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Biotechnology Advances xx (2005) xxx – xxx

www.elsevier.com/locate/biotechadv

Advances and applications of de novo designed

affinity ligands in proteomics
A. Cecı́lia A. Roque, Christopher R. Lowe*
Institute of Biotechnology, University of Cambridge, Tennis Court Road, CB2 1QT, Cambridge, UK
Received 29 April 2005; accepted 9 May 2005

Abstract

Affinity chromatography represents a promising technique for decoding the proteomics universe.
While conventional affinity purification is being used in conjunction with two-dimensional
electrophoresis (2D-PAGE) and mass spectrometry (MS) for the study of proteomes and
subproteomes, scientists are still confronted with the need for specific and tailor-made affinity
ligands to target desired groups and families of proteins. Evidence has shown that, in many
situations, synthetic affinity ligands can circumvent inconveniences associated with the utilisation of
biological ligands for the chromatography-based purification of biomolecules. This review will
highlight the potential applications of affinity chromatography and synthetic de novo designed
ligands as separation tools for proteomics.
D 2005 Elsevier Inc. All rights reserved.

Keywords: Affinity chromatography; Synthetic ligands; Biomimetics; Proteomics

1. Introduction

The availability of complete genome sequences of many eukaryotic and prokaryotic

organisms builds enthusiasm and challenges to biological researchers who wish to

* Corresponding author. Tel.: +44 1223 334157; fax: +44 1223 334162.
E-mail address: crl1@biotech.cam.ac.uk (C.R. Lowe).

0734-9750/$ - see front matter D 2005 Elsevier Inc. All rights reserved.
doi:10.1016/j.biotechadv.2005.05.001

JBA-05983; No of Pages 14
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2 A.C.A. Roque, C.R. Lowe / Biotechnology Advances xx (2005) xxx–xxx

unravel the secrets of the gene products, the proteins. The equivalence between genes
and the proteins they code for is generally a non-straightforward process, not only
because many post-transcriptional and post-translational modifications take place,
but many cellular regulation mechanisms also control the expression of genes.
Proteomics can be defined as the analysis of part or all of the protein complements of
a complex biological system at any given moment in time and it includes the
characterization and quantitation of protein expression, function and structure (Shi et
al., 2004). Proteome analysis requires techniques that could provide high throughput,
high sensitivity and resolution, as well as the possibility of quantifying and identifying
PTM (post-translational modifications) in proteins. Conventional experimental techni-
ques used in proteomics include two-dimensional electrophoresis (2D-PAGE) and mass
spectrometry (MS).
Two-dimensional electrophoresis is widely used for the separation and quantitation of
thousands of intact proteins in a single run. It also presents the possibility of applying
labelling techniques for the detection of PTM and comparative protein expression in
selected cell populations. It is therefore possible to use general protein detection
reagents for a holistic approach (organic dyes, silver stain, radiolabelling and fluorescent
stains, amongst others) and specific detection methods to reveal the status of proteins,
such as the level of phosphorylation (e.g. autoradiography 32P and 33P), glycosylation
(e.g. dansyl hydrazine), proteolytic modifications (e.g. zymographic assays for serine
proteases), S-nitrosylation (e.g. Biotin Switch method), arginine methylation (e.g.
immunoblotting) and ADP-ribosylation (e.g. 1,6-etheno NAD+) (Patton, 2002). Another
option employs recombinant-DNA strategies to couple affinity tags or reporter enzymes
to proteins and this approach has proven useful both at the detection and purification
levels. Examples of these affinity tags include the FLAG and oligohistidine peptides,
the green fluorescent protein and the enzyme h-glucuronidase. Differential display
proteomics is based on the comparison of different protein profiles — examples of this
approach using gel electrophoresis are difference gel-electrophoresis (DIGE) and
multiplexed proteomics (MP). Isotope-encoded affinity tagging is another powerful
strategy that combines affinity chromatography, gel electrophoresis and peptide mass
profiling by MS (Patton, 2002). Despite the developments achieved in 2D-PAGE, there
are still major technical disadvantages such as: poor reproducibility, difficult detection
of extremely acidic or basic proteins (pI b 3.5 and N9.5), hydrophobic or membrane-
located proteins, as well as proteins with extreme range of molecular weights, and
limitations on the amount of proteins that can be loaded and deficient detection of low
abundance proteins.
Mass spectrometry-based matrix-assisted laser desorption/ionization (MALDI) and
electrospray ionization (ESI) have been the most popular MS methodologies used for
protein and peptide identification in proteomics (Newton et al., 2004). Other strategies
have included, for example, quadrupole ion-trap (LCQ) and Fourier transform ion
cyclotron resonance (FTICR). MS-based techniques for the separation and sequencing of
peptides are usually a bbottom-upQ approach, complementary to upstream electrophoretic
or chromatographic methods (for the separation of intact proteins) and digestion of
proteins to smaller peptide fragments (Jensen, 2004). This bbottom-upQ tactic to
proteomics has proved highly flexible and versatile. Intact-protein btop-downQ
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approaches, where individual proteins are selected for MS analysis without any previous
chemical or enzymatic proteolysis, have also been used in some situations as a means to
complement peptide-level measurements with more information on the protein
modification state. However, not all intact proteins are amenable to this btop-downQ
methodology mainly due to intrinsic factors related with low solubility and molecular
weight (Jacobs et al., 2005, Loo et al., 2005, Fountoulakis and Vlahou, 2005).

