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Rendošová M, Gyepes R, Gucký A, Kožurková M, Vilková M, Olejníková P, Kello M, Liška A, Kléri I, Havlíčková J, Tamáš A, Vargová Z. In(III) pyridinecarboxylate complexes: Composition, solution equilibria estimation, bioevaluation and interactions with HSA. J Inorg Biochem 2024; 262:112738. [PMID: 39293328 DOI: 10.1016/j.jinorgbio.2024.112738] [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: 04/19/2024] [Revised: 09/02/2024] [Accepted: 09/09/2024] [Indexed: 09/20/2024]
Abstract
Two In(III) - pyridinecarboxylates ([In(Pic)2(NO3)(H2O)] (InPic; HPic = picolinic acid), [In(HDpic)(Dpic)(H2O)2]·5H2O (InDpic; H2Dpic = dipicolinic acid), have been synthesized by one-step procedure. The complexes composition was confirmed by physicochemical analyses and X-ray diffraction confirmed molecular structure of both complexes. Moreover, complex species speciation was described in both systems by potentiometry and 1H NMR spectroscopy and mononuclear complex species were determined; [In(Pic)]2+ (logβ011 = 6.94(4)), [In(Pic)2]+ (logβ021 = 11.98(9)), [In(Dpic)]+ (logβ011 = 10.42(6)), [In(Dpic)2]- (logβ021 = 17.58(7)) and [In(Dpic)2(OH)]2- (logβ-121 = 10.18(6)). To confirm the complexes stability in 1 % DMSO, 1H NMR spectra were measured (immediately after dissolution up to 96 h). Antimicrobial and anticancer assays indicate a more significant sensitivity of S. aureus bacteria and MDA-MB-231 cancer cells to the InPic complex (IC50 = 25 and 340.7 μM) than to the InDpic (IC50 = 50 and 975.4 μM). The interaction and binding mechanism of picolinic/dipicolinic acid and their indium(III) complexes with HSA (human serum albumin) were studied using fluorescence and CD spectroscopy. The results confirmed that the studied compounds had bound successfully to HSA, and the binding parameters and constants (KSV, Kq, Kb) were calculated together with the number of binding sites. The binding forces were identified based on calculated thermodynamic parameters (ΔG, ΔH, ΔS). Synchronous spectra were used to study the microenvironment of Tyr and Trp residues and displacement assays revealed that site I was the preferred binding site. After binding, conformational changes were found to have occurred in the HSA molecule and the % α-helical content had decreased.
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Affiliation(s)
- Michaela Rendošová
- Department of Inorganic Chemistry, P. J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovak Republic
| | - Róbert Gyepes
- Department of Inorganic Chemistry, Charles University, Hlavova 2030, 128 00 Prague, Czech Republic
| | - Adrián Gucký
- Department of Biochemistry, P. J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovak Republic
| | - Mária Kožurková
- Department of Biochemistry, P. J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovak Republic
| | - Mária Vilková
- NMR Laboratory, P. J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovak Republic
| | - Petra Olejníková
- Department of Biochemistry and Microbiology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovak Republic
| | - Martin Kello
- Department of Pharmacology, P. J. Šafárik University, Trieda SNP 1, 040 11 Košice, Slovak Republic
| | - Alan Liška
- Department of Molecular Electrochemistry and Catalysis, J. Heyrovský Institute of Physical Chemistry of the CAS, Dolejškova 3/2155, 182 23, Prague 8, Czech Republic
| | - Ivana Kléri
- Department of Biochemistry, P. J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovak Republic
| | - Jana Havlíčková
- Department of Inorganic Chemistry, Charles University, Hlavova 2030, 128 00 Prague, Czech Republic
| | - Adrián Tamáš
- Department of Inorganic Chemistry, P. J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovak Republic
| | - Zuzana Vargová
- Department of Inorganic Chemistry, P. J. Šafárik University, Moyzesova 11, 041 54 Košice, Slovak Republic.
