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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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2
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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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3
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Diniz-Sousa R, Silva CCA, Pereira SS, da Silva SL, Fernandes PA, Teixeira LMC, Zuliani JP, Soares AM. Therapeutic applications of snake venoms: An invaluable potential of new drug candidates. Int J Biol Macromol 2023; 238:124357. [PMID: 37028634 DOI: 10.1016/j.ijbiomac.2023.124357] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/01/2023] [Accepted: 04/03/2023] [Indexed: 04/09/2023]
Abstract
Animal venoms and their chemical compounds have aroused both empirical and scientific attention for ages. However, there has been a significant increase in scientific investigations in recent decades, allowing the production of various formulations that are helping in the development of many important tools for biotechnological, diagnostic, or therapeutic use, both in human and animal health, as well as in plants. Venoms are composed of biomolecules and inorganic compounds that may have physiological and pharmacological activities that are not related to their principal actions (prey immobilization, digestion, and defense). Snake venom toxins, mainly enzymatic and non-enzymatic proteins, and peptides have been identified as potential prototypes for new drugs and/or models for the development of pharmacologically active structural domains for the treatment of cancer, cardiovascular diseases, neurodegenerative and autoimmune diseases, pain, and infectious-parasitic diseases. This minireview aims to provide an overview of the biotechnological potential of animal venoms, with a focus on snakes, and to introduce the reader to the fascinating world of Applied Toxinology, where animal biodiversity can be used to develop therapeutic and diagnostic applications for humans.
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Affiliation(s)
- Rafaela Diniz-Sousa
- Laboratório de Biotecnologia de Proteínas e Compostos Bioativos Aplicados à Saúde (LABIOPROT), Fundação Oswaldo Cruz, FIOCRUZ, Unidade Rondônia, Porto Velho, Rondônia, Brazil; Centro Universitário São Lucas (UniSL), Porto Velho, Rondônia, Brazil
| | - Cleópatra C A Silva
- Laboratório de Biotecnologia de Proteínas e Compostos Bioativos Aplicados à Saúde (LABIOPROT), Fundação Oswaldo Cruz, FIOCRUZ, Unidade Rondônia, Porto Velho, Rondônia, Brazil; Instituto Nacional de Ciência e Tecnologia de Epidemiologia da Amazônia Ocidental (INCT-EpiAmO), Porto Velho, Rondônia, Brazil
| | - Soraya S Pereira
- Laboratório de Engenharia de Anticorpos, Fundação Oswaldo Cruz, FIOCRUZ, Unidade Rondônia, Porto Velho, Rondônia, Brazil
| | - Saulo L da Silva
- LAQV/Requimte, University of Porto, Rua do Campo Alegre s/n, Porto, Portugal; Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, Porto, Portugal; Faculty of Chemical Sciences, University of Cuenca, Cuenca, Azuay, Ecuador
| | - Pedro A Fernandes
- LAQV/Requimte, University of Porto, Rua do Campo Alegre s/n, Porto, Portugal; Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, Porto, Portugal
| | - Luís M C Teixeira
- LAQV/Requimte, University of Porto, Rua do Campo Alegre s/n, Porto, Portugal; Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, Porto, Portugal
| | - Juliana P Zuliani
- Laboratório de Imunologia Celular Aplicada à Saúde, Fundação Oswaldo Cruz, FIOCRUZ, Unidade Rondônia, Porto Velho, Rondônia, Brazil
| | - Andreimar M Soares
- Laboratório de Biotecnologia de Proteínas e Compostos Bioativos Aplicados à Saúde (LABIOPROT), Fundação Oswaldo Cruz, FIOCRUZ, Unidade Rondônia, Porto Velho, Rondônia, Brazil; Centro Universitário São Lucas (UniSL), Porto Velho, Rondônia, Brazil; Instituto Nacional de Ciência e Tecnologia de Epidemiologia da Amazônia Ocidental (INCT-EpiAmO), Porto Velho, Rondônia, Brazil; Faculdade Católica de Rondônia (FCR), Porto Velho, Rondônia, Brazil.
