1
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Ople R, Ramos-Gonzalez N, Li Q, Sobecks BL, Aydin D, Powers AS, Faouzi A, Polacco BJ, Bernhard SM, Appourchaux K, Sribhashyam S, Eans SO, Tsai BA, Dror RO, Varga BR, Wang H, Hüttenhain R, McLaughlin JP, Majumdar S. Signaling Modulation Mediated by Ligand Water Interactions with the Sodium Site at μOR. ACS CENTRAL SCIENCE 2024; 10:1490-1503. [PMID: 39220695 PMCID: PMC11363324 DOI: 10.1021/acscentsci.4c00525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/19/2024] [Accepted: 06/20/2024] [Indexed: 09/04/2024]
Abstract
The mu opioid receptor (μOR) is a target for clinically used analgesics. However, adverse effects, such as respiratory depression and physical dependence, necessitate the development of alternative treatments. Recently we reported a novel strategy to design functionally selective opioids by targeting the sodium binding allosteric site in μOR with a supraspinally active analgesic named C6guano. Presently, to improve systemic activity of this ligand, we used structure-based design, identifying a new ligand named RO76 where the flexible alkyl linker and polar guanidine guano group is swapped with a benzyl alcohol, and the sodium site is targeted indirectly through waters. A cryoEM structure of RO76 bound to the μOR-Gi complex confirmed that RO76 interacts with the sodium site residues through a water molecule, unlike C6guano which engages the sodium site directly. Signaling assays coupled with APEX based proximity labeling show binding in the sodium pocket modulates receptor efficacy and trafficking. In mice, RO76 was systemically active in tail withdrawal assays and showed reduced liabilities compared to those of morphine. In summary, we show that targeting water molecules in the sodium binding pocket may be an avenue to modulate signaling properties of opioids, and which may potentially be extended to other G-protein coupled receptors where this site is conserved.
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Affiliation(s)
- Rohini
S. Ople
- Center
for Clinical Pharmacology, University of
Health Sciences & Pharmacy at St. Louis and Washington University
School of Medicine, St. Louis, Missouri 63110, United States
- Department
of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Nokomis Ramos-Gonzalez
- Center
for Clinical Pharmacology, University of
Health Sciences & Pharmacy at St. Louis and Washington University
School of Medicine, St. Louis, Missouri 63110, United States
- Department
of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Qiongyu Li
- Department
of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94158, United States
| | - Briana L. Sobecks
- Department of Computer Science, Stanford
University, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Department
of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Deniz Aydin
- Department of Computer Science, Stanford
University, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Department
of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Alexander S. Powers
- Department of Computer Science, Stanford
University, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Department
of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Abdelfattah Faouzi
- Center
for Clinical Pharmacology, University of
Health Sciences & Pharmacy at St. Louis and Washington University
School of Medicine, St. Louis, Missouri 63110, United States
- Department
of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Benjamin J. Polacco
- Department of Computer Science, Stanford
University, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
| | - Sarah M. Bernhard
- Center
for Clinical Pharmacology, University of
Health Sciences & Pharmacy at St. Louis and Washington University
School of Medicine, St. Louis, Missouri 63110, United States
- Department
of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Kevin Appourchaux
- Center
for Clinical Pharmacology, University of
Health Sciences & Pharmacy at St. Louis and Washington University
School of Medicine, St. Louis, Missouri 63110, United States
- Department
of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Sashrik Sribhashyam
- Center
for Clinical Pharmacology, University of
Health Sciences & Pharmacy at St. Louis and Washington University
School of Medicine, St. Louis, Missouri 63110, United States
- Department
of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Shainnel O. Eans
- Department
of Pharmacodynamics, University of Florida, Gainesville, Florida 032610, United
States
| | - Bowen A. Tsai
- Department
of Pharmacodynamics, University of Florida, Gainesville, Florida 032610, United
States
| | - Ron O. Dror
- Department of Computer Science, Stanford
University, Stanford, California 94305, United States
- Department
of Structural Biology, Stanford University
School of Medicine, Stanford, California 94305, United States
- Department
of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Balazs R. Varga
- Center
for Clinical Pharmacology, University of
Health Sciences & Pharmacy at St. Louis and Washington University
School of Medicine, St. Louis, Missouri 63110, United States
- Department
of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Haoqing Wang
- Department
of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Ruth Hüttenhain
- Department
of Molecular & Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, United States
| | - Jay P. McLaughlin
- Department
of Pharmacodynamics, University of Florida, Gainesville, Florida 032610, United
States
| | - Susruta Majumdar
- Center
for Clinical Pharmacology, University of
Health Sciences & Pharmacy at St. Louis and Washington University
School of Medicine, St. Louis, Missouri 63110, United States
- Department
of Anesthesiology and Washington University Pain Center, Washington University School of Medicine, St. Louis, Missouri 63110, United States
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2
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Che T, Varga B, Bernhard SM, El Daibani A, Zaidi S, Lam J, Aguilar J, Appourchaux K, Nazarova A, Kouvelis A, Eans S, Margolis E, Fay J, Pradhan A, Katritch V, McLaughlin J, Majumdar S. Structure-Guided Design of Partial Agonists at an Opioid Receptor. RESEARCH SQUARE 2024:rs.3.rs-4664764. [PMID: 39070616 PMCID: PMC11276012 DOI: 10.21203/rs.3.rs-4664764/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The persistence of chronic pain and continuing overdose deaths from pain-relieving opioids targeting μ opioid receptor (μOR) have fueled the need for reliable long-term analgesics which use different targets and mechanisms. The δ opioid receptor (δOR) is a potential alternative target for non-addictive analgesics to alleviate chronic pain, made more attractive by its lack of respiratory depression associated with μOR agonists. However, early δOR full agonists were found to induce seizures, precluding clinical use. Partial δOR agonists may offer more controlled activation of the receptor compared to full agonists, but the development of such ligands has been hindered by uncertainty over the molecular mechanism mediating partial agonism. Using a structure-based approach, we explored the engagement of the sodium binding pocket in δOR and developed a bitopic ligand, C6-Quino, predicted to be a selective δOR partial agonist. Functional studies of C6-Quino revealed that it displayed δOR partial agonist activity at both G-protein and arrestin pathways. Its interaction with the sodium pocket was confirmed and analyzed using a single particle cryo-EM. Additionally, C6-Quino demonstrated favorable chemical and physiological properties like oral activity, and analgesic activity in multiple chronic pain models. Notably, μOR-related hyperlocomotion and respiratory depression, and δOR-related convulsions, were not observed at analgesic doses of C6-Quino. This fundamentally new approach to designing δOR ligands provides a blueprint for the development of partial agonists as safe analgesics and acts as a generic method to optimize signaling profiles of other Class A GPCRs.
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Affiliation(s)
- Tao Che
- Washington University in St. Louis
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3
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Heinzke AL, Pahl A, Zdrazil B, Leach AR, Waldmann H, Young RJ, Leeson PD. Occurrence of "Natural Selection" in Successful Small Molecule Drug Discovery. J Med Chem 2024; 67:11226-11241. [PMID: 38949112 PMCID: PMC11247505 DOI: 10.1021/acs.jmedchem.4c00811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/08/2024] [Accepted: 06/13/2024] [Indexed: 07/02/2024]
Abstract
Published compounds from ChEMBL version 32 are used to seek evidence for the occurrence of "natural selection" in drug discovery. Three measures of natural product (NP) character were applied, to compare time- and target-matched compounds reaching the clinic (clinical compounds in phase 1-3 development and approved drugs) with background compounds (reference compounds). Pseudo-NPs (PNPs), containing NP fragments combined in ways inaccessible by nature, are increasing over time, reaching 67% of clinical compounds first disclosed since 2010. PNPs are 54% more likely to be found in post-2008 clinical versus reference compounds. The majority of target classes show increased clinical compound NP character versus their reference compounds. Only 176 NP fragments appear in >1000 clinical compounds published since 2008, yet these make up on average 63% of the clinical compound's core scaffolds. There is untapped potential awaiting exploitation, by applying nature's building blocks─"natural intelligence"─to drug design.
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Affiliation(s)
- A. Lina Heinzke
- European
Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridgeshire, U.K.
| | - Axel Pahl
- Compound
Management and Screening Center, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Barbara Zdrazil
- European
Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridgeshire, U.K.
| | - Andrew R. Leach
- European
Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridgeshire, U.K.
| | - Herbert Waldmann
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
- Faculty
of Chemistry and Chemical Biology, Technical
University Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | | | - Paul D. Leeson
- Paul Leeson
Consulting Ltd., Nuneaton CV13 6LZ, Warwickshire, U.K.
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4
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Szwabowski GL, Griffing M, Mugabe EJ, O’Malley D, Baker LN, Baker DL, Parrill AL. G Protein-Coupled Receptor-Ligand Pose and Functional Class Prediction. Int J Mol Sci 2024; 25:6876. [PMID: 38999982 PMCID: PMC11241240 DOI: 10.3390/ijms25136876] [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: 05/24/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
G protein-coupled receptor (GPCR) transmembrane protein family members play essential roles in physiology. Numerous pharmaceuticals target GPCRs, and many drug discovery programs utilize virtual screening (VS) against GPCR targets. Improvements in the accuracy of predicting new molecules that bind to and either activate or inhibit GPCR function would accelerate such drug discovery programs. This work addresses two significant research questions. First, do ligand interaction fingerprints provide a substantial advantage over automated methods of binding site selection for classical docking? Second, can the functional status of prospective screening candidates be predicted from ligand interaction fingerprints using a random forest classifier? Ligand interaction fingerprints were found to offer modest advantages in sampling accurate poses, but no substantial advantage in the final set of top-ranked poses after scoring, and, thus, were not used in the generation of the ligand-receptor complexes used to train and test the random forest classifier. A binary classifier which treated agonists, antagonists, and inverse agonists as active and all other ligands as inactive proved highly effective in ligand function prediction in an external test set of GPR31 and TAAR2 candidate ligands with a hit rate of 82.6% actual actives within the set of predicted actives.
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Affiliation(s)
| | | | | | | | | | - Daniel L. Baker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA; (G.L.S.); (M.G.); (E.J.M.); (D.O.); (L.N.B.)
| | - Abby L. Parrill
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA; (G.L.S.); (M.G.); (E.J.M.); (D.O.); (L.N.B.)
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5
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Pan B, Guo C, Liu D, Wüthrich K. Fluorine-19 labeling of the tryptophan residues in the G protein-coupled receptor NK1R using the 5-fluoroindole precursor in Pichia pastoris expression. JOURNAL OF BIOMOLECULAR NMR 2024:10.1007/s10858-024-00439-6. [PMID: 38554216 DOI: 10.1007/s10858-024-00439-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/16/2024] [Indexed: 04/01/2024]
Abstract
In NMR spectroscopy of biomolecular systems, the use of fluorine-19 probes benefits from a clean background and high sensitivity. Therefore, 19F-labeling procedures are of wide-spread interest. Here, we use 5-fluoroindole as a precursor for cost-effective residue-specific introduction of 5-fluorotryptophan (5F-Trp) into G protein-coupled receptors (GPCRs) expressed in Pichia pastoris. The method was successfully implemented with the neurokinin 1 receptor (NK1R). The 19F-NMR spectra of 5F-Trp-labeled NK1R showed one well-separated high field-shifted resonance, which was assigned by mutational studies to the "toggle switch tryptophan". Residue-selective labeling thus enables site-specific investigations of this functionally important residue. The method described here is inexpensive, requires minimal genetic manipulation and can be expected to be applicable for yeast expression of GPCRs at large.
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Affiliation(s)
- Benxun Pan
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Canyong Guo
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Dongsheng Liu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Kurt Wüthrich
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, 92037, USA.
- Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, Zürich, 8093, Switzerland.
