1
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Timofeeva AM, Shayakhmetova LS, Nikitin AO, Sedykh TA, Matveev AL, Shanshin DV, Volosnikova EA, Merkuleva IA, Shcherbakov DN, Tikunova NV, Sedykh SE, Nevinsky GA. Natural Antibodies Produced in Vaccinated Patients and COVID-19 Convalescents Hydrolyze Recombinant RBD and Nucleocapsid (N) Proteins. Biomedicines 2024; 12:1007. [PMID: 38790969 PMCID: PMC11118737 DOI: 10.3390/biomedicines12051007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/30/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Antibodies are protein molecules whose primary function is to recognize antigens. However, recent studies have demonstrated their ability to hydrolyze specific substrates, such as proteins, oligopeptides, and nucleic acids. In 2023, two separate teams of researchers demonstrated the proteolytic activity of natural plasma antibodies from COVID-19 convalescents. These antibodies were found to hydrolyze the S-protein and corresponding oligopeptides. Our study shows that for antibodies with affinity to recombinant structural proteins of the SARS-CoV-2: S-protein, its fragment RBD and N-protein can only hydrolyze the corresponding protein substrates and are not cross-reactive. By using strict criteria, we have confirmed that this proteolytic activity is an intrinsic property of antibodies and is not caused by impurities co-eluting with them. This discovery suggests that natural proteolytic antibodies that hydrolyze proteins of the SARS-CoV-2 virus may have a positive impact on disease pathogenesis. It is also possible for these antibodies to work in combination with other antibodies that bind specific epitopes to enhance the process of virus neutralization.
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Affiliation(s)
- Anna M. Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia (S.E.S.)
- Advanced Engineering School, Novosibirsk State University, 630090 Novosibirsk, Russia
| | | | - Artem O. Nikitin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia (S.E.S.)
- Advanced Engineering School, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Tatyana A. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia (S.E.S.)
| | - Andrey L. Matveev
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia (S.E.S.)
| | - Daniil V. Shanshin
- State Research Center of Virology and Biotechnology Vector, 630559 Koltsovo, Russia (D.N.S.)
| | | | - Iuliia A. Merkuleva
- State Research Center of Virology and Biotechnology Vector, 630559 Koltsovo, Russia (D.N.S.)
| | - Dmitriy N. Shcherbakov
- State Research Center of Virology and Biotechnology Vector, 630559 Koltsovo, Russia (D.N.S.)
- Department of Physical-Chemistry, Biology and Biotechnology, Altay State University, 656049 Barnaul, Russia
| | - Nina V. Tikunova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia (S.E.S.)
- Advanced Engineering School, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia (S.E.S.)
- Advanced Engineering School, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Georgy A. Nevinsky
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia (S.E.S.)
- Advanced Engineering School, Novosibirsk State University, 630090 Novosibirsk, Russia
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2
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Ouyang Y, O'Hagan MP, Willner B, Willner I. Aptamer-Modified Homogeneous Catalysts, Heterogenous Nanoparticle Catalysts, and Photocatalysts: Functional "Nucleoapzymes", "Aptananozymes", and "Photoaptazymes". ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2210885. [PMID: 37083210 DOI: 10.1002/adma.202210885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/18/2023] [Indexed: 05/03/2023]
Abstract
Conjugation of aptamers to homogeneous catalysts ("nucleoapzymes"), heterogeneous nanoparticle catalysts ("aptananozymes"), and photocatalysts ("photoaptazymes") yields superior catalytic/photocatalytic hybrid nanostructures emulating functions of native enzymes and photosystems. The concentration of the substrate in proximity to the catalytic sites ("molarity effect") or spatial concentration of electron-acceptor units in spatial proximity to the photosensitizers, by aptamer-ligand complexes, leads to enhanced catalytic/photocatalytic efficacies of the hybrid nanostructures. This is exemplified by sets of "nucleoapzymes" composed of aptamers conjugated to the hemin/G-quadruplex DNAzymes or metal-ligand complexes as catalysts, catalyzing the oxidation of dopamine to aminochrome, oxygen-insertion into the Ar─H moiety of tyrosinamide and the subsequent oxidation of the catechol product into aminochrome, or the hydrolysis of esters or ATP. Also, aptananozymes consisting of aptamers conjugated to Cu2+ - or Ce4+ -ion-modified C-dots or polyadenine-stabilized Au nanoparticles acting as catalysts oxidizing dopamine or operating bioreactor biocatalytic cascades, are demonstrated. In addition, aptamers conjugated to the Ru(II)-tris-bipyridine photosensitizer or the Zn(II) protoporphyrin IX photosensitizer provide supramolecular photoaptazyme assemblies emulating native photosynthetic reaction centers. Effective photoinduced electron transfer followed by the catalyzed synthesis of NADPH or the evolution of H2 is demonstrated by the photosystems. Structure-function relationships dictate the catalytic and photocatalytic efficacies of the systems.
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Affiliation(s)
- Yu Ouyang
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Michael P O'Hagan
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Bilha Willner
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Itamar Willner
- The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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3
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Lin M, Eubanks LM, Karadkhelkar NM, Blake S, Janda KD. Catalytic Antibody Blunts Carfentanil-Induced Respiratory Depression. ACS Pharmacol Transl Sci 2023; 6:802-811. [PMID: 37200811 PMCID: PMC10186356 DOI: 10.1021/acsptsci.3c00031] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Indexed: 05/20/2023]
Abstract
Carfentanil, the most potent of the fentanyl analogues, is at the forefront of synthetic opioid-related deaths, second to fentanyl. Moreover, the administration of the opioid receptor antagonist naloxone has proven inadequate for an increasing number of opioid-related conditions, often requiring higher/additional doses to be effective, as such interest in alternative strategies to combat more potent synthetic opioids has intensified. Increasing drug metabolism would be one strategy to detoxify carfentanil; however, carfentanil's major metabolic pathways involve N-dealkylation or monohydroxylation, which do not lend themselves readily to exogenous enzyme addition. Herein, we report, to our knowledge, the first demonstration that carfentanil's methyl ester when hydrolyzed to its acid was found to be 40,000 times less potent than carfentanil in activating the μ-opioid receptor. Physiological consequences of carfentanil and its acid were also examined through plethysmography, and carfentanil's acid was found to be incapable of inducing respiratory depression. Based upon this information, a hapten was chemically synthesized and immunized, allowing the generation of antibodies that were screened for carfentanil ester hydrolysis. From the screening campaign, three antibodies were found to accelerate the hydrolysis of carfentanil's methyl ester. From this series of catalytic antibodies, the most active underwent extensive kinetic analysis, allowing us to postulate its mechanism of hydrolysis against this synthetic opioid. In the context of potential clinical applications, the antibody, when passively administered, was able to reduce respiratory depression induced by carfentanil. The data presented supports further development of antibody catalysis as a biologic strategy to complement carfentanil overdose reversal.
