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.     

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.     

Pyridoxal-5'-phosphate-dependent catalytic antibodies

Cofactors--i.e., metal ions and coenzymes--extend the catalytic scope of enzymes and might have been among the first biological catalysts. They may be expected to efficiently extend the catalytic potential of antibodies. Monoclonal antibodies (MAbs) against Nalpha-phosphopyridoxyl-L-lysine were screened for 1) binding of 5'-phosphopyridoxyl amino acids, 2) binding of the planar Schiff base of pyridoxal-5'-phosphate (PLP) and amino acids, the first intermediate of all PLP-dependent reactions, and 3) catalysis of the PLP-dependent alpha, beta-elimination reaction with beta-chloro-D/L-alanine. Antibody 15A9 fulfilled all criteria and was also found to catalyze the cofactor-dependent transamination reaction of hydrophobic D-amino acids and oxo acids (k'cat = 0.42 min(-1) with D-alanine at 25 degrees C). No other reactions with either D- or L-amino acids were detected. PLP markedly contributes to catalytic efficacy-it is a 10(4) times more efficient acceptor of the amino group than pyruvate. The antibody ensures reaction specificity, stereospecificity, and substrate specificity, and further accelerates the transamination reaction (k'cat(Ab)/k'cat(PLP) = 5 x 10(3)). The successive screening steps simulate the selection criteria that might have been operative in the evolution of protein-assisted pyridoxal catalysis.     

Nonspecific catalysis by protein surfaces

Catalytic antibodies are the best availablea llaround enzyme mimics. They provide a unique experimental approach and some special insights into general questions about catalysis by enzymes. They offer enantiospecific reactions and levels of substrate binding that compare well with typical enzyme reactions, but not—so far—comparable catalytic efficiency. We and others have used the Kemp elimination as a probe of catalytic efficiency in antibodies. We compare these reactions with nonspecific catalysis by other proteins, and with catalysis by enzymes. Several simple reactions are catalyzed by theserum albumins with Michaelis-Menten kinetics, and can be shown to involve substrate binding and catalysis by local functional groups. Here, we report the details of one investigation, which implicate known binding sites on the protein surface and discuss implications for catalyst design and efficiency.     

催化剂筛选：火山型曲线成因理论解析及其在多相催化中的应用

多相催化对于现代社会来说具有极其重要的意义,催化剂的理性设计/筛选是现代催化化学研究者的一个重要的目标。其中,火山型曲线是一个的重要工具。它指出对于一个催化反应来说,其催化活性针对关键物种吸附能来说呈一条先上升后下降的曲线,要求最佳催化剂对中间体的吸附能不能太高也不能太低。近几十年来,密度泛函理论等第一性原理计算方法的发展让许多催化剂表面反应微观物理量的计算成为了可能,这极大地拓展了火山型曲线的应用范围。 然而,对于火山型曲线根源的解释,人们却并非了解得十分清楚;一些基本科学概念的理解很多还是基于经验性的Sabatier原理：吸附太弱不利于吸附、太强不利于脱附。针对该问题的科学解析,本文进行了详细的动力学探究,试图以完全数学解析的方式回答催化反应中火山型曲线的必然存在性、产生根源及在催化活性预测中的内涵。本文采用了两步催化模型以及微动力学来进行速率方程的推导,并考虑BEP关系(基元反应的能垒与其反应焓存在线性关系)的应用,最终将整体反应速率转化为中间体吸附能相关的单值函数。基于对该函数的系列推导和分析,得到如下基本结论：(1)从数学上以一个完全的解析形式证明了催化反应中火山型曲线的存在。(2)通过对比催化反应与与之对应的气相反应,我们证明了：若无催化剂参与反应,则火山型曲线不会产生;由于催化剂表面的参与,随着催化剂吸附能力的增强,其表面会因为吸附作用而被占据毒化,导致反应速率存在一个最大值,即形成火山型曲线。从概念上讲,火山型曲线的根源是由“吸附过程引发表面活性位占据”这一自毒化效应造成的,它的存在可能体现为多相催化的基本属性。(3)数值模拟解析展示了表面反应与气相反应的区别,印证了我们的数学解析结论。同时,通过一定的简化,我们对火山型曲线中各部分的斜率进行了研究。结果发现,对于吸附决速过程,催化反应和气相反应斜率相同,其差别主要出现在脱附决速过程。在此阶段由于吸附能过大,表面被毒化,表面反应速率开始下降;而气相反应的速率依然上升。(4)表面反应速率方程的分解和简化结果表明,最佳催化剂在反应中的空活性位点覆盖度和其BEP关系的斜率存在内在关联关系(θ*opt=1–α),据此讨论了其在催化剂寻优过程中的意义。尝试解释了(a)合成氨反应中正逆反应所需最佳催化剂不同的现象;(b)合成氨或CO甲烷化反应最佳催化剂为前过渡金属、而CO/NO氧化等为后过渡金属这一典型催化现象的物理图像。最后,针对火山型曲线理论框架在实际催化剂理论筛选寻优中的应用,我们简要综述了本课题组近年来在光解水制氢Pt基助催化剂和染料敏化太阳能电池的对电极材料设计方面的理论进展。     

