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Ma XB, Yue CX, Liu Y, Yang Y, Wang J, Yang XN, Huang LD, Zhu MX, Hattori M, Li CZ, Yu Y, Guo CR. A shared mechanism for TNP-ATP recognition by members of the P2X receptor family. Comput Struct Biotechnol J 2024; 23:295-308. [PMID: 38173879 PMCID: PMC10762375 DOI: 10.1016/j.csbj.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/30/2023] [Accepted: 12/03/2023] [Indexed: 01/05/2024] Open
Abstract
P2X receptors (P2X1-7) are non-selective cation channels involved in many physiological activities such as synaptic transmission, immunological modulation, and cardiovascular function. These receptors share a conserved mechanism to sense extracellular ATP. TNP-ATP is an ATP derivative acting as a nonselective competitive P2X antagonist. Understanding how it occupies the orthosteric site in the absence of agonism may help reveal the key allostery during P2X gating. However, TNP-ATP/P2X complexes (TNP-ATP/human P2X3 (hP2X3) and TNP-ATP/chicken P2X7 (ckP2X7)) with distinct conformations and different mechanisms of action have been proposed. Whether these represent species and subtype variations or experimental differences remains unclear. Here, we show that a common mechanism of TNP-ATP recognition exists for the P2X family members by combining enhanced conformation sampling, engineered disulfide bond analysis, and covalent occupancy. In this model, the polar triphosphate moiety of TNP-ATP interacts with the orthosteric site, while its TNP-moiety is deeply embedded in the head and dorsal fin (DF) interface, creating a restrictive allostery in these two domains that results in a partly enlarged yet ion-impermeable pore. Similar results were obtained from multiple P2X subtypes of different species, including ckP2X7, hP2X3, rat P2X2 (rP2X2), and human P2X1 (hP2X1). Thus, TNP-ATP uses a common mechanism for P2X recognition and modulation by restricting the movements of the head and DF domains which are essential for P2X activation. This knowledge is applicable to the development of new P2X inhibitors.
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Affiliation(s)
- Xiao-Bo Ma
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chen-Xi Yue
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Yan Liu
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yang Yang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jin Wang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao-Na Yang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Li-Dong Huang
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Michael X. Zhu
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Motoyuki Hattori
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Neurobiology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chang-Zhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Ye Yu
- Department of Pharmacology and Chemical Biology, Institute of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- School of Basic Medicine and Clinical Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Chang-Run Guo
- School of Traditional Chinese Pharmacy, and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
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Elbahnsi A, Dudas B, Cisternino S, Declèves X, Miteva MA. Mechanistic insights into P-glycoprotein ligand transport and inhibition revealed by enhanced molecular dynamics simulations. Comput Struct Biotechnol J 2024; 23:2548-2564. [PMID: 38989058 PMCID: PMC11233806 DOI: 10.1016/j.csbj.2024.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/07/2024] [Accepted: 06/07/2024] [Indexed: 07/12/2024] Open
Abstract
P-glycoprotein (P-gp) plays a crucial role in cellular detoxification and drug efflux processes, transitioning between inward-facing (IF) open, occluded, and outward-facing (OF) states to facilitate substrate transport. Its role is critical in cancer therapy, where P-gp contributes to the multidrug resistance phenotype. In our study, classical and enhanced molecular dynamics (MD) simulations were conducted to dissect the structural and functional features of the P-gp conformational states. Our advanced MD simulations, including kinetically excited targeted MD (ketMD) and adiabatic biasing MD (ABMD), provided deeper insights into state transition and translocation mechanisms. Our findings suggest that the unkinking of TM4 and TM10 helices is a prerequisite for correctly achieving the outward conformation. Simulations of the IF-occluded conformations, characterized by kinked TM4 and TM10 helices, consistently demonstrated altered communication between the transmembrane domains (TMDs) and nucleotide binding domain 2 (NBD2), suggesting the implication of this interface in inhibiting P-gp's efflux function. A particular emphasis was placed on the unstructured linker segment connecting the NBD1 to TMD2 and its role in the transporter's dynamics. With the linker present, we specifically noticed a potential entrance of cholesterol (CHOL) through the TM4-TM6 portal, shedding light on crucial residues involved in accommodating CHOL. We therefore suggest that this entry mechanism could be employed for some P-gp substrates or inhibitors. Our results provide critical data for understanding P-gp functioning and developing new P-gp inhibitors for establishing more effective strategies against multidrug resistance.
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Affiliation(s)
- Ahmad Elbahnsi
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
| | - Balint Dudas
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
| | - Salvatore Cisternino
- Université Paris Cité, Inserm UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Paris, France
| | - Xavier Declèves
- Université Paris Cité, Inserm UMRS 1144, Optimisation Thérapeutique en Neuropsychopharmacologie, Paris, France
| | - Maria A. Miteva
- Université Paris Cité, CNRS UMR 8038 CiTCoM, Inserm U1268 MCTR, Paris, France
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3
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Gao Y, Bai Q, Zhang XC, Zhao Y. Structural insights into the allosteric effects of the antiepileptic drug topiramate on the Ca V2.3 channel. Biochem Biophys Res Commun 2024; 725:150271. [PMID: 38901222 DOI: 10.1016/j.bbrc.2024.150271] [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: 05/14/2024] [Revised: 05/16/2024] [Accepted: 06/15/2024] [Indexed: 06/22/2024]
Abstract
The R-type voltage-gated calcium channel CaV2.3 is predominantly located in the presynapse and is implicated in distinct types of epileptic seizures. It has consequently emerged as a molecular target in seizure treatment. Here, we determined the cryo-EM structure of the CaV2.3-α2δ1-β1 complex in the topiramate-bound state at a 3.0 Å resolution. We provide a snapshot of the binding site of topiramate, a widely prescribed antiepileptic drug, on a voltage-gated ion channel. The binding site is located at an intracellular juxtamembrane hydrophilic cavity. Further structural analysis revealed that topiramate may allosterically facilitate channel inactivation. These findings provide fundamental insights into the mechanism underlying the inhibitory effect of topiramate on CaV and NaV channels, elucidating a previously unseen modulator binding site and thus pointing toward a route for the development of new drugs.
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Affiliation(s)
- Yiwei Gao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qinru Bai
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuejun Cai Zhang
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yan Zhao
- Key Laboratory of Biomacromolecules (CAS), National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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4
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Drop M, Koczurkiewicz-Adamczyk P, Bento O, Pietruś W, Satała G, Blicharz-Futera K, Canale V, Grychowska K, Bantreil X, Pękala E, Kurczab R, Bojarski AJ, Chaumont-Dubel S, Marin P, Lamaty F, Zajdel P. 5-HT 6 receptor neutral antagonists protect astrocytes: A lesson from 2-phenylpyrrole derivatives. Eur J Med Chem 2024; 275:116615. [PMID: 38936149 DOI: 10.1016/j.ejmech.2024.116615] [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: 04/26/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024]
Abstract
The serotonin type 6 receptor (5-HT6R) displays a strong constitutive activity, suggesting it participates largely in the physiological and pathological processes controlled by the receptor. The active states of 5-HT6R engage particular signal transduction pathways that lead to different biological responses. In this study, we present the development of 5-HT6R neutral antagonists at Gs signaling built upon the 2-phenylpyrrole scaffold. Using molecular dynamics simulations, we outline the relationship between the exposure of the basic center of the molecules and their ability to target the agonist-activated state of the receptor. Our study identifies compound 30 as a potent and selective neutral antagonist at 5-HT6R-operated Gs signaling. Furthermore, we demonstrate the cytoprotective effects of 30 and structurally diverse 5-HT6R neutral antagonists at Gs signaling in C8-D1A cells and human astrocytes exposed to rotenone. This effect is not observed for 5-HT6R agonists or inverse agonists. In light of these findings, we propose compound 30 as a valuable molecular probe to study the biological effects associated with the agonist-activated state of 5-HT6R and provide insight into the glioprotective properties of 5-HT6R neutral antagonists at Gs signaling.
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Affiliation(s)
- Marcin Drop
- Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Str., 30-688, Kraków, Poland; IBMM, Université de Montpellier, CNRS, ENSCM, 34095, Montpellier, France
| | | | - Ophélie Bento
- IBMM, Université de Montpellier, CNRS, ENSCM, 34095, Montpellier, France; Institut de Génomique Fonctionelle, Université de Montpellier, CNRS INSERM, 34094, Montpellier, France
| | - Wojciech Pietruś
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Str., 31-343, Kraków, Poland
| | - Grzegorz Satała
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Str., 31-343, Kraków, Poland
| | - Klaudia Blicharz-Futera
- Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Str., 30-688, Kraków, Poland
| | - Vittorio Canale
- Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Str., 30-688, Kraków, Poland
| | - Katarzyna Grychowska
- Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Str., 30-688, Kraków, Poland
| | - Xavier Bantreil
- IBMM, Université de Montpellier, CNRS, ENSCM, 34095, Montpellier, France; Institut Universitaire de France (IUF), France
| | - Elżbieta Pękala
- Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Str., 30-688, Kraków, Poland
| | - Rafał Kurczab
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Str., 31-343, Kraków, Poland
| | - Andrzej J Bojarski
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Str., 31-343, Kraków, Poland
| | - Severine Chaumont-Dubel
- Institut de Génomique Fonctionelle, Université de Montpellier, CNRS INSERM, 34094, Montpellier, France
| | - Philippe Marin
- Institut de Génomique Fonctionelle, Université de Montpellier, CNRS INSERM, 34094, Montpellier, France
| | - Frédéric Lamaty
- IBMM, Université de Montpellier, CNRS, ENSCM, 34095, Montpellier, France
| | - Paweł Zajdel
- Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Str., 30-688, Kraków, Poland.
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5
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Elmore G, Ahern BM, McVay NM, Barker KW, Lohano SS, Ali N, Sebastian A, Andres DA, Satin J, Levitan BM. The C-terminus of Rad is required for membrane localization and L-type calcium channel regulation. J Gen Physiol 2024; 156:e202313518. [PMID: 38990175 PMCID: PMC11244639 DOI: 10.1085/jgp.202313518] [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: 12/05/2023] [Revised: 05/17/2024] [Accepted: 06/26/2024] [Indexed: 07/12/2024] Open
Abstract
L-type CaV1.2 current (ICa,L) links electrical excitation to contraction in cardiac myocytes. ICa,L is tightly regulated to control cardiac output. Rad is a Ras-related, monomeric protein that binds to L-type calcium channel β subunits (CaVβ) to promote inhibition of ICa,L. In addition to CaVβ interaction conferred by the Rad core motif, the highly conserved Rad C-terminus can direct membrane association in vitro and inhibition of ICa,L in immortalized cell lines. In this work, we test the hypothesis that in cardiomyocytes the polybasic C-terminus of Rad confers t-tubular localization, and that membrane targeting is required for Rad-dependent ICa,L regulation. We introduced a 3xFlag epitope to the N-terminus of the endogenous mouse Rrad gene to facilitate analysis of subcellular localization. Full-length 3xFlag-Rad (Flag-Rad) mice were compared with a second transgenic mouse model, in which the extended polybasic C-termini of 3xFlag-Rad was truncated at alanine 277 (Flag-RadΔCT). Ventricular cardiomyocytes were isolated for anti-Flag-Rad immunocytochemistry and ex vivo electrophysiology. Full-length Flag-Rad showed a repeating t-tubular pattern whereas Flag-RadΔCT failed to display membrane association. ICa,L in Flag-RadΔCT cardiomyocytes showed a hyperpolarized activation midpoint and an increase in maximal conductance. Additionally, current decay was faster in Flag-RadΔCT cells. Myocardial ICa,L in a Rad C-terminal deletion model phenocopies ICa,L modulated in response to β-AR stimulation. Mechanistically, the polybasic Rad C-terminus confers CaV1.2 regulation via membrane association. Interfering with Rad membrane association constitutes a specific target for boosting heart function as a treatment for heart failure with reduced ejection fraction.
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Affiliation(s)
- Garrett Elmore
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Brooke M Ahern
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Nicholas M McVay
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Kyle W Barker
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Sarisha S Lohano
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Nemat Ali
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Andrea Sebastian
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Douglas A Andres
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Jonathan Satin
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Bryana M Levitan
- Department of Physiology, University of Kentucky, Lexington, KY, USA
- Gill Heart and Vascular Institute , Lexington, KY, USA
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6
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Matsingos C, Howell LA, McCormick PJ, Fornili A. Elucidating the Activation Mechanism of the Proton-sensing GPR68 Receptor. J Mol Biol 2024; 436:168688. [PMID: 38936694 DOI: 10.1016/j.jmb.2024.168688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 06/08/2024] [Accepted: 06/20/2024] [Indexed: 06/29/2024]
Abstract
GPR68 is a proton-sensing G-protein Coupled Receptor (GPCR) involved in a variety of physiological processes and disorders including neoplastic pathologies. While GPR68 and few other GPCRs have been shown to be activated by a decrease in the extracellular pH, the molecular mechanism of their activation remains largely unknown. In this work, we used a combined computational and in vitro approach to provide new insight into the activation mechanism of the receptor. Molecular Dynamics simulations of GPR68 were used to model the changes in residue interactions and motions triggered by pH. Global and local rearrangements consistent with partial activation were observed upon protonation of the inactive state. Selected extracellular histidine and transmembrane acidic residues were found to have significantly upshifted pKa values during the simulations, consistently with their previously hypothesised role in activation through changes in protonation state. Moreover, a novel pairing between histidine and acidic residues in the extracellular region was highlighted by both sequence analyses and simulation data and tested through site-directed mutagenesis. At last, we identified a previously unknown hydrophobic lock in the extracellular region that might stabilise the inactive conformation and regulate the transition to the active state.
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Affiliation(s)
- Christos Matsingos
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.
| | - Lesley A Howell
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Peter J McCormick
- Centre for Endocrinology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, United Kingdom; Department of Pharmacology and Therapeutics, University of Liverpool, Liverpool L69 7BE, United Kingdom
| | - Arianna Fornili
- Department of Chemistry, School of Physical and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom.