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Affiliation(s)
- Mingliang Lin
- Departments of Chemistry
and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute
of Research and Medicine (WIRM), The Scripps
Research Institute, La Jolla, California 92037, United States
| | - Lisa M. Eubanks
- Departments of Chemistry
and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute
of Research and Medicine (WIRM), The Scripps
Research Institute, La Jolla, California 92037, United States
| | - Nishant M. Karadkhelkar
- Departments of Chemistry
and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute
of Research and Medicine (WIRM), The Scripps
Research Institute, La Jolla, California 92037, United States
| | - Steven Blake
- Departments of Chemistry
and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute
of Research and Medicine (WIRM), The Scripps
Research Institute, La Jolla, California 92037, United States
| | - Kim D. Janda
- Departments of Chemistry
and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute
of Research and Medicine (WIRM), The Scripps
Research Institute, La Jolla, California 92037, United States
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4
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Catalytic Antibodies: Design, Expression, and Their Applications in Medicine. Appl Biochem Biotechnol 2023; 195:1514-1540. [PMID: 36222989 PMCID: PMC9554387 DOI: 10.1007/s12010-022-04183-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 01/24/2023]
Abstract
Catalytic antibodies made it feasible to develop new catalysts, which had previously been the subject of research. Scientists have discovered natural antibodies that can hydrolyze substrates such as nucleic acids, proteins, and polysaccharides during decades of research, as well as several ways of producing antibodies with specialized characteristics and catalytic functions. These antibodies are widely used in chemistry, biology, and medicine. Catalytic antibodies can continue to play a role and even fully prevent the emergence of autoimmune disorders, especially in the field of infection and immunity, where the process of its occurrence and development often takes a long time. In this work, the development, design and evolution methodologies, and the expression systems and applications of catalytic antibodies, are discussed. Trial registration: not applicable.
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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Prabhakar R. Promiscuous Catalytic Activity of a Binuclear Metallohydrolase: Peptide and Phosphoester Hydrolyses. J Chem Inf Model 2022; 62:2466-2480. [PMID: 35451306 DOI: 10.1021/acs.jcim.2c00214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, chemical promiscuity of a binuclear metallohydrolase Streptomyces griseus aminopeptidase (SgAP) has been investigated using DFT calculations. SgAP catalyzes two diverse reactions, peptide and phosphoester hydrolyses, using its binuclear (Zn-Zn) core. On the basis of the experimental information, mechanisms of these reactions have been investigated utilizing leucine p-nitro aniline (Leu-pNA) and bis(4-nitrophenyl) phosphate (BNPP) as the substrates. The computed barriers of 16.5 and 16.8 kcal/mol for the most plausible mechanisms proposed by the DFT calculations are in good agreement with the measured values of 13.9 and 18.3 kcal/mol for the Leu-pNA and BNPP hydrolyses, respectively. The former was found to occur through the transfer of two protons, while the latter with only one proton transfer. They are in line with the experimental observations. The cleavage of the peptide bond was the rate-determining process for the Leu-pNA hydrolysis. However, the creation of the nucleophile and its attack on the electrophile phosphorus atom was the rate-determining step for the BNPP hydrolysis. These calculations showed that the chemical nature of the substrate and its binding mode influence the nucleophilicity of the metal bound hydroxyl nucleophile. Additionally, the nucleophilicity was found to be critical for the Leu-pNA hydrolysis, whereas double Lewis acid activation was needed for the BNPP hydrolysis. That could be one of the reasons why peptide hydrolysis can be catalyzed by both mononuclear and binuclear metal cofactors containing hydrolases, while phosphoester hydrolysis is almost exclusively by binuclear metallohydrolases. These results will be helpful in the development of versatile catalysts for chemically distinct hydrolytic reactions.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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6
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Essential Protective Role of Catalytically Active Antibodies (Abzymes) with Redox Antioxidant Functions in Animals and Humans. Int J Mol Sci 2022; 23:ijms23073898. [PMID: 35409256 PMCID: PMC8999700 DOI: 10.3390/ijms23073898] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/24/2022] [Accepted: 03/26/2022] [Indexed: 12/13/2022] Open
Abstract
During the life of aerobic organisms, the oxygen resulting from numerous reactions is converted into reactive oxygen species (ROS). Many ROS are dangerous due to their high reactivity; they are strong oxidants, and react with various cell components, leading to their damage. To protect against ROS overproduction, enzymatic and non-enzymatic systems are evolved in aerobic cells. Several known non-enzymatic antioxidants have a relatively low specific antioxidant activity. Superoxide dismutases, catalase, glutathione peroxidase, glutathione S-transferase, thioredoxin, and the peroxiredoxin families are the most important enzyme antioxidants. Artificial antibodies catalyzing redox reactions using different approaches have been created. During the past several decades, it has been shown that the blood and various biological fluids of humans and animals contain natural antibodies that catalyze different redox reactions, such as classical enzymes. This review, for the first time, summarizes data on existing non-enzymatic antioxidants, canonical enzymes, and artificial or natural antibodies (abzymes) with redox functions. Comparing abzymes with superoxide dismutase, catalase, peroxide-dependent peroxidase, and H2O2-independent oxidoreductase activities with the same activities as classical enzymes was carried out. The features of abzymes with the redox activities are described, including their exceptional diversity in the optimal pH values, dependency and independence on various metal ions, and the reaction rate constants for healthy donors and patients with different autoimmune diseases. The entire body of evidence indicates that abzymes with redox antioxidant activities existing in the blood for a long time compared to enzymes are an essential part of the protection system of humans and animals from oxidative stress.
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7
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Lyu Y, Scrimin P. Mimicking Enzymes: The Quest for Powerful Catalysts from Simple Molecules to Nanozymes. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01219] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yanchao Lyu
- University of Padova, Department of Chemical Sciences, via Marzolo, 1, 35131 Padova, Italy
| | - Paolo Scrimin
- University of Padova, Department of Chemical Sciences, via Marzolo, 1, 35131 Padova, Italy
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8
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Lin M, Ellis B, Eubanks LM, Janda KD. Pharmacokinetic Approach to Combat the Synthetic Cannabinoid PB-22. ACS Chem Neurosci 2021; 12:2573-2579. [PMID: 34254505 DOI: 10.1021/acschemneuro.1c00360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Synthetic cannabinoids are part of a group of drugs called new psychoactive substances. Most of these cannabinoids are unregulated, and there are no therapeutic treatments for their addictive properties or reversing a potential overdose. Vaccination and catalytic antibodies strategies were investigated to assess their ability to blunt the psychoactive properties of the cannabinoid PB-22. To complement these antibody concentric investigations, we also disclose the discovery of the enzymatic degradation of this cannabinoid. Serum factors including albumin and carboxylesterase were found to catalyze the hydrolysis of PB-22. Affinity, kinetics, animal behavior, and biodistribution studies were utilized to evaluate the efficiency of these pharmacokinetic approaches. Our findings suggest simple antibody binding as the most efficacious means for altering PB-22's effect on the brain. Catalytic approaches only translated to esterases being capable of PB-22's degradation with a catalytic antibody approach providing no proclivity for PB-22's hydrolysis. Pharmacokinetic approaches provide a powerful strategy for treating substance abuse disorders and overdose for drugs where no therapeutic is available.