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6
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Hong X, Ma J, Zheng S, Zhao G, Fu C. Advances in the research and application of neurokinin-1 receptor antagonists. J Zhejiang Univ Sci B 2024; 25:91-105. [PMID: 38303494 PMCID: PMC10835208 DOI: 10.1631/jzus.b2300455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 09/07/2023] [Indexed: 02/03/2024]
Abstract
Recently, the substance P (SP)/neurokinin-1 receptor (NK-1R) system has been found to be involved in various human pathophysiological disorders including the symptoms of coronavirus disease 2019 (COVID-19). Besides, studies in the oncological field have demonstrated an intricate correlation between the upregulation of NK-1R and the activation of SP/NK-1R system with the progression of multiple carcinoma types and poor clinical prognosis. These findings indicate that the modulation of SP/NK-1R system with NK-1R antagonists can be a potential broad-spectrum antitumor strategy. This review updates the latest potential and applications of NK-1R antagonists in the treatment of human diseases and cancers, as well as the underlying mechanisms. Furthermore, the strategies to improve the bioavailability and efficacy of NK-1R antagonist drugs are summarized, such as solid dispersion systems, nanonization, and nanoencapsulation. As a radiopharmaceutical therapeutic, the NK-1R antagonist aprepitant was originally developed as radioligand receptor to target NK-1R-overexpressing tumors. However, combining NK-1R antagonists with other drugs can produce a synergistic effect, thereby enhancing the therapeutic effect, alleviating the symptoms, and improving patients quality of life in several diseases and cancers.
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Affiliation(s)
- Xiangyu Hong
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Junjie Ma
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Shanshan Zheng
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Guangyu Zhao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Caiyun Fu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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7
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Soltani A, Hashemy SI. Homology modeling, virtual screening, molecular docking, and ADME approaches to identify a potent agent targeting NK2R protein. Biotechnol Appl Biochem 2024; 71:213-222. [PMID: 37904319 DOI: 10.1002/bab.2533] [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: 12/03/2022] [Accepted: 08/24/2023] [Indexed: 11/01/2023]
Abstract
Neurokinin/tachykinin receptors are classified as the G-protein coupled receptor superfamily. The neurokinin 2 receptor (NK2R) is widely expressed in different tissues. NK2R is associated with a range of biological events, such as inflammation, smooth muscle contraction, intestinal motor functions, and asthma. Despite these diverse activities, no approved drugs targeting NK2R have been developed yet. Our study focuses on finding potential inhibitors for NK2R using virtual screening, molecular docking, and ADME (absorption, distribution, metabolism, and excretion) approaches. We used a homology modeling approach and AlphaFold DB to obtain the three-dimensional structure of mouse and human NK2R proteins, respectively. The homology model of NK2R was predicted using MODELLER v10.3 and further refined and validated using the 3Drefine tool and RAMPAGE server, respectively. Molecular docking was performed using a library of 910 structurally similar molecules to four NK1R antagonists: aprepitant, casopitant, fosaprepitant, and rolapitant. Molecular docking revealed six small molecules that displayed high Chemscore fitness scores, and binding energies with desirable ligand-NK2R interactions. The evaluation of the in silico ADME profile, solubility, and permeability of the ligand molecules has revealed that the small molecules are potentially nontoxic and have the chance of exhibiting biological activity after oral administration. Further experimental studies (in vitro and in vivo assays) are required to evaluate the effectiveness of these inhibitors as therapeutic targets.
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Affiliation(s)
- Arash Soltani
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Isaac Hashemy
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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8
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Madsen JJ, Petersen JE, Christensen DP, Hansen JB, Schwartz TW, Frimurer TM, Olsen OH. Deciphering specificity and cross-reactivity in tachykinin NK1 and NK2 receptors. J Biol Chem 2023; 299:105438. [PMID: 37944618 PMCID: PMC10724690 DOI: 10.1016/j.jbc.2023.105438] [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: 09/03/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
The tachykinin receptors neurokinin 1 (NK1R) and neurokinin 2 (NK2R) are G protein-coupled receptors that bind preferentially to the natural peptide ligands substance P and neurokinin A, respectively, and have been targets for drug development. Despite sharing a common C-terminal sequence of Phe-X-Gly-Leu-Met-NH2 that helps direct biological function, the peptide ligands exhibit some degree of cross-reactivity toward each other's non-natural receptor. Here, we investigate the detailed structure-activity relationships of the ligand-bound receptor complexes that underlie both potent activation by the natural ligand and cross-reactivity. We find that the specificity and cross-reactivity of the peptide ligands can be explained by the interactions between the amino acids preceding the FxGLM consensus motif of the bound peptide ligand and two regions of the receptor: the β-hairpin of the extracellular loop 2 (ECL2) and a N-terminal segment leading into transmembrane helix 1. Positively charged sidechains of the ECL2 (R177 of NK1R and K180 of NK2R) are seen to play a vital role in the interaction. The N-terminal positions 1 to 3 of the peptide ligand are entirely dispensable. Mutated and chimeric receptor and ligand constructs neatly swap around ligand specificity as expected, validating the structure-activity hypotheses presented. These findings will help in developing improved agonists or antagonists for NK1R and NK2R.
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Affiliation(s)
- Jesper J Madsen
- Global and Planetary Health, College of Public Health, University of South Florida, Tampa, Florida, USA; Center for Global Health and Infectious Diseases Research, College of Public Health, University of South Florida, Tampa, Florida, USA; Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Jacob E Petersen
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Thue W Schwartz
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Thomas M Frimurer
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Ole H Olsen
- Section for Metabolic Receptology, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
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9
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Witoszka K, Matalińska J, Misicka A, Lipiński PFJ. Moving out of CF 3 -Land: Synthesis, Receptor Affinity, and in silico Studies of NK1 Receptor Ligands Containing a Pentafluorosulfanyl (SF 5 ) Group. ChemMedChem 2023; 18:e202300315. [PMID: 37821725 DOI: 10.1002/cmdc.202300315] [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: 06/17/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 10/13/2023]
Abstract
The NK1 receptor (NK1R) is a molecular target for both approved and experimental drugs intended for a variety of conditions, including emesis, pain, and cancers. While contemplating modifications to the typical NK1R pharmacophore, we wondered whether the CF3 groups common for many NK1R ligands, could be replaced with some other moiety. Our attention was drawn by the SF5 group, and so we designed, synthesized, and tested ten novel SF5 -containing compounds for NK1R affinity. All analogues exhibit detectable NK1R binding, with the best of them, compound 5 a, (3-bromo-5-(pentafluoro-λ6 -sulfanyl)benzyl acetyl-L-tryptophanate) binding only slightly worse (IC50 =34.3 nM) than the approved NK1R-targeting drug, aprepitant (IC50 =27.7 nM). Molecular docking provided structural explanation of SAR. According to our analysis, the SF5 group in our compounds occupies a position similar to that of one of the CF3 groups of aprepitant as found in the crystal structure. Additionally, we checked whether the docking scoring function or energies derived from Fragment Molecular Orbital quantum chemical calculations may be helpful in explaining and predicting the experimental receptor affinities for our analogues. Both these methods produce moderately good results. Overall, this is the first demonstration of the utility of the SF5 group in the design of NK1R ligands.
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Affiliation(s)
- Katarzyna Witoszka
- Department of Neuropeptides, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
| | - Joanna Matalińska
- Department of Neuropeptides, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
| | - Aleksandra Misicka
- Department of Neuropeptides, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
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10
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Coveñas R, Rodríguez FD, Robinson P, Muñoz M. The Repurposing of Non-Peptide Neurokinin-1 Receptor Antagonists as Antitumor Drugs: An Urgent Challenge for Aprepitant. Int J Mol Sci 2023; 24:15936. [PMID: 37958914 PMCID: PMC10650658 DOI: 10.3390/ijms242115936] [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: 09/24/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
The substance P (SP)/neurokinin-1 receptor (NK-1R) system is involved in cancer progression. NK-1R, activated by SP, promotes tumor cell proliferation and migration, angiogenesis, the Warburg effect, and the prevention of apoptosis. Tumor cells overexpress NK-1R, which influences their viability. A typical specific anticancer strategy using NK-1R antagonists, irrespective of the tumor type, is possible because these antagonists block all the effects mentioned above mediated by SP on cancer cells. This review will update the information regarding using NK-1R antagonists, particularly Aprepitant, as an anticancer drug. Aprepitant shows a broad-spectrum anticancer effect against many tumor types. Aprepitant alone or in combination therapy with radiotherapy or chemotherapy could reduce the sequelae and increase the cure rate and quality of life of patients with cancer. Current data open the door to new cancer research aimed at antitumor therapeutic strategies using Aprepitant. To achieve this goal, reprofiling the antiemetic Aprepitant as an anticancer drug is urgently needed.
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Affiliation(s)
- Rafael Coveñas
- Laboratory of Neuroanatomy of the Peptidergic Systems, Institute of Neurosciences of Castilla y León (INCYL), University of Salamanca, 37007 Salamanca, Spain;
- Group GIR-BMD (Bases Moleculares del Desarrollo), University of Salamanca, 37007 Salamanca, Spain;
| | - Francisco D. Rodríguez
- Group GIR-BMD (Bases Moleculares del Desarrollo), University of Salamanca, 37007 Salamanca, Spain;
- Department of Biochemistry and Molecular Biology, Faculty of Chemical Sciences, University of Salamanca, 37007 Salamanca, Spain
| | - Prema Robinson
- Department of Infectious Diseases, Infection Control, and Employee Health, MD Anderson Cancer Center, The University of Texas, Houston, TX 77030, USA
| | - Miguel Muñoz
- Pediatric Intensive Care Unit, Research Laboratory on Neuropeptides (IBIS), Virgen del Rocío University Hospital, 41013 Seville, Spain;
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11
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Maurer SK, Mayer MP, Ward SJ, Boudjema S, Halawa M, Zhang J, Caulton SG, Emsley J, Dreveny I. Ubiquitin-specific protease 11 structure in complex with an engineered substrate mimetic reveals a molecular feature for deubiquitination selectivity. J Biol Chem 2023; 299:105300. [PMID: 37777157 PMCID: PMC10637973 DOI: 10.1016/j.jbc.2023.105300] [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: 05/22/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/02/2023] Open
Abstract
Ubiquitin-specific proteases (USPs) are crucial for controlling cellular proteostasis and signaling pathways but how deubiquitination is selective remains poorly understood, in particular between paralogues. Here, we developed a fusion tag method by mining the Protein Data Bank and trapped USP11, a key regulator of DNA double-strand break repair, in complex with a novel engineered substrate mimetic. Together, this enabled structure determination of USP11 as a Michaelis-like complex that revealed key S1 and S1' binding site interactions with a substrate. Combined mutational, enzymatic, and binding experiments identified Met77 in linear diubiquitin as a significant residue that leads to substrate discrimination. We identified an aspartate "gatekeeper" residue in the S1' site of USP11 as a contributing feature for discriminating against linear diubiquitin. When mutated to a glycine, the corresponding residue in paralog USP15, USP11 acquired elevated activity toward linear diubiquitin in-gel shift assays, but not controls. The reverse mutation in USP15 confirmed that this position confers paralog-specific differences impacting diubiquitin cleavage rates. The results advance our understanding of the molecular basis for the higher selectivity of USP11 compared to USP15 and may aid targeted inhibitor development. Moreover, the reported carrier-based crystallization strategy may be applicable to other challenging targets.
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Affiliation(s)
- Sigrun K Maurer
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Matthias P Mayer
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Stephanie J Ward
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Sana Boudjema
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Mohamed Halawa
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Jiatong Zhang
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Simon G Caulton
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Jonas Emsley
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Ingrid Dreveny
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom.
