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Opportunities for New Chemical Libraries Unnatural Biopolymers and Diversomers.

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Opportunities for New Chemical Libraries : Unnatural Biopolymers and
Rob M. J. Liskamp*
The solid-phase methodology for the synthesis of biopolymers is nowadays indispensable in chemistry. pharmacology,
immunology, physiology. biology, and biophysics. Using this
fantastic tool,"] it is not only possible to prepare (large) peptides
in a (semi)autoniatic manner in which amino acids and other
reagents are added, and excess of reagents and waste are removed (without the tedious purification of intermediates), but
this methodology has also been successfully applied to the synthesis of nucleic acids and recently carbohydrates.['. 31 Once developed the next logical step was the adaptation of the efficient
solid-phase methodology to the sinnrltmneous synthesis of . ~ e i w ( i / peptidcs. This led to the development of several multiple
peptide synthesis strategies with a large range of
A significant step further are the peptide libraries. for example,
aimed ;it the systematic synthesis of many -if not all- possible
peptides of a certain length. When each amino acid residue is
one ofthe 20 proteinogenic L-amino acids, there are 400 possible
dipeptidcs. 8000 possible tripeptides etc. in a library: with each
amino ncid increment the number of peptidcs increases 20-fold.
HoweLer. there will be intrinsic difficulties in preparing and
handling such large libraries.'"' in addition to difficulties in identification. selection. and enrichment of promising compounds
from ;I library. I n order to facilitate identification and enrichment, encoded libraries might be very interesting. In one particular promising type of these libraries a chemically synthesized
entity. for example a peptide, is linked to a particular oligonucleotide sequence. It is proposed that the use of the encoding
genetic tag should serve to identify and to enrich the promising
compounds from the library.".
Peptide libraries are undeniably useful in the discovery of chemical lead compounds. However. the chemical lead discoveries from these libraries still require extensive modifications before suitable drug candidates
are produced. This is due to the disadvantages of peptides, such
as their water solubility and in many cases their facile degradation by proteases. which limit their use in biological systems.
Therefore the results described by Cho et al. and Hobbs DeWitt
et al. are the next significant steps on the way to new librarie5.l'.
which first may-to a certain extent-circumvent
Dr. R M . I. Liskamp
Utrcchl In\titute for Pharmaceutical Sciences
Departiiicnt of Pharmaceutics, Section Orpanic and
Medicinal Chemistry. Utrecht University
P . 0 BOA800x2. NL-350X TB Utrecht (The Netherlands)
TcIda\. Int. code + (303516674
these disadvantages. second provide lead compounds. possibly
requiring less extensive modifications, and third may provide
new frameworks for generating macromolecules with novel
Cho et al. described the principles of the solid-phase synthesis
of an ohgocarbamate as well as the generation of an oligocarbamate library.['] This oligocarbaniate was referred to as "an unnatural biopolyiner".''] "unnatural" because it is obviously not
found in nature and "biopolymer" to hint at the origin of the
monomers which were derived from proteinogenic amino acids.
The term "biopolymer mimetic" is perhaps a better alternative,
as "unnatural biopolymer" is a contradiction in itself. The
monomeric, N-protected aminoalkylcarbonates were conveniently prepared from the corresponding N-protected amino
acids or from amino alcohols derived from amino acids
(Scheme 1). By using the base-labile Fmoc-protecting group, an
oligocarbamate was synthesized by standard solid-phase niethods; the coupling yields were greater than 99% per step. Even
more interesting was the use of the photolabile nitroveratryloxycarbonyl (Nvoc) amino-protecting group (Scheme 1). This enabled the authors to prepare a library containing 256 oligocarbamates, by employing a binary masking strategy as was
described by Fodor et al. in their light-directed parallel synthesis
The liof libraries of oligopeptides and
brary contains all of the compounds that can be formed by
deleting one or more carbamate units from the parent sequence
Ac-Tyr'-Phe"-Ah'-Sere-Lys'-He"-Phe'-Leu"(the superscript "c"
indicates the presence of a carbamate linkage). The library was
attached to a glass surface of approximately 1.3 cm by 1.3 cm
and screened for its ability to bind a monoclonal antibody
against Ac-Tyr'-Lys'-Phe"-Leu'. It was found that the oligocarbamates Ac-Lys'-Phe"-Leu"-GIy-OH (Gly is the linker in the
keyhole limpet hemocyanin conjugate of this oligocarbamate),
Ac-Phe'-Lys"-Phe'-Leu'-Gly-OH, Ac-Tyr'-Lys'-Phe'-Leu"-GlyOH. Ac-Ah'-Lys"-Phe'-Leu"-Gly-OH, and Ac-1le"-Phe'-Leu"Gly-OH were among the ten highest affinity ligands based on
fluorescence intensities. Competitive enzyme-linked immunosorbent assay experiments in solution using the free oligocarbamates resulted in Ic,, values between 60 and 180 nM. It was
therefore suggested that the dominant epitope of the antibody
was Phe'-Leu'. Although, Ac-Tyr'-Phe'-Leu'-Gly-OH containing this epitope did bind in solution with an IC,, value of about
160 nM, the fluorescence signal associated with this oligocarbamate on the solid support, that is the glass surt'ace in the library.
