1
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Slanska M, Stackova L, Marques SM, Stacko P, Martínek M, Jílek L, Toul M, Damborsky J, Bednar D, Klán P, Prokop Z. Azobenzene-Based Photoswitchable Substrates for Advanced Mechanistic Studies of Model Haloalkane Dehalogenase Enzyme Family. ACS Catal 2024; 14:11635-11645. [PMID: 39114093 PMCID: PMC11301625 DOI: 10.1021/acscatal.4c03503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024]
Abstract
The engineering of efficient enzymes for large-scale production of industrially relevant compounds is a challenging task. Utilizing rational protein design, which relies on a comprehensive understanding of mechanistic information, holds significant promise for achieving success in this endeavor. Pre-steady-state kinetic measurements, obtained either through fast-mixing techniques or photoswitchable substrates, provide crucial mechanistic insights. The latter approach not only furnishes mechanistic clarity but also affords real-time structural elucidation of reaction intermediates via time-resolved femtosecond crystallography. Unfortunately, only a limited number of such valuable mechanistic probes are available. To address this gap, we applied a multidisciplinary approach, including computational analysis, chemical synthesis, physicochemical property screening, and enzyme kinetics to identify promising candidates for photoswitchable probes. We demonstrate the approach by designing an azobenzene-based photoswitchable substrate tailored for haloalkane dehalogenases, a prototypic class of enzymes pivotal in developing computational tools for rational protein design. The probe was subjected to steady-state and pre-steady-state kinetic analysis, which revealed new insights about the catalytic behavior of the model biocatalysts. We employed laser-triggered Z-to-E azobenzene photoswitching to generate the productive isomer in situ, opening avenues for advanced mechanistic studies using time-resolved femtosecond crystallography. Our results not only pave the way for the mechanistic understanding of this model enzyme family, incorporating both kinetic and structural dimensions, but also propose a systematic approach to the rational design of photoswitchable enzymatic substrates.
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Affiliation(s)
- Michaela Slanska
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Lenka Stackova
- RECETOX,
Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk
University, Brno 625 00, Czech Republic
| | - Sergio M. Marques
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Brno 625 00, Czech Republic
- International
Clinical Research Centre, St. Ann’s Hospital, Brno 625 00, Czech Republic
| | - Peter Stacko
- RECETOX,
Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk
University, Brno 625 00, Czech Republic
| | - Marek Martínek
- RECETOX,
Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk
University, Brno 625 00, Czech Republic
| | - Luboš Jílek
- RECETOX,
Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk
University, Brno 625 00, Czech Republic
| | - Martin Toul
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Brno 625 00, Czech Republic
- International
Clinical Research Centre, St. Ann’s Hospital, Brno 625 00, Czech Republic
| | - Jiri Damborsky
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Brno 625 00, Czech Republic
- International
Clinical Research Centre, St. Ann’s Hospital, Brno 625 00, Czech Republic
| | - David Bednar
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Brno 625 00, Czech Republic
- International
Clinical Research Centre, St. Ann’s Hospital, Brno 625 00, Czech Republic
| | - Petr Klán
- RECETOX,
Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- Department
of Chemistry, Faculty of Science, Masaryk
University, Brno 625 00, Czech Republic
| | - Zbynek Prokop
- Loschmidt
Laboratories, Department of Experimental Biology and RECETOX, Faculty
of Science, Masaryk University, Brno 625 00, Czech Republic
- International
Clinical Research Centre, St. Ann’s Hospital, Brno 625 00, Czech Republic
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2
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Aboomar NM, Essam O, Hassan A, Bassiouny AR, Arafa RK. Exploring a repurposed candidate with dual hIDO1/hTDO2 inhibitory potential for anticancer efficacy identified through pharmacophore-based virtual screening and in vitro evaluation. Sci Rep 2024; 14:9386. [PMID: 38653790 PMCID: PMC11039737 DOI: 10.1038/s41598-024-59353-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
