Immune versus natural selection: antibody aldolases with enzymic rates but broader scope

Asymmetric organocatalysis with glycosyl-β-amino acids: direct asymmetric aldol reaction of acetone with aldehydes

Direct asymmetric aldol reaction of acetone with aromatic aldehydes was achieved in good yields and high enantioselectivity using 5-amino-5-deoxy-beta-L-ido-(alpha-D-gluco)-heptofuranuronic acids as a new class of organocatalysts.

Genetic introduction of a diketone-containing amino acid into proteins

An orthogonal tRNA/aminoacyl-tRNA synthetase pair was evolved that makes possible the site-specific incorporation of an unnatural amino acid bearing a beta-diketone side chain into proteins in Escherichia coli with high translational efficiency and fidelity. Proteins containing this unnatural amino acid can be efficiently and selectively modified with hydroxylamine derivatives of fluorophores and other biophysical probes.

Structural Basis for D-Amino Acid Transamination by the Pyridoxal 5′-Phosphate-dependent Catalytic Antibody 15A9

Antibody 15A9, raised with 5'-phosphopyridoxyl (PPL)-N(epsilon)-acetyl-L-lysine as hapten, catalyzes the reversible transamination of hydrophobic D-amino acids with pyridoxal 5'-phosphate (PLP). The crystal structures of the complexes of Fab 15A9 with PPL-L-alanine, PPL-D-alanine, and the hapten were determined at 2.3, 2.3, and 2.5A resolution, respectively, and served for modeling the complexes with the corresponding planar imine adducts. The conformation of the PLP-amino acid adduct and its interactions with 15A9 are similar to those occurring in PLP-dependent enzymes, except that the amino acid substrate is only weakly bound, and, due to the immunization and selection strategy, the lysine residue that covalently binds PLP in these enzymes is missing. However, the N-acetyl-L-lysine moiety of the hapten appears to have selected for aromatic residues in hypervariable loop H3 (Trp-H100e and Tyr-H100b), which, together with Lys-H96, create an anion-binding environment in the active site. The structural situation and mutagenesis experiments indicate that two catalytic residues facilitate the transamination reaction of the PLP-D-alanine aldimine. The space vacated by the absent L-lysine side chain of the hapten can be filled, in both PLP-alanine aldimine complexes, by mobile Tyr-H100b. This group can stabilize a hydroxide ion, which, however, abstracts the C alpha proton only from D-alanine. Together with the absence of any residue capable of deprotonating C alpha of L-alanine, Tyr-H100b thus underlies the enantiomeric selectivity of 15A9. The reprotonation of C4' of PLP, the rate-limiting step of 15A9-catalyzed transamination, is most likely performed by a water molecule that, assisted by Lys-H96, produces a hydroxide ion stabilized by the anion-binding environment.

Breaking the one antibody-one target axiom

Studies at the interface of chemistry and biology have allowed us to develop an immunotherapeutic approach called chemically programmed antibodies (cpAbs), which combines the merits of traditional small-molecule drug design with immunotherapy. In this approach, a catalytic antibody catalyzes the covalent conjugation of a small molecule or peptide to the active site of the antibody, effectively recruiting the binding specificity of the conjugated molecule to the antibody. In essence, this technology provides the tools for breaking the "one antibody-one target axiom" of immunochemistry. Our studies in this area have focused on using the chemistry of the well studied aldolase catalytic antibodies of which mAb 38C2 is a member. Previously, we explored reversible assembly of cpAbs available through diketone chemistry. In this article, we explore a unique proadapter assembly strategy wherein an antibody 38C2-catalyzed transformation unveils a reactive tag that then reacts to form a stable covalent bond with the antibody. An integrin alpha(v)beta 3 antagonist was synthesized with the designed proadapter and studied using human breast cancer cell lines MDA-MB-231 and MDA-MB-435. We demonstrate that this approach allows for (i) the effective assembly of cpAbs in vitro and in vivo, (ii) selective retargeting of 38C2 to integrin alpha(v)beta 3 expressing breast cancer cell lines, (iii) intracellular delivery of cpAbs into cells, (iv) dramatically increased circulatory half-life, and (v) substantial enhancement of the therapeutic effect over the peptidomimetic itself in animal models of breast cancer metastasis. We believe that this technology possesses potential for the treatment and diagnosis of disease.

Control of function of a small peptide by a protein

A peptide that functions only in the presence of a protein has been developed using reaction-based selection from peptide phage libraries. The peptide was not functional in the absence of the protein, but formed enaminones with 1,3-diketone derivatives when bound to the protein.

Enhancing Heterogeneous Catalysis through Cooperative Hybrid Organic–Inorganic Interfaces

Active-site/surface cooperativity can enhance heterogeneous organic and organometallic catalysis. We review the powerful role of the solid surface in this context for generating local acidity and, as an inner-sphere ligand, for stabilizing immobilized supramolecular assemblies and unsaturated organometallic complexes that are often unstable in solution.

(3,4)-Connected Zincophosphites as Structural Analogues of Zinc Hydrogen Phosphate

The synthesis and crystal structures of three new open-framework zincophosphites with helical channels are reported here in the context of the synthetic design of an open architecture from three- and four-connected polyhedral centers. These zincophosphites were prepared under hydrothermal conditions from HF-containing media in mixed water-ethylene glycol solvents. Their three-dimensional frameworks consist of alternating ZnO4(6-) tetrahedra and HPO3(2-) trigonal pyramids with an overall framework composition of [Zn3(HPO3)4]2-. The topology was analyzed by converting these zincophosphites from their (3,4)-connected network into a four-connected framework. The symmetry and charge density of three different structure-directing agents dictate the symmetry and framework density of resulting inorganic frameworks. These zincophosphites are structural analogues of a known hydrogen phosphate, suggesting that the bonding difference between -P-H and -P-OH plays an insignificant role in the formation of phosphite and hydrogen phosphate open frameworks.

