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1
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Takayama I, Araki N, Tewari J, Yohda M, Matsunami H, Fukutani Y. Antagonists Enhance Cell-Surface Expression of Mammalian Odorant Receptors. Int J Mol Sci 2025; 26:1458. [PMID: 40003926 PMCID: PMC11855683 DOI: 10.3390/ijms26041458] [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: 12/10/2024] [Revised: 01/31/2025] [Accepted: 02/08/2025] [Indexed: 02/27/2025] Open
Abstract
Functional characterization of vertebrate odorant receptors (ORs), members of the G protein-coupled receptor (GPCR) family, is essential for understanding olfaction. However, the functional expression of ORs in heterologous cells is often challenging, at least partly caused by structural instability in non-olfactory cells. Antagonists have been shown to restore membrane expression of some non-olfactory GPCR mutants, likely by transient increase in structural stability upon antagonist binding. Based on this premise, we examined whether antagonists could enhance OR membrane expression in heterologous cells. Using phenyl salicylate (PES) on cells expressing the mouse OR Or11g7, we observed increased cell surface expression exceeding the effects of co-expression with the OR chaperone RTP1S. After removing the antagonist, Or11g7 retained normal agonist responsiveness. Similar enhancements in cell surface expression were observed for a human OR OR2T11 treated with its antagonists. These findings suggest that small-molecule antagonists act as pharmacological chaperones to stabilize OR conformation, enhancing surface expression in a manner similar to molecular chaperones. Our study reveals a novel role for odorant antagonists in OR biogenesis and may inform future research on olfactory training mechanisms.
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Affiliation(s)
- Ikumi Takayama
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei 184-8588, Tokyo, Japan; (I.T.); (N.A.); (M.Y.)
| | - Nako Araki
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei 184-8588, Tokyo, Japan; (I.T.); (N.A.); (M.Y.)
| | - Jeevan Tewari
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei 184-8588, Tokyo, Japan; (I.T.); (N.A.); (M.Y.)
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Yosuke Fukutani
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei 184-8588, Tokyo, Japan; (I.T.); (N.A.); (M.Y.)
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2
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Wang J, Zhang Q, Fan W, Shi Q, Mao J, Xie J, Chai G, Zhang C. Deciphering olfactory receptor binding mechanisms: a structural and dynamic perspective on olfactory receptors. Front Mol Biosci 2025; 11:1498796. [PMID: 39845900 PMCID: PMC11751049 DOI: 10.3389/fmolb.2024.1498796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Accepted: 12/23/2024] [Indexed: 01/24/2025] Open
Abstract
Olfactory receptors, classified as G-protein coupled receptors (GPCRs), have been a subject of scientific inquiry since the early 1950s. Historically, investigations into the sensory mechanisms of olfactory receptors were often confined to behavioral characteristics in model organisms or the expression of related proteins and genes. However, with the development of cryo-electron microscopy techniques, it has gradually become possible to decipher the specific structures of olfactory receptors in insects and humans. This has provided new insights into the binding mechanisms between odor molecules and olfactory receptors. Furthermore, due to the rapid advancements in related fields such as computer simulations, the prediction and exploration of odor molecule binding to olfactory receptors have been progressively achieved through molecular dynamics simulations. Through this comprehensive review, we aim to provide a thorough analysis of research related to the binding mechanisms between odor molecules and olfactory receptors from the perspectives of structural biology and molecular dynamics simulations. Finally, we will provide an outlook on the future of research in the field of olfactory receptor sensory mechanisms.