2. Affinity chromatography in proteomics

Liquid chromatography is already considered an indispensable tool in proteomics by

allowing the separation of macromolecules by different properties (Shi et al., 2004). The
type of interactions and techniques explored may include reverse-phase, ion exchange,
size-exclusion, and hydrophobic or affinity chromatography.
The affinity concept relies on specific, reversible and non-covalent interactions
between two biological entities forming a complex. Affinity technology exploits these
natural specific recognition phenomena and the predictive and rational character of the
binding between the proteins to purify and the complementary ligand. Association
constants between the ligand and the protein in the range 103–108 (M 1) are normally
the most suitable for purification purposes (Janson, 1984). As this binding is highly
specific, the use of affinity purification reduces non-specific interactions, increases
operational yields and facilitates the elimination of undesirable contaminants. The
adsorption is efficient even from diluted crude extracts, which makes possible a one-step
purification of the target proteins. Therefore, affinity chromatography, in particular,
represents an appealing option to complement proteomics analysis, not only by
separating target proteins based on their specific interaction with immobilized ligands
but also by allowing the identification of protein–protein interactions that can allow the
function or activity of the proteins to be inferred.
Whilst the first protein to be purified by affinity chromatography was a-amylase
(1910) by adsorption onto insoluble starch, the term baffinity chromatographyQ was
coined in 1968 by Cuatrecasas. Since then, affinity chromatography has matured as a
technique with acknowledged contributions in small and preparative-scale, as well as in
large-scale purification of biomolecules, and has also suffered major refinements in
order to comply with exigencies from regulatory agencies (Lowe, 2001; Roque et al.,
2004a). The type of affinity ligand utilised has also evolved substantially: Group-
specific adsorbents, such as coenzymes, lectins, boronates and nucleic acids, were the
first to be used as affinity ligands in the early 1970s, whilst textile dyes became
popular in the late 1970s–1980s and inspired the introduction of designer dyes or
biomimetic textile dyes (Lowe et al., 1992) and, later, the evolution into de novo
designed ligands (Lowe et al., 2001). In these terms, affinity chromatography has
actually been used in its more general sense of battractionQ: Not only the natural ligand
involved in a biological interaction with the target protein is considered but also
unnatural ligands that interact with protein’s binding site by non-biospecific
interactions. The first group of ligands is referred to as bbiospecific ligandsQ, whereas
the second group of ligands is termed bpseudobiospecific ligandsQ (Fig. 1).
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Fig. 1. Classification of affinity ligands for the purification of proteins by affinity chromatography. Biospecific
ligands are naturally occurring molecules with affinity for the target protein-binding site. Pseudobiospecific
ligands can be biological or non-biological molecules that interact with the target protein but do not occur
naturally in the biological systems. Biomimetic ligands are a new class of pseudobiospecific ligands that are
tailor-made to a specific target protein in order to increase specificity and the overall operational performance of
the affinity adsorbents. HCIC — hydrophobic charge induction chromatography; IMAC — immobilized metal
affinity chromatography.

