1
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Wujieti B, Feng X, Liu E, Li D, Hao M, Zhou L, Cui W. A theoretical study on the activity and selectivity of IDO/TDO inhibitors. Phys Chem Chem Phys 2024; 26:16747-16764. [PMID: 38818624 DOI: 10.1039/d3cp06036e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO) is a tryptophan (Trp) metabolic enzyme along the kynurenine (NFK) pathway. Under pathological conditions, IDO overexpressed by tumor cells causes depletion of tryptophan and the accumulation of metabolic products, which inhibit the local immune response and form immune escape. Therefore, the suppression of IDO activity is one of the strategies for tumor immunotherapy, and drug design for this target has been the focus of research for more than two decades. Apart from IDO, tryptophan dioxygenase (TDO) of the same family can also catalyze the same biochemical reaction in the human body, but it has different tissue distribution and substrate selectivity from IDO. Based on the principle of drug design with high potency and low cross-reactivity to specific targets, in this subject, the activity and selectivity of IDO and TDO toward small molecular inhibitors were studied from the perspective of thermodynamics and kinetics. The aim was to elucidate the structural requirements for achieving favorable biological activity and selectivity of IDO and TDO inhibitors. Specifically, the interactions of inhibitors from eight families with IDO and TDO were initially investigated through molecular docking and molecular dynamics simulations, and the thermodynamic data for binding of inhibitors were predicted by the molecular mechanics/generalized Born surface area (MM/GBSA) method. Secondly, we explored the free energy landscape of JKloops, the kinetic control element of IDO/TDO, using temperature replica exchange molecular dynamics (T-REMD) simulations and elucidated the connection between the rules of IDO/TDO conformational changes and the inhibitor selectivity mechanism. Furthermore, the binding and dissociation processes of the C1 inhibitor (NLG919) were simulated by the adaptive steering molecular dynamics (ASMD) method, which not only addressed the possible stable, metastable, and transition states for C1 inhibitor-IDO/TDO interactions, but also accurately predicted kinetic data for C1 inhibitor binding and dissociation. In conclusion, we have constructed a complete process from enzyme (IDO/TDO) conformational activation to inhibitor binding/dissociation and used the thermodynamic and kinetic data of each link as clues to verify the control mechanism of IDO/TDO on inhibitor selectivity. This is of great significance for us to understand the design principles of tumor immunotherapy drugs and to avoid drug resistance of immunotherapy drugs.
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Affiliation(s)
- Baerlike Wujieti
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Xinping Feng
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Erxia Liu
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Deqing Li
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Mingtian Hao
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Luqi Zhou
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Wei Cui
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
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2
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Mousavi H, Rimaz M, Zeynizadeh B. Practical Three-Component Regioselective Synthesis of Drug-Like 3-Aryl(or heteroaryl)-5,6-dihydrobenzo[ h]cinnolines as Potential Non-Covalent Multi-Targeting Inhibitors To Combat Neurodegenerative Diseases. ACS Chem Neurosci 2024; 15:1828-1881. [PMID: 38647433 DOI: 10.1021/acschemneuro.4c00055] [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] [Indexed: 04/25/2024] Open
Abstract
Neurodegenerative diseases (NDs) are one of the prominent health challenges facing contemporary society, and many efforts have been made to overcome and (or) control it. In this research paper, we described a practical one-pot two-step three-component reaction between 3,4-dihydronaphthalen-1(2H)-one (1), aryl(or heteroaryl)glyoxal monohydrates (2a-h), and hydrazine monohydrate (NH2NH2•H2O) for the regioselective preparation of some 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnoline derivatives (3a-h). After synthesis and characterization of the mentioned cinnolines (3a-h), the in silico multi-targeting inhibitory properties of these heterocyclic scaffolds have been investigated upon various Homo sapiens-type enzymes, including hMAO-A, hMAO-B, hAChE, hBChE, hBACE-1, hBACE-2, hNQO-1, hNQO-2, hnNOS, hiNOS, hPARP-1, hPARP-2, hLRRK-2(G2019S), hGSK-3β, hp38α MAPK, hJNK-3, hOGA, hNMDA receptor, hnSMase-2, hIDO-1, hCOMT, hLIMK-1, hLIMK-2, hRIPK-1, hUCH-L1, hPARK-7, and hDHODH, which have confirmed their functions and roles in the neurodegenerative diseases (NDs), based on molecular docking studies, and the obtained results were compared with a wide range of approved drugs and well-known (with IC50, EC50, etc.) compounds. In addition, in silico ADMET prediction analysis was performed to examine the prospective drug properties of the synthesized heterocyclic compounds (3a-h). The obtained results from the molecular docking studies and ADMET-related data demonstrated that these series of 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnolines (3a-h), especially hit ones, can really be turned into the potent core of new drugs for the treatment of neurodegenerative diseases (NDs), and/or due to the having some reactionable locations, they are able to have further organic reactions (such as cross-coupling reactions), and expansion of these compounds (for example, with using other types of aryl(or heteroaryl)glyoxal monohydrates) makes a new avenue for designing novel and efficient drugs for this purpose.
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Affiliation(s)
- Hossein Mousavi
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia 5756151818, Iran
| | - Mehdi Rimaz
- Department of Chemistry, Payame Noor University, P.O. Box 19395-3697, Tehran 19395-3697, Iran
| | - Behzad Zeynizadeh
- Department of Organic Chemistry, Faculty of Chemistry, Urmia University, Urmia 5756151818, Iran
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3
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Röhrig UF, Majjigapu SR, Vogel P, Reynaud A, Pojer F, Dilek N, Reichenbach P, Ascenção K, Irving M, Coukos G, Michielin O, Zoete V. Structure-based optimization of type III indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors. J Enzyme Inhib Med Chem 2022; 37:1773-1811. [PMID: 35758198 PMCID: PMC9246256 DOI: 10.1080/14756366.2022.2089665] [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] [Indexed: 11/25/2022] Open
Abstract
The haem enzyme indoleamine 2,3-dioxygenase 1 (IDO1) catalyses the rate-limiting step in the kynurenine pathway of tryptophan metabolism and plays an essential role in immunity, neuronal function, and ageing. Expression of IDO1 in cancer cells results in the suppression of an immune response, and therefore IDO1 inhibitors have been developed for use in anti-cancer immunotherapy. Here, we report an extension of our previously described highly efficient haem-binding 1,2,3-triazole and 1,2,4-triazole inhibitor series, the best compound having both enzymatic and cellular IC50 values of 34 nM. We provide enzymatic inhibition data for almost 100 new compounds and X-ray diffraction data for one compound in complex with IDO1. Structural and computational studies explain the dramatic drop in activity upon extension to pocket B, which has been observed in diverse haem-binding inhibitor scaffolds. Our data provides important insights for future IDO1 inhibitor design.
