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Activated Aryl Halides
Aryl Bromides and Iodides
Biological Research Tools
Boronic Acids and Pinacolates
Exotic Heterocycles (RubyScaffolds)
Fragments for FBLD
Heterocycles (5-membered ring)
Heterocycles (7-membered ring)
Heterocycles-Tricyclic and Polycyclic
Indoles and Azaindoles
InFarmatik for North America Only
Leadlike Rule of 3 (RubyRO3)
New Products April 2013
New Products June 2013
New Products May 2013
Rare and Unique Substructures
Rare Building Blocks
Sonogashira Coupling Reactants
Suzuki Coupling Reactants
TIDEA screening compounds
Download the Focus Synthesis catalog in the format of your choice:
Focus Synthesis is a new research chemical supplier that uses rational principles based in chemoinformatics in the design
of chemical building blocks that are ideally suited for DOS (diversity-oriented synthesis). Focus Synthesis products include
members of unique and underrepresented substructure classes, building blocks designed for thorough chemical space coverage,
exotic heterocycles and precursors for highly focused combinatorial libraries. If you purchase rare chemicals from Focus
Synthesis, you will have a time-saving tool set for discovering the drugs of the future by exploring uncharted chemical
space, expanding SAR knowledge, and bolstering your IP position.
Focus Synthesis offers synthons, building blocks, and research chemicals that are optimized for drug discovery using cheminformatics-based design. In addition to being a research chemical supplier specializing in drug candidate intermediates and other organic chemicals, Focus Synthesis also provides custom synthesis outsourcing, in-house custom chemistry, and proprietary design services.
Many of the building blocks in the Focus Synthesis catalog belong to substructure classes that are rare or unavailable in other chemical catalogs. For these molecules, a substructure search in the Available Chemicals Directory (Symyx software) will yield 0 or 1 structure. The underrepresented substructures in these synthons make them ideal for the development of non-obvious variations on current lead molecules, thereby strengthening intellectual property positions. In addition, these distinctive building blocks are excellent tools for improving diversity and chemical space coverage. Click here to see an online subcatalog of building blocks with rare and unique substructures®. Our Rare and Unique Subcatalog listing is updated every 6 months, removing products that are no longer rare. The last update was made in July 2009.
Focus Synthesis has also developed subsets of the Rare and Unique Substructure® Classes that are even more
distinctive and unusual.
RubyScaffoldsTM are exotic heterocycles in which the unsubstituted heterocycle is found in fewer than 1 in 10,000 (<0.01%) of the molecules in emolecules.com when a substructure search. These distinctive heterocycles can help you to explore new areas of chemical structure space. They can also help to enhance your IP position because few if any derivatives are commercially available and most test molecules that you make from them will be patentable. Click here to see an online catalog of RubyScaffoldTM exotic heterocycles. Examples of 4 RubyScaffoldsTM currently in stock are shown here, with the rare heterocyclic substructure highlighted red:
For RubyShapesTM, the substructure is rare or unique in commercial catalogs for all possible heavy atom substitutions. The substructure is a graph consisting of "wild card" atoms and bonds, and yields at most 1 structure when used in a substructure search in the Available Chemicals Directory (Symyx software). As building blocks, RubyShapesTM are ideal for improving the diversity of molecular shapes in your corporate collection. The following figure depicts 4 RubyShapesTM molecular structures from the Focus catalog, alongside their rare substructure shapes (substructures highlighted in green):
RubySynthonsTM are ultra-rare molecules containing substructures that are not found in the very large Emolecules database (>10 million organic structures from the literature as well as commercial sources). RubySynthonsTM are ideal as starting points for improving the overall diversity of your corporate compound collections and for helping you create highly novel, patentable leads. Examples of RubySynthonsTM are shown below, with rare substructures highlighted in blue:
Focus Synthesis has introduced Cheminformatic Gap Fillers in order to provide druggable
building blocks that significantly improve the diversity of commercially available building blocks. One approach to
measuring chemical diversity involves determining how evenly distributed a set of molecules are in chemical property space,
where the dimensions of the space can be physical properties, chemical properties, topological or geometric parameters
based on structure, etc. Useful descriptors for this type of cheminformatic analysis include chemical properties, physical
properties, and structure based parameters, and various combinations thereof that can be independently increased or
decreased in a straightforward, intuitive manner using structural changes. Polar Surface Area (FISA, area in angstroms of
O and N atoms) and Weakly Polar Surface Area (WPSA, area in angstroms of F, Cl, Br, I, S, and P) were chosen here because
of their relationship to drug bioavailability in mammals (Wessel et al, 1998; Votano et al, 2004).
In the example given here, the parameters were determined using QikProp software from Schrodinger. In the scatter plot shown in the example below, many gaps are evident in the distribution of commercial bromopyridines (ACD) because many of these compounds share similar properties and cluster together. The Focus Gap Fillers have been designed to occupy the gaps, so that their FISA and WPSA values differ by at least 10 angstom squared units from any bromopyridine available from another vendor. Inclusion of Focus Gap Filler building blocks will therefore significantly enhance the diversity of combinatorial libraries derived from bromoarenes. Click here to view structures, prices and availability for Cheminformatic Gap Filler building blocks.
References for cheminformatic gap fillers:
ACD: abbreviation for Available Chemicals Directory (a product of MDL Information Systems).