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2
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Fan J, Ke H, Lei J, Wang J, Tominaga M, Lei X. Structural basis of TRPV1 inhibition by SAF312 and cholesterol. Nat Commun 2024; 15:6689. [PMID: 39107321 PMCID: PMC11303535 DOI: 10.1038/s41467-024-51085-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 07/29/2024] [Indexed: 08/10/2024] Open
Abstract
Transient Receptor Potential Vanilloid 1 (TRPV1) plays a central role in pain sensation and is thus an attractive pharmacological drug target. SAF312 is a potent, selective, and non-competitive antagonist of TRPV1 and shows promising potential in treating ocular surface pain. However, the precise mechanism by which SAF312 inhibits TRPV1 remains poorly understood. Here, we present the cryo-EM structure of human TRPV1 in complex with SAF312, elucidating the structural foundation of its antagonistic effects on TRPV1. SAF312 binds to the vanilloid binding pocket, preventing conformational changes in S4 and S5 helices, which are essential for channel gating. Unexpectedly, a putative cholesterol was found to contribute to SAF312's inhibition. Complemented by mutagenesis experiments and molecular dynamics simulations, our research offers substantial mechanistic insights into the regulation of TRPV1 by SAF312, highlighting the interplay between the antagonist and cholesterol in modulating TRPV1 function. This work not only expands our understanding of TRPV1 inhibition by SAF312 but also lays the groundwork for further developments in the design and optimization of TRPV1-related therapies.
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Affiliation(s)
- Junping Fan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Organic Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
| | - Han Ke
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Organic Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jing Lei
- Division of Cell Signaling, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan
- Thermal Biology Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan
| | - Jin Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Organic Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Makoto Tominaga
- Division of Cell Signaling, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan
- Thermal Biology Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan
- Thermal Biology Research Group, Nagoya Advanced Research and Development Center, Nagoya City University, Nagoya, 467-8601, Japan
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Organic Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- Institute for Cancer Research, Shenzhen Bay Laboratory, Shenzhen, 518107, China.
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3
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Guo Z, Zhu AT, Wei X, Jiang Y, Yu Y, Noh I, Gao W, Fang RH, Zhang L. A genetically engineered neuronal membrane-based nanotoxoid elicits protective immunity against neurotoxins. Bioact Mater 2024; 38:321-330. [PMID: 38764446 PMCID: PMC11101676 DOI: 10.1016/j.bioactmat.2024.05.006] [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: 01/07/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/21/2024] Open
Abstract
Given their dangerous effects on the nervous system, neurotoxins represent a significant threat to public health. Various therapeutic approaches, including chelating agents, receptor decoys, and toxin-neutralizing antibodies, have been explored. While prophylactic vaccines are desirable, it is oftentimes difficult to effectively balance their safety and efficacy given the highly dangerous nature of neurotoxins. To address this, we report here on a nanovaccine against neurotoxins that leverages the detoxifying properties of cell membrane-coated nanoparticles. A genetically modified cell line with constitutive overexpression of the α7 nicotinic acetylcholine receptor is developed as a membrane source to generate biomimetic nanoparticles that can effectively and irreversibly bind to α-bungarotoxin, a model neurotoxin. This abrogates the biological activity of the toxin, enabling the resulting nanotoxoid to be safely delivered into the body and processed by the immune system. When co-administered with an immunological adjuvant, a strong humoral response against α-bungarotoxin is generated that protects vaccinated mice against a lethal dose of the toxin. Overall, this work highlights the potential of using genetic modification strategies to develop nanotoxoid formulations against various biological threats.