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Affiliation(s)
- Ute F Röhrig
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland
| | - Somi Reddy Majjigapu
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland.,Laboratory of Glycochemistry and Asymmetric Synthesis, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pierre Vogel
- Laboratory of Glycochemistry and Asymmetric Synthesis, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Aline Reynaud
- Protein Production and Structure Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Florence Pojer
- Protein Production and Structure Core Facility, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Nahzli Dilek
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland
| | - Patrick Reichenbach
- Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, Epalinges, Switzerland
| | - Kelly Ascenção
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland
| | - Melita Irving
- Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, Epalinges, Switzerland
| | - George Coukos
- Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, Epalinges, Switzerland
| | - Olivier Michielin
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne (CHUV), Ludwig Cancer Research-Lausanne Branch, Lausanne, CH-1011, Switzerland
| | - Vincent Zoete
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Lausanne, Switzerland.,Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, Epalinges, Switzerland
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4
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Ogbechi J, Huang YS, Clanchy FIL, Pantazi E, Topping LM, Darlington LG, Williams RO, Stone TW. Modulation of immune cell function, IDO expression and kynurenine production by the quorum sensor 2-heptyl-3-hydroxy-4-quinolone (PQS). Front Immunol 2022; 13:1001956. [PMID: 36389710 PMCID: PMC9650388 DOI: 10.3389/fimmu.2022.1001956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/05/2022] [Indexed: 12/29/2023] Open
Abstract
Many invasive micro-organisms produce 'quorum sensor' molecules which regulate colony expansion and may modulate host immune responses. We have examined the ability of Pseudomonas Quorum Sensor (PQS) to influence cytokine expression under conditions of inflammatory stress. The administration of PQS in vivo to mice with collagen-induced arthritis (CIA) increased the severity of disease. Blood and inflamed paws from treated mice had fewer regulatory T cells (Tregs) but normal numbers of Th17 cells. However, PQS (1μM) treatment of antigen-stimulated lymph node cells from collagen-immunised mice in vitro inhibited the differentiation of CD4+IFNγ+ cells, with less effect on CD4+IL-17+ cells and no change in CD4+FoxP3+Tregs. PQS also inhibited T cell activation by anti-CD3/anti-CD28 antibodies. PQS reduced murine macrophage polarisation and inhibited expression of IL1B and IL6 genes in murine macrophages and human THP-1 cells. In human monocyte-derived macrophages, IDO1 gene, protein and enzyme activity were all inhibited by exposure to PQS. TNF gene expression was inhibited in THP-1 cells but not murine macrophages, while LPS-induced TNF protein release was increased by high PQS concentrations. PQS is known to have iron scavenging activity and its suppression of cytokine release was abrogated by iron supplementation. Unexpectedly, PQS decreased the expression of indoleamine-2, 3-dioxygenase genes (IDO1 and IDO2), IDO1 protein expression and enzyme activity in mouse and human macrophages. This is consistent with evidence that IDO1 inhibition or deletion exacerbates arthritis, while kynurenine reduces its severity. It is suggested that the inhibition of IDO1 and cytokine expression may contribute to the quorum sensor and invasive actions of PQS.
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Affiliation(s)
- Joy Ogbechi
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculo-skeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | - Yi-Shu Huang
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculo-skeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | - Felix I. L. Clanchy
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculo-skeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | - Eirini Pantazi
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculo-skeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | - Louise M. Topping
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculo-skeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | | | - Richard O. Williams
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculo-skeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
| | - Trevor W. Stone
- The Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculo-skeletal Sciences (NDORMS), University of Oxford, Oxford, United Kingdom
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5
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Ebokaiwe AP, Ushang OR, Ogunwa TH, Kikiowo B, Olusanya O. Quercetin attenuates cyclophosphamide induced-immunosuppressive indoleamine 2,3-dioxygenase in the hippocampus and cerebral cortex of male Wister rats. J Biochem Mol Toxicol 2022; 36:e23179. [PMID: 35906875 DOI: 10.1002/jbt.23179] [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: 01/25/2022] [Revised: 06/17/2022] [Accepted: 07/21/2022] [Indexed: 12/16/2022]
Abstract
This study investigated the protective effect of quercetin against cyclophosphamide-induced immunosuppressive indoleamine 2,3-dioxygenase (IDO) via the mechanism of oxidative-inflammatory stress and behavioral indices. Cyclophosphamide (CYP) was administered to male Wister rats at a dose of 100 mg/kg with or without quercetin 50 mg/kg every other day for 7 days. Experimental techniques including western blotting, immunohistochemistry analysis, and inflammatory and oxidative stress marker assays were carried out. We also conducted behavioral analyses such as open field, tail suspension, and Y-maze tests for cognitive assessment. The results indicated that quercetin attenuated oxidative-inflammatory stress induced by CYP in the hippocampus and cerebral cortex of male Wister rats by augmenting the activities of antioxidant enzymes and suppressing lipid peroxidation as well as inflammatory mediators such as interleukin-6 and interferon-γ. Concomitantly, quercetin partially prevented the alteration in brain tissue histological architecture and mitigated the activities of IDO/tryptophan 2,3-dioxygenase (TDO) and protein expression of IDO1. This was corroborated by the IDO-quercetin model obtained in silico, revealing a favorable inhibitory interaction between quercetin and the enzyme. Finally, the results of behavioral tests suggested that quercetin significantly prevented the depressive-like posture of the CYP-treated rats. Our study for the first time revealed that quercetin ameliorates the effect of CYP-instigated IDO/TDO activities in the cerebral cortex and hippocampus via restoration of antioxidant enzymes and preventing oxidative-inflammatory stress.
