wasting resources on insignificant entries.
Still, a comprehensive evalution of the entire Chemical Space is conducted, ensuring that every potential molecule has the opportunity to be featured as a result.

Chemical Spaces — Commercial Sources for Compounds

Several applications developed by BioSolveIT are available to mine relevant chemistry from the ultra-vast Spaces.
The accessibility of retrieved molecules can be coupled to widely popular on-demand services: Compounds retrieved from one of our various partners' Chemical Spaces can be purchased and delivered to your location within a few weeks typically.

Available Commercial Chemical Spaces

AMBrosia CHEMriya eXplore Freedom Space GalaXi REAL Space

Exclusive Commercial Chemical Spaces

xREAL Space

Virtual Chemical Spaces

KnowledgeSpace
In partnership with Enamine Ltd. we built the world's largest collection of commercially available compounds, featuring 70,363,810,611 virtual products based on 167 in-house reactions.
Using our CoLibri technology, we coded the Enamine synthesis protocols and in-stock starting materials as a searchable Chemical Space. REAL Space allows for efficient hit exploration, from finding previously unknown analogs to scaffold hopping. It provides an escape from an availability bias of current stock screening collections towards intellectual property-free areas. Additionally, 170,202 reagents and building blocks are encoded to ensure precise, relevant results for early-stage drug discovery.

Traits
  • Make-on-demand
  • Drug-like properties
  • Rapid synthesis and delivery
Download
7.0 x 1010
REAL Space
This ultra-large compound molecule collection of drug-like compounds has been created in close collaboration with Ambinter (a brand of Greenpharma).
It is based on unique in-house building blocks and chemical reactions, leading to a stunning amount of 110,496,278,572 compounds with favorable physicochemical properties for early stages of drug discovery. Furthermore, all AMBrosia entries can be ordered directly from Ambinter to be synthesized and delivered straight to you.

Traits
  • Make-on-demand
  • Drug-like properties
  • Plethora of decorated scaffolds
Download
1.1 x 1011
AMBrosia
Created in collaboration with eMolecules, eXplore represents the largest commercial Chemical Space so far. In its very first iteration it already featured 5 trillion compounds based on robust chemical reactions. Users can order the building blocks and synthesize the compounds themselves in a 'do it yourself'-manner — or request the already synthesized compounds from eMolecules. eXplore's compounds are created with curated building blocks to provide accessible results that can be shipped within few business days to customers.

We have created a Cookbook as an introduction to eXplore that can be downloaded here (PDF).

Traits
  • Do-it-yourself: Order the building blocks and synthesize the compounds in-house
  • Largest commercial Chemical Space featuring drug- and lead-like compounds
  • Make-on-demand via CRO possible
Download
5.0 x 1012
eXplore
The Freedom Space by Chemspace has been conceived to maximize the accessibility of your molecules. The Freedom Space features molecules created based on robust chemical reactions; its compounds can be ordered as either already final, synthesized products, or as their building blocks for a convenient and indepedent synthesis in your own labs. The Freedom Space was created by taking a selected set of in-stock building blocks from several suppliers and combining them utilizing ten well-validated chemical transformations. The reactions include acylation, reductive amination, arylation, etc, resulting in 5 x 109 accessible compounds.

Traits
  • Make-on-demand and do-it-yourself possible
  • Robust chemical reactions
  • Focus on accessibility of compounds
Download
5.1 x 109
Freedom Space
The latest and so far largest update of the 'GalaXi' Chemical Space now covers 12 billions of tangible molecules. In close collaboration with WuXi LabNetwork we created a novel Chemical Space ready for you to download and search. This space contains a lot of unique chemical intellectual property for your research, and compounds can be created on demand upon request with WuXi. GalaXi has been shaped from WuXi LabNetwork’s building blocks and reaction schemes that have been properly checked to deliver high quality results. High quality processing has been ensured using our CoLibri software.

Traits
  • Make-on-demand
  • Contains unique building blocks with sp3-rich spiro motifs
  • Versatile building blocks
Download
1.2 x 1010
GalaXi
CHEMriya, OTAVA's on-demand Chemical Space, features over 11.8 billion accessible molecules, based on 10,000 building blocks and 66 in-house reactions. Several multi-component and ring-closure reactions provide a vast chemical diversity with a broad range of molecular scaffolds. As every Chemical Space is based on in-house knowledge and ressources, CHEMriya will further expand the search horizon of infiniSee, allowing you to search in new areas of tangible molecules.

Traits
  • Make-on-demand
  • Contains unique ring-closing reactions
  • Covering drug- and lead-like structures, as well as beyond rule-of-five entries
Download
1.2 x 1010
CHEMriya

xREAL Space

infiniSee xREAL is the result of a long-standing collaboration between BioSolveIT and Enamine Ltd., offering access to over 2.4 trillion compounds exclusievely through infiniSee xREAL, making it the largest commercially available Chemical Space. xREAL incorporates Enamine's synthesis protocols and starting materials into a searchable Chemical Space, enabling efficient hit exploration, scaffold hopping, and the discovery of novel analogs. With a high synthesis success rate exceeding 80%, xREAL ensures rapid synthesis and delivery of commercially available compounds.

Traits
  • Trillions Sized combinatorial compound collection
  • Exclusive access through infiniSee xREAL
  • High synthesis success rates (80%+)
  • Constantly evolving with machine learning approaches

Download infiniSee xREAL!

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KnowledgeSpace has a focus on size: The space is comprised of more than one hundred literature reactions including ring-closures, couplings, substitutions, and multi-component reactions. The result is a literature-driven virtual Chemical Space covering hundreds of billions of virtual products with high likelihood of synthetic accessibility. This space is ready for searching — but it can also serve as a blueprint for customization, capitalizing on your proprietary building blocks and chemistry protocols.