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Affiliation(s)
- Mingliang Lin
- Department of Chemistry, Department of Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, and The Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Beverly Ellis
- Department of Chemistry, Department of Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, and The Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Lisa M. Eubanks
- Department of Chemistry, Department of Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, and The Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Kim D. Janda
- Department of Chemistry, Department of Immunology and Microbial Science, The Skaggs Institute for Chemical Biology, and The Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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9
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Harmon NM, Huang X, Hsiao CHC, Wiemer AJ, Wiemer DF. Incorporation of a FRET pair within a phosphonate diester. Bioorg Chem 2021; 114:105048. [PMID: 34126576 DOI: 10.1016/j.bioorg.2021.105048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/25/2021] [Accepted: 05/28/2021] [Indexed: 10/21/2022]
Abstract
Cell-cleavable protecting groups are an effective tactic for construction of biological probes because such compounds can improve problems with instability, solubility, and cellular uptake. Incorporation of fluorescent groups in the protecting groups may afford useful probes of cellular functions, especially for payloads containing phosphonates that would be highly charged if not protected, but little is known about the steric or electronic factors that impede release of the payload. In this report we present a strategy for the synthesis of a coumarin fluorophore and a 4-((4-(dimethylamino)phenyl)diazenyl)benzoic acid (DABCYL) ester chromophore incorporated as a FRET pair within a single phosphonate. Such compounds were designed to deliver a BTN3A1 ligand payload to its intracellular receptor. Both final products and some synthetic intermediates were evaluated for their ability to undergo metabolic activation in γδ T cell functional assays, and for their photophysical properties by spectrophotometry. One phosphonate bearing a DABCYL acyloxyester and a novel tyramine-linked coumarin fluorophore exhibited strong, rapid, and potent cellular activity for γδ T cell stimulation and also showed FRET interactions. This strategy demonstrates that bioactivatable phosphonates containing FRET pairs can be utilized to develop probes to monitor cellular uptake of otherwise charged payloads.
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Affiliation(s)
- Nyema M Harmon
- Department of Chemistry, The University of Iowa, Iowa City, IA 52245, United States
| | - Xueting Huang
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, United States
| | | | - Andrew J Wiemer
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269, United States; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, United States
| | - David F Wiemer
- Department of Chemistry, The University of Iowa, Iowa City, IA 52245, United States; Department of Pharmacology, University of Iowa, Iowa City, IA 52242, United States.
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10
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Bhaskaran A, Aitken HM, Xiao Z, Blyth M, Nothling MD, Kamdar S, O'Mara ML, Connal LA. Enzyme inspired polymer functionalized with an artificial catalytic triad. POLYMER 2021. [DOI: 10.1016/j.polymer.2021.123735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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11
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Zhang Q, Shu J, Zhang Y, Xu Z, Yue J, Liu X, Xu B, Chen Z, Jiang W. Structures and esterolytic reactivity of novel binuclear copper(ii) complexes with reduced l-serine Schiff bases as mimic carboxylesterases. Dalton Trans 2020; 49:10261-10269. [PMID: 32672259 DOI: 10.1039/d0dt01823f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three novel binuclear copper(ii) complexes with reduced l-serine Schiff bases were synthesized and their structures were analyzed with single-crystal X-ray diffraction and DFT calculations. The crystal data revealed that all of these binuclear complexes are chiral. Both 5-halogenated (bromo- and chloro-) binuclear complexes exhibit right-handed helix structural character. Interestingly, the 5-methyl-containing analogue has a two-dimensional pore structure. In this paper, the esterolysis reactivity of the as-prepared complexes shows that in the hydrolysis of p-nitrophenyl acetate (PNPA) these three complexes provide 26, 18, 40-fold rate acceleration as compared to the spontaneous hydrolysis of PNPA at pH 7.0, respectively. Under selected conditions, in excess buffered aqueous solution a rate enhancement by three orders of magnitude was observed for the catalytic hydrolysis of another carboxylic ester, p-nitrophenyl picolinate (PNPP). These complexes efficiently promoted PNPP hydrolysis in a micellar solution of cetyltrimethylammonium bromide (CTAB), giving rise to a rate enhancement in excess of four orders of magnitude, which is approximately 2.0-3.2 times higher than that in the buffer.
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Affiliation(s)
- Qin Zhang
- School of Chemistry and Environmental Engineering, Sichuan University of Science & Engineering, Sichuan Zigong 643000, P. R. China.
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12
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Abstract
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The enormous rate accelerations observed
for many enzyme catalysts
are due to strong stabilizing interactions between the protein and
reaction transition state. The defining property of these catalysts
is their specificity for binding the transition state with a much
higher affinity than substrate. Experimental results are presented
which show that the phosphodianion-binding energy of phosphate monoester
substrates is used to drive conversion of their protein catalysts
from flexible and entropically rich ground states to stiff and catalytically
active Michaelis complexes. These results are generalized to other
enzyme-catalyzed reactions. The existence of many enzymes in flexible,
entropically rich, and inactive ground states provides a mechanism
for utilization of ligand-binding energy to mold these catalysts into
stiff and active forms. This reduces the substrate-binding energy
expressed at the Michaelis complex, while enabling the full and specific
expression of large transition-state binding energies. Evidence is
presented that the complexity of enzyme conformational changes increases
with increases in the enzymatic rate acceleration. The requirement
that a large fraction of the total substrate-binding energy be utilized
to drive conformational changes of floppy enzymes is proposed to favor
the selection and evolution of protein folds with multiple flexible
unstructured loops, such as the TIM-barrel fold. The effect of protein
motions on the kinetic parameters for enzymes that undergo ligand-driven
conformational changes is considered. The results of computational
studies to model the complex ligand-driven conformational change in
catalysis by triosephosphate isomerase are presented.