Pyridoxal-5′-phosphate-dependent catalytic antibodies

Cofactors—i.e., metal ions and coenzymes—extend the catalytic scope of enzymes and might have been among the first biological catalysts. They may be expected to efficiently extend the catalytic potential of antibodies. Monoclonal antibodies (MAbs) against N^α-phosphopyridoxyl-l-lysine were screened for 1) binding of 5′-phosphopyridoxyl amino acids, 2) binding of the planar Schiff base of pyridoxal-5′-phosphate (PLP) and amino acids, the first intermediate of all PLP-dependent reactions, and 3), catalysis of the PLP-dependent α, β-elimination reaction with β-chloro-D/L-alanine. Antibody 15A9 fulfilled all criteria and was also found to catalyze the cofactor-dependent transamination reaction of hydrophobic D-amino acids and oxo acids (k′ _cat=0.42 min⁻¹ with D-alanine at 25°C). No other reactions with either D- or L-amino acids were detected. PLP markedly contributes to catalytic effecacy—it is a 10⁴ times more efficient acceptor of the amino group than pyruvate. The antibody ensures reaction specificity, stereospecificity, and substrate specificity, and further accelerates the transamination reaction (k′ _cat(Ab)/k′ _cat(PLP)=5×10³). The successive screening steps simulate the selection criteria that might have been operative in the evolution of protein-assisted psyridoxal catalysis.     

Substrate binding and activation via pendant hydrogen-bonding groups as an approach to biomimetic homogeneous catalysis

In a biomimetic approach to organometallic catalysis, pendant hydrogen-bonding groups are shown to influence the chemistry of ligand binding and activation in an iridium complex. Such groups can bind a substrate by hydrogen bonding and so offer the possibility of a biomimetic approach to catalysis where binding is controlled via molecular recognition. Because catalyst design in this area may be challenging, combinatorial and rapid screening methods may be needed to assay potential catalysts and initial progress on developing these methods for hydrosilation of alkenes and imines is described. Catalysis of aldehyde imination and the origin of pK_a changes of bound H₂ are discussed.     

Binding site optimisation for artificial enzymes by diffusion NMR of small molecules