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4
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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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5
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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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Stevens BR, Pepine CJ, Richards EM, Kim S, Raizada MK. Depressive hypertension: A proposed human endotype of brain/gut microbiome dysbiosis. Am Heart J 2021; 239:27-37. [PMID: 33984318 DOI: 10.1016/j.ahj.2021.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/04/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Hypertension (HTN) is frequently linked with depression (DEP) in adults with cardiovascular disease (CVD), yet the underlying mechanism and successful management remain elusive. We approached this knowledge gap through the lens that humans are eukaryote-prokaryote "meta-organisms," such that cardiovascular disease dysregulation is a mosaic disorder involving dysbiosis of the gut. We hypothesized that patients diagnosed with hypertension plus depression harbor a unique gut microbial ecology with attending functional genomics engaged with their hosts' gut/brain axis physiology. METHODS Stool microbiome DNA was analyzed by whole metagenome shotgun sequencing in 54 subjects parsed into cohorts diagnosed with HTN only (N = 18), DEP only (N = 7), DEP plus HTN (DEP-HTN) (N = 8), or reference subjects with neither HTN nor DEP (N = 21). A novel battery of machine-learning multivariate analyses of de-noised data yielded effect sizes and permutational covariance-based dissimilarities that significantly differentiated the cohorts (false discovery rate (FDR)-adjusted P ≤ .05); data clustering within 95% confidence interval). RESULTS Metagenomic significant differences extricated the four cohorts. Data of the cohort exhibiting DEP-HTN were germane to the interplay of central control of blood pressure concomitant with the neuropathology of depressive disorders. DEP-HTN gut bacterial community ecology was defined by co-occurrence of Eubacterium siraeum, Alistipes obesi, Holdemania filiformis, and Lachnospiraceae bacterium 1.1.57FAA with Streptococcus salivariu. The corresponding microbial functional genomics of DEP-HTN engaged pathways degrading GABA and beneficial short chain fatty acids (SCFA), and are associated with enhanced sodium absorption and inflammasome induction. CONCLUSIONS These data suggest a new putative endotype of hypertension, which we denote "depressive-hypertension" (DEP-HTN), for which we posit a model that is distinctive from either HTN alone or DEP alone. An "endotype" is a subtype of a heterogeneous pathophysiological mechanism. The DEP-HTN model incorporates a unique signature of microbial taxa and functional genomics with crosstalk that putatively intertwines host pathophysiology involving the gastrointestinal tract with disruptions in central control of blood pressure and mood. The DEP-HTN endotype model engages cardiology with gastroenterology and psychiatry, providing a proof-of-concept foundation to explore future treatments, diagnosis, and prevention of HTN-coupled mood disorders.
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Ali S, Alam M, Hasan GM, Hassan MI. Potential therapeutic targets of Klebsiella pneumoniae: a multi-omics review perspective. Brief Funct Genomics 2021; 21:63-77. [PMID: 34448478 DOI: 10.1093/bfgp/elab038] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/15/2022] Open
Abstract
The multidrug resistance developed in many organisms due to the prolonged use of antibiotics has been an increasing global health crisis. Klebsiella pneumoniae is a causal organism for various infections, including respiratory, urinary tract and biliary diseases. Initially, immunocompromised individuals are primarily affected by K. pneumoniae. Due to the emergence of hypervirulent strains recently, both healthy and immunocompetent individuals are equally susceptible to K. pneumoniae infections. The infections caused by multidrug-resistant and hypervirulent K. pneumoniae strains are complicated to treat, illustrating an urgent need to develop novel and more practical approaches to combat the pathogen. We focused on the previously performed high-throughput analyses by other groups to discover several novel enzymes that may be considered attractive drug targets of K. pneumoniae. These targets qualify most of the selection criteria for drug targeting, including an absence of its homolog's gene in the host. The capsule, lipopolysaccharide, fimbriae, siderophores and essential virulence factors facilitate the pathogen entry, infection and survival inside the host. This review discusses K. pneumoniae pathophysiology, including its virulence determinants and further the potential drug targets that might facilitate the discovery of novel drugs and effective treatment regimens shortly.