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Affiliation(s)
- Azubuike P Ebokaiwe
- Toxicology and Immunotherapy Research Unit, Department of Biochemistry, Alex Ekwueme Federal University Ndufu Alike, Abakaliki, Nigeria
| | - Odobi R Ushang
- Toxicology and Immunotherapy Research Unit, Department of Biochemistry, Alex Ekwueme Federal University Ndufu Alike, Abakaliki, Nigeria
| | - Tomisin H Ogunwa
- Center for Bio-Computing and Drug Design, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria.,Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Babatomiwa Kikiowo
- Center for Bio-Computing and Drug Design, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria.,Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Olasiende Olusanya
- Institute of Biophysics, University of Chinese Academy of Sciences, Beijing, Chaoyang, China.,Department of Biochemistry, University of Benin, Benin City, Nigeria
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6
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Mammoli A, Bianconi E, Ruta L, Riccio A, Bigiotti C, Souma M, Carotti A, Rossini S, Suvieri C, Pallotta MT, Grohmann U, Camaioni E, Macchiarulo A. Critical Assessment of a Structure-Based Screening Campaign for IDO1 Inhibitors: Tips and Pitfalls. Int J Mol Sci 2022; 23:ijms23073981. [PMID: 35409342 PMCID: PMC8999677 DOI: 10.3390/ijms23073981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 11/26/2022] Open
Abstract
Over the last two decades, indoleamine 2,3-dioxygenase 1 (IDO1) has attracted wide interest as a key player in immune regulation, fostering the design and development of small molecule inhibitors to restore immune response in tumor immunity. In this framework, biochemical, structural, and pharmacological studies have unveiled peculiar structural plasticity of IDO1, with different conformations and functional states that are coupled to fine regulation of its catalytic activity and non-enzymic functions. The large plasticity of IDO1 may affect its ligand recognition process, generating bias in structure-based drug design campaigns. In this work, we report a screening campaign of a fragment library of compounds, grounding on the use of three distinct conformations of IDO1 that recapitulate its structural plasticity to some extent. Results are instrumental to discuss tips and pitfalls that, due to the large plasticity of the enzyme, may influence the identification of novel and differentiated chemical scaffolds of IDO1 ligands in structure-based screening campaigns.
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Affiliation(s)
- Andrea Mammoli
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo n.1, 06123 Perugia, Italy; (A.M.); (E.B.); (L.R.); (A.R.); (C.B.); (M.S.); (A.C.); (E.C.)
| | - Elisa Bianconi
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo n.1, 06123 Perugia, Italy; (A.M.); (E.B.); (L.R.); (A.R.); (C.B.); (M.S.); (A.C.); (E.C.)
| | - Luana Ruta
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo n.1, 06123 Perugia, Italy; (A.M.); (E.B.); (L.R.); (A.R.); (C.B.); (M.S.); (A.C.); (E.C.)
| | - Alessandra Riccio
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo n.1, 06123 Perugia, Italy; (A.M.); (E.B.); (L.R.); (A.R.); (C.B.); (M.S.); (A.C.); (E.C.)
| | - Carlo Bigiotti
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo n.1, 06123 Perugia, Italy; (A.M.); (E.B.); (L.R.); (A.R.); (C.B.); (M.S.); (A.C.); (E.C.)
| | - Maria Souma
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo n.1, 06123 Perugia, Italy; (A.M.); (E.B.); (L.R.); (A.R.); (C.B.); (M.S.); (A.C.); (E.C.)
| | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo n.1, 06123 Perugia, Italy; (A.M.); (E.B.); (L.R.); (A.R.); (C.B.); (M.S.); (A.C.); (E.C.)
| | - Sofia Rossini
- Department of Medicine and Surgery, University of Perugia, P.le Gambuli, 06132 Perugia, Italy; (S.R.); (C.S.); (M.T.P.); (U.G.)
| | - Chiara Suvieri
- Department of Medicine and Surgery, University of Perugia, P.le Gambuli, 06132 Perugia, Italy; (S.R.); (C.S.); (M.T.P.); (U.G.)
| | - Maria Teresa Pallotta
- Department of Medicine and Surgery, University of Perugia, P.le Gambuli, 06132 Perugia, Italy; (S.R.); (C.S.); (M.T.P.); (U.G.)
| | - Ursula Grohmann
- Department of Medicine and Surgery, University of Perugia, P.le Gambuli, 06132 Perugia, Italy; (S.R.); (C.S.); (M.T.P.); (U.G.)
| | - Emidio Camaioni
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo n.1, 06123 Perugia, Italy; (A.M.); (E.B.); (L.R.); (A.R.); (C.B.); (M.S.); (A.C.); (E.C.)
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo n.1, 06123 Perugia, Italy; (A.M.); (E.B.); (L.R.); (A.R.); (C.B.); (M.S.); (A.C.); (E.C.)
- Correspondence: ; Tel.: +39-(075)-585-5131
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7
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Mirgaux M, Leherte L, Wouters J. Temporary Intermediates of L-Trp Along the Reaction Pathway of Human Indoleamine 2,3-Dioxygenase 1 and Identification of an Exo Site. Int J Tryptophan Res 2021; 14:11786469211052964. [PMID: 34949925 PMCID: PMC8689440 DOI: 10.1177/11786469211052964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/19/2021] [Indexed: 12/28/2022] Open
Abstract
Protein dynamics governs most of the fundamental processes in the human body.
Particularly, the dynamics of loops located near an active site can be involved
in the positioning of the substrate and the reaction mechanism. The
understanding of the functioning of dynamic loops is therefore a challenge, and
often requires the use of a multi-disciplinary approach mixing, for example,
crystallographic experiments and molecular dynamics simulations. In the present
work, the dynamic behavior of the JK-loop of the human indoleamine
2,3-dioxygenase 1 hemoprotein, a target for immunotherapy, is investigated. To
overcome the lack of knowledge on this dynamism, the study reported here is
based on 3 crystal structures presenting different conformations of the loop,
completed with molecular dynamics trajectories and MM-GBSA analyses, in order to
trace the reaction pathway of the enzyme. In addition, the crystal structures
identify an exo site in the small unit of the enzyme, that is populated
redundantly by the substrate or the product of the reaction. The role of this
newer reported exo site still needs to be investigated.