Theory of proteolytic antibody occurrence

Antibodies (Abs) with proteolytic and other catalytic activities have been characterized in the blood and mucosal secretions of humans and experimental animals. The catalytic activity can be traced to nucleophilic sites of innate origin located in Ab germline variable regions. Discoveries of the natural chemical reactivity of Abs were initially met with bewilderment, as the notion had taken hold that catalytic activities can be introduced into Abs by artificial means, but somatically operative selection pressures are designed only to adapt non-covalent Ab binding to antigen ground states. Unsurprisingly, initial efforts to engineer Abs with catalytic activity were oriented towards improving the non-covalent binding at the atoms immediately within the transition state reaction center. Slowly, however, dogmatic approaches to Ab catalysis have given way to the realization that efficient and specific catalytic Abs can be prepared by improving the natural nucleophilic reactivity combined with non-covalent recognition of epitope regions remote from the reaction center. The field remains beset, however, with controversy. This article attempts to provide a rational basis for natural Ab catalysis, in the hope that understanding this phenomenon will stimulate medical and basic science advances in the field.

Development of protein, peptide, and small molecule catalysts using catalysis-based selection strategies

We have developed peptide catalysts and antibody catalysts that catalyze aldol, retro-aldol, and Michael reactions via an enamine mechanism using reaction-based selections with 1,3-diketone derivatives. Nucleophilic amino groups of the catalysts were covalently trapped during the selections. We have also developed fluorogenic substrates that are useful for real-time monitoring of the progress of bond-forming reactions, such as aldol reactions, by an increase in fluorescence. These fluorogenic substrates have been used to monitor peptide-catalyzed, antibody-catalyzed, enzyme-catalyzed, and small molecule-catalyzed reactions. Catalysis-based screening using fluorogenic substrates will accelerate rapid identification of superior catalysts and reaction conditions.

Dual mechanism of zinc-proline catalyzed aldol reactions in water

The aldol reaction of acetone with aldehydes in aqueous medium under catalysis by zinc-proline (Zn(L-Pro)2) and secondary amines such as proline, (2S,4R)-4-hydroxyproline (Hyp) and (S)-(+)-1-(2-pyrrolidinomethyl)pyrrolidine (PMP) is shown to proceed by an enamine mechanism, as evidenced by reductive trapping of the iminium intermediate, while the aldol reaction of dihydroxyacetone (DHA) under catalysis by zinc-proline and by general bases such as N-methylmorpholine (NMM) is shown to occur under rate-limiting deprotonation of the alpha-carbon and formation of an enolate intermediate.

Squaric monoamide monoester as a new class of reactive immunization hapten for catalytic antibodies

A squaric monoester monoamide motif was employed as an effective reactive immunogen for the discovery of monoclonal antibodies with reactive residue(s) in their combining sites. Two antibodies, 2D4 and 3C8, were uncovered that enhance paraoxon hydrolysis over background. Kinetic analysis of these antibodies was performed and interestingly both undergo a single turnover event due to covalent modification within the antibody combining site. Because antibodies 2D4 and 3C8 result in covalent attachment and thus inactivation of paraoxon, they could be useful probes for investigating paraoxon intoxication.

Biocatalytic Approaches to Hetero-Diels-Alder Adducts of Carbonyl Compounds

Very little information is available on hetero-Diels-Alderases for the assembly of heterocyclic products despite the synthetic value of these [4+2] cycloadditions. Hetero-Diels-Alderase antibodies raised against a bicyclic transition state analogue have been generated for the cycloaddition of ethylglyoxylate with an all-carbon diene. More recently, a conceptually novel biocatalytic approach to hetero-Diels-Alder (HDA) adducts derived from carbonyl dienophiles has been developed mirroring a stepwise aldol Michael mechanism instead of a concerted pathway. In this approach, the two key steps are an antibody-mediated kinetic resolution of beta-hydroxyenones and a subsequent ring-closure process. An attractive feature of this methodology is the possibility to convert the enantioenriched aldol intermediates into tetrahydropyranones or dihydropyranones. This bioorganic route is best applied for the preparation of enantioenriched HDA adducts derived from poorly electrophilic acceptors, therefore complementing existing catalytic routes to these adducts based on the use of small organocatalysts or chiral Lewis acids.

Organocatalytic Entry to Chiral Bicyclo[3.n.1]alkanones via Direct Asymmetric Intramolecular Aldolization

[reaction: see text] The facile stereoselective syntheses of endo-8-hydroxybicyclo[3.3.1]nonan-2-one and endo-7-hydroxybicyclo[3.2.1]octan-2-one, featuring an alpha-amino acid catalyzed intramolecular aldolization of sigma-symmetric substrates, are described. A high enantioselectivity and a high catalytic efficiency have been exhibited by (4R,2S)-tetrabutylammonium 4-TBDPSoxy-prolinate in the aldolization of 3-(4-oxocyclohexyl)propionaldehyde to give highly enantiomerically enriched (1S,5R,8R)-8-hydroxybicyclo[3.3.1]nonan-2-one.