ranked in the bottom 30%. This suggests that the conformation
of the oligocarbamate on the solid support may be different
from that in solution. This problem certainly has to be addressed in the future before a general application of the use of
libraries can be recommended for affinity studies.” ‘ I
compounds (comparable to an in-house sample collection of a
pharmaceutical company), which can be offered to the often
automated, fast high throughput biological screening assays.
In contrast to the well-known procedure in which
polyethylene rods or pins were used as a solid support for mul-
Amino acid
Amino alcohol
PG: Frnoc
R’ = CH$H(CH&
R‘ = Bn
R3 = (CHz),-NH,
one of 256
i Pr, 3-Melnd
R4 = a.0. Ph, Chx
R~ = a.0. H, CI, NO,
array of 40
Scheme 1. Solid-phase synthesis of oligocarbamates and benzodiazepines starting with a resin-bound amino acid. The Fmoc-protected 4-nitrophenyl carbonate monomers derived from ;mino acids or amino alcohols were used in a normal solid-phase synthesis of an oligocarbamate. whereas the corresponding
Nvoc-protected monomers were used in the generation of a library of 256 oligocarbamates of which one representative (Ac-Lys’-Phe‘-Leu‘-Gly-OH) is shown.
An array of 40 diarepines uas synthesized by reacting the resin-hound amino acid hith eight different 2-aminohenzophenone imines followed by cycliration.
Ind = indolyl. Chx = cyclohexyl.
Although the oligocarbamate differs significantly from the
corresponding polypeptide, for example, it is more extended
(that is there are four atoms located between the side chains
instead of two atoms as in a peptide), some inherent disadvantages of peptides seem to be less pronounced in oligocarbamates: a) the oligocarbamates are significantly more hydrophobic, as was determined from a comparison of the water/octanol
partitioning coefficients; b) the oligocarbamates are resistant to
degradation by trypsin and pepsin.
Contrary to the Berkeley and Affymax report, the diversomer
paper by Hobbs De Witt et al. placed no emphasis on the preparation of an oligomer library but focussed entirely on the generation of a library of diverse, albeit related, organic compounds
called “diversomers”.[*]An important reason for the creation of
these libraries is to discover lead compounds, which will be
structurally more related to the ultimate drug. since lead compounds discovered from peptide or nucleotide libraries still require extensive modifications (vide supra). Another equally important reason is to rapidly obtain a large library of organic
tiple peptide synthesis in the “PEPSCAN” method,C4,l 2 I hollow
pins, ending in a glass frit were used, each containing approximately 100 mg resin to which a Fmoc amino acid was attached
by a linker. The removal of the Fmoc-group from eight amino
acid resins and treatment of each resin with five different isocyanates followed by cyclization led to 39 of the 40 desired
hydantoins in 4-81 YOyield. Similarly, by starting from Bocprotected amino acid Merrifield resins (five), 40 different benzodiazepines were synthesized by reacting with eight different
2-aminobenzophenone imines followed by cyclization
(Scheme 1 ) . The 40 products were obtained in 9-63 % yield and
their purity was typically >90 % (determined by ‘H NMR spectroscopy). These compounds were then used in an assay for
inhibition of fluoronitrazepam. A report by Bunin and Ellman
had earlier described the solid-phase synthesis of ten benzodiazepine derivatives using an alternative approach.“ 31
An important message from the reports is that the authors are
able by carrying out synthesis on a solid support-to prepare
an array of unnatural compounds, which can be used for screen-
ing purposes to discover new lead compounds. These lead compounds m a y then be closer to ultimate drugs, because they are
obtained from an array of compounds further removed from
naturd systems such as peptides and nucleotides.
Using the solid-phase strategy also libraries of other biopolymer miinetics may become accessible, for example. oligoureas,
oligosulfonex, peptid~sulfonamides,['~]
peptidophosphoramidates, and peptoids (Scheme 2).r1s1These compounds will undoubtedly provide new biologically active compounds and also
opportunities for the construction of biopolymers with novel
tance of creating library compounds with defined conformations that are similar if not identical in different environments.