Discovering effective anti-cancer agents poses a formidable challenge given the limited efficacy of current therapeutic modalities against various cancer types due to intrinsic resistance mechanisms. Cancer immunochemotherapy is an alternative strategy for breast cancer treatment and overcoming cancer resistance. Human Indoleamine 2,3-dioxygenase (hIDO1) and human Tryptophan 2,3-dioxygenase 2 (hTDO2) play pivotal roles in tryptophan metabolism, leading to the generation of kynurenine and other bioactive metabolites. This process facilitates the de novo synthesis of Nicotinamide Dinucleotide (NAD), promoting cancer resistance. This study identified a new dual hIDO1/hTDO2 inhibitor using a drug repurposing strategy of FDA-approved drugs. Herein, we delineate the development of a ligand-based pharmacophore model based on a training set of 12 compounds with reported hIDO1/hTDO2 inhibitory activity. We conducted a pharmacophore search followed by high-throughput virtual screening of 2568 FDA-approved drugs against both enzymes, resulting in ten hits, four of them with high potential of dual inhibitory activity. For further in silico and in vitro biological investigation, the anti-hypercholesterolemic drug Pitavastatin deemed the drug of choice in this study. Molecular dynamics (MD) simulations demonstrated that Pitavastatin forms stable complexes with both hIDO1 and hTDO2 receptors, providing a structural basis for its potential therapeutic efficacy. At nanomolar (nM) concentration, it exhibited remarkable in vitro enzyme inhibitory activity against both examined enzymes. Additionally, Pitavastatin demonstrated potent cytotoxic activity against BT-549, MCF-7, and HepG2 cell lines (IC50 = 16.82, 9.52, and 1.84 µM, respectively). Its anticancer activity was primarily due to the induction of G1/S phase arrest as discovered through cell cycle analysis of HepG2 cancer cells. Ultimately, treating HepG2 cancer cells with Pitavastatin affected significant activation of caspase-3 accompanied by down-regulation of cellular apoptotic biomarkers such as IDO, TDO, STAT3, P21, P27, IL-6, and AhR.
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Affiliation(s)
- Nourhan M Aboomar
- Drug Design and Discovery Lab, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, Cairo, 12578, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo, 12578, Egypt
| | - Omar Essam
- Drug Design and Discovery Lab, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, Cairo, 12578, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo, 12578, Egypt
| | - Afnan Hassan
- Drug Design and Discovery Lab, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, Cairo, 12578, Giza, Egypt
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo, 12578, Egypt
- Euro-Mediterranean Master in Neuroscience and Biotechnology Program, Alexandria University, Alexandria, 21511, Egypt
| | - Ahmad R Bassiouny
- Department of Biochemistry, Faculty of Science, Alexandria University, Alexandria, 21511, Egypt
| | - Reem K Arafa
- Drug Design and Discovery Lab, Zewail City of Science and Technology, Ahmed Zewail Road, October Gardens, Cairo, 12578, Giza, Egypt.
- Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Cairo, 12578, Egypt.
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3
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Kassab SE, Mowafy S. Structural Basis of Selective Human Indoleamine-2,3-dioxygenase 1 (hIDO1) Inhibition. ChemMedChem 2021; 16:3149-3164. [PMID: 34174026 DOI: 10.1002/cmdc.202100253] [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: 04/07/2021] [Revised: 06/23/2021] [Indexed: 11/08/2022]
Abstract
hIDO1 is a heme-dioxygenase overexpressed in the tumor microenvironment and is implicated in the survival of cancer cells. Metabolism of tryptophan to N-formyl-kynurenine by hIDO1 leads to immune suppression to result in cancer cell immune escape. In this article, we discuss the discovery of selective hIDO1 inhibitors for therapeutic intervention that have been promoted to clinical trials and for which crystallographic structural information is available for the respective inhibitor-enzyme complex. The structural insights are based on the complex crystal structures and the relative biological data profiles. The structural basis of selective hIDO1 inhibition, as discussed herein, opens new avenues to the discovery of novel inhibitors with improved activity profiles, selectivity, and distinct structure frameworks.