Development of Small Designer Aldolase Enzymes: Catalytic Activity, Folding, and Substrate Specificity†

Small (24-35 amino acid residues) peptides that catalyze carbon-carbon bond transformations including aldol, retro-aldol, and Michael reactions in aqueous buffer via an enamine mechanism have been developed. Peptide phage libraries were created by appending six randomized amino acid residues to the C-terminus or to the N-terminus of an 18-mer alpha-helix peptide containing lysine residues. Reaction-based selection with 1,3-diketones was performed to trap the amino groups of reactive lysine residues that were necessary for the catalysis via an enamine mechanism by formation of stable enaminones. The selected 24-mer peptides catalyzed the reactions with improved activities. The improved activities were correlated with improved folded states of the peptides. The catalyst was then improved with respect to substrate specificity by appending a phage display-derived substrate-binding module. The resulting 35-mer peptide functioned with a significant proportion of the catalytic proficiency of larger protein catalysts. These results indicate that small designer enzymes with good rate acceleration and excellent substrate specificity can be created by combination of design and reaction-based selection from libraries.

A catalytic asymmetric bioorganic route to enantioenriched tetrahydro- and dihydropyranones

A conceptually novel approach to hetero Diels-Alder adducts of carbonyl compounds is described using as the key steps an antibody-mediated kinetic resolution of hydroxyenones followed by a ring-closure process. Various beta-hydroxyenones proved to be very good substrates for antibodies 84G3- and 93F3-catalyzed retro-aldol reactions, allowing the preparation of highly enantiomerically enriched (up to 99% ee) precursors of pyranones. An attractive feature of this methodology is the possibility to convert these acyclic-enantioenriched beta-hydroxyenones into tetrahydropyranones by a conventional Michael-type addition procedure or into the corresponding dihydropyranones using an alternative palladium-catalyzed oxidative ring closure. For the palladium-mediated cyclization, a biphasic system has been implemented that allows the direct preparation of enantiopure dihydropyranones from the corresponding racemic aldol precursors using a sequential antibody-resolution/palladium-cyclization strategy, without isolation of the intermediate enantioenriched hydroxyenones. This bioorganic route is best applied to the preparation of hetero Diels-Alder adducts otherwise derived from less nucleophilic dienes and unactivated dienophiles.

Improved pKa calculations through flexibility based sampling of a water-dominated interaction scheme

Ionizable groups play critical roles in biological processes. Computation of pK(a)s is complicated by model approximations and multiple conformations. Calculated and experimental pK(a)s are compared for relatively inflexible active-site side chains, to develop an empirical model for hydration entropy changes upon charge burial. The modification is found to be generally small, but large for cysteine, consistent with small molecule ionization data and with partial charge distributions in ionized and neutral forms. The hydration model predicts significant entropic contributions for ionizable residue burial, demonstrated for components in the pyruvate dehydrogenase complex. Conformational relaxation in a pH-titration is estimated with a mean-field assessment of maximal side chain solvent accessibility. All ionizable residues interact within a low protein dielectric finite difference (FD) scheme, and more flexible groups also access water-mediated Debye-Hückel (DH) interactions. The DH method tends to match overall pH-dependent stability, while FD can be more accurate for active-site groups. Tolerance for side chain rotamer packing is varied, defining access to DH interactions, and the best fit with experimental pK(a)s obtained. The new (FD/DH) method provides a fast computational framework for making the distinction between buried and solvent-accessible groups that has been qualitatively apparent from previous work, and pK(a) calculations are significantly improved for a mixed set of ionizable residues. Its effectiveness is also demonstrated with computation of the pH-dependence of electrostatic energy, recovering favorable contributions to folded state stability and, in relation to structural genomics, with substantial improvement (reduction of false positives) in active-site identification by electrostatic strain.

Analysis of the class I aldolase binding site architecture based on the crystal structure of 2-deoxyribose-5-phosphate aldolase at 0.99A resolution

The crystal structure of the bacterial (Escherichia coli) class I 2-deoxyribose-5-phosphate aldolase (DERA) has been determined by Se-Met multiple anomalous dispersion (MAD) methods at 0.99A resolution. This structure represents the highest-resolution X-ray structure of an aldolase determined to date and enables a true atomic view of the enzyme. The crystal structure shows the ubiquitous TIM alpha/beta barrel fold. The enzyme contains two lysine residues in the active site. Lys167 forms the Schiff base intermediate, whereas Lys201, which is in close vicinity to the reactive lysine residue, is responsible for the perturbed pK(a) of Lys167 and, hence, also a key residue in the reaction mechanism. DERA is the only known aldolase that is able to use aldehydes as both aldol donor and acceptor molecules in the aldol reaction and is, therefore, of particular interest as a biocatalyst in synthetic organic chemistry. The uncomplexed DERA structure enables a detailed comparison with the substrate complexes and highlights a conformational change in the phosphate-binding site. Knowledge of the enzyme active-site environment has been the basis for exploration of catalysis of non-natural substrates and of mutagenesis of the phosphate-binding site to expand substrate specificity. Detailed comparison with other class I aldolase enzymes and DERA enzymes from different organisms reveals a similar geometric arrangement of key residues and implies a potential role for water as a general base in the catalytic mechanism.

