1
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Tang Q, Tillmann M, Cohen JD. Analytical methods for stable isotope labeling to elucidate rapid auxin kinetics in Arabidopsis thaliana. PLoS One 2024; 19:e0303992. [PMID: 38776314 PMCID: PMC11111016 DOI: 10.1371/journal.pone.0303992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/04/2024] [Indexed: 05/24/2024] Open
Abstract
The phytohormone auxin plays a critical role in plant growth and development. Despite significant progress in elucidating metabolic pathways of the primary bioactive auxin, indole-3-acetic acid (IAA), over the past few decades, key components such as intermediates and enzymes have not been fully characterized, and the dynamic regulation of IAA metabolism in response to environmental signals has not been completely revealed. In this study, we established a protocol employing a highly sensitive liquid chromatography-mass spectrometry (LC-MS) instrumentation and a rapid stable isotope labeling approach. We treated Arabidopsis seedlings with two stable isotope labeled precursors ([13C6]anthranilate and [13C8, 15N1]indole) and monitored the label incorporation into proposed indolic compounds involved in IAA biosynthetic pathways. This Stable Isotope Labeled Kinetics (SILK) method allowed us to trace the turnover rates of IAA pathway precursors and product concurrently with a time scale of seconds to minutes. By measuring the entire pathways over time and using different isotopic tracer techniques, we demonstrated that these methods offer more detailed information about this complex interacting network of IAA biosynthesis, and should prove to be useful for studying auxin metabolic network in vivo in a variety of plant tissues and under different environmental conditions.
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Affiliation(s)
- Qian Tang
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Molly Tillmann
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Jerry D. Cohen
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota, United States of America
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2
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Drago VN, Devos JM, Blakeley MP, Forsyth VT, Parks JM, Kovalevsky A, Mueser TC. Neutron diffraction from a microgravity-grown crystal reveals the active site hydrogens of the internal aldimine form of tryptophan synthase. CELL REPORTS. PHYSICAL SCIENCE 2024; 5:101827. [PMID: 38645802 PMCID: PMC11027755 DOI: 10.1016/j.xcrp.2024.101827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Pyridoxal 5'-phosphate (PLP), the biologically active form of vitamin B6, is an essential cofactor in many biosynthetic pathways. The emergence of PLP-dependent enzymes as drug targets and biocatalysts, such as tryptophan synthase (TS), has underlined the demand to understand PLP-dependent catalysis and reaction specificity. The ability of neutron diffraction to resolve the positions of hydrogen atoms makes it an ideal technique to understand how the electrostatic environment and selective protonation of PLP regulates PLP-dependent activities. Facilitated by microgravity crystallization of TS with the Toledo Crystallization Box, we report the 2.1 Å joint X-ray/neutron (XN) structure of TS with PLP in the internal aldimine form. Positions of hydrogens were directly determined in both the α- and β-active sites, including PLP cofactor. The joint XN structure thus provides insight into the selective protonation of the internal aldimine and the electrostatic environment of TS necessary to understand the overall catalytic mechanism.
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Affiliation(s)
- Victoria N. Drago
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Juliette M. Devos
- Life Sciences Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
- Partnership for Structural Biology (PSB), 38000 Grenoble, France
| | - Matthew P. Blakeley
- Large Scale Structures Group, Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - V. Trevor Forsyth
- Faculty of Medicine, Lund University, and LINXS Institute for Advanced Neutron and X-ray Science, Lund, Sweden
| | - Jerry M. Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy C. Mueser
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
- Lead contact
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3
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Martins NF, Viana MJA, Maigret B. Fungi Tryptophan Synthases: What Is the Role of the Linker Connecting the α and β Structural Domains in Hemileia vastatrix TRPS? A Molecular Dynamics Investigation. Molecules 2024; 29:756. [PMID: 38398508 PMCID: PMC10893352 DOI: 10.3390/molecules29040756] [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: 12/27/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Tryptophan synthase (TRPS) is a complex enzyme responsible for tryptophan biosynthesis. It occurs in bacteria, plants, and fungi as an αββα heterotetramer. Although encoded by independent genes in bacteria and plants, in fungi, TRPS is generated by a single gene that concurrently expresses the α and β entities, which are linked by an elongated peculiar segment. We conducted 1 µs all-atom molecular dynamics simulations on Hemileia vastatrix TRPS to address two questions: (i) the role of the linker segment and (ii) the comparative mode of action. Since there is not an experimental structure, we started our simulations with homology modeling. Based on the results, it seems that TRPS makes use of an already-existing tunnel that can spontaneously move the indole moiety from the α catalytic pocket to the β one. Such behavior was completely disrupted in the simulation without the linker. In light of these results and the αβ dimer's low stability, the full-working TRPS single genes might be the result of a particular evolution. Considering the significant losses that Hemileia vastatrix causes to coffee plantations, our next course of action will be to use the TRPS to look for substances that can block tryptophan production and therefore control the disease.
