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Kelley EH, Osipiuk J, Korbas M, Endres M, Bland A, Ehrman V, Joachimiak A, Olsen KW, Becker DP. N α -acetyl-L-ornithine deacetylase from Escherichia coli and a ninhydrin-based assay to enable inhibitor identification. Front Chem 2024; 12:1415644. [PMID: 39055043 PMCID: PMC11270798 DOI: 10.3389/fchem.2024.1415644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/14/2024] [Indexed: 07/27/2024] Open
Abstract
Bacteria are becoming increasingly resistant to antibiotics, therefore there is an urgent need for new classes of antibiotics to fight antibiotic resistance. Mammals do not express N ɑ -acetyl-L-ornithine deacetylase (ArgE), an enzyme that is critical for bacterial survival and growth, thus ArgE represents a promising new antibiotic drug target, as inhibitors would not suffer from mechanism-based toxicity. A new ninhydrin-based assay was designed and validated that included the synthesis of the substrate analog N 5, N 5-di-methyl N α-acetyl-L-ornithine (kcat/Km = 7.32 ± 0.94 × 104 M-1s-1). This new assay enabled the screening of potential inhibitors that absorb in the UV region, and thus is superior to the established 214 nm assay. Using this new ninhydrin-based assay, captopril was confirmed as an ArgE inhibitor (IC50 = 58.7 μM; Ki = 37.1 ± 0.85 μM), and a number of phenylboronic acid derivatives were identified as inhibitors, including 4-(diethylamino)phenylboronic acid (IC50 = 50.1 μM). Selected inhibitors were also tested in a thermal shift assay with ArgE using SYPRO Orange dye against Escherichia coli ArgE to observe the stability of the enzyme in the presence of inhibitors (captopril Ki = 35.9 ± 5.1 μM). The active site structure of di-Zn EcArgE was confirmed using X-ray absorption spectroscopy, and we reported two X-ray crystal structures of E. coli ArgE. In summary, we describe the development of a new ninhydrin-based assay for ArgE, the identification of captopril and phenylboronic acids as ArgE inhibitors, thermal shift studies with ArgE + captopril, and the first two published crystal structures of ArgE (mono-Zn and di-Zn).
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Affiliation(s)
- Emma H. Kelley
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Jerzy Osipiuk
- Structural Biology Center, Argonne National Laboratory, X-ray Science Division, Lemont, IL, United States
- eBERlight, Argonne National Laboratory, X-ray Science Division, Lemont, IL, United States
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States
| | | | - Michael Endres
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States
| | - Alayna Bland
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Victoria Ehrman
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Andrzej Joachimiak
- Structural Biology Center, Argonne National Laboratory, X-ray Science Division, Lemont, IL, United States
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, United States
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Kenneth W. Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
| | - Daniel P. Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, United States
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2
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Shestakova A, Fatkulin A, Surkova D, Osmolovskiy A, Popova E. First Insight into the Degradome of Aspergillus ochraceus: Novel Secreted Peptidases and Their Inhibitors. Int J Mol Sci 2024; 25:7121. [PMID: 39000228 PMCID: PMC11241649 DOI: 10.3390/ijms25137121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/07/2024] [Accepted: 06/14/2024] [Indexed: 07/16/2024] Open
Abstract
Aspergillus fungi constitute a pivotal element within ecosystems, serving as both contributors of biologically active compounds and harboring the potential to cause various diseases across living organisms. The organism's proteolytic enzyme complex, termed the degradome, acts as an intermediary in its dynamic interaction with the surrounding environment. Using techniques such as genome and transcriptome sequencing, alongside protein prediction methodologies, we identified putative extracellular peptidases within Aspergillus ochraceus VKM-F4104D. Following manual annotation procedures, a total of 11 aspartic, 2 cysteine, 2 glutamic, 21 serine, 1 threonine, and 21 metallopeptidases were attributed to the extracellular degradome of A. ochraceus VKM-F4104D. Among them are enzymes with promising applications in biotechnology, potential targets and agents for antifungal therapy, and microbial antagonism factors. Thus, additional functionalities of the extracellular degradome, extending beyond mere protein substrate digestion for nutritional purposes, were demonstrated.