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Affiliation(s)
- Jingtao Wang
- College of Chemistry, Zhengzhou University, Zhengzhou, Henan, China
- Department of tobacco flavor, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, Henan, China
| | - Qidong Zhang
- Department of tobacco flavor, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, Henan, China
| | - Wu Fan
- Department of tobacco flavor, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, Henan, China
| | - Qingzhao Shi
- Department of tobacco flavor, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, Henan, China
| | - Jian Mao
- Department of tobacco flavor, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, Henan, China
| | - Jianping Xie
- Department of tobacco flavor, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, Henan, China
| | - Guobi Chai
- Department of tobacco flavor, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, Henan, China
- Food Laboratory of Zhongyuan, Flavour Science Research Center of Zhengzhou University, Zhengzhou, Henan, China
| | - Chenglei Zhang
- Medical Laboratory, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
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Yang P, Luo T, Yang S, Zhang A, Tang Y, Chen L, Wang J, Zhao Y, Zhong Z, Li X, Han Z, Zhang Y, Tang Y, Ma J, Jin L, Long K, Li M, Lu L. Identification of Olfactory Receptors Responding to Androstenone and the Key Structure Determinant in Domestic Pig. Curr Issues Mol Biol 2024; 47:13. [PMID: 39852128 PMCID: PMC11763519 DOI: 10.3390/cimb47010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2024] [Revised: 12/13/2024] [Accepted: 12/21/2024] [Indexed: 01/26/2025] Open
Abstract
Olfactory receptors (ORs) are members of the transmembrane G protein-coupled receptor superfamily, playing a crucial role in odor recognition, which further mediates crucial biological processes in mammals. In sows, androstenone can trigger sexual behaviors through olfaction, but the underlying mechanism remains to be explored. To efficiently and accurately screen pig olfactory receptors responding to androstenone and the key structure determinant, we adapted the high-throughput RNA-seq strategy to screen the altered genes upon androstenone treatment in the olfactory epithelium of pigs, yielding 1397 downregulated genes. Of which, 15 OR genes and 49 OR-like genes were candidate androstenone-responsive genes, and 5 ORs (OR2D2, OR8D1, OR8D2, OR10Z1 and OR7D4) were proven as responsible for androstenone-mediated olfaction in vitro. Among the five ORs, pig OR7D4 has the highest level of androstenone response. To further find the structural determinant, we performed ligand-binding cavity analysis on pig OR7D4 with androstenone, predicted seven potential structural sites and further confirmed that F178 and T203 are the key sites for recognizing androstenone. Nevertheless, the natural non-synonymous mutation M133V (rs696400829) of pig OR7D4 was proven to significantly impair the respondence to androstenone. This is the first time the ORs responding to androstenone in pigs and the key structural determinant of pig OR7D4 were identified, which highlights the significance of investigating the role of OR7D4 in pig reproduction performance in the future.
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Affiliation(s)
- Peidong Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (P.Y.); (T.L.); (S.Y.); (Y.T.); (Z.Z.); (X.L.); (Z.H.); (Y.Z.); (Y.T.); (J.M.); (L.J.); (K.L.)
| | - Tingting Luo
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (P.Y.); (T.L.); (S.Y.); (Y.T.); (Z.Z.); (X.L.); (Z.H.); (Y.Z.); (Y.T.); (J.M.); (L.J.); (K.L.)
| | - Shuqi Yang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (P.Y.); (T.L.); (S.Y.); (Y.T.); (Z.Z.); (X.L.); (Z.H.); (Y.Z.); (Y.T.); (J.M.); (L.J.); (K.L.)
| | - Anjing Zhang
- Department of Pig Production, Chongqing Academy of Animal Science, Chongqing 402460, China; (A.Z.); (L.C.); (J.W.)
| | - Yuan Tang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (P.Y.); (T.L.); (S.Y.); (Y.T.); (Z.Z.); (X.L.); (Z.H.); (Y.Z.); (Y.T.); (J.M.); (L.J.); (K.L.)
| | - Li Chen
- Department of Pig Production, Chongqing Academy of Animal Science, Chongqing 402460, China; (A.Z.); (L.C.); (J.W.)
| | - Jinyong Wang
- Department of Pig Production, Chongqing Academy of Animal Science, Chongqing 402460, China; (A.Z.); (L.C.); (J.W.)