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7
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Eberle SA, Gustavsson M. Bilayer lipids modulate ligand binding to atypical chemokine receptor 3. Structure 2024; 32:1174-1183.e5. [PMID: 38776922 DOI: 10.1016/j.str.2024.04.018] [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: 10/18/2023] [Revised: 02/28/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Chemokine receptors belong to the large class of G protein-coupled receptors (GPCRs) and are involved in a number of (patho)physiological processes. Previous studies highlighted the importance of membrane lipids for modulating GPCR structure and function. However, the underlying mechanisms of how lipids regulate GPCRs are often poorly understood. Here, we report that anionic lipid bilayers increase the binding affinity of the chemokine CXCL12 for the atypical chemokine receptor 3 (ACKR3) by modulating the CXCL12 binding kinetics. Notably, the anionic bilayer favors CXCL12 over the more positively charged chemokine CXCL11, which we explained by bilayer interactions orienting CXCL12 but not CXCL11 for productive ACKR3 binding. Furthermore, our data suggest a stabilization of active ACKR3 conformations in anionic bilayers. Taken together, the described regulation of chemokine selectivity of ACKR3 by the lipid bilayer proposes an extended version of the classical model of chemokine binding including the lipid environment of the receptor.
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Affiliation(s)
- Stefanie Alexandra Eberle
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Martin Gustavsson
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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8
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Zeng W, Wang Y, Gao R, Wen H, Yu M. Unlocking the Reverse Targeting Mechanisms of Cannabidiol: Unveiling New Therapeutic Avenues. J Med Chem 2024. [PMID: 39092992 DOI: 10.1021/acs.jmedchem.4c01353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Cannabidiol (CBD) and Δ9-tetrahydrocannabinol (THC), the main components of Cannabis sativa plants, have attracted a significant amount of attention due to their biological activities. This study identified GPR18 as the target of partial agonist CBD activating the p42/p44 MAPK pathway leading to migration of endometrial epithelial cells. Induced fit docking (IFD) showed that the affinity of THC for GPR18 is higher than that of CBD, and molecular dynamics (MD) simulations showed that CBD-GPR18 complexes at 130/200 ns might have stable conformations, potentially activating GPR18 by changing the distances of key residues in its active pocket. In contrast, THC maintains "metastable" conformations, generating a "shrinking space" leading to full agonism of THC by adding mechanical constraints in GPR18's active pocket. Steered molecular dynamics (SMD) revealed GPR18's active pocket was influenced more by CBD's partial agonism compared with THC. This combined IFD-MD-SMD method may be used to explain the mechanism of activation of partial or full agonists of GPR18.
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Affiliation(s)
- Wen Zeng
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing 314019, China
| | - Yifei Wang
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Rui Gao
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Hongliang Wen
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Yangtze Delta Region Academy of Beijing Institute of Technology, Jiaxing 314019, China
| | - Mingjia Yu
- School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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9
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De Salis SKF, Chen JZ, Skarratt KK, Fuller SJ, Balle T. Deep learning structural insights into heterotrimeric alternatively spliced P2X7 receptors. Purinergic Signal 2024; 20:431-447. [PMID: 38032425 DOI: 10.1007/s11302-023-09978-3] [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: 08/16/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
P2X7 receptors (P2X7Rs) are membrane-bound ATP-gated ion channels that are composed of three subunits. Different subunit structures may be expressed due to alternative splicing of the P2RX7 gene, altering the receptor's function when combined with the wild-type P2X7A subunits. In this study, the application of the deep-learning method, AlphaFold2-Multimer (AF2M), for the generation of trimeric P2X7Rs was validated by comparing an AF2M-generated rat wild-type P2X7A receptor with a structure determined by cryogenic electron microscopy (cryo-EM) (Protein Data Bank Identification: 6U9V). The results suggested AF2M could firstly, accurately predict the structures of P2X7Rs and secondly, accurately identify the highest quality model through the ranking system. Subsequently, AF2M was used to generate models of heterotrimeric alternatively spliced P2X7Rs consisting of one or two wild-type P2X7A subunits in combination with one or two P2X7B, P2X7E, P2X7J, and P2X7L splice variant subunits. The top-ranking models were deemed valid based on AF2M's confidence measures, stability in molecular dynamics simulations, and consistent flexibility of the conserved regions between the models. The structure of the heterotrimeric receptors, which were missing key residues in the ATP binding sites and carboxyl terminal domains (CTDs) compared to the wild-type receptor, help to explain their observed functions. Overall, the models produced in this study (available as supplementary material) unlock the possibility of structure-based studies into the heterotrimeric P2X7Rs.
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Affiliation(s)
- Sophie K F De Salis
- Brain and Mind Centre, The University of Sydney, Camperdown, NSW, 2050, Australia
- Sydney Pharmacy School, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Jake Zheng Chen
- Brain and Mind Centre, The University of Sydney, Camperdown, NSW, 2050, Australia
- Sydney Pharmacy School, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Kristen K Skarratt
- The University of Sydney, Nepean Clinical School, Kingswood, NSW, 2747, Australia
| | - Stephen J Fuller
- The University of Sydney, Nepean Clinical School, Kingswood, NSW, 2747, Australia
| | - Thomas Balle
- Brain and Mind Centre, The University of Sydney, Camperdown, NSW, 2050, Australia.
- Sydney Pharmacy School, The University of Sydney, Camperdown, NSW, 2050, Australia.
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10
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Khanal P, Zargari F, Dey YN, Nikfarjam Z. Olanzapine manipulates neuroactive signals and may onset metabolic disturbances. J Biomol Struct Dyn 2024; 42:6613-6627. [PMID: 37477254 DOI: 10.1080/07391102.2023.2235617] [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: 01/04/2023] [Accepted: 07/06/2023] [Indexed: 07/22/2023]
Abstract
Olanzapine is one of the most prescribed atypical antipsychotics to treat psychiatric illness and is associated with weight gain and metabolic disturbance. The present study investigated the olanzapine-regulated metabolic pathways using functional enrichent analysis including binding affinity with G-protein-coupled receptors (GPCRs). Proteins modulated by olanzapine were retrieved from SwissTargetPrediction, DIGEP-Pred, and BindingDB and then enriched in Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) to assess molecular function, biological process, and cellular components including Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. We used homology modeling to improve the 3D structure for GPCR synapse proteins including dopamine, serotonin, muscarinic, and histamine receptors which were then optimized using molecular dynamics (MD) simulations. The protein-olanzapine binding mechanisms for different GPCR binders were evaluated using molecular docking; later refined by MD simulations. Binding mechanism of olanzapine with D2, 5HT1A, 5HT2A, 5HT2B, 5HT2C, M1, and M2 receptors were created using homology modeling and optimized using MD simulations. In target identification, it was observed that olanzapine majority targeted G-protein coupled receptors. Further, enrichment analysis identified around 76% of the total genes regulated in molecular function, biological process, and cellular components were common including KEGG pathways. Moreover, it was observed that olanzapine had a major potency over the neurotransmitter synapse including neuroactive signals . Olanzapine-induced weight gain and metabolic alterations could be due to the deregulation of multiple synapses like dopamine, serotonin, muscarinic, and histamine at the feeding center followed by cGMP-PKG, cAMP, and PI3K-Akt signaling pathways. HIGHLIGHTSOlanzapine is used in the management of psychiatric illnesses.Olanzapine causes disturbance in lipids and glucosehomeostasis and manipulates energy expenditure.Olanzapine-induced weight gain may occur due to the deregulation of the multiple synapse and cGMP-PKG, cAMP, and PI3K-Akt signaling pathwayCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pukar Khanal
- Department of Pharmacology, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, India
| | - Farshid Zargari
- Pharmacology Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
- Department of Chemistry, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran
| | - Yadu Nandan Dey
- Department of Pharmacology, B.C. Roy College of Pharmacy and Allied Health Sciences, Durgapur, India
| | - Zahra Nikfarjam
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
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11
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Daniel P, Balušíková K, Truksa J, Černý J, Jaček M, Jelínek M, Mulenga MJV, Voráčová K, Chen L, Wei L, Sun Y, Ojima I, Kovář J. Effect of substituents at the C3´, C3´N, C10 and C2-meta-benzoate positions of taxane derivatives on their activity against resistant cancer cells. Toxicol Appl Pharmacol 2024; 489:116993. [PMID: 38870637 PMCID: PMC11257372 DOI: 10.1016/j.taap.2024.116993] [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: 01/24/2024] [Revised: 04/25/2024] [Accepted: 06/05/2024] [Indexed: 06/15/2024]
Abstract
We tested the effect of substituents at the (1) C3´, C3´N, (2) C10, and (3) C2-meta-benzoate positions of taxane derivatives on their activity against sensitive versus counterpart paclitaxel-resistant breast (MCF-7) and ovarian (SK-OV-3) cancer cells. We found that (1) non-aromatic groups at both C3´ and C3´N positions, when compared with phenyl groups at the same positions of a taxane derivative, significantly reduced the resistance of ABCB1 expressing MCF-7/PacR and SK-OV-3/PacR cancer cells. This is, at least in the case of the SB-T-1216 series, accompanied by an ineffective decrease of intracellular levels in MCF-7/PacR cells. The low binding affinity of SB-T-1216 in the ABCB1 binding cavity can elucidate these effects. (2) Cyclopropanecarbonyl group at the C10 position, when compared with the H atom, seems to increase the potency and capability of the derivative in overcoming paclitaxel resistance in both models. (3) Derivatives with fluorine and methyl substituents at the C2-meta-benzoate position were variously potent against sensitive and resistant cancer cells. All C2 derivatives were less capable of overcoming acquired resistance to paclitaxel in vitro than non-substituted analogs. Notably, fluorine derivatives SB-T-121205 and 121,206 were more potent against sensitive and resistant SK-OV-3 cells, and derivatives SB-T-121405 and 121,406 were more potent against sensitive and resistant MCF-7 cells. (4) The various structure-activity relationships of SB-T derivatives observed in two cell line models known to express ABCB1 favor their complex interaction not based solely on ABCB1.
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Affiliation(s)
- Petr Daniel
- Division of Cell and Molecular Biology, Department of Biochemistry, Cell and Molecular Biology, Third Faculty of Medicine, Charles University, Prague, Czech Republic.
| | - Kamila Balušíková
- Division of Cell and Molecular Biology, Department of Biochemistry, Cell and Molecular Biology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Jaroslav Truksa
- Division of Cell and Molecular Biology, Department of Biochemistry, Cell and Molecular Biology, Third Faculty of Medicine, Charles University, Prague, Czech Republic; Laboratory of Tumor Resistance, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Centre, Vestec, Czech Republic
| | - Jiří Černý
- Laboratory of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV Research Centre, Vestec, Czech Republic
| | - Martin Jaček
- Department of Hygiene, Epidemiology and Preventive Medicine, Third Faculty of Medicine, Charles Univesity, Prague, Czech Republic
| | - Michael Jelínek
- Division of Cell and Molecular Biology, Department of Biochemistry, Cell and Molecular Biology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Mutale Jane Vobruba Mulenga
- Division of Cell and Molecular Biology, Department of Biochemistry, Cell and Molecular Biology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Kateřina Voráčová
- Division of Cell and Molecular Biology, Department of Biochemistry, Cell and Molecular Biology, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lei Chen
- Institute of Chemical Biology and Drug Discovery, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Longfei Wei
- Institute of Chemical Biology and Drug Discovery, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Yi Sun
- Institute of Chemical Biology and Drug Discovery, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Iwao Ojima
- Institute of Chemical Biology and Drug Discovery, State University of New York at Stony Brook, Stony Brook, NY, USA
| | - Jan Kovář
- Division of Cell and Molecular Biology, Department of Biochemistry, Cell and Molecular Biology, Third Faculty of Medicine, Charles University, Prague, Czech Republic.
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12
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Kotova PD, Dymova EA, Lyamin OO, Rogachevskaja OA, Kolesnikov SS. PI3 kinase inhibitor PI828 uncouples aminergic GPCRs and Ca 2+ mobilization irrespectively of its primary target. Biochim Biophys Acta Gen Subj 2024; 1868:130649. [PMID: 38823731 DOI: 10.1016/j.bbagen.2024.130649] [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: 02/23/2024] [Revised: 04/20/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
The phosphoinositide 3-kinase (PI3K) is involved in regulation of multiple intracellular processes. Although the inhibitory analysis is generally employed for validating a physiological role of PI3K, increasing body of evidence suggests that PI3K inhibitors can exhibit PI3K-unrelated activity as well. Here we studied Ca2+ signaling initiated by aminergic agonists in a variety of different cells and analyzed effects of the PI3K inhibitor PI828 on cell responsiveness. It turned out that PI828 inhibited Ca2+ transients elicited by acetylcholine (ACh), histamine, and serotonin, but did not affect Ca2+ responses to norepinephrine and ATP. Another PI3K inhibitor wortmannin negligibly affected Ca2+ signaling initiated by any one of the tested agonists. Using the genetically encoded PIP3 sensor PH(Akt)-Venus, we confirmed that both PI828 and wortmannin effectively inhibited PI3K and ascertained that this kinase negligibly contributed to ACh transduction. These findings suggested that PI828 inhibited Ca2+ responses to aminergic agonists tested, involving an unknown cellular mechanism unrelated to the PI3K inhibition. Complementary physiological experiments provided evidence that PI828 could inhibit Ca2+ signals induced by certain agonists, by acting extracellularly, presumably, through their surface receptors. For the muscarinic M3 receptor, this possibility was verified with molecular docking and molecular dynamics. As demonstrated with these tools, wortmannin could be bound in the extracellular vestibule at the muscarinic M3 receptor but this did not preclude binding of ACh to the M3 receptor followed by its activation. In contrast, PI828 could sterically block the passage of ACh into the allosteric site, preventing activation of the muscarinic M3 receptor.