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Affiliation(s)
- John P Richard
- Department of Chemistry , SUNY, University at Buffalo , Buffalo , New York 14260-3000 , United States
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13
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Sivakumar R, Thanikachalam V, Kim BG, Kim SD. Synthesis of Secondary and Tertiary Oxime Carbamate Derivatives and their Structure-Dependent Bioactivity. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Bong-Gi Kim
- Department of Organic and Nano System Engineering; Konkuk University; Seoul 05029 Korea
| | - Sung Dong Kim
- Department of Organic and Nano System Engineering; Konkuk University; Seoul 05029 Korea
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14
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Shahsavarian MA, Chaaya N, Costa N, Boquet D, Atkinson A, Offmann B, Kaveri SV, Lacroix-Desmazes S, Friboulet A, Avalle B, Padiolleau-Lefèvre S. Multitarget selection of catalytic antibodies with β-lactamase activity using phage display. FEBS J 2017; 284:634-653. [PMID: 28075071 DOI: 10.1111/febs.14012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 10/29/2016] [Accepted: 01/09/2017] [Indexed: 01/24/2023]
Abstract
β-lactamase enzymes responsible for bacterial resistance to antibiotics are among the most important health threats to the human population today. Understanding the increasingly vast structural motifs responsible for the catalytic mechanism of β-lactamases will help improve the future design of new generation antibiotics and mechanism-based inhibitors of these enzymes. Here we report the construction of a large murine single chain fragment variable (scFv) phage display library of size 2.7 × 109 with extended diversity by combining different mouse models. We have used two molecularly different inhibitors of the R-TEM β-lactamase as targets for selection of catalytic antibodies with β-lactamase activity. This novel methodology has led to the isolation of five antibody fragments, which are all capable of hydrolyzing the β-lactam ring. Structural modeling of the selected scFv has revealed the presence of different motifs in each of the antibody fragments potentially responsible for their catalytic activity. Our results confirm (a) the validity of using our two target inhibitors for the in vitro selection of catalytic antibodies endowed with β-lactamase activity, and (b) the plasticity of the β-lactamase active site responsible for the wide resistance of these enzymes to clinically available inhibitors and antibiotics.
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Affiliation(s)
- Melody A Shahsavarian
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, France.,UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France
| | - Nancy Chaaya
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, France.,UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France
| | - Narciso Costa
- Service de Pharmacologie et d'Immuno-analyse (SPI), IBITECS, CEA, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Didier Boquet
- Service de Pharmacologie et d'Immuno-analyse (SPI), IBITECS, CEA, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alexandre Atkinson
- Unité Fonctionnalité et Ingénierie des Protéines (UFIP), UMR CNRS 6286, Université de Nantes, France
| | - Bernard Offmann
- Unité Fonctionnalité et Ingénierie des Protéines (UFIP), UMR CNRS 6286, Université de Nantes, France
| | - Srini V Kaveri
- UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U 1138, Paris, France.,Equipe Immunopathology and Therapeutic Immunointervention, Centre de Recherche des Cordeliers, Paris, France.,International Associated Laboratory IMPACT, Institut National de la Santé et de la Recherche Médicale-France and Indian Council of Medical Research-India, National Institute of Immunohaemotology, Mumbai, India
| | - Sébastien Lacroix-Desmazes
- UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U 1138, Paris, France.,Equipe Immunopathology and Therapeutic Immunointervention, Centre de Recherche des Cordeliers, Paris, France.,International Associated Laboratory IMPACT, Institut National de la Santé et de la Recherche Médicale-France and Indian Council of Medical Research-India, National Institute of Immunohaemotology, Mumbai, India
| | - Alain Friboulet
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, France.,UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France
| | - Bérangère Avalle
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, France.,UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France
| | - Séverine Padiolleau-Lefèvre
- Génie Enzymatique et Cellulaire (GEC), FRE 3580 CNRS, Université de Technologie de Compiègne, France.,UMR S 1138, Sorbonne Universités, Université Pierre et Marie Curie - Paris VI, France
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15
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16
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Subramanyam C, Madhava G, Thaslim Basha SK, Rasheed S, Sankar AU, Raju CN. Bismuth(III) Chloride Mediated Michaelis–Arbuzov Reaction: A Facile Synthesis of Substituted Arylphosphonates/Phosphinates and Bioactivity Evaluation. PHOSPHORUS SULFUR 2015. [DOI: 10.1080/10426507.2015.1043048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Ch. Subramanyam
- Department of Chemistry, Sri Venkateswara University, Tirupati, 517 502, India
| | - G. Madhava
- Department of Chemistry, Sri Venkateswara University, Tirupati, 517 502, India
| | - S. K. Thaslim Basha
- Department of Chemistry, Sri Venkateswara University, Tirupati, 517 502, India
| | - S. Rasheed
- Department of Chemistry, Sri Venkateswara University, Tirupati, 517 502, India
| | - A. Uday Sankar
- Department of Biotechnology, Vikrama Simhapuri University, Nellore, India
| | - C. Naga Raju
- Department of Chemistry, Sri Venkateswara University, Tirupati, 517 502, India
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17
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Moroz YS, Dunston TT, Makhlynets OV, Moroz OV, Wu Y, Yoon JH, Olsen AB, McLaughlin JM, Mack KL, Gosavi PM, van Nuland NAJ, Korendovych IV. New Tricks for Old Proteins: Single Mutations in a Nonenzymatic Protein Give Rise to Various Enzymatic Activities. J Am Chem Soc 2015; 137:14905-11. [PMID: 26555770 DOI: 10.1021/jacs.5b07812] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Design of a new catalytic function in proteins, apart from its inherent practical value, is important for fundamental understanding of enzymatic activity. Using a computationally inexpensive, minimalistic approach that focuses on introducing a single highly reactive residue into proteins to achieve catalysis we converted a 74-residue-long C-terminal domain of calmodulin into an efficient esterase. The catalytic efficiency of the resulting stereoselective, allosterically regulated catalyst, nicknamed AlleyCatE, is higher than that of any previously reported de novo designed esterases. The simplicity of our design protocol should complement and expand the capabilities of current state-of-art approaches to protein design. These results show that even a small nonenzymatic protein can efficiently attain catalytic activities in various reactions (Kemp elimination, ester hydrolysis, retroaldol reaction) as a result of a single mutation. In other words, proteins can be just one mutation away from becoming entry points for subsequent evolution.