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Affiliation(s)
- Manon Mirgaux
- Laboratoire de Chimie Biologique Structurale, Namur Institute of Structured Matter (NISM), Namur Research Institute for Life Sciences (NARILIS), University of Namur, Department of Chemistry, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Laurence Leherte
- Laboratoire de Chimie Biologique Structurale, Namur Institute of Structured Matter (NISM), Namur Research Institute for Life Sciences (NARILIS), University of Namur, Department of Chemistry, Rue de Bruxelles 61, 5000 Namur, Belgium
| | - Johan Wouters
- Laboratoire de Chimie Biologique Structurale, Namur Institute of Structured Matter (NISM), Namur Research Institute for Life Sciences (NARILIS), University of Namur, Department of Chemistry, Rue de Bruxelles 61, 5000 Namur, Belgium
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8
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Röhrig UF, Michielin O, Zoete V. Structure and Plasticity of Indoleamine 2,3-Dioxygenase 1 (IDO1). J Med Chem 2021; 64:17690-17705. [PMID: 34907770 DOI: 10.1021/acs.jmedchem.1c01665] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Since the discovery of the implication of indoleamine 2,3-dioxygenase 1 (IDO1) in tumoral immune resistance in 2003, the search for inhibitors has been intensely pursued both in academia and in pharmaceutical companies, supported by the publication of the first crystal structure of IDO1 in 2006. More recently, it has become clear that IDO1 is an important player in various biological pathways and diseases ranging from neurodegenerative diseases to infection and autoimmunity. Its inhibition may lead to clinical benefit in different therapeutic settings. At present, over 50 experimental structures of IDO1 in complex with different ligands are available in the Protein Data Bank. Our analysis of this wealth of structural data sheds new light on several open issues regarding IDO1's structure and function.
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Affiliation(s)
- Ute F Röhrig
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Olivier Michielin
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne (CHUV), Ludwig Cancer Research─Lausanne Branch, 1011 Lausanne, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.,Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, 1066 Epalinges, Switzerland
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9
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Tang K, Wang B, Yu B, Liu HM. Indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors and PROTAC-based degraders for cancer therapy. Eur J Med Chem 2021; 227:113967. [PMID: 34752953 DOI: 10.1016/j.ejmech.2021.113967] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 12/30/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1), a known immunosuppressive enzyme that catalyzes the rate-limiting step in the oxidation of tryptophan (Trp) to kynurenine (Kyn), has received increasing attention as an attractive immunotherapeutic target for cancer therapy. Up to now, eleven small-molecule IDO1 inhibitors have entered clinical trials for the treatment of cancers. In addition, proteolysis targeting chimera (PROTAC) based degraders also provide prospects for cancer therapy. Herein we present a comprehensive overview of the medicinal chemistry strategies and potential therapeutic applications of IDO1 inhibitors in nonclinical trials and IDO1-PROTAC degraders.
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Affiliation(s)
- Kai Tang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China
| | - Bo Wang
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China
| | - Bin Yu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China.
| | - Hong-Min Liu
- School of Pharmaceutical Sciences & Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, China.
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10
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Basran J, Booth ES, Campbell LP, Thackray SJ, Jesani MH, Clayden J, Moody PCE, Mowat CG, Kwon H, Raven EL. Binding of l-kynurenine to X. campestris tryptophan 2,3-dioxygenase. J Inorg Biochem 2021; 225:111604. [PMID: 34571402 DOI: 10.1016/j.jinorgbio.2021.111604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/31/2021] [Accepted: 09/10/2021] [Indexed: 11/18/2022]
Abstract
The kynurenine pathway is the major route of tryptophan metabolism. The first step of this pathway is catalysed by one of two heme-dependent dioxygenase enzymes - tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) - leading initially to the formation of N-formylkynurenine (NFK). In this paper, we present a crystal structure of a bacterial TDO from X. campestris in complex with l-kynurenine, the hydrolysed product of NFK. l-kynurenine is bound at the active site in a similar location to the substrate (l-Trp). Hydrogen bonding interactions with Arg117 and the heme 7-propionate anchor the l-kynurenine molecule into the pocket. A mechanism for the hydrolysis of NFK in the active site is presented.
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Affiliation(s)
- Jaswir Basran
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 9HN, UK
| | - Elizabeth S Booth
- Department of Chemistry, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Laura P Campbell
- EastChem School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Sarah J Thackray
- EastChem School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Mehul H Jesani
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Jonathan Clayden
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Peter C E Moody
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester LE1 9HN, UK
| | - Christopher G Mowat
- EastChem School of Chemistry, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, UK
| | - Hanna Kwon
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Emma L Raven
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
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11
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Gonnet L, Baron M, Baltas M. Synthesis of Biologically Relevant 1,2,3- and 1,3,4-Triazoles: From Classical Pathway to Green Chemistry. Molecules 2021; 26:5667. [PMID: 34577138 PMCID: PMC8464795 DOI: 10.3390/molecules26185667] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/06/2021] [Accepted: 09/14/2021] [Indexed: 01/15/2023] Open
Abstract
Green Chemistry has become in the last two decades an increasing part of research interest. Nonconventional «green» sources for chemical reactions include micro-wave, mechanical mixing, visible light and ultrasound. 1,2,3-triazoles have important applications in pharmaceutical chemistry while their 1,2,4 counterparts are developed to a lesser extent. In the review presented here we will focus on synthesis of 1,2,3 and 1,2,4-triazole systems by means of classical and « green chemistry » conditions involving ultrasound chemistry and mechanochemistry. The focus will be on compounds/scaffolds that possess biological/pharmacophoric properties. Finally, we will also present the formal cycloreversion of 1,2,3-triazole compounds under mechanical forces and its potential use in biological systems.
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Affiliation(s)
- Lori Gonnet
- IMT Mines Albi, UMR CNRS 5302, Centre Rapsodee, Campus Jarlard, Allée des Sciences, Université de Toulouse, CEDEX 09, 81013 Albi, France; (L.G.); (M.B.)
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, QC H3A 0B8, Canada
| | - Michel Baron
- IMT Mines Albi, UMR CNRS 5302, Centre Rapsodee, Campus Jarlard, Allée des Sciences, Université de Toulouse, CEDEX 09, 81013 Albi, France; (L.G.); (M.B.)