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Affiliation(s)
- Polina D Kotova
- Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institutskaya Street 3, Pushchino, Russia.
| | - Ekaterina A Dymova
- Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institutskaya Street 3, Pushchino, Russia
| | - Oleg O Lyamin
- Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institutskaya Street 3, Pushchino, Russia
| | - Olga A Rogachevskaja
- Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institutskaya Street 3, Pushchino, Russia
| | - Stanislav S Kolesnikov
- Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institutskaya Street 3, Pushchino, Russia
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13
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Bertalan É, Konno M, Del Carmen Marín M, Bagherzadeh R, Nagata T, Brown L, Inoue K, Bondar AN. Hydrogen-Bonding and Hydrophobic Interaction Networks as Structural Determinants of Microbial Rhodopsin Function. J Phys Chem B 2024; 128:7407-7426. [PMID: 39024507 DOI: 10.1021/acs.jpcb.4c02946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Microbial pump rhodopsins are highly versatile light-driven membrane proteins that couple protein conformational dynamics with ion translocation across the cell membranes. Understanding how microbial pump rhodopsins use specific amino acid residues at key functional sites to control ion selectivity and ion pumping direction is of general interest for membrane transporters, and could guide site-directed mutagenesis for optogenetics applications. To enable direct comparisons between proteins with different sequences we implement, for the first time, a unique numbering scheme for the microbial pump rhodopsin residues, NS-mrho. We use NS-mrho to show that distinct microbial pump rhodopsins typically have hydrogen-bond networks that are less conserved than anticipated from the amino acid residue conservation, whereas their hydrophobic interaction networks are largely conserved. To illustrate the role of the hydrogen-bond networks as structural elements that determine the functionality of microbial pump rhodopsins, we performed experiments, atomic-level simulations, and hydrogen bond network analyses on GR, the outward proton pump from Gloeobacter violaceus, and KR2, the outward sodium pump from Krokinobacter eikastus. The experiments indicate that multiple mutations that recover KR2 amino acid residues in GR not only fail to convert it into a sodium pump, but completely inactivate GR by abolishing photoisomerization of the retinal chromophore. This observation could be attributed to the drastically altered hydrogen-bond interaction network identified with simulations and network analyses. Taken together, our findings suggest that functional specificity could be encoded in the collective hydrogen-bond network of microbial pump rhodopsins.
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Affiliation(s)
- Éva Bertalan
- Department of Mathematics and Natural Sciences, RWTH Aachen University, Templergraben 59, 52062 Aachen, Germany
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa 277-8581, Chiba, Japan
| | - María Del Carmen Marín
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa 277-8581, Chiba, Japan
| | - Reza Bagherzadeh
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa 277-8581, Chiba, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa 277-8581, Chiba, Japan
| | - Leonid Brown
- Department of Physics, University of Guelph, 488 Gordon Street, Guelph, Ontario N1G 2W1, Canada
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa 277-8581, Chiba, Japan
| | - Ana-Nicoleta Bondar
- Institute of Computational Biomedicine, Forschungszentrum Jülich, IAS-5/INM-9, Wilhelm-Johnen Straße, 5428 Jülich, Germany
- Faculty of Physics, University of Bucharest, Atomiştilor 405, 077125 Măgurele, Romania
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14
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Puls K, Olivé-Marti AL, Hongnak S, Lamp D, Spetea M, Wolber G. Discovery of Novel, Selective, and Nonbasic Agonists for the Kappa-Opioid Receptor Determined by Salvinorin A-Based Virtual Screening. J Med Chem 2024. [PMID: 39088801 DOI: 10.1021/acs.jmedchem.4c00590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
Modulating the kappa-opioid receptor (KOR) is a promising strategy for treating various human diseases. KOR agonists show potential for treating pain, pruritus, and epilepsy, while KOR antagonists show potential for treating depression, anxiety, and addiction. The diterpenoid Salvinorin A (SalA), a secondary metabolite of Salvia divinorum, is a potent and selective KOR agonist. Unlike typical opioids, SalA lacks a basic nitrogen, which encouraged us to search for nonbasic KOR ligands. Through structure-based virtual screening using 3D pharmacophore models based on the binding mode of SalA, we identified novel, nonbasic, potent, and selective KOR agonists. In vitro studies confirmed two virtual hits, SalA-VS-07 and SalA-VS-08, as highly selective for the KOR and showing G protein-biased KOR agonist activity. Both KOR ligands share a novel spiro-moiety and a nonbasic scaffold. Our findings provide novel starting points for developing therapeutics aimed at treating pain and other conditions in which KOR is a central player.
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Affiliation(s)
- Kristina Puls
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2-4, 14195 Berlin, Germany
| | - Aina-Leonor Olivé-Marti
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Siriwat Hongnak
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - David Lamp
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Mariana Spetea
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Gerhard Wolber
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2-4, 14195 Berlin, Germany
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15
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Huang X, Chorianopoulou A, Kalkounou P, Georgiou M, Pousias A, Davies A, Pearce A, Harris M, Lambrinidis G, Marakos P, Pouli N, Kolocouris A, Lougiakis N, Ladds G. Hit-to-Lead Optimization of Heterocyclic Carbonyloxycarboximidamides as Selective Antagonists at Human Adenosine A3 Receptor. J Med Chem 2024. [PMID: 39073853 DOI: 10.1021/acs.jmedchem.4c01092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Antagonism of the human adenosine A3 receptor (hA3R) has potential therapeutic application. Alchemical relative binding free energy calculations of K18 and K32 suggested that the combination of a 3-(2,6-dichlorophenyl)-isoxazolyl group with 2-pyridinyl at the ends of a carbonyloxycarboximidamide group should improve hA3R affinity. Of the 25 new analogues synthesized, 37 and 74 showed improved hA3R affinity compared to K18 (and K32). This was further improved through the addition of a bromine group to the 2-pyridinyl at the 5-position, generating compound 39. Alchemical relative binding free energy calculations, mutagenesis studies and MD simulations supported the compounds' binding pattern while suggesting that the bromine of 39 inserts deep into the hA3R orthosteric pocket, so highlighting the importance of rigidification of the carbonyloxycarboximidamide moiety. MD simulations highlighted the importance of rigidification of the carbonyloxycarboximidamide, while suggesting that the bromine of 39 inserts deep into the hA3R orthosteric pocket, which was supported through mutagenesis studies 39 also selectively antagonized endogenously expressed hA3R in nonsmall cell lung carcinoma cells, while pharmacokinetic studies indicated low toxicity enabling in vivo evaluation. We therefore suggest that 39 has potential for further development as a high-affinity hA3R antagonist.
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Affiliation(s)
- Xianglin Huang
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Anna Chorianopoulou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou 15771, Athens, Greece
| | - Panagoula Kalkounou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou 15771, Athens, Greece
| | - Maria Georgiou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou 15771, Athens, Greece
| | - Athanasios Pousias
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou 15771, Athens, Greece
| | - Amy Davies
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Abigail Pearce
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Matthew Harris
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - George Lambrinidis
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou 15771, Athens, Greece
| | - Panagiotis Marakos
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou 15771, Athens, Greece
| | - Nicole Pouli
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou 15771, Athens, Greece
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou 15771, Athens, Greece
| | - Nikolaos Lougiakis
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou 15771, Athens, Greece
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
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16
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Yue Z, Wu J, Teng D, Wang Z, Voth GA. Activation of the influenza B M2 proton channel (BM2). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605324. [PMID: 39091734 PMCID: PMC11291123 DOI: 10.1101/2024.07.26.605324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Influenza B viruses have co-circulated during most seasonal flu epidemics and can cause significant human morbidity and mortality due to their rapid mutation, emerging drug resistance, and severe impact on vulnerable populations. The influenza B M2 proton channel (BM2) plays an essential role in viral replication, but the mechanisms behind its symmetric proton conductance and the involvement of a second histidine (His27) cluster remain unclear. Here we perform the membrane- enabled continuous constant-pH molecular dynamics simulations on wildtype BM2 and a key H27A mutant to explore its pH-dependent conformational switch. Simulations capture the activation as the first histidine (His19) protonates and reveal the transition at lower pH values compared to AM2 is a result of electrostatic repulsions between His19 and pre-protonated His27. Crucially, we provide an atomic-level understanding of the symmetric proton conduction by identifying pre-activating channel hydration in the C-terminal portion. This research advances our understanding of the function of BM2 function and lays the groundwork for further chemically reactive modeling of the explicit proton transport process as well as possible anti-flu drug design efforts.
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Affiliation(s)
- Zhi Yue
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Frank Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Jiangbo Wu
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Frank Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Da Teng
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Frank Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | | | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Frank Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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17
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Lazaridi S, Yuan J, Lemmin T. Atomic insights into the signaling landscape of E. coli PhoQ histidine kinase from molecular dynamics simulations. Sci Rep 2024; 14:17659. [PMID: 39085378 PMCID: PMC11291726 DOI: 10.1038/s41598-024-68206-z] [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: 04/18/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
Bacteria rely on two-component systems to sense environmental cues and regulate gene expression for adaptation. The PhoQ/PhoP system exemplifies this crucial role, playing a key part in sensing magnesium (Mg2+) levels, antimicrobial peptides, mild acidic pH, osmotic upshift, and long-chain unsaturated fatty acids, promoting virulence in certain bacterial species. However, the precise details of PhoQ activation remain elusive. To elucidate PhoQ's signaling mechanism at atomic resolution, we combined AlphaFold2 predictions with molecular modeling and carried out extensive Molecular Dynamics (MD) simulations. Our MD simulations revealed three distinct PhoQ conformations that were validated by experimental data. Notably, one conformation was characterized by Mg2+ bridging the acidic patch in the sensor domain to the membrane, potentially representing a repressed state. Furthermore, the high hydration observed in a putative intermediate state lends support to the hypothesis of water-mediated conformational changes during PhoQ signaling. Our findings not only revealed specific conformations within the PhoQ signaling pathway, but also hold significant promise for understanding the broader histidine kinase family due to their shared structural features. Our approach paves the way for a more comprehensive understanding of histidine kinase signaling mechanisms across various bacterial species and opens the door for developing novel therapeutics that target PhoQ modulation.
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Affiliation(s)
- Symela Lazaridi
- Institute of Biochemistry and Molecular Medicine (IBMM), University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences (GCB), University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
| | - Jing Yuan
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, Karl-Von-Frisch-Strasse 14, 35043, Marburg, Germany
| | - Thomas Lemmin
- Institute of Biochemistry and Molecular Medicine (IBMM), University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland.
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18
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Shen M, Huang Y, Cai Z, Cherny VV, DeCoursey TE, Shen J. Interior pH-sensing residue of human voltage-gated proton channel H v1 is histidine 168. Biophys J 2024:S0006-3495(24)00486-7. [PMID: 39054673 DOI: 10.1016/j.bpj.2024.07.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 07/07/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024] Open
Abstract
The molecular mechanisms governing the human voltage-gated proton channel hHv1 remain elusive. Here, we used membrane-enabled hybrid-solvent continuous constant pH molecular dynamics (CpHMD) simulations with pH replica exchange to further evaluate the structural models of hHv1 in the closed (hyperpolarized) and open (depolarized) states recently obtained with MD simulations and explore potential pH-sensing residues. The CpHMD titration at a set of symmetric pH conditions revealed three residues that can gain or lose protons upon channel depolarization. Among them, residue H168 at the intracellular end of the S3 helix switches from the deprotonated to the protonated state and its protonation is correlated with the increased tilting of the S3 helix during the transition from the closed to the open state. Thus, the simulation data suggest H168 as an interior pH sensor, in support of a recent finding based on electrophysiological experiments of Hv1 mutants. We propose that protonation of H168 acts as a key that unlocks the closed channel configuration by increasing the flexibility of the S2-S3 linker, which increases the tilt angle of S3 and enhances the mobility of the S4 helix, thus promoting channel opening. Our work represents an important step toward deciphering the pH-dependent gating mechanism of hHv1.
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Affiliation(s)
- Mingzhe Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Yandong Huang
- College of Computer Engineering, Jimei University, Xiamen, Fujian Province, China.
| | - Zhitao Cai
- College of Computer Engineering, Jimei University, Xiamen, Fujian Province, China
| | - Vladimir V Cherny
- Department of Physiology & Biophysics, Rush University Medical Center, Chicago, Illinois
| | - Thomas E DeCoursey
- Department of Physiology & Biophysics, Rush University Medical Center, Chicago, Illinois
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland.
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19
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Freites JA, Tobias DJ. Molecular Dynamics Simulations of the Eye Lens Water Channel Aquaporin 0 from Fish. J Phys Chem B 2024. [PMID: 39052430 DOI: 10.1021/acs.jpcb.4c03015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Aquaporin 0 (AQP0) plays a key role in water circulation in the eye lens through a variety of functions. In contrast to mammalian genomes, zebrafish contains two aqp0 genes leading to a separation of AQP0 multiple functions between the two gene products, Aqp0a and Aqp0b. A notable feature of the zebrafish AQP0 paralogs is the increased water permeability of Aqp0b relative to Aqp0a as well as a severa lfold increase relative to mammalian AQP0. Here, we report equilibrium molecular dynamics (MD) simulations on the microsecond timescale to identify the structural basis underlying the differences in water permeability between zebrafish AQP0 paralogs and between AQP0 mammalian and fish orthologs. Our simulations are able to reproduce the experimental trends in water permeability. Our results suggest that a substitution of a key Y23 residue in mammalian AQP0 for F23 in fish AQP0 orthologs introduces significant changes in the conformational dynamics of the CS-I structural motif, which, in conjunction with different levels of hydration of the channel vestibule, can account for the differences in permeabilities between fish and mammalian AQP0 orthologs and between zebrafish AQP0 paralogs.