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Affiliation(s)
- Shaymaa Emam Kassab
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Damanhour University, Damanhour, El-Buhaira, 22516, Egypt
| | - Samar Mowafy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Misr International University, Cairo, 11431, Egypt.,Department of Chemistry, University of Washington, Seattle, Washington, 98195, United States of America
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4
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Liu X, Zhang Y, Duan H, Luo Q, Liu W, Liang L, Wan H, Chang S, Hu J, Shi H. Inhibition Mechanism of Indoleamine 2, 3-Dioxygenase 1 (IDO1) by Amidoxime Derivatives and Its Revelation in Drug Design: Comparative Molecular Dynamics Simulations. Front Mol Biosci 2020; 6:164. [PMID: 32047753 PMCID: PMC6997135 DOI: 10.3389/fmolb.2019.00164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 12/31/2019] [Indexed: 02/05/2023] Open
Abstract
For cancer treatment, in addition to the three standard therapies of surgery, chemotherapy, and radiotherapy, immunotherapy has become the fourth internationally-recognized alternative treatment. Indoleamine 2, 3-dioxygenase 1 (IDO1) catalyzes the conversion of tryptophan to kynurenine causing lysine depletion, which is an important target in the research and development of anticancer drugs. Epacadostat (INCB024360) is currently one of the most potent IDO1 inhibitors, nevertheless its inhibition mechanism still remains elusive. In this work, comparative molecular dynamics simulations were performed to reveal that the high inhibitory activity of INCB024360 mainly comes from two aspects: disturbing the ligand delivery tunnel and then preventing small molecules such as oxygen and water molecules from accessing the active site, as well as hindering the shuttle of substrate tryptophan with product kynurenine through the heme binding pocket. The scanning of key residues showed that L234 and R231 residues both were crucial to the catalytic activity of IDO1. With the association with INCB024360, L234 forms a stable hydrogen bond with G262, which significantly affects the spatial position of G262-A264 loop and then greatly disturbs the orderliness of ligand delivery tunnel. In addition, the cleavage of hydrogen bond between G380 and R231 increases the mobility of the GTGG conserved region, leading to the closure of the substrate tryptophan channel. This work provides new ideas for understanding action mechanism of amidoxime derivatives, improving its inhibitor activity and developing novel inhibitors of IDO1.
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Affiliation(s)
- Xinyu Liu
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Yiwen Zhang
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Huaichuan Duan
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Qing Luo
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Wei Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Hua Wan
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, China
| | - Shan Chang
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Hubing Shi
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, China
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5
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Greco FA, Albini E, Coletti A, Dolciami D, Carotti A, Orabona C, Grohmann U, Macchiarulo A. Tracking Hidden Binding Pockets Along the Molecular Recognition Path ofl‐Trp to Indoleamine 2,3‐Dioxygenase 1. ChemMedChem 2019; 14:2084-2092. [DOI: 10.1002/cmdc.201900529] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/17/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Francesco A. Greco
- Department of Pharmaceutical SciencesUniversity of Perugia via del liceo n.1 06123 Perugia Italy
| | - Elisa Albini
- Department of Experimental MedicineUniversity of Perugia P.le Gambuli 06132 Perugia Italy
| | - Alice Coletti
- Department of Pharmaceutical SciencesUniversity of Perugia via del liceo n.1 06123 Perugia Italy
| | - Daniela Dolciami
- Department of Pharmaceutical SciencesUniversity of Perugia via del liceo n.1 06123 Perugia Italy
| | - Andrea Carotti
- Department of Pharmaceutical SciencesUniversity of Perugia via del liceo n.1 06123 Perugia Italy
| | - Ciriana Orabona
- Department of Experimental MedicineUniversity of Perugia P.le Gambuli 06132 Perugia Italy
| | - Ursula Grohmann
- Department of Experimental MedicineUniversity of Perugia P.le Gambuli 06132 Perugia Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical SciencesUniversity of Perugia via del liceo n.1 06123 Perugia Italy