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Affiliation(s)
- Sabeeha Ali
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Manzar Alam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar New Delhi 110025, India
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8
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Metal-ion promiscuity of microbial enzyme DapE at its second metal-binding site. J Biol Inorg Chem 2021; 26:569-582. [PMID: 34241683 DOI: 10.1007/s00775-021-01875-7] [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: 02/01/2021] [Accepted: 05/28/2021] [Indexed: 10/20/2022]
Abstract
Metalloenzymes are ubiquitous in nature catalyzing a number of crucial biochemical processes in animal and plant kingdoms. For better adaptation to the relative abundance of different metal ions in different cellular fluids, many of these enzymes exhibit metal promiscuity. The microbial enzyme DapE, an essential enzyme for bacterial growth and survival and a potentially safe target for antibiotics, continues to show enzyme activity when the two zinc ions in its active site are replaced by other transition metal ions. The effect of metal-ion substitution at the second metal-binding site of DapE on its substrate affinity and catalytic efficiency is investigated by QM/MM treatment of the enzyme-substrate complex, by modelling the enzyme with Mn(II), Co(II), Ni(II), or Cu(II) ion in place of Zn(II) at its second metal-binding site, while retaining Zn(II) ion at the first metal-binding site. On the basis of substrate binding energy and activation energy barrier for the chemical catalysis, it is found that Zn-Mn DapE shows poor binding affinity as well as inefficient chemical catalysis. Although Zn-Cu and Zn-Ni DapEs show activation energy barriers comparable to that of wild-type Zn-Zn DapE, their weaker substrate affinity renders these mixed-metal enzymes less efficient. On the other hand, Zn-Co DapE is found to outperform the naturally occurring Zn-Zn DapE, both in terms of substrate affinity and chemical catalysis. The observed metal promiscuity may have played an important role in the survival of bacteria even in those cellular media where Zn ions are in limited supply. Metal nonspecificity in the catalysis of DapE enzyme allows bacteria to thrive in different cellular media.
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9
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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] [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, 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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11
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Li L, Chang L, Zhang X, Ning Z, Mayne J, Ye Y, Stintzi A, Liu J, Figeys D. Berberine and its structural analogs have differing effects on functional profiles of individual gut microbiomes. Gut Microbes 2020; 11:1348-1361. [PMID: 32372706 PMCID: PMC7524264 DOI: 10.1080/19490976.2020.1755413] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The understanding of the effects of compounds on the gut microbiome is limited. In particular, it is unclear whether structurally similar compounds would have similar or distinct effects on the gut microbiome. Here, we selected berberine (BBR), an isoquinoline quaternary alkaloid, and 16 structural analogs and evaluated their effects on seven individual gut microbiomes cultured in vitro. The responses of the individual microbiomes were evaluated by metaproteomic profiles and by assessing butyrate production. We show that both interindividual differences and compound treatments significantly contributed to the variance of metaproteomic profiles. BBR and eight analogs led to changes in proteins involved in microbial defense and stress responses and enrichment of proteins from Verrucomicrobia, Proteobacteria, and Bacteroidetes phyla. It also led to a decrease in proteins from the Firmicutes phylum and its Clostridiales order which correlated to decrease proteins involved in the butyrate production pathway and butyrate concentration. Three of the compounds, sanguinarine, chelerythrine, and ethoxysanguinarine, activated bacterial protective mechanisms, enriched Proteobacteria, increased opacity proteins, and markedly reduced butyrate production. Dihydroberberine had a similar function to BBR in enriching the Akkermansia genus. In addition, it showed less overall adverse impacts on the functionality of the gut microbiome, including a better maintenance of the butyrate level. Our study shows that ex vivo microbiome assay can assess differential regulating effects of compounds with subtle differences and reveals that compound analogs can have distinct effects on the microbiome.