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Affiliation(s)
- Anna Shestakova
- Department of Microbiology, Lomonosov MSU, Moscow 119234, Russia; (A.S.); (A.O.)
| | - Artem Fatkulin
- Laboratory of Molecular Physiology, HSE University, Moscow 101000, Russia
| | - Daria Surkova
- Department of Microbiology, Lomonosov MSU, Moscow 119234, Russia; (A.S.); (A.O.)
| | | | - Elizaveta Popova
- Department of Microbiology, Lomonosov MSU, Moscow 119234, Russia; (A.S.); (A.O.)
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3
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Terrazas-López M, González-Segura L, Díaz-Vilchis A, Aguirre-Mendez KA, Lobo-Galo N, Martínez-Martínez A, Díaz-Sánchez ÁG. The three-dimensional structure of DapE from Enterococcus faecium reveals new insights into DapE/ArgE subfamily ligand specificity. Int J Biol Macromol 2024; 270:132281. [PMID: 38740150 DOI: 10.1016/j.ijbiomac.2024.132281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/25/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
DapE is a Zn2+-metallohydrolase recognized as a drug target for bacterial control. It is a homodimer that requires the exchange of interface strands by an induced fit essential for catalysis. Identifying novel anti-DapE agents requires greater structural details. Most of the characterized DapEs are from the Gram-negative group. Here, two high-resolution DapE crystal structures from Enterococcus faecium are presented for the first time with novel aspects. A loosened enzyme intermediate between the open and closed conformations is observed. Substrates may bind to loose state, subsequently it closes, where hydrolysis occurs, and finally, the change to the open state leads to the release of the products. Mutation of His352 suggests a role, along with His194, in the oxyanion stabilization in the mono-metalated Zn2+ isoform, while in the di-metalated isoform, the metal center 2 complements it function. An aromatic-π box potentially involved in the interaction of DapE with other proteins, and a peptide flip could determine the specificity in the Gram-positive ArgE/DapE group. Finally, details of two extra-catalytic cavities whose geometry changes depending on the conformational state of the enzyme are presented. These cavities could be a target for developing non-competitive agents that trap the enzyme in an inactive state.
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Affiliation(s)
- Manuel Terrazas-López
- Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Instituto de Ciencias Biomédicas, Departamento de Ciencias Químico-Biológicas, Chihuahua, CP 32310, Mexico
| | - Lilian González-Segura
- Universidad Nacional Autónoma de México, Facultad de Química, Departamento de Bioquímica, Ciudad Universitaria, Ciudad de México, 04510, Mexico.
| | - Adelaida Díaz-Vilchis
- Universidad Nacional Autónoma de México, Facultad de Química, Departamento de Bioquímica, Ciudad Universitaria, Ciudad de México, 04510, Mexico
| | - Kelly Annecy Aguirre-Mendez
- Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Instituto de Ciencias Biomédicas, Departamento de Ciencias Químico-Biológicas, Chihuahua, CP 32310, Mexico
| | - Naún Lobo-Galo
- Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Instituto de Ciencias Biomédicas, Departamento de Ciencias Químico-Biológicas, Chihuahua, CP 32310, Mexico
| | - Alejandro Martínez-Martínez
- Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Instituto de Ciencias Biomédicas, Departamento de Ciencias Químico-Biológicas, Chihuahua, CP 32310, Mexico
| | - Ángel G Díaz-Sánchez
- Universidad Autónoma de Ciudad Juárez, Ciudad Juárez, Instituto de Ciencias Biomédicas, Departamento de Ciencias Químico-Biológicas, Chihuahua, CP 32310, Mexico.