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12
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Mishra S, Rout M, Singh MK, Dehury B, Pati S. Illuminating the structural basis of human neurokinin 1 receptor (NK1R) antagonism through classical all-atoms molecular dynamics simulations. J Cell Biochem 2023; 124:1848-1869. [PMID: 37942587 DOI: 10.1002/jcb.30493] [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: 07/13/2023] [Revised: 09/26/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023]
Abstract
Advances in structural biology have bestowed insights into the pleiotropic effects of neurokinin 1 receptors (NK1R) in diverse patho-physiological processes, thereby highlighting the potential therapeutic value of antagonists directed against NK1R. Herein, we investigate the mode of antagonist recognition to discern the obscure atomic facets germane for the function and molecular determinants of NK1R. To commence discernment of potent antagonists and the conformational changes in NK1R, induced upon antagonist binding, state-of-the-art classical all-atoms molecular dynamics (MD) simulations in lipid mimetic bilayers have been utilized. MD simulations of structural ensembles reveals the involvement of TM5 and TM6 in tight anchoring of antagonists through a network of interhelical hydrogen-bonds, while, the extracellular loop 2 (ECL2) governs the overall size and nature of the pocket, thereby modulating NK1R. Consistent comparison between experiments and MD simulation results discerns the predominant role of TM3, TM4, and TM6 in lipid-NK1R interaction. Correlation between hydrophobic index and helicity of TM domains elucidates their importance in maintaining the structural stability in addition to regulating NK1R antagonism. Taken together, we anticipate that our computational study marks a comprehensive structural basis of NK1R antagonism in lipid bilayers, which may facilitate designing of new therapeutics against associated diseases targeting human neurokinin receptors.
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Affiliation(s)
- Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Mahender Kumar Singh
- Data Science Laboratory, National Brain Research Centre, Gurgaon, Haryana, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
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13
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Hegron A, Peach CJ, Tonello R, Seemann P, Teng S, Latorre R, Huebner H, Weikert D, Rientjes J, Veldhuis NA, Poole DP, Jensen DD, Thomsen ARB, Schmidt BL, Imlach WL, Gmeiner P, Bunnett NW. Therapeutic antagonism of the neurokinin 1 receptor in endosomes provides sustained pain relief. Proc Natl Acad Sci U S A 2023; 120:e2220979120. [PMID: 37216510 PMCID: PMC10235985 DOI: 10.1073/pnas.2220979120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/04/2023] [Indexed: 05/24/2023] Open
Abstract
The hypothesis that sustained G protein-coupled receptor (GPCR) signaling from endosomes mediates pain is based on studies with endocytosis inhibitors and lipid-conjugated or nanoparticle-encapsulated antagonists targeted to endosomes. GPCR antagonists that reverse sustained endosomal signaling and nociception are needed. However, the criteria for rational design of such compounds are ill-defined. Moreover, the role of natural GPCR variants, which exhibit aberrant signaling and endosomal trafficking, in maintaining pain is unknown. Herein, substance P (SP) was found to evoke clathrin-mediated assembly of endosomal signaling complexes comprising neurokinin 1 receptor (NK1R), Gαq/i, and βarrestin-2. Whereas the FDA-approved NK1R antagonist aprepitant induced a transient disruption of endosomal signals, analogs of netupitant designed to penetrate membranes and persist in acidic endosomes through altered lipophilicity and pKa caused sustained inhibition of endosomal signals. When injected intrathecally to target spinal NK1R+ve neurons in knockin mice expressing human NK1R, aprepitant transiently inhibited nociceptive responses to intraplantar injection of capsaicin. Conversely, netupitant analogs had more potent, efficacious, and sustained antinociceptive effects. Mice expressing C-terminally truncated human NK1R, corresponding to a natural variant with aberrant signaling and trafficking, displayed attenuated SP-evoked excitation of spinal neurons and blunted nociceptive responses to SP. Thus, sustained antagonism of the NK1R in endosomes correlates with long-lasting antinociception, and domains within the C-terminus of the NK1R are necessary for the full pronociceptive actions of SP. The results support the hypothesis that endosomal signaling of GPCRs mediates nociception and provides insight into strategies for antagonizing GPCRs in intracellular locations for the treatment of diverse diseases.
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Affiliation(s)
- Alan Hegron
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University, New York, NY10010
- Pain Research Center, College of Dentistry, New York University, New York, NY10010
| | - Chloe J. Peach
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University, New York, NY10010
- Pain Research Center, College of Dentistry, New York University, New York, NY10010
| | - Raquel Tonello
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University, New York, NY10010
- Pain Research Center, College of Dentistry, New York University, New York, NY10010
| | - Philipp Seemann
- Department of Chemistry and Pharmacy, Friedrich-Alexander Universität Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Shavonne Teng
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University, New York, NY10010
- Pain Research Center, College of Dentistry, New York University, New York, NY10010
| | - Rocco Latorre
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University, New York, NY10010
- Pain Research Center, College of Dentistry, New York University, New York, NY10010
| | - Harald Huebner
- Department of Chemistry and Pharmacy, Friedrich-Alexander Universität Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Dorothee Weikert
- Department of Chemistry and Pharmacy, Friedrich-Alexander Universität Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Jeanette Rientjes
- Gene Modification Platform, Monash University, Clayton, VIC3168, Australia
| | - Nicholas A. Veldhuis
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC3052, Australia
| | - Daniel P. Poole
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC3052, Australia
| | - Dane D. Jensen
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University, New York, NY10010
- Pain Research Center, College of Dentistry, New York University, New York, NY10010
- NYU Dentistry Translational Research Center, College of Dentistry, New York University, New York, NY10010
| | - Alex R. B. Thomsen
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University, New York, NY10010
- Pain Research Center, College of Dentistry, New York University, New York, NY10010
| | - Brian L. Schmidt
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University, New York, NY10010
- Pain Research Center, College of Dentistry, New York University, New York, NY10010
- NYU Dentistry Translational Research Center, College of Dentistry, New York University, New York, NY10010
| | - Wendy L. Imlach
- Department of Physiology and Monash Biomedicine Discovery Institute, Monash University, VIC3800, Australia
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Friedrich-Alexander Universität Erlangen-Nürnberg, 91058, Erlangen, Germany
| | - Nigel W. Bunnett
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY10010
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University, New York, NY10010
- Pain Research Center, College of Dentistry, New York University, New York, NY10010
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14
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Ye L, Yang Y, Li C, Zhang J, Wang W, Ma M, Xu H, Zhang W, Zou F, Hu Z, Wang H, Tian J. Synthesis and evaluation of piperazinotriazoles. Discovery of a potent and orally bioavailable neurokinin-3 receptor inhibitor. Eur J Med Chem 2023; 257:115486. [PMID: 37247507 DOI: 10.1016/j.ejmech.2023.115486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/31/2023]
Abstract
The neurokinin-3 receptor (NK3R) is one of three receptors that recognize neurokinins. The finding that pharmacological blockade of neurokinin B (NKB) signaling with an oral NK3R antagonist can significantly improve hot flash symptoms independent of any hormonal effect fits strongly suggest that NK3R is a viable drug target and that drugs targeting this receptor could be novel pharmacotherapies. Currently no NK3R ligands have been approved for the treatment of human disorders. Herein, we designed and synthesized a series of novel imidazolepiperazine derivatives (16a-16x, 20a-20f, 29a-29m) and performed molecular docking to confirm the design, among which the target compound 16x exhibited promising inhibitory activity against NK3R (IC50 = 430.60 nM) with excellent membrane permeability (Papp, A-B = 37.6 × 10-6 cm/s, ER < 1) and oral bioavailability (F% = 93.6%). Our in vivo studies demonstrated that 16x was orally active, efficacious, and well-tolerated in ovariectomy (OVX) model to suppress blood luteinizing hormone levels, which suggests that 16x is a viable lead compound for further optimization and development.
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Affiliation(s)
- Liang Ye
- School of Public Health and Management, Binzhou Medical University, Yantai, PR China.
| | - Yifei Yang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, 264005, PR China
| | - Chunmei Li
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, 264005, PR China
| | - Jianzhao Zhang
- College of Life Sciences, Yantai University, Yantai, Shangdong, 264005, PR China
| | - Wenyan Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, 264005, PR China
| | - Mingxu Ma
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, 264005, PR China
| | - Hengwei Xu
- R & D Center, Luye Pharma Group Ltd., Yantai, 264003, PR China
| | - Wenjing Zhang
- R & D Center, Luye Pharma Group Ltd., Yantai, 264003, PR China
| | - Fangxia Zou
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, 264005, PR China
| | - Zhengping Hu
- Medicine & Pharmacy Research Center, Binzhou Medical University, Yantai, PR China
| | - Hongbo Wang
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, 264005, PR China.
| | - Jingwei Tian
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, 264005, PR China.
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15
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Martins MS, Almeida IF, Cruz MT, Sousa E. Chronic pruritus: from pathophysiology to drug design. Biochem Pharmacol 2023; 212:115568. [PMID: 37116666 DOI: 10.1016/j.bcp.2023.115568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/30/2023]
Abstract
Pruritus, the most common symptom in dermatology, is an innate response capable of protecting skin against irritants. Nonetheless, when it lasts more than six weeks it is assumed to be a chronic pathology having a negative impact on people's lives. Chronic pruritus (CP) can occur in common and rare skin diseases, having a high prevalence in global population. The existing therapies are unable to counteract CP or are associated with adverse effects, so the development of effective treatments is a pressing issue. The pathophysiological mechanisms underlying CP are not yet completely dissected but, based on current knowledge, involve a wide range of receptors, namely neurokinin 1 receptor (NK1R), Janus kinase (JAK), and transient receptor potential (TRP) ion channels, especially transient receptor potential vanilloid 1 (TRPV1) and transient receptor potential ankyrin 1 (TRPA1). This review will address the relevance of these molecular targets for the treatment of CP and molecules capable of modulating these receptors that have already been studied clinically or have the potential to possibly alleviate this pathology. According to scientific and clinical literature, there is an increase in the expression of these molecular targets in the lesioned skin of patients experiencing CP when compared with non-lesioned skin, highlighting their importance for the development of potential efficacious drugs through the design of antagonists/inhibitors.
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Affiliation(s)
- Márcia S Martins
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal; Laboratory of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Isaobel F Almeida
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; UCIBIO-Applied Molecular Biosciences Unit, MedTech, Laboratory of Pharmaceutical Technology, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal.
| | - Maria T Cruz
- CNC-Center for Neuroscience and Cell Biology, CIBB-Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Emília Sousa
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, 4450-208 Matosinhos, Portugal; Laboratory of Organic and Pharmaceutical Chemistry, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal.
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16
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Liessmann F, Künze G, Meiler J. Improving the Modeling of Extracellular Ligand Binding Pockets in RosettaGPCR for Conformational Selection. Int J Mol Sci 2023; 24:7788. [PMID: 37175495 PMCID: PMC10178219 DOI: 10.3390/ijms24097788] [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: 04/03/2023] [Revised: 04/19/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of drug targets and undergo substantial conformational changes in response to ligand binding. Despite recent progress in GPCR structure determination, static snapshots fail to reflect the conformational space of putative binding pocket geometries to which small molecule ligands can bind. In comparative modeling of GPCRs in the absence of a ligand, often a shrinking of the orthosteric binding pocket is observed. However, the exact prediction of the flexible orthosteric binding site is crucial for adequate structure-based drug discovery. In order to improve ligand docking and guide virtual screening experiments in computer-aided drug discovery, we developed RosettaGPCRPocketSize. The algorithm creates a conformational ensemble of biophysically realistic conformations of the GPCR binding pocket between the TM bundle, which is consistent with a knowledge base of expected pocket geometries. Specifically, tetrahedral volume restraints are defined based on information about critical residues in the orthosteric binding site and their experimentally observed range of Cα-Cα-distances. The output of RosettaGPCRPocketSize is an ensemble of binding pocket geometries that are filtered by energy to ensure biophysically probable arrangements, which can be used for docking simulations. In a benchmark set, pocket shrinkage observed in the default RosettaGPCR was reduced by up to 80% and the binding pocket volume range and geometric diversity were increased. Compared to models from four different GPCR homology model databases (RosettaGPCR, GPCR-Tasser, GPCR-SSFE, and GPCRdb), the here-created models showed more accurate volumes of the orthosteric pocket when evaluated with respect to the crystallographic reference structure. Furthermore, RosettaGPCRPocketSize was able to generate an improved realistic pocket distribution. However, while being superior to other homology models, the accuracy of generated model pockets was comparable to AlphaFold2 models. Furthermore, in a docking benchmark using small-molecule ligands with a higher molecular weight between 400 and 700 Da, a higher success rate in creating native-like binding poses was observed. In summary, RosettaGPCRPocketSize can generate GPCR models with realistic orthosteric pocket volumes, which are useful for structure-based drug discovery applications.