The origin of enantioselectivity in aldolase antibodies: crystal structure, site-directed mutagenesis, and computational analysis

Catalytic aldolase antibodies, generated by reactive immunization, catalyze the aldol reaction with the efficiency of natural enzymes, but accept a much broader range of substrates. Two separate groups of aldolase antibodies that catalyze the same aldol reactions with antipodal selectivity were analyzed by comparing their amino acid sequences with their crystal structures, site-directed mutagenesis data, and computational docking of the transition states of the aldol reaction. The crystal structure of aldolase antibody 93F3 Fab' at 2.5A resolution revealed a combining site with two lysine residues, including LysL89 that reacts to form the covalent enamine intermediate. In contrast, antibody 33F12 has one active site lysine, LysH93. The reactive lysine residues in each group of antibodies are differentially located on the heavy and light chain variable regions in pseudo-symmetric opposite orientations, but both within highly hydrophobic environments. Thus, the defining feature for the observed enantioselectivities of these aldolase antibody catalysts is the respective location and relative disposition of the reactive lysine residues within the active sites of these catalysts.

Enzymes in the synthesis of bioactive compounds: the prodigious decades

The growing demand for enantiomerically pure pharmaceuticals has impelled research on enzymes as catalysts for asymmetric synthetic transformations. However, the use of enzymes for this purpose was rather limited until the discovery that enzymes can work in organic solvents. Since the advent of the PCR the number of available enzymes has been growing rapidly and the tailor-made biocatalysts are becoming a reality. Thus, it has been possible the use of enzymes for the synthesis of new innovative medicines such as carbohydrates and their incorporation to modern methods for drug development, such as combinatorial chemistry. Finally, the genomic research is allowing the manipulation of whole genomes opening the door to the combinatorial biosynthesis of compounds. In this review, our intention is to highlight the main landmarks that have led to transfer the chemical efficiency shown by the enzymes in the cell to the synthesis of bioactive molecules in the lab during the last 20 years.

Calorimetric determination of thermodynamic parameters of 2'-dUMP binding to Leishmania major dUTPase

We have investigated the binding of 2'-deoxyuridine 5'-monophosphate (2'-dUMP) to Leishmania major deoxyuridine 5'-triphosphate nucleotide hydrolase (dUTPase) by isothermal titration microcalorimetry under different experimental conditions. Binding to dimeric L. major dUTPase is a non-cooperative process, with a stoichiometry of 1 molecule of 2'-dUMP per subunit. The utilization of buffers with different ionization enthalpies has allowed us to conclude that the formation of the 2'-dUMP-dUTPase complex, at pH 7.5 and 30 degrees C, is accompanied by the uptake of 0.33 +/- 0.05 protons per dUTPase subunit from the buffer media. Moreover, 2'-dUMP shows a moderate affinity for the enzyme, and binding is enthalpically driven across the temperature range studied. Besides, whereas DeltaG degrees remains practically invariant as a function of temperature, both DeltaH and DeltaS degrees decrease with increasing temperature. The TS and TH were 23.4 and 13.6 degrees C, respectively. The temperature dependence of the enthalpy change yields a heat capacity change of DeltaCp degrees = -618.1 +/- 126.4 cal x mol(-1) x K(-1), a value low enough to discard major conformational changes, in agreement with the fitting model. An interpretation of this value in terms of solvent-accessible surface areas is provided.

Catalytic antibodies: hapten design strategies and screening methods

Catalytic antibodies have emerged as powerful tools for the efficient and specific catalysis of a wide range of chemical transformations. Generating antibody catalysts that achieve enzymatic efficiency remains a challenging task, which has long been the source of great interest both in the design of more effective haptens for immunization and in the development of more direct and efficient screening methods for the selection of antibodies with desired catalytic capacities. In this review, we describe the development of different hapten design strategies, including a transition state analog (TSA) approach, 'bait-and-switch' catalysis, and reactive immunization. We also comment on recent developments in the screening process that allow for a more efficient identification of antibody catalysts.

Small Peptides Catalyze Highly Enantioselective Direct Aldol Reactions of Aldehydes with Hydroxyacetone: Unprecedented Regiocontrol in Aqueous Media

[reaction: see text] L-Proline-based small peptides have been developed as efficient catalysts for the asymmetric direct aldol reactions of hydroxyacetone with aldehydes. Chiral 1,4-diols 7, which are disfavored products in similar aldol reactions catalyzed by either aldolases or L-proline, were obtained in high yields and enantioselectivities of up to 96% ee with peptides 3 and 4 in aqueous media.

New mechanistic studies on the proline-catalyzed aldol reaction

The mechanism of the proline-catalyzed aldol reaction has stimulated considerable debate, and despite limited experimental data, at least five different mechanisms have been proposed. Complementary to recent theoretical studies we have initiated an experimental program with the goal of clarifying some of the basic mechanistic questions concerning the proline-catalyzed aldol reaction. Here we summarize our discoveries in this area and provide further evidence for the involvement of enamine intermediates.

Chiral phosphoramide-catalyzed, enantioselective, directed cross-aldol reactions of aldehydes

Catalytic, enantioselective, directed cross-aldol reactions of aldehydes are described. The addition of isobutyraldehyde trichlorosilyl enolate 2 to various aldehydes in the presence of 10 mol % bisphosphoramide 4 provides aldol products in high yields with moderate to good enantioselectivities. The reaction works well with a wide range of aromatic, olefinic, and aliphatic aldehydes. Enantioselectivities are highly dependent on the electronic nature of the aldehyde substituent. Hammett studies reveal that enantioselectivity increases as aldehydes become either more electron rich or more electron poor.