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Haeger G, Probst J, Jaeger K, Bongaerts J, Siegert P. Novel aminoacylases from Streptomyces griseus DSM 40236 and their recombinant production in Streptomyces lividans. FEBS Open Bio 2023; 13:2224-2238. [PMID: 37879963 PMCID: PMC10699109 DOI: 10.1002/2211-5463.13723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/15/2023] [Accepted: 10/20/2023] [Indexed: 10/27/2023] Open
Abstract
Amino acid-based surfactants are valuable compounds for cosmetic formulations. The chemical synthesis of acyl amino acids is conventionally performed by the Schotten-Baumann reaction using fatty acyl chlorides, but aminoacylases have also been investigated for use in biocatalytic synthesis with free fatty acids. Aminoacylases and their properties are diverse; they belong to different peptidase families and show differences in substrate specificity and biocatalytic potential. Bacterial aminoacylases capable of synthesis have been isolated from Burkholderia, Mycolicibacterium, and Streptomyces. Although several proteases and peptidases from S. griseus have been described, no aminoacylases from this species have been identified yet. In this study, we investigated two novel enzymes produced by S. griseus DSM 40236T . We identified and cloned the respective genes and recombinantly expressed an α-aminoacylase (EC3.5.1.14), designated SgAA, and an ε-lysine acylase (EC3.5.1.17), designated SgELA, in S. lividans TK23. The purified aminoacylase SgAA was biochemically characterized, focusing on its hydrolytic activity to determine temperature- and pH optima and stabilities. The aminoacylase could hydrolyze various acetyl amino acids at the Nα -position with a broad specificity regarding the sidechain. Substrates with longer acyl chains, like lauroyl amino acids, were hydrolyzed to a lesser extent. Purified aminoacylase SgELA specific for the hydrolysis of Nε -acetyl-l-lysine was unstable and lost its enzymatic activity upon storage for a longer period but could initially be characterized. The pH optimum of SgELA was pH 8.0. While synthesis of acyl amino acids was not observed with SgELA, SgAA catalyzed the synthesis of lauroyl-methionine.
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Affiliation(s)
- Gerrit Haeger
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
| | - Johanna Probst
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme TechnologyHeinrich Heine University DüsseldorfJülichGermany
- Institute of Bio‐ and Geosciences IBG‐1: BiotechnologyForschungszentrum Jülich GmbHJülichGermany
| | - Johannes Bongaerts
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
| | - Petra Siegert
- Institute of Nano‐ and BiotechnologiesAachen University of Applied SciencesJülichGermany
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5
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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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Liveris ZJ, Kelley EH, Simmons E, Konczak K, Lutz MR, Ballicora M, Olsen KW, Becker DP. Synthesis and characterization of the N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) alternate substrate analog N,N-dimethyl-l,l-SDAP. Bioorg Med Chem 2023; 91:117415. [PMID: 37459673 DOI: 10.1016/j.bmc.2023.117415] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 08/01/2023]
Abstract
Growing antibiotic resistance by pathogenic bacteria has led to a global crisis. The bacterial enzyme N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) provides a very attractive target for the discovery of a new class of antibiotics, as it resides exclusively in many pathogenic bacterial strains and is a key enzyme in the lysine biosynthetic pathway. This pathway is responsible for the production of lysine as well as meso-diaminopimelate (m-DAP), both of which are required for peptidoglycan cell-wall synthesis, and lysine for peptide synthesis. The enzyme DapE catalyzes the hydrolysis of N-succinyl-l,l-diaminopimelic acid (l,l-SDAP) to succinate and l,l-diaminopimelic acid (l,l-DAP), and due to its absence in humans, inhibition of DapE avoids mechanism-based side effects. We have executed the asymmetric synthesis of N,N-dimethyl-SDAP, an l,l-SDAP substrate analog and an analog of the synthetic substrate of our previously described DapE assay. Previous modeling studies advocated that N,N-dimethyl-SDAP might function as an inhibitor, however the compound behaves as a substrate, and we have demonstrated the use of N,N-dimethyl-SDAP as the substrate in a modified ninhydrin-based DapE assay. Thermal shift experiments of DapE in the presence of N,N-dimethyl-SDAP are consistent with a melt temperature (Tm) shifted by succinate, the product of enzymatic hydrolysis.
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Affiliation(s)
- Zachary J Liveris
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Emma H Kelley
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Emma Simmons
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Katherine Konczak
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Marlon R Lutz
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Miguel Ballicora
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Kenneth W Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States
| | - Daniel P Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, United States.