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Affiliation(s)
- Fabian Liessmann
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
| | - Georg Künze
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
| | - Jens Meiler
- Institute for Drug Discovery, Medical Faculty, Leipzig University, 04103 Leipzig, Germany; (F.L.)
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37235, USA
- Center for Scalable Data Analytics and Artificial Intelligence, Leipzig University, 04105 Leipzig, Germany
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17
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Vinay CM, Mehta CH, Bhat C, Kamath A, B Joshi M, Paul B, Nayak UY, Rai PS. Integrated LC-MS/MS and network pharmacology approach for predictingactive ingredients and pharmacological mechanisms of Tribulus terrestris L. against cardiac diseases. J Biomol Struct Dyn 2023; 41:11930-11945. [PMID: 37042962 DOI: 10.1080/07391102.2023.2199076] [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: 08/29/2022] [Accepted: 12/24/2022] [Indexed: 04/13/2023]
Abstract
Tribulus terrestris L. (Gokshura) is a medicinal herb used for treating cardiac diseases and several other diseases. However, the active ingredients and the possible mechanism of action for treating cardiac diseases remain unclear. Hence, the study was designed to identify the active ingredients and to explore the potential mechanism of action of Tribulus terrestris L. for treating cardiac diseases by an integrated approach of metabolomics and network pharmacology. We performed HPLC-QTOF-MS/MS analysis to identify putative compounds and network pharmacology approach for predictive key targets and pathways. Using molecular docking and molecular dynamics simulation, we identified the active ingredients in Tribulus terrestris L. that can act as putative lead compounds to treat cardiac diseases. A total of 55 putative compounds were identified using methanolic extract of Tribulus terrestris L. using HPLC-QTOF-MS/MS analysis. Network pharmacology analysis predicted 32 human protein targets from 25 secondary metabolites, which have shown direct interaction with cardiac diseases. Based on the degrees of interaction, the hub targets such as TACR1, F2, F2R, ADRA1B, CHRM5, ADRA1A, ADRA1D, HTR2B, and AVPR1A were identified. In silico molecular docking and simulation resulted in the identification of active ingredients such as Kaempferol 3-rutinoside 7-glucuronide, Keioside, rutin, moupinamide, aurantiamide, quercetin-3-o-α-rhamnoside, tribuloside, and 3'',6''- Di-O-p-coumaroyltrifolin against hub protein targets. Hence, these compounds could be potential lead compounds for treating cardiac diseases. A further assessment of its efficacy can be made based on in vivo and in vitro studies for better understanding and strong assertion.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chigateri M Vinay
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Chetan Hasmukh Mehta
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Chandrakanth Bhat
- Department of Dravyaguna, Muniyal Institute of Ayurveda Medical Sciences, Manipal, India
| | - Archana Kamath
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Manjunath B Joshi
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Bobby Paul
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Usha Yogendra Nayak
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Padmalatha S Rai
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, India
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18
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Klenk C, Scrivens M, Niederer A, Shi S, Mueller L, Gersz E, Zauderer M, Smith ES, Strohner R, Plückthun A. A Vaccinia-based system for directed evolution of GPCRs in mammalian cells. Nat Commun 2023; 14:1770. [PMID: 36997531 PMCID: PMC10063554 DOI: 10.1038/s41467-023-37191-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/06/2023] [Indexed: 04/03/2023] Open
Abstract
Directed evolution in bacterial or yeast display systems has been successfully used to improve stability and expression of G protein-coupled receptors for structural and biophysical studies. Yet, several receptors cannot be tackled in microbial systems due to their complex molecular composition or unfavorable ligand properties. Here, we report an approach to evolve G protein-coupled receptors in mammalian cells. To achieve clonality and uniform expression, we develop a viral transduction system based on Vaccinia virus. By rational design of synthetic DNA libraries, we first evolve neurotensin receptor 1 for high stability and expression. Second, we demonstrate that receptors with complex molecular architectures and large ligands, such as the parathyroid hormone 1 receptor, can be readily evolved. Importantly, functional receptor properties can now be evolved in the presence of the mammalian signaling environment, resulting in receptor variants exhibiting increased allosteric coupling between the ligand binding site and the G protein interface. Our approach thus provides insights into the intricate molecular interplay required for GPCR activation.
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Affiliation(s)
- Christoph Klenk
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| | - Maria Scrivens
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Anina Niederer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Shuying Shi
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Loretta Mueller
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Elaine Gersz
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Maurice Zauderer
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Ernest S Smith
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Ralf Strohner
- MorphoSys AG, Semmelweisstr. 7, 82152, Planegg, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
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19
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Matalińska J, Lipiński PFJ. Docking is not enough: 17-trifluoromethylphenyl trinor PGF2α is only a very weak ligand of neurokinin-1 receptor. Exp Mol Pathol 2023; 129:104849. [PMID: 36526011 DOI: 10.1016/j.yexmp.2022.104849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
17-trifluoromethylphenyl trinor prostaglandin F2α (17-CF3PTPGF2α) was reported recently to exhibit in vitro and in vivo anticancer activity. Based solely on the results of in silico molecular docking, it was claimed that this compound is NK1 receptor (NK1R) antagonist and that its activity is through this receptor. In this contribution we show that 17-CF3PTPGF2α is only a very weak NK1R ligand (IC50 > 200 μM). In connection with that we discuss the issue of this compound's molecular target. Finally, we briefly narrate on the proper use of molecular docking in biomedical research.
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Affiliation(s)
- Joanna Matalińska
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106, Warsaw, Poland.
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, 5 Pawińskiego Street, PL 02-106, Warsaw, Poland.
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20
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Faouzi A, Wang H, Zaidi SA, DiBerto JF, Che T, Qu Q, Robertson MJ, Madasu MK, El Daibani A, Varga BR, Zhang T, Ruiz C, Liu S, Xu J, Appourchaux K, Slocum ST, Eans SO, Cameron MD, Al-Hasani R, Pan YX, Roth BL, McLaughlin JP, Skiniotis G, Katritch V, Kobilka BK, Majumdar S. Structure-based design of bitopic ligands for the µ-opioid receptor. Nature 2023; 613:767-774. [PMID: 36450356 PMCID: PMC10328120 DOI: 10.1038/s41586-022-05588-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022]
Abstract
Mu-opioid receptor (µOR) agonists such as fentanyl have long been used for pain management, but are considered a major public health concern owing to their adverse side effects, including lethal overdose1. Here, in an effort to design safer therapeutic agents, we report an approach targeting a conserved sodium ion-binding site2 found in µOR3 and many other class A G-protein-coupled receptors with bitopic fentanyl derivatives that are functionalized via a linker with a positively charged guanidino group. Cryo-electron microscopy structures of the most potent bitopic ligands in complex with µOR highlight the key interactions between the guanidine of the ligands and the key Asp2.50 residue in the Na+ site. Two bitopics (C5 and C6 guano) maintain nanomolar potency and high efficacy at Gi subtypes and show strongly reduced arrestin recruitment-one (C6 guano) also shows the lowest Gz efficacy among the panel of µOR agonists, including partial and biased morphinan and fentanyl analogues. In mice, C6 guano displayed µOR-dependent antinociception with attenuated adverse effects, supporting the µOR sodium ion-binding site as a potential target for the design of safer analgesics. In general, our study suggests that bitopic ligands that engage the sodium ion-binding pocket in class A G-protein-coupled receptors can be designed to control their efficacy and functional selectivity profiles for Gi, Go and Gz subtypes and arrestins, thus modulating their in vivo pharmacology.
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MESH Headings
- Animals
- Mice
- Analgesics, Opioid/chemistry
- Analgesics, Opioid/metabolism
- Arrestins/metabolism
- Cryoelectron Microscopy
- Fentanyl/analogs & derivatives
- Fentanyl/chemistry
- Fentanyl/metabolism
- Ligands
- Morphinans/chemistry
- Morphinans/metabolism
- Receptors, Opioid, mu/agonists
- Receptors, Opioid, mu/chemistry
- Receptors, Opioid, mu/metabolism
- Receptors, Opioid, mu/ultrastructure
- Binding Sites
- Nociception
- Drug Design
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Affiliation(s)
- Abdelfattah Faouzi
- Center for Clinical Pharmacology, University of Health Sciences and Pharmacy and Washington University School of Medicine, St Louis, MO, USA
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Saheem A Zaidi
- Department of Quantitative and Computational Biology, Department of Chemistry, Bridge Institute and Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA
| | - Jeffrey F DiBerto
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Tao Che
- Center for Clinical Pharmacology, University of Health Sciences and Pharmacy and Washington University School of Medicine, St Louis, MO, USA
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Qianhui Qu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Robertson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Manish K Madasu
- Center for Clinical Pharmacology, University of Health Sciences and Pharmacy and Washington University School of Medicine, St Louis, MO, USA
| | - Amal El Daibani
- Center for Clinical Pharmacology, University of Health Sciences and Pharmacy and Washington University School of Medicine, St Louis, MO, USA
| | - Balazs R Varga
- Center for Clinical Pharmacology, University of Health Sciences and Pharmacy and Washington University School of Medicine, St Louis, MO, USA
| | - Tiffany Zhang
- Department of Neurology and Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Claudia Ruiz
- Department of Chemistry, Scripps Research, Jupiter, FL, USA
| | - Shan Liu
- Department of Anesthesiology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Jin Xu
- Department of Anesthesiology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Kevin Appourchaux
- Center for Clinical Pharmacology, University of Health Sciences and Pharmacy and Washington University School of Medicine, St Louis, MO, USA
| | - Samuel T Slocum
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Shainnel O Eans
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | | | - Ream Al-Hasani
- Center for Clinical Pharmacology, University of Health Sciences and Pharmacy and Washington University School of Medicine, St Louis, MO, USA
| | - Ying Xian Pan
- Department of Neurology and Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Anesthesiology, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jay P McLaughlin
- Department of Pharmacodynamics, University of Florida, Gainesville, FL, USA
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Vsevolod Katritch
- Department of Quantitative and Computational Biology, Department of Chemistry, Bridge Institute and Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA.
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Susruta Majumdar
- Center for Clinical Pharmacology, University of Health Sciences and Pharmacy and Washington University School of Medicine, St Louis, MO, USA.
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21
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Okladnikov I, Boyko Y, Nelyubina Y, Ioffe S, Sukhorukov A. Asymmetric Synthesis of a Pyrrolizidinone‐Based hNK1 Antagonist through Reductive Ring Contraction of a Six‐Membered Cyclic Nitronate. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ilya Okladnikov
- Zelinsky Institute of Organic Chemistry RAS: Institut organiceskoj himii imeni N D Zelinskogo RAN Laboratory of organic and metal-organic nitrogen-oxygen systems RUSSIAN FEDERATION
| | - Yaroslav Boyko
- University of Illinois Urbana-Champaign Roger Adams Laboratory, Department of Chemistry UNITED STATES
| | - Yulia Nelyubina
- A N Nesmeyanov Institute of Organoelement Compounds RAS: Institut elementoorganiceskih soedinenij imeni A N Nesmeanova RAN Center for molecular composition studies RUSSIAN FEDERATION
| | - Sema Ioffe
- Zelinsky Institute of Organic Chemistry RAS: Institut organiceskoj himii imeni N D Zelinskogo RAN Laboratory of organic and metal-organic nitrogen-oxygen systems RUSSIAN FEDERATION
| | - Alexey Sukhorukov
- Zelinsky Institute of Organic Chemistry RAS: Institut organiceskoj himii imeni N D Zelinskogo RAN Laboratory of Organic and Metal-organic Nitrogen-oxygen Systems Leninsky prospect, 47 119991 Moscow RUSSIAN FEDERATION
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22
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Sustained endosomal release of a neurokinin-1 receptor antagonist from nanostars provides long-lasting relief of chronic pain. Biomaterials 2022; 285:121536. [PMID: 35533442 PMCID: PMC10064865 DOI: 10.1016/j.biomaterials.2022.121536] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/31/2022] [Accepted: 04/20/2022] [Indexed: 12/21/2022]
Abstract
Soft polymer nanoparticles designed to disassemble and release an antagonist of the neurokinin 1 receptor (NK1R) in endosomes provide efficacious yet transient relief from chronic pain. These micellar nanoparticles are unstable and rapidly release cargo, which may limit the duration of analgesia. We examined the efficacy of stable star polymer nanostars containing the NK1R antagonist aprepitant-amine for the treatment of chronic pain in mice. Nanostars continually released cargo for 24 h, trafficked through the endosomal system, and disrupted NK1R endosomal signaling. After intrathecal injection, nanostars accumulated in endosomes of spinal neurons. Nanostar-aprepitant reversed mechanical, thermal and cold allodynia and normalized nociceptive behavior more efficaciously than free aprepitant in preclinical models of neuropathic and inflammatory pain. Analgesia was maintained for >10 h. The sustained endosomal delivery of antagonists from slow-release nanostars provides effective and long-lasting reversal of chronic pain.