Wessel MD, Jurs PC, Tolan JW, Muskal SM, J Chem Inf Comput Sci. 1998 V38(4): pp726-35
Votano JR, Parham M, Hall LH, Kier LB. Mol Divers. 2004 V8: pp379-91
Many of the synthons and building blocks offered by Focus Synthesis are so unusual that their synthetic chemistry as
precursors is not common knowledge. Beginning with isothiazole (FS000701), this section will briefly review synthetic
chemistry using a chemical structure schematic with literature references. Where applicable, biological activity will be
tabulated for selected end-products formed from Focus Synthesis precursors. These schematics are not meant to be at all
comprehensive, but will provide a representative sample of the organic and medicinal chemistry publications for products
formed from Focus Synthesis building blocks.
The chemistry of isothiazole (FS000701) is reviewed in the schematic below. Click here to see current pricing and availability for isothiazole.
The chemistry of 7-Bromo-benzo[b]thiophene (FS001166) is reviewed below. Click here to see current pricing and availability for 7-Bromo-benzo[b]thiophene.
Focus Synthesis now offers confidential building block design services to help meet your specific requirements for
diversity and property space coverage in medicinal and high-throughput chemistry. The synthetic intermediates made
through Synthon Design ServicesSM, known as SDS Building BlocksTM, will be substantially distinct
from commercially available building blocks. All rights to the molecules and their method of synthesis will be made
available to you, and your will be able to specify a period of exclusivity (no listing in the Focus Synthesis catalog)
ranging from 6 months to 6 years. Differentiation from commercial building blocks will be based on Rare and Unique
SubstructuresTM, ultrarare substructures (RubySynthonsTM), exotic heterocycles
(RubyScaffoldsTM), rare molecular graphs (RubyShapesTM), and Cheminformatic Gap FillersTM.
More detailed descriptions of the corresponding catalog products can be found on the
A more focused service, also requiring the protection of a nondisclosure agreement, would provide the most useful diversity by identify building blocks that are distinct relative to your corporate compound collection as well as commercial databases. SDS Building BlocksTM will be designed to meet other specifications that you define, such as PSA, ClogP, FW, EA, type of functionality, ring system, complexity, rule-of-five, etc.
Care will be taken to ensure synthetic accessibility. If warranted, in-house trial runs of key synthetic steps can be carried out in house on small (~100 mg) scales to better determine feasibility. In-house custom synthesis of larger quantities (up to 20 grams) by Focus Synthesis will be provided as an option. Part of the design cost will be discounted if you choose Focus Synthesis to synthesize the SDS blocksTM.
Focus Synthesis is chemical manufacturer and distributor with particular strength in synthons and building blocks with rare substructures and functional groups such as aryl bromides, boronic acids and boron pinacolates, (suitable for Suzuki coupling). Other strengths include functional groups such as aryl iodides and, terminal alkynes for Sonogashira coupling, alkoxyamines, and bromoketones. As a chemical manufacturer, Focus Synthesis is also carries distinctive heterocycles, including derivatives of azetidine, , pyridazine, and isothiazole. To improve your i.p position and explore uncharted regions of chemical space, purchase exotic heterocycles such as diazocane, thiadiazinane, oxazepane, oxa-aza-spirooctane, isothiazolo-pyridine, diaza-bicyclooctane, and thieno-pyridazine. Focus Synthesis carries unusual biological research tools such as kinase inhibitors, APIs, and other life science chemicals. Our in-house and outsourced custom organic synthesis services are detailed here.
All Focus Synthesis catalog items are > 95% pure unless otherwise indicated. Analysis will always include HNMR. Additional data (LC/MS, HPLC, GC, or mass spec,13CNMR, FNMR, IR, TLC, melting point) will be included when required. A COA, NMR data, and (when available) other spectroscopic and analytical data will be made available on request for all Focus Synthesis products currently or formerly in stock.
As of June, 2010, customers can buy chemicals from over 800 chemicals in stock, mostly building blocks and synthons.
More than 290 of these stock items are the high-value synthons containing Rare and Unique Substructures®.
As a chemical distributor, Focus Synthesis emphasizes distinctiveness and drugability over number of different products
because our main goal is to help pharmaceutical and biotechnology companies find the right molecule and design better
drugs. Stock availability ranges from 10mg to 1000 grams.
Many Focus Synthesis building blocks can be scaled up to multikilogram quantities on request--Focus Synthesis has filled
orders as large as 225 kilograms.
Click on the following links for overviews concerning these Focus building block product lines: Rare and Unique Substructure Classes, "Rule of Three" Building Blocks, and Cheminformatic Gap Fillers.
Focus Synthesis is particularly strong in the following areas: 1)Suzuki reaction substrates (boronic acids and aryl bromides), 2) Derivatives of isothiazole, azetidine, pyridine, pyridazine, and numerous exotic heterocycles. 3) Alkoxyamines, bromoketones, sulfonyl chlorides, difluoromethyl and difluroethyl molecules, and (4) molecules with unusual regiochemistry, such as 6-Bromo-benzo[b]thiophene (FS002042), 8-Bromo-imidazo[1,2-a]pyridine (FS000684), 6-Bromoisoquinoline (FS002008), and 6-Bromoquinazoline (FS002067). These intermediates provide combinatorial and medicinal chemists with precursors for highly diverse libraries and compound collections containing numerous patentable scaffolds and exhibiting superior property space coverage. These molecule types are represented in the Featured Molecule online catalog.
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