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Affiliation(s)
- Zhongyuan Guo
- Department of NanoEngineering, Chemical Engineering Program, Shu and K.C. Chien and Peter Farrell Collaboratory, University of California San Diego, La Jolla, CA, 92093, USA
| | - Audrey T. Zhu
- Department of NanoEngineering, Chemical Engineering Program, Shu and K.C. Chien and Peter Farrell Collaboratory, University of California San Diego, La Jolla, CA, 92093, USA
| | - Xiaoli Wei
- Department of NanoEngineering, Chemical Engineering Program, Shu and K.C. Chien and Peter Farrell Collaboratory, University of California San Diego, La Jolla, CA, 92093, USA
| | - Yao Jiang
- Department of NanoEngineering, Chemical Engineering Program, Shu and K.C. Chien and Peter Farrell Collaboratory, University of California San Diego, La Jolla, CA, 92093, USA
| | - Yiyan Yu
- Department of NanoEngineering, Chemical Engineering Program, Shu and K.C. Chien and Peter Farrell Collaboratory, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ilkoo Noh
- Department of NanoEngineering, Chemical Engineering Program, Shu and K.C. Chien and Peter Farrell Collaboratory, University of California San Diego, La Jolla, CA, 92093, USA
| | - Weiwei Gao
- Department of NanoEngineering, Chemical Engineering Program, Shu and K.C. Chien and Peter Farrell Collaboratory, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ronnie H. Fang
- Department of NanoEngineering, Chemical Engineering Program, Shu and K.C. Chien and Peter Farrell Collaboratory, University of California San Diego, La Jolla, CA, 92093, USA
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Liangfang Zhang
- Department of NanoEngineering, Chemical Engineering Program, Shu and K.C. Chien and Peter Farrell Collaboratory, University of California San Diego, La Jolla, CA, 92093, USA
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Obi P, Gc JB, Mariasoosai C, Diyaolu A, Natesan S. Application of Generative Artificial Intelligence in Predicting Membrane Partitioning of Drugs: Combining Denoising Diffusion Probabilistic Models and MD Simulations Reduces the Computational Cost to One-Third. J Chem Theory Comput 2024; 20:5866-5881. [PMID: 38942732 DOI: 10.1021/acs.jctc.4c00315] [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] [Indexed: 06/30/2024]
Abstract
The optimal interaction of drugs with plasma membranes and membranes of subcellular organelles is a prerequisite for desirable pharmacology. Importantly, for drugs targeting the transmembrane lipid-facing sites of integral membrane proteins, the relative affinity of a drug to the bilayer lipids compared to the surrounding aqueous phase affects the partitioning, access, and binding of the drug to the target site. Molecular dynamics (MD) simulations, including enhanced sampling techniques such as steered MD, umbrella sampling (US), and metadynamics, offer valuable insights into the interactions of drugs with the membrane lipids and water in atomistic detail. However, these methods are computationally prohibitive for the high-throughput screening of drug candidates. This study shows that applying denoising diffusion probabilistic models (DDPMs), a generative AI method, to US simulation data reduces the computational cost significantly. Specifically, the models used only partial (one-third) data from the US simulations and reproduced the complete potential of mean force (PMF) profiles for three FDA-approved drugs (β2-adrenergic agonists) and ∼20 biologically relevant chemicals with known experimentally characterized bilayer locations. Intriguingly, the model can predict the solvation-free energies for partitioning and crossing the bilayer, preferred bilayer locations (low-energy well), and orientations of the ligands with high accuracy. The results indicate that DDPMs can be used to characterize the complete membrane partitioning profile of drug molecules using fewer umbrella sampling simulations at select positions along the bilayer normal (z-axis), irrespective of their amphiphilic-lipophilic-cephalophilic characteristics.