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Affiliation(s)
- Yurii S Moroz
- Department of Chemistry, Syracuse University , 111 College Place, Syracuse, New York 13244, United States
| | - Tiffany T Dunston
- Department of Chemistry, Syracuse University , 111 College Place, Syracuse, New York 13244, United States
| | - Olga V Makhlynets
- Department of Chemistry, Syracuse University , 111 College Place, Syracuse, New York 13244, United States
| | - Olesia V Moroz
- Department of Chemistry, Syracuse University , 111 College Place, Syracuse, New York 13244, United States
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, University of California-San Francisco , 555 Mission Bay Boulevard South, San Francisco, California 94158, United States
| | - Jennifer H Yoon
- Department of Chemistry, Syracuse University , 111 College Place, Syracuse, New York 13244, United States
| | - Alissa B Olsen
- Department of Chemistry, Syracuse University , 111 College Place, Syracuse, New York 13244, United States
| | - Jaclyn M McLaughlin
- Department of Chemistry, Syracuse University , 111 College Place, Syracuse, New York 13244, United States
| | - Korrie L Mack
- Department of Chemistry, Syracuse University , 111 College Place, Syracuse, New York 13244, United States
| | - Pallavi M Gosavi
- Department of Chemistry, Syracuse University , 111 College Place, Syracuse, New York 13244, United States
| | - Nico A J van Nuland
- Jean Jeener NMR Centre, Structural Biology Brussels, Vrije Universiteit Brussel , Pleinlaan 2, 1050 Brussels, Belgium
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University , 111 College Place, Syracuse, New York 13244, United States
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18
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Marconi PL, Alvarez MA. The expression of the 14D9 catalytic antibody in suspended cells of Nicotiana tabacum cultures increased by the addition of protein stabilizers and by transference from Erlenmeyer flasks to a 2-L bioreactor. Biotechnol Prog 2014; 30:1185-9. [PMID: 24930706 DOI: 10.1002/btpr.1940] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 05/25/2014] [Indexed: 11/08/2022]
Abstract
The effect of two protein stabilizers (polyvinylpyrrolidone [PVP] and gelatine) on growth and 14D9 yield of Nicotiana tabacum cell suspension cultures (Ab-KDEL and sec-Ab) was analyzed. The addition of PVP at a concentration of 1.0 g L(-1) produced the highest total 14D9 yield (biomass + culture medium) in the Ab-KDEL line (4.82% total soluble protein [TSP]). With the addition of gelatine, the highest total 14D9 yield (2.48% TSP) was attained in the Ab-KDEL line at 5.0 g L(-1) gelatine. When the Ab-KDEL suspended cells were cultured in a 2-L bioreactor, the highest 14D9 yield was 8.1% TSP at a 5% w/v inoculum size, which was the best 14D9 yield so far obtained in the platforms tested (E. coli, N. tabacum leaves and seeds, N. tabacum hairy roots, and cell suspension cultures).
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Affiliation(s)
- Patricia L Marconi
- Cátedra de Farmacobotánica y Farmacognosia, Carreras de Farmacia y Bioquímica, Facultad de Ciencias de la Salud, Universidad Maimónides, Ciudad de Buenos Aires, Argentina
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19
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Fanlo-Virgós H, Alba ANR, Hamieh S, Colomb-Delsuc M, Otto S. Transient substrate-induced catalyst formation in a dynamic molecular network. Angew Chem Int Ed Engl 2014; 53:11346-50. [PMID: 25169198 DOI: 10.1002/anie.201403480] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 07/02/2014] [Indexed: 11/06/2022]
Abstract
In biology enzyme concentrations are continuously regulated, yet for synthetic catalytic systems such regulatory mechanisms are underdeveloped. We now report how a substrate of a chemical reaction induces the formation of its own catalyst from a dynamic molecular network. After complete conversion of the substrate, the network disassembles the catalyst. These results open up new opportunities for controlling catalysis in synthetic chemical systems.
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Affiliation(s)
- Hugo Fanlo-Virgós
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands) http://www.otto-lab.com
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20
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Fanlo-Virgós H, Alba ANR, Hamieh S, Colomb-Delsuc M, Otto S. Transient Substrate-Induced Catalyst Formation in a Dynamic Molecular Network. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403480] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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21
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Tsumuraya T, Fujii I. Directed Evolution of Hydrolytic Antibodies in Phage-displayed Combinatorial Libraries. CHEM LETT 2014. [DOI: 10.1246/cl.131220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Takeshi Tsumuraya
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University
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22
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Huang WR, Chen YL, Lee CY, Chiu HT. Fabrication of gold/polypyrrole core/shell nanowires on a flexible substrate for molecular imprinted electrochemical sensors. RSC Adv 2014. [DOI: 10.1039/c4ra11774c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Gold/polypyrrole core/shell nanowires electrochemically grown on flexible substrates are used as molecular imprinted polymer biosensors for dopamine detection.
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Affiliation(s)
- Wei-Ren Huang
- Department of Applied Chemistry
- National Chiao Tung University
- Hsinchu, Republic of China
| | - Yu-Liang Chen
- Department of Applied Chemistry
- National Chiao Tung University
- Hsinchu, Republic of China
| | - Chi-Young Lee
- Department of Materials Science and Engineering
- National Tsing Hua University
- Hsinchu, Republic of China
| | - Hsin-Tien Chiu
- Department of Applied Chemistry
- National Chiao Tung University
- Hsinchu, Republic of China
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23
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Eleniste PP, Hofstetter H, Hofstetter O. Expression and characterization of an enantioselective antigen-binding fragment directed against α-amino acids. Protein Expr Purif 2013; 91:20-9. [PMID: 23827208 PMCID: PMC3816624 DOI: 10.1016/j.pep.2013.06.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 06/19/2013] [Accepted: 06/24/2013] [Indexed: 11/18/2022]
Abstract
This work describes the design and expression of a stereoselective Fab that possesses binding properties comparable to those displayed by the parent monoclonal antibody. Utilizing mRNA from hybridoma clones that secrete a stereoselective anti-l-amino acid antibody, a corresponding biotechnologically produced Fab was generated. For that, appropriate primers were designed based on extensive literature and databank searches. Using these primers in PCR resulted in successful amplification of the VH, VL, CL and CH1 gene fragments. Overlap PCR was utilized to combine the VH and CH1 sequences and the VL and CL sequences, respectively, to obtain the genes encoding the HC and LC fragments. These sequences were separately cloned into the pEXP5-CT/TOPO expression vector and used for transfection of BL21(DE3) cells. Separate expression of the two chains, followed by assembly in a refolding buffer, yielded an Fab that was demonstrated to bind to l-amino acids but not to recognize the corresponding d-enantiomers.
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Affiliation(s)
| | - Heike Hofstetter
- Department of Chemistry and Biochemistry, Northern Illinois University,
DeKalb, Illinois 60115, USA
| | - Oliver Hofstetter
- Department of Chemistry and Biochemistry, Northern Illinois University,
DeKalb, Illinois 60115, USA
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24
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Cai X, Whitfield T, Hixon MS, Grant Y, Koob GF, Janda KD. Probing active cocaine vaccination performance through catalytic and noncatalytic hapten design. J Med Chem 2013; 56:3701-9. [PMID: 23627877 DOI: 10.1021/jm400228w] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Presently, there are no FDA-approved medications to treat cocaine addiction. Active vaccination has emerged as one approach to intervene through the rapid sequestering of the circulating drug, thus terminating both psychoactive effects and drug toxicity. Herein, we report our efforts examining two complementary, but mechanistically distinct active vaccines, i.e., noncatalytic and catalytic, for cocaine treatment. A cocaine-like hapten GNE and a cocaine transition-state analogue GNT were used to generate the active vaccines, respectively. GNE-KLH (keyhole limpet hemocyannin) was found to elicit persistent high-titer, cocaine-specific antibodies and blunt cocaine-induced locomotor behaviors. Catalytic antibodies induced by GNT-KLH were also shown to produce potent titers and suppress locomotor response in mice; however, upon repeated cocaine challenges, the vaccine's protecting effects waned. In depth kinetic analysis suggested that loss of catalytic activity was due to antibody modification by cocaine. The work provides new insights for the development of active vaccines for the treatment of cocaine abuse.