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23
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Liolios C, Patsis C, Lambrinidis G, Tzortzini E, Roscher M, Bauder-Wüst U, Kolocouris A, Kopka K. Investigation of Tumor Cells and Receptor-Ligand Simulation Models for the Development of PET Imaging Probes Targeting PSMA and GRPR and a Possible Crosstalk between the Two Receptors. Mol Pharm 2022; 19:2231-2247. [PMID: 35467350 DOI: 10.1021/acs.molpharmaceut.2c00070] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Prostate-specific membrane antigen (PSMA) and gastrin-releasing peptide receptor (GRPR) have both been used in nuclear medicine as targets for molecular imaging and therapy of prostate (PCa) and breast cancer (BCa). Three bioconjugate probes, the PSMA specific: [68Ga]Ga-1, ((HBED-CC)-Ahx-Lys-NH-CO-NH Glu or PSMA-11), the GRPR specific: [68Ga]Ga-2, ((HBED-CC)-4-amino-1-carboxymethyl piperidine-[D-Phe6, Sta13]BN(6-14), a bombesin (BN) analogue), and 3 (the BN analogue: 4-amino-1-carboxymethyl piperidine-[(R)-Phe6, Sta13]BN(6-14) connected with the fluorescent dye, BDP-FL), were synthesized and tested in vitro with PCa and BCa cell lines, more specifically, with PCa cells, PC-3 and LNCaP, with BCa cells, T47D, MDA-MB-231, and with the in-house created PSMA-overexpressing PC-3(PSMA), T47D(PSMA), and MDA-MB-231(PSMA). In addition, biomolecular simulations were conducted on the association of 1 and 2 with PSMA and GRPR. The PSMA overexpression resulted in an increase of cell-bound radioligand [68Ga]Ga-1 (PSMA) for PCa and BCa cells and also of [68Ga]Ga-2 (GRPR), especially in those cell lines already expressing GRPR. The results were confirmed by fluorescence-activated cell sorting with a PE-labeled PSMA-specific antibody and the fluorescence tracer 3. The docking calculations and molecular dynamics simulations showed how 1 enters the PSMA funnel region and how pharmacophore Glu-urea-Lys interacts with the arginine patch, the S1', and S1 subpockets by forming hydrogen and van der Waals bonds. The chelating moiety of 1, that is, HBED-CC, forms additional stabilizing hydrogen bonding and van der Waals interactions in the arene-binding site. Ligand 2 is diving into the GRPR transmembrane (TM) helical cavity, thereby forming hydrogen bonds through its amidated end, water-mediated hydrogen bonds, and π-π interactions. Our results provide valuable information regarding the molecular mechanisms involved in the interactions of 1 and 2 with PSMA and GRPR, which might be useful for the diagnostic imaging and therapy of PCa and BCa.
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Affiliation(s)
- Christos Liolios
- Division of Radiopharmaceutical Chemistry, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Radiochemical Studies Laboratory, INRASTES, N.C.S.R. "Demokritos", Agia Paraskevi Attikis, 15310 Athens, Greece.,Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Christos Patsis
- Division of Cell Plasticity and Epigenetic Remodelling, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.,Department of Translational Oncology, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - George Lambrinidis
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Mareike Roscher
- Division of Radiopharmaceutical Chemistry, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Ulrike Bauder-Wüst
- Division of Radiopharmaceutical Chemistry, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimioupolis-Zografou, 15771 Athens, Greece
| | - Klaus Kopka
- Institute of Radiopharmaceutical Cancer Research, Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Bautzner Landstraße 400, 01328 Dresden, Germany.,Faculty of Chemistry and Food Chemistry, School of Science, Technical University Dresden, Lebensmittelchemie Chemiegebäude, Raum 413 Bergstr. 66, 01069 Dresden, Germany
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24
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GPCR large-amplitude dynamics by 19F-NMR of aprepitant bound to the neurokinin 1 receptor. Proc Natl Acad Sci U S A 2022; 119:e2122682119. [PMID: 35377814 PMCID: PMC9169749 DOI: 10.1073/pnas.2122682119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Comparisons of G protein-coupled receptor (GPCR) complexes with agonists and antagonists based on X-ray crystallography and cryo-electron microscopy structure determinations show differences in the width of the orthosteric ligand binding groove over the range from 0.3 to 2.9 Å. Here, we show that there are transient structure fluctuations with amplitudes up to at least 6 Å. The experiments were performed with the neurokinin 1 receptor (NK1R), a GPCR of class A that is involved in inflammation, pain, and cancer. We used 19F-NMR observation of aprepitant, which is an approved drug that targets NK1R for the treatment of chemotherapy-induced nausea and vomiting. Aprepitant includes a bis-trifluoromethyl-phenyl ring attached with a single bond to the core of the molecule; 19F-NMR revealed 180° flipping motions of this ring about this bond. In the picture emerging from the 19F-NMR data, the GPCR transmembrane helices undergo large-scale floating motions in the lipid bilayer. The functional implication is of extensive promiscuity of initial ligand binding, primarily determined by size and shape of the ligand, with subsequent selection by unique interactions between atom groups of the ligand and the GPCR within the binding groove. This second step ensures the wide range of different efficacies documented for GPCR-targeting drugs. The NK1R data also provide a rationale for the observation that diffracting GPCR crystals are obtained for complexes with only very few of the ligands from libraries of approved drugs and lead compounds that bind to the receptors.
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25
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In Vitro Biological Evaluation of Aprepitant Based 177Lu-Radioconjugates. Pharmaceutics 2022; 14:pharmaceutics14030607. [PMID: 35335981 PMCID: PMC8949964 DOI: 10.3390/pharmaceutics14030607] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 12/27/2022] Open
Abstract
Currently, the search for promising NK1R-positive tumor-targeting radiopharmaceuticals based on the structure of small molecular antagonists of neurokinin-1 receptor can be observed. Following this trend, we continued our evaluation of aprepitant-based 177Lu-radioconjugates in terms of future oncological applications. For this purpose, three novel aprepitant homologues were synthesized to broaden the previously obtained derivative portfolio, functionalized with the DOTA chelator and labeled with 68Ga and 177Lu. The newly evaluated radioconjugates showed the intended significant increase in lipophilicity compared to the previous ones, while maintaining stability in the human serum. Then, in a receptor binding study to the human NK1 receptor, we compared the two series of 177Lu-radioconjugates of aprepitant with each other and with the reference Substance P derivative currently used in glioblastoma therapy, clearly indicating the high affinity and better binding capacity of the novel radioconjugates. The in vitro experimental results included in the presented study, supported by labeling optimization, radioconjugate characterization and docking modeling of new aprepitant-derived radioagents, confirm our assumptions about the usefulness of aprepitant as a NK1R targeting vector and point out the perspectives for the forthcoming first in vivo trials.
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26
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Lipiński PFJ, Matalińska J. Fentanyl Structure as a Scaffold for Opioid/Non-Opioid Multitarget Analgesics. Int J Mol Sci 2022; 23:ijms23052766. [PMID: 35269909 PMCID: PMC8910985 DOI: 10.3390/ijms23052766] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022] Open
Abstract
One of the strategies in the search for safe and effective analgesic drugs is the design of multitarget analgesics. Such compounds are intended to have high affinity and activity at more than one molecular target involved in pain modulation. In the present contribution we summarize the attempts in which fentanyl or its substructures were used as a μ-opioid receptor pharmacophoric fragment and a scaffold to which fragments related to non-opioid receptors were attached. The non-opioid ‘second’ targets included proteins as diverse as imidazoline I2 binding sites, CB1 cannabinoid receptor, NK1 tachykinin receptor, D2 dopamine receptor, cyclooxygenases, fatty acid amide hydrolase and monoacylglycerol lipase and σ1 receptor. Reviewing the individual attempts, we outline the chemistry, the obtained pharmacological properties and structure-activity relationships. Finally, we discuss the possible directions for future work.
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27
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Schöppe J, Ehrenmann J, Waltenspühl Y, Plückthun A. Universal platform for the generation of thermostabilized GPCRs that crystallize in LCP. Nat Protoc 2022; 17:698-726. [PMID: 35140409 DOI: 10.1038/s41596-021-00660-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/08/2021] [Indexed: 12/13/2022]
Abstract
Structural studies of G-protein-coupled receptors (GPCRs) are often limited by difficulties in obtaining well-diffracting crystals suitable for high-resolution structure determination. During the past decade, crystallization in lipidic cubic phase (LCP) has become the most successful and widely used technique for obtaining such crystals. Despite often intense efforts, many GPCRs remain refractory to crystallization, even if receptors can be purified in sufficient amounts. To address this issue, we have developed a highly efficient screening and stabilization strategy for GPCRs, based on a fluorescence thermal stability assay readout, which seems to correlate particularly well with those GPCR constructs that remain native during incorporation into the LCP. Detailed protocols are provided for rapid and cost-efficient mutant and construct generation using sequence- and ligation-independent cloning, high-throughput magnetic bead-based protein purification from small-scale expressions in mammalian cells, the screening and optimal combination of mutations for increased receptor thermostability and the rapid identification of suitable chimeric fusion protein constructs for successful crystallization in LCP. We exemplify the method on three receptors from two different classes: the neurokinin 1 receptor, the oxytocin receptor and the parathyroid hormone 1 receptor.
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Affiliation(s)
- Jendrik Schöppe
- Department of Biochemistry, University of Zürich, Zurich, Switzerland.,Novo Nordisk A/S, Måløv, Denmark
| | - Janosch Ehrenmann
- Department of Biochemistry, University of Zürich, Zurich, Switzerland.,leadXpro AG, PARK InnovAARE, Villigen, Switzerland
| | - Yann Waltenspühl
- Department of Biochemistry, University of Zürich, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Zurich, Switzerland.
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28
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Salim C, Kan AK, Batsaikhan E, Patterson EC, Jee C. Neuropeptidergic regulation of compulsive ethanol seeking in C. elegans. Sci Rep 2022; 12:1804. [PMID: 35110557 PMCID: PMC8810865 DOI: 10.1038/s41598-022-05256-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 01/07/2022] [Indexed: 11/09/2022] Open
Abstract
Despite the catastrophic consequences of alcohol abuse, alcohol use disorders (AUD) and comorbidities continue to strain the healthcare system, largely due to the effects of alcohol-seeking behavior. An improved understanding of the molecular basis of alcohol seeking will lead to enriched treatments for these disorders. Compulsive alcohol seeking is characterized by an imbalance between the superior drive to consume alcohol and the disruption or erosion in control of alcohol use. To model the development of compulsive engagement in alcohol seeking, we simultaneously exploited two distinct and conflicting Caenorhabditis elegans behavioral programs, ethanol preference and avoidance of aversive stimulus. We demonstrate that the C. elegans model recapitulated the pivotal features of compulsive alcohol seeking in mammals, specifically repeated attempts, endurance, and finally aversion-resistant alcohol seeking. We found that neuropeptide signaling via SEB-3, a CRF receptor-like GPCR, facilitates the development of ethanol preference and compels animals to seek ethanol compulsively. Furthermore, our functional genomic approach and behavioral elucidation suggest that the SEB-3 regulates another neuropeptidergic signaling, the neurokinin receptor orthologue TKR-1, to facilitate compulsive ethanol-seeking behavior.