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7
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Muduli S, Karmakar S, Mishra S. The coordinated action of the enzymes in the L-lysine biosynthetic pathway and how to inhibit it for antibiotic targets. Biochim Biophys Acta Gen Subj 2023; 1867:130320. [PMID: 36813209 DOI: 10.1016/j.bbagen.2023.130320] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 01/19/2023] [Accepted: 02/02/2023] [Indexed: 02/22/2023]
Abstract
BACKGROUND Antimicrobial resistance is a global health issue that requires immediate attention in terms of new antibiotics and new antibiotic targets. The l-lysine biosynthesis pathway (LBP) is a promising avenue for drug discovery as it is essential for bacterial growth and survival and is not required by human beings. SCOPE OF REVIEW The LBP involves a coordinated action of fourteen different enzymes distributed over four distinct sub-pathways. The enzymes involved in this pathway belong to different classes, such as aspartokinase, dehydrogenase, aminotransferase, epimerase, etc. This review provides a comprehensive account of the secondary and tertiary structure, conformational dynamics, active site architecture, mechanism of catalytic action, and inhibitors of all enzymes involved in LBP of different bacterial species. MAJOR CONCLUSIONS LBP offers a wide scope for novel antibiotic targets. The enzymology of a majority of the LBP enzymes is well understood, although these enzymes are less widely studied in the critical pathogens (according to the 2017 WHO report) that require immediate attention. In particular, the enzymes in the acetylase pathway, DapAT, DapDH, and Aspartokinase in critical pathogens have received little attention. High throughput screening for inhibitor design against the enzymes of lysine biosynthetic pathway is rather limited, both in number and in the extent of success. GENERAL SIGNIFICANCE This review can serve as a guide for the enzymology of LBP and help in identifying new drug targets and designing potential inhibitors.
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Affiliation(s)
- Sunita Muduli
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Soumyajit Karmakar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India.
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8
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DiPuma T, Thabthimthong T, Kelley EH, Konczak K, Beulke M, Herbert C, S Habeeb Mohammad T, Starus A, Nocek B, Olsen KW, Holz RC, Becker DP. Tetrazole-based inhibitors of the bacterial enzyme N-succinyl-l,l-2,6-diaminopimelic acid desuccinylase as potential antibiotics. Bioorg Med Chem Lett 2023; 83:129177. [PMID: 36764468 DOI: 10.1016/j.bmcl.2023.129177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/27/2022] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Based on a hit from a high-throughput screen, a series of phenyltetrazole amides was synthesized and assayed for inhibitory potency against DapE from Haemophilus influenzae (HiDapE). The inhibitory potency was modest but confirmed, with the most potent analog containing an aminothiazole moiety displaying an IC50 = 50.2 ± 5.0 μM. Docking reveals a potential binding mode wherein the amide carbonyl bridges both zinc atoms in the active site, and the tetrazole forms key hydrogen bonds with Arg330.
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Affiliation(s)
- Thomas DiPuma
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA
| | - Teerana Thabthimthong
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA
| | - Emma H Kelley
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA
| | - Katherine Konczak
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA
| | - Megan Beulke
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA
| | - Claire Herbert
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA
| | - Thahani S Habeeb Mohammad
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA
| | - Anna Starus
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA
| | - Boguslaw Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Kenneth W Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA
| | - Richard C Holz
- Department of Chemistry, Colorado School of Mines, 1500 Illinois St., Golden, CO 80401, USA.
| | - Daniel P Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, IL 60660, USA.