Pseudobiospecific ligands may be synthetic (dyes) or biological (peptides, oligonucle-

otide aptamers) and some belong to the youngest class of biomimetic ligands. These
ligands are tailor-made molecules that mimic the natural biological recognition between
a target protein and a natural ligand. Biospecific ligand affinity chromatography has
some inherent drawbacks that are difficult to overcome. The ligand has to be produced,
usually at high cost, and biases its full characterization. On the other hand, the
coupling yield is often low and the immobilization may modify the ligand. There is
also a high probability of ligand leaching during harsh elution steps (Lowe, 2001). The
drawbacks of pseudobiospecific affinity chromatography can be more easily
surmounted, but they are dependent on the biological or synthetic source of the
ligand. Still, combinatorial methods allied with molecular modelling and genetic
engineering have contributed enormously to the development of highly resistant
pseudobiospecific ligands.
Affinity chromatography can be utilised in different stages of a proteomics analysis
(Lee and Lee, 2004). A general scheme of the possible strategies to incorporate
affinity chromatography in proteomics is depicted in Fig. 2. Affinity chromatography
can be utilised as a depletion method, where certain proteins or a specific group of
proteins, especially if present in high concentrations, can be removed to enhance the
probability to visualize low abundance proteins in 2D-PAGE gels. This method can be
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Fig. 2. Affinity chromatography and its possible applications in proteomic analysis.

problematic by diluting the sample during the washing step and also by losing low-
abundance proteins if they present affinity for the immobilized ligands. Another option
is the concentration/extraction method, where affinity chromatography can be helpful
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in the isolation of a small group of proteins before proceeding to analysis by 2D-

PAGE or by MS after proteolytic digestion. The concentration mode proves
particularly useful for increasing the amount of low-abundance proteins or for the
study of subproteomes. In the latter case, analysis of the phosphoproteome, for
example, can be accomplished by immunoaffinity chromatography or by IMAC
(Kalume et al., 2003) as these steps help in the enrichment of both phosphorylated
proteins and peptides. Some comment should be made on the fact that multiple affinity
columns might be required since only a single-protein or group of proteins can be
enriched at any time when employing affinity chromatography. In general, when
affinity chromatography is positioned prior to 2D-PAGE to separate proteins, the
affinity ligands immobilized are a specific antigen, group-specific adsorbents (e.g.
lectin to capture glycoproteins) or IMAC-ligands. When affinity chromatography is
placed after enzyme digestion and peptides are being separated, then it is more
common additionally to exploit ligands related to previous peptide chemical
modifications (Jensen, 2004; Roque and Lowe, in press). In a more general approach,
proteins and peptides can be modified or tagged to facilitate downstream separation
(Scheich et al., 2003; Jensen, 2004).