Traits
  • Virtual Chemical Space (compounds cannot be ordered)
  • Source for ideation
  • Largest Space available
Download
2.9 x 1014
KnowledgeSpace

FAQ

Let’s compare Chemical Spaces to sauerkraut. The concept of fermented cabbage exists in many world cuisines; kimchi in Korea, kapusta kiszona in Poland, curtido in El Salvador. Although they follow similar preparation steps, the taste varies greatly due to the local ingredients used. Chemical Spaces behave alike: The knowledge and building blocks used to build up the Chemical Space differ between companies and methods involved. The overlaps between two Chemical Spaces can be surprisingly minuscule (Lessel et al. 2019 and Rarey et al. 2021).
By searching in several Chemical Spaces you will maximize your success rate to find diverse, promising molecules.
After performing a search with infiniSee your results will be presented in a table. The column "Source" tells you the origin of the Chemical Space that contains your solution; the ID of the respective result molecule is shown in the "Name" column.
Compounds can be ordered by sending a quote request to the compound vendor with the following information:
Requested structures in SMILES or SD format, Compound ID (concatenated), and amount requested.

For compounds from Ambinter's AMBrosia Space, send your request to ambrosia@greenpharma.com.
For compounds from eMolecule's eXplore Space, send your request to explore@emolecules.com.
For compounds from Enamine's REAL Space, send your request to libraries@enamine.net.
For compounds from WuXi's GalaXi Space please send your request to contact@labnetwork.com
For compounds from OTAVA's CHEMriya Space please send your request to info@otava.ca.
For compounds from Chemspace's Freedom Space please send your request to sales@chem-space.com.
In this post, we explain the difference between combinatorial, ultra-vast Chemical Spaces and their exhaustive counterpart, enumerated compound libraries.
The building blocks and chemical reactions used in the creation of our partners' Chemical Spaces are not available to the general public.

As for the eXplore Chemical Space, a is available here (PDF). It contains the reactions as SMARTS definitions that were cherry-picked by eMolecules for the creation of the Space.

A helpful collection robust chemistry reactions for computational chemists can be foundfollowing this link.
infiniSee

infiniSee

infiniSee is your Chemical Space navigation platform.
Based on similarity it finds molecules of interest in ultra-large Chemical Spaces in a flash on any standard hardware.
Various modes, each employing distinct algorithms, are available to provide you with the most relevant chemistry tailored to the project needs.
  • Scaffold Hopper (FTrees): Retrieves compounds based on fuzzy pharmacophore similarity.
  • Analog Hunter (SpaceLight): Screens for close analogs of a compounds based on Tanimoto fingerprint similarity.
  • Motif Matcher (SpaceMACS): Mines for molecules containing an exact substructure of interest or those with highest maximum common substructure to the query.
Learn More

Sophisticated Software Solutions for Computational Chemists

infiniSee comes with a state-of-the-art graphical user interface that is is easy to operate, enabling effortless navigation for medicinal and computational chemists, as well as other drug hunters, to seamlessly search for compounds and assess the results.
The various Chemical Space search methods (so-called "Components") are also available as command line tools that can be integrated into your consisting workflows. Computational chemists can use advanced setting for large-scale mining of relevant compounds to fine-tune their results.
Those additional settings include:
  • FTrees: expansion of alternative results/alternative synthesis routes
  • SpaceLight: selection of different fingerprints (e.g., ECFP, fCSFP, iCSFP, tCSFP and their respective variants)
  • SpaceMACS: SMARTS definition
  • ... and many more for each tool

Available Command Line Tools for Chemical Space Exploration

FTrees SpaceLight SpaceMACS

Conquer the Chemical Space with BioSolveIT

The fact that the enumeration of compounds has computational limits led to the widespread acceptance within the pharmaceutical industry of utilizing combinatorial Chemical Spaces to harness the potential of in-house building blocks and expertise in chemistry.
The accessibility of results, coupled with intellectual property considerations, further reinforces the adoption of this approach. Expanding the hunting grounds for novel compounds within these Chemical Spaces not only addresses the limitations posed by computational constraints but also opens up new avenues for discovery, allowing pharmaceutical researchers to explore a broader spectrum of potential drug candidates.
CoLibri

CoLibri

The heartbeat of ultra-large Chemical Spaces is the synthetic accessibility of mined compounds. What can be made – easily enough – decides what eventually will be made.
CoLibri is our toolkit for Chemical Space creation that transforms synthetic know-how into a Chemical Space, constituting huge numbers of virtual, yet synthetically accessible compounds.

Given a set of building blocks and chemical reactions, CoLibri processes the input and writes it into a *.space file. This turns in-house resources into the largest hunting grounds for drug discovery.
Learn More
create your own custom chemical space with colibri

Create Your Own Chemical Space
... Or Ask Us to Create One for You

Sometimes the perfect solution is within reach in your own compound library without realization. Design your own, bespoke Chemical Space with your accumulated, in-house knowledge and resources. Reactions and building blocks can be defined to create massive numbers of virtual compounds. Multiple big pharma companies have built their own corporate, in-house Chemical Spaces to search for scaffold alternatives to reduce costs and time.

With years of experience in getting the most out of your resources, BioSolveIT has created dozens of Chemical Spaces. The Spaces generated by our software are recognized as the largest compound sets among pharmaceutical companies.
Considering your in-house proprietary building blocks and chemistry knowledge, we tailor a unique Chemical Space that encompasses the full spectrum of synthesizable potentials as a source for ideation of accessible compounds.
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