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Affiliation(s)
- Peter Obi
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington 99202, United States
| | - Jeevan B Gc
- The Center for Protein Degradation, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, United States
| | - Charles Mariasoosai
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington 99202, United States
| | - Ayobami Diyaolu
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington 99202, United States
| | - Senthil Natesan
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington 99202, United States
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5
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Labrecque C, Fuglestad B. Ligandability at the Membrane Interface of GPx4 Revealed through a Reverse Micelle Fragment Screening Platform. JACS AU 2024; 4:2676-2686. [PMID: 39055139 PMCID: PMC11267533 DOI: 10.1021/jacsau.4c00427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024]
Abstract
While they account for a large portion of drug targets, membrane proteins present a unique challenge for drug discovery. Peripheral membrane proteins (PMPs), a class of water-soluble proteins that bind to membranes, are also difficult targets, particularly those that function only when bound to membranes. The protein-membrane interface in PMPs is often where functional interactions and catalysis occur, making it a logical target for inhibition. However, protein-membrane interfaces are underexplored spaces in inhibitor design, and there is a need for enhanced methods for small-molecule ligand discovery. In an effort to better initiate drug discovery efforts for PMPs, this study presents a screening methodology using membrane-mimicking reverse micelles (mmRM) and NMR-based fragment screening to assess ligandability at the protein-membrane interface. The proof-of-principle target, glutathione peroxidase 4 (GPx4), is a lipid hydroperoxidase that is essential for the oxidative protection of membranes and thereby the prevention of ferroptosis. GPx4 inhibition is promising for therapy-resistant cancer therapy, but current inhibitors are generally covalent ligands with limited clinical utility. Presented here is the discovery of noncovalent small-molecule ligands for membrane-bound GPx4 revealed through the mmRM fragment screening methodology. The fragments were tested against GPx4 under bulk aqueous conditions and displayed little to no binding to the protein without embedment into the membrane. The 9 hits had varying affinities and partitioning coefficients and revealed properties of fragments that bind within the protein-membrane interface. Additionally, a secondary screen confirmed the potential to progress the fragments by enhancing the affinity from >200 to ∼15 μM with the addition of certain hydrophobic groups. This study presents an advancement of screening capabilities for membrane-associated proteins, reveals ligandability within the GPx4 protein-membrane interface, and may serve as a starting point for developing noncovalent inhibitors of GPx4.
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Affiliation(s)
- Courtney
L. Labrecque
- Department
of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Brian Fuglestad
- Department
of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- Institute
for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
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6
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Tang T, Sun J, Li C. The role of Phafin proteins in cell signaling pathways and diseases. Open Life Sci 2024; 19:20220896. [PMID: 38947768 PMCID: PMC11211877 DOI: 10.1515/biol-2022-0896] [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: 02/11/2024] [Revised: 05/14/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
Membrane-associated proteins are important membrane readers that mediate and facilitate the signaling and trafficking pathways in eukaryotic membrane-bound compartments. The protein members in the Phafin family are membrane readers containing two phosphoinositide recognition domains: the Pleckstrin Homology domain and the FYVE (Fab1, YOTB, Vac1, and early endosome antigen 1) domain. Phafin proteins, categorized into two subfamilies, Phafin1 and Phafin2, associate with cellular membranes through interactions involving membrane-embedded phosphoinositides and phosphoinositide-binding domains. These membrane-associated Phafin proteins play pivotal roles by recruiting binding partners and forming complexes, which contribute significantly to apoptotic, autophagic, and macropinocytotic pathways. Elevated expression levels of Phafin1 and Phafin2 are observed in various cancers. A recent study highlights a significant increase in Phafin1 protein levels in the lungs of idiopathic pulmonary fibrosis patients compared to normal subjects, suggesting a crucial role for Phafin1 in the pathogenesis of pulmonary fibrosis. Additionally, phosphatidylinositol-3-phosphate-binding 2 (Pib2), a close relative of the Phafin1 protein, functions as an amino acid sensor activating the TOCR1 pathway in yeasts. This review focuses on delineating the involvement of Phafin proteins in cellular signaling and their implications in diseases and briefly discusses the latest research findings concerning Pib2.