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6
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Kashi AA, Davis RW, Phair RD. The IDO Metabolic Trap Hypothesis for the Etiology of ME/CFS. Diagnostics (Basel) 2019; 9:E82. [PMID: 31357483 PMCID: PMC6787624 DOI: 10.3390/diagnostics9030082] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023] Open
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating noncommunicable disease brandishing an enormous worldwide disease burden with some evidence of inherited genetic risk. Absence of measurable changes in patients' standard blood work has necessitated ad hoc symptom-driven therapies and a dearth of mechanistic hypotheses regarding its etiology and possible cure. A new hypothesis, the indolamine-2,3-dioxygenase (IDO) metabolic trap, was developed and formulated as a mathematical model. The historical occurrence of ME/CFS outbreaks is a singular feature of the disease and implies that any predisposing genetic mutation must be common. A database search for common damaging mutations in human enzymes produces 208 hits, including IDO2 with four such mutations. Non-functional IDO2, combined with well-established substrate inhibition of IDO1 and kinetic asymmetry of the large neutral amino acid transporter, LAT1, yielded a mathematical model of tryptophan metabolism that displays both physiological and pathological steady-states. Escape from the pathological one requires an exogenous perturbation. This model also identifies a critical point in cytosolic tryptophan abundance beyond which descent into the pathological steady-state is inevitable. If, however, means can be discovered to return cytosolic tryptophan below the critical point, return to the normal physiological steady-state is assured. Testing this hypothesis for any cell type requires only labelled tryptophan, a means to measure cytosolic tryptophan and kynurenine, and the standard tools of tracer kinetics.
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Affiliation(s)
- Alex A Kashi
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
| | - Ronald W Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA
- Departments of Biochemistry and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Robert D Phair
- Integrative Bioinformatics Inc., Mountain View, CA 94041, USA.
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7
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Yuasa HJ. A comprehensive comparison of the metazoan tryptophan degrading enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140247. [PMID: 31276825 DOI: 10.1016/j.bbapap.2019.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 01/15/2023]
Abstract
Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) have an independent origin; however, they have distinctly evolved to catalyze the same reaction. In general, TDO is a single-copy gene in each metazoan species, and TDO enzymes demonstrate similar enzyme activity regardless of their biological origin. In contrast, multiple IDO paralogues are observed in many species, and they display various enzymatic properties. Similar to vertebrate IDO2, invertebrate IDOs generally show low affinity/catalytic efficiency for L-Trp. Meanwhile, two IDO isoforms from scallop (IDO-I and -III) and sponge IDOs show high L-Trp catalytic activity, which is comparable to vertebrate IDO1. Site-directed mutagenesis experiments have revealed that primarily two residues, Tyr located at the 2nd residue on the F-helix (F2nd) and His located at the 9th residue on the G-helix (G9th), are crucial for the high affinity/catalytic efficiency of these 'high performance' invertebrate IDOs. Conversely, those two amino acid substitutions (F2nd/Tyr and G9th/His) resulted in high affinity and catalytic activity in other molluscan 'low performance' IDOs. In human IDO1, G9th is Ser167, whereas the counterpart residue of G9th in human TDO is His76. Previous studies have shown that Ser167 could not be substituted by His because the human IDO1 Ser167His variant showed significantly low catalytic activity. However, this may be specific for human IDO1 because G9th/His was demonstrated to be very effective in increasing the L-Trp affinity even in vertebrate IDOs. Therefore, these findings indicate that the active sites of TDO and IDO are more similar to each other than previously expected.
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Affiliation(s)
- Hajime Julie Yuasa
- Laboratory of Biochemistry, Department of Applied Science, Faculty of Science and Technology, National University Corporation Kochi University, Kochi 780-8520, Japan.