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Affiliation(s)
- Xiaoqing Cai
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, The Worm Institute of Research and Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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25
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Richter F, Blomberg R, Khare SD, Kiss G, Kuzin AP, Smith AJT, Gallaher J, Pianowski Z, Helgeson RC, Grjasnow A, Xiao R, Seetharaman J, Su M, Vorobiev S, Lew S, Forouhar F, Kornhaber GJ, Hunt JF, Montelione GT, Tong L, Houk KN, Hilvert D, Baker D. Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. J Am Chem Soc 2012; 134:16197-206. [PMID: 22871159 DOI: 10.1021/ja3037367] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nucleophilic catalysis is a general strategy for accelerating ester and amide hydrolysis. In natural active sites, nucleophilic elements such as catalytic dyads and triads are usually paired with oxyanion holes for substrate activation, but it is difficult to parse out the independent contributions of these elements or to understand how they emerged in the course of evolution. Here we explore the minimal requirements for esterase activity by computationally designing artificial catalysts using catalytic dyads and oxyanion holes. We found much higher success rates using designed oxyanion holes formed by backbone NH groups rather than by side chains or bridging water molecules and obtained four active designs in different scaffolds by combining this motif with a Cys-His dyad. Following active site optimization, the most active of the variants exhibited a catalytic efficiency (k(cat)/K(M)) of 400 M(-1) s(-1) for the cleavage of a p-nitrophenyl ester. Kinetic experiments indicate that the active site cysteines are rapidly acylated as programmed by design, but the subsequent slow hydrolysis of the acyl-enzyme intermediate limits overall catalytic efficiency. Moreover, the Cys-His dyads are not properly formed in crystal structures of the designed enzymes. These results highlight the challenges that computational design must overcome to achieve high levels of activity.
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Affiliation(s)
- Florian Richter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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26
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Geibel B, Merschky M, Rether C, Schmuck C. Artificial Enzyme Mimics. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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28
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Lei Y, Luo W, Zhu Y. A matching algorithm for catalytic residue site selection in computational enzyme design. Protein Sci 2011; 20:1566-75. [PMID: 21714026 DOI: 10.1002/pro.685] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 06/07/2011] [Indexed: 11/07/2022]
Abstract
A loop closure-based sequential algorithm, PRODA_MATCH, was developed to match catalytic residues onto a scaffold for enzyme design in silico. The computational complexity of this algorithm is polynomial with respect to the number of active sites, the number of catalytic residues, and the maximal iteration number of cyclic coordinate descent steps. This matching algorithm is independent of a rotamer library that enables the catalytic residue to take any required conformation during the reaction coordinate. The catalytic geometric parameters defined between functional groups of transition state (TS) and the catalytic residues are continuously optimized to identify the accurate position of the TS. Pseudo-spheres are introduced for surrounding residues, which make the algorithm take binding into account as early as during the matching process. Recapitulation of native catalytic residue sites was used as a benchmark to evaluate the novel algorithm. The calculation results for the test set show that the native catalytic residue sites were successfully identified and ranked within the top 10 designs for 7 of the 10 chemical reactions. This indicates that the matching algorithm has the potential to be used for designing industrial enzymes for desired reactions.
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Affiliation(s)
- Yulin Lei
- Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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29
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Drag M, Salvesen GS. Emerging principles in protease-based drug discovery. Nat Rev Drug Discov 2010; 9:690-701. [PMID: 20811381 DOI: 10.1038/nrd3053] [Citation(s) in RCA: 403] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteases have an important role in many signalling pathways, and represent potential drug targets for diseases ranging from cardiovascular disorders to cancer, as well as for combating many parasites and viruses. Although inhibitors of well-established protease targets such as angiotensin-converting enzyme and HIV protease have shown substantial therapeutic success, developing drugs for new protease targets has proved challenging in recent years. This in part could be due to issues such as the difficulty of achieving selectivity when targeting protease active sites. This Perspective discusses the general principles in protease-based drug discovery, highlighting the lessons learned and the emerging strategies, such as targeting allosteric sites, which could help harness the therapeutic potential of new protease targets.
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Affiliation(s)
- Marcin Drag
- Program in Apoptosis and Cell Death Research, Burnham Institute for Medical Research, La Jolla, California 92037, USA.
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30
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Soluble artificial metalloproteases with broad substrate selectivity, high reactivity, and high thermal and chemical stabilities. J Biol Inorg Chem 2010; 15:1023-31. [DOI: 10.1007/s00775-010-0662-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 04/12/2010] [Indexed: 10/19/2022]
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31
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The catalytic efficiency (kcat/Km) of the class A β-lactamase Toho-1 correlates with the thermal stability of its catalytic intermediate analog. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:684-91. [DOI: 10.1016/j.bbapap.2009.10.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 10/20/2009] [Accepted: 10/26/2009] [Indexed: 11/20/2022]
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32
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Acevedo O. Role of water in the multifaceted catalytic antibody 4B2 for allylic isomerization and Kemp elimination reactions. J Phys Chem B 2010; 113:15372-81. [PMID: 19860435 DOI: 10.1021/jp9069114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Specificity toward a single reaction is a well-known characteristic of catalytic antibodies. However, contrary to convention, catalytic antibody 4B2 possesses the ability to efficiently catalyze two unrelated reactions: a Kemp elimination and an allylic isomerization of a beta,gamma-unsaturated ketone. To elucidate how this multifaceted antibody operates, mixed quantum and molecular mechanics calculations coupled to Monte Carlo simulations were carried out. The antibody was determined to derive its adaptability for the mechanistically different reactions through the rearrangement of water molecules in the active site into advantageous geometric orientations for enhanced electrostatic stabilization. In the case of the Kemp elimination, a general base, Glu L34, carried out the proton abstraction from the isoxazole ring of 5-nitro-benzisoxazole while water molecules delivered specific stabilization at the transition state. The role of water was found to be more pronounced in the allylic isomerization because the solvent actively participated in the stepwise mechanism. A rate-limiting abstraction of the alpha-proton from the beta,gamma-unsaturated ketone via Glu L34 led to the formation of a neutral dienol intermediate, which was rapidly reprotonated at the gamma-position via a solvent hydronium ion. Preferential channeling of H(3)O(+) in the active site ensured a stereoselective proton exchange from the alpha- to the gamma-position, in good agreement with deuterium exchange NMR and HPLC experiments. Ideas for improved water-mediated catalytic antibody designs are presented. In a technical advancement, improvements to a recent polynomial fitting and integration technique utilizing free energy perturbation theory delivered greater accuracy and speed gains.
