3.4.3 Catalytic Antibodies and Computational De-Novo
Design of Enzymes
One of the most striking drawbacks of enzyme catalysis is that proteins cannot be
designed and synthesized from scratch due to the boundaries of ribosomal protein
synthesis [634]. As a consequence, some synthetically useful transformations,
which are not (or only rudimentary) found in nature, are impossible by enzymatic
catalysis, in particular cycloadditions or rearrangement reactions. Furthermore, a
search for biocatalysts possessing opposite stereochemical properties is usually a
tedious empirical undertaking which is often unsuccessful. This gap may be filled
by the development of synthetic enzymes [635–637].
Like all catalysts, enzymes accelerate a reaction by stabilizing its transition state.
If the latter is known for a given organic transformation, an idealized cavity can be
designed possessing matching properties to that of the transition state, such as
H-bond donor/acceptor, δ
+
/δ
À pairs, π-donor/acceptor, lipophilic binding sites,
etc.
13 This entity will bind the transition state, thereby lower its ΔG and diminish
the activation energy (E a ). Consequently, the reaction will be accelerated (Fig. 1.7).
For the de novo creation of transition state stabilizing proteins, two strategies were
evolved: (i) catalytic antibodies [638–642] and (ii) computational design of existing
protein scaffolds [643].
Catalytic Antibodies
The immune system produces a vast repertoire – in the range of 10
8 –10
10 [644] – of
exquisitely specific proteins (antibodies) that protect vertebrates from ‘foreign’
invaders such as pathogenic bacteria and viruses, parasites and cancer cells. Antibodies have become invaluable tools in the detection, isolation and analysis of
biological materials and are the key elements in many diagnostic procedures. Their
potential, however, is not limited to biology and medicine, because they can also be
elicited to a large array of synthetic molecules. In a very simplified version they can
be regarded as enzymes possessing an active site, but no chemical operator. To
indicate their derivation, catalytic antibodies are also called ‘abzymes’ – antibodies
as enzymes.
Antibodies are large proteins consisting of four peptide chains which have a
molecular weight of about 150,000 Da (Fig. 3.12). There are two identical heavy
(H, 50,000 Da) and light chains (L, 25,000 Da) which are crosslinked by disulfide
bonds. The light chains are divided into variable (V) and constant (C) regions (V L , C L ),
while the heavy chains consist of V H , C H 1, C H 2, and C H 3 domains. The variable V H
and V L domains (located within the first ~110 amino acids of the heavy and light
chains) are highly polymorphic and are adapted to the antigen (hapten) they are
supposed to trap. Consequently, binding occurs in this region. On the other
hand, the constant regions represent the basic framework of the antibody and are
relatively invariant. Antibodies bind molecules ranging in size from about 6 to 34 Å
13 The transition state is related to the binding cavity like the ‘negative’ to a photographic picture.
386
3 Special Techniques
Design of Enzymes
One of the most striking drawbacks of enzyme catalysis is that proteins cannot be
designed and synthesized from scratch due to the boundaries of ribosomal protein
synthesis [634]. As a consequence, some synthetically useful transformations,
which are not (or only rudimentary) found in nature, are impossible by enzymatic
catalysis, in particular cycloadditions or rearrangement reactions. Furthermore, a
search for biocatalysts possessing opposite stereochemical properties is usually a
tedious empirical undertaking which is often unsuccessful. This gap may be filled
by the development of synthetic enzymes [635–637].
Like all catalysts, enzymes accelerate a reaction by stabilizing its transition state.
If the latter is known for a given organic transformation, an idealized cavity can be
designed possessing matching properties to that of the transition state, such as
H-bond donor/acceptor, δ
+
/δ
À pairs, π-donor/acceptor, lipophilic binding sites,
etc.
13 This entity will bind the transition state, thereby lower its ΔG and diminish
the activation energy (E a ). Consequently, the reaction will be accelerated (Fig. 1.7).
For the de novo creation of transition state stabilizing proteins, two strategies were
evolved: (i) catalytic antibodies [638–642] and (ii) computational design of existing
protein scaffolds [643].
Catalytic Antibodies
The immune system produces a vast repertoire – in the range of 10
8 –10
10 [644] – of
exquisitely specific proteins (antibodies) that protect vertebrates from ‘foreign’
invaders such as pathogenic bacteria and viruses, parasites and cancer cells. Antibodies have become invaluable tools in the detection, isolation and analysis of
biological materials and are the key elements in many diagnostic procedures. Their
potential, however, is not limited to biology and medicine, because they can also be
elicited to a large array of synthetic molecules. In a very simplified version they can
be regarded as enzymes possessing an active site, but no chemical operator. To
indicate their derivation, catalytic antibodies are also called ‘abzymes’ – antibodies
as enzymes.
Antibodies are large proteins consisting of four peptide chains which have a
molecular weight of about 150,000 Da (Fig. 3.12). There are two identical heavy
(H, 50,000 Da) and light chains (L, 25,000 Da) which are crosslinked by disulfide
bonds. The light chains are divided into variable (V) and constant (C) regions (V L , C L ),
while the heavy chains consist of V H , C H 1, C H 2, and C H 3 domains. The variable V H
and V L domains (located within the first ~110 amino acids of the heavy and light
chains) are highly polymorphic and are adapted to the antigen (hapten) they are
supposed to trap. Consequently, binding occurs in this region. On the other
hand, the constant regions represent the basic framework of the antibody and are
relatively invariant. Antibodies bind molecules ranging in size from about 6 to 34 Å
13 The transition state is related to the binding cavity like the ‘negative’ to a photographic picture.
386
3 Special Techniques