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9
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Muduli S, Mishra S. Ligands-induced open-close conformational change during DapE catalysis: Insights from molecular dynamics simulations. Proteins 2023; 91:781-797. [PMID: 36633566 DOI: 10.1002/prot.26466] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/20/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023]
Abstract
The microbial enzyme DapE plays a critical role in the lysine biosynthetic pathway and is considered as a potentially safe antibiotic target. In this study, atomistic simulations are employed to identify the modes of essential dynamics that define the conformational response of the enzyme to ligand binding and unbinding. The binding modes and the binding affinities of the products to the DapE enzyme are estimated from the MM-PBSA method, and the residues contributing to the ligand binding are identified. Various structural analyses and the principal component analysis of the molecular dynamics trajectories reveal that the removal of products from the active site causes a significant change in the overall enzyme structure. Both Cartesian and dihedral principal component analyses are used to characterize the structural changes in terms of domain unfolding and domain twisting motions. In the most dominant mode, that is, the domain unfolding motion, the two catalytic domains move away from the two dimerization domains of the dimeric enzyme, representing a closed-to-open conformational change. The conformational changes are initiated by the coordinated movement of three loops (Asp75-Pro82, Gly240-Asn244, and Thr347-Glu353) that trigger a domain-level movement. From multiple short trajectories, the time constant associated with the domain opening motion is estimated as 43.6 ns. Physiologically, this close-to-open conformational change is essential for the regeneration of the initial state of the enzyme for the subsequent cycle of catalytic action and provides the apo enzyme enough flexibility for efficient substrate binding.
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Affiliation(s)
- Sunita Muduli
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
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10
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Abstract
Proteins have shown promise as therapeutics and diagnostics, but their effectiveness is limited by our inability to spatially target their activity. To overcome this limitation, we developed a computationally guided method to design inactive proenzymes or zymogens, which are activated through cleavage by a protease. Since proteases are differentially expressed in various tissues and disease states, including cancer, these proenzymes could be targeted to the desired microenvironment. We tested our method on the therapeutically relevant protein carboxypeptidase G2 (CPG2). We designed Pro-CPG2s that are inhibited by 80 to 98% and are partially to fully reactivatable following protease treatment. The developed methodology, with further refinements, could pave the way for routinely designing protease-activated protein-based therapeutics and diagnostics that act in a spatially controlled manner. Confining the activity of a designed protein to a specific microenvironment would have broad-ranging applications, such as enabling cell type-specific therapeutic action by enzymes while avoiding off-target effects. While many natural enzymes are synthesized as inactive zymogens that can be activated by proteolysis, it has been challenging to redesign any chosen enzyme to be similarly stimulus responsive. Here, we develop a massively parallel computational design, screening, and next-generation sequencing-based approach for proenzyme design. For a model system, we employ carboxypeptidase G2 (CPG2), a clinically approved enzyme that has applications in both the treatment of cancer and controlling drug toxicity. Detailed kinetic characterization of the most effectively designed variants shows that they are inhibited by ∼80% compared to the unmodified protein, and their activity is fully restored following incubation with site-specific proteases. Introducing disulfide bonds between the pro- and catalytic domains based on the design models increases the degree of inhibition to 98% but decreases the degree of restoration of activity by proteolysis. A selected disulfide-containing proenzyme exhibits significantly lower activity relative to the fully activated enzyme when evaluated in cell culture. Structural and thermodynamic characterization provides detailed insights into the prodomain binding and inhibition mechanisms. The described methodology is general and could enable the design of a variety of proproteins with precise spatial regulation.
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11
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Kochert M, Nocek BP, Habeeb Mohammad TS, Gild E, Lovato K, Heath TK, Holz RC, Olsen KW, Becker DP. Atomic-Resolution 1.3 Å Crystal Structure, Inhibition by Sulfate, and Molecular Dynamics of the Bacterial Enzyme DapE. Biochemistry 2021; 60:908-917. [PMID: 33721990 DOI: 10.1021/acs.biochem.0c00926] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the atomic-resolution (1.3 Å) X-ray crystal structure of an open conformation of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE, EC 3.5.1.18) from Neisseria meningitidis. This structure [Protein Data Bank (PDB) entry 5UEJ] contains two bound sulfate ions in the active site that mimic the binding of the terminal carboxylates of the N-succinyl-l,l-diaminopimelic acid (l,l-SDAP) substrate. We demonstrated inhibition of DapE by sulfate (IC50 = 13.8 ± 2.8 mM). Comparison with other DapE structures in the PDB demonstrates the flexibility of the interdomain connections of this protein. This high-resolution structure was then utilized as the starting point for targeted molecular dynamics experiments revealing the conformational change from the open form to the closed form that occurs when DapE binds l,l-SDAP and cleaves the amide bond. These simulations demonstrated closure from the open to the closed conformation, the change in RMS throughout the closure, and the independence in the movement of the two DapE subunits. This conformational change occurred in two phases with the catalytic domains moving toward the dimerization domains first, followed by a rotation of catalytic domains relative to the dimerization domains. Although there were no targeting forces, the substrate moved closer to the active site and bound more tightly during the closure event.