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China;
| | - Zhining Zhong
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (P.Y.); (T.L.); (S.Y.); (Y.T.); (Z.Z.); (X.L.); (Z.H.); (Y.Z.); (Y.T.); (J.M.); (L.J.); (K.L.)
| | - Xuemin Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (P.Y.); (T.L.); (S.Y.); (Y.T.); (Z.Z.); (X.L.); (Z.H.); (Y.Z.); (Y.T.); (J.M.); (L.J.); (K.L.)
| | - Ziyin Han
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (P.Y.); (T.L.); (S.Y.); (Y.T.); (Z.Z.); (X.L.); (Z.H.); (Y.Z.); (Y.T.); (J.M.); (L.J.); (K.L.)
| | - Yupei Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (P.Y.); (T.L.); (S.Y.); (Y.T.); (Z.Z.); (X.L.); (Z.H.); (Y.Z.); (Y.T.); (J.M.); (L.J.); (K.L.)
| | - Yue Tang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (P.Y.); (T.L.); (S.Y.); (Y.T.); (Z.Z.); (X.L.); (Z.H.); (Y.Z.); (Y.T.); (J.M.); (L.J.); (K.L.)
| | - Jideng Ma
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (P.Y.); (T.L.); (S.Y.); (Y.T.); (Z.Z.); (X.L.); (Z.H.); (Y.Z.); (Y.T.); (J.M.); (L.J.); (K.L.)
| | - Long Jin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (P.Y.); (T.L.); (S.Y.); (Y.T.); (Z.Z.); (X.L.); (Z.H.); (Y.Z.); (Y.T.); (J.M.); (L.J.); (K.L.)
| | - Keren Long
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (P.Y.); (T.L.); (S.Y.); (Y.T.); (Z.Z.); (X.L.); (Z.H.); (Y.Z.); (Y.T.); (J.M.); (L.J.); (K.L.)
| | - Mingzhou Li
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (P.Y.); (T.L.); (S.Y.); (Y.T.); (Z.Z.); (X.L.); (Z.H.); (Y.Z.); (Y.T.); (J.M.); (L.J.); (K.L.)
| | - Lu Lu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 610000, China; (P.Y.); (T.L.); (S.Y.); (Y.T.); (Z.Z.); (X.L.); (Z.H.); (Y.Z.); (Y.T.); (J.M.); (L.J.); (K.L.)
- Department of Pig Production, Chongqing Academy of Animal Science, Chongqing 402460, China; (A.Z.); (L.C.); (J.W.)
- College of Animal Science and Technology, Southwest University, Chongqing 402460, China;
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Pirona L, Ballabio F, Alfonso-Prieto M, Capelli R. Calcium-Driven In Silico Inactivation of a Human Olfactory Receptor. J Chem Inf Model 2024; 64:2971-2978. [PMID: 38523266 DOI: 10.1021/acs.jcim.4c00249] [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: 03/26/2024]
Abstract
Conformational changes as well as molecular determinants related to the activation and inactivation of olfactory receptors are still poorly understood due to the intrinsic difficulties in the structural determination of this GPCR family. Here, we perform, for the first time, the in silico inactivation of human olfactory receptor OR51E2, highlighting the possible role of calcium in this receptor state transition. Using molecular dynamics simulations, we show that a divalent ion in the ion binding site, coordinated by two acidic residues at positions 2.50 and 3.39 conserved across most ORs, stabilizes the receptor in its inactive state. In contrast, protonation of the same two acidic residues is not sufficient to drive inactivation within the microsecond timescale of our simulations. Our findings suggest a novel molecular mechanism for OR inactivation, potentially guiding experimental validation and offering insights into the possible broader role of divalent ions in GPCR signaling.