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Affiliation(s)
- Natália F Martins
- EMBRAPA Agroindústria Tropical, Planalto do Pici, Fortaleza 60511-110, CE, Brazil
| | - Marcos J A Viana
- EMBRAPA Agroindústria Tropical, Planalto do Pici, Fortaleza 60511-110, CE, Brazil
| | - Bernard Maigret
- LORIA, UMR 7504 CNRS, Université de Lorraine, 54000 Vandoeuvre les Nancy, France
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4
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Konas D, Cho S, Thomas OD, Bhatti MM, Leon Hernandez K, Moran C, Booter H, Candela T, Lacap J, McFadden P, van den Berg S, Welter AM, Peralta A, Janson CA, Catalano J, Goodey NM. Investigating the Roles of Active Site Residues in Mycobacterium tuberculosis Indole-3-glycerol Phosphate Synthase, a Potential Target for Antitubercular Agents. ACS BIO & MED CHEM AU 2023; 3:438-447. [PMID: 37876495 PMCID: PMC10591298 DOI: 10.1021/acsbiomedchemau.3c00029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 10/26/2023]
Abstract
Mycobacterium tuberculosis drug resistance is emerging and new drug targets are needed. Tryptophan biosynthesis is necessary for M. tuberculosis replication and virulence. Indole-3-glycerol phosphate synthase (IGPS) catalyzes a step in M. tuberculosis tryptophan biosynthesis and has been suggested as a potential anti-infective target, but our understanding of this enzyme is limited. To aid in inhibitor design and gain a greater mechanistic picture of this enzyme, there is a need to understand the roles of active site amino acids in ligand binding and catalysis. In this work, we explored the roles of conserved active site amino acids Glu57, Lys59, Lys119, Glu168, and Glu219. Mutation of each to Ala results in loss of all detectable activity. The Glu57Gln, Lys59Arg, Lys119Arg, Glu168Gln, and Glu219Asp mutations result in large activity losses, while Glu219Gln has enhanced activity. Analysis of the enzymatic data yields the following main conclusions: (A) Lys119 is the likely catalytic acid in the CdRP ring closure step. (B) Glu168 stabilizes a charged reaction intermediate and may also be the catalytic base. (C) Glu57, Glu219, and Lys119 form a closely arranged triad in which Glu57 and Glu219 modulate the pKa of Lys119, and thus overall activity. This increased understanding of inter- and intramolecular interactions and demonstration of the highly coordinated nature of the M. tuberculosis IGPS active site provide new mechanistic information and guidance for future work with this potential new drug target.
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Affiliation(s)
- David
W. Konas
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Sarah Cho
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Oshane D. Thomas
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Maryum M. Bhatti
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Katherine Leon Hernandez
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Cinthya Moran
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Hedda Booter
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Thomas Candela
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Joseph Lacap
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Paige McFadden
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Savannah van den Berg
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Alyssa M. Welter
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Ashley Peralta
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Cheryl A. Janson
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Jaclyn Catalano
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
| | - Nina M. Goodey
- Department of Chemistry and
Biochemistry, Montclair State University 1 Normal Avenue, Montclair, New Jersey 07043, United States
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5
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Yang J, Zhang L, Qiao W, Luo Y. Mycobacterium tuberculosis: Pathogenesis and therapeutic targets. MedComm (Beijing) 2023; 4:e353. [PMID: 37674971 PMCID: PMC10477518 DOI: 10.1002/mco2.353] [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: 02/20/2023] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 09/08/2023] Open
Abstract
Tuberculosis (TB) remains a significant public health concern in the 21st century, especially due to drug resistance, coinfection with diseases like immunodeficiency syndrome (AIDS) and coronavirus disease 2019, and the lengthy and costly treatment protocols. In this review, we summarize the pathogenesis of TB infection, therapeutic targets, and corresponding modulators, including first-line medications, current clinical trial drugs and molecules in preclinical assessment. Understanding the mechanisms of Mycobacterium tuberculosis (Mtb) infection and important biological targets can lead to innovative treatments. While most antitubercular agents target pathogen-related processes, host-directed therapy (HDT) modalities addressing immune defense, survival mechanisms, and immunopathology also hold promise. Mtb's adaptation to the human host involves manipulating host cellular mechanisms, and HDT aims to disrupt this manipulation to enhance treatment effectiveness. Our review provides valuable insights for future anti-TB drug development efforts.
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Affiliation(s)
- Jiaxing Yang
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Laiying Zhang
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
| | - Wenliang Qiao
- Department of Thoracic Surgery, West China HospitalSichuan UniversityChengduSichuanChina
- Lung Cancer Center, West China HospitalSichuan UniversityChengduSichuanChina
| | - Youfu Luo
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China HospitalSichuan UniversityChengduChina
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6
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D'Amico RN, Boehr DD. Allostery, engineering and inhibition of tryptophan synthase. Curr Opin Struct Biol 2023; 82:102657. [PMID: 37467527 DOI: 10.1016/j.sbi.2023.102657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023]
Abstract
The final two steps of tryptophan biosynthesis are catalyzed by the enzyme tryptophan synthase (TS), composed of alpha (αTS) and beta (βTS) subunits. Recently, experimental and computational methods have mapped "allosteric networks" that connect the αTS and βTS active sites. In αTS, allosteric networks change across the catalytic cycle, which might help drive the conformational changes associated with its function. Directed evolution studies to increase catalytic function and expand the substrate profile of stand-alone βTS have also revealed the importance of αTS in modulating the conformational changes in βTS. These studies also serve as a foundation for the development of TS inhibitors, which can find utility against Mycobacterium tuberculosis and other bacterial pathogens.
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Affiliation(s)
- Rebecca N D'Amico
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA, 16802
| | - David D Boehr
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA, 16802.