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Affiliation(s)
- J Alfredo Freites
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, California 92697-2025, United States
| | - Douglas J Tobias
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences 2, Irvine, California 92697-2025, United States
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20
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Guvench O. Effect of Lipid Bilayer Anchoring on the Conformational Properties of the Cytochrome P450 2D6 Binding Site. J Phys Chem B 2024; 128:7188-7198. [PMID: 39016537 DOI: 10.1021/acs.jpcb.4c03097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
Human cytochrome P450 (CYP) proteins metabolize 75% of small-molecule pharmaceuticals, which makes structure-based modeling of CYP metabolism and inhibition, bolstered by the current availability of X-ray crystal structures of CYP globular catalytic domains, an attractive prospect. Accounting for this broad metabolic capacity is a combination of the existence of multiple different CYP proteins and the capacity of a single CYP protein to metabolize multiple different small molecules. It is thought that structural plasticity and flexibility contribute to this latter property; therefore, incorporating diverse conformational states of a particular CYP is likely an important consideration in structure-based CYP metabolism and inhibition modeling. While all-atom explicit-solvent molecular dynamics simulations can be used to generate conformational ensembles under biologically relevant conditions, existing CYP crystal structures are of the globular domain only, whereas human CYPs contain N-terminal transmembrane and linker peptides that anchor the globular catalytic domain to the endoplasmic reticulum. To determine whether this can cause significant differences in the sampled binding site conformations, microsecond scale all-atom explicit-solvent molecular dynamics simulations of the CYP2D6 globular domain in an aqueous environment were compared with those of the full-length protein anchored in a POPC lipid bilayer. While bilayer-anchoring damped some structural fluctuations in the globular domain relative to the aqueous simulations, none of the affected residues included binding site pocket residues. Furthermore, clustering of molecular dynamics snapshots based on either pairwise binding site pocket RMSD or volume differences demonstrated a lack of separation of snapshots from the two simulation conditions into different clusters. These results suggest the substantially simpler and computationally cheaper aqueous simulation approach can be used to generate a relevant conformational ensemble of the CYP2D6 binding site for structure-based metabolism and inhibition modeling.
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Affiliation(s)
- Olgun Guvench
- Department of Pharmaceutical Sciences and Administration, School of Pharmacy, Westbrook College of Health Professions, University of New England, 716 Stevens Ave, Portland, Maine 04103, United States
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21
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Llinas Del Torrent C, Raïch I, Gonzalez A, Lillo J, Casajuana-Martin N, Franco R, Pardo L, Navarro G. Allosterism in the adenosine A 2A and cannabinoid CB 2 heteromer. Br J Pharmacol 2024. [PMID: 39044481 DOI: 10.1111/bph.16502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 01/24/2024] [Accepted: 03/18/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND AND PURPOSE Allosterism is a regulatory mechanism for GPCRs that can be attained by ligand-binding or protein-protein interactions with another GPCR. We have studied the influence of the dimer interface on the allosteric properties of the A2A receptor and CB2 receptor heteromer. EXPERIMENTAL APPROACH We have evaluated cAMP production, phosphorylation of signal-regulated kinases (pERK1/2), label-free dynamic mass redistribution, β-arrestin 2 recruitment and bimolecular fluorescence complementation assays in the absence and presence of synthetic peptides that disrupt the formation of the heteromer. Molecular dynamic simulations provided converging evidence that the heteromeric interface influences the allosteric properties of the A2AR-CB2R heteromer. KEY RESULTS Apo A2AR blocks agonist-induced signalling of CB2R. The disruptive peptides, with the amino acid sequence of transmembrane (TM) 6 of A2AR or CB2R, facilitate CB2R activation, suggesting that A2AR allosterically prevents the outward movement of TM 6 of CB2R for G protein binding. Significantly, binding of the selective antagonist SCH 58261 to A2AR also facilitated agonist-induced activation of CB2R. CONCLUSIONS AND IMPLICATIONS It is proposed that the A2AR-CB2R heteromer contains distinct dimerization interfaces that govern its functional properties. The molecular interface between protomers of the A2AR-CB2R heteromer interconverted from TM 6 for apo or agonist-bound A2AR, blocking CB2R activation, to mainly the TM 1/7 interface for antagonist-bound A2AR, facilitating the independent opening of intracellular cavities for G protein binding. These novel results shed light on a different type of allosteric mechanism and extend the repertoire of GPCR heteromer signalling.
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Affiliation(s)
- Claudia Llinas Del Torrent
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Iu Raïch
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Institute of Neuroscience, University of Barcelona (NeuroUB), Barcelona, Spain
| | - Angel Gonzalez
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Jaume Lillo
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Nil Casajuana-Martin
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Rafael Franco
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Leonardo Pardo
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Gemma Navarro
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Institute of Neuroscience, University of Barcelona (NeuroUB), Barcelona, Spain
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22
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Liu A, Liu Y, Zhang W, Ye RD. Structural insights into ligand recognition and activation of the succinate receptor SUCNR1. Cell Rep 2024; 43:114381. [PMID: 38923454 DOI: 10.1016/j.celrep.2024.114381] [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: 04/18/2024] [Revised: 05/24/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Succinate, a citric acid cycle intermediate, serves important functions in energy homeostasis and metabolic regulation. Extracellular succinate acts as a stress signal through succinate receptor (SUCNR1), a class A G protein-coupled receptor. Research on succinate signaling is hampered by the lack of high-resolution structures of the agonist-bound receptor. We present cryoelectron microscopy (cryo-EM) structures of SUCNR1-Gi complexes bound to succinate and its non-metabolite derivative cis-epoxysuccinate. Key determinants for the recognition of succinate in cis conformation include R2817.39 and Y832.64, while Y301.39 and R993.29 participate in the binding of both succinate and cis-epoxysuccinate. Extracellular loop 2, through F175ECL2 in its β-hairpin, forms a hydrogen bond with succinate and caps the binding pocket. At the receptor-Gi interface, agonist binding induces the rearrangement of a hydrophobic network on transmembrane (TM)5 and TM6, leading to TM signaling through TM3 and TM7. These findings extend our understanding of succinate recognition by SUCNR1, aiding the development of therapeutics for the succinate receptor.
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Affiliation(s)
- Aijun Liu
- Dongguan Songshan Lake Central Hospital, Dongguan Third People's Hospital, The Affiliated Dongguan Songshan Lake Central Hospital, Guangdong Medical University, Dongguan, Guangdong 523326, China; Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China; The Chinese University of Hong Kong, Shenzhen Futian Biomedical Innovation R&D Center, Shenzhen, Guangdong 518000, China.
| | - Yezhou Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China; The Chinese University of Hong Kong, Shenzhen Futian Biomedical Innovation R&D Center, Shenzhen, Guangdong 518000, China
| | - Weijia Zhang
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Richard D Ye
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China; The Chinese University of Hong Kong, Shenzhen Futian Biomedical Innovation R&D Center, Shenzhen, Guangdong 518000, China.
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23
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Kokkaliari S, Grauso L, Mangoni A, Seabra G, Paul VJ, Luesch H. Isolation, Structure Elucidation, and Biological Activity of the Selective TACR2 Antagonist Tumonolide and its Aldehyde from a Marine Cyanobacterium. Chemistry 2024:e202401393. [PMID: 39023398 DOI: 10.1002/chem.202401393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The macrocyclic tumonolide (1) with enamide functionality and the linear tumonolide aldehyde (2) are new interconverting natural products from a marine cyanobacterium with a peptide-polyketide skeleton, representing a hybrid of apratoxins and palmyrolides or laingolides. The planar structures were established by NMR and mass spectrometry. The relative configuration of the stereogenically-rich apratoxin-like polyketide portion was determined using J-based configuration analysis. The absolute configuration of tumonolide (1) was determined by chiral analysis of the amino acid units and computational methods, followed by NMR chemical shift and ECD spectrum prediction, indicating all-R configuration for the polyketide portion, as in palmyrolide A and contrary to the all-S configuration in apratoxins. Functional screening against a panel of 168 GPCR targets revealed tumonolide (1) as a selective antagonist of TACR2 with an IC50 of 7.0 μM, closely correlating with binding affinity. Molecular docking studies established the binding mode and rationalized the selectivity for TACR2 over TACR1 and TACR3. RNA sequencing upon treatment of HCT116 colorectal cancer cells demonstrated activation of the pulmonary fibrosis idiopathic signaling pathway and the insulin secretion signaling pathway at 20 μM, indicating its potential to modulate these pathways.
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Affiliation(s)
- Sofia Kokkaliari
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Laura Grauso
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, 80055 Portici, Napoli, Italy
| | - Alfonso Mangoni
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131, Napoli, Italy
| | - Gustavo Seabra
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
| | - Valerie J Paul
- Smithsonian Marine Station at Ft. Pierce, 701 Seaway Drive, Ft. Pierce, Florida 34949, United States
| | - Hendrik Luesch
- Department of Medicinal Chemistry and Center for Natural Products, Drug Discovery and Development (CNPD3), University of Florida, 1345 Center Drive, Gainesville, Florida 32610, United States
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24
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Mobilia M, Karakashian A, Neupane KR, Hage O, Whitus C, Carter A, Voy C, Johnson LA, Graf GA, Gordon SM. Enhancement of high-density lipoprotein-associated protease inhibitor activity prevents atherosclerosis progression. Atherosclerosis 2024; 396:118544. [PMID: 39126769 DOI: 10.1016/j.atherosclerosis.2024.118544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/28/2024] [Accepted: 07/11/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND AND AIMS Inflammatory cells within atherosclerotic lesions secrete proteolytic enzymes that contribute to lesion progression and destabilization, increasing the risk for an acute cardiovascular event. Elastase is a serine protease, secreted by macrophages and neutrophils, that may contribute to the development of unstable plaque. We previously reported interaction of endogenous protease-inhibitor proteins with high-density lipoprotein (HDL), including alpha-1-antitrypsin, an inhibitor of elastase. These findings support a potential role for HDL as a modulator of protease activity. In this study, we test the hypothesis that enhancement of HDL-associated elastase inhibitor activity is protective against atherosclerotic lesion progression. METHODS We designed an HDL-targeting protease inhibitor (HTPI) that binds to HDL and confers elastase inhibitor activity. Lipoprotein binding and the impact of HTPI on atherosclerosis were examined using mouse models. Histology and immunofluorescence staining of aortic root sections were used to examine the impact of HTPI on lesion morphology and inflammatory features. RESULTS HTPI is a small (1.6 kDa) peptide with an elastase inhibitor domain, a soluble linker, and an HDL-targeting domain. When incubated with human plasma ex vivo, HTPI predominantly binds to HDL. Intravenous administration of HTPI to mice resulted in its binding to plasma HDL and increased elastase inhibitor activity on isolated HDL. Accumulation of HTPI within plaque was observed after administration to Apoe-/- mice. To examine the effect of HTPI treatment on atherosclerosis, prevention and progression studies were performed using Ldlr-/- mice fed Western diet. In both study designs, HTPI-treated mice had reduced lipid deposition in plaque. CONCLUSIONS These data support the hypothesis that HDL-associated anti-elastase activity can improve the atheroprotective potential of HDL and highlight the potential utility of HDL enrichment with anti-protease activity as an approach for stabilization of atherosclerotic lesions.
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Affiliation(s)
- Maura Mobilia
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA
| | | | - Khaga R Neupane
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA
| | - Olivia Hage
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Callie Whitus
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA
| | - Abigail Carter
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA
| | - Clairity Voy
- Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Lance A Johnson
- Department of Physiology, University of Kentucky, Lexington, KY, USA; Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Gregory A Graf
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA; Department of Physiology, University of Kentucky, Lexington, KY, USA
| | - Scott M Gordon
- Saha Cardiovascular Research Center, University of Kentucky, Lexington, KY, USA; Department of Physiology, University of Kentucky, Lexington, KY, USA.
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25
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Liebl K, Voth GA. Lipid Organization by the Caveolin-1 Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.10.602986. [PMID: 39026816 PMCID: PMC11257593 DOI: 10.1101/2024.07.10.602986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Caveolins are lipid-binding proteins that can organize membrane remodeling and oligomerize into the 8S-complex. The CAV1 8S-complex comprises a disk-like structure, about 15nm in diameter, with a central beta barrel. Further oligomerization of 8S-complexes remodels the membrane into caveolae vessels, with a dependence on cholesterol concentration. However, the molecular mechanisms behind membrane remodeling and cholesterol filtering are still not understood. Performing atomistic Molecular Dynamics simulations in combination with advanced sampling techniques, we describe how the CAV1-8S complex bends the membrane and accumulates cholesterol. Here, our simulations show an enhancing effect by the palmitoylations of CAV1, and we predict that the CAV1-8S complex can extract cholesterol molecules from the lipid bilayer and accommodate them in its beta barrel. Through backmapping to the all-atom level we also conclude that the Martini v2 coarse-grained forcefield overestimates membrane bending, as the atomistic simulations exhibit only very localized bending.
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Affiliation(s)
- Korbinian Liebl
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637
| | - Gregory A. Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, IL 60637
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26
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Koh JYP, Itahana Y, Krah A, Mostafa H, Ong M, Iwamura S, Vincent DM, Radha Krishnan S, Ye W, Yim PWC, Khopade TM, Chen K, Kong PS, Wang LF, Bates RW, Kimura Y, Viswanathan R, Bond PJ, Itahana K. Exploring bat-inspired cyclic tryptophan diketopiperazines as ABCB1 Inhibitors. Commun Chem 2024; 7:158. [PMID: 39003409 PMCID: PMC11246513 DOI: 10.1038/s42004-024-01225-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 06/18/2024] [Indexed: 07/15/2024] Open
Abstract
Chemotherapy-induced drug resistance remains a major cause of cancer recurrence and patient mortality. ATP binding cassette subfamily B member 1 (ABCB1) transporter overexpression in tumors contributes to resistance, yet current ABCB1 inhibitors have been unsuccessful in clinical trials. To address this challenge, we propose a new strategy using tryptophan as a lead molecule for developing ABCB1 inhibitors. Our idea stems from our studies on bat cells, as bats have low cancer incidences and high ABCB1 expression. We hypothesized that potential ABCB1 substrates in bats could act as competitive inhibitors in humans. By molecular simulations of ABCB1-substrate interactions, we generated a benzylated Cyclo-tryptophan (C3N-Dbn-Trp2) that inhibits ABCB1 activity with efficacy comparable to or better than the classical inhibitor, verapamil. C3N-Dbn-Trp2 restored chemotherapy sensitivity in drug-resistant human cancer cells with no adverse effect on cell proliferation. Our unique approach presents a promising lead toward developing effective ABCB1 inhibitors to treat drug-resistant cancers.