A binding site optimisation protocol for the design of artificial enzymes based on "small molecule-small molecule" binding studies by diffusion NMR is presented. Since the reaction chosen was the hydrolysis of ester 1 ([4-(4-carboxy-1-oxobutyl)-aminobenzyl]-phenethyl ester), an analogous phosphonate ester 2 ([4-(4-carboxy-1-oxobutyl)-aminobenzyl]-phosphonic phenethyl ester) was selected as a suitable transition state analogue (TSA). The key objective of the NMR studies was to find a unit with functional groups capable of binding to the acidic sites of the TSA. Nine dipeptides, mainly with basic and hydroxyl groups, were used and their affinity to the TSA was studied by measuring the change in the diffusion coefficient, D(pep), upon binding by pulse field gradient NMR. The value of D(pep) at 298 K in D(2)O at pD 5, 7 and 10 was measured both in free solution, and mixtures containing one dipeptide and the TSA. As both components are low molecular weight species with M < 500, a TSA-to-dipeptide ratio of 10:1 was used to detect significant changes in D(pep). The results revealed that dipeptides with basic residues show higher affinity to the TSA than those with hydroxyl or aliphatic side chains in aqueous solutions. The dipeptide showing the most significant relative change in D(pep) was H-Arg-Arg-OH, and the binding constant was estimated to be 86 L M(-1) by measuring D(pep) at varying concentrations of the TSA. In addition, binding of the TSA to a new water-soluble polymer with a polyallylamine backbone and randomly distributed Arg-Arg binding sites was examined, and the binding constant was estimated to be > or =1500 L M(-1). As confirmed by further catalytic activity tests, polymers containing Arg-Arg as a binding site are capable of significant rate accelerations in the hydrolysis of ester 1.     

The origins of noncovalent catalysis of intermolecular Diels-Alder reactions by cyclodextrins,self-assembling capsules,antibodies, and RNAses

The catalysis of Diels-Alder reactions by noncovalent binding by synthetic, protein, and nucleic acid hosts has been surveyed and compared. These catalysts consist of binding cavities that form complexes containing both the diene and the dienophile; the cycloaddition reaction occurs in the cavity. The binding requires no formation of covalent bonds and is driven principally by the hydrophobic (or solvophobic) effect. A molecular mechanics and dynamics study of the cyclodextrin catalysis of a Diels-Alder reaction is used to exemplify and probe this form of catalysis. Detailed kinetic data is available for catalysis by antibodies, RNA, cyclodextrins, and Rebek's tennis ball capsules. Some of these catalysts stabilize the reactants more than the transition state and consequently will only have catalytic effect under conditions of low substrate-to-catalyst ratios. None of the hosts achieve significant specific binding of transition states that is the hallmark of enzyme catalysis.     

Designing a new Diels-Alderase: a combinatorial, semirational approach including dynamic optimization

A computationally inexpensive design strategy involving 'semirational' screening for enzymatic catalysis is presented. The protocol is based on well-established computational methods and represents a holistic approach to the catalytic process. The model reaction studied here is the Diels-Alder, for which a successful computational design has recently been published (Siegel, J. B. et al. Science 2010, 329, 309-313). While it is a leap forward in the field of computational design, the focus on designing only a small fraction of the active site gives little control over dynamics. Our approach explicitly incorporates mutagenesis and the analysis of binding events and transition states, and a promising enzyme-substrate candidate is generated with relatively little effort. We estimate catalytic rate accelerations of up to 10?.     

A Phage Display-Identified Short Peptide Capable of Hydrolyzing Calcium Pyrophosphate Crystals—The Etiological Factor of Chondrocalcinosis

Chondrocalcinosis is a metabolic disease caused by the presence of calcium pyrophosphate dihydrate crystals in the synovial fluid. The goal of our endeavor was to find out whether short peptides could be used as a dissolving factor for such crystals. In order to identify peptides able to dissolve crystals of calcium pyrophosphate, we screened through a random library of peptides using a phage display. The first screening was designed to select phages able to bind the acidic part of alendronic acid (pyrophosphate analog). The second was a catalytic assay in the presence of crystals. The best-performing peptides were subsequently chemically synthesized and rechecked for catalytic properties. One peptide, named R25, turned out to possess some hydrolytic activity toward crystals. Its catalysis is Mg²⁺-dependent and also works against soluble species of pyrophosphate.     

Towards Platinum(II) Complexes for in cellulo Applications: Synthesis,Characterization, Biological and Catalytic Evaluation

With the aim of achieving bioorthogonal intracellular catalysis, a library of platinum(II) complexes was synthesized. Their non-toxicity to living cells was demonstrated and their catalytic activity was evaluated on a cyclization reaction leading to a highly fluorescent coumarin. None of the platinum complexes showed any catalytic activity for coumarin synthesis. Still, we demonstrated that the silver salt AgSbF₆ commonly used to ‘activate’ metal catalysts by removing a chloride is a very efficient catalyst for the studied intramolecular cyclization reaction.     

