First-principle studies of intermolecular and intramolecular catalysis of protonated cocaine

We have performed a series of first-principles electronic structure calculations to examine the reaction pathways and the corresponding free energy barriers for the ester hydrolysis of protonated cocaine in its chair and boat conformations. The calculated free energy barriers for the benzoyl ester hydrolysis of protonated chair cocaine are close to the corresponding barriers calculated for the benzoyl ester hydrolysis of neutral cocaine. However, the free energy barrier calculated for the methyl ester hydrolysis of protonated cocaine in its chair conformation is significantly lower than for the methyl ester hydrolysis of neutral cocaine and for the dominant pathway of the benzoyl ester hydrolysis of protonated cocaine. The significant decrease of the free energy barrier, approximately 4 kcal/mol, is attributed to the intramolecular acid catalysis of the methyl ester hydrolysis of protonated cocaine, because the transition state structure is stabilized by the strong hydrogen bond between the carbonyl oxygen of the methyl ester moiety and the protonated tropane N. The relative magnitudes of the free energy barriers calculated for different pathways of the ester hydrolysis of protonated chair cocaine are consistent with the experimental kinetic data for cocaine hydrolysis under physiologic conditions. Similar intramolecular acid catalysis also occurs for the benzoyl ester hydrolysis of (protonated) boat cocaine in the physiologic condition, although the contribution of the intramolecular hydrogen bonding to transition state stabilization is negligible. Nonetheless, the predictability of the intramolecular hydrogen bonding could be useful in generating antibody-based catalysts that recruit cocaine to the boat conformation and an analog that elicited antibodies to approximate the protonated tropane N and the benzoyl O more closely than the natural boat conformer might increase the contribution from hydrogen bonding. Such a stable analog of the transition state for intramolecular catalysis of cocaine benzoyl-ester hydrolysis was synthesized and used to successfully elicit a number of anticocaine catalytic antibodies.     

Modeling the catalysis of anti-cocaine catalytic antibody: competing reaction pathways and free energy barriers

The competing reaction pathways and the corresponding free energy barriers for cocaine hydrolysis catalyzed by an anti-cocaine catalytic antibody, mAb15A10, were studied by using a novel computational strategy based on the binding free energy calculations on the antibody binding with cocaine and transition states. The calculated binding free energies were used to evaluate the free energy barrier shift from the cocaine hydrolysis in water to the antibody-catalyzed cocaine hydrolysis for each reaction pathway. The free energy barriers for the antibody-catalyzed cocaine hydrolysis were predicted to be the corresponding free energy barriers for the cocaine hydrolysis in water plus the calculated free energy barrier shifts. The calculated free energy barrier shift of -6.87 kcal/mol from the dominant reaction pathway of the cocaine benzoyl ester hydrolysis in water to the dominant reaction pathway of the antibody-catalyzed cocaine hydrolysis is in good agreement with the experimentally derived free energy barrier shift of -5.93 kcal/mol. The calculated mutation-caused shifts of the free energy barrier are also reasonably close to the available experimental activity data. The good agreement suggests that the protocol for calculating the free energy barrier shift from the cocaine hydrolysis in water to the antibody-catalyzed cocaine hydrolysis may be used in future rational design of possible high-activity mutants of the antibody as anti-cocaine therapeutics. The general strategy of the free energy barrier shift calculation may also be valuable in studying a variety of chemical reactions catalyzed by other antibodies or proteins through noncovalent bonding interactions with the substrates.     

X-Ray structures of two families of hydrolytic antibodies

The catalytic mechanisms of two esterase-like catalytic antibodies (Abs) have been determined, based on kinetic data and on structures of the complexes with transition-state analogs and with a stable substrate analog of the reactions they catalyze. Both Abs stabilize the oxyanion intermediate close to the transition state in ester hydrolysis. The different geometries of the hydrogen bonds that participate in this stabilization account for most of the difference between the efficiencies of these two Abs.     