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Affiliation(s)
- Tuoxian Tang
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jing Sun
- Department of Biostatistics and Epidemiology, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Chen Li
- Department of Biology, Chemistry, Pharmacy, Free University of Berlin, Berlin, Germany
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7
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Inan T, Flinko R, Lewis GK, MacKerell AD, Kurkcuoglu O. Identifying and Assessing Putative Allosteric Sites and Modulators for CXCR4 Predicted through Network Modeling and Site Identification by Ligand Competitive Saturation. J Phys Chem B 2024; 128:5157-5174. [PMID: 38647430 PMCID: PMC11139592 DOI: 10.1021/acs.jpcb.4c00925] [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: 02/12/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
The chemokine receptor CXCR4 is a critical target for the treatment of several cancer types and HIV-1 infections. While orthosteric and allosteric modulators have been developed targeting its extracellular or transmembrane regions, the intramembrane region of CXCR4 may also include allosteric binding sites suitable for the development of allosteric drugs. To investigate this, we apply the Gaussian Network Model (GNM) to the monomeric and dimeric forms of CXCR4 to identify residues essential for its local and global motions located in the hinge regions of the protein. Residue interaction network (RIN) analysis suggests hub residues that participate in allosteric communication throughout the receptor. Mutual residues from the network models reside in regions with a high capacity to alter receptor dynamics upon ligand binding. We then investigate the druggability of these potential allosteric regions using the site identification by ligand competitive saturation (SILCS) approach, revealing two putative allosteric sites on the monomer and three on the homodimer. Two screening campaigns with Glide and SILCS-Monte Carlo docking using FDA-approved drugs suggest 20 putative hit compounds including antifungal drugs, anticancer agents, HIV protease inhibitors, and antimalarial drugs. In vitro assays considering mAB 12G5 and CXCL12 demonstrate both positive and negative allosteric activities of these compounds, supporting our computational approach. However, in vivo functional assays based on the recruitment of β-arrestin to CXCR4 do not show significant agonism and antagonism at a single compound concentration. The present computational pipeline brings a new perspective to computer-aided drug design by combining conformational dynamics based on network analysis and cosolvent analysis based on the SILCS technology to identify putative allosteric binding sites using CXCR4 as a showcase.
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Affiliation(s)
- Tugce Inan
- Department
of Chemical Engineering, Istanbul Technical
University, Istanbul 34469, Turkey
| | - Robin Flinko
- Institute
of Human Virology, University of Maryland
School of Medicine, Baltimore, Maryland 21201, United States
| | - George K. Lewis
- Institute
of Human Virology, University of Maryland
School of Medicine, Baltimore, Maryland 21201, United States
| | - Alexander D. MacKerell
- University
of Maryland Computer-Aided Drug Design Center, Department of Pharmaceutical
Sciences, School of Pharmacy, University
of Maryland, Baltimore, Maryland 21201, United States
| | - Ozge Kurkcuoglu
- Department
of Chemical Engineering, Istanbul Technical
University, Istanbul 34469, Turkey
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8
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Labrecque CL, Fuglestad B. Ligandability at the membrane interface of GPx4 revealed through a reverse micelle fragment screening platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593437. [PMID: 38766018 PMCID: PMC11100811 DOI: 10.1101/2024.05.09.593437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
While they account for a large portion of drug targets, membrane proteins (MPs) present a unique challenge for drug discovery. Peripheral membrane proteins (PMPs), a class of proteins that bind reversibly to membranes, are also difficult targets, particularly those that function only while bound to membranes. The protein-membrane interface in PMPs is often where functional interactions and catalysis occur, making it a logical target for inhibition. However, interfaces are underexplored spaces in inhibitor design and there is a need for enhanced methods for small-molecule ligand discovery. In an effort to better initiate drug discovery efforts for PMPs, this study presents a screening methodology using membrane-mimicking reverse micelles (mmRM) and NMR-based fragment screening to assess ligandability in the protein-membrane interface. The proof-of-principle target, glutathione peroxidase 4 (GPx4), is a lipid hydroperoxidase which is essential for the oxidative protection of membranes and thereby the prevention of ferroptosis. GPx4 inhibition is promising for therapy-resistant cancer therapy, but current inhibitors are generally covalent ligands with limited clinical utility. Presented here is the discovery of non-covalent small-molecule ligands for membrane-bound GPx4 revealed through the mmRM fragment screening methodology. The fragments were tested against GPx4 in bulk aqueous conditions and displayed little to no binding to the protein without embedment into the membrane. The 9 hits had varying affinities and partitioning coefficients and revealed properties of fragments that bind within the protein-membrane interface. Additionally, a secondary screen confirmed the potential to progress the fragments by enhancing the affinity from > 200 μM to ~15 μM with the addition of certain hydrophobic groups. This study presents an advancement of screening capabilities for membrane associated proteins, reveals ligandability within the GPx4 protein-membrane interface, and may serve as a starting point for developing non-covalent inhibitors of GPx4.