The direct organocatalytic asymmetric mannich reaction: unmodified aldehydes as nucleophiles

The unprecedented application of unmodified aldehydes as nucleophilic donors in direct catalytic asymmetric Mannich-type reactions is disclosed in a full account. Our efforts in broadening the applicability of chiral pyrrolidine-based catalysts in direct asymmetric Mannich-type reactions led to the highly diastereo- and enantioselective and concise synthesis of functionalized alpha- and beta-amino acids, beta-lactams, and amino alcohols.

Prodrugs of dynemicin analogs for selective chemotherapy mediated by an aldolase catalytic Ab

Prodrugs of dynemicin analogs were synthesized, and their activation by aldolase antibody (Ab) 38C2 was evaluated by DNA-cleaving activity, as well as tumor cell growth inhibition. Further, we provide evidence that the activated enediynes underwent covalent crosscoupling with the aldolase Ab, which appears to be a limiting factor of their tumor cell growth-inhibiting activity and should be of general interest in the field of enediyne chemotherapy. These findings might open new avenues for defined conjugations of small molecule drugs to mAbs in general and aldolase Abs in particular.

Tandem aminoxylation–allylation reactions: a rapid, asymmetric conversion of aldehydes to mono-substituted 1,2-diols

A facile and rapid synthesis of enantiopure mono-substituted 1,2-diols was achieved by the tandem aminoxylation-allylation reactions of aldehydes.

Evolution of Aldolase Antibodies in Vitro : Correlation of Catalytic Activity and Reaction-based Selection

Aldolase antibodies that operate via an enamine mechanism were developed by in vitro selection. Antibody Fab phage display libraries were created where the catalytic active site residues of aldolase antibodies 38C2 and 33F12 were combined with a naive human antibody V gene repertoire. Selection from these libraries with 1,3-diketones covalently trapped the amino groups of reactive lysine residues by formation of stable enaminones. The selected aldolase antibodies retained the essential catalytic lysine residue and its function in altered and humanized primary antibody structures. The substrate specificity of the aldolase antibodies was directly related to the structure of the diketone used for selection. The k(cat) values of the antibody-catalyzed retro-aldol reactions were correlated with the K(d) values, i.e. the reactivities of the selected aldolase antibodies for the corresponding diketones. Antibodies that bound to the diketone with a lower K(d) value displayed a higher k(cat) value in the retro-aldol reaction, and a linear relationship was observed in the plots of logk(cat) versus logK(d). These results indicate that selections with diketones directed the evolution of aldolase antibodies in vitro that operate via an enamine mechanism. This strategy provides a route to tailor-made aldol catalysts with different substrate specificities.

Induced fit movements and metal cofactor selectivity of class II aldolases: structure of Thermus aquaticus fructose-1,6-bisphosphate aldolase

Fructose-1,6-bisphosphate (FBP) aldolase is an essential glycolytic enzyme that reversibly cleaves its ketohexose substrate into triose phosphates. Here we report the crystal structure of a metallo-dependent or class II FBP aldolase from an extreme thermophile, Thermus aquaticus (Taq). The quaternary structure reveals a tetramer composed of two dimers related by a 2-fold axis. Taq FBP aldolase subunits exhibit two distinct conformational states corresponding to loop regions that are in either open or closed position with respect to the active site. Loop closure remodels the disposition of chelating active site histidine residues. In subunits corresponding to the open conformation, the metal cofactor, Co(2+), is sequestered in the active site, whereas for subunits in the closed conformation, the metal cation exchanges between two mutually exclusive binding loci, corresponding to a site at the active site surface and an interior site vicinal to the metal-binding site in the open conformation. Cofactor site exchange is mediated by rotations of the chelating histidine side chains that are coupled to the prior conformational change of loop closure. Sulfate anions are consistent with the location of the phosphate-binding sites of the FBP substrate and determine not only the previously unknown second phosphate-binding site but also provide a mechanism that regulates loop closure during catalysis. Modeling of FBP substrate into the active site is consistent with binding by the acyclic keto form, a minor solution species, and with the metal cofactor mediating keto bond polarization. The Taq FBP aldolase structure suggests a structural basis for different metal cofactor specificity than in Escherichia coli FBP aldolase structures, and we discuss its potential role during catalysis. Comparison with the E. coli structure also indicates a structural basis for thermostability by Taq FBP aldolase.

The specificity of cross-reactivity: promiscuous antibody binding involves specific hydrogen bonds rather than nonspecific hydrophobic stickiness

Proteins are renowned for their specificity of function. There is, however, accumulating evidence that many proteins, from enzymes to antibodies, are functionally promiscuous. Promiscuity is of considerable physiological importance. In the immune system, cross-reactive or multispecific antibodies are implicated in autoimmune and allergy conditions. In most cases, however, the mechanism behind promiscuity and the relationship between specific and promiscuous activities are unknown. Are the two contradictory? Or can a protein exhibit several unrelated activities each of which is highly specific? To address these questions, we studied a multispecific IgE antibody (SPE7) elicited against a 2,4-dinitrophenyl hapten (DNP). SPE7 is able to distinguish between closely related derivatives such as NP (nitrophenol) and DNP, yet it can also bind a number of unrelated ligands. We find that, like DNP, the cross-reactants are themselves bound specifically-close derivatives of these cross-reactants show very low or no binding to SPE7. It has been suggested that cross-reactivity is simply due to "hydrophobic stickiness", nonspecific interactions between hydrophobic ligands and binding sites. However, partitioning experiments reveal that affinity for SPE7 is unrelated to ligand hydrophobicity. These data, combined with crystal structures of SPE7 in complex with four different ligands, demonstrate that each cross-reactant is bound specifically, forming different hydrogen bonds dependant upon its particular chemistry and the availability of complementary antibody residues. SPE7 is highly homologous to the germline antinitrophenol (NP) antibody B1-8. By comparing the sequences and binding patterns of SPE7 and B1-8, we address the relationship between affinity maturation, specificity, and cross-reactivity.