Rational design of an enzyme mutant for anti-cocaine therapeutics

(-)-Cocaine is a widely abused drug and there is no available anti-cocaine therapeutic. The disastrous medical and social consequences of cocaine addiction have made the development of an effective pharmacological treatment a high priority. An ideal anti-cocaine medication would be to accelerate (-)-cocaine metabolism producing biologically inactive metabolites. The main metabolic pathway of cocaine in body is the hydrolysis at its benzoyl ester group. Reviewed in this article is the state-of-the-art computational design of high-activity mutants of human butyrylcholinesterase (BChE) against (-)-cocaine. The computational design of BChE mutants have been based on not only the structure of the enzyme, but also the detailed catalytic mechanisms for BChE-catalyzed hydrolysis of (-)-cocaine and (+)-cocaine. Computational studies of the detailed catalytic mechanisms and the structure-and-mechanism-based computational design have been carried out through the combined use of a variety of state-of-the-art techniques of molecular modeling. By using the computational insights into the catalytic mechanisms, a recently developed unique computational design strategy based on the simulation of the rate-determining transition state has been employed to design high-activity mutants of human BChE for hydrolysis of (-)-cocaine, leading to the exciting discovery of BChE mutants with a considerably improved catalytic efficiency against (-)-cocaine. One of the discovered BChE mutants (i.e., A199S/S287G/A328W/Y332G) has a approximately 456-fold improved catalytic efficiency against (-)-cocaine. The encouraging outcome of the computational design and discovery effort demonstrates that the unique computational design approach based on the transition-state simulation is promising for rational enzyme redesign and drug discovery.     

Catalytic Antibodies by Fluorescence Screening

A series of eleven immunizations against transition-state analogs were carried out to improve the catalytic properties of Ab 9D9, a catalytic antibody that catalyzes a fluorogenic retro-Diels-Alder reaction liberating nitroxyl. By a direct fluorescence assay of cell-culture supernatant, eight new hybridoma cell lines producing catalytic antibodies for the reaction were readily identified among more than 14000 individual samples. Our results demonstrate that early catalysis screening by fluorescence allows an efficient survey of large antibody libraries, and may lead to rapid and significant improvement in catalysis.     

Synthesis, properties, and reactivity of cocaine benzoylthio ester possessing the cocaine absolute configuration

One aspect of immunopharmacotherapy for cocaine abuse involves the use of a catalytic monoclonal antibody (mAb) to degrade cocaine via hydrolysis of the benzoate ester. A cocaine benzoylthio ester analogue provides a means to implement high-throughput selection strategies to potentially isolate mAbs with high activity. The required analogue was synthesized starting from (-)-cocaine hydrochloride and possessed the cocaine absolute configuration. Key points in the preparation were the introduction of the sulfur atom at C-3 via a bromomagnesium thiolate addition to the exo face of anhydroecgonine, separation of C-2 diastereomers, recycling of a C-2 thio ester byproduct, and formation of the necessary C-2 methyl and C-3 benzoylthio esters. Effects resulting from the lower electronegativity and greater hydrophobicity of sulfur compared to oxygen were observed. These characteristics could result in interesting drug properties. Furthermore, the analogue was found to be a substrate for catalytic mAbs that hydrolyze cocaine as monitored by HPLC and also spectrophotometry by coupling cleavage of the benzoylthio ester to the disulfide exchange with Ellman's reagent. Screening antibody libraries with the new cocaine analogue using the spectroscopic assay provides an avenue for the high-throughput identification of catalysts that efficiently breakdown cocaine.     

Catalytic antibodies for complex reactions: hapten design and the importance of screening for catalysis in the generation of catalytic antibodies for the NDA/CN reaction

Success in generating catalytic antibodies as enzyme mimics lies in the strategic design of the transition-state analog (TSA) for the reaction of interest, and careful development of screening processes for the selection of antibodies that are catalysts. Typically, the choice of TSA structure is straightforward, and the criterion for selection in screening is often binding of the TSA to the antibody in a microtiter-plate assay. This article emphasizes the problems of TSA design in complex reactions and the importance of selecting antibodies on the basis of catalysis as well as binding to the TSA. The target reaction is the derivatization of primary amines with naphthalene-2,3-dicarboxaldehyde (NDA) in the presence of cyanide ion. The desired outcome is selective catalysis of formation of the fluorescent derivative in preference to nonfluorescent side-products. In the study, TSA design was directed toward the reaction branch leading to the fluorescent product. Here, we describe a microtiter plate-based assay that is capable of detecting antibodies showing catalytic activity at an early stage. Of the antibodies selected, 36% showed no appreciable binding to any of the substrates tested, but did show catalytic activity in derivatizing one or more of the amino acids screened. In contrast, only two out of 77 clones that showed binding did not show catalysis. Thus, in this complex system, observation of binding is a good predictor of the presence of catalytic activity, and failure to observe binding is a poor predictor of the absence of catalytic activity.     