The scientist has an innate desire to be able to rclfio/?d/L'
design a compound with a predicted (biological) activity. c'omputer-assisted molecular modeling techniques, X-ray crystallographic analysis, and N M R methods have intensified this desire
and the belief that this should ultimately be possible for all
drugs. Nevertheless, many of the current drugs or at least the
lead coinpounds which initiated their development have been
obtained by screening approaches. that is, by an "irrtitimncil"
approach. Although it is expected that the rational design of
R4 0 0
Scheme Z A peptide [ 1 ) . the correspondins oligocai-bamate (2). oligoureas (3 and 4). pepioid (5).I7eptrdosiilfonainide (6). and oligosulfone (7)
The diversomer library shows that an array of organic compounds can be synthesized. and. although the number is much
smaller than that which can be achieved by most of the current
methods for generating peptide libraries, a significant number of
structural analogues can be obtained in a faster way than is the
case when each of the compounds is synthesized separately.
Furthermore, it should be possible to adapt the method to many
more organic reactions, so that it is likely that a number of
diversomcr libraries will be appear in the near future.
Another challenge is the development of "conformationally
restricted" libraries in which the conformation of iiii oligomer is
more ;iccurately defined, for example, by introducing rigid
monomers at different locations in an oligomer. This is noteworth). since there is ample evidence in the literature that in
inany cases merely the presence of functional groups delivered,
for example, by an amino acid sequence is not sufficient for an
optimal biological activity, but that a proper orientation of
functional groups is essential too.1161In addition, the conformation on the solid support o f the library may be different from
that in solution (vide supra), which may diminish the reliability
o f a library for the selection process. This underlines the impor-
drugs will become increasingly important. screening approaches
will gain more momentum too, since they will contribute to a
faster and more direct access to information. Therefore the rational design of irrational screening procedures holds promises
for the future, and as a result there will be plenty of opportunities for the creation and applications o f new libraries."
German vcrsion: A q q w . C h o ~1994.
1116. 661
[ I ] R . B. Merrifield. J.
h i . C h 7 7 . Soc . 1963. 85. 2149. A y r u ( ' i i l ~ 7 l . 1985. 97,
801 ; . A n p w C ' h c i n I n / . W E17fi/. 1985. 24. 799.
121 For i i recent rcvieh: S. L. Beaucage. K. P. lyer, 7iwfrhi~.ih.ori1993, 48. 2223.
[i] R. Verduyn. P. A. M. van der Klein. M. Douwes. G. A van dcr M a d . J. H .
van Boom, R P ~Trui,.
U i i m PNI~(-Bu.\1993. 11-7. 464; S. J. Danishefsky. K . E
McClure. .I. 7. Randolph. R. B. Ruggeri, S ~ . i ~ z c1993.
260. 1307: S. P. Douglas. D. M. Whitfield. J. J. Krepinsky, J Am C ' / w v . Soc. 1991. 111. 5OY5. (i.
H. Veeneman. R. M. J. Liskainp, G. A. van drr Marcl, I. H. w n Boom,
7i./roherlrori Le// 1987, 28, 6695.
141 F o r a recent review on multiple peptide synthesis: G. Jung. A . G. BeckSickmger, Anficw Chciii. 1992. 104. 375; A n g i w Clierii. Iii1. €</,&/. 1992. .</.
[5] S. Brenner. R. A. Lerner. Pro<. .bur/.Acnrl. S c i L'SA 1992. 89. 53x1 ; 1. A m a h
S o c r i c . c 1992, -757. 330, J. Nielsen, S. Brenner. K . D. Janda, J. A m . C'hcwl. So<
1993. 115. 9812
[6] I n principle. it should also be possible to assign coding dements to compound?
othcr than peptides. for example. carbohydrates. Tor the identification of a
coinpound This would cxpand the possibilities for the crcation of new libraries.
171 C. Y Cho. E. J. Moran. S. R. Chci-I-).J. C Steplians. S. P A. Fodor. C.L.
Adams. .4 Sundaram, J. 6'.Jacobs. P. G. Schultz. Smww 1993. 261.
[8] S. Hobbs DeWilt. J. S. Kiely. C. J. Stankovic. M . C. Schrocder. D M Reynolds
Cody. M . R. Pa\ia. Pror.. .z'iiil. A < o d S < i .L S A 1993. 90. 6909.
[9] The anlisense oligonucleotides are a n earlier category of "uniiatiiral biopolyiners". A . Peyman. C/irw. Rcjr. 1990. YO. 543.
[lo] S . P. A. Fodor. J. L. Leightoii Read, M . C. Piri-imp. L. Strqer. A T Lu. D.
Solas. S&iiw 1991. 3.71. 767. a highlight \ + a s deboted to this topic: G. von
Kicdcrowksi. A q e w C h w . 1991. I(J3.X39: A i i g r b i . C i i o i z . I i i r . Ed. Ei?g/. 1991,
3(/. 822
[ 1 1 ] This is one the critic;d questions raised iii the highlight by von Kiederowski
[I?] H M. Gcysen. R. H. Meloen. S. J. Barteling. Pror. ?/a//.Amd. SU. CS.4 1984.