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Affiliation(s)
- Matthew Kochert
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Boguslaw P Nocek
- The Center for Structural Genomics of Infectious Diseases, Computation Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Thahani S Habeeb Mohammad
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Elliot Gild
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Kaitlyn Lovato
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Tahirah K Heath
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Richard C Holz
- Department of Chemistry, Colorado School of Mines, 1500 Illinois Street, Golden, Colorado 80401, United States
| | - Kenneth W Olsen
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
| | - Daniel P Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1032 West Sheridan Road, Chicago, Illinois 60660, United States
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Terrazas-López M, Lobo-Galo N, Aguirre-Reyes LG, Bustos-Jaimes I, Marcos-Víquez JÁ, González-Segura L, Díaz-Sánchez ÁG. Interaction of N-succinyl diaminopimelate desuccinylase with orphenadrine and disulfiram. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Terrazas-López M, Lobo-Galo N, Aguirre-Reyes LG, Cuen-Andrade JL, de la Rosa LA, Alvarez-Parrilla E, Martínez-Martínez A, Díaz-Sánchez ÁG. Interaction of N-succinyl-diaminopimelate desuccinylase with flavonoids. Biochimie 2020; 177:198-212. [DOI: 10.1016/j.biochi.2020.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 08/03/2020] [Accepted: 08/21/2020] [Indexed: 12/27/2022]
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14
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Nocek B, Reidl C, Starus A, Heath T, Bienvenue D, Osipiuk J, Jedrzejczak R, Joachimiak A, Becker DP, Holz RC. Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism. Biochemistry 2018; 57:574-584. [PMID: 29272107 PMCID: PMC6886521 DOI: 10.1021/acs.biochem.7b01151] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The X-ray crystal structure of the dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase from Haemophilus influenzae (HiDapE) bound by the products of hydrolysis, succinic acid and l,l-DAP, was determined at 1.95 Å. Surprisingly, the structure bound to the products revealed that HiDapE undergoes a significant conformational change in which the catalytic domain rotates ∼50° and shifts ∼10.1 Å (as measured at the position of the Zn atoms) relative to the dimerization domain. This heretofore unobserved closed conformation revealed significant movements within the catalytic domain compared to that of wild-type HiDapE, which results in effectively closing off access to the dinuclear Zn(II) active site with the succinate carboxylate moiety bridging the dinculear Zn(II) cluster in a μ-1,3 fashion forming a bis(μ-carboxylato)dizinc(II) core with a Zn-Zn distance of 3.8 Å. Surprisingly, His194.B, which is located on the dimerization domain of the opposing chain ∼10.1 Å from the dinuclear Zn(II) active site, forms a hydrogen bond (2.9 Å) with the oxygen atom of succinic acid bound to Zn2, forming an oxyanion hole. As the closed structure forms upon substrate binding, the movement of His194.B by more than ∼10 Å is critical, based on site-directed mutagenesis data, for activation of the scissile carbonyl carbon of the substrate for nucleophilic attack by a hydroxide nucleophile. Employing the HiDapE product-bound structure as the starting point, a reverse engineering approach called product-based transition-state modeling provided structural models for each major catalytic step. These data provide insight into the catalytic reaction mechanism and also the future design of new, potent inhibitors of DapE enzymes.