3. Rational design in affinity chromatography

The concept of the bbiomimeticQ ligand was initially introduced as an upgrade of

textile dyes, i.e.bdyestuffsQ designed to better mimic the structure and binding of
natural biological ligands (Lowe et al., 1992). Due to developments in computational
technology, combinatorial libraries and high-throughput screening techniques, this
concept has been extended to include not only synthetic biomimetic dyes and triazine
non-dye ligands (designed de novo ligands), but also peptides and minimised protein
domains (Roque et al., 2004a). A good example of biomimetic affinity ligands is
the group of protein A ligands applied in the purification of antibodies, which
includes a protein A mimetic multimeric peptide ligand (PAM-TG19318) (Fassina et
al., 1996) and the de novo designed artificial protein A (ApA) (Li et al., 1998; Teng
et al., 2000).
The availability of crystallographic structures of proteins and complexes, together
with the development of computer-based molecular modelling techniques, has
prompted the bintelligentQ design and synthesis of affinity ligands with improved
characteristics over their natural counterparts. These improvements include chemically
defined and characterized ligands which are easy to synthesize with moderate to high
specificity, the possibility of using mild elution conditions, the high stability of the
ligand to sterilization-in-place and cleaning-in-place procedures, the high yield of
ligand utilisation, and the low cost and high scalability (Roque et al., 2004a).
Lowe and co-workers have been pioneers in de novo ligand design and synthesis of
triazine scaffolded affinity ligands for the purification of different target biomolecules
(Lowe et al., 1992, 2001; Lowe, 2001). The methodology represents an integrated
procedure by combining structure-based design with combinatorial chemistry and
integrating solid-phase synthesis of ligands with screening in parallel for affinity
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chromatography of proteins (Fig. 3). Three main design strategies have been followed: (i)
the template for design is a natural partner involved in binding to the target protein (Li et al.,
1998); (ii) the template for design is a molecule that binds to the target site of the protein
(Teng et al., 1999; Filippusson et al., 2000); and (iii) direct mimicking of natural biological
recognition interactions (Palanisamy et al., 1999, 2000) (Table 1). Although it is possible
to rationalise several factors in the ligand design, numerous indefinite factors are
introduced upon immobilization on the solid support: the matrix and the coupling
chemistry in addition to the ligand play an important role in binding to the target molecule
(Lowe, 2001). However, performing the synthesis and screening on the solid-support helps
to minimise these effects when considering the final application of the ligand as an affinity
adsorbent.

Fig. 3. General strategy followed for the finding of a lead ligand following the design, synthesis and screening of
a solid-phase combinatorial library of de novo designed ligands. Different strategies can be applied at the
molecular modelling stage of de novo design of synthetic ligands (DESIGN), followed by the synthesis of a nxn
combinatorial library of immobilized ligands (SYNTHESIS) further assessed for affinity and specificity for the
target proteins (SCREENING). Screening procedures can involve, for example, FITC-based systems (a) or
affinity chromatography (b). Potential lead ligands selected at this stage are synthesized in solution-phase,
characterized by NMR and MS and further immobilized onto agarose beads to confirm affinity for target protein.
A lead ligand is chosen and subsequent studies were performed to optimise its performance. A second generation
of ligands might be designed, synthesized and tested.