Gold‐Triggered Uncaging Chemistry in Living Systems

Recent advances in bioorthogonal catalysis are increasing the capacity of researchers to manipulate the fate of molecules in complex biological systems. A bioorthogonal uncaging strategy is presented, which is triggered by heterogeneous gold catalysis and facilitates the activation of a structurally diverse range of therapeutics in cancer cell culture. Furthermore, this solid‐supported catalytic system enabled locally controlled release of a fluorescent dye into the brain of a zebrafish for the first time, offering a novel way to modulate the activity of bioorthogonal reagents in the most fragile and complex organs.     

Array-based split-pool combinatorial screening of potential catalysts

A new method for screening split-pool combinatorial libraries for catalytic activity is described. Site-selective detection of catalytic activity for solution-based reactions was made possible without cofunctionalizing beads or adding diffusion-limiting matrixes. This was done by spatially separating resin-bound catalysts on an adhesive array on a microscope slide and introducing the reacting liquid to the top of the slide. Convective mixing and evaporation was controlled using a cover slide and imaging both the formation of products within active beads and the diffusion of products out of the beads. Colored reaction products and pH-sensitive indicators were used to visually detect catalytically active beads in the presence of inactive ones. Quantitative analyses of the images support the assumption that color intensities can be used to assess the quality of hits from a combinatorial screen. The Knoevenagel condensation reaction catalysis as well as esterase screening using methyl red were used to validate the approach. Using the esterase data, it was shown that some information on activity could also be extracted from the colored plume surrounding individual beads although the precision is not as good as that from direct measurement of absorbance through the bead. It was also found that the distribution of products within a single bead can also be gleaned from the absorbance data for different-sized beads.     

New fluorogenic probes for oxygen and carbene transfer: a sensitive assay for single bead-supported catalysts.

A high-throughput screening assay for atom transfer catalysis has been developed. This assay is based on two probes, developed herein, which generate highly fluorescent products upon carbene or oxygen atom transfer. The emission wavelength of probes 1 and 5 shift significantly (up to 90 nm) upon epoxidation, allowing detection of product at 3% conversion. Probe 7 is not fluorescent, while fluorescence emission by carbene insertion/rearrangement product 8 allows detection at less than 1% conversion. Such sensitivity allows for examination of single-bead reactions in a high throughput array format (1536 wells per plate), and provides a broad detection window ranging from single to high turnover numbers. Thousands of metal complexes are evaluated in a single screening experiment. Preliminary screening of a diverse ligand library with probe 7 in the presence of Rh(II) uncovered new catalysts capable of cyclopropanation and C-H insertion.     

Selection and rapid purification of murine antibody fragments that bind a transition-state analog by phage display

Functional antibody fragments may be displayed on the surface of filamentous bacteriophage by introducing variable region genes into the viral genome at a gene encoding a viral coat protein. “Phage display” enables the isolation of antibody genes from large libraries according to the binding specificities they encode. We have constructed a new phage-display vector encoding a polyhistidine tag that has been used for rapid purification of soluble antibody fragments. An antibody library derived from immunized mice was cloned into this vector. This library was panned against the transition state analog RT3, and a high proportion of binders isolated after two rounds of panning. PCR analysis revealed that there were 24 different pattern groups. Sequencing of 15 clones within the major pattern group revealed 10 related clones with a range of point mutations. Thus, phage display can provide a large diverse repertoire of candidate catalytic antibodies based on TSA selection and screening.     

Millisecond dynamics in glutaredoxin during catalytic turnover is dependent on substrate binding and absent in the resting states