| | - Michel Baltas
- CNRS, LCC (Laboratoire de Chimie de Coordination), Université de Toulouse, UPS, INPT, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, CEDEX 4, F-31077 Toulouse, France
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12
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Zheng Y, Stafford PM, Stover KR, Mohan DC, Gupta M, Keske EC, Schiavini P, Villar L, Wu F, Kreft A, Thomas K, Raaphorst E, Pasangulapati JP, Alla SR, Sharma S, Mittapalli RR, Sagamanova I, Johnson SL, Reed MA, Weaver DF. A Series of 2-((1-Phenyl-1H-imidazol-5-yl)methyl)-1H-indoles as Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors. ChemMedChem 2021; 16:2195-2205. [PMID: 33759400 DOI: 10.1002/cmdc.202100107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/19/2021] [Indexed: 12/17/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1) is a promising therapeutic target in cancer immunotherapy and neurological disease. Thus, searching for highly active inhibitors for use in human cancers is now a focus of widespread research and development efforts. In this study, we report the structure-based design of 2-(5-imidazolyl)indole derivatives, a series of novel IDO1 inhibitors which have been designed and synthesized based on our previous study using N1-substituted 5-indoleimidazoles. Among these, we have identified one with a strong IDO1 inhibitory activity (IC50 =0.16 μM, EC50 =0.3 μM). Structural-activity relationship (SAR) and computational docking simulations suggest that a hydroxyl group favorably interacts with a proximal Ser167 residue in Pocket A, improving IDO1 inhibitory potency. The brain penetrance of potent compounds was estimated by calculation of the Blood Brain Barrier (BBB) Score and Brain Exposure Efficiency (BEE) Score. Many compounds had favorable scores and the two most promising compounds were advanced to a pharmacokinetic study which demonstrated that both compounds were brain penetrant. We have thus discovered a flexible scaffold for brain penetrant IDO1 inhibitors, exemplified by several potent, brain penetrant, agents. With this promising scaffold, we provide herein a basis for further development of brain penetrant IDO1 inhibitors.
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Affiliation(s)
- Yong Zheng
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Paul M Stafford
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Kurt R Stover
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Darapaneni Chandra Mohan
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Mayuri Gupta
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Eric C Keske
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Paolo Schiavini
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Laura Villar
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Fan Wu
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Alexander Kreft
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Kiersten Thomas
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Elana Raaphorst
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Jagadeesh P Pasangulapati
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Siva R Alla
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Simmi Sharma
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Ramana R Mittapalli
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Irina Sagamanova
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Shea L Johnson
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada
| | - Mark A Reed
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON M55 3H6, Canada
| | - Donald F Weaver
- Krembil Research Institute, University Health Network, 60 Leonard Avenue, Toronto, ON M5T 2S8, Canada.,Department of Chemistry, University of Toronto, Toronto, ON M55 3H6, Canada.,Department of Medicine, Division of Neurology, University of Toronto, Toronto, ON M5S 1A8, Canada
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13
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Röhrig UF, Majjigapu SR, Reynaud A, Pojer F, Dilek N, Reichenbach P, Ascencao K, Irving M, Coukos G, Vogel P, Michielin O, Zoete V. Azole-Based Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors. J Med Chem 2021; 64:2205-2227. [PMID: 33557523 DOI: 10.1021/acs.jmedchem.0c01968] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The heme enzyme indoleamine 2,3-dioxygenase 1 (IDO1) plays an essential role in immunity, neuronal function, and aging through catalysis of the rate-limiting step in the kynurenine pathway of tryptophan metabolism. Many IDO1 inhibitors with different chemotypes have been developed, mainly targeted for use in anti-cancer immunotherapy. Lead optimization of direct heme iron-binding inhibitors has proven difficult due to the remarkable selectivity and sensitivity of the heme-ligand interactions. Here, we present experimental data for a set of closely related small azole compounds with more than 4 orders of magnitude differences in their inhibitory activities, ranging from millimolar to nanomolar levels. We investigate and rationalize their activities based on structural data, molecular dynamics simulations, and density functional theory calculations. Our results not only expand the presently known four confirmed chemotypes of sub-micromolar heme binding IDO1 inhibitors by two additional scaffolds but also provide a model to predict the activities of novel scaffolds.
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Affiliation(s)
- Ute F Röhrig
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Somi Reddy Majjigapu
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Laboratory of Glycochemistry and Asymmetric Synthesis, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Aline Reynaud
- Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Florence Pojer
- Protein Production and Structure Core Facility, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Nahzli Dilek
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Patrick Reichenbach
- Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, University of Lausanne, 1066 Epalinges, Switzerland
| | - Kelly Ascencao
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Melita Irving
- Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, University of Lausanne, 1066 Epalinges, Switzerland
| | - George Coukos
- Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, University of Lausanne, 1066 Epalinges, Switzerland.,Department of Oncology, Ludwig Cancer Research-Lausanne Branch, University Hospital of Lausanne (CHUV), 1011 Lausanne, Switzerland
| | - Pierre Vogel
- Laboratory of Glycochemistry and Asymmetric Synthesis, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Olivier Michielin
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Oncology, Ludwig Cancer Research-Lausanne Branch, University Hospital of Lausanne (CHUV), 1011 Lausanne, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Department of Oncology UNIL-CHUV, Ludwig Lausanne Branch, University of Lausanne, 1066 Epalinges, Switzerland
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14
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Feng X, Liao D, Liu D, Ping A, Li Z, Bian J. Development of Indoleamine 2,3-Dioxygenase 1 Inhibitors for Cancer Therapy and Beyond: A Recent Perspective. J Med Chem 2020; 63:15115-15139. [PMID: 33215494 DOI: 10.1021/acs.jmedchem.0c00925] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1) has received increasing attention due to its immunosuppressive function in connection with various diseases, including cancer. A recent increase in the understanding of IDO1 has significantly contributed to the discovery of numerous novel inhibitors, but the latest clinical outcomes raised questions and have indicated a future direction of IDO1 inhibition for therapeutic approaches. Herein, we present a comprehensive review of IDO1, discussing the latest advances in understanding the IDO1 structure and mechanism, an overview of recent IDO1 inhibitor discoveries and potential therapeutic applications to provide helpful information for medicinal chemists investigating IDO1 inhibitors.
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Affiliation(s)
- Xi Feng
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, People's Republic of China
| | - Dongdong Liao
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, People's Republic of China
| | - Dongyu Liu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, People's Republic of China
| | - An Ping
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, People's Republic of China
| | - Zhiyu Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, People's Republic of China
| | - Jinlei Bian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, People's Republic of China
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15
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Mirgaux M, Leherte L, Wouters J. Influence of the presence of the heme cofactor on the JK-loop structure in indoleamine 2,3-dioxygenase 1. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:1211-1221. [DOI: 10.1107/s2059798320013510] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/08/2020] [Indexed: 01/13/2023]
Abstract
Indoleamine 2,3-dioxygenase 1 has sparked interest as an immunotherapeutic target in cancer research. Its structure includes a loop, named the JK-loop, that controls the orientation of the substrate or inhibitor within the active site. However, little has been reported about the crystal structure of this loop. In the present work, the conformation of the JK-loop is determined for the first time in the presence of the heme cofactor in the active site through X-ray diffraction experiments (2.44 Å resolution). Molecular-dynamics trajectories were also obtained to provide dynamic information about the loop according to the presence of cofactor. This new structural and dynamic information highlights the importance of the JK-loop in confining the labile heme cofactor to the active site.