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Affiliation(s)
- Boguslaw Nocek
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Cory Reidl
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60626, United States
| | - Anna Starus
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60626, United States
| | - Tahirah Heath
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60626, United States
| | - David Bienvenue
- 19010 33rd Avenue Northeast, Seattle, Washington 98155, United States
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, United States
| | - Jerzy Osipiuk
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Robert Jedrzejczak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Daniel P. Becker
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 West Sheridan Road, Chicago, Illinois 60626, United States
| | - Richard C. Holz
- Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, United States
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Dutta D, Mishra S. Active Site Dynamics in Substrate Hydrolysis Catalyzed by DapE Enzyme and Its Mutants from Hybrid QM/MM-Molecular Dynamics Simulation. J Phys Chem B 2017; 121:7075-7085. [DOI: 10.1021/acs.jpcb.7b04431] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Debodyuti Dutta
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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16
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Yachnin BJ, Khare SD. Engineering carboxypeptidase G2 circular permutations for the design of an autoinhibited enzyme. Protein Eng Des Sel 2017; 30:321-331. [PMID: 28160000 PMCID: PMC6283397 DOI: 10.1093/protein/gzx005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/11/2017] [Accepted: 01/18/2017] [Indexed: 11/14/2022] Open
Abstract
Carboxypeptidase G2 (CPG2) is an Food and Drug Administration (FDA)-approved enzyme drug used to treat methotrexate (MTX) toxicity in cancer patients receiving MTX treatment. It has also been used in directed enzyme-prodrug chemotherapy, but this strategy has been hampered by off-site activation of the prodrug by the circulating enzyme. The development of a tumor protease activatable CPG2, which could be achieved using a circular permutation of CPG2 fused to an inactivating 'prodomain', would aid in these applications. We report the development of a protease accessibility-based screen to identify candidate sites for circular permutation in proximity of the CPG2 active site. The resulting six circular permutants showed similar expression, structure, thermal stability, and, in four cases, activity levels compared to the wild-type enzyme. We rationalize these results based on structural models of the permutants obtained using the Rosetta software. We developed a cell growth-based selection system, and demonstrated that when fused to periplasm-directing signal peptides, one of our circular permutants confers MTX resistance in Escherichia coli with equal efficiency as the wild-type enzyme. As the permutants have similar properties to wild-type CPG2, these enzymes are promising starting points for the development of autoinhibited, protease-activatable zymogen forms of CPG2 for use in therapeutic contexts.
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Affiliation(s)
- Brahm J. Yachnin
- Department of Chemistry & Chemical Biology and the Center for Integrative Proteomics, Rutgers University, Piscataway, NJ 08854, USA
| | - Sagar D. Khare
- Department of Chemistry & Chemical Biology and the Center for Integrative Proteomics, Rutgers University, Piscataway, NJ 08854, USA
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17
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Dutta D, Mishra S. Structural and mechanistic insight into substrate binding from the conformational dynamics in apo and substrate-bound DapE enzyme. Phys Chem Chem Phys 2016; 18:1671-80. [DOI: 10.1039/c5cp06024a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Conformational dynamics induced by substrate binding in DapE enzyme.
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Affiliation(s)
- Debodyuti Dutta
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur
- India
| | - Sabyashachi Mishra
- Department of Chemistry
- Indian Institute of Technology Kharagpur
- Kharagpur
- India
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18
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Forlani G, Makarova KS, Ruszkowski M, Bertazzini M, Nocek B. Evolution of plant δ(1)-pyrroline-5-carboxylate reductases from phylogenetic and structural perspectives. FRONTIERS IN PLANT SCIENCE 2015; 6:567. [PMID: 26284089 PMCID: PMC4522605 DOI: 10.3389/fpls.2015.00567] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/09/2015] [Indexed: 05/23/2023]
Abstract
Proline plays a crucial role in cell growth and stress responses, and its accumulation is essential for the tolerance of adverse environmental conditions in plants. Two routes are used to biosynthesize proline in plants. The main route uses glutamate as a precursor, while in the other route proline is derived from ornithine. The terminal step of both pathways, the conversion of δ(1)-pyrroline-5-carboxylate (P5C) to L-proline, is catalyzed by P5C reductase (P5CR) using NADH or NADPH as a cofactor. Since P5CRs are important housekeeping enzymes, they are conserved across all domains of life and appear to be relatively unaffected throughout evolution. However, global analysis of these enzymes unveiled significant functional diversity in the preference for cofactors (NADPH vs. NADH), variation in metal dependence and the differences in the oligomeric state. In our study we investigated evolutionary patterns through phylogenetic and structural analysis of P5CR representatives from all kingdoms of life, with emphasis on the plant species. We also attempted to correlate local sequence/structure variation among the functionally and structurally characterized members of the family.