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Affiliation(s)
- Chinnu Salim
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center (UTHSC), 71 S. Manassas St., Suite 217, Memphis, TN, 38103, USA
| | - Ann Ke Kan
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center (UTHSC), 71 S. Manassas St., Suite 217, Memphis, TN, 38103, USA
| | - Enkhzul Batsaikhan
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center (UTHSC), 71 S. Manassas St., Suite 217, Memphis, TN, 38103, USA
| | - E Clare Patterson
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center (UTHSC), 71 S. Manassas St., Suite 217, Memphis, TN, 38103, USA
| | - Changhoon Jee
- Department of Pharmacology, Addiction Science and Toxicology, College of Medicine, University of Tennessee Health Science Center (UTHSC), 71 S. Manassas St., Suite 217, Memphis, TN, 38103, USA.
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29
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Novel NK1R-Targeted 68Ga-/ 177Lu-Radioconjugates with Potential Application against Glioblastoma Multiforme: Preliminary Exploration of Structure-Activity Relationships. Int J Mol Sci 2022; 23:ijms23031214. [PMID: 35163139 PMCID: PMC8835841 DOI: 10.3390/ijms23031214] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 02/06/2023] Open
Abstract
Locoregionally administered, NK1 receptor (NK1R) targeted radionuclide therapy is a promising strategy for the treatment of glioblastoma multiforme. So far, the radiopharmaceuticals used in this approach have been based on the endogenous agonist of NK1R, Substance P or on its close analogues. Herein, we used a well-known, small molecular NK1R antagonist, L732,138, as the basis for the radiopharmaceutical vector. First, 14 analogues of this compound were evaluated to check whether extending the parent structure with linkers of different lengths would not deteriorate the NK1R binding. The tested analogues had affinity similar to or better than the parent compound, and none of the linkers had a negative impact on the binding. Next, five DOTA conjugates were synthesized and used for labelling with 68Ga and 177Lu. The obtained radioconjugates turned out to be fairly lipophilic but showed rather limited stability in human plasma. Evaluation of the receptor affinity of the (radio)conjugates showed that neither the chelator nor the metal negatively impacts the NK1R binding. The 177Lu-radioconjugates exhibited the binding characteristics towards NK1R similar or better than that of the 177Lu-labelled derivative of Substance P, which is in current clinical use. The experimental results presented herein, along with their structural rationalization provided by modelling, give insight for the further molecular design of small molecular NK1R-targeting vectors.
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30
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Harris JA, Faust B, Gondin AB, Dämgen MA, Suomivuori CM, Veldhuis NA, Cheng Y, Dror RO, Thal DM, Manglik A. Selective G protein signaling driven by substance P-neurokinin receptor dynamics. Nat Chem Biol 2022; 18:109-115. [PMID: 34711980 PMCID: PMC8712391 DOI: 10.1038/s41589-021-00890-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/27/2021] [Indexed: 12/20/2022]
Abstract
The neuropeptide substance P (SP) is important in pain and inflammation. SP activates the neurokinin-1 receptor (NK1R) to signal via Gq and Gs proteins. Neurokinin A also activates NK1R, but leads to selective Gq signaling. How two stimuli yield distinct G protein signaling at the same G protein-coupled receptor remains unclear. We determined cryogenic-electron microscopy structures of active NK1R bound to SP or the Gq-biased peptide SP6-11. Peptide interactions deep within NK1R are critical for receptor activation. Conversely, interactions between SP and NK1R extracellular loops are required for potent Gs signaling but not Gq signaling. Molecular dynamics simulations showed that these superficial contacts restrict SP flexibility. SP6-11, which lacks these interactions, is dynamic while bound to NK1R. Structural dynamics of NK1R agonists therefore depend on interactions with the receptor extracellular loops and regulate G protein signaling selectivity. Similar interactions between other neuropeptides and their cognate receptors may tune intracellular signaling.
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Affiliation(s)
- Julian A Harris
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, CA, USA
| | - Bryan Faust
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | - Arisbel B Gondin
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash University, Parkville, Victoria, Australia
| | - Marc André Dämgen
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Carl-Mikael Suomivuori
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Nicholas A Veldhuis
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash University, Parkville, Victoria, Australia
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA.
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA.
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA.
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31
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Thom C, Ehrenmann J, Vacca S, Waltenspühl Y, Schöppe J, Medalia O, Plückthun A. Structures of neurokinin 1 receptor in complex with G q and G s proteins reveal substance P binding mode and unique activation features. SCIENCE ADVANCES 2021; 7:eabk2872. [PMID: 34878828 PMCID: PMC8654284 DOI: 10.1126/sciadv.abk2872] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
The neurokinin 1 receptor (NK1R) is involved in inflammation and pain transmission. This pathophysiologically important G protein–coupled receptor is predominantly activated by its cognate agonist substance P (SP) but also by the closely related neurokinins A and B. Here, we report cryo–electron microscopy structures of SP-bound NK1R in complex with its primary downstream signal mediators, Gq and Gs. Our structures reveal how a polar network at the extracellular, solvent-exposed receptor surface shapes the orthosteric pocket and that NK1R adopts a noncanonical active-state conformation with an interface for G protein binding, which is distinct from previously reported structures. Detailed comparisons with antagonist-bound NK1R crystal structures reveal that insurmountable antagonists induce a distinct and long-lasting receptor conformation that sterically blocks SP binding. Together, our structures provide important structural insights into ligand and G protein promiscuity, the lack of basal signaling, and agonist- and antagonist-induced conformations in the neurokinin receptor family.
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Xu S, Zhou L, Guo S, Hu Q, Shi X, Xia C, Zhang H, Ye C, Jia Y, Hu G. Different pituitary action of NK3Ra and NK3Rb in grass carp. Gen Comp Endocrinol 2021; 313:113829. [PMID: 34087185 DOI: 10.1016/j.ygcen.2021.113829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/03/2021] [Accepted: 05/31/2021] [Indexed: 10/21/2022]
Abstract
In mammals, NK3R is the specific receptor for NKB, which played an important role in reproduction. Recently, two NK3R isoforms, namely NK3Ra and NK3Rb, have been identified in fish. However, little is known about the pituitary actions of the two NK3R isoforms in fish. In this study, both NK3Ra and NK3Rb were isolated from grass carp pituitary. Although their sequence similarity was only 61.6%, the two NK3R isoforms displayed similar ligand selectivity and binding affinity to TAC3 gene products (NKBa, NKBRPa and NKBRPb). In addition, both NK3Ra and NK3Rb displayed similar signaling pathways, including PKA, PKC, MAPK and Ca2+ cascades. Tissue distribution indicated that both NK3Ra and NK3Rb were highly detected in grass carp pituitary. Further study found that NK3Ra was mainly located in pituitary LHβ cells, while NK3Rb was only detected in pituitary SLα cells. Furthermore, NK3Ra and NK3Rb activation could induce LHβ and SLα promoter activity, respectively. These results suggested that the two NK3R isoforms displayed different pituitary actions in fish. Using grass carp pituitary cells as model, we found that PACAP could significantly reduce NK3Ra, but induce NK3Rb mRNA expression coupled with cAMP/PKA and PLC/PKC pathways. Interestingly, PACAP could also significantly inhibit LHβ, but stimulate SLα mRNA expression in grass carp pituitary cells. Furthermore, NK3R antagonist could not only inhibit LHβ mRNA expression, but also block PACAP-induced SLα mRNA expression in grass carp pituitary cells. These results suggested that NK3Ra and NK3Rb could mediate PACAP-reduced LHβ and -induced SLα mRNA expression in grass carp pituitary, respectively.
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Affiliation(s)
- Shaohua Xu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Lingling Zhou
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuming Guo
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiongyao Hu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuetao Shi
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Chuanhui Xia
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Huiying Zhang
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Ye
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongyi Jia
- Agriculture Ministry Key Laboratory of Healthy Freshwater Aquaculture, Key Laboratory of Fish Health and Nutrition of Zhejiang Province, Zhejiang Institute of Freshwater Fisheries, Huzhou 313001, China.
| | - Guangfu Hu
- College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
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Atre I, Mizrahi N, Levavi-Sivan B. Characteristics of Neurokinin-3 Receptor and Its Binding Sites by Mutational Analysis. BIOLOGY 2021; 10:biology10100968. [PMID: 34681067 PMCID: PMC8533089 DOI: 10.3390/biology10100968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/13/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022]
Abstract
NKB (Neurokinin B) is already known to play a crucial role in fish reproduction, but little is known about the structure and function of NKB receptors. Based on an in silico model of the tilapia NKB receptor Tachykinin 3 receptor a (tiTac3Ra) found in the current study, we determined the key residues involved in binding to tilapia NKB and its functional homologue NKF (Neurokinin F). Despite studies in humans suggesting the crucial role of F2516.44 and M2897.43 in NKB binding, no direct peptide interaction was observed in tilapia homologs. In-silico, Ala mutations on residues F2516.44 and M2897.43 did not influence binding affinity, but significantly affected the stability of tiTac3Ra. Moreover, in vitro studies indicated them to be critical to tiNKB/tiNKF-induced receptor activity. The binding of NKB antagonists to tiTac3Ra both in-vitro and in vivo inhibits FSH (follicle stimulating hormone) and LH (luteinizing hormone) release and sperm production in mature tilapia males. Non-peptide NKB antagonist SB-222200 had a strong inhibitory effect on the Tac3Ra activation. SB-222200 also decreased LH plasma levels; two hours post intraperitoneal injection, changed sperm volume and the ratios of the different stages along the spermatogenesis in tilapia testes.
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Satarker S, Maity S, Mudgal J, Nampoothiri M. In silico screening of neurokinin receptor antagonists as a therapeutic strategy for neuroinflammation in Alzheimer's disease. Mol Divers 2021; 26:443-466. [PMID: 34331670 PMCID: PMC8885547 DOI: 10.1007/s11030-021-10276-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/07/2021] [Indexed: 02/08/2023]
Abstract
Neuroinflammation is one of the detrimental factors leading to neurodegeneration in Alzheimer’s disease (AD) and other neurodegenerative disorders. The activation of microglial neurokinin 1 receptor (NK1R) by substance P (SP) enhances neuroinflammation which is mediated through pro-inflammatory pathways involving NFkB, ERK1/2, and P38 and thus projects the scope and importance of NK1R inhibitors. Emphasizing the inhibitory role of N Acetyl l Tryptophan (l-NAT) on NK1R, this is the first in silico screening of l-NAT mediated NK1R antagonism. In addition, FDA- approved ligands were screened for their potential NK1R antagonism. The l-NAT was docked in XP (Extra Precision) mode while FDA-approved ligands were screened in HTVS (High Throughput Virtual Screening), SP (Standard Precision), and XP mode onto NK1R (PDB:6HLO). The l-NAT and top 3 compounds FDA-approved ligands were subjected to molecular dynamics (MD) studies of 100 ns simulation time. The XP docking of l-NAT, indacaterol, modafinil and alosetron showed good docking scores. Their 100 ns MD showed brief protein–ligand interactions with an acceptable root mean square deviation. The protein–ligand contacts depicted pi-pi stacking, pi-cation, hydrogen bonds, and water bridges with the amino acids necessary for NK1R inhibition. The variable colour band intensities on the protein–ligand contact map indicated their binding strength with amino acids. The molecular mechanics/generalized born surface area (MM-GBSA) scores suggested favourable binding free energy of the complexes. Thus, our study predicted the ability of l-NAT, indacaterol, modafinil, and alosetron as capable NK1R inhibitors that can aid to curb neuroinflammation in conditions of AD which could be further ascertained in subsequent studies.