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Affiliation(s)
- Lorenza Pirona
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Federico Ballabio
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, I-20133 Milano, Italy
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, D-54248 Jülich, Germany
| | - Riccardo Capelli
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, I-20133 Milano, Italy
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5
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Wu C, Xu M, Dong J, Cui W, Yuan S. The structure and function of olfactory receptors. Trends Pharmacol Sci 2024; 45:268-280. [PMID: 38296675 DOI: 10.1016/j.tips.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/02/2024]
Abstract
Olfactory receptors (ORs) form the most important chemosensory receptor family responsible for our sense of smell in the nasal olfactory epithelium. This receptor family belongs to the class A G protein-coupled receptors (GPCRs). Recent research has indicated that ORs are involved in many nonolfactory physiological processes in extranasal tissue, such as the brain, pancreas, and testes, and implies the possible role of their dysregulation in various diseases. The recently released structures of OR51E2 and consensus OR52 have also unveiled the uniqueness of ORs from other class A GPCR members. In this review, we discuss these recent developments and computational modeling efforts toward understanding the structural properties of unresolved ORs, which could guide potential future OR-targeted drug discovery.
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Affiliation(s)
- Chenyang Wu
- The AlphaMol-SIAT Joint Laboratory, Shenzhen 518055, China; The Research Center for Computer-aided Drug Discovery, The Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Marc Xu
- The AlphaMol-SIAT Joint Laboratory, Shenzhen 518055, China; The Research Center for Computer-aided Drug Discovery, The Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junlin Dong
- The AlphaMol-SIAT Joint Laboratory, Shenzhen 518055, China; The Research Center for Computer-aided Drug Discovery, The Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqiang Cui
- The AlphaMol-SIAT Joint Laboratory, Shenzhen 518055, China
| | - Shuguang Yuan
- The AlphaMol-SIAT Joint Laboratory, Shenzhen 518055, China; AlphaMol Science Ltd, Shenzhen 518055, China.
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6
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Scharf MM, Humphrys LJ, Berndt S, Di Pizio A, Lehmann J, Liebscher I, Nicoli A, Niv MY, Peri L, Schihada H, Schulte G. The dark sides of the GPCR tree - research progress on understudied GPCRs. Br J Pharmacol 2024. [PMID: 38339984 DOI: 10.1111/bph.16325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/24/2023] [Accepted: 01/08/2024] [Indexed: 02/12/2024] Open
Abstract
A large portion of the human GPCRome is still in the dark and understudied, consisting even of entire subfamilies of GPCRs such as odorant receptors, class A and C orphans, adhesion GPCRs, Frizzleds and taste receptors. However, it is undeniable that these GPCRs bring an untapped therapeutic potential that should be explored further. Open questions on these GPCRs span diverse topics such as deorphanisation, the development of tool compounds and tools for studying these GPCRs, as well as understanding basic signalling mechanisms. This review gives an overview of the current state of knowledge for each of the diverse subfamilies of understudied receptors regarding their physiological relevance, molecular mechanisms, endogenous ligands and pharmacological tools. Furthermore, it identifies some of the largest knowledge gaps that should be addressed in the foreseeable future and lists some general strategies that might be helpful in this process.