Table 1
A summary of de novo designed biomimetic ligands based on a triazine-scaffold for the affinity purification of proteins
Design strategy
Kallikrein Complex kallikrein/kininogen; ligands
designed to mimic Phe–Arg dipeptide
on the substrate
Elastase Complex elastase/turkey ovomucoid
inhibitor; ligands designed to mimic
the natural inhibitor
IgG (Fab fragment) Complex PpL–IgG; ligands designed
towards mimicking the natural PpL
binding interfaces to IgG
IgG Complex SpA–IgG; ligands designed
to mimic the Phe132–Tyr133 dipeptide
on SpA
IgG Refinement of SpA mimicking ligand
(Li et al., 1998)
Human recombinant factor VIIa Complex tissue factor/factor VIIa;
ligands designed to bind to the
Gla-domain in Factor VIIa
Sugar moieties on glycoproteins Protein–carbohydrate complexes:
identification and mimicking of key
residues determining monosaccharide
specificity
Recombinant insulin precursor MI3 Study of the target protein per se and
selection of appropriate binding sites
Human a1-antitrypsin Study of the target protein per se and
selection of appropriate binding sites
Prion protein Study of the target protein per se and
selection of appropriate binding sites
SpA — staphylococcal protein A; PpL — protein L from Peptostreptococcus magnus; IgG — immunoglobulin G; Gla — g-carboxyglutamic acid.
8
Synthesis References
Solution-phase synthesis (Burton, 1992)
A.C.A. Roque, C.R. Lowe / Biotechnology Advances xx (2005) xxx–xxx
Solid-phase combinatorial chemistry (Filippusson et al., 2000)
ARTICLE IN PRESS
(12 ligands)
Solid-phase combinatorial chemistry (Roque et al., 2004b, 2005a,
(169 ligands) 2005b)
Solution-phase synthesis (Li et al., 1998)
Solid-phase combinatorial chemistry (Teng et al., 1999, 2000)
(88 ligands)
Solid-phase combinatorial chemistry; (Morrill et al., 2002, 2003)
solution-phase synthesis of a sub-library
Solid-phase combinatorial chemistry (Palanisamy et al., 1999, 2000;
(80 ligands) Gupta and Lowe, 2004)
Solid-phase combinatorial chemistry (Sproule et al., 2000)
(64 ligands); solution-phase synthesis
of a sub-library
Solid-phase combinatorial chemistry (Lowe et al., 2001)
Solid-phase combinatorial chemistry (Renou et al., 2004)
(49 ligands)
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4. Synthetic de novo affinity ligands in proteomics

From a proteomics point of view, de novo designed synthetic ligands represent a good
alternative to biological ligands and an opportunity to attain new classes of ligands for
specific target proteins, as the power of designed ligands lies on the btailor-madeQ
approach. As already presented in Table 1, the concepts of de novo designed synthetic
ligands has already lead to the development of a series of triazine scaffolded molecules
presenting affinity to different proteins or families of proteins. The utilisation of affinity
chromatography as a depletion method has been recently reported to eliminate the
immunoglobulin content from crude samples to be further submitted to 2D-PAGE or MS
techniques (Lee and Lee, 2004). Similarly, affinity chromatography has also been utilised
recently to separate, in a concentration mode, glycoproteins and glycosylated peptides
resulting from proteomic analysis (Hashim et al., 2001; Hirabayashi et al., 2001). In the
former, both general synthetic ligands (e.g. Cibacron blue F-3GA) and immunoadsorbents
(e.g. bovine IgG-specific IgG immobilized on Sepharose) were utilised; in the latter,
lectins were utilised as the ligand molecule. This section will focus particularly on the
work accomplished in our group regarding the design, synthesis, evaluation and
application of (i) immunoglobulin-binding ligands and (ii) glycoprotein-binding ligands
(Fig. 4). Although displaying high selectivity, adsorbents based on proteins A/L and
carbohydrate-binding systems suffer from high costs of production and purification, low
binding capacities, limited life cycles and low scale-up potential, which is attributable to
the biological nature of the ligands. The biomimetic ligands described below are fully

Fig. 4. De novo designed affinity ligands for mimicking proteins A and L. Crystallographic structure of the
complex between protein A and Fc fragment of IgG (A) and of the complex between protein L and Fab fragments
of IgG (D). Structure of the ligands artificial protein A (B) and L (E) and respective superimposition at the
proteins A and L binding sites (C) and (F).
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synthetic in nature and can circumvent problems associated with biological ligands, while
maintaining the affinity and specificity for the target proteins.