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Affiliation(s)
- Sairaj Satarker
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Swastika Maity
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Jayesh Mudgal
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Madhavan Nampoothiri
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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Waltenspühl Y, Ehrenmann J, Klenk C, Plückthun A. Engineering of Challenging G Protein-Coupled Receptors for Structure Determination and Biophysical Studies. Molecules 2021; 26:molecules26051465. [PMID: 33800379 PMCID: PMC7962830 DOI: 10.3390/molecules26051465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 01/14/2023] Open
Abstract
Membrane proteins such as G protein-coupled receptors (GPCRs) exert fundamental biological functions and are involved in a multitude of physiological responses, making these receptors ideal drug targets. Drug discovery programs targeting GPCRs have been greatly facilitated by the emergence of high-resolution structures and the resulting opportunities to identify new chemical entities through structure-based drug design. To enable the determination of high-resolution structures of GPCRs, most receptors have to be engineered to overcome intrinsic hurdles such as their poor stability and low expression levels. In recent years, multiple engineering approaches have been developed to specifically address the technical difficulties of working with GPCRs, which are now beginning to make more challenging receptors accessible to detailed studies. Importantly, successfully engineered GPCRs are not only valuable in X-ray crystallography, but further enable biophysical studies with nuclear magnetic resonance spectroscopy, surface plasmon resonance, native mass spectrometry, and fluorescence anisotropy measurements, all of which are important for the detailed mechanistic understanding, which is the prerequisite for successful drug design. Here, we summarize engineering strategies based on directed evolution to reduce workload and enable biophysical experiments of particularly challenging GPCRs.
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Abstract
![]()
Developing
drugs for the central nervous system (CNS) requires
fine chemical modifications, as a strict balance between size and
lipophilicity is necessary to improve the permeability through the
blood-brain barrier (BBB).
In this context, morpholine and its analogues represent valuable heterocycles,
due to their conformational and physicochemical properties. In fact,
the presence of a weak basic nitrogen atom and of an oxygen atom at
the opposite position provides a peculiar pKa value and a flexible conformation to the ring, thus allowing
it to take part in several lipophilic–hydrophilic interactions,
and to improve blood solubility and brain permeability of the overall
structure. In CNS-active compounds, morpholines are used (1) to enhance
the potency through molecular interactions, (2) to act as a scaffold
directing the appendages in the correct position, and (3) to modulate
pharmacokinetic/pharmacodynamic (PK/PD) properties. In this perspective,
selected morpholine-containing CNS drug candidates are discussed to
reveal the active pharmacophores accountable for the (1) modulation
of receptors involved in mood disorders and pain, (2) bioactivity
toward enzymes and receptors responsible for neurodegenerative diseases,
and (3) inhibition of enzymes involved in the pathology of CNS tumors.
The medicinal chemistry/pharmacological activity of morpholine derivatives
is discussed, in the effort to highlight the importance of morpholine
ring interactions in the active site of different targets, particularly
reporting binding features retrieved from PDB data, when available.
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Affiliation(s)
- Elena Lenci
- Department of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 13, 50019 Sesto Fiorentino, Florence, Italy
| | - Lorenzo Calugi
- Department of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 13, 50019 Sesto Fiorentino, Florence, Italy
| | - Andrea Trabocchi
- Department of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 13, 50019 Sesto Fiorentino, Florence, Italy
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Mishra V. A Comprehensive Guide to the Commercial Baculovirus Expression Vector Systems for Recombinant Protein Production. Protein Pept Lett 2020; 27:529-537. [PMID: 31721691 DOI: 10.2174/0929866526666191112152646] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/24/2019] [Accepted: 10/25/2019] [Indexed: 12/17/2022]
Abstract
The Baculovirus Expression Vector System (BEVS) is a workhorse for recombinant protein expression for over thirty-five years. Ever since it was first used to overexpress the human IFN-β protein, the system has been engineered and modified several times for quick and easy expression and scale-up of the recombinant proteins. Multiple gene assemblies performed on the baculovirus genome using synthetic biology methods lead to optimized overexpression of the multiprotein complexes. Nowadays, several commercially available BEVS platforms offer a variety of customizable features, and often it is confusing which one to choose for a novice user. This short review is intended to be a one-stop guide to the commercially available baculovirus technology for heterologous protein expression in the insect cells, which users can refer to choose from popular and desirable BEVS products or services.
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Affiliation(s)
- Vibhor Mishra
- Howard Hughes Medical Institute and Department of Biology, Indiana University, Bloomington, IN 47405, United States
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38
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Zhang H, Li Y, Nie J, Ren J, Zeng AP. Structure-based dynamic analysis of the glycine cleavage system suggests key residues for control of a key reaction step. Commun Biol 2020; 3:756. [PMID: 33311647 PMCID: PMC7733448 DOI: 10.1038/s42003-020-01401-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 10/19/2020] [Indexed: 12/16/2022] Open
Abstract
Molecular shuttles play decisive roles in many multi-enzyme systems such as the glycine cleavage system (GCS) for one-carbon (C1) metabolism. In GCS, a lipoate swinging arm containing an aminomethyl moiety is attached to protein H and serves as a molecular shuttle among different proteins. Protection of the aminomethyl moiety in a cavity of protein H and its release induced by protein T are key processes but barely understood. Here, we present a detailed structure-based dynamic analysis of the induced release of the lipoate arm of protein H. Based on molecular dynamics simulations of interactions between proteins H and T, four major steps of the release process showing significantly different energy barriers and time scales can be distinguished. Mutations of a key residue, Ser-67 in protein H, led to a bidirectional tuning of the release process. This work opens ways to target C1 metabolism in biomedicine and the utilization of formate and CO2 for biosynthesis.
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Affiliation(s)
- Han Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, 100029, Beijing, China
| | - Yuchen Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, 100029, Beijing, China
| | - Jinglei Nie
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, 100029, Beijing, China
| | - Jie Ren
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, 100029, Beijing, China. .,State Key Laboratory for Biology of Plant Diseases and Insect Pests/Key Laboratory of Control of Biological Hazard Factors (Plant Origin) for Agri-product Quality and Safety, Ministry of Agriculture, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - An-Ping Zeng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, North Third Ring Road 15, Chaoyang District, 100029, Beijing, China. .,Hamburg University of Technology, Institute of Bioprocess and Biosystems Engineering, Denickestrasse 15, D-21073, Hamburg, Germany.
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39
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Kleynhans J, Kruger HG, Cloete T, Zeevaart JR, Ebenhan T. In Silico Modelling in the Development of Novel Radiolabelled Peptide Probes. Curr Med Chem 2020; 27:7048-7063. [DOI: 10.2174/0929867327666200504082256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/28/2020] [Accepted: 02/19/2020] [Indexed: 12/11/2022]
Abstract
This review describes the usefulness of in silico design approaches in the design of
new radiopharmaceuticals, especially peptide-based radiotracers (including peptidomimetics).
Although not part of the standard arsenal utilized during radiopharmaceutical design, the use
of in silico strategies is steadily increasing in the field of radiochemistry as it contributes to a
more rational and scientific approach. The development of new peptide-based radiopharmaceuticals
as well as a short introduction to suitable computational approaches are provided in
this review. The first section comprises a concise overview of the three most useful computeraided
drug design strategies used, namely i) a Ligand-based Approach (LBDD) using pharmacophore
modelling, ii) a Structure-based Design Approach (SBDD) using molecular docking
strategies and iii) Absorption-Distribution-Metabolism-Excretion-Toxicity (ADMET)
predictions. The second section summarizes the challenges connected to these computer-aided
techniques and discusses successful applications of in silico radiopharmaceutical design in
peptide-based radiopharmaceutical development, thereby improving the clinical procedure in
Nuclear Medicine. Finally, the advances and future potential of in silico modelling as a design
strategy is highlighted.
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Affiliation(s)
- Janke Kleynhans
- Nuclear Medicine Research Infrastructure (NuMeRI) NPC, Pelindaba 0420, South Africa
| | | | - Theunis Cloete
- Center of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom 2520, South Africa
| | - Jan Rijn Zeevaart
- Nuclear Medicine Research Infrastructure (NuMeRI) NPC, Pelindaba 0420, South Africa
| | - Thomas Ebenhan
- Nuclear Medicine Research Infrastructure (NuMeRI) NPC, Pelindaba 0420, South Africa
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40
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Matalińska J, Lipiński PFJ, Kosson P, Kosińska K, Misicka A. In Vivo, In Vitro and In Silico Studies of the Hybrid Compound AA3266, an Opioid Agonist/NK1R Antagonist with Selective Cytotoxicity. Int J Mol Sci 2020; 21:E7738. [PMID: 33086743 PMCID: PMC7588979 DOI: 10.3390/ijms21207738] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/14/2020] [Accepted: 10/17/2020] [Indexed: 12/14/2022] Open
Abstract
AA3266 is a hybrid compound consisting of opioid receptor agonist and neurokinin-1 receptor (NK1R) antagonist pharmacophores. It was designed with the desire to have an analgesic molecule with improved properties and auxiliary anticancer activity. Previously, the compound was found to exhibit high affinity for μ- and δ-opioid receptors, while moderate binding to NK1R. In the presented contribution, we report on a deeper investigation of this hybrid. In vivo, we have established that AA3266 has potent antinociceptive activity in acute pain model, comparable to that of morphine. Desirably, with prolonged administration, our hybrid induces less tolerance than morphine does. AA3266, contrary to morphine, does not cause development of constipation, which is one of the main undesirable effects of opioid use. In vitro, we have confirmed relatively strong cytotoxic activity on a few selected cancer cell lines, similar to or greater than that of a reference NK1R antagonist, aprepitant. Importantly, our compound affects normal cells to smaller extent what makes our compound more selective against cancer cells. In silico methods, including molecular docking, molecular dynamics simulations and fragment molecular orbital calculations, have been used to investigate the interactions of AA3266 with MOR and NK1R. Insights from these will guide structural optimization of opioid/antitachykinin hybrid compounds.
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Affiliation(s)
- Joanna Matalińska
- Department of Neuropeptides, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawińskiego 5, 02-106 Warsaw, Poland; (K.K.); (A.M.)
| | - Piotr F. J. Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawińskiego 5, 02-106 Warsaw, Poland; (K.K.); (A.M.)
| | - Piotr Kosson
- Toxicology Research Laboratory, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawińskiego 5, 02-106 Warsaw, Poland;
| | - Katarzyna Kosińska
- Department of Neuropeptides, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawińskiego 5, 02-106 Warsaw, Poland; (K.K.); (A.M.)
| | - Aleksandra Misicka
- Department of Neuropeptides, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawińskiego 5, 02-106 Warsaw, Poland; (K.K.); (A.M.)
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41
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Nielsen CDT, Dhasmana D, Floresta G, Wohland T, Cilibrizzi A. Illuminating the Path to Target GPCR Structures and Functions. Biochemistry 2020; 59:3783-3795. [PMID: 32956586 DOI: 10.1021/acs.biochem.0c00606] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
G-Protein-coupled receptors (GPCRs) are ubiquitous within eukaryotes, responsible for a wide array of physiological and pathological processes. Indeed, the fact that they are the most drugged target in the human genome is indicative of their importance. Despite the clear interest in GPCRs, most information regarding their activity has been so far obtained by analyzing the response from a "bulk medium". As such, this Perspective summarizes some of the common methods for this indirect observation. Nonetheless, by inspecting approaches applying super-resolution imaging, we argue that imaging is perfectly situated to obtain more detailed structural and spatial information, assisting in the development of new GPCR-targeted drugs and clinical strategies. The benefits of direct optical visualization of GPCRs are analyzed in the context of potential future directions in the field.
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Affiliation(s)
- Christian D-T Nielsen
- Imperial College London, White City Campus, Molecular Sciences Research Hub, 80 Wood Lane, London W12 0BZ, U.K
| | - Divya Dhasmana
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Giuseppe Floresta
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Agostino Cilibrizzi
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
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The Neurokinin-1 Receptor Antagonist Aprepitant: An Intelligent Bullet against Cancer? Cancers (Basel) 2020; 12:cancers12092682. [PMID: 32962202 PMCID: PMC7564414 DOI: 10.3390/cancers12092682] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 12/21/2022] Open
Abstract
Neurokinin-1 receptor (NK-1R) antagonists exert antitumor action, are safe and do not cause serious side-effects. These antagonists (via the NK-1R) exert multiple actions against cancer: antiproliferative and anti-Warburg effects and apoptotic, anti-angiogenic and antimetastatic effects. These multiple effects have been shown for a broad spectrum of cancers. The drug aprepitant (an NK-1R antagonist) is currently used in clinical practice as an antiemetic. In in vivo and in vitro studies, aprepitant also showed the aforementioned multiple antitumor actions against many types of cancer. A successful combination therapy (aprepitant and radiotherapy) has recently been reported in a patient suffering from lung carcinoma: the tumor mass disappeared and side-effects were not observed. Aprepitant could be considered as an intelligent bullet against cancer. The administration of aprepitant in cancer patients to prevent recurrence and metastasis after surgical procedures, thrombosis and thromboembolism is discussed, as is the possible link, through the substance P (SP)/NK-1R system, between cancer and depression. Our main aim is to review the multiple antitumor actions exerted by aprepitant, and the use of this drug is suggested in cancer patients. Altogether, the data support the reprofiling of aprepitant for a new therapeutic use as an antitumor agent.