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7
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Ito S, Yagi K, Sugita Y. Allosteric regulation of β-reaction stage I in tryptophan synthase upon the α-ligand binding. J Chem Phys 2023; 158:115101. [PMID: 36948822 DOI: 10.1063/5.0134117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Tryptophan synthase (TRPS) is a bifunctional enzyme consisting of α- and β-subunits that catalyzes the last two steps of L-tryptophan (L-Trp) biosynthesis. The first stage of the reaction at the β-subunit is called β-reaction stage I, which converts the β-ligand from an internal aldimine [E(Ain)] to an α-aminoacrylate [E(A-A)] intermediate. The activity is known to increase 3-10-fold upon the binding of 3-indole-D-glycerol-3'-phosphate (IGP) at the α-subunit. The effect of α-ligand binding on β-reaction stage I at the distal β-active site is not well understood despite the abundant structural information available for TRPS. Here, we investigate the β-reaction stage I by carrying out minimum-energy pathway searches based on a hybrid quantum mechanics/molecular mechanics (QM/MM) model. The free-energy differences along the pathway are also examined using QM/MM umbrella sampling simulations with QM calculations at the B3LYP-D3/aug-cc-pVDZ level of theory. Our simulations suggest that the sidechain orientation of βD305 near the β-ligand likely plays an essential role in the allosteric regulation: a hydrogen bond is formed between βD305 and the β-ligand in the absence of the α-ligand, prohibiting a smooth rotation of the hydroxyl group in the quinonoid intermediate, whereas the dihedral angle rotates smoothly after the hydrogen bond is switched from βD305-β-ligand to βD305-βR141. This switch could occur upon the IGP-binding at the α-subunit, as evidenced by the existing TRPS crystal structures.
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Affiliation(s)
- Shingo Ito
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kiyoshi Yagi
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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8
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Fernandes GFS, Thompson AM, Castagnolo D, Denny WA, Dos Santos JL. Tuberculosis Drug Discovery: Challenges and New Horizons. J Med Chem 2022; 65:7489-7531. [PMID: 35612311 DOI: 10.1021/acs.jmedchem.2c00227] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Over the past 2000 years, tuberculosis (TB) has claimed more lives than any other infectious disease. In 2020 alone, TB was responsible for 1.5 million deaths worldwide, comparable to the 1.8 million deaths caused by COVID-19. The World Health Organization has stated that new TB drugs must be developed to end this pandemic. After decades of neglect in this field, a renaissance era of TB drug discovery has arrived, in which many novel candidates have entered clinical trials. However, while hundreds of molecules are reported annually as promising anti-TB agents, very few successfully progress to clinical development. In this Perspective, we critically review those anti-TB compounds published in the last 6 years that demonstrate good in vivo efficacy against Mycobacterium tuberculosis. Additionally, we highlight the main challenges and strategies for developing new TB drugs and the current global pipeline of drug candidates in clinical studies to foment fresh research perspectives.
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Affiliation(s)
- Guilherme F S Fernandes
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Andrew M Thompson
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Daniele Castagnolo
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - William A Denny
- Auckland Cancer Society Research Centre, Faculty of Medical and Health Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jean L Dos Santos
- School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara 14800903, Brazil
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9
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Ito S, Yagi K, Sugita Y. Computational Analysis on the Allostery of Tryptophan Synthase: Relationship between α/β-Ligand Binding and Distal Domain Closure. J Phys Chem B 2022; 126:3300-3308. [PMID: 35446577 PMCID: PMC9083551 DOI: 10.1021/acs.jpcb.2c01556] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tryptophan synthase (TRPS) is a bifunctional enzyme consisting of α and β-subunits and catalyzes the last two steps of l-tryptophan (L-Trp) biosynthesis, namely, cleavage of 3-indole-d-glycerol-3'-phosphate (IGP) into indole and glyceraldehyde-3-phosphate (G3P) in the α-subunit, and a pyridoxal phosphate (PLP)-dependent reaction of indole and l-serine (L-Ser) to produce L-Trp in the β-subunit. Importantly, the IGP binding at the α-subunit affects the β-subunit conformation and its ligand-binding affinity, which, in turn, enhances the enzymatic reaction at the α-subunit. The intersubunit communications in TRPS have been investigated extensively for decades because of the fundamental and pharmaceutical importance, while it is still difficult to answer how TRPS allostery is regulated at the atomic detail. Here, we investigate the allosteric regulation of TRPS by all-atom classical molecular dynamics (MD) simulations and analyze the potential of mean-force (PMF) along conformational changes of the α- and β-subunits. The present simulation has revealed a widely opened conformation of the β-subunit, which provides a pathway for L-Ser to enter into the β-active site. The IGP binding closes the α-subunit and induces a wide opening of the β-subunit, thereby enhancing the binding affinity of L-Ser to the β-subunit. Structural analyses have identified critical hydrogen bonds (HBs) at the interface of the two subunits (αG181-βS178, αP57-βR175, etc.) and HBs between the β-subunit (βT110 - βH115) and a complex of PLP and L-Ser (an α-aminoacrylate intermediate). The former HBs regulate the allosteric, β-subunit opening, whereas the latter HBs are essential for closing the β-subunit in a later step. The proposed mechanism for how the interdomain communication in TRPS is realized with ligand bindings is consistent with the previous experimental data, giving a general idea to interpret the allosteric regulations in multidomain proteins.