Investigation of the enzymatic and nonenzymatic cope rearrangement of carbaprephenate to carbachorismate

The dimethyl esters of carbaprephenate and 4-epi-carbaprephenate were prepared by modification of published procedures. In methanol these compounds are converted quantitatively to isomeric 6-hydroxytricyclo[3.3.1.0(2,7)]non-3-en-1,3-dimethyl esters via a two-step sequence involving an initial Cope rearrangement, followed by intramolecular Diels-Alder reaction of the dimethyl carbachorismate or 4-epi-carbachorismate intermediates. Carbaprephenate and its epimer were obtained by alkaline hydrolysis of the corresponding dimethyl esters. These compounds, in contrast to their ester precursors, undergo spontaneous acid-catalyzed decarboxylation in aqueous solution. Only at high pH does the Cope rearrangement compete with decarboxylation. At pH 12 and 90 degrees C, carbaprephenate slowly rearranges to carbachorismate, which rapidly loses water to give 3-(2-carboxyallyl)benzoic acid as the major product. A small amount of the intramolecular Diels-Alder adduct derived from carbachorismate is also observed by NMR as a minor product. Carbaprephenate is not a substrate for the enzyme chorismate mutase from Bacillus subtilis (BsCM), nor does carbaprephenate inhibit the normal chorismate mutase activity of this enzyme, even when present in 200-fold excess over chorismate. Its low affinity for the enzyme-active site is presumably a consequence of placing a methylene group rather than an oxygen atom proximal to the essential cationic residue Arg90. Nevertheless, BsCM variants that lack this cation (R90G and R90A) do not accelerate the Cope rearrangement of carbaprephenate either, and a catalytic antibody 1F7, which exhibits modest chorismate mutase activity, is similarly inactive. Poor substrate binding and the relatively high barrier for the Cope compared to the Claisen rearrangement presumably account for the lack of detectable catalysis. Acceleration of this sigmatropic rearrangement apparently requires more than an active site that is complementary in shape to the reactive substrate conformer.     

Catalytic antibodies for complex reactions

Success in generating catalytic antibodies as enzyme mimics lies in the strategic design of the transition-state analog (TSA) for the reaction of interest, and careful development of screening processes for the selection of antibodies that are catalysts. Typically, the choice of TSA structure is straightforward, and the criterion for selection in screening is often binding of the TSA to the antibody in a microtiter-plate assay. This article emphasizes the problems of TSA design in complex reactions and the importance of selecting antibodies on the basis of catalysis as well as binding to the TSA. The target reaction is the derivatization of primary amines with naphthalene-2,3-dicarboxaldehyde (NDA) in the presence of cyanideion. The desired outcome is selective catalysis of formation of the fluorescent derivative in preference to nonfluorescent side-products. In the study, TSA design was directed toward the reaction branch leading to the fluorescent product. Here, we describe a microtiter plate-based assay that is capable of detecting antibodies showing catalytic activity atan early stage. Of the antibodies selected, 36% showed no appreciable binding to any of the substrates tested, but did show catalytic activity in deriving one or more of the amino acids screened. In contrast, only two out of 77 clones that showed binding did not show catalysis. Thus, in this complex system, observation of binding is a good predictor of the presence of catalytic activity, and failure to observe binding is a poor predictor of the absence of catalytic activity.     

Hydrolysis of substituted 8-acetoxyquinolines

In the absence of metal ions, the hydrolysis of 2-methyl-8-acetoxyquinoline and of 5-chloro-8-acetoxyquinoline follow the same reaction paths as those of the parent ester 8-acetoxyquinoline, including an intramolecular catalysis by the quinoline nitrogen. Unlike the hydrolysis of the other esters, that of the 2-methyl compound appears not to be catalysed by metal ions, and this is consistent with the view that catalysis by a metal ion involves the formation of a 7-membered chelate structure.     

Hapten design for the generation of catalytic antibodies

This article brings together all of the kinetic data on catalytic antibodies available in the published literature at the time of writing (September, 1993). The data have been presented so that they can be analyzed for any significant trends that arise from relating the structure of the transition-state analog/hapten to the type and efficiency of the catalytic antibody activity elicited.     

Catalytic hydrolysis of α-amino esters in the presence of chiral palladacycles

The rate of hydrolysis of esters derived from optically active α-amino acids, catalyzed by chiral cyclopalladated benzylamines, depends on the configuration of chiral centers in the substrate and catalyst. The catalytic hydrolysis of sulfur-containing amino esters follows an intramolecular mechanism, and the difference in the reaction rates for the stereoisomers increases in going from ortho-palladated primary benzylamines (k _S/k _R = 1.1) to tertiary amines (k _S/k _R = 1.5); the strongest catalytic effect is observed for an ester and a complex with the same absolute configuration of the chiral centers. The efficiency of intermolecular catalysis is greater for a complex and ester with opposite absolute configurations of the chiral centers, and the rate constants of catalytic hydrolysis for two pairs of stereoisomers coincide within experimental error. The maximal difference in the reaction rates is observed for cyclopalladated secondary benzylamines; it reaches 2.3 for the phenylalanine ester.     