4.1. The artificial protein A

Staphylococcus aureus protein A (SpA) was used as a template for the design of a
synthetic ligand to bind specifically to immunoglobulin G (Li et al., 1998). The dipeptide
motif Phe132–Tyr133 was crucial for the complex SpA–IgG (Deisenhofer, 1981) and was
thus used as a starting point for the design of a series of biomimetic ligands. The most
suitable ligand was able to bind IgG selectively from human plasma (98% purity after
elution) and competitively to SpA, with affinity constants between 105–106 M 1 (Li et al.,
1998). The lead compound was further refined by the synthesis of an IgG-binding
combinatorial solid-phase ligand library comprising 88 adsorbents. The ligand library was
assessed for its ability to bind pure human IgG and selected ligands further tested for their
specificity to purify IgG from human plasma (Teng et al., 1999). Ligand 22/8 (ApA—
artificial protein A) proved to be the most efficient for binding hIgG, (K a = 1.4  105 M 1)
and for the separation of IgG from human plasma with recoveries of 67–69% and purities
of 98–99% (Teng et al., 2000). This adsorbent also proved effective in the purification of
antibodies from different species (chicken, cow, rabbit, pig, horse, rat, goat, sheep and
mouse) and from different human classes (IgA and IgM) and IgG subclasses, including
IgG3. Stability studies of ligand 22/8 in 1M NaOH over N140 h proved that it can
withstand general procedures of cleaning-in-place and sterilisation, which represents an
important advance over natural SpA (Teng et al., 2000).

4.2. The artificial protein L

The lack of existence of a synthetic affinity ligand with a universal affinity for the scFv,
Fab or F(abV)2 small antibody fragments prompted the design, synthesis and evaluation of
a protein L mimic. Until then, affinity ligands binding specifically to the Fab fragments of
immunoglobulins comprised anti-antibodies raised against the immunoglobulin of interest,
molecules interacting with CDR regions (antigen or epitope/mimotope peptides) or
microbial binding proteins (protein L). However, anti-antibodies represent an expensive
and labour intensive option (Huse et al., 2002); ligands interacting with CDR regions are
usually unique to each antibody and, therefore, do not represent a universal ligand (Murray
et al., 1998). Protein L from Peptostreptococcus magnus was discovered in 1985 and is an
immunoglobulin light chain binding protein particularly suitable for the purification of
scFv, Fab and F(abV)2 biomolecules (Housden et al., 2003). Protein L binds with high
affinity (K d of 1n M) to a large number of immunoglobulins with n1, n3 and n4 light
chains (but not to n2 and E subgroups) and thus recognises 50% of human and more than
75% of murine immunoglobulins (Stura et al., 2002).
A solid phase combinatorial triazine-scaffolded library of affinity ligands was designed
de novo, synthesized and screened for the discovery of a protein L mimic. The thirteen
compounds included in the combinatorial library were selected on the basis of the structure
of the eleven different amino acid residues from the protein L domain recognised as being
involved in the interaction with the n-light chains (Wikstrom et al., 1995; Graille et al.,
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2001). The solid-phase library was synthesized by a bmix-and-splitQ procedure on

Sepharose beads as a solid support. The members of the library were screened by an
iterative procedure for their binding to human IgG and specificity towards the Fab moiety
(Roque et al., 2005b). Using an FITC-based screening protocol, a total of 110 ligands were
shown to bind N20% of loaded human IgG and these were subsequently assessed for
selectivity for human Fab (Roque et al., 2004b). A total of 73 ligands displayed N20%
binding to human Fab and, from these, 43 ligands showed b20% binding of loaded human
Fc. Ligands 8/7, 5/9 and 12/3 were identified as putative lead ligands for mimicking the
protein L interaction with the Fab moiety of immunoglobulins (Roque et al., 2005b).
Ligand 8/7 was selected as the lead ligand and was further studied (Roque et al., 2005a).
This ligand has shown to inhibit the interaction of PpL with IgG and Fab in competitive
ELISA assays. Ligand 8/7 adsorbents bind 0.32 mg/g of human IgG and 0.28 mg/g of Fab
with estimated K a of 104 M 1, while a commercial PpL adsorbent binds 0.47 and 0.36 mg/
g, respectively (mg/g of resin). Binding to Fc was negligible to both resins. Ligand 8/7-
adsorbent binds to immunoglobulins from different classes and sources that PpL also
interacts with. Additionally, ligand 8/7 binds to IgG1 with n and E isotypes (92% and
100% of loaded protein) and polyclonal IgG from sheep, cow, goat and chicken. These
properties were reflected in the isolation of immunoglobulins from crude samples, under
non-optimised conditions, achieving purification factors of 7-fold and purities up to 95%
(Roque et al., 2005a).
The artificial protein A, ligand 22/8 (triazine scaffold substituted with 3-aminophenol
and 4-amino-1-naphthol), possessed a more hydrophobic nature compared to ligand 8/7.
This reflects the type of amino acid residues that are involved in the interaction of proteins
A and L with immunoglobulins. In protein A, the Phe132–Tyr133 motif was shown to be
relevant, whereas in protein L, a series of predominantly hydrophilic amino acid residues
and a hydrogen-bond based interaction formed the basis of the complex with the light
chains.