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16
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Dolšak A, Gobec S, Sova M. Indoleamine and tryptophan 2,3-dioxygenases as important future therapeutic targets. Pharmacol Ther 2020; 221:107746. [PMID: 33212094 DOI: 10.1016/j.pharmthera.2020.107746] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023]
Abstract
Conversion of tryptophan to N-formylkynurenine is the first and rate-limiting step of the tryptophan metabolic pathway (i.e., the kynurenine pathway). This conversion is catalyzed by three enzyme isoforms: indoleamine 2,3-dioxygenase 1 (IDO1), indoleamine 2,3-dioxygenase 2 (IDO2), and tryptophan 2,3-dioxygenase (TDO). As this pathway generates numerous metabolites that are involved in various pathological conditions, IDOs and TDO represent important targets for therapeutic intervention. This pathway has especially drawn attention due to its importance in tumor resistance. Over the last decade, a large number of IDO and TDO inhibitors have been developed, many of which have entered clinical trials. Here, detailed structural comparisons of these three enzymes (with emphasis on their active sites), their involvement in cellular signaling, and their role(s) in pathological conditions are discussed. Furthermore, the most important recent inhibitors described in papers and patents and involved in clinical trials are reviewed, with a focus on both selective and multiple inhibitors. A short overview of the biochemical and cellular assays used for inhibitory potency evaluation is also presented. This review summarizes recent advances on IDO and TDO as potential drug targets, and provides the key features and perspectives for further research and development of potent inhibitors of the kynurenine pathway.
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Affiliation(s)
- Ana Dolšak
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Stanislav Gobec
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Matej Sova
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, SI-1000 Ljubljana, Slovenia.
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17
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Identification of potential indoleamine 2, 3-dioxygenase 1 (IDO1) inhibitors by an FBG-based 3D QSAR pharmacophore model. J Mol Graph Model 2020; 99:107628. [DOI: 10.1016/j.jmgm.2020.107628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 01/08/2023]
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18
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Mammoli A, Coletti A, Ballarotto M, Riccio A, Carotti A, Grohmann U, Camaioni E, Macchiarulo A. New Insights from Crystallographic Data: Diversity of Structural Motifs and Molecular Recognition Properties between Groups of IDO1 Structures. ChemMedChem 2020; 15:891-899. [PMID: 32190988 DOI: 10.1002/cmdc.202000116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Indexed: 01/04/2023]
Abstract
A large number of crystallographic structures of IDO1 in different ligand-bound and -unbound states have been disclosed over the last decade. Yet, only a few of them have been exploited for structure-based drug design (SBDD) campaigns. In this study, we analyzed the structural motifs and molecular-recognition properties of three groups of IDO1 structures: 1) structures containing the heme group and inhibitors in the catalytic site; 2) heme-free structures of IDO1; 3) substrate-bound structures of IDO1. The results suggest that unrelated conformations of the enzyme have been solved with different ligand-induced changes of secondary motifs that localize even in regions remote from the catalytic site. Moreover, the study identified an uncharted region of molecular-recognition space covered by IDO1 binding sites that could guide the selection of diverse structures for additional SBDD studies aimed at the identification of novel lead compounds with differentiated chemical scaffolds.
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Affiliation(s)
- Andrea Mammoli
- Department of Pharmaceutical Sciences, University of Perugia, via del liceo n.1, 06123, Perugia, Italy
| | - Alice Coletti
- Department of Pharmacy, University of Chieti-Pescara, via dei Vestini n. 31, 66100, Chieti, Italy
| | - Marco Ballarotto
- Department of Pharmaceutical Sciences, University of Perugia, via del liceo n.1, 06123, Perugia, Italy
| | - Alessandra Riccio
- Department of Pharmaceutical Sciences, University of Perugia, via del liceo n.1, 06123, Perugia, Italy
| | - Andrea Carotti
- Department of Pharmaceutical Sciences, University of Perugia, via del liceo n.1, 06123, Perugia, Italy
| | - Ursula Grohmann
- Department of Experimental Medicine, University of Perugia, P.le Gambuli, 06132, Perugia, Italy
| | - Emidio Camaioni
- Department of Pharmaceutical Sciences, University of Perugia, via del liceo n.1, 06123, Perugia, Italy
| | - Antonio Macchiarulo
- Department of Pharmaceutical Sciences, University of Perugia, via del liceo n.1, 06123, Perugia, Italy
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19
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Positive allosteric modulation of indoleamine 2,3-dioxygenase 1 restrains neuroinflammation. Proc Natl Acad Sci U S A 2020; 117:3848-3857. [PMID: 32024760 DOI: 10.1073/pnas.1918215117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
l-tryptophan (Trp), an essential amino acid for mammals, is the precursor of a wide array of immunomodulatory metabolites produced by the kynurenine and serotonin pathways. The kynurenine pathway is a paramount source of several immunoregulatory metabolites, including l-kynurenine (Kyn), the main product of indoleamine 2,3-dioxygenase 1 (IDO1) that catalyzes the rate-limiting step of the pathway. In the serotonin pathway, the metabolite N-acetylserotonin (NAS) has been shown to possess antioxidant, antiinflammatory, and neuroprotective properties in experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS). However, little is known about the exact mode of action of the serotonin metabolite and the possible interplay between the 2 Trp metabolic pathways. Prompted by the discovery that NAS neuroprotective effects in EAE are abrogated in mice lacking IDO1 expression, we investigated the NAS mode of action in neuroinflammation. We found that NAS directly binds IDO1 and acts as a positive allosteric modulator (PAM) of the IDO1 enzyme in vitro and in vivo. As a result, increased Kyn will activate the ligand-activated transcription factor aryl hydrocarbon receptor and, consequently, antiinflammatory and immunoregulatory effects. Because NAS also increased IDO1 activity in peripheral blood mononuclear cells of a significant proportion of MS patients, our data may set the basis for the development of IDO1 PAMs as first-in-class drugs in autoimmune/neuroinflammatory diseases.