An approach to sequence-specific antibody proteases

We describe here a novel strategy for the isolation of antibodies with sequence-specific protease activity: the synthesis of dipeptide haptens in which the targeted peptide bond has been replaced by a ring-strained or torsionally strained hydroxyethylene transition-state analog. Thus, the analogs mimic both a peptide bond in a distorted, reactive conformation and the transition state for peptide bond hydrolysis. In order to obtain sequence-specific antibody proteases, these analogs have been flanked with additional amino acid residues in preparation for immunization. In particular, we have synthesized peptides containing analogs such as 2-cis-amino-3-cis-hydroxycyclobutane carboxylic acid andendo-(3-amino-2-hydroxy)bicyclo[2.2.1]heptane-7-anti-carboxylic acid. We have also prepared a series of peptide derivatives containing analogs, such as 2-[3-amino-2-oxo-1-azetidinyl]-3-methylbutanoic acid, in which the targeted peptide bond has been incorporated into a β-lactam ring. Since the “peptide bond” has been left intact, these species mimic only a distorted ground state. At present, antibodies are being elicited against a number of the above peptide derivatives.     

Nucleophilic proteolytic antibodies

Proteolytic antibodies appear to utilizecatalytic mechanisms akin to nonantibody serine proteases, assessed from mutagenesis and protease-inhibitor studies. The catalytic efficiency derives substantially from the ability to recognize the ground state with high affinity. Because the proteolytic activity is germline-encoded, catalysts with specificity for virtually any target polypeptide could potentially be developed by applying appropriate immunogens and selection strategies. Analysis of transition-state stabilizing interactions suggests that chemical reactivity ofactive-site serine residues is an important contributor to catalysis. A prototype antigen analog capable of reacting covalently with nucleophilic serine residues permitted enrichment of the catalysts from a phage-displayed lupus light-chain library. Further mechanistic developments in understanding proteolytic antibodies may lead to the isolation of catalysts suitable for passive immunotherapy of major diseases, and elicitation of catalytic immunity as a component of prophylactic vaccination.     

Molecular organization of reactants in the kinetics and catalysis of liquid phase reactions: XII. Mechanism of the boron trifluoride-catalyzed Curtius thermal rearrangement of benzoyl azide into phenyl isocyanate

The kinetics of the thermal decomposition and rearrangement of benzoyl azide into phenyl isocyanate was studied in n-heptane in the presence of boron trifluoride etherate as the catalyst. The apparent activation energy of the noncatalytic reaction is 28.0 kcal/mol, and that of the catalytic reaction is 11.0 kcal/mol. The electronic structure and geometry of various complexes between benzoyl azide and BF₃ were studied using the PBE/TZ2P density functional method, and fragments of the potential energy surface were calculated for the catalytic rearrangement. Comparatively stable 1: 1 and 1: 2 complexes between the syn conformer of benzoyl azide and the catalyst can form in the system by coordination to the oxygen and nitrogen atoms of the acyl azide group. The heats of formation of these complexes are between ?1.7 and ?6.4 kcal/mol. The main consequence of the formation of these complexes is that the acyl azide group comes out of the benzene ring plane and thus becomes more reactive. The effective activation energies calculated for the catalytic rearrangement involving complexes of different compositions are 12–15 kcal/mol lower the effective activation energy of the noncatalytic reaction. Information has been obtained about the structure of the transition state of the catalytic reaction, in which a nitrogen molecule is abstracted from benzoyl azide with a synchronous rearrangement of other atoms, resulting in the formation of the ultimate product.     

Aspects of antibody-catalyzed primary amide hydrolysis

Because there are many known C-terminally amidated peptides of biological importance, there is great potential in medicine and organic synthesis for antibodies that catalyze primary amide bond hydrolysis or formation. We characterized a catalytic antibody, 13D11, raised to a phosphinate hapten, that hydrolyzed the primary amide of a dansyl-alkylated derivative of (R)-phenylalaninamide (DNS-(R)F-NH₂). At pH 9.0, 13D11 hydrolyzed DNS-(R)F-NH₂ with a k_cat of 1.65 × 10^-7 s^-1 (k_cat/k_uncat = 132) and a K_m of 432 μM, and was stereospecifically hapten-inhibited (K_i = 14.0 μM). Control experiments indicated that the catalytic activity was not the result of a contaminating protease. In accordance with the hapten being a transition-state analog of base hydrolysis, the rate of DNS-(R)F-NH₂ hydrolysis increased with hydroxide concentration to an optimum pH of 9.5. Above pH 9.5, activity declined rapidly suggesting the antibody was inactivated during the long incubation period. This work demonstrates the feasibility of generating catalytic antibodies to hydrolyze unactivated amide bonds without cofactor assistance.     