Conformational dynamics is important for enzyme function. Which motions of enzymes determine catalytic efficiency and whether the same motions are important for all enzymes, however, are not well understood. Here we address conformational dynamics in glutaredoxin during catalytic turnover with a combination of NMR magnetization transfer, R(2) relaxation dispersion, and ligand titration experiments. Glutaredoxins catalyze a glutathione exchange reaction, forming a stable glutathinoylated enzyme intermediate. The equilibrium between the reduced state and the glutathionylated state was biochemically tuned to exchange on the millisecond time scale. The conformational changes of the protein backbone during catalysis were followed by (15)N nuclear spin relaxation dispersion experiments. A conformational transition that is well described by a two-state process with an exchange rate corresponding to the glutathione exchange rate was observed for 23 residues. Binding of reduced glutathione resulted in competitive inhibition of the reduced enzyme having kinetics similar to that of the reaction. This observation couples the motions observed during catalysis directly to substrate binding. Backbone motions on the time scale of catalytic turnover were not observed for the enzyme in the resting states, implying that alternative conformers do not accumulate to significant concentrations. These results infer that the turnover rate in glutaredoxin is governed by formation of a productive enzyme-substrate encounter complex, and that catalysis proceeds by an induced fit mechanism rather than by conformer selection driven by intrinsic conformational dynamics.     

When does the Michaelis-Menten equation hold for fluctuating enzymes?

Enzymes are dynamic entities: both their conformation and catalytic activity fluctuate over time. When such fluctuations are relatively fast, it is not surprising that the classical Michaelis-Menten (MM) relationship between the steady-state enzymatic velocity and the substrate concentration still holds. However, recent single-molecule experiments have shown that this is the case even for an enzyme whose catalytic activity fluctuates on the 10(-4)-10 s range. The purpose of this paper is to examine various scenarios in which slowly fluctuating enzymes would still obey the MM relationship. Specifically, we consider (1) the quasi-static condition (e.g., the conformational fluctuation of the enzyme-substrate complex is much slower than binding, catalysis, and the conformational fluctuations of the free enzyme), (2) the quasi-equilibrium condition (when the substrate dissociation is much faster than catalysis, irrespective of the time scales or amplitudes of conformational fluctuations), and (3) the conformational-equilibrium condition (when the dissociation and catalytic rates depend on the conformational coordinate in the same way). For each of these scenarios, the physical meaning of the apparent Michaelis constant and catalytic rate constant is provided. Finally, as an example, the theoretical analysis of a recent single-molecule enzyme assay is considered in light of the perspectives presented in this paper.     

Characterizing the protonation states of the catalytic residues in apo and substrate-bound human T-cell leukemia virus type 1 protease

Human T-cell leukemia virus type 1 (HTLV-1) protease is an attractive target when developing inhibitors to treat HTLV-1 associated diseases. To study the catalytic mechanism and design novel HTLV-1 protease inhibitors, the protonation states of the two catalytic aspartic acid residues must be determined. Free energy simulations have been conducted to study the proton transfer reaction between the catalytic residues of HTLV-1 protease using a combined quantum mechanical and molecular mechanical (QM/MM) molecular dynamics simulation. The free energy profiles for the reaction in the apo-enzyme and in an enzyme – substrate complex have been obtained. In the apo-enzyme, the two catalytic residues are chemically equivalent and are expected to be both unprotonated. Upon substrate binding, the catalytic residues of HTLV-1 protease evolve to a singly protonated state, in which the OD1 of Asp32 is protonated and forms a hydrogen bond with the OD1 of Asp32′, which is unprotonated. The HTLV-1 protease–substrate complex structure obtained from this simulation can serve as the Michaelis complex structure for further mechanistic studies of HTLV-1 protease while providing a receptor structure with the correct protonation states for the active site residues toward the design of novel HTLV-1 protease inhibitors through virtual screening.     

聚合物稳定的金纳米簇催化：理论计算与实验的相互影响

平均粒径为2–10 nm的聚合物稳定的Au纳米簇(NCs)表现出独特的催化性能。多个研究表明，影响聚合物稳定的Au NCs催化活性的主要因素为： Au NC尺寸的控制、聚合物的选择以及反应条件的优化。这是由于聚合物稳定的Au NCs在多个催化反应中表现出明显的尺寸效应，其催化活性也因所采用的聚合物和反应条件的不同而不同。为了阐明影响聚合物稳定的Au NCs催化活性的内在原因，众多研究者关注于聚合物稳定的Au NCs催化中的理论计算与实验的相互影响。本文主要总结了聚合物稳定的Au NCs中这种相互影响的研究进展。