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20
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Pham KN, Lewis-Ballester A, Yeh SR. Structural Basis of Inhibitor Selectivity in Human Indoleamine 2,3-Dioxygenase 1 and Tryptophan Dioxygenase. J Am Chem Soc 2019; 141:18771-18779. [PMID: 31682426 DOI: 10.1021/jacs.9b08871] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (hIDO1) and tryptophan dioxygenase (hTDO) are two of the only three heme-based dioxygenases in humans. They have recently been identified as key cancer immunotherapeutic drug targets. While structures of hIDO1 in complex with inhibitors have been documented, so far there are no structures of hTDO-inhibitor complexes available. Here we use PF-06840003 (IPD), a hIDO1-selective inhibitor in clinical trials, as a structural probe to elucidate inhibitor-selectivity in hIDO1 versus hTDO. Spectroscopic studies show that IPD exhibits 400-fold higher inhibition activity toward hIDO1 with respect to hTDO. Crystallographic structures reveal that the binding pocket of IPD in the active site in hIDO1 is much more flexible as compared to that in hTDO, which offers a molecular explanation for the superior inhibition activity of IPD in hIDO1 with respect to hTDO. In addition to the IPD bound in the active site, a second IPD molecule was identified in an inhibitory site on the proximal side of the heme in hIDO1 and in an exosite that is ∼40 Å away from the active site in hTDO. Taken together the data provide new insights into structure-based design of mono and dual inhibitors targeting hIDO1 and/or hTDO.
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Affiliation(s)
- Khoa N Pham
- Department of Physiology and Biophysics , Albert Einstein College of Medicine , The Bronx , New York 10461 , United States
| | - Ariel Lewis-Ballester
- Department of Physiology and Biophysics , Albert Einstein College of Medicine , The Bronx , New York 10461 , United States
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics , Albert Einstein College of Medicine , The Bronx , New York 10461 , United States
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21
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Röhrig UF, Reynaud A, Majjigapu SR, Vogel P, Pojer F, Zoete V. Inhibition Mechanisms of Indoleamine 2,3-Dioxygenase 1 (IDO1). J Med Chem 2019; 62:8784-8795. [PMID: 31525930 DOI: 10.1021/acs.jmedchem.9b00942] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1) catalyzes the rate-limiting step in the kynurenine pathway of tryptophan metabolism, which is involved in immunity, neuronal function, and aging. Its implication in pathologies such as cancer and neurodegenerative diseases has stimulated the development of IDO1 inhibitors. However, negative phase III clinical trial results of the IDO1 inhibitor epacadostat in cancer immunotherapy call for a better understanding of the role and the mechanisms of IDO1 inhibition. In this work, we investigate the molecular inhibition mechanisms of four known IDO1 inhibitors and of two quinones in detail, using different experimental and computational approaches. We also determine for the first time the X-ray structure of the highly efficient 1,2,3-triazole inhibitor MMG-0358. Based on our results and a comprehensive literature overview, we propose a classification scheme for IDO1 inhibitors according to their inhibition mechanism, which will be useful for further developments in the field.
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Affiliation(s)
- Ute F Röhrig
- Molecular Modeling Group , SIB Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland
| | - Aline Reynaud
- Protein Production and Structure Core Facility, School of Life Sciences , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Somi Reddy Majjigapu
- Molecular Modeling Group , SIB Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland.,Laboratory of Glycochemistry and Asymmetric Synthesis , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Pierre Vogel
- Laboratory of Glycochemistry and Asymmetric Synthesis , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Florence Pojer
- Protein Production and Structure Core Facility, School of Life Sciences , École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Vincent Zoete
- Molecular Modeling Group , SIB Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland.,Department of Fundamental Oncology , University of Lausanne, Ludwig Lausanne Branch , 1066 Epalinges , Switzerland
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22
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Wang XX, Sun SY, Dong QQ, Wu XX, Tang W, Xing YQ. Recent advances in the discovery of indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors. MEDCHEMCOMM 2019; 10:1740-1754. [PMID: 32055299 DOI: 10.1039/c9md00208a] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO1), an important immunoregulatory enzyme ubiquitously expressed in various tissues and cells, plays a key role in tryptophan metabolism via the kynurenine pathway and has emerged as an attractive therapeutic target for the treatment of cancer and other diseases, such as Alzheimer's disease and arthritis. IDO1 has diverse biological roles in immune suppression and tumor progression by tryptophan catabolism. In addition, IDO1-mediated immune tolerance assists tumor cells in escaping the immune surveillance. Recently, extensive and enormous investigations have been made in the discovery of IDO1 inhibitors in both academia and pharmaceutical companies. In this review, IDO1 inhibitors are grouped as tryptophan derivatives, inhibitors with an imidazole, 1,2,3-triazole or tetrazole scaffold, inhibitors with quinone or iminoquinone, N-hydroxyamidines and other derivatives, and their enzymatic inhibitory activity, selectivity and other biological activities are also introduced and summarized.
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Affiliation(s)
- Xiu-Xiu Wang
- Department of Pharmacy , The Second Affliated Hospital of Bengbu Medical College , Bengbu , Anhuir 233040 , P.R. China .
| | - Si-Yu Sun
- Department of Pharmacy , The Second Affliated Hospital of Bengbu Medical College , Bengbu , Anhuir 233040 , P.R. China .
| | - Qing-Qing Dong
- Department of Pharmacy , The Second Affliated Hospital of Bengbu Medical College , Bengbu , Anhuir 233040 , P.R. China .
| | - Xiao-Xiang Wu
- Department of Pharmacy , The Second Affliated Hospital of Bengbu Medical College , Bengbu , Anhuir 233040 , P.R. China .
| | - Wei Tang
- Department of Pharmacy , The Second Affliated Hospital of Bengbu Medical College , Bengbu , Anhuir 233040 , P.R. China .
| | - Ya-Qun Xing
- Department of Pharmacy , The Second Affliated Hospital of Bengbu Medical College , Bengbu , Anhuir 233040 , P.R. China .
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23
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Ye Z, Yue L, Shi J, Shao M, Wu T. Role of IDO and TDO in Cancers and Related Diseases and the Therapeutic Implications. J Cancer 2019; 10:2771-2782. [PMID: 31258785 PMCID: PMC6584917 DOI: 10.7150/jca.31727] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 04/10/2019] [Indexed: 02/06/2023] Open
Abstract
Kynurenine (Kyn) pathway is a significant metabolic pathway of tryptophan (Trp). The metabolites of the Kyn pathway are closely correlated with numerous diseases. Two main enzymes, indoleamine-2,3-dioxygenase (IDO) and tryptophan-2,3-dioxygenase (TDO or TDO2), regulate the first and rate-limiting step of the Kyn pathway. These enzymes are directly or indirectly involved in various diseases, including inflammatory diseases, cancer, diabetes, and mental disorders. Presently, an increasing number of potential mechanisms have been revealed. In the present review, we depict the structure of IDO and TDO and explicate their functions in various diseases to facilitate a better understanding of them and to indicate new therapeutic plans to target them. Moreover, we summarize the inhibitors of IDO/TDO that are currently under development and their efficacy in the treatment of cancer and other diseases.