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8
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Horn M, Nienhaus K, Nienhaus GU. Kinetic Study of Ligand Binding and Conformational Changes in Inducible Nitric Oxide Synthase. J Phys Chem B 2018; 122:11048-11057. [PMID: 29965771 DOI: 10.1021/acs.jpcb.8b05137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Nitric oxide synthases (NOSs) are heme enzymes that generate highly reactive nitric oxide from l-arginine (l-Arg) in a complex mechanism that is still only partially understood. We have studied carbon monoxide (CO) binding to the oxygenase domain of murine inducible NOS (iNOS) by using flash photolysis. The P420 and P450 forms of the enzyme, assigned to a protonated and unprotonated proximal cysteine, through which the heme is anchored to the protein, show markedly different CO rebinding properties. The data suggest that P420 has a widely open distal pocket that admits water. CO rebinding to the P450 form strongly depends on the presence of the substrate l-Arg, the intermediate Nω-hydroxy-l-arginine, and the cofactor tetrahydrobiopterin. After adding these small molecules to the enzyme solution, the CO kinetics change slowly over the hours. This process can be described as a relaxation from a fast rebinding, metastable species to a slowly rebinding, thermodynamically stable species, which we associate with the enzymatically active form. Our results allow us to determine kinetic parameters of l-Arg binding to the ferrous deoxy iNOS protein for the first time and also provide clues regarding the nature of structural differences between the two interconverting species.
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Affiliation(s)
- Michael Horn
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Str. 1 , D-76131 Karlsruhe , Germany
| | - Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Str. 1 , D-76131 Karlsruhe , Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Str. 1 , D-76131 Karlsruhe , Germany.,Institute of Nanotechnology (INT) and Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT) , D-76344 Eggenstein-Leopoldshafen , Germany.,Department of Physics , University of Illinois at Urbana-Champaign , 1110 West Green Street , Urbana , Illinois 61801 , United States
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9
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Nienhaus K, Nienhaus GU. Different Mechanisms of Catalytic Complex Formation in Two L-Tryptophan Processing Dioxygenases. Front Mol Biosci 2018; 4:94. [PMID: 29354636 PMCID: PMC5758539 DOI: 10.3389/fmolb.2017.00094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/18/2017] [Indexed: 01/25/2023] Open
Abstract
The human heme enzymes tryptophan 2,3-dioxygenase (hTDO) and indoleamine 2,3 dioxygenase (hIDO) catalyze the initial step in L-tryptophan (L-Trp) catabolism, the insertion of dioxygen into L-Trp. Overexpression of these enzymes causes depletion of L-Trp and accumulation of metabolic products, and thereby contributes to tumor immune tolerance and immune dysregulation in a variety of disease pathologies. Understanding the assembly of the catalytically active, ternary enzyme-substrate-ligand complexes is not yet fully resolved, but an essential prerequisite for designing efficient and selective de novo inhibitors. Evidence is mounting that the ternary complex forms by sequential binding of ligand and substrate in a specific order. In hTDO, the apolar L-Trp binds first, decreasing active-site solvation and, as a result, reducing non-productive oxidation of the heme iron by the dioxygen ligand, which may leave the substrate bound to a ferric heme iron. In hIDO, by contrast, dioxygen must first coordinate to the heme iron because a bound substrate would occlude ligand access to the heme iron, so the ternary complex can no longer form. Consequently, faster association of L-Trp at high concentrations results in substrate inhibition. Here, we summarize our present knowledge of ternary complex formation in hTDO and hIDO and relate these findings to structural peculiarities of their active sites.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany.,Institute of Nanotechnology and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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10