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43
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Dorokhov VS, Nelyubina YV, Ioffe SL, Sukhorukov AY. Asymmetric Synthesis of Merck's Potent hNK 1 Antagonist and Its Stereoisomers via Tandem Acylation/[3,3]-Rearrangement of 1,2-Oxazine N-Oxides. J Org Chem 2020; 85:11060-11071. [PMID: 32786617 DOI: 10.1021/acs.joc.0c01322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An asymmetric total synthesis of Merck's hNK1 antagonist and three of its stereoisomers was accomplished in 10 steps. The synthesis involves a stereoselective assembly of 1,2-oxazine N-oxide by the [4 + 2]-cycloaddition, site-selective C-H oxygenation using a novel tandem acylation/[3,3]-rearrangement process and the reductive 1,2-oxazine ring contraction into a pyrrolidine ring as key stages. Using this strategy, the fused pyrrolidine subunit was constructed with exceptionally high regio- and stereoselectivities. The approach described here can be used to access enantiopure 3,4-disubstituted prolinols, which are frequently found in pharmaceutically relevant molecules and organocatalysts.
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Affiliation(s)
- Valentin S Dorokhov
- N. D. Zelinsky Institute of Organic Chemistry, Leninsky prospect, 47, Moscow 119991, Russia
| | - Yulia V Nelyubina
- A. N. Nesmeyanov Institute of Organoelement Compounds, Vavilov str. 28, Moscow 119991, Russia
| | - Sema L Ioffe
- N. D. Zelinsky Institute of Organic Chemistry, Leninsky prospect, 47, Moscow 119991, Russia
| | - Alexey Yu Sukhorukov
- N. D. Zelinsky Institute of Organic Chemistry, Leninsky prospect, 47, Moscow 119991, Russia.,Plekhanov Russian University of Economics, Stremyanny per. 36, Moscow 117997, Russia
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Radiochemical Synthesis and Evaluation of Novel Radioconjugates of Neurokinin 1 Receptor Antagonist Aprepitant Dedicated for NK1R-Positive Tumors. Molecules 2020; 25:molecules25163756. [PMID: 32824729 PMCID: PMC7466001 DOI: 10.3390/molecules25163756] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/13/2020] [Accepted: 08/15/2020] [Indexed: 12/18/2022] Open
Abstract
Aprepitant, a lipophilic and small molecular representative of neurokinin 1 receptor antagonists, is known for its anti-proliferative activity on numerous cancer cell lines that are sensitive to Substance P mitogen action. In the presented research, we developed two novel structural modifications of aprepitant to create aprepitant conjugates with different radionuclide chelators. All of them were radiolabeled with 68Ga and 177Lu radionuclides and evaluated in terms of their lipophilicity and stability in human serum. Furthermore, fully stable conjugates were examined in molecular modelling with a human neurokinin 1 receptor structure and in a competitive radioligand binding assay using rat brain homogenates in comparison to the aprepitant molecule. This initial research is in the conceptual stage to give potential theranostic-like radiopharmaceutical pairs for the imaging and therapy of neurokinin 1 receptor-overexpressing cancers.
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Waltenspühl Y, Schöppe J, Ehrenmann J, Kummer L, Plückthun A. Crystal structure of the human oxytocin receptor. SCIENCE ADVANCES 2020; 6:eabb5419. [PMID: 32832646 PMCID: PMC7439316 DOI: 10.1126/sciadv.abb5419] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/29/2020] [Indexed: 05/24/2023]
Abstract
The peptide hormone oxytocin modulates socioemotional behavior and sexual reproduction via the centrally expressed oxytocin receptor (OTR) across several species. Here, we report the crystal structure of human OTR in complex with retosiban, a nonpeptidic antagonist developed as an oral drug for the prevention of preterm labor. Our structure reveals insights into the detailed interactions between the G protein-coupled receptor (GPCR) and an OTR-selective antagonist. The observation of an extrahelical cholesterol molecule, binding in an unexpected location between helices IV and V, provides a structural rationale for its allosteric effect and critical influence on OTR function. Furthermore, our structure in combination with experimental data allows the identification of a conserved neurohypophyseal receptor-specific coordination site for Mg2+ that acts as potent, positive allosteric modulator for agonist binding. Together, these results further our molecular understanding of the oxytocin/vasopressin receptor family and will facilitate structure-guided development of new therapeutics.
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Jain AR, Britton ZT, Markwalter CE, Robinson AS. Improved ligand-binding- and signaling-competent human NK2R yields in yeast using a chimera with the rat NK2R C-terminus enable NK2R-G protein signaling platform. Protein Eng Des Sel 2020; 32:459-469. [PMID: 32400863 DOI: 10.1093/protein/gzaa009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 03/09/2020] [Accepted: 04/16/2020] [Indexed: 02/07/2023] Open
Abstract
The tachykinin 2 receptor (NK2R) plays critical roles in gastrointestinal, respiratory and mental disorders and is a well-recognized target for therapeutic intervention. To date, therapeutics targeting NK2R have failed to meet regulatory agency approval due in large part to the limited characterization of the receptor-ligand interaction and downstream signaling. Herein, we report a protein engineering strategy to improve ligand-binding- and signaling-competent human NK2R that enables a yeast-based NK2R signaling platform by creating chimeras utilizing sequences from rat NK2R. We demonstrate that NK2R chimeras incorporating the rat NK2R C-terminus exhibited improved ligand-binding yields and downstream signaling in engineered yeast strains and mammalian cells, where observed yields were better than 4-fold over wild type. This work builds on our previous studies that suggest exchanging the C-termini of related and well-expressed family members may be a general protein engineering strategy to overcome limitations to ligand-binding and signaling-competent G protein-coupled receptor yields in yeast. We expect these efforts to result in NK2R drug candidates with better characterized signaling properties.
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Affiliation(s)
- Abhinav R Jain
- Department of Chemical and Biomolecular Engineering, Tulane University, 6823 St Charles Ave, New Orleans, LA, 70118, USA
| | - Zachary T Britton
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St, Newark, DE, 19716, USA.,AstraZeneca, Antibody Discovery and Protein Engineering, Gaithersburg, MD 20878, USA
| | - Chester E Markwalter
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St, Newark, DE, 19716, USA.,Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Anne S Robinson
- Department of Chemical and Biomolecular Engineering, Tulane University, 6823 St Charles Ave, New Orleans, LA, 70118, USA.,Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St, Newark, DE, 19716, USA.,Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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Errey JC, Fiez-Vandal C. Production of membrane proteins in industry: The example of GPCRs. Protein Expr Purif 2020; 169:105569. [DOI: 10.1016/j.pep.2020.105569] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/07/2020] [Accepted: 01/12/2020] [Indexed: 01/08/2023]
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Yu J, Gimenez LE, Hernandez CC, Wu Y, Wein AH, Han GW, McClary K, Mittal SR, Burdsall K, Stauch B, Wu L, Stevens SN, Peisley A, Williams SY, Chen V, Millhauser GL, Zhao S, Cone RD, Stevens RC. Determination of the melanocortin-4 receptor structure identifies Ca 2+ as a cofactor for ligand binding. Science 2020; 368:428-433. [PMID: 32327598 PMCID: PMC7567314 DOI: 10.1126/science.aaz8995] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/09/2020] [Indexed: 12/27/2022]
Abstract
The melanocortin-4 receptor (MC4R) is involved in energy homeostasis and is an important drug target for syndromic obesity. We report the structure of the antagonist SHU9119-bound human MC4R at 2.8-angstrom resolution. Ca2+ is identified as a cofactor that is complexed with residues from both the receptor and peptide ligand. Extracellular Ca2+ increases the affinity and potency of the endogenous agonist α-melanocyte-stimulating hormone at the MC4R by 37- and 600-fold, respectively. The ability of the MC4R crystallized construct to couple to ion channel Kir7.1, while lacking cyclic adenosine monophosphate stimulation, highlights a heterotrimeric GTP-binding protein (G protein)-independent mechanism for this signaling modality. MC4R is revealed as a structurally divergent G protein-coupled receptor (GPCR), with more similarity to lipidic GPCRs than to the homologous peptidic GPCRs.
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MESH Headings
- Calcium/chemistry
- Crystallography, X-Ray
- Cyclic AMP/chemistry
- Humans
- Ligands
- Melanocyte-Stimulating Hormones/chemistry
- Melanocyte-Stimulating Hormones/pharmacology
- Mutation
- Potassium Channels, Inwardly Rectifying/chemistry
- Protein Binding
- Protein Multimerization
- Protein Structure, Secondary
- Receptor, Melanocortin, Type 4/antagonists & inhibitors
- Receptor, Melanocortin, Type 4/chemistry
- Receptor, Melanocortin, Type 4/genetics
- Receptors, G-Protein-Coupled/antagonists & inhibitors
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/genetics
- Signal Transduction
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Affiliation(s)
- Jing Yu
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Luis E Gimenez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ciria C Hernandez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
| | - Ariel H Wein
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Gye Won Han
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Kyle McClary
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Sanraj R Mittal
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Kylie Burdsall
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Benjamin Stauch
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Lijie Wu
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
| | - Sophia N Stevens
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
| | - Alys Peisley
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Valerie Chen
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Glenn L Millhauser
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Roger D Cone
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
- Department of Molecular and Integrative Physiology, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Raymond C Stevens
- iHuman Institute, ShanghaiTech University, Pudong, Shanghai 201210, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
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Matalińska J, Lipiński PFJ, Kotlarz A, Kosson P, Muchowska A, Dyniewicz J. Evaluation of Receptor Affinity, Analgesic Activity and Cytotoxicity of a Hybrid Peptide, AWL3020. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-020-10051-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
AbstractIn the present contribution we report design, synthesis and evaluation of receptor affinity, analgesic activity and cytotoxicity of a hybrid peptide, AWL3020. The peptide includes two pharmacophores, one of δ-opioid receptor (δOR) agonists and one of neurokinin-1 receptor (NK1R) antagonists. The design was motivated by the desire to obtain a compound with strong analgesic action and potential additional antiproliferative action. The compound displays high δOR affinity (IC50 = 29.5 nM). On the other hand, it has only poor affinity for the NK1R (IC50 = 70.28 μM). The substance shows good analgesic action which is however weaker than that of morphine. Regarding the effect on proliferation, the compound exhibits no pro-proliferative action in the assayed range. In higher concentrations, it has also cytotoxic activity. This effect is however not selective. The strongest effect of AWL3020 was found for melanoma MeW164 cell line (EC50 = 46.27 μM in reduction of cell numbers after a few days of incubation; EC50 = 37.78 μM in MTT assay).
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50
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The application of helix fusion methods in structural biology. Curr Opin Struct Biol 2020; 60:110-116. [PMID: 31968282 DOI: 10.1016/j.sbi.2019.12.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 10/31/2019] [Accepted: 12/05/2019] [Indexed: 12/18/2022]
Abstract
Methods generating fusion proteins with rigid and predictable structures have been developed in recent years. Among them, helix fusion methods that link two proteins by connecting their terminal alpha helices into a single and extended alpha helix can be particularly useful because designing fusion helices is conceptually and technically simple. These methods have been shown crucial in obtaining crystals that diffract x-rays to high resolution or attaching large and symmetrical backbone proteins to small target proteins for cryo-EM analysis. The structural rigidity of the fusion helix is crucial for these applications, and the reduction of structural ambiguity and flexibility at the fusion sites will further enhance the usefulness of this method.
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