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Affiliation(s)
- Magdalena M Scharf
- Karolinska Institutet, Dept. Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Stockholm, Sweden
| | - Laura J Humphrys
- Institute of Pharmacy, University of Regensburg, Regensburg, Germany
| | - Sandra Berndt
- Rudolf Schönheimer Institute for Biochemistry, Molecular Biochemistry, University of Leipzig, Leipzig, Germany
| | - Antonella Di Pizio
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
| | - Juliane Lehmann
- Rudolf Schönheimer Institute for Biochemistry, Molecular Biochemistry, University of Leipzig, Leipzig, Germany
| | - Ines Liebscher
- Rudolf Schönheimer Institute for Biochemistry, Molecular Biochemistry, University of Leipzig, Leipzig, Germany
| | - Alessandro Nicoli
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
| | - Masha Y Niv
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Lior Peri
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Hannes Schihada
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gunnar Schulte
- Karolinska Institutet, Dept. Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Stockholm, Sweden
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7
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Choi C, Bae J, Kim S, Lee S, Kang H, Kim J, Bang I, Kim K, Huh WK, Seok C, Park H, Im W, Choi HJ. Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family. Nat Commun 2023; 14:8105. [PMID: 38062020 PMCID: PMC10703812 DOI: 10.1038/s41467-023-43983-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Structural and mechanistic studies on human odorant receptors (ORs), key in olfactory signaling, are challenging because of their low surface expression in heterologous cells. The recent structure of OR51E2 bound to propionate provided molecular insight into odorant recognition, but the lack of an inactive OR structure limited understanding of the activation mechanism of ORs upon odorant binding. Here, we determined the cryo-electron microscopy structures of consensus OR52 (OR52cs), a representative of the OR52 family, in the ligand-free (apo) and octanoate-bound states. The apo structure of OR52cs reveals a large opening between transmembrane helices (TMs) 5 and 6. A comparison between the apo and active structures of OR52cs demonstrates the inward and outward movements of the extracellular and intracellular segments of TM6, respectively. These results, combined with molecular dynamics simulations and signaling assays, shed light on the molecular mechanisms of odorant binding and activation of the OR52 family.
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Affiliation(s)
- Chulwon Choi
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jungnam Bae
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seonghan Kim
- Department of Bioengineering, Lehigh University, Bethlehem, PA, 18015, USA
| | - Seho Lee
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyunook Kang
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jinuk Kim
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Injin Bang
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Kiheon Kim
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Won-Ki Huh
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hahnbeom Park
- Brain Science Institute, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Wonpil Im
- Department of Bioengineering, Lehigh University, Bethlehem, PA, 18015, USA
- Departments of Biological Sciences, Chemistry, and Computer Science and Engineering, Lehigh University, Bethlehem, PA, 18015, USA
| | - Hee-Jung Choi
- Department of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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8
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Nicoli A, Haag F, Marcinek P, He R, Kreißl J, Stein J, Marchetto A, Dunkel A, Hofmann T, Krautwurst D, Di Pizio A. Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1. J Chem Inf Model 2023; 63:2014-2029. [PMID: 36696962 PMCID: PMC10091413 DOI: 10.1021/acs.jcim.2c00752] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
With approximately 400 encoding genes in humans, odorant receptors (ORs) are the largest subfamily of class A G protein-coupled receptors (GPCRs). Despite its high relevance and representation, the odorant-GPCRome is structurally poorly characterized: no experimental structures are available, and the low sequence identity of ORs to experimentally solved GPCRs is a significant challenge for their modeling. Moreover, the receptive range of most ORs is unknown. The odorant receptor OR5K1 was recently and comprehensively characterized in terms of cognate agonists. Here, we report two additional agonists and functional data of the most potent compound on two mutants, L1043.32 and L2556.51. Experimental data was used to guide the investigation of the binding modes of OR5K1 ligands into the orthosteric binding site using structural information from AI-driven modeling, as recently released in the AlphaFold Protein Structure Database, and from homology modeling. Induced-fit docking simulations were used to sample the binding site conformational space for ensemble docking. Mutagenesis data guided side chain residue sampling and model selection. We obtained models that could better rationalize the different activity of active (agonist) versus inactive molecules with respect to starting models and also capture differences in activity related to minor structural differences. Therefore, we provide a model refinement protocol that can be applied to model the orthosteric binding site of ORs as well as that of GPCRs with low sequence identity to available templates.
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Affiliation(s)
- Alessandro Nicoli
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Franziska Haag
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Patrick Marcinek
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Ruiming He
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany.,Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Johanna Kreißl
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Jörg Stein
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Alessandro Marchetto
- Computational Biomedicine, Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.,Department of Biology, Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52074 Aachen, Germany
| | - Andreas Dunkel
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, 85354 Freising, Germany
| | - Dietmar Krautwurst
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Antonella Di Pizio
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
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