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Affiliation(s)
- Shingo Ito
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kiyoshi Yagi
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Computational Biophysics Research Team, RIKEN Center for Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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10
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Bosken YK, Ai R, Hilario E, Ghosh RK, Dunn MF, Kan S, Niks D, Zhou H, Ma W, Mueller LJ, Fan L, Chang CA. Discovery of antimicrobial agent targeting tryptophan synthase. Protein Sci 2022; 31:432-442. [PMID: 34767267 PMCID: PMC8820114 DOI: 10.1002/pro.4236] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/27/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023]
Abstract
Antibiotic resistance is a continually growing challenge in the treatment of various bacterial infections worldwide. New drugs and new drug targets are necessary to curb the threat of infectious diseases caused by multidrug-resistant pathogens. The tryptophan biosynthesis pathway is essential for bacterial growth but is absent in higher animals and humans. Drugs that can inhibit the bacterial biosynthesis of tryptophan offer a new class of antibiotics. In this work, we combined a structure-based strategy using in silico docking screening and molecular dynamics (MD) simulations to identify compounds targeting the α subunit of tryptophan synthase with experimental methods involving the whole-cell minimum inhibitory concentration (MIC) test, solution state NMR, and crystallography to confirm the inhibition of L-tryptophan biosynthesis. Screening 1,800 compounds from the National Cancer Institute Diversity Set I against α subunit revealed 28 compounds for experimental validation; four of the 28 hit compounds showed promising activity in MIC testing. We performed solution state NMR experiments to demonstrate that a one successful inhibitor, 3-amino-3-imino-2-phenyldiazenylpropanamide (Compound 1) binds to the α subunit. We also report a crystal structure of Salmonella enterica serotype Typhimurium tryptophan synthase in complex with Compound 1 which revealed a binding site at the αβ interface of the dimeric enzyme. MD simulations were carried out to examine two binding sites for the compound. Our results show that this small molecule inhibitor could be a promising lead for future drug development.
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Affiliation(s)
- Yuliana K. Bosken
- Department of ChemistryUniversity of California at RiversideRiversideCalifornia
| | - Rizi Ai
- Department of ChemistryUniversity of California at RiversideRiversideCalifornia
| | - Eduardo Hilario
- Department of ChemistryUniversity of California at RiversideRiversideCalifornia
| | - Rittik K. Ghosh
- Department of BiochemistryUniversity of California at RiversideRiversideCalifornia
| | - Michael F. Dunn
- Department of BiochemistryUniversity of California at RiversideRiversideCalifornia
| | - Shih‐Hsin Kan
- Department of ChemistryUniversity of California at RiversideRiversideCalifornia,Present address:
CHOC Research InstituteOrangeCalifornia
| | - Dimitri Niks
- Department of BiochemistryUniversity of California at RiversideRiversideCalifornia
| | - Huanbin Zhou
- Department of Microbiology and Plant PathologyUniversity of California at RiversideRiversideCalifornia,Present address:
Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina
| | - Wenbo Ma
- Department of Microbiology and Plant PathologyUniversity of California at RiversideRiversideCalifornia,Present address:
The Sainsbury LaboratoryNorwich Research ParkNorwichUK
| | - Leonard J. Mueller
- Department of ChemistryUniversity of California at RiversideRiversideCalifornia
| | - Li Fan
- Department of BiochemistryUniversity of California at RiversideRiversideCalifornia
| | - Chia‐En A. Chang
- Department of ChemistryUniversity of California at RiversideRiversideCalifornia
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11
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Klein A, Rovó P, Sakhrani VV, Wang Y, Holmes JB, Liu V, Skowronek P, Kukuk L, Vasa SK, Güntert P, Mueller LJ, Linser R. Atomic-resolution chemical characterization of (2x)72-kDa tryptophan synthase via four- and five-dimensional 1H-detected solid-state NMR. Proc Natl Acad Sci U S A 2022; 119:e2114690119. [PMID: 35058365 PMCID: PMC8795498 DOI: 10.1073/pnas.2114690119] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/13/2021] [Indexed: 02/07/2023] Open
Abstract
NMR chemical shifts provide detailed information on the chemical properties of molecules, thereby complementing structural data from techniques like X-ray crystallography and electron microscopy. Detailed analysis of protein NMR data, however, often hinges on comprehensive, site-specific assignment of backbone resonances, which becomes a bottleneck for molecular weights beyond 40 to 45 kDa. Here, we show that assignments for the (2x)72-kDa protein tryptophan synthase (665 amino acids per asymmetric unit) can be achieved via higher-dimensional, proton-detected, solid-state NMR using a single, 1-mg, uniformly labeled, microcrystalline sample. This framework grants access to atom-specific characterization of chemical properties and relaxation for the backbone and side chains, including those residues important for the catalytic turnover. Combined with first-principles calculations, the chemical shifts in the β-subunit active site suggest a connection between active-site chemistry, the electrostatic environment, and catalytically important dynamics of the portal to the β-subunit from solution.