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Affiliation(s)
- Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA.
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33
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Kasturirangan S, Brune D, Sierks M. Promoting alpha-secretase cleavage of beta-amyloid with engineered proteolytic antibody fragments. Biotechnol Prog 2009; 25:1054-63. [PMID: 19572401 DOI: 10.1002/btpr.190] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Deposition of beta-amyloid (A beta) is considered as an important early event in the pathogenesis of Alzheimer's Disease (AD), and reduction of A beta levels by various therapeutic approaches is actively being pursued. A potentially non-inflammatory approach to facilitate clearance and reduce toxicity is to hydrolyze A beta at its alpha-secretase site. We have previously identified a light chain fragment, mk18, with alpha-secretase-like catalytic activity, producing the 1-16 and 17-40 amino acid fragments of A beta 40 as primary products, although hydrolysis is also observed following other lysine and arginine residues. To improve the specific activity of the recombinant antibody by affinity maturation, we constructed a single chain variable fragment (scFv) library containing a randomized CDR3 heavy chain region. A biotinylated covalently reactive analog mimicking alpha-secretase site cleavage was synthesized, immobilized on streptavidin beads, and used to select yeast surface expressed scFvs with increased specificity for A beta. After two rounds of selection against the analog, yeast cells were individually screened for proteolytic activity towards an internally quenched fluorogenic substrate that contains the alpha-secretase site of A beta. From 750 clones screened, the two clones with the highest increase in proteolytic activity compared to the parent mk18 were selected for further study. Kinetic analyses using purified soluble scFvs showed a 3- and 6-fold increase in catalytic activity (k(cat)/K(M)) toward the synthetic A beta substrate compared to the original scFv primarily due to an expected decrease in K(M) rather than an increase in k(cat). This affinity maturation strategy can be used to select for scFvs with increased catalytic specificity for A beta. These proteolytic scFvs have potential therapeutic applications for AD by decreasing soluble A beta levels in vivo.
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Affiliation(s)
- Srinath Kasturirangan
- Harrington Department of Bioengineering, Arizona State University, Tempe, AZ 85287, USA
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34
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Kalek M, Stawinski J. Efficient synthesis of mono- and diarylphosphinic acids: a microwave-assisted palladium-catalyzed cross-coupling of aryl halides with phosphinate. Tetrahedron 2009. [DOI: 10.1016/j.tet.2009.10.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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35
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YANG GS, QI YD, OU ZM, YAO SJ. Enzymological Characteristics of Catalytic Antibody-catalyzed Enantioselective Hydrolysis of Ibuprofen Ester in Water-in-oil Microemulsion*. PROG BIOCHEM BIOPHYS 2009. [DOI: 10.3724/sp.j.1206.2008.00347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Malisi C, Kohlbacher O, Höcker B. Automated scaffold selection for enzyme design. Proteins 2009; 77:74-83. [DOI: 10.1002/prot.22418] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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37
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38
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Ikeda K, Katsumata T, Sugiyama Y, Miyamoto K, Tanaka K, Sato M. Regioselective Ester Hydrolysis of Sialic Acid Derivatives Catalyzed by Molecularly Imprinted Polymers. HETEROCYCLES 2009. [DOI: 10.3987/com-09-11820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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39
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Tsumuraya T, Fujii I. Molecular Basis for Transition-State Stabilization in Catalytic Antibodies. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2008. [DOI: 10.1246/bcsj.81.1039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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40
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Zhang X, DeChancie J, Gunaydin H, Chowdry AB, Clemente FR, Smith, Handel TM, Houk KN. Quantum Mechanical Design of Enzyme Active Sites. J Org Chem 2008; 73:889-99. [DOI: 10.1021/jo701974n] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiyun Zhang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093 and the Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Jason DeChancie
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093 and the Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Hakan Gunaydin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093 and the Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Arnab B. Chowdry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093 and the Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Fernando R. Clemente
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093 and the Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - Smith
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093 and the Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - T. M. Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093 and the Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
| | - K. N. Houk
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California 92093 and the Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095
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41
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Simón L, Muñiz FM, Sáez S, Raposo C, Morán JR. From Theozymes to Artificial Enzymes: Enzyme-Like Receptors for Michael Additions with Oxyanion Holes and Active Amino Groups. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700565] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Ma X, Sun S, Ma X, Li T, Meng J, Fan J. Polyclonal Antibodies from Hen Egg Yolk (IgY) with Hydrolysis Activity. Protein J 2007; 26:499-505. [PMID: 17763927 DOI: 10.1007/s10930-007-9091-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Polyclonal catalytic antibodies (abzymes) play an important role in immunology research. In this study, we report polyclonal antibodies IgYs isolated from chicken egg yolk with hydrolysis activity for the first time. The IgYs were raised in hens using HNPBV [4-(hydroxy (naphthalen-2-yloxy) phosphoryl) butanoic acid] attached to BSA (Bovine serum albumin) as an immunogen. Anti-(HNPBV-BSA) IgYs were isolated from yolks of the eggs laid using a two-step salt precipitation and one-step gel filtration protocol. NA (naphthalen-2-yl acetate) was selected as the substrate and the hydrolysis reaction of the IgYs for it was examined. The result reveals that the rate of the hydrolysis reaction is higher (Kcat/K (uncat) approximately 2x10(4)). The purified IgYs were digested with pepsin and the smaller fragment (Fab') with specific antigen binding properties was produced. The research indicates that the enzymatic properties of Fab' are similar to IgYs. The catalytic activity of the IgYs was further determined by measuring the rate of hydrolysis of NA in the presence of inhibitor. These findings show that chicken egg is an excellent donor for polyclonal catalytic antibodies.
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Affiliation(s)
- Xianghui Ma
- Department of Chemistry, College of Science, Tianjin University, Tianjin, 300072, China
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Sakakura M, Takahashi H, Shimba N, Fujii I, Shimada I. Structural Basis of the Transition-state Stabilization in Antibody-catalyzed Hydrolysis. J Mol Biol 2007; 367:133-47. [PMID: 17239396 DOI: 10.1016/j.jmb.2006.12.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Revised: 12/12/2006] [Accepted: 12/14/2006] [Indexed: 11/23/2022]
Abstract
The catalytic antibody 6D9, which was raised against a transition-state analogue (TSA), catalyzes the hydrolysis of a non-bioactive chloramphenicol monoester to generate chloramphenicol. It has been shown that 6D9 utilizes the binding affinity in the catalysis; the differential affinity of the TSA relative to the substrate is equal to the rate enhancement. To reveal the recognition mechanism of 6D9 for the TSA and the substrate, we performed NMR analysis of the Fv fragment of 6D9 (6D9-Fv), together with site-directed mutagenesis and stopped-flow kinetic analyses. Among six 6D9-Fv mutants, Y58(H)A and W100i(H)A displayed significant reductions in their affinities to the TSA, while their substrate-binding affinities were identical with that of the wild-type 6D9-Fv. The stopped-flow kinetic studies revealed that the TSA binding to 6D9-Fv occurred by an induced-fit mechanism. In contrast, no induced-fit type of TSA-binding mechanism was observed for Y58(H)A and W100i(H)A. From NMR experiments, we identified the residues with chemical shifts that were perturbed by the ligand-binding. The residues affected by the TSA binding were located on the TSA-binding site determined by the X-ray study, and on the regions far from the binding site. On the other hand, the residues affected by the substrate binding were localized on the TSA-binding site. As for W100i(H)A, no residue other than those in the binding site was affected by the ligand binding. On the basis of these results and the crystal structure, we concluded that the TSA binding induced a conformational change involving the formation of aromatic-aromatic interactions and a hydrogen bond. These interactions can account for the differential affinity for the TSA relative to the substrate. W100i(H) probably plays an important role in inducing the conformational changes. The present NMR studies have enabled us to visualize the concept of transition-state stabilization in enzymatic catalysis, in which the transition-state contacts are better than those of the substrate.