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Affiliation(s)
- Javier Yu Peng Koh
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Yoko Itahana
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Alexander Krah
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore
| | - Habib Mostafa
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh, India
| | - Mingmin Ong
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Sahana Iwamura
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Dona Mariya Vincent
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh, India
| | | | - Weiying Ye
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Pierre Wing Chi Yim
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Tushar M Khopade
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh, India
| | - Kunihiko Chen
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Pui San Kong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Roderick W Bates
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore, Singapore
| | - Yasuhisa Kimura
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Rajesh Viswanathan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Andhra Pradesh, India.
| | - Peter J Bond
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), Singapore, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
| | - Koji Itahana
- Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.
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27
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Licht JA, Berry SP, Gutierrez MA, Gaudet R. They all rock: A systematic comparison of conformational movements in LeuT-fold transporters. Structure 2024:S0969-2126(24)00233-8. [PMID: 39025067 DOI: 10.1016/j.str.2024.06.015] [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: 01/24/2024] [Revised: 05/30/2024] [Accepted: 06/21/2024] [Indexed: 07/20/2024]
Abstract
Many membrane transporters share the LeuT fold-two five-helix repeats inverted across the membrane plane. Despite hundreds of structures, whether distinct conformational mechanisms are supported by the LeuT fold has not been systematically determined. After annotating published LeuT-fold structures, we analyzed distance difference matrices (DDMs) for nine proteins with multiple available conformations. We identified rigid bodies and relative movements of transmembrane helices (TMs) during distinct steps of the transport cycle. In all transporters, the bundle (first two TMs of each repeat) rotates relative to the hash (third and fourth TMs). Motions of the arms (fifth TM) to close or open the intracellular and outer vestibules are common, as is a TM1a swing, with notable variations in the opening-closing motions of the outer vestibule. Our analyses suggest that LeuT-fold transporters layer distinct motions on a common bundle-hash rock and demonstrate that systematic analyses can provide new insights into large structural datasets.
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Affiliation(s)
- Jacob A Licht
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Samuel P Berry
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael A Gutierrez
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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28
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Ananya, Panchariya DC, Karthic A, Singh SP, Mani A, Chawade A, Kushwaha S. Vaccine design and development: Exploring the interface with computational biology and AI. Int Rev Immunol 2024:1-20. [PMID: 38982912 DOI: 10.1080/08830185.2024.2374546] [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: 03/22/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024]
Abstract
Computational biology involves applying computer science and informatics techniques in biology to understand complex biological data. It allows us to collect, connect, and analyze biological data at a large scale and build predictive models. In the twenty first century, computational resources along with Artificial Intelligence (AI) have been widely used in various fields of biological sciences such as biochemistry, structural biology, immunology, microbiology, and genomics to handle massive data for decision-making, including in applications such as drug design and vaccine development, one of the major areas of focus for human and animal welfare. The knowledge of available computational resources and AI-enabled tools in vaccine design and development can improve our ability to conduct cutting-edge research. Therefore, this review article aims to summarize important computational resources and AI-based tools. Further, the article discusses the various applications and limitations of AI tools in vaccine development.
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Affiliation(s)
- Ananya
- National Institute of Animal Biotechnology, Hyderabad, India
| | | | | | | | - Ashutosh Mani
- Motilal Nehru National Institute of Technology, Prayagraj, India
| | - Aakash Chawade
- Swedish University of Agricultural Sciences, Alnarp, Sweden
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29
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Selvaraj SP, Lin KH, Lin WC, You MF, Li TL, Chen JY. Rejuvenation of Meropenem by Conjugation with Tilapia Piscidin-4 Peptide Targeting NDM-1 Escherichia coli. ACS OMEGA 2024; 9:29756-29764. [PMID: 39005813 PMCID: PMC11238198 DOI: 10.1021/acsomega.4c03352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/13/2024] [Accepted: 06/21/2024] [Indexed: 07/16/2024]
Abstract
Gram-negative pathogens that produce β-lactamases pose a serious public health threat as they can render β-lactam antibiotics inactive via hydrolysis. This action contributes to the waning effectiveness of clinical antibiotics and creates an urgent need for new antimicrobials. Antimicrobial peptides (AMPs) exhibiting multimodal functions serve as a potential source in spite of a few limitations. Thus, the conjugation of conventional antibiotics with AMPs may be an effective strategy to leverage the advantages of each component. In this study, we conjugated meropenem to the AMP Tilapia piscidin 4 (TP4) using a typical coupling reaction. The conjugate was characterized by using HPLC-MS, HR-MS, and MS-MS fragmentation analysis. It was then evaluated in terms of antibacterial potency, hemolysis, and cytotoxicity toward RAW264.7 and CCD-966SK cell lines. The conjugation of meropenem with TP4 significantly reduced the cytotoxicity compared to TP4. Conjugation of unprotected TP4 with meropenem resulted in cross-linking at the N-terminal and lysine sites. The structural activity relationship of the two isomers of the TP4-meropenem conjugate was investigated. Both the isomers showed notable antibacterial activities against NDM-1 Escherichia coli and reduced red blood cell hemolysis as compared to TP4. Lysine conjugate (TP4-K-Mero) showed lesser hemolysis than the N-terminal conjugate (TP4-N-Mero). Molecular modeling further revealed that the conjugates can bind to lipopolysaccharides and inhibit NDM-1 β-lactamase. Together, these data show that conjugation of antibiotics with AMP can be a feasible approach to increase the therapeutic profile and effectively target multidrug-resistant pathogens. Furthermore, antibiotic conjugation at different AMP sites tends to show unique biological properties.
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Affiliation(s)
- Sanjay Prasad Selvaraj
- Molecular and Biological Agricultural Science Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Wen-Chun Lin
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10 Dahuen Rd, Jiaushi, Ilan 262, Taiwan
| | - Ming-Feng You
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10 Dahuen Rd, Jiaushi, Ilan 262, Taiwan
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung City 402, Taiwan
| | - Jyh-Yih Chen
- Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10 Dahuen Rd, Jiaushi, Ilan 262, Taiwan
- The iEGG and Animal Biotechnology Center and the Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
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30
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Mellouk A, Jaouen P, Ruel LJ, Lê M, Martini C, Moraes TF, El Bakkouri M, Lagüe P, Boisselier E, Calmettes C. POTRA domains of the TamA insertase interact with the outer membrane and modulate membrane properties. Proc Natl Acad Sci U S A 2024; 121:e2402543121. [PMID: 38959031 PMCID: PMC11252910 DOI: 10.1073/pnas.2402543121] [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: 02/08/2024] [Accepted: 05/22/2024] [Indexed: 07/04/2024] Open
Abstract
The outer membrane (OM) of gram-negative bacteria serves as a vital organelle that is densely populated with OM proteins (OMPs) and plays pivotal roles in cellular functions and virulence. The assembly and insertion of these OMPs into the OM represent a fundamental process requiring specialized molecular chaperones. One example is the translocation and assembly module (TAM), which functions as a transenvelope chaperone promoting the folding of specific autotransporters, adhesins, and secretion systems. The catalytic unit of TAM, TamA, comprises a catalytic β-barrel domain anchored within the OM and three periplasmic polypeptide-transport-associated (POTRA) domains that recruit the TamB subunit. The latter acts as a periplasmic ladder that facilitates the transport of unfolded OMPs across the periplasm. In addition to their role in recruiting the auxiliary protein TamB, our data demonstrate that the POTRA domains mediate interactions with the inner surface of the OM, ultimately modulating the membrane properties. Through the integration of X-ray crystallography, molecular dynamic simulations, and biomolecular interaction methodologies, we located the membrane-binding site on the first and second POTRA domains. Our data highlight a binding preference for phosphatidylglycerol, a minor lipid constituent present in the OM, which has been previously reported to facilitate OMP assembly. In the context of the densely OMP-populated membrane, this association may serve as a mechanism to secure lipid accessibility for nascent OMPs through steric interactions with existing OMPs, in addition to creating favorable conditions for OMP biogenesis.
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Affiliation(s)
- Abdelkader Mellouk
- Institut National de la Rechyuerche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Laval, QCH7V 1B7, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
| | - Paul Jaouen
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
- Faculty of Medicine, Department of Ophthalmology and Otolaryngology—Head and Neck Surgery, centre hospitalier universitaire de Québec, Université Laval, Québec City, QCG1S 4L8, Canada
| | - Louis-Jacques Ruel
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec City, QCG1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QCG1V 0A6, Canada
| | - Michel Lê
- Institut National de la Rechyuerche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Laval, QCH7V 1B7, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
| | - Cyrielle Martini
- Institut National de la Rechyuerche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Laval, QCH7V 1B7, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
| | - Trevor F. Moraes
- Department of Biochemistry, University of Toronto, Toronto, ONM5G 1M1, Canada
| | - Majida El Bakkouri
- National Research Council Canada, Human Health Therapeutics, Montréal, QCH4P 2R2, Canada
| | - Patrick Lagüe
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec City, QCG1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QCG1V 0A6, Canada
| | - Elodie Boisselier
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
- Faculty of Medicine, Department of Ophthalmology and Otolaryngology—Head and Neck Surgery, centre hospitalier universitaire de Québec, Université Laval, Québec City, QCG1S 4L8, Canada
| | - Charles Calmettes
- Institut National de la Rechyuerche Scientifique (INRS), Centre Armand-Frappier Santé Biotechnologie, Laval, QCH7V 1B7, Canada
- Regroupement Québécois de recherche sur la fonction, la structure et l’ingénierie des protéines (PROTEO), Université du Québec à Montréal, Montréal, QCH2X 3Y7, Canada
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31
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Stary D, Bajda M. Structural Studies of the Taurine Transporter: A Potential Biological Target from the GABA Transporter Subfamily in Cancer Therapy. Int J Mol Sci 2024; 25:7339. [PMID: 39000444 PMCID: PMC11242302 DOI: 10.3390/ijms25137339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 06/28/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
The taurine transporter (TauT, SLC6A6) is a member of the solute carrier 6 (SLC6) family, which plays multiple physiological roles. The SLC6 family is divided into four subfamilies: GABA (γ-aminobutyric acid), monoamine, glycine and neutral amino acid transporters. Proteins from the GABA group, including the taurine transporter, are primarily considered therapeutic targets for treating central nervous system disorders. However, recent studies have suggested that inhibitors of SLC6A6 could also serve as anticancer agents. Overexpression of TauT has been associated with the progression of colon and gastric cancer. The pool of known ligands of this transporter is limited and the exact spatial structure of taurine transporter remains unsolved. Understanding its structure could aid in the development of novel inhibitors. Therefore, we utilized homology modelling techniques to create models of TauT. Docking studies and molecular dynamics simulations were conducted to describe protein-ligand interactions. We compared the obtained information for TauT with literature data on other members of the GABA transporter group. Our in silico analysis allowed us to characterize the transporter structure and point out amino acids crucial for ligand binding: Glu406, Gly62 and Tyr138. The significance of selected residues was confirmed through structural studies of mutants. These results will aid in the development of novel taurine transporter inhibitors, which can be explored as anticancer agents.
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Affiliation(s)
- Dorota Stary
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Cracow, Poland
- Doctoral School of Medical and Health Sciences, Jagiellonian University Medical College, św. Łazarza 16, 31-530 Cracow, Poland
| | - Marek Bajda
- Department of Physicochemical Drug Analysis, Faculty of Pharmacy, Jagiellonian University Medical College, Medyczna 9, 30-688 Cracow, Poland
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32
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Moqadam M, Gartan P, Talandashti R, Chiapparino A, Titeca K, Gavin AC, Reuter N. A Membrane-Assisted Mechanism for the Release of Ceramide from the CERT START Domain. J Phys Chem B 2024; 128:6338-6351. [PMID: 38903016 PMCID: PMC11228987 DOI: 10.1021/acs.jpcb.4c02398] [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: 04/12/2024] [Revised: 05/26/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
Ceramide transfer protein CERT is the mediator of nonvesicular transfer of ceramide from the ER to Golgi. In CERT, START is the domain responsible for the binding and transport of ceramide. A wealth of structural data has revealed a helix-grip fold surrounding a large hydrophobic cavity holding the ceramide. Yet, little is known about the mechanisms by which START releases the ceramide through the polar region and into the packed environment of cellular membranes. As such events do not lend themselves easily to experimental investigations, we used multiple unbiased microsecond-long molecular simulations. We propose a membrane-assisted mechanism in which the membrane acts as an allosteric effector initiating the release of ceramide and where the passage of the ceramide acyl chains is facilitated by the intercalation of a single phosphatidylcholine lipid in the cavity, practically greasing the ceramide way out. We verify using free energy calculation and experimental lipidomics data that CERT forms stable complexes with phosphatidylcholine lipids, in addition to ceramide, thus providing validation for the proposed mechanism.