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Affiliation(s)
- Alexander Klein
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Petra Rovó
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
| | - Varun V Sakhrani
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Yangyang Wang
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Jacob B Holmes
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Viktoriia Liu
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Patricia Skowronek
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
| | - Laura Kukuk
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Suresh K Vasa
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
| | - Peter Güntert
- Institute of Biophysical Chemistry, Goethe University, 60438 Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
- Department of Chemistry, Tokyo Metropolitan University, Tokyo 192-0397, Japan
| | - Leonard J Mueller
- Department of Chemistry, University of California, Riverside, CA 92521
| | - Rasmus Linser
- Department of Chemistry and Pharmacy, Ludwig Maximilians University, 81377 Munich, Germany;
- Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany
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12
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Esposito N, Konas DW, Goodey NM. Indole-3-Glycerol Phosphate Synthase From Mycobacterium tuberculosis: A Potential New Drug Target. Chembiochem 2022; 23:e202100314. [PMID: 34383995 PMCID: PMC9041893 DOI: 10.1002/cbic.202100314] [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: 06/26/2021] [Revised: 07/29/2021] [Indexed: 01/21/2023]
Abstract
Tuberculosis (TB), caused by the pathogen Mycobacterium tuberculosis, affects millions of people worldwide. Several TB drugs have lost efficacy due to emerging drug resistance and new anti-TB targets are needed. Recent research suggests that indole-3-glycerol phosphate synthase (IGPS) in M. tuberculosis (MtIGPS) could be such a target. IGPS is a (β/α)8 -barrel enzyme that catalyzes the conversion of 1-(o-carboxyphenylamino)-1-deoxyribulose 5'-phosphate (CdRP) into indole-glycerol-phosphate (IGP) in the bacterial tryptophan biosynthetic pathway. M. tuberculosis over expresses the tryptophan pathway genes during an immune response and inhibition of MtIGPS allows CD4 T-cells to more effectively fight against M. tuberculosis. Here we review the published data on MtIGPS expression, kinetics, mechanism, and inhibition. We also discuss MtIGPS crystal structures and compare them to other IGPS structures to reveal potential structure-function relationships of interest for the purposes of drug design and biocatalyst engineering.
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Affiliation(s)
| | | | - Nina M. Goodey
- Corresponding author: Nina M. Goodey: Phone: (973) 655 3410; , Twitter: @ninagoodey
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13
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Bajad NG, Singh SK, Singh SK, Singh TD, Singh M. Indole: A promising scaffold for the discovery and development of potential anti-tubercular agents. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2022; 3:100119. [PMID: 35992375 PMCID: PMC9389259 DOI: 10.1016/j.crphar.2022.100119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 04/13/2022] [Accepted: 07/05/2022] [Indexed: 11/08/2022] Open
Abstract
Indole-containing small molecules have been reported to have diverse pharmacological activities. The aromatic heterocyclic scaffold, which resembles various protein structures, has received attention from organic and medicinal chemists. Exploration of indole derivatives in drug discovery has rapidly yielded a vast array of biologically active compounds with broad therapeutic potential. Nature is the major source of indole scaffolds, but various classical and advanced synthesis methods for indoles have also been reported. One-pot synthesis is widely considered an efficient approach in synthetic organic chemistry and has been used to synthesize some indole compounds. The rapid emergence of drug-resistant tuberculosis is a major challenge to be addressed. Identifying novel targets and drug candidates for tuberculosis is therefore crucial. Researchers have extensively explored indole derivatives as potential anti-tubercular agents or drugs. Indole scaffolds containing the novel non-covalent (decaprenylphosphoryl-β-D-ribose2′-epimerase) DprE1 inhibitor 1,4-azaindole is currently in clinical trials to treat Mycobacterium tuberculosis. In addition, DG167 indazole sulfonamide with potent anti-tubercular activity is undergoing early-stage development in preclinical studies. Indole bearing cationic amphiphiles with high chemical diversity have been reported to depolarize and disrupt the mycobacterial membrane. Some indole-based compounds have potential inhibitory activities against distinct anti-tubercular targets, including the inhibition of cell wall synthesis, replication, transcription, and translation, as summarized in the graphical abstract. The success of computer-aided drug design in the fields of cancer and anti-viral drugs has accelerated in silico studies in antibacterial drug development. This review describes the sources of indole scaffolds, the potential for novel indole derivatives to serve as anti-tubercular agents, in silico findings, and proposed actions to facilitate the design of novel compounds with anti-tubercular activity. The Indole derivatives emerged as an efficient bioactive compoundes with wide range of therapeutic potential. Identifying novel drug candidates with indole derivatives can curtail the rapid emergence of drug-resistant tuberculosis. The current review highlights the sources of indole scaffolds, their derivatives, and in silico findings as anti-tubercular agents. Currently, DprE1 inhibitor 1,4-azaindole and DG167 indazole sulfonamide are in clinical trials to treat Mycobacterium tuberculosis.
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14
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An Outline of the Latest Crystallographic Studies on Inhibitor-Enzyme Complexes for the Design and Development of New Therapeutics against Tuberculosis. Molecules 2021; 26:molecules26237082. [PMID: 34885662 PMCID: PMC8659263 DOI: 10.3390/molecules26237082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/04/2022] Open
Abstract
The elucidation of the structure of enzymes and their complexes with ligands continues to provide invaluable insights for the development of drugs against many diseases, including bacterial infections. After nearly three decades since the World Health Organization’s (WHO) declaration of tuberculosis (TB) as a global health emergency, Mycobacterium tuberculosis (Mtb) continues to claim millions of lives, remaining among the leading causes of death worldwide. In the last years, several efforts have been devoted to shortening and improving treatment outcomes, and to overcoming the increasing resistance phenomenon. The structural elucidation of enzyme-ligand complexes is fundamental to identify hot-spots, define possible interaction sites, and elaborate strategies to develop optimized molecules with high affinity. This review offers a critical and comprehensive overview of the most recent structural information on traditional and emerging mycobacterial enzymatic targets. A selection of more than twenty enzymes is here discussed, with a special emphasis on the analysis of their binding sites, the definition of the structure–activity relationships (SARs) of their inhibitors, and the study of their main intermolecular interactions. This work corroborates the potential of structural studies, substantiating their relevance in future anti-mycobacterial drug discovery and development efforts.