Chemically Fueled Dissipative Self‐Assembly that Exploits Cooperative Catalysis

In living systems, dissipative processes are driven by the endergonic hydrolysis of chemical fuels such as nucleoside triphosphates. Now, through a simple model system, a transient self‐assembled state is realized by utilizing the catalytic effect of histidine on the formation and breaking of ester bonds. First, histidine facilitates the ester bond formation, which then rapidly co‐assembles to form a self‐supporting gel. An out‐of‐equilibrium state is realized owing to the cooperative catalysis by the proximal histidines in the assembled state, driving the second pathway and resulting in disassembly to sol. Cooperative effects that use the dual role of imidazoles as nucleophile and as proton donor is utilized to achieve transient assemblies. This simple system mimics the structural journey seen in microtubule formation where the substrate GTP facilitates the non‐covalent assembly and triggers a cooperative catalytic process, leading to substrate hydrolysis and subsequent disassembly.     

Trimethyl lock: a stable chromogenic substrate for esterases

p-Nitrophenyl acetate is the most commonly used substrate for detecting the catalytic activity of esterases, including those that activate prodrugs in human cells. This substrate is unstable in aqueous solution, limiting its utility. Here, a stable chromogenic substrate for esterases is produced by the structural isolation of an acetyl ester and p-nitroaniline group using a trimethyl lock moiety. Upon ester hydrolysis, unfavorable steric interactions between the three methyl groups of this o-hydroxycinnamic acid derivative encourage rapid lactonization to form a hydrocoumarin and release p-nitroaniline. This "prochromophore" could find use in a variety of assays.     

Catalytic activity of anti-ground state antibodies,antibody subunits,and human autoantibodies

Catalytic antibodies may be produced over the natural course of antibody-affinity maturation by placement of chemically reactive residues in antibody-active sites by somatic hypermutation or V-D-J-gene rearrangement. This hypothesis has received support from recent observations on the chemical reactivity of antibodies to vasoactive intestinal peptide (VIP), DNA, and steroid-and dinitrophenyl-esters. Recent studies reveal that monoclonal antibodies raised against the ground state of VIP can accelerate the cleavage of peptide bonds. The light-chain (L-chain) subunit of human autoantibodies display increased hydrolytic rate and diminished VIP-binding affinity compared to the parent antibody, consistent with increased turnover owing to weaker binding of the substrate ground state. These observations reveal an essential limitation of catalytic antibodies, i.e., large turnover rates may be associated with diminished substrate specificity. The hydrolysis of VIP by IgG purified by affinity chromatography from asthma patients and nonasthmatic controls was compared. IgG from the majority of asthma patients displayed VIP-hydrolyzing activity. V_max values for IgG from asthmatics tended to be higher than those from the nonasthmatic group. In principle, catalysis by antibodies may be an important mediator of immunological defense, regulation, and autoimmune dysfunction. The verification of these possibilities will require studies that utilize efficient assays of antibody catalysis during experimental immunization and autoimmune disease, as well as mechanistic investigation of catalysis by antibodies and their subunits.     

A catalytic antibody against a tocopherol cyclase inhibitor

The cyclic ammonium cation 5 and its guanidinium analogue 4 are inhibitors of tocopherol cyclase. Monoclonal antibodies were raised against protein conjugates of the haptens 1-3 and screened for catalytic reactions with alkene 8, a short chain analogue of the natural substrate phytyl-hydroquinone 6, and its enol ether analogues 10a,b. Antibody 16E7 raised against hapten 3 was found to catalyze the hydrolysis of Z enol ether 10a to form hemiacetal 12 with an apparent rate acceleration of k(cat)/k(uncat)=1400. Antibody 16E7 also catalyzed the elimination of Kemp's benzisoxazole 59. The absence of cyclization in the reaction of enol ether 10a was attributed to the competition of water molecules for the oxocarbonium cation intermediate within the antibody binding pocket. Hapten and reaction design features contributing to this outcome are discussed. Antibody 16E7 provides the first example of a carboxyl group acting both as an acid in an intrinsically acid-catalyzed process and as a base in an intrinsically base-catalyzed process, as expected from first principles. In contrast to the many examples of general-acid-catalyzed processes known to be catalyzed by catalytic antibodies, the specific-acid-catalyzed cyclization of phytyl-hydroquinone 6 or its analogue 8 still eludes antibody catalysis.