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Affiliation(s)
- Mahmoud Moqadam
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Parveen Gartan
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Reza Talandashti
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Antonella Chiapparino
- European
Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1, Heidelberg D-69117, Germany
| | - Kevin Titeca
- European
Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1, Heidelberg D-69117, Germany
- Department
of Cell Physiology and Metabolism, University
of Geneva, CMU Rue Michel-Servet 1, Genève 4 1211, Switzerland
| | - Anne-Claude Gavin
- Department
of Cell Physiology and Metabolism, University
of Geneva, CMU Rue Michel-Servet 1, Genève 4 1211, Switzerland
| | - Nathalie Reuter
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
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33
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Rigobello L, Lugli F, Caporali L, Bartocci A, Fadanni J, Zerbetto F, Iommarini L, Carelli V, Ghelli AM, Musiani F. A computational study to assess the pathogenicity of single or combinations of missense variants on respiratory complex I. Int J Biol Macromol 2024; 273:133086. [PMID: 38871105 DOI: 10.1016/j.ijbiomac.2024.133086] [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: 03/21/2024] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 06/15/2024]
Abstract
Variants found in the respiratory complex I (CI) subunit genes encoded by mitochondrial DNA can cause severe genetic diseases. However, it is difficult to establish a priori whether a single or a combination of CI variants may impact oxidative phosphorylation. Here we propose a computational approach based on coarse-grained molecular dynamics simulations aimed at investigating new CI variants. One of the primary CI variants associated with the Leber hereditary optic neuropathy (m.14484T>C/MT-ND6) was used as a test case and was investigated alone or in combination with two additional rare CI variants whose role remains uncertain. We found that the primary variant positioned in the E-channel region, which is fundamental for CI function, stiffens the enzyme dynamics. Moreover, a new mechanism for the transition between π- and α-conformation in the helix carrying the primary variant is proposed. This may have implications for the E-channel opening/closing mechanism. Finally, our findings show that one of the rare variants, located next to the primary one, further worsens the stiffening, while the other rare variant does not affect CI function. This approach may be extended to other variants candidate to exert a pathogenic impact on CI dynamics, or to investigate the interaction of multiple variants.
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Affiliation(s)
- Laura Rigobello
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna I-40127, Italy
| | - Francesca Lugli
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Bologna I-40126, Italy.
| | - Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna I-40124, Italy
| | - Alessio Bartocci
- Department of Physics, University of Trento, Trento I-38123, Italy; INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento I-38123, Italy
| | - Jacopo Fadanni
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Bologna I-40126, Italy
| | - Francesco Zerbetto
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Bologna I-40126, Italy
| | - Luisa Iommarini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna I-40127, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna I-40124, Italy; Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna I-40123, Italy
| | - Anna Maria Ghelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna I-40127, Italy; IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna I-40124, Italy
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna I-40127, Italy.
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34
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Pujol-Giménez J, Baumann SP, Ho TM, Augustynek B, Hediger MA. Functional Characterization of the Lysosomal Peptide/Histidine Transporter PHT1 ( SLC15A4) by Solid Supported Membrane Electrophysiology (SSME). Biomolecules 2024; 14:771. [PMID: 39062485 PMCID: PMC11275134 DOI: 10.3390/biom14070771] [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: 06/07/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
The peptide/histidine transporter PHT1 (SLC15A4) is expressed in the lysosomal membranes of immune cells where it plays an important role in metabolic and inflammatory signaling. PHT1 is an H+-coupled/histidine symporter that can transport a wide range of oligopeptides, including a variety of bacterial-derived peptides. Moreover, it enables the scaffolding of various metabolic signaling molecules and interacts with key regulatory elements of the immune response. Not surprisingly, PHT1 has been implicated in the pathogenesis of autoimmune diseases such as systemic lupus erythematosus (SLE). Unfortunately, the pharmacological development of PHT1 modulators has been hampered by the lack of suitable transport assays. To address this shortcoming, a novel transport assay based on solid-supported membrane-based electrophysiology (SSME) is presented. Key findings of the present SSME studies include the first recordings of electrophysiological properties, a pH dependence analysis, an assessment of PHT1 substrate selectivity, as well as the transport kinetics of the identified substrates. In contrast to previous work, PHT1 is studied in its native lysosomal environment. Moreover, observed substrate selectivity is validated by molecular docking. Overall, this new SSME-based assay is expected to contribute to unlocking the pharmacological potential of PHT1 and to deepen the understanding of its functional properties.
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Affiliation(s)
- Jonai Pujol-Giménez
- Department of Nephrology and Hypertension, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland (T.M.H.); (B.A.); (M.A.H.)
- Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland
| | - Sven P. Baumann
- Department of Nephrology and Hypertension, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland (T.M.H.); (B.A.); (M.A.H.)
- Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Tin Manh Ho
- Department of Nephrology and Hypertension, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland (T.M.H.); (B.A.); (M.A.H.)
- Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland
| | - Bartlomiej Augustynek
- Department of Nephrology and Hypertension, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland (T.M.H.); (B.A.); (M.A.H.)
- Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland
| | - Matthias A. Hediger
- Department of Nephrology and Hypertension, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland (T.M.H.); (B.A.); (M.A.H.)
- Department of Biomedical Research, Inselspital, University of Bern, Kinderklinik, Freiburgstrasse 15, 3010 Bern, Switzerland
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35
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Wang Y, Qiu L, Wang B, Guan Z, Dong Z, Zhang J, Cao S, Yang L, Wang B, Gong Z, Zhang L, Ma W, Liu Z, Zhang D, Wang G, Yin P. Structural basis for odorant recognition of the insect odorant receptor OR-Orco heterocomplex. Science 2024; 384:1453-1460. [PMID: 38870272 DOI: 10.1126/science.adn6881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/29/2024] [Indexed: 06/15/2024]
Abstract
Insects detect and discriminate a diverse array of chemicals using odorant receptors (ORs), which are ligand-gated ion channels comprising a divergent odorant-sensing OR and a conserved odorant receptor co-receptor (Orco). In this work, we report structures of the ApOR5-Orco heterocomplex from the pea aphid Acyrthosiphon pisum alone and bound to its known activating ligand, geranyl acetate. In these structures, three ApOrco subunits serve as scaffold components that cannot bind the ligand and remain relatively unchanged. Upon ligand binding, the pore-forming helix S7b of ApOR5 shifts outward from the central pore axis, causing an asymmetrical pore opening for ion influx. Our study provides insights into odorant recognition and channel gating of the OR-Orco heterocomplex and offers structural resources to support development of innovative insecticides and repellents for pest control.
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Affiliation(s)
- Yidong Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Synthetic Biology Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Liang Qiu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Bing Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhi Dong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Song Cao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Synthetic Biology Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lulu Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bo Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhou Gong
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Liwei Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Weihua Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhu Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Guirong Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Synthetic Biology Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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36
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Clews AC, Ulch BA, Jesionowska M, Hong J, Mullen RT, Xu Y. Variety of Plant Oils: Species-Specific Lipid Biosynthesis. PLANT & CELL PHYSIOLOGY 2024; 65:845-862. [PMID: 37971406 DOI: 10.1093/pcp/pcad147] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/03/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023]
Abstract
Plant oils represent a large group of neutral lipids with important applications in food, feed and oleochemical industries. Most plants accumulate oils in the form of triacylglycerol within seeds and their surrounding tissues, which comprises three fatty acids attached to a glycerol backbone. Different plant species accumulate unique fatty acids in their oils, serving a range of applications in pharmaceuticals and oleochemicals. To enable the production of these distinctive oils, select plant species have adapted specialized oil metabolism pathways, involving differential gene co-expression networks and structurally divergent enzymes/proteins. Here, we summarize some of the recent advances in our understanding of oil biosynthesis in plants. We compare expression patterns of oil metabolism genes from representative species, including Arabidopsis thaliana, Ricinus communis (castor bean), Linum usitatissimum L. (flax) and Elaeis guineensis (oil palm) to showcase the co-expression networks of relevant genes for acyl metabolism. We also review several divergent enzymes/proteins associated with key catalytic steps of unique oil accumulation, including fatty acid desaturases, diacylglycerol acyltransferases and oleosins, highlighting their structural features and preference toward unique lipid substrates. Lastly, we briefly discuss protein interactomes and substrate channeling for oil biosynthesis and the complex regulation of these processes.
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Affiliation(s)
- Alyssa C Clews
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Brandon A Ulch
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Monika Jesionowska
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Jun Hong
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
- Department of Genetics and Developmental Science, Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Robert T Mullen
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Yang Xu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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37
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Ananya YK, Ramya L. Deciphering the conformational dynamics of Myelin Oligodendrocyte glycoprotein in the myelin sheath. J Biomol Struct Dyn 2024:1-8. [PMID: 38910432 DOI: 10.1080/07391102.2024.2337956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/25/2024] [Indexed: 06/25/2024]
Abstract
Myelin Oligodendrocyte Glycoprotein (MOG) is a transmembrane protein in the myelin sheath. It acts as an auto-antigen under certain unknown conditions causing demyelination, thus resulting in Myelin Oligodendrocyte Glycoprotein Antibody-associated Disease (MOGAD). The significance of glycosylation in the conformational dynamics of the extracellular region (EC1) of the MOG were evident from the previous computational studies. Here, in this study, we performed the molecular dynamics simulation of the entire human MOG in the myelin sheath for 100 ns using the NAMD program. The results indicated that the EC1 and cytoplasmic region (CP) dominate the conformational rigidity of the protein, and enhance its interaction with lipids. This in turn helps in maintaining the myelin integrity in the presence of glycan. The transmembrane regions have reduced interaction with lipids in the glycosylated system. Moreover, the C-terminal extracellular region 2 (EC2) behaves exactly opposite to that of EC1 in the glycan presence. This may be attributed to the glycosylation site in the EC1 region. Hence, not only the region EC1 (having 3 crucial epitopes) but even the CP region were important for understanding the proper function of MOG in the glycan presence.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Y K Ananya
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thirumalaisamudram, Thanjavur, Tamilnadu, India
| | - L Ramya
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thirumalaisamudram, Thanjavur, Tamilnadu, India
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38
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Liu HL, Zhong HY, Zhang YX, Xue HR, Zhang ZS, Fu KQ, Cao XD, Xiong XC, Guo D. Structural basis of tolvaptan binding to the vasopressin V 2 receptor. Acta Pharmacol Sin 2024:10.1038/s41401-024-01325-5. [PMID: 38902502 DOI: 10.1038/s41401-024-01325-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 05/26/2024] [Indexed: 06/22/2024] Open
Abstract
The vasopressin V2 receptor (V2R) is a validated therapeutic target for autosomal dominant polycystic kidney disease (ADPKD), with tolvaptan being the first FDA-approved antagonist. Herein, we used Gaussian accelerated molecular dynamics simulations to investigate the spontaneous binding of tolvaptan to both active and inactive V2R conformations at the atomic-level. Overall, the binding process consists of two stages. Tolvaptan binds initially to extracellular loops 2 and 3 (ECL2/3) before overcoming an energy barrier to enter the pocket. Our simulations result highlighted key residues (e.g., R181, Y205, F287, F178) involved in this process, which were experimentally confirmed by site-directed mutagenesis. This work provides structural insights into tolvaptan-V2R interactions, potentially aiding the design of novel antagonists for V2R and other G protein-coupled receptors.
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Affiliation(s)
- Hong-Li Liu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Hai-Yang Zhong
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Yi-Xiao Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Hua-Rui Xue
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Zheng-Shuo Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Ke-Quan Fu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xu-Dong Cao
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xiao-Chun Xiong
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China.
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221004, China.
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39
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Mittal A, Martin MF, Levin EJ, Adams C, Yang M, Provins L, Hall A, Procter M, Ledecq M, Hillisch A, Wolff C, Gillard M, Horanyi PS, Coleman JA. Structures of synaptic vesicle protein 2A and 2B bound to anticonvulsants. Nat Struct Mol Biol 2024:10.1038/s41594-024-01335-1. [PMID: 38898101 DOI: 10.1038/s41594-024-01335-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
Epilepsy is a common neurological disorder characterized by abnormal activity of neuronal networks, leading to seizures. The racetam class of anti-seizure medications bind specifically to a membrane protein found in the synaptic vesicles of neurons called synaptic vesicle protein 2 (SV2) A (SV2A). SV2A belongs to an orphan subfamily of the solute carrier 22 organic ion transporter family that also includes SV2B and SV2C. The molecular basis for how anti-seizure medications act on SV2s remains unknown. Here we report cryo-electron microscopy structures of SV2A and SV2B captured in a luminal-occluded conformation complexed with anticonvulsant ligands. The conformation bound by anticonvulsants resembles an inhibited transporter with closed luminal and intracellular gates. Anticonvulsants bind to a highly conserved central site in SV2s. These structures provide blueprints for future drug design and will facilitate future investigations into the biological function of SV2s.
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Affiliation(s)
- Anshumali Mittal
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew F Martin
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Jonathan A Coleman
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA.
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40
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Zhang C, Tong F, Zhou B, He M, Liu S, Zhou X, Ma Q, Feng T, Du WJ, Yang H, Xu H, Xiao L, Xu ZZ, Zhu C, Wu R, Wang YQ, Han Q. TMC6 functions as a GPCR-like receptor to sense noxious heat via Gαq signaling. Cell Discov 2024; 10:66. [PMID: 38886367 PMCID: PMC11183229 DOI: 10.1038/s41421-024-00678-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 04/08/2024] [Indexed: 06/20/2024] Open
Abstract
Thermosensation is vital for the survival, propagation, and adaption of all organisms, but its mechanism is not fully understood yet. Here, we find that TMC6, a membrane protein of unknown function, is highly expressed in dorsal root ganglion (DRG) neurons and functions as a Gαq-coupled G protein-coupled receptor (GPCR)-like receptor to sense noxious heat. TMC6-deficient mice display a substantial impairment in noxious heat sensation while maintaining normal perception of cold, warmth, touch, and mechanical pain. Further studies show that TMC6 interacts with Gαq via its intracellular C-terminal region spanning Ser780 to Pro810. Specifically disrupting such interaction using polypeptide in DRG neurons, genetically ablating Gαq, or pharmacologically blocking Gαq-coupled GPCR signaling can replicate the phenotype of TMC6 deficient mice regarding noxious heat sensation. Noxious heat stimulation triggers intracellular calcium release from the endoplasmic reticulum (ER) of TMC6- but not control vector-transfected HEK293T cell, which can be significantly inhibited by blocking PLC or IP3R. Consistently, noxious heat-induced intracellular Ca2+ release from ER and action potentials of DRG neurons largely reduced when ablating TMC6 or blocking Gαq/PLC/IP3R signaling pathway as well. In summary, our findings indicate that TMC6 can directly function as a Gαq-coupled GPCR-like receptor sensing noxious heat.