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15
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Yang L, Hu X, Chai X, Ye Q, Pang J, Li D, Hou T. Opportunities for overcoming tuberculosis: Emerging targets and their inhibitors. Drug Discov Today 2021; 27:326-336. [PMID: 34537334 DOI: 10.1016/j.drudis.2021.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/24/2021] [Accepted: 09/10/2021] [Indexed: 12/28/2022]
Abstract
Tuberculosis (TB), an airborne infectious disease mainly caused by Mycobacterium tuberculosis (Mtb), remains a leading cause of human morbidity and mortality worldwide. Given the alarming rise of resistance to anti-TB drugs and latent TB infection (LTBI), new targets and novel bioactive compounds are urgently needed for the treatment of this disease. We provide an overview of the recent advances in anti-TB drug discovery, emphasizing several newly validated targets for which an inhibitor has been reported in the past five years. Our review presents several attractive directions that have potential for the development of next-generation therapies.
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Affiliation(s)
- Liu Yang
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xueping Hu
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xin Chai
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qing Ye
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jinping Pang
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dan Li
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Lab of Computer-aided Design and Computer Graphics (CAD&CG), Zhejiang University, Hangzhou, Zhejiang 310058, China.
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16
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The tryptophan biosynthetic pathway is essential for Mycobacterium tuberculosis to cause disease. Biochem Soc Trans 2021; 48:2029-2037. [PMID: 32915193 PMCID: PMC7609029 DOI: 10.1042/bst20200194] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 12/19/2022]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), is the most significant cause of death from a single infectious agent worldwide. Antibiotic-resistant strains of M. tuberculosis represent a threat to effective treatment, and the long duration, toxicity and complexity of current chemotherapy for antibiotic-resistant disease presents a need for new therapeutic approaches with novel modes of action. M. tuberculosis is an intracellular pathogen that must survive phagocytosis by macrophages, dendritic cells or neutrophils to establish an infection. The tryptophan biosynthetic pathway is required for bacterial survival in the phagosome, presenting a target for new classes of antitubercular compound. The enzymes responsible for the six catalytic steps that produce tryptophan from chorismate have all been characterised in M. tuberculosis, and inhibitors have been described for some of the steps. The innate immune system depletes cellular tryptophan in response to infection in order to inhibit microbial growth, and this effect is likely to be important for the efficacy of tryptophan biosynthesis inhibitors as new antibiotics. Allosteric inhibitors of both the first and final enzymes in the pathway have proven effective, including by a metabolite produced by the gut biota, raising the intriguing possibility that the modulation of tryptophan biosynthesis may be a natural inter-bacterial competition strategy.
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17
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Tillmann M, Tang Q, Cohen JD. Protocol: analytical methods for visualizing the indolic precursor network leading to auxin biosynthesis. PLANT METHODS 2021; 17:63. [PMID: 34158074 PMCID: PMC8220744 DOI: 10.1186/s13007-021-00763-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 06/07/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND The plant hormone auxin plays a central role in regulation of plant growth and response to environmental stimuli. Multiple pathways have been proposed for biosynthesis of indole-3-acetic acid (IAA), the primary auxin in a number of plant species. However, utilization of these different pathways under various environmental conditions and developmental time points remains largely unknown. RESULTS Monitoring incorporation of stable isotopes from labeled precursors into proposed intermediates provides a method to trace pathway utilization and characterize new biosynthetic routes to auxin. These techniques can be aided by addition of chemical inhibitors to target specific steps or entire pathways of auxin synthesis. CONCLUSIONS Here we describe techniques for pathway analysis in Arabidopsis thaliana seedlings using multiple stable isotope-labeled precursors and chemical inhibitors coupled with highly sensitive liquid chromatography-mass spectrometry (LC-MS) methods. These methods should prove to be useful to researchers studying routes of IAA biosynthesis in vivo in a variety of plant tissues.
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Affiliation(s)
- Molly Tillmann
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, MN, USA.
| | - Qian Tang
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, MN, USA
| | - Jerry D Cohen
- Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, MN, USA
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18
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Libardo MDJ, Duncombe CJ, Green SR, Wyatt PG, Thompson S, Ray PC, Ioerger TR, Oh S, Goodwin MB, Boshoff HIM, Barry CE. Resistance of Mycobacterium tuberculosis to indole 4-carboxamides occurs through alterations in drug metabolism and tryptophan biosynthesis. Cell Chem Biol 2021; 28:1180-1191.e20. [PMID: 33765439 PMCID: PMC8379015 DOI: 10.1016/j.chembiol.2021.02.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/22/2021] [Accepted: 02/25/2021] [Indexed: 01/22/2023]
Abstract
Tryptophan biosynthesis represents an important potential drug target for new anti-TB drugs. We identified a series of indole-4-carboxamides with potent antitubercular activity. In vitro, Mycobacterium tuberculosis (Mtb) acquired resistance to these compounds through three discrete mechanisms: (1) a decrease in drug metabolism via loss-of-function mutations in the amidase that hydrolyses these carboxamides, (2) an increased biosynthetic rate of tryptophan precursors via loss of allosteric feedback inhibition of anthranilate synthase (TrpE), and (3) mutation of tryptophan synthase (TrpAB) that decreased incorporation of 4-aminoindole into 4-aminotryptophan. Thus, these indole-4-carboxamides act as prodrugs of a tryptophan antimetabolite, 4-aminoindole.
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Affiliation(s)
- M Daben J Libardo
- Tuberculosis Research Section, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Caroline J Duncombe
- Tuberculosis Research Section, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Simon R Green
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Paul G Wyatt
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Stephen Thompson
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Peter C Ray
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Sangmi Oh
- Tuberculosis Research Section, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael B Goodwin
- Tuberculosis Research Section, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Helena I M Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Clifton E Barry
- Tuberculosis Research Section, Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7935, South Africa.