X I , 3998.
[13] B. A Bunin. J. A . Ellman. J Ant. Chrw Six. 1992. / I d . 10997.
[14] R. M. J. Liskamp. W J. Moree. unpublished results.
[15] Peptoids were recently highlighted by H. Kessler. . 4 r i , q v Chrrii. 1993. /(I.<,
572: Air,qcii.. C./ii,ifi. 1171. Ed. Efi,?/ 1993, 32. 543.
[I61 See for example the rccent review o n peptidoinimetics: A. Giannis. T. Kolter.
A i f , q r i i . C/wii?.1993, 105. 1303, A i i g e i i . C/zeiv I i i / . Ed. Eiigl. 1993. 32. 1144.
[17] A highlight was devoted to the "rationality of random screening":
Pluckthun, L. Ge. .3iigor. Chmii. 1991. 103. 301 ; .411,gri1.C h m . I n r . Ed Ennpl.
1991, .W, 296.
Construction of Carbon Frameworks with the Help of Ruthenium Complexes :
1,5-Cyclooctadiene as a Reagent in Transition Metal Catalyzed Reactions
Holger Butenschon"
A communication by B. M. Trost et al.['] which appeared last
year is one of several important papers that have been published
recently from the rapidly developing area of ruthenium -organic chemistry. 1.5-Cyclooctadiene (COD) is frequently used in
transition metal complexes as a bidentate. neutral ligand, which
can be removed again often under mild conditions with the
formation of free coordination sites. The perfect example of this
is bis( 1.5-cyclooctadiene)nickel(o) as a precursor of "naked
nickel". with which G . Wilke et al. carried out a large number
of important reactions and thus emphasized the special value of
organometallic chemistry for the synthesis of organic compounds at a very early stage.I2l It is noteworthy that there have
been very few reports on the reactions of COD at the metal
center despite its frequent use as a ligand. One such example is
the formation of the bicyclo[3.3.0]octadienylcobalt complex 1 from the reaction of
cobalt reagents with COD, as reported by
Lehmkuhl et al. as well as Otsuka et
Scheme 1. a ) 5 % [CpRu(COD)CI] (3). MeOH: R' = Me. Et. CH,OSi(iPr),.
H: R' = CH,OH. CH,OSi(iPr),. C H 2 C H 2 0 H . />CH,C,H,OCH,. CO,Me. CH,CH2CH,C0,Me. 78-100% (see text)
ficient alkynes react particularly slowly and no reaction takes
place with dimethyl butynedioate. Steric hindrance slows down
the reaction; 5 is obtained only in 51 YO(98 % brsm) after 80 h
at reflux. This can. however. be used for the differentiation of
triple bonds in alkynes with several triple bonds, as shown by
the selective formation of 6 in 63 % (72% brsm, Scheme 2).
The relatively narrow spectrum of the
organic chemistry of COD has been considerably extended by B. M. Trost et a1."'
who discovered that COD can formally function a s a bis-homodiene in metal-catalyzed [4 + 2]cycloadditions. A 0.1 M solution
of the alkyne 2 reacts with 1.1 equivalents of COD in the presence of 5 mol Yo chloro(q"-cycl~octadiene)(~~~-cyclopentadi- The catalytic cycle proposed by the authors starts from a
enyl)rutheniuni(ii) [CpRu(COD)CI] (3)["]in boiling methanol to
cationic cyclopentadienylruthenium complex. bearing one C O D
give derivatives 4 of tricyclo['. 'Idec-7-ene (Scheme 1 ) .
ligand and one solvent molecule. The latter is displaced by the
Yields of between 78 and 100% are achieved in seven out of
alkyne, which subsequently reacts with a double bond of the
eight examples, in the other case the yield is only 22 YO(however,
COD ligand to give a metallacyclopentene. An intramolecular
as the authors note, this is in fact "65X0 yield brsm". where brsm
carbometalation of the remaining double bond of the eightstands for "based on recovered starting material"). Electron-demembered ring with successive reductive elimination leads to
the elimination of the products 4; renewed complexation of a
[*I Prof. Dr. H Butenrchdn
COD molecule regenerates the catalytically active species. The
lnstitu[ fur Orgmische Chemie der Universitit
authors point out that the reaction is also catalyzed by other
Schneiderberp 1B. D-30167 Hannobcr (FRG)
coordinatively highly unsaturated ruthenium complexes and fiT e l e f n Int. code + (511)762-.30lI
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chemical, opportunities, diversomers, libraries, unnatural, biopolymers, new
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