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Affiliation(s)
- Chen Zhang
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Fang Tong
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Bin Zhou
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Mingdong He
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Shuai Liu
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Xiaomeng Zhou
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Qiang Ma
- School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tianyu Feng
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Wan-Jie Du
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Huan Yang
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Hao Xu
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Lei Xiao
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China
| | - Zhen-Zhong Xu
- School of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Cheng Zhu
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
| | - Ruiqi Wu
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China.
| | - Yan-Qing Wang
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China.
| | - Qingjian Han
- Shanghai Stomatological Hospital & School of Stomatology, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Integrative Medicine and Neurobiology, School of Basic Medical Science, Fudan University, Shanghai, China.
- Shanghai Key Laboratory of Craniomaxillofacial Development and Diseases, Fudan University, Shanghai, China.
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41
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Clarke A, Skerjanz J, Gsell MAF, Wiedner P, Erkan-Candag H, Groschner K, Stockner T, Tiapko O. PIP 2 modulates TRPC3 activity via TRP helix and S4-S5 linker. Nat Commun 2024; 15:5220. [PMID: 38890374 PMCID: PMC11189476 DOI: 10.1038/s41467-024-49396-6] [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: 11/16/2023] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
The transient receptor potential canonical type 3 (TRPC3) channel plays a pivotal role in regulating neuronal excitability in the brain via its constitutive activity. The channel is intricately regulated by lipids and has previously been demonstrated to be positively modulated by PIP2. Using molecular dynamics simulations and patch clamp techniques, we reveal that PIP2 predominantly interacts with TRPC3 at the L3 lipid binding site, located at the intersection of pre-S1 and S1 helices. We demonstrate that PIP2 sensing involves a multistep mechanism that propagates from L3 to the pore domain via a salt bridge between the TRP helix and S4-S5 linker. Notably, we find that both stimulated and constitutive TRPC3 activity require PIP2. These structural insights into the function of TRPC3 are invaluable for understanding the role of the TRPC subfamily in health and disease, in particular for cardiovascular diseases, in which TRPC3 channels play a major role.
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Affiliation(s)
- Amy Clarke
- Department of Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Julia Skerjanz
- Division of Medical Physics and Biophysics, Medical University of Graz, Graz, Austria
| | - Mathias A F Gsell
- Division of Medical Physics and Biophysics, Medical University of Graz, Graz, Austria
| | - Patrick Wiedner
- Division of Medical Physics and Biophysics, Medical University of Graz, Graz, Austria
| | - Hazel Erkan-Candag
- Division of Medical Physics and Biophysics, Medical University of Graz, Graz, Austria
| | - Klaus Groschner
- Division of Medical Physics and Biophysics, Medical University of Graz, Graz, Austria
| | - Thomas Stockner
- Department of Pharmacology, Medical University of Vienna, Vienna, Austria.
| | - Oleksandra Tiapko
- Division of Medical Physics and Biophysics, Medical University of Graz, Graz, Austria.
- BioTechMed, 8010, Graz, Austria.
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42
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Erramilli SK, Dominik PK, Ogbu CP, Kossiakoff AA, Vecchio AJ. Structural and biophysical insights into targeting of claudin-4 by a synthetic antibody fragment. Commun Biol 2024; 7:733. [PMID: 38886509 PMCID: PMC11183071 DOI: 10.1038/s42003-024-06437-6] [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: 01/04/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024] Open
Abstract
Claudins are a 27-member family of ~25 kDa membrane proteins that integrate into tight junctions to form molecular barriers at the paracellular spaces between endothelial and epithelial cells. As the backbone of tight junction structure and function, claudins are attractive targets for modulating tissue permeability to deliver drugs or treat disease. However, structures of claudins are limited due to their small sizes and physicochemical properties-these traits also make therapy development a challenge. Here we report the development of a synthetic antibody fragment (sFab) that binds human claudin-4 and the determination of a high-resolution structure of it bound to claudin-4/enterotoxin complexes using cryogenic electron microscopy. Structural and biophysical results reveal this sFabs mechanism of select binding to human claudin-4 over other homologous claudins and establish the ability of sFabs to bind hard-to-target claudins to probe tight junction structure and function. The findings provide a framework for tight junction modulation by sFabs for tissue-selective therapies.
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Affiliation(s)
- Satchal K Erramilli
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
- Pfizer, San Diego, CA, 92121, USA
| | - Chinemerem P Ogbu
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Structural Biology, University at Buffalo, Buffalo, NY, 14203, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Alex J Vecchio
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Department of Structural Biology, University at Buffalo, Buffalo, NY, 14203, USA.
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43
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Iraci N, Carotenuto L, Ciaglia T, Belperio G, Di Matteo F, Mosca I, Carleo G, Giovanna Basilicata M, Ambrosino P, Turcio R, Puzo D, Pepe G, Gomez-Monterrey I, Soldovieri MV, Di Sarno V, Campiglia P, Miceli F, Bertamino A, Ostacolo C, Taglialatela M. In Silico Assisted Identification, Synthesis, and In Vitro Pharmacological Characterization of Potent and Selective Blockers of the Epilepsy-Associated KCNT1 Channel. J Med Chem 2024; 67:9124-9149. [PMID: 38782404 PMCID: PMC11181338 DOI: 10.1021/acs.jmedchem.4c00268] [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: 01/30/2024] [Revised: 03/28/2024] [Accepted: 04/09/2024] [Indexed: 05/25/2024]
Abstract
Gain-of-function (GoF) variants in KCNT1 channels cause severe, drug-resistant forms of epilepsy. Quinidine is a known KCNT1 blocker, but its clinical use is limited due to severe drawbacks. To identify novel KCNT1 blockers, a homology model of human KCNT1 was built and used to screen an in-house library of compounds. Among the 20 molecules selected, five (CPK4, 13, 16, 18, and 20) showed strong KCNT1-blocking ability in an in vitro fluorescence-based assay. Patch-clamp experiments confirmed a higher KCNT1-blocking potency of these compounds when compared to quinidine, and their selectivity for KCNT1 over hERG and Kv7.2 channels. Among identified molecules, CPK20 displayed the highest metabolic stability; this compound also blocked KCNT2 currents, although with a lower potency, and counteracted GoF effects prompted by 2 recurrent epilepsy-causing KCNT1 variants (G288S and A934T). The present results provide solid rational basis for future design of novel compounds to counteract KCNT1-related neurological disorders.
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Affiliation(s)
- Nunzio Iraci
- Department
of Chemical, Biological, Pharmaceutical and Environmental Sciences
(CHIBIOFARAM), University of Messina, Viale F. Stagno d’Alcontres
31, 98166 Messina, Italy
| | - Lidia Carotenuto
- Department
of Neuroscience, Reproductive Sciences and Dentistry, University Federico II of Naples, Via S. Pansini, 5, 80131 Naples, Italy
| | - Tania Ciaglia
- Department
of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084 Fisciano, SA, Italy
| | - Giorgio Belperio
- Department
of Science and Technology, University of
Sannio, Via F. De Sanctis, 82100 Benevento, Italy
| | - Francesca Di Matteo
- Department
of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084 Fisciano, SA, Italy
| | - Ilaria Mosca
- Department
of Medicine and Health Science Vincenzo Tiberio, University of Molise, Via C. Gazzani, 86100 Campobasso, Italy
| | - Giusy Carleo
- Department
of Neuroscience, Reproductive Sciences and Dentistry, University Federico II of Naples, Via S. Pansini, 5, 80131 Naples, Italy
| | - Manuela Giovanna Basilicata
- Department
of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, P.zza L. Miraglia 2, 80138 Naples, Italy
| | - Paolo Ambrosino
- Department
of Science and Technology, University of
Sannio, Via F. De Sanctis, 82100 Benevento, Italy
| | - Rita Turcio
- Department
of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084 Fisciano, SA, Italy
| | - Deborah Puzo
- Department
of Medicine and Health Science Vincenzo Tiberio, University of Molise, Via C. Gazzani, 86100 Campobasso, Italy
| | - Giacomo Pepe
- Department
of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084 Fisciano, SA, Italy
| | - Isabel Gomez-Monterrey
- Department
of Pharmacy, University Federico II of Naples, Via D. Montesano 49, 80131 Naples, Italy
| | - Maria Virginia Soldovieri
- Department
of Medicine and Health Science Vincenzo Tiberio, University of Molise, Via C. Gazzani, 86100 Campobasso, Italy
| | - Veronica Di Sarno
- Department
of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084 Fisciano, SA, Italy
| | - Pietro Campiglia
- Department
of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084 Fisciano, SA, Italy
| | - Francesco Miceli
- Department
of Neuroscience, Reproductive Sciences and Dentistry, University Federico II of Naples, Via S. Pansini, 5, 80131 Naples, Italy
| | - Alessia Bertamino
- Department
of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084 Fisciano, SA, Italy
| | - Carmine Ostacolo
- Department
of Pharmacy, University of Salerno, Via G. Paolo II 132, 84084 Fisciano, SA, Italy
| | - Maurizio Taglialatela
- Department
of Neuroscience, Reproductive Sciences and Dentistry, University Federico II of Naples, Via S. Pansini, 5, 80131 Naples, Italy
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44
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Ben Mariem O, Palazzolo L, Torre B, Wei Y, Bianchi D, Guerrini U, Laurenzi T, Saporiti S, De Fabiani E, Pochini L, Indiveri C, Eberini I. Atomistic description of the OCTN1 recognition mechanism via in silico methods. PLoS One 2024; 19:e0304512. [PMID: 38829838 PMCID: PMC11146731 DOI: 10.1371/journal.pone.0304512] [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: 11/30/2023] [Accepted: 05/14/2024] [Indexed: 06/05/2024] Open
Abstract
The Organic Cation Transporter Novel 1 (OCTN1), also known as SLC22A4, is widely expressed in various human tissues, and involved in numerous physiological and pathological processes remains. It facilitates the transport of organic cations, zwitterions, with selectivity for positively charged solutes. Ergothioneine, an antioxidant compound, and acetylcholine (Ach) are among its substrates. Given the lack of experimentally solved structures of this protein, this study aimed at generating a reliable 3D model of OCTN1 to shed light on its substrate-binding preferences and the role of sodium in substrate recognition and transport. A chimeric model was built by grafting the large extracellular loop 1 (EL1) from an AlphaFold-generated model onto a homology model. Molecular dynamics simulations revealed domain-specific mobility, with EL1 exhibiting the highest impact on overall stability. Molecular docking simulations identified cytarabine and verapamil as highest affinity ligands, consistent with their known inhibitory effects on OCTN1. Furthermore, MM/GBSA analysis allowed the categorization of substrates into weak, good, and strong binders, with molecular weight strongly correlating with binding affinity to the recognition site. Key recognition residues, including Tyr211, Glu381, and Arg469, were identified through interaction analysis. Ach demonstrated a low interaction energy, supporting the hypothesis of its one-directional transport towards to outside of the membrane. Regarding the role of sodium, our model suggested the involvement of Glu381 in sodium binding. Molecular dynamics simulations of systems at increasing levels of Na+ concentrations revealed increased sodium occupancy around Glu381, supporting experimental data associating Na+ concentration to molecule transport. In conclusion, this study provides valuable insights into the 3D structure of OCTN1, its substrate-binding preferences, and the role of sodium in the recognition. These findings contribute to the understanding of OCTN1 involvement in various physiological and pathological processes and may have implications for drug development and disease management.
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Affiliation(s)
- Omar Ben Mariem
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Beatrice Torre
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Yao Wei
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Davide Bianchi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Uliano Guerrini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Tommaso Laurenzi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Simona Saporiti
- Analytical Excellence and Program Management, Merck Serono S.p.A., Rome, Italy
| | - Emma De Fabiani
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
| | - Lorena Pochini
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata CS, Italy
| | - Cesare Indiveri
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata CS, Italy
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, Italy
- DSRC, Università degli Studi di Milano, Milan, Italy
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45
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Garisetti V, Dhanabalan AK, Dasararaju G. Orphan receptor GPR88 as a potential therapeutic target for CNS disorders - an in silico approach. J Biomol Struct Dyn 2024; 42:4745-4758. [PMID: 37306437 DOI: 10.1080/07391102.2023.2222820] [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: 01/16/2023] [Accepted: 06/02/2023] [Indexed: 06/13/2023]
Abstract
The G-protein-coupled receptors are a part of the largest and most physiologically relevant family of membrane proteins. One-third of the medications, now on the market, target the GPCR receptor family, which is one of the most important therapeutic targets for many disorders. In the reported work, we have focussed on orphan GPR88 receptor which is a part of the GPCR protein family and a potential target for central nervous system disorders. GPR88 is known to show the highest expression in the striatum, which is a key region in motor control and cognitive functions. Recent studies have reported that GPR88 is activated by two agonists, 2-PCCA and RTI-13951-33. In this study, we have predicted the three-dimensional protein structure for the orphan GPR88 using the homology modeling approach. We then used shape-based screening techniques based on known agonists and structure-based virtual screening methods employing docking to uncover novel GPR88 ligands. The screened GPR88-ligand complexes were further subjected to molecular dynamics simulation studies. The selected ligands could fasten the development of novel treatments for the vast list of movement and central nervous system disorders.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vasavi Garisetti
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, Tamil Nadu, India
| | - Anantha Krishnan Dhanabalan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, Tamil Nadu, India
| | - Gayathri Dasararaju
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, Tamil Nadu, India
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46
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Shen Q, Tang X, Wen X, Cheng S, Xiao P, Zang S, Shen D, Jiang L, Zheng Y, Zhang H, Xu H, Mao C, Zhang M, Hu W, Sun J, Zhang Y, Chen Z. Molecular Determinant Underlying Selective Coupling of Primary G-Protein by Class A GPCRs. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310120. [PMID: 38647423 PMCID: PMC11187927 DOI: 10.1002/advs.202310120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/02/2024] [Indexed: 04/25/2024]
Abstract
G-protein-coupled receptors (GPCRs) transmit downstream signals predominantly via G-protein pathways. However, the conformational basis of selective coupling of primary G-protein remains elusive. Histamine receptors H2R and H3R couple with Gs- or Gi-proteins respectively. Here, three cryo-EM structures of H2R-Gs and H3R-Gi complexes are presented at a global resolution of 2.6-2.7 Å. These structures reveal the unique binding pose for endogenous histamine in H3R, wherein the amino group interacts with E2065.46 of H3R instead of the conserved D1143.32 of other aminergic receptors. Furthermore, comparative analysis of the H2R-Gs and H3R-Gi complexes reveals that the structural geometry of TM5/TM6 determines the primary G-protein selectivity in histamine receptors. Machine learning (ML)-based structuromic profiling and functional analysis of class A GPCR-G-protein complexes illustrate that TM5 length, TM5 tilt, and TM6 outward movement are key determinants of the Gs and Gi/o selectivity among the whole Class A family. Collectively, the findings uncover the common structural geometry within class A GPCRs that determines the primary Gs- and Gi/o-coupling selectivity.