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19
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Ostrowska K, Leśniak A, Czarnocka Z, Chmiel J, Bujalska-Zadrożny M, Trzaskowski B. Design, Synthesis, and Biological Evaluation of a Series of 5- and 7-Hydroxycoumarin Derivatives as 5-HT 1A Serotonin Receptor Antagonists. Pharmaceuticals (Basel) 2021; 14:ph14030179. [PMID: 33668396 PMCID: PMC7996328 DOI: 10.3390/ph14030179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/19/2021] [Accepted: 02/20/2021] [Indexed: 11/16/2022] Open
Abstract
We have designed and synthesized a series of 60 new 5- and 7-hydroxycoumarin derivatives bearing the piperazine moiety with the expected binding to 5-HT1A and 5-HT2A receptors. Molecular docking of all investigated compounds revealed subnanomolar estimates of 5-HT1AR Ki for three ligands and 5-HT2AR Ki for one ligand as well as numerous low nanomolar estimates of Ki for both receptors. Intrigued by these results we synthesized all 60 new derivatives using microwave-assisted protocols. We show that three new compounds show a relatively high antagonistic activity against the 5HT1A receptor, although lower than the reference compound WAY-100635. These compounds also showed relatively low binding affinities to the 5-HT2A receptor. We also provide a detailed structure-activity analysis of this series of compounds and compare it with previously obtained results for an exhaustive series of coumarin derivatives.
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Affiliation(s)
- Kinga Ostrowska
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha Str., 02-097 Warsaw, Poland; (Z.C.); (J.C.)
- Correspondence: ; Tel.: +48-22-572-0669
| | - Anna Leśniak
- Department of Pharmacodynamics, Faculty of Pharmacy, Centre for Preclinical Research and Technology, Medical University of Warsaw, 1 Banacha Str., 02-097 Warsaw, Poland; (A.L.); (M.B.-Z.)
| | - Zuzanna Czarnocka
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha Str., 02-097 Warsaw, Poland; (Z.C.); (J.C.)
| | - Jagoda Chmiel
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Warsaw, 1 Banacha Str., 02-097 Warsaw, Poland; (Z.C.); (J.C.)
| | - Magdalena Bujalska-Zadrożny
- Department of Pharmacodynamics, Faculty of Pharmacy, Centre for Preclinical Research and Technology, Medical University of Warsaw, 1 Banacha Str., 02-097 Warsaw, Poland; (A.L.); (M.B.-Z.)
| | - Bartosz Trzaskowski
- Centre of New Technologies, University of Warsaw, 2C Banacha Str., 02-097 Warsaw, Poland;
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20
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Computational investigations of allostery in aromatic amino acid biosynthetic enzymes. Biochem Soc Trans 2021; 49:415-429. [PMID: 33544132 DOI: 10.1042/bst20200741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022]
Abstract
Allostery, in which binding of ligands to remote sites causes a functional change in the active sites, is a fascinating phenomenon observed in enzymes. Allostery can occur either with or without significant conformational changes in the enzymes, and the molecular basis of its mechanism can be difficult to decipher using only experimental techniques. Computational tools for analyzing enzyme sequences, structures, and dynamics can provide insights into the allosteric mechanism at the atomic level. Combining computational and experimental methods offers a powerful strategy for the study of enzyme allostery. The aromatic amino acid biosynthesis pathway is essential in microorganisms and plants. Multiple enzymes involved in this pathway are sensitive to feedback regulation by pathway end products and are known to use allostery to control their activities. To date, four enzymes in the aromatic amino acid biosynthesis pathway have been computationally investigated for their allosteric mechanisms, including 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase, anthranilate synthase, chorismate mutase, and tryptophan synthase. Here we review the computational studies and findings on the allosteric mechanisms of these four enzymes. Results from these studies demonstrate the capability of computational tools and encourage future computational investigations of allostery in other enzymes of this pathway.
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21
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O'Rourke KF, D'Amico RN, Sahu D, Boehr DD. Distinct conformational dynamics and allosteric networks in alpha tryptophan synthase during active catalysis. Protein Sci 2020; 30:543-557. [PMID: 33314435 DOI: 10.1002/pro.4011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/21/2020] [Accepted: 12/06/2020] [Indexed: 12/13/2022]
Abstract
Experimental observations of enzymes under active turnover conditions have brought new insight into the role of protein motions and allosteric networks in catalysis. Many of these studies characterize enzymes under dynamic chemical equilibrium conditions, in which the enzyme is actively catalyzing both the forward and reverse reactions during data acquisition. We have previously analyzed conformational dynamics and allosteric networks of the alpha subunit of tryptophan synthase under such conditions using NMR. We have proposed that this working state represents a four to one ratio of the enzyme bound with the indole-3-glycerol phosphate substrate (E:IGP) to the enzyme bound with the products indole and glyceraldehyde-3-phosphate (E:indole:G3P). Here, we analyze the inactive D60N variant to deconvolute the contributions of the substrate- and products-bound states to the working state. While the D60N substitution itself induces small structural and dynamic changes, the D60N E:IGP and E:indole:G3P states cannot entirely account for the conformational dynamics and allosteric networks present in the working state. The act of chemical bond breakage and/or formation, or possibly the generation of an intermediate, may alter the structure and dynamics present in the working state. As the enzyme transitions from the substrate-bound to the products-bound state, millisecond conformational exchange processes are quenched and new allosteric connections are made between the alpha active site and the surface which interfaces with the beta subunit. The structural ordering of the enzyme and these new allosteric connections may be important in coordinating the channeling of the indole product into the beta subunit.
