Skeletal diversity construction via a branching synthetic strategy

Article abstract of DOI:10.1039/b607710b

A branching synthetic strategy was used to efficiently generate structurally diverse scaffolds, which span a broad area of chemical descriptor space, and their biological activity against MRSA was demonstrated. The Royal Society of Chemistry 2006.

Full text of DOI:10.1039/b607710b

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Skeletal diversity construction via a branching synthetic strategy{{
Emma E. Wyatt,a Suzanne Fergus,a Warren R. J. D. Galloway,a Andreas Bender,a David J. Fox,a
Alleyn T. Plowright,b Alan S. Jessiman,c Martin Welchd and David R. Spring*a
Received (in Cambridge, UK) 1st June 2006, Accepted 28th June 2006
First published as an Advance Article on the web 10th July 2006
DOI: 10.1039/b607710b
esters. The diversity of scaffold-forming reactions possible with
diazoacetates leads to skeletally-diverse products. Secondly,
polyfluorocarbon tag technology enables solution phase combi-
natorial synthesis with the generic purification of product from
reagents by fluorous solid-phase extraction (SPE), reverse fluorous
SPE or liquid–liquid extraction.8 A reliable, multigram scale
synthesis of the diazoacetate (1) was achieved and the product was
stable to chromatography and could be stored for months without
significant decomposition.
A branching synthetic strategy was used to efficiently generate
structurally diverse scaffolds, which span a broad area of
chemical descriptor space, and their biological activity against
MRSA was demonstrated.
Small molecule modulation of protein gene products (chemical
genetics) is a powerful approach for the study of biological
systems,1 and is complementary to nucleic acid based approaches
(such as siRNA) that target the gene locus or mRNA. In order to
find a selective small molecule modulator of any protein function a
structurally diverse compound collection is required. Natural
products are structurally diverse;2 however, there are many
disadvantages with using extracts in chemical genetic experiments
(e.g. limited availability, bioactive constituent identification, and
complex analogue synthesis). These problems have led to a
complementary approach of synthesizing structurally diverse small
molecules directly and efficiently, an approach known as diversity-
oriented synthesis (DOS).3 Whereas compound collections of a
common scaffold decorated with diverse building blocks have been
synthesized efficiently,4 there are limited examples of the synthesis
of small molecules with a high degree of skeletal diversity.5 Nature
synthesizes many diverse molecular frameworks using a divergent
synthetic strategy from the basic ‘two-carbon’ starting unit acetyl
CoA (Fig. 1).6 Herein, we report the use of a fluorous-tagged
diazoacetate (1) as a basic ‘two-carbon’ starting unit in divergent
reaction pathways to synthesize drug-like and natural product-like
compounds in just 2–4 synthetic steps.
In the first step of the diversity-oriented synthesis, 1 was
exploited in three general divergent reaction pathways: (i) three-
membered ring formation (shown in Scheme 1); (ii) 1,3-dipolar
cycloadditions (b and d, Scheme 2); and (iii) a-deprotonation and
subsequent quenching with an electrophile and carbenoid forma-
tion (c, Scheme 2). The second steps of the synthesis involve
complexity-generating reactions to diversify the molecular frame-
works further. For example, as illustrated in Scheme 1, step 1
involved cyclopropanation of benzene to give cycloheptatriene 3,
via 2.9 Treatment of 3 with primary amines gives ecgonine
analogues (5, cf. cocaine scaffold);10 alternatively, heating 3 with
dienophiles forms polycarbocyclic adducts (6). Alkynes react with
1 to yield cyclopropenes 4, which were rearranged to furans (not
shown) or used as dienophiles to give cis-fused [4.1.0] ring
systems (7) with cyclopentadiene.7 Further divergent reaction
pathways included: uncatalyzed 1,3-dipolar cycloadditions with
electron-deficient alkenes to give 2-pyrazolines (b, Scheme 2),
The fluorous-tagged diazoacetate (1) was identified as an
attractive DOS starting unit for two key reasons. Firstly, the
reactive diazo functionality permits a wide range of complexity-
generating, C–C bond-forming reactions,7 which can be used to
generate a wide range of scaffolds with versatile functionality that
can be diversified further. The diazoacetate functionality can be
nucleophilic and/or electrophilic under controllable conditions
allowing ultimate mechanistic flexibility. This versatility makes
diazoacetate 1 a more powerful starting unit than simple acetate
aDepartment of Chemistry, University of Cambridge, Lensfield Road,
Cambridge, UK CB2 1EW. E-mail: drspring@ch.cam.ac.uk;
Fax: +44 (0)1223-336362; Tel: +44 (0)1223-336498
bAstraZeneca, Cardiovascular and Gastro-Intestinal Research Area,
Alderley Park, Cheshire, UK
cPfizer Global Research & Development, Discovery Chemistry,
Sandwich, Kent, UK
Fig. 1 The biosynthesis of many natural products originates from the
‘two-carbon’ starting unit acetyl CoA in divergent biosynthetic pathways.
In our complementary diversity-oriented synthesis approach the fluorous-
tagged a-diazoacetate ‘two-carbon’ unit 1 was used in divergent reaction
pathways to yield drug-like and natural product-like small molecules.
Coenzyme A and the fluorous tag act as handles with which the synthetic
units can be manipulated.6
dDepartment of Biochemistry, University of Cambridge, Downing Site,
Cambridge, UK CB2 1QW
{ Electronic supplementary information (ESI) available: Full experimental
details, characterization and spectra of key compounds. See DOI: 10.1039/
b607710b
{ The HTML version of this article has been enhanced with colour
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3296 | Chem. Commun., 2006, 3296–3298