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Affiliation(s)
- Giuseppe Forlani
- Department of Life Science and Biotechnology, University of FerraraFerrara, Italy
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, BethesdaMD, USA
| | - Milosz Ruszkowski
- Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Argonne National Laboratory, ArgonneIL, USA
| | - Michele Bertazzini
- Department of Life Science and Biotechnology, University of FerraraFerrara, Italy
| | - Boguslaw Nocek
- The Bioscience Division, Argonne National Laboratory, ArgonneIL, USA
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Starus A, Nocek B, Bennett B, Larrabee JA, Shaw DL, Sae-Lee W, Russo MT, Gillner DM, Makowska-Grzyska M, Joachimiak A, Holz RC. Inhibition of the dapE-Encoded N-Succinyl-L,L-diaminopimelic Acid Desuccinylase from Neisseria meningitidis by L-Captopril. Biochemistry 2015; 54:4834-44. [PMID: 26186504 DOI: 10.1021/acs.biochem.5b00475] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Binding of the competitive inhibitor L-captopril to the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase from Neisseria meningitidis (NmDapE) was examined by kinetic, spectroscopic, and crystallographic methods. L-Captopril, an angiotensin-converting enzyme (ACE) inhibitor, was previously shown to be a potent inhibitor of the DapE from Haemophilus influenzae (HiDapE) with an IC50 of 3.3 μM and a measured Ki of 1.8 μM and displayed a dose-responsive antibiotic activity toward Escherichia coli. L-Captopril is also a competitive inhibitor of NmDapE with a Ki of 2.8 μM. To examine the nature of the interaction of L-captopril with the dinuclear active site of DapE, we have obtained electron paramagnetic resonance (EPR) and magnetic circular dichroism (MCD) data for the enzymatically hyperactive Co(II)-substituted forms of both HiDapE and NmDapE. EPR and MCD data indicate that the two Co(II) ions in DapE are antiferromagnetically coupled, yielding an S = 0 ground state, and suggest a thiolate bridge between the two metal ions. Verification of a thiolate-bridged dinuclear complex was obtained by determining the three-dimensional X-ray crystal structure of NmDapE in complex with L-captopril at 1.8 Å resolution. Combination of these data provides new insights into binding of L-captopril to the active site of DapE enzymes as well as important inhibitor-active site residue interaction's. Such information is critical for the design of new, potent inhibitors of DapE enzymes.
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Affiliation(s)
- Anna Starus
- †Department of Chemistry and Biochemistry, Loyola University-Chicago, 1068 West Sheridan Road, Chicago, Illinois 60626, United States
| | - Boguslaw Nocek
- ‡Center for Structural Genomics of Infectious Diseases, Computation Institute, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Brian Bennett
- §Department of Physics, Marquette University, Milwaukee, Wisconsin 53201, United States
| | - James A Larrabee
- ∥Department of Chemistry and Biochemistry, Middlebury College, Middlebury, Vermont 05753, United States
| | - Daniel L Shaw
- ∥Department of Chemistry and Biochemistry, Middlebury College, Middlebury, Vermont 05753, United States
| | - Wisath Sae-Lee
- ∥Department of Chemistry and Biochemistry, Middlebury College, Middlebury, Vermont 05753, United States
| | - Marie T Russo
- ∥Department of Chemistry and Biochemistry, Middlebury College, Middlebury, Vermont 05753, United States
| | - Danuta M Gillner
- ⊥Department of Chemistry, Silesian University of Technology, 44-100 Gliwice, Poland
| | - Magdalena Makowska-Grzyska
- ‡Center for Structural Genomics of Infectious Diseases, Computation Institute, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Andrzej Joachimiak
- ‡Center for Structural Genomics of Infectious Diseases, Computation Institute, University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Richard C Holz
- #Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, United States
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