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Affiliation(s)
- Kathleen F O'Rourke
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Debashish Sahu
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
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22
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Kovács E, Faigl F, Mucsi Z. Regio- and Diastereoselective Synthesis of 2-Arylazetidines: Quantum Chemical Explanation of Baldwin's Rules for the Ring-Formation Reactions of Oxiranes†. J Org Chem 2020; 85:11226-11239. [PMID: 32786621 PMCID: PMC7498157 DOI: 10.1021/acs.joc.0c01310] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
A general,
scalable two-step regio- and diastereoselective method
has been described for the synthesis of versatile alkaloid-type azetidines
from simple building blocks with excellent overall yields. In the
kinetically controlled reaction, only the formation of the strained
four-membered ring can be achieved instead of the thermodynamically
favorable five-membered rings under appropriate conditions. Remarkable
functional group tolerance has also been demonstrated. In this paper,
we give a new scope of Baldwin’s rules by density functional
theory (DFT) calculations with an explicit solvent model, confirming
the proposed reaction mechanisms and the role of kinetic controls
in the stereochemical outcome of the reported transition-metal-free
carbon–carbon bond formation reactions.
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Affiliation(s)
- Ervin Kovács
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1117, Hungary.,MTA-BME Organic Chemical Technology Research Group, Budapest University of Technology and Economics, Budafoki út 8, H-1111 Budapest, Hungary.,Femtonics Ltd., Budapest H-1094, Hungary
| | - Ferenc Faigl
- MTA-BME Organic Chemical Technology Research Group, Budapest University of Technology and Economics, Budafoki út 8, H-1111 Budapest, Hungary
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23
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Pyridoxal 5'-Phosphate-Dependent Enzymes at the Crossroads of Host-Microbe Tryptophan Metabolism. Int J Mol Sci 2020; 21:ijms21165823. [PMID: 32823705 PMCID: PMC7461572 DOI: 10.3390/ijms21165823] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/06/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
The chemical processes taking place in humans intersects the myriad of metabolic pathways occurring in commensal microorganisms that colonize the body to generate a complex biochemical network that regulates multiple aspects of human life. The role of tryptophan (Trp) metabolism at the intersection between the host and microbes is increasingly being recognized, and multiple pathways of Trp utilization in either direction have been identified with the production of a wide range of bioactive products. It comes that a dysregulation of Trp metabolism in either the host or the microbes may unbalance the production of metabolites with potential pathological consequences. The ability to redirect the Trp flux to restore a homeostatic production of Trp metabolites may represent a valid therapeutic strategy for a variety of pathological conditions, but identifying metabolic checkpoints that could be exploited to manipulate the Trp metabolic network is still an unmet need. In this review, we put forward the hypothesis that pyridoxal 5′-phosphate (PLP)-dependent enzymes, which regulate multiple pathways of Trp metabolism in both the host and in microbes, might represent critical nodes and that modulating the levels of vitamin B6, from which PLP is derived, might represent a metabolic checkpoint to re-orienteer Trp flux for therapeutic purposes.
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24
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Michalska K, Chang C, Maltseva NI, Jedrzejczak R, Robertson GT, Gusovsky F, McCarren P, Schreiber SL, Nag PP, Joachimiak A. Allosteric inhibitors of Mycobacterium tuberculosis tryptophan synthase. Protein Sci 2020; 29:779-788. [PMID: 31930594 PMCID: PMC7020977 DOI: 10.1002/pro.3825] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/13/2022]
Abstract
Global dispersion of multidrug resistant bacteria is very common and evolution of antibiotic-resistance is occurring at an alarming rate, presenting a formidable challenge for humanity. The development of new therapeuthics with novel molecular targets is urgently needed. Current drugs primarily affect protein, nucleic acid, and cell wall synthesis. Metabolic pathways, including those involved in amino acid biosynthesis, have recently sparked interest in the drug discovery community as potential reservoirs of such novel targets. Tryptophan biosynthesis, utilized by bacteria but absent in humans, represents one of the currently studied processes with a therapeutic focus. It has been shown that tryptophan synthase (TrpAB) is required for survival of Mycobacterium tuberculosis in macrophages and for evading host defense, and therefore is a promising drug target. Here we present crystal structures of TrpAB with two allosteric inhibitors of M. tuberculosis tryptophan synthase that belong to sulfolane and indole-5-sulfonamide chemical scaffolds. We compare our results with previously reported structural and biochemical studies of another, azetidine-containing M. tuberculosis tryptophan synthase inhibitor. This work shows how structurally distinct ligands can occupy the same allosteric site and make specific interactions. It also highlights the potential benefit of targeting more variable allosteric sites of important metabolic enzymes.
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Affiliation(s)
- Karolina Michalska
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Changsoo Chang
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Natalia I. Maltseva
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Robert Jedrzejczak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
| | - Gregory T. Robertson
- Colorado State UniversityMycobacteria Research Laboratories, Department of Microbiology, Immunology and PathologyFort CollinsColorado
| | | | | | | | - Partha P. Nag
- Broad Institute of MIT and HarvardCambridgeMassachusetts
| | - Andrzej Joachimiak
- Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and EngineeringUniversity of ChicagoChicagoIllinois
- Structural Biology Center, X‐ray Science DivisionArgonne National LaboratoryArgonneIllinois
- Department of Biochemistry and Molecular BiologyUniversity of ChicagoChicagoIllinois
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