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Affiliation(s)
- Courtney L. Labrecque
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 22384, United States
| | - Brian Fuglestad
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 22384, United States
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
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9
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Bedini A, Elisi GM, Fanini F, Retini M, Scalvini L, Pasquini S, Contri C, Varani K, Spadoni G, Mor M, Vincenzi F, Rivara S. Binding and unbinding of potent melatonin receptor ligands: Mechanistic simulations and experimental evidence. J Pineal Res 2024; 76:e12941. [PMID: 38606814 DOI: 10.1111/jpi.12941] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 04/13/2024]
Abstract
The labeled ligand commonly employed in competition binding studies for melatonin receptor ligands, 2-[125I]iodomelatonin, showed slow dissociation with different half-lives at the two receptor subtypes. This may affect the operational measures of affinity constants, which at short incubation times could not be obtained in equilibrium conditions, and structure-activity relationships, as the Ki values of tested ligands could depend on either interaction at the binding site or the dissociation path. To address these issues, the kinetic and saturation binding parameters of 2-[125I]iodomelatonin as well as the competition constants for a series of representative ligands were measured at a short (2 h) and a long (20 h) incubation time. Concurrently, we simulated by molecular modeling the dissociation path of 2-iodomelatonin from MT1 and MT2 receptors and investigated the role of interactions at the binding site on the stereoselectivity observed for the enantiomers of the subtype-selective ligand UCM1014. We found that equilibrium conditions for 2-[125I]iodomelatonin binding can be reached only with long incubation times, particularly for the MT2 receptor subtype, for which a time of 20 h approximates this condition. On the other hand, measured Ki values for a set of ligands including agonists, antagonists, nonselective, and subtype-selective compounds were not significantly affected by the length of incubation, suggesting that structure-activity relationships based on data collected at shorter time reflect different interactions at the binding site. Molecular modeling simulations evidenced that the slower dissociation of 2-iodomelatonin from the MT2 receptor can be related to the restricted mobility of a gatekeeper tyrosine along a lipophilic path from the binding site to the membrane bilayer. The enantiomers of the potent, MT2-selective agonist UCM1014 were separately synthesized and tested. Molecular dynamics simulations of the receptor-ligand complexes provided an explanation for their stereoselectivity as due to the preference shown by the eutomer at the binding site for the most abundant axial conformation adopted by the ligand in solution. These results suggest that, despite the slow-binding kinetics occurring for the labeled ligand, affinity measures at shorter incubation times give robust results consistent with known structure-activity relationships and with interactions taken at the receptor binding site.
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Affiliation(s)
- Annalida Bedini
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Urbino, Italy
| | - Gian Marco Elisi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parma, Italy
| | - Fabiola Fanini
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Urbino, Italy
| | - Michele Retini
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Urbino, Italy
| | - Laura Scalvini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parma, Italy
| | - Silvia Pasquini
- Dipartimento di Scienze Chimiche, Farmaceutiche ed Agrarie, Università degli Studi di Ferrara, Ferrara, Italy
| | - Chiara Contri
- Dipartimento di Medicina Traslazionale, Università degli Studi di Ferrara, Ferrara, Italy
| | - Katia Varani
- Dipartimento di Medicina Traslazionale, Università degli Studi di Ferrara, Ferrara, Italy
| | - Gilberto Spadoni
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Carlo Bo, Urbino, Italy
| | - Marco Mor
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parma, Italy
| | - Fabrizio Vincenzi
- Dipartimento di Medicina Traslazionale, Università degli Studi di Ferrara, Ferrara, Italy
| | - Silvia Rivara
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parma, Italy
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10
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Eyal S. Tuning Sodium Channel Blockers to the Near-Atomic Level. Epilepsy Curr 2024; 24:123-125. [PMID: 39280048 PMCID: PMC11394411 DOI: 10.1177/15357597231225065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2024] Open
Abstract
[Box: see text]
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Affiliation(s)
- Sara Eyal
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem
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11