A humanized aldolase antibody for selective chemotherapy and adaptor immunotherapy

Mouse monoclonal antibody 38C2 is the prototype of a new class of catalytic antibodies that were generated by reactive immunization. Through a reactive lysine, 38C2 catalyzes aldol and retro-aldol reactions using the enamine mechanism of natural aldolases. In addition to its remarkable versatility and efficacy in synthetic organic chemistry, 38C2 has been used for the selective activation of prodrugs in vitro and in vivo and thereby emerged as a promising tool for selective chemotherapy. Adding another application with relevance for cancer therapy, designated adaptor immunotherapy, we have recently shown that 38C2 can be chemically programmed to target tumors by formation of a covalent bond of defined stoichiometry with a beta-diketone derivative of an integrin alpha(v)beta(3) targeting RGD peptidomimetic. However, a major limitation for the transition from preclinical to clinical evaluation is the human anti-mouse antibody immune response that mouse 38C2 is likely to elicit in a majority of patients after single administration. Here, we report the humanization of mouse 38C2 based on rational design guided by molecular modeling. In essence, the catalytic center of mouse 38C2, which encompasses a deep hydrophobic pocket with a reactive lysine residue at the bottom, was grafted into a human antibody framework. Humanized 38C2 IgG1 was found to bind to beta-diketone haptens with conserved affinities and revealed strong catalytic activity with identical k(cat) and slightly higher K(M) values compared to the parental mouse antibody. Furthermore, humanized 38C2 IgG1 revealed efficiency in prodrug activation and chemical programming comparable to the parental mouse antibody.

Discovery of new peptide-based catalysts for the direct asymmetric aldol reaction

A series of oligo-peptide based catalysts were prepared using Fmoc solid-phase peptide synthesis. It was found that peptides with N-terminal proline residues catalyzed an aldol reaction yielding enantiomeric enriched product. Peptide H-Pro-Glu-Leu-Phe-OH catalyzed the reaction with good activity and moderate enantioselectivity (66% ee). Furthermore, it was shown that an acidic side chain and/or C-termini are essential to catalysis.

Fluorescent detection of carbon-carbon bond formation

We have developed a new spectroscopic system for detecting carbon-carbon bond formation by fluorescence to enhance high-throughput catalyst screening and rapid characterization of catalysts on a small scale. Fluorogenic substrates composed of a fluorophore possessing an amino group are readily prepared as amides of alpha,beta-unsaturated carbonyl compounds and generally exhibit low fluorescence, while Michael or Diels-Alder reactions of these fluorogenic substrates provide products of significantly increased fluorescence. The product's fluorescence is approximately 20- to 100-fold higher than that of the substrate. The assay system was validated by screening potential catalysts of the Michael reaction and in solvent optimization experiments. The covalent combination of fluorophores possessing an amino group with alpha,beta-unsaturated carbonyl compounds should provide a diverse range of fluorogenic substrates that may be used to rapidly screen catalysts and to optimize reaction conditions.

Turnover-based in vitro selection and evolution of biocatalysts from a fully synthetic antibody library

This report describes the selection of highly efficient antibody catalysts by combining chemical selection from a synthetic library with directed in vitro protein evolution. Evolution started from a naive antibody library displayed on phage made from fully synthetic, antibody-encoding genes (the Human Combinatorial Antibody Library; HuCAL-scFv). HuCAL-scFv was screened by direct selection for catalytic antibodies exhibiting phosphatase turnover. The substrate used was an aryl phosphate, which is spontaneously transformed into an electrophilic trapping reagent after cleavage. Chemical selection identified an efficient biocatalyst that then served as a template for error-prone PCR (epPCR) to generate randomized repertoires that were subjected to further selection cycles. The resulting superior catalysts displayed cumulative mutations throughout the protein sequence; the ten-fold improvement of their catalytic proficiencies (>10(10) M(-1)) resulted from increased kcat values, thus demonstrating direct selection for turnover. The strategy described here makes the search for new catalysts independent of the immune system and the antibody framework.

Bioorganic chemistry à la baguette: studies on molecular recognition in biological systems using rigid-rod molecules

Initial studies using rigid-rod molecules or "baguettes" to address bioorganic topics of current scientific concern are reported. It is illustrated how transmembrane oligo(p-phenylene)s as representative model rods can be tuned to recognize lipid bilayer membranes either by their thickness or polarization. The construction of otherwise problematic hydrogen-bonded chains along transmembrane rods yields "proton wires," which act by a mechanism that is central in bioenergetics but poorly explored by means of synthetic models. Another example focuses on multivalent ligands assembling rigid-rod cell-surface receptors into transmembrane dynamic arene arrays. The potassium transport mediated by these ligand-receptor complexes provides experimental support for the potential biological importances of the controversial cation-pi mechanism. More complex supramolecular architecture is portrayed in the first artificial beta-barrels. It is shown how programmed assembly of toroidal rigid-rod supramolecules in detergent-free water permits control of diameter of the chemical nature of their interior. Reversed rigid-rod beta-barrels are assembled to function as self-assembled ionophores, ion channel models, and transmembrane nanopores. The potential of future intratoroidal chemistry is exemplified by encapsulation and planarization of beta-carotene in water and the construction of transmembrane B-DNA at the center of a second-sphere host-guest complex à al baguette.