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Affiliation(s)
- Qingya Shen
- Department of Pharmacology and Department of Pathology of Sir Run Run Shaw Hospital & Liangzhu LaboratoryHangzhou310058China
- MOE Frontier Science Center for Brain Research and Brain‐Machine IntegrationZhejiang University School of MedicineHangzhou310058China
| | - Xinyan Tang
- Department of Pharmacology and Department of Pharmacy of the Second Affiliated HospitalNHC and CAMS Key Laboratory of Medical NeurobiologySchool of Basic Medical SciencesZhejiang University School of MedicineHangzhou310058China
| | - Xin Wen
- Advanced Medical Research InstituteMeili Lake Translational Research ParkCheeloo College of MedicineShandong UniversityJinan250012China
- Department of Biochemistry and Molecular BiologyShandong University School of MedicineJinan250012China
| | - Shizhuo Cheng
- Department of Pharmacology and Department of Pathology of Sir Run Run Shaw Hospital & Liangzhu LaboratoryHangzhou310058China
- MOE Frontier Science Center for Brain Research and Brain‐Machine IntegrationZhejiang University School of MedicineHangzhou310058China
- College of Computer Science and TechnologyZhejiang UniversityHangzhou310027China
| | - Peng Xiao
- Advanced Medical Research InstituteMeili Lake Translational Research ParkCheeloo College of MedicineShandong UniversityJinan250012China
- Department of Biochemistry and Molecular BiologyShandong University School of MedicineJinan250012China
| | - Shao‐Kun Zang
- Department of Pharmacology and Department of Pathology of Sir Run Run Shaw Hospital & Liangzhu LaboratoryHangzhou310058China
- MOE Frontier Science Center for Brain Research and Brain‐Machine IntegrationZhejiang University School of MedicineHangzhou310058China
| | - Dan‐Dan Shen
- Department of Pharmacology and Department of Pathology of Sir Run Run Shaw Hospital & Liangzhu LaboratoryHangzhou310058China
- MOE Frontier Science Center for Brain Research and Brain‐Machine IntegrationZhejiang University School of MedicineHangzhou310058China
| | - Lei Jiang
- Department of Pharmacology and Department of Pharmacy of the Second Affiliated HospitalNHC and CAMS Key Laboratory of Medical NeurobiologySchool of Basic Medical SciencesZhejiang University School of MedicineHangzhou310058China
| | - Yanrong Zheng
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang ProvinceZhejiang Chinese Medical UniversityHangzhou310053China
| | - Huibing Zhang
- Department of Pharmacology and Department of Pathology of Sir Run Run Shaw Hospital & Liangzhu LaboratoryHangzhou310058China
- MOE Frontier Science Center for Brain Research and Brain‐Machine IntegrationZhejiang University School of MedicineHangzhou310058China
| | - Haomang Xu
- Department of Pharmacology and Department of Pathology of Sir Run Run Shaw Hospital & Liangzhu LaboratoryHangzhou310058China
- MOE Frontier Science Center for Brain Research and Brain‐Machine IntegrationZhejiang University School of MedicineHangzhou310058China
| | - Chunyou Mao
- Department of Pharmacology and Department of Pathology of Sir Run Run Shaw Hospital & Liangzhu LaboratoryHangzhou310058China
- Department of General SurgerySir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouZhejiang310016China
- Zhejiang Research and Development Engineering Laboratory of Minimally Invasive Technology and EquipmentZhejiang UniversityHangzhou310016China
| | - Min Zhang
- College of Computer Science and TechnologyZhejiang UniversityHangzhou310027China
| | - Weiwei Hu
- Department of Pharmacology and Department of Pharmacy of the Second Affiliated HospitalNHC and CAMS Key Laboratory of Medical NeurobiologySchool of Basic Medical SciencesZhejiang University School of MedicineHangzhou310058China
| | - Jin‐Peng Sun
- Advanced Medical Research InstituteMeili Lake Translational Research ParkCheeloo College of MedicineShandong UniversityJinan250012China
- Department of Biochemistry and Molecular BiologyShandong University School of MedicineJinan250012China
- Department of Physiology and Pathophysiology, School of Basic Medical SciencesPeking UniversityKey Laboratory of Molecular Cardiovascular ScienceMinistry of EducationBeijing100191China
| | - Yan Zhang
- Department of Pharmacology and Department of Pathology of Sir Run Run Shaw Hospital & Liangzhu LaboratoryHangzhou310058China
- MOE Frontier Science Center for Brain Research and Brain‐Machine IntegrationZhejiang University School of MedicineHangzhou310058China
| | - Zhong Chen
- Department of Pharmacology and Department of Pharmacy of the Second Affiliated HospitalNHC and CAMS Key Laboratory of Medical NeurobiologySchool of Basic Medical SciencesZhejiang University School of MedicineHangzhou310058China
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang ProvinceZhejiang Chinese Medical UniversityHangzhou310053China
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47
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Hu K, Zhang Q, Chen Y, Yang J, Xia Y, Rao B, Li S, Shen Y, Cao M, Lu H, Qin A, Jiang XC, Yao D, Zhao J, Zhou L, Cao Y. Cryo-EM structure of human sphingomyelin synthase and its mechanistic implications for sphingomyelin synthesis. Nat Struct Mol Biol 2024; 31:884-895. [PMID: 38388831 DOI: 10.1038/s41594-024-01237-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 01/31/2024] [Indexed: 02/24/2024]
Abstract
Sphingomyelin (SM) has key roles in modulating mammalian membrane properties and serves as an important pool for bioactive molecules. SM biosynthesis is mediated by the sphingomyelin synthase (SMS) family, comprising SMS1, SMS2 and SMS-related (SMSr) members. Although SMS1 and SMS2 exhibit SMS activity, SMSr possesses ceramide phosphoethanolamine synthase activity. Here we determined the cryo-electron microscopic structures of human SMSr in complexes with ceramide, diacylglycerol/phosphoethanolamine and ceramide/phosphoethanolamine (CPE). The structures revealed a hexameric arrangement with a reaction chamber located between the transmembrane helices. Within this structure, a catalytic pentad E-H/D-H-D was identified, situated at the interface between the lipophilic and hydrophilic segments of the reaction chamber. Additionally, the study unveiled the two-step synthesis process catalyzed by SMSr, involving PE-PLC (phosphatidylethanolamine-phospholipase C) hydrolysis and the subsequent transfer of the phosphoethanolamine moiety to ceramide. This research provides insights into the catalytic mechanism of SMSr and expands our understanding of sphingolipid metabolism.
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Affiliation(s)
- Kexin Hu
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qing Zhang
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Frontiers Science Center of Degeneration and Regeneration in Skeletal System, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yang Chen
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jintong Yang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Ying Xia
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bing Rao
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shaobai Li
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yafeng Shen
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mi Cao
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongliang Lu
- College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - An Qin
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Frontiers Science Center of Degeneration and Regeneration in Skeletal System, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xian-Cheng Jiang
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | - Deqiang Yao
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Institute of Aging & Tissue Regeneration, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jie Zhao
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Frontiers Science Center of Degeneration and Regeneration in Skeletal System, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Lu Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China.
| | - Yu Cao
- Institute of Precision Medicine, the Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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48
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Weinstein JJ, Saikia C, Karbat I, Goldenzweig A, Reuveny E, Fleishman SJ. One-shot design elevates functional expression levels of a voltage-gated potassium channel. Protein Sci 2024; 33:e4995. [PMID: 38747377 PMCID: PMC11094769 DOI: 10.1002/pro.4995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 05/19/2024]
Abstract
Membrane proteins play critical physiological roles as receptors, channels, pumps, and transporters. Despite their importance, however, low expression levels often hamper the experimental characterization of membrane proteins. We present an automated and web-accessible design algorithm called mPROSS (https://mPROSS.weizmann.ac.il), which uses phylogenetic analysis and an atomistic potential, including an empirical lipophilicity scale, to improve native-state energy. As a stringent test, we apply mPROSS to the Kv1.2-Kv2.1 paddle chimera voltage-gated potassium channel. Four designs, encoding 9-26 mutations relative to the parental channel, were functional and maintained potassium-selective permeation and voltage dependence in Xenopus oocytes with up to 14-fold increase in whole-cell current densities. Additionally, single-channel recordings reveal no significant change in the channel-opening probability nor in unitary conductance, indicating that functional expression levels increase without impacting the activity profile of individual channels. Our results suggest that the expression levels of other dynamic channels and receptors may be enhanced through one-shot design calculations.
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Affiliation(s)
- Jonathan Jacob Weinstein
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
Scala Biodesign LtdTel AvivIsrael
| | - Chandamita Saikia
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
- Present address:
Institute for BiochemistryUniversity of LübeckLübeckGermany
| | - Izhar Karbat
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | | | - Eitan Reuveny
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
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49
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Ganwir P, Bhadane R, Chaturbhuj GU. In-silico screening and identification of glycomimetic as potential human sodium-glucose co-transporter 2 inhibitor. Comput Biol Chem 2024; 110:108074. [PMID: 38678730 DOI: 10.1016/j.compbiolchem.2024.108074] [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: 01/15/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024]
Abstract
Sodium-glucose co-transporter 2 (SGLT2) is one of the important targets against type II diabetes mellitus. A typical SGLT2 inhibitor acts by inhibiting glucose reabsorption, thus lowering the blood glucose level. Unlike SGLT1, SGLT2 is responsible for almost 90% glucose reabsorption from glomerular filtrate. The current SGLT2 inhibitors include gliflozins, often prescribed as second or third-line agents in diabetes mellitus. The SGLT2 inhibitors also benefit patients with heart and kidney disease. Due to instability issues with the natural O-aryl glycoside analogues C-glycoside analogues were developed and showed improved stability. Despite enhanced bioavailability and selectivity of newer derivatives, some serious side effects are associated with gliflozin analogues. At the present study, we applied in-silico approaches to find new glycomimetic compounds as potent SGLT2 inhibitors that could show improvement in side effects associated with current analogues. This work applied both ligand-based and structure-based drug approaches to find potential compounds. We developed a 3D-QSAR method to screen potential inhibitors from a library of ten thousand compounds and performed docking studies. The compounds were ranked based on predicted pIC50 and docking score. An initial screening of five thousand compounds was conducted, and the subsequently selected top 12 compounds were based on binding free energy calculations. These selected compounds were subjected to molecular dynamics (MD) simulations. Remarkably, our simulations identified nine compounds that exhibited significant and sustained binding affinity compared to the co-crystallized Empagliflozin. Collectively, considering the anticipated pharmacokinetic profiles and toxicity assessments, several of these compounds emerged as promising candidates for further in-depth evaluation.
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Affiliation(s)
- Prerna Ganwir
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, India; Department of Pharmaceutical Chemistry, Dr Bhanuben Nanavati College of Pharmacy, Vile Parle West, Mumbai 400056, India
| | - Rajendra Bhadane
- Pharmaceutical Sciences Laboratory, Åbo Akademi University, Tykistökatu 6 A, Biocity, Turku FI-20520, Finland; Institute of Biomedicine, Research Unit for Infection and Immunity, University of Turku, Kiinamyllynkatu 10, Turku FI-20520, Finland.
| | - Ganesh U Chaturbhuj
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai 400019, India.
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50
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Mukhaleva E, Ma N, van der Velden WJC, Gogoshin G, Branciamore S, Bhattacharya S, Rodin AS, Vaidehi N. Bayesian network models identify cooperative GPCR:G protein interactions that contribute to G protein coupling. J Biol Chem 2024; 300:107362. [PMID: 38735478 PMCID: PMC11176750 DOI: 10.1016/j.jbc.2024.107362] [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: 11/03/2023] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/14/2024] Open
Abstract
Cooperative interactions in protein-protein interfaces demonstrate the interdependency or the linked network-like behavior and their effect on the coupling of proteins. Cooperative interactions also could cause ripple or allosteric effects at a distance in protein-protein interfaces. Although they are critically important in protein-protein interfaces, it is challenging to determine which amino acid pair interactions are cooperative. In this work, we have used Bayesian network modeling, an interpretable machine learning method, combined with molecular dynamics trajectories to identify the residue pairs that show high cooperativity and their allosteric effect in the interface of G protein-coupled receptor (GPCR) complexes with Gα subunits. Our results reveal six GPCR:Gα contacts that are common to the different Gα subtypes and show strong cooperativity in the formation of interface. Both the C terminus helix5 and the core of the G protein are codependent entities and play an important role in GPCR coupling. We show that a promiscuous GPCR coupling to different Gα subtypes, makes all the GPCR:Gα contacts that are specific to each Gα subtype (Gαs, Gαi, and Gαq). This work underscores the potential of data-driven Bayesian network modeling in elucidating the intricate dependencies and selectivity determinants in GPCR:G protein complexes, offering valuable insights into the dynamic nature of these essential cellular signaling components.
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Affiliation(s)
- Elizaveta Mukhaleva
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Wijnand J C van der Velden
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Grigoriy Gogoshin
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Sergio Branciamore
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California, USA.
| | - Supriyo Bhattacharya
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA.
| | - Andrei S Rodin
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California, USA.
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California, USA; Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California, USA.
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