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Nienhaus K, Hahn V, Hüpfel M, Nienhaus GU. Substrate Binding Primes Human Tryptophan 2,3-Dioxygenase for Ligand Binding. J Phys Chem B 2017; 121:7412-7420. [PMID: 28715185 DOI: 10.1021/acs.jpcb.7b03463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The human heme enzyme tryptophan 2,3-dioxygenase (hTDO) catalyzes the insertion of dioxygen into its cognate substrate, l-tryptophan (l-Trp). Its active site structure is highly dynamic, and the mechanism of enzyme-substrate-ligand complex formation and the ensuing enzymatic reaction is not yet understood. Here we have studied complex formation in hTDO by using time-resolved optical and infrared spectroscopy with carbon monoxide (CO) as a ligand. We have observed that both substrate-free and substrate-bound hTDO coexist in two discrete conformations with greatly different ligand binding rates. In the fast rebinding hTDO conformation, there is facile ligand access to the heme iron, but it is greatly hindered in the slowly rebinding conformation. Spectroscopic evidence implicates active site solvation as playing a crucial role for the observed kinetic differences. Substrate binding shifts the conformational equilibrium markedly toward the fast species and thus primes the active site for subsequent ligand binding, ensuring that formation of the ternary complex occurs predominantly by first binding l-Trp and then the ligand. Consequently, the efficiency of catalysis is enhanced because O2 binding prior to substrate binding, resulting in nonproductive oxidation of the heme iron, is greatly suppressed.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
| | - Vincent Hahn
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
| | - Manuel Hüpfel
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT) , Wolfgang-Gaede-Straße 1, 76131 Karlsruhe, Germany.,Institute of Nanotechnology (INT) and Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT) , 76344 Eggenstein-Leopoldshafen, Germany.,Department of Physics, University of Illinois at Urbana-Champaign , 1110 W. Green Street, Urbana, Illinois 61801, United States
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11
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Coletti A, Greco FA, Dolciami D, Camaioni E, Sardella R, Pallotta MT, Volpi C, Orabona C, Grohmann U, Macchiarulo A. Advances in indoleamine 2,3-dioxygenase 1 medicinal chemistry. MEDCHEMCOMM 2017; 8:1378-1392. [PMID: 30108849 PMCID: PMC6072487 DOI: 10.1039/c7md00109f] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/11/2017] [Indexed: 12/11/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1) mediates multiple immunoregulatory processes including the induction of regulatory T cell differentiation and activation, suppression of T cell immune responses and inhibition of dendritic cell function, which impair immune recognition of cancer cells and promote tumor growth. On this basis, this enzyme is widely recognized as a valuable drug target for the development of immunotherapeutic small molecules in oncology. Although medicinal chemistry has made a substantial contribution to the discovery of numerous chemical classes of potent IDO1 inhibitors in the past 20 years, only very few compounds have progressed in clinical trials. In this review, we provide an overview of the current understanding of structure-function relationships of the enzyme, and discuss structure-activity relationships of selected classes of inhibitors that have shaped the hitherto few successes of IDO1 medicinal chemistry. An outlook opinion is also given on trends in the design of next generation inhibitors of the enzyme.
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Affiliation(s)
- Alice Coletti
- Department of Pharmaceutical Sciences , University of Perugia , via del Liceo 1 , 06123 Perugia , Italy . ; ; Tel: +39 075 585 5160
| | - Francesco Antonio Greco
- Department of Pharmaceutical Sciences , University of Perugia , via del Liceo 1 , 06123 Perugia , Italy . ; ; Tel: +39 075 585 5160
| | - Daniela Dolciami
- Department of Pharmaceutical Sciences , University of Perugia , via del Liceo 1 , 06123 Perugia , Italy . ; ; Tel: +39 075 585 5160
| | - Emidio Camaioni
- Department of Pharmaceutical Sciences , University of Perugia , via del Liceo 1 , 06123 Perugia , Italy . ; ; Tel: +39 075 585 5160
| | - Roccaldo Sardella
- Department of Pharmaceutical Sciences , University of Perugia , via del Liceo 1 , 06123 Perugia , Italy . ; ; Tel: +39 075 585 5160
| | - Maria Teresa Pallotta
- Department of Experimental Medicine , University of Perugia , P.le Gambuli , 06132 Perugia , Italy
| | - Claudia Volpi
- Department of Experimental Medicine , University of Perugia , P.le Gambuli , 06132 Perugia , Italy
| | - Ciriana Orabona
- Department of Experimental Medicine , University of Perugia , P.le Gambuli , 06132 Perugia , Italy
| | - Ursula Grohmann
- Department of Experimental Medicine , University of Perugia , P.le Gambuli , 06132 Perugia , Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences , University of Perugia , via del Liceo 1 , 06123 Perugia , Italy . ; ; Tel: +39 075 585 5160
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