Chemically programmed monoclonal antibodies for cancer therapy: adaptor immunotherapy based on a covalent antibody catalyst

Proposing that a blend of the chemical diversity of small synthetic molecules with the immunological characteristics of the antibody molecule will lead to therapeutic agents with superior properties, we here present a device that equips small synthetic molecules with both effector function and long serum half-life of a generic antibody molecule. As a prototype, we developed a targeting device that is based on the formation of a covalent bond of defined stoichiometry between a 1,3-diketone derivative of an integrin alpha(v)beta(3) and alpha(v)beta(5) targeting Arg-Gly-Asp peptidomimetic and the reactive lysine of aldolase antibody 38C2. The resulting complex was shown to (i) spontaneously assemble in vitro and in vivo, (ii) selectively retarget antibody 38C2 to the surface of cells expressing integrins alpha(v)beta(3) and alpha(v)beta(5), (iii) dramatically increase the circulatory half-life of the Arg-Gly-Asp peptidomimetic, and (iv) effectively reduce tumor growth in animal models of human Kaposi's sarcoma and colon cancer. This immunotherapeutic has the potential to target a variety of human cancers, acting on both the vasculature that supports tumor growth as well as the tumor cells themselves. Further, by use of a generic antibody molecule that forms a covalent bond with a 1,3-diketone functionality, essentially any compound can be turned into an immunotherapeutic agent thereby not only increasing the diversity space that can be accessed but also multiplying the therapeutic effect.

Noncovalent binding of a reaction intermediate by a designed helix-loop-helix motif-implications for catalyst design

In our search for a catalyst for the transamination reaction of aspartic acid to form oxaloacetate, twenty-five forty-two-residue sequences were designed to fold into helix-loop-helix dimers and form binding sites for the key intermediate along the reaction pathway, the aldimine. This intermediate is formed from aspartic acid and the cofactor pyridoxal phosphate. The design of the binding sites followed a strategy in which exclusively noncovalent forces were used for binding the aldimine. Histidine residues were incorporated to catalyse the rate-limiting 1,3 proton transfer reaction that converts the aldimine into the ketimine, an intermediate that is subsequently hydrolysed to form oxaloacetate and pyridoxamine phosphate. The two most efficient catalysts, T-4 and T-16, selected from the pool of sequences by a simple screening procedure, were shown by CD and NMR spectroscopies to bind the aldimine intermediate with dissociation constants in the millimolar range. The mean residue ellipticity of T-4 in aqueous solution at pH 7.4 and a concentration of 0.75 mM was -18500 deg x cm(2) dmol(-1). Upon addition of 6 mm l-aspartic acid and 1.5 mM pyridoxal phosphate to form the aldimine, the mean residue ellipticity changed to -19900 deg x cm(2) dmol(-1). The corresponding mean residue ellipticities of T-16 were -21200 deg x cm(2) dmol(-1) and -24000 deg x cm(2) dmol(-1). These results show that the helical content increased in the presence of the aldimine, and that the folded polypeptides bound the aldimine. The (1)H NMR relaxation time of the imine CH proton of the aldimine was affected by the presence of T-4 as was the (31)P NMR resonance linewidth. The catalytic efficiencies of T-4 and T-16 were compared to that of imidazole and found to be more than three orders of magnitude larger. The designed binding sites were thus shown to be capable of binding the aldimine in close proximity to His residues, by noncovalent forces, into conformations that proved to be catalytically active. The results show for the first time the design of well-defined catalytic sites that bind a reaction intermediate with enzyme-like affinities under equilibrium conditions and represent an important advance in de novo catalyst design.

Active site in RrmJ, a heat shock-induced methyltransferase

The heat shock protein RrmJ (FtsJ), highly conserved from eubacteria to eukarya, is responsible for the 2'-O-ribose methylation of the universally conserved base U2552 in the A-loop of the 23 S rRNA. Absence of this methylation, which occurs late in the maturation process of the ribosome, appears to cause the destabilization and premature dissociation of the 50 S ribosomal subunit. To understand the mechanism of 2'-O-ribose methyltransfer reactions, we characterized the enzymatic parameters of RrmJ and conducted site-specific mutagenesis of RrmJ. A structure based sequence alignment with VP39, a structurally related 2'-O-methyltransferase from vaccinia virus, guided our mutagenesis studies. We analyzed the function of our RrmJ mutants in vivo and characterized the methyltransfer reaction of the purified proteins in vitro. The active site of RrmJ appears to be formed by a catalytic triad consisting of two lysine residues, Lys-38 and Lys-164, and the negatively charged residue Asp-124. Another highly conserved residue, Glu-199, that is present in the active site of RrmJ and VP39 appears to play only a minor role in the methyltransfer reaction in vivo. Based on these results, a reaction mechanism for the methyltransfer activity of RrmJ is proposed.