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Affiliation(s)
- Zixiang Ye
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Linxiu Yue
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jiachen Shi
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Mingmei Shao
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Tao Wu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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24
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Serafini M, Torre E, Aprile S, Massarotti A, Fallarini S, Pirali T. Synthesis, Docking and Biological Evaluation of a Novel Class of Imidazothiazoles as IDO1 Inhibitors. Molecules 2019; 24:E1874. [PMID: 31096672 PMCID: PMC6572114 DOI: 10.3390/molecules24101874] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 12/21/2022] Open
Abstract
IDO1, a key dioxygenase in tryptophan-kynurenine metabolism, appeared in the last 10 years at the vanguard of druggable targets in cancer therapy due to its well-established role both in immune escape and inflammatory neovascularization. Among the pool of IDO1 inhibitors that have entered clinical trials, none have reached approval. The identification of novel inhibitors endowed with better clinical profile, together with the further comprehension of the interactions with residues in IDO1 active site, are still a need. In this context, we have synthesized a novel class of imidazothiazole derivatives as IDO1 inhibitors and identified three compounds with inhibitory potency in the low micromolar range. This report strengthens the role played by pocket C in the active site of IDO1, providing novel directions in the design of IDO1 inhibitors.
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Affiliation(s)
- Marta Serafini
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy.
| | - Enza Torre
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy.
| | - Silvio Aprile
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy.
| | - Alberto Massarotti
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy.
| | - Silvia Fallarini
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy.
| | - Tracey Pirali
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy.
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25
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Acúrcio RC, Scomparin A, Satchi‐Fainaro R, Florindo HF, Guedes RC. Computer‐aided drug design in new druggable targets for the next generation of immune‐oncology therapies. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Rita C. Acúrcio
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Anna Scomparin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine Tel Aviv University Tel Aviv Israel
| | - Ronit Satchi‐Fainaro
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine Tel Aviv University Tel Aviv Israel
| | - Helena F. Florindo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy Universidade de Lisboa Lisbon Portugal
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26
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Luo S, Xu K, Xiang S, Chen J, Chen C, Guo C, Tong Y, Tong L. High-resolution structures of inhibitor complexes of human indoleamine 2,3-dioxygenase 1 in a new crystal form. Acta Crystallogr F Struct Biol Commun 2018; 74:717-724. [PMID: 30387777 PMCID: PMC6213978 DOI: 10.1107/s2053230x18012955] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/13/2018] [Indexed: 11/11/2022] Open
Abstract
Human indoleamine 2,3-dioxygenase 1 (IDO1) is a heme-dependent enzyme with important roles in many cellular processes and is a potential target for drug discovery against cancer and other diseases. Crystal structures of IDO1 in complex with various inhibitors have been reported. Many of these crystals belong to the same crystal form and most of the reported structures have resolutions in the range 3.2-2.3 Å. Here, three new crystal forms of human IDO1 obtained by introducing a surface mutation, K116A/K117A, distant from the active site are reported. One of these crystal forms diffracted to 1.5 Å resolution and can be readily used for soaking experiments to determine high-resolution structures of IDO1 in complex with the substrate tryptophan or inhibitors that coordinate the heme. In addition, this mutant was used to produce crystals of a complex with an inhibitor that targets the apo form of the enzyme under the same conditions; the structure of this complex was determined at 1.7 Å resolution. Overall, this mutant represents a robust platform for determining the structures of inhibitor and substrate complexes of IDO1 at high resolution.
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Affiliation(s)
- Shukun Luo
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Ke Xu
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Shaoyun Xiang
- Suzhou Kintor Pharmaceuticals Inc., Suzhou Industrial Park, Suzhou 215123, People’s Republic of China
| | - Jie Chen
- Suzhou Kintor Pharmaceuticals Inc., Suzhou Industrial Park, Suzhou 215123, People’s Republic of China
| | - Chunyun Chen
- Suzhou Kintor Pharmaceuticals Inc., Suzhou Industrial Park, Suzhou 215123, People’s Republic of China
| | - Chuangxin Guo
- Suzhou Kintor Pharmaceuticals Inc., Suzhou Industrial Park, Suzhou 215123, People’s Republic of China
| | - Youzhi Tong
- Suzhou Kintor Pharmaceuticals Inc., Suzhou Industrial Park, Suzhou 215123, People’s Republic of China
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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27
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Pham KN, Yeh SR. Mapping the Binding Trajectory of a Suicide Inhibitor in Human Indoleamine 2,3-Dioxygenase 1. J Am Chem Soc 2018; 140:14538-14541. [PMID: 30347977 DOI: 10.1021/jacs.8b07994] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Human indoleamine 2,3-dioxygenase 1 (hIDO1) is an important heme-containing enzyme that is a key drug target for cancer immunotherapy. Several hIDO1 inhibitors have entered clinical trials, among which BMS-986205 (BMS) stands out as the only suicide inhibitor. Despite its "best-in-class" activity, the action mechanism of BMS remains elusive. Here, we report three crystal structures of hIDO1-BMS complexes that define the complete binding trajectory of the inhibitor. BMS first binds in a solvent exposed surface cleft near the active site in an extended conformation. The initial binding partially unfolds the active site, which triggers heme release, thereby exposing a new binding pocket. The inhibitor then undergoes a large scale movement to this new binding pocket, where it binds by adopting a high energy kinked conformation. Finally, the inhibitor relaxes to a bent conformation, via an additional large scale rearrangement, culminating in the energy minimum state. The structural data offer a molecular explanation for the remarkable efficacy and suicide inhibition activity of the inhibitor. They also suggest a novel strategy that can be applied for drug development targeting hIDO1 and related enzymes.
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Affiliation(s)
- Khoa N Pham
- Department of Physiology and Biophysics , Albert Einstein College of Medicine , Bronx , New York 10461 , United States
| | - Syun-Ru Yeh
- Department of Physiology and Biophysics , Albert Einstein College of Medicine , Bronx , New York 10461 , United States
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