4.3. The artificial glycoprotein-binding ligands

Group-specific immobilized lectins or biospecific antibodies traditionally carry out

isolation of the glycosylated form of proteins and peptides. These adsorbents, however,
present the usual disadvantages of biological ligands and can contaminate the final product
by leaching. Lectins have proven to be toxic and damaging to mammalian cells in culture.
Immobilized boronates are a family of synthetic ligands able to purify glycoproteins but
require alkaline conditions to bind to sugars, which can be detrimental to the protein
structure; other supramolecular structures have shown to have affinity for saccharides, but
only in non-aqueous media (Gupta and Lowe, 2004).
Rational design and solid-phase combinatorial chemistry were initially applied to the
development of affinity adsorbents for glycoproteins and, from these preliminary studies,
the triazine-based ligand 8/10 (histamine/tryptamine) presented affinity for the carbohy-
drate moiety of glucose oxidase and other mannosylated proteins (Palanisamy et al.,
1999). In a follow-up study, analogues of histamine and tryptamine were investigated in
order to find a ligand more suitable for facile solution-phase synthesis. Ligand 18/18, a 5-
aminoindan bis-substituted triazine molecule, has been shown to bind selectively to
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glucose oxidase with a K a in the order of 4.3  105 M 1 (Palanisamy et al., 2000). This
biomimetic ligand displayed affinity for mannose, glucose and fucose moieties and the
ability to bind to glycoproteins but was unable to bind selectively to the different
saccharides (Palanisamy et al., 2000). Rational design and combinatorial chemistry were
further employed on the discovery of ligand 11/11, a benzylamine bis-substituted triazine
molecule, showing the following monosaccharide specificity mannoside N glucoside N
galactoside, and affinity constants for binding to glycoproteins in the order of 104 M 1
(Gupta and Lowe, 2004). This biomimetic ligand also enhanced the understanding of
saccharide selectivity, showing that the resolving power might be based on the formation
of hydrogen bonds between the equatorial 3- and 4-hydroxyl groups from sugars and the
planar, polar nitrogen groups of the triazine ligand. Ligand 11/11, like other triazine-based
biomimetic ligands, has shown to be chemically stable and easy to synthesize, to possess
non-fissile bonds and to withstand sterilization and cleaning in situ (Gupta and Lowe,
2004).

5. Concluding remarks

Although it might be difficult to apply affinity chromatography as a stand-alone

one-dimensional assay in proteomics, there is no doubt that the technique is very
useful not only for the separation of specific groups of proteins but also for the
exploration of post-translational modifications and the study of protein–protein
interactions. The application of affinity chromatography for the enrichment or depletion
of proteins, where group-specific ligands can be applied, is a powerful way of
increasing resolution and sensitivity in subsequent 2D-PAGE or MS analysis (Lee and
Lee, 2004). Synthetic biomimetic ligands have been shown to circumvent many of the
disadvantages associated with natural biological ligands for the downstream processing
of therapeutic proteins. It is also time to consider these molecules as an alternative to
group-specific ligands utilised in proteomics analysis. In particular, the recently
developed artificial proteins A and L and artificial lectin ligands represent a promising
group of de novo designed affinity ligands to complement current proteomic analysis
techniques.

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