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Ashrafuzzaman M, Koeppe RE, Andersen OS. Intrinsic Lipid Curvature and Bilayer Elasticity as Regulators of Channel Function: A Comparative Single-Molecule Study. Int J Mol Sci 2024; 25:2758. [PMID: 38474005 PMCID: PMC10931550 DOI: 10.3390/ijms25052758] [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: 01/06/2024] [Revised: 02/13/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
Perturbations in bilayer material properties (thickness, lipid intrinsic curvature and elastic moduli) modulate the free energy difference between different membrane protein conformations, thereby leading to changes in the conformational preferences of bilayer-spanning proteins. To further explore the relative importance of curvature and elasticity in determining the changes in bilayer properties that underlie the modulation of channel function, we investigated how the micelle-forming amphiphiles Triton X-100, reduced Triton X-100 and the HII lipid phase promoter capsaicin modulate the function of alamethicin and gramicidin channels. Whether the amphiphile-induced changes in intrinsic curvature were negative or positive, amphiphile addition increased gramicidin channel appearance rates and lifetimes and stabilized the higher conductance states in alamethicin channels. When the intrinsic curvature was modulated by altering phospholipid head group interactions, however, maneuvers that promote a negative-going curvature stabilized the higher conductance states in alamethicin channels but destabilized gramicidin channels. Using gramicidin channels of different lengths to probe for changes in bilayer elasticity, we found that amphiphile adsorption increases bilayer elasticity, whereas altering head group interactions does not. We draw the following conclusions: first, confirming previous studies, both alamethicin and gramicidin channels are modulated by changes in lipid bilayer material properties, the changes occurring in parallel yet differing dependent on the property that is being changed; second, isolated, negative-going changes in curvature stabilize the higher current levels in alamethicin channels and destabilize gramicidin channels; third, increases in bilayer elasticity stabilize the higher current levels in alamethicin channels and stabilize gramicidin channels; and fourth, the energetic consequences of changes in elasticity tend to dominate over changes in curvature.
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Affiliation(s)
- Mohammad Ashrafuzzaman
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA;
| | - Roger E. Koeppe
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA;
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12
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Su R, Fu H, Ding L, Fu B, He S, Ma H, Hu H, Ren H. Long-term impact of nano zero-valent iron on methanogenic activity, microbial community structure, and transcription activity in anaerobic wastewater treatment system. BIORESOURCE TECHNOLOGY 2024; 393:130028. [PMID: 37977494 DOI: 10.1016/j.biortech.2023.130028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Nano zero-valent iron (NZVI) is commonly used in industrial wastewater treatment. However, its long-term impact mechanisms of metabolization in anaerobic systems are not well understood. This study investigated the effects of long-term and continuous addition of NZVI on methanogenic activity, microbial community, and transcription activity. The results demonstrated that low levels of NZVI (1000 mg/L) induced inhibition of methanogenesis after 80 days, while high levels of NZVI (5000 mg/L) immediately led to a sharp decrease of cumulative methane production and chemical oxygen demand removal, which arrived at a steady state (14.4 % of control and 17 %) after 30 days. NZVI adversely affected cell viability, adenosine triphosphate production, and fatty acid evolution of cell membranes played a crucial role in resisting chronic NZVI toxicity. Moreover, high NZVI levels hindered the transcription of key enzymes CoM and mcrA, while low NZVI levels maintained its high CoM and mcrA activity, but down-regulated the transcription of cdh and hdr. Besides, amino-utilizing bacteria was reduced under the high NZVI concentration, while low NZVI changed dominant genus with potential protein hydrolysis function from Candidatus Cloacamonas to Sedimentibacter. These results provide a guideline for proper NZVI utilization in wastewater treatment.
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Affiliation(s)
- Runhua Su
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Huimin Fu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China; National Research Base of Intelligent Manufacturing Service, Chongqing Technology and Business University, Chongqing 400067, China
| | - Lili Ding
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China.
| | - Bo Fu
- School of Environmental and Civil Engineering, Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Su He
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Haijun Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Haidong Hu
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environment, Nanjing University, Nanjing 210023, China
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13
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Melancon