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Affiliation(s)
- Leyuan Li
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Lu Chang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xu Zhang
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Zhibin Ning
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Janice Mayne
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada
| | - Yang Ye
- State Key Laboratory of Drug Research & Natural Products Chemistry Department, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China,Shanghai Institute of Materia Medica, University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, Shanghai, China
| | - Alain Stintzi
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada,Shanghai Institute of Materia Medica, University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, Shanghai, China
| | - Jia Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China,Shanghai Institute of Materia Medica, University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, Shanghai, China,Jia Liu Shanghai Institute of Materia Medica, University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, China
| | - Daniel Figeys
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Canada,Shanghai Institute of Materia Medica, University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, Shanghai, China,Canadian Institute for Advanced Research, Toronto, Canada,CONTACT Daniel Figeys
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Li HB, Yang T, Richards EM, Pepine CJ, Raizada MK. Maternal Treatment With Captopril Persistently Alters Gut-Brain Communication and Attenuates Hypertension of Male Offspring. Hypertension 2020; 75:1315-1324. [PMID: 32200676 DOI: 10.1161/hypertensionaha.120.14736] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Maternal-fetal crosstalk has been implicated in long-term control of the health of offspring, including transgenerational hypertension. However, current knowledge is limited regarding maternal influences on the gut and its microbiome in blood pressure control in offspring. Therefore, the current study was designed to test the hypothesis that maternal factors influence the gut-brain axis impacting hypertension in offspring. We elected to use captopril, an antihypertensive angiotensin-converting enzyme inhibitor that possesses antibacterial properties, for the study. Pregnant female spontaneously hypertensive rats and normotensive Wistar Kyoto rats were treated with captopril water (100 mg/[kg·day]) or sterile water throughout pregnancy and lactation. At weaning, the pups from dams drinking sterile water were continued with sterile water until 12 weeks of age. The male pups from dams drinking captopril water were divided at weaning into 2 groups: offspring drinking captopril water and offspring withdrawn from captopril water, then drinking sterile water until 12 weeks of age. Captopril changed gut microbiota of spontaneously hypertensive rat dams, and some of these changes were reflected in their 12-week-old male offspring. These 12-week-old spontaneously hypertensive rat male offspring exposed to captopril via dams demonstrated persistently decreased systolic blood pressure, decreased number of activated microglia and neuroinflammation, as well as improvement of gut inflammation and permeability. Therefore, maternal captopril treatment improves the dysregulated gut-brain axis in spontaneously hypertensive rat male offspring, providing conceptual support that targeting the gut-brain axis via the mother may be a viable strategy for control of hypertension in the offspring.
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Affiliation(s)
- Hong-Bao Li
- From the Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University, China (H.-B.L.).,Department of Physiology and Functional Genomics (H.-B.L, T.Y., E.M.R., M.K.R.), College of Medicine, University of Florida, Gainesville
| | - Tao Yang
- Department of Physiology and Functional Genomics (H.-B.L, T.Y., E.M.R., M.K.R.), College of Medicine, University of Florida, Gainesville.,Microbiome Consortium and Center for Hypertension and Precision Medicine, Department of Physiology and Pharmacology, College of Medicine and Life Sciences, University of Toledo, OH (T.Y.)
| | - Elaine M Richards
- Department of Physiology and Functional Genomics (H.-B.L, T.Y., E.M.R., M.K.R.), College of Medicine, University of Florida, Gainesville
| | - Carl J Pepine
- Division of Cardiovascular Medicine, Department of Medicine (C.J.P.), College of Medicine, University of Florida, Gainesville
| | - Mohan K Raizada
- Department of Physiology and Functional Genomics (H.-B.L, T.Y., E.M.R., M.K.R.), College of Medicine, University of Florida, Gainesville
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