The elicitation of carboxylesterase activity in antibodies by reactive immunization with labile organophosphorus antigens: a role for flexibility

For the creation of powerfully catalytic antibodies, the technique of reactive immunization solves the problem inherent in immunization with transition-state analogs (TSAs), namely, that many interesting target reactions are multistep reactions, with multiple transition states, and thus in general, no single analog can adequately simulate all the transition states along the reaction path. In contrast, immunization with chemically reactive antigens such as phosphonylating agents, which phosphonylate B-cells during the immune response, produces antibodies that have been "trained" to recognize, bind, and stabilize all the actual transition states involved in the phosphonylation reaction. Therefore, catalytic antibodies have been selected by the immune system on the basis of their capacity to stabilize any number of transition states that occur during the target reaction. Somewhat surprisingly, phosphonolysis catalysts generated in this way commonly also catalyze esterolysis reactions. Esterolysis reactions should pass through transition states with a roughly tetrahedral disposition of ligands about a central carbon atom, while phosphonolysis reactions should pass through transition states with a roughly trigonal-bipyramidal disposition of ligands about a central phosphorus atom. These two divergent transition-state geometries suggest that the same active site should have difficulty recognizing and stabilizing both kinds of transition state. The observations thus indicate a puzzling form of "cross-reactivity" toward transition states. A possible explanation arises from evidence that at least some nucleophilic displacements at phosphorus do not pass through a trigonal-bipyramidal adduct, with a bond-formation transition state preceding it and a bond-fission transition state succeeding it. Instead a single transition state is traversed in which both bond-formation and bond-fission occur simultaneously. Such a concerted-reaction transition state should have two weak, partial bonds to phosphorus, one for formation of the nucleophile-P bond and one for fission of the P-leaving group bond. In a stepwise reaction through an intermediate, only one bond is partial and weak in each of the two transition states. The concerted-reaction transition state, with two weak bonds to phosphorus, may be more easily compressed, expanded, and otherwise distorted because of the lower force constants associated with partial bonds; particularly distortions of angles involving the two partial bonds should require relatively low energies. This may lend a high level of flexibility to phosphonolysis transition states, allowing them to be accommodated within an active site (or a range of active sites) with strong catalytic stabilization. Included among these active sites may be a majority that can also stabilize esterolysis transition states. Indeed many of the target esterolysis reactions studied to date may occur through a single concerted-reaction transition state rather than through separate transition states before and after a tetrahedral intermediate. Thus, the esterolysis transition states may also be highly flexible. Finally, flexibility present in germline antibodies may be specifically preserved in reactive immunization. The high flexibility of both kinds of ligands and of the antibody combining site may then account for the catalytic "cross-reactivity" of these antibodies.

Reactive immunization: a unique approach to catalytic antibodies

The development of antibody catalysts and indeed natural antibody responses has in the past been based on non-covalent binding to antigens. In contrast to this, reactive immunization utilizes reactive immunogens that covalently react with antibodies during the course of their induction through a designed chemical transformation. The inducing chemical transformation is designed to become part of the catalytic mechanism when the antibody is subsequently challenged with substrate molecules. Reactive immunization has proven to be an efficient approach to generating highly proficient catalytic antibodies with unusually broad substrate scope. This review describes catalytic antibodies generated by reactive immunization, their features and applications, as well as in vitro selection of catalytic antibodies based on reactive compounds.

Catalytic antibodies with acetylcholinesterase activity

We describe three catalytic cholinesterase-like catalytic antibodies (Ab1), as well as anti-idiotypic (Ab2) and idiotypic (Ab3) antibodies, to one of the Ab1s. The Ab1s were raised against the human erythrocyte acetylcholinesterase (AChE), and are unusual in that they both recognise and resemble acetylcholinesterase in their catalytic activity. No contamination of the antibody preparations with either acetylcholinesterase or butyrylcholinesterase (BChE) was found. None of the Ab2s showed catalytic activity, whereas four Ab3s did (an incidence of 1.26% of all Ab3s). Although there is considerable resemblance between Ab1s and Ab3s, there are significant differences between the two groups. All the antibodies were inhibited by phenylmethylsulphonyl fluoride (PMSF), indicating the presence of a serine residue in their active sites, and were inhibited by the cholinesterase active site inhibitors iso-OMPA and pyridostigmine, suggesting the similarity of the sites to those of cholinesterases. The Ab3s resemble the Ab1s in their ability to hydrolyse both acetyl and butyrylthiocholine (BTCh). However, the Ab3s appear to be better catalysts, having significantly reduced K(m) values (for acetyl, but not for butyrylthiocholine) and increased turnover numbers (K(cat)), rate enhancements (K(cat)/K(uncat)) and K(cat)/K(m) ratios, for both substrates, although these values by no means approach those of the natural enzymes. The Ab1s appear to have structures resembling the anionic sites of cholinesterases, as shown by their reaction with the anionic site inhibitors (edrophonium and tetramethylammonium). No such reactions were observed in the Ab3s. None of the antibodies show evidence of the sites resembling the peripheral anionic site (PAS) of acetylcholinesterase. All the antibodies recognise, to varying degrees, the peripheral anionic site of acetylcholinesterase. This was shown by their ability to inhibit acetylcholinesterase, to compete with peripheral site inhibitors, and to block acetylcholinesterase-mediated cell adhesion, a property of this site. The results indicate idiotypic mimicry of a catalytic antibody's active site, and suggest that the development of the catalytic activity in the anti-acetylcholinesterase antibodies may be related to the structural features of the peripheral anionic site of acetylcholinesterase.

Immunologically driven chemical engineering of antibodies for catalytic activity

We describe a new strategy for the preparation of catalytic antibodies based on a two-step procedure. Firstly, monoclonal antibodies are selected only if displaying the following binding features: binding both the substrate and a reactive group in such a way that the two groups are in a reactive position towards each other. Secondly, the selected monoclonal antibodies (mAbs) are chemically engineered by covalently binding the reactive group into the binding pocket of the antibody. Using previously isolated monoclonal antibodies, we have focused our studies on the control of this second step.