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Affiliation(s)
- Masayoshi Sakakura
- Laboratory of Physical Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
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Takahashi-Ando N, Shimazaki K, Kakinuma H, Fujii I, Nishi Y. Molecular mechanisms of improvement of hydrolytic antibody 6D9 by site-directed mutagenesis. J Biochem 2006; 140:509-15. [PMID: 16921165 DOI: 10.1093/jb/mvj179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We performed a series of site-directed mutagenesis experiments of catalytic antibody, 6D9, which hydrolyzes a prodrug of chloramphenicol, based on our previous directed evolution study [Takahashi et al. (2001) Nat. Biotechnol. 19, 563-567]. Since we previously found that the variants with a mutation of Ser(L27e)Tyr afforded a one order of magnitude increase in catalytic rate, we created a site-directed mutant containing this mutation. The resulting mutant, 6D9-Ser(L27e)Tyr, had 6.5-fold higher k(cat)/k(uncat) and 9.8-fold higher k(cat)/K(m) than wild-type 6D9. We also created 6D9-Thr(L27a)Pro, since this mutation occurred frequently in the previous directed evolution, and it had 2.1-fold higher k(cat)/k(uncat) and k(cat)/K(m) than 6D9. Kinetic and computational analyses suggest that Tyr at L27e contributes to transition-state stabilization, while Pro at L27a does not interact with the transition-state structure directly, but obviously contributes to enhanced catalytic activity. Including double mutants that combined favourable substitutions, we created seven site-directed mutants. However, none of them had higher catalytic activities than some of highly improved variants obtained in the previous directed evolution. The present study gives direct evidence that not only a specific amino acid residue which obviously contributes to transition-state stabilization, but also a group of amino acid residues working in concert is important for efficient catalysis of a given transformation.
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Affiliation(s)
- Naoko Takahashi-Ando
- Laboratory of Life Science & Biomolecular Engineering, Japan Tobacco, Inc. 6-2, Umegaoka, Aoba-ku, Yokohama, Kanagawa 227-8512.
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Sinha SC, Li LS, Watanabe SI, Kaltgrad E, Tanaka F, Rader C, Lerner RA, Barbas CF. Aldolase antibody activation of prodrugs of potent aldehyde-containing cytotoxics for selective chemotherapy. Chemistry 2006; 10:5467-72. [PMID: 15378729 DOI: 10.1002/chem.200400419] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Prodrugs of potent aldehyde analogues of the anticancer drug doxorubicin (Dox) were synthesized. These prodrugs were efficiently activated by antibody 93F3 and no drug formation was observed in the absence of 93F3 in either phosphate buffered saline or cell culture media. In the presence of antibody 93F3, these prodrugs were activated and decreased the proliferation of human cancer cells in in vitro proliferation assays.
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Affiliation(s)
- Subhash C Sinha
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Zhu X, Dickerson TJ, Rogers CJ, Kaufmann GF, Mee JM, McKenzie KM, Janda KD, Wilson IA. Complete reaction cycle of a cocaine catalytic antibody at atomic resolution. Structure 2006; 14:205-16. [PMID: 16472740 DOI: 10.1016/j.str.2005.10.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2005] [Revised: 09/27/2005] [Accepted: 10/04/2005] [Indexed: 11/30/2022]
Abstract
Antibody 7A1 hydrolyzes cocaine to produce nonpsychoactive metabolites ecgonine methyl ester and benzoic acid. Crystal structures of 7A1 Fab' and six complexes with substrate cocaine, the transition state analog, products ecgonine methyl ester and benzoic acid together and individually, as well as heptaethylene glycol have been analyzed at 1.5-2.3 angstroms resolution. Here, we present snapshots of the complete cycle of the cocaine hydrolytic reaction at atomic resolution. Significant structural rearrangements occur along the reaction pathway, but they are generally limited to the binding site, including the ligands themselves. Several interacting side chains either change their rotamers or alter their mobility to accommodate the different reaction steps. CDR loop movements (up to 2.3 angstroms) and substantial side chain rearrangements (up to 9 angstroms) alter the shape and size (approximately 320-500 angstroms3) of the antibody active site from "open" to "closed" to "open" for the substrate, transition state, and product states, respectively.
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Affiliation(s)
- Xueyong Zhu
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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Paul S, Nishiyama Y, Planque S, Taguchi H. Theory of proteolytic antibody occurrence. Immunol Lett 2006; 103:8-16. [PMID: 16290203 DOI: 10.1016/j.imlet.2005.10.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Revised: 10/09/2005] [Accepted: 10/09/2005] [Indexed: 11/22/2022]
Abstract
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.
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Affiliation(s)
- Sudhir Paul
- Chemical Immunology and Therapeutics Research Center, Department of Pathology and Laboratory Medicine, University of Texas-Houston Medical School, 6431 Fannin, 77030, USA.
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Heng BC, Cao T, Stojkovic M, Vajta G. Mammalian oocyte polarity can be exploited for the automation of somatic cell nuclear transfer – in the development of a ‘cloning biochip’. Med Hypotheses 2006; 67:420-1. [PMID: 16377096 DOI: 10.1016/j.mehy.2005.11.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2005] [Accepted: 11/13/2005] [Indexed: 11/27/2022]
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Hofstetter H, Hofstetter O. Antibodies as tailor-made chiral selectors for detection and separation of stereoisomers. Trends Analyt Chem 2005. [DOI: 10.1016/j.trac.2005.04.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Tanaka F, Fuller R, Barbas CF. Development of Small Designer Aldolase Enzymes: Catalytic Activity, Folding, and Substrate Specificity†. Biochemistry 2005; 44:7583-92. [PMID: 15896002 DOI: 10.1021/bi050216j] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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.
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Affiliation(s)
- Fujie Tanaka
- The Skaggs Institute for Chemical Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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