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223 small molecules that have 30 discrete molecular frameworks
among other unique structural features. The library was made
using parallel synthetic techniques leading to 2–15 mg of each final
product (molecular weight range 140–614). All library members
were assessed for their identity and quality, and purified if
necessary by recrystallization, chromatography or extraction to
ensure . 90% purity of final products (1H NMR, HPLC and
LCMS).13 Full characterization of 20 demonstration compounds
representing each divergent reaction pathway was also undertaken.
In order to assess the degree of overall diversity obtained in our
diversity-oriented synthesis we compared the diversity of our
library to the chemical space spanned by ‘benchmark collections’:
(1) known pharmacologically active small molecules (MDL Drug
Data Report database)14 and (2) a focused library (conventional
combinatorial chemistry).15 A visual representation of the diversity
of the collections in ‘chemical space’ is depicted in Fig. 2.
Scheme 1 Example of diversity-oriented synthesis with fluorous-tagged
diazoacetate (1). (a) C6H6, Rh2(O2CCF3)4, 70%; (b) RCCH, Rh2(OAc)4,
[BuCCH, 57%]; (c) RNH2, NaOH then MeOH, H2SO4, [MeNH2, 35%];
(d) dienophile [dimethyl acetylenedicarboxylate, 59%]; (e) C5H6, 92%.
Perhaps the biggest challenge for synthetic chemists involved in
diversity-oriented synthesis is to achieve efficiently, high levels of
skeletal diversity and complexity in order to explore biologically-
relevant regions of chemical space. We have presented a new
strategy of starting from a fluorous-tagged ‘two-carbon’ (diazo-
acetate) unit and using divergent, complexity-generating reaction
pathways to create maximum skeletal diversity in final products. A
library of 223 small molecules was synthesized, which have
30 distinct molecular frameworks. Significantly, the physico-
chemical and topological diversity of the compounds synthesized
compared favourably with databases of known drugs, which
include pharmacologically active synthetic small molecules and
natural products. Phenotypic screening experiments showed that a
high number of the compounds, with diverse scaffolds, modulate
the growth of pathogenic strains of methicillin resistant
Staphylococcus aureus (MRSA).16 We will provide a full account
of our screening experiments and the discovery of new antibacter-
ials with novel modes of action in due course.
three-component ylide-mediated cycloadditions to form 2,5-trans-
substituted pyrrolidines (d, Scheme 2),11 and 1,3-keto ester
formation (8 and 9; c, Scheme 2).7 The b-dicarbonyl compounds
were exploited to generate diverse heterocyclic products, such as
coumarins and amino pyrimidinones. A wide range of naturally-
occurring and synthetic coumarins and pyrimidine derivatives are
known to be pharmacologically active, such as the anticoagulant
warfarin and batzelladine alkaloids. These molecular frameworks
are considered to be privileged scaffolds and are therefore desirable
to include in a structurally diverse compound collection for use in
chemical genetic screens. The dihydropyrimidine derivatives were
further modified by reaction with a range of 3-formylchromones to
form unusual pyrimido[1,2-a]pyrimidines.12 Fluorous-tagged ester
products were varied divergently by ester hydrolysis, transester-
ification, ester reduction and transamidation; thereby, both
carbons of the ‘two-carbon’ starting unit were diversified
structurally.
We gratefully acknowledge financial support from EPSRC,
AstraZeneca (E.E.W.), Pfizer (W.R.J.D.G.), Gates Cambridge
The divergent chemistry of the fluorous-tagged diazoacetate
described above was exploited in the diversity-oriented synthesis of
Scheme 2 Divergent reaction pathways lead to skeletal diversity. (a) Rh2(OAc)4, furan, then I2, 60% (91%). (b) DMAD, 84% (88%). (c) LDA, RCOR9,
then Rh2(OAc)4; 8: 49% (90%); 9: 68% (97%). (d) PhCHO, PhNH2, then DMAD, Rh2(OAc)4, d.r. 5 20 : 1, 51% (80%). (e) Guanidine carbonate 62%
(96%). (f) Resorcinol, H2SO4, 74% (95%). (g) NH2OH, 77% (89%). (h) Thiophene-2-carboxaldehyde, guanidine carbonate, then 3-formylchromone, 43%
(98%). Yields and purity (in brackets) of the product example following generic purification using (reverse) fluorous SPE or precipitation shown. Purity
1
determined by HPLC, LCMS or H NMR. DMAD 5 dimethyl acetylenedicarboxylate.
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Fig. 2 Visual representation of the diversity of different chemical
collections in physicochemical and topological space using MOE
descriptors followed by principal component analysis (PCA). The DOS
library synthesized in this paper is depicted in small diamonds. For
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Repository (small grey dots) are depicted. Library diversity can be
described as the standard deviation of properties in this PCA space,
normalized to a per-compound-basis. Normalization to give a value of
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products were not of sufficient purity, and were therefore purified
further.
Trust (A.B.) and BBSRC. We also acknowledge the EPSRC
National Mass Spectrometry Service Centre, Swansea, for
providing mass spectrometric data.
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16 Staphylococcus aureus strain MRSA-15 (common pathogenic strain in
UK hospitals) were used for inhibition of proliferation phenotypic
experiments. Compounds modulated growth over a range of concentra-
tions: 100 mM concentration (29%), 50 mM (6%), 25 mM (4%), 10 mM
(2%). The most active compounds were found to have Minimal
Inhibitory Concentrations (MIC) of 3.56 and 6.05 mg/ml.
3298 | Chem. Commun., 2006, 3296–3298
This journal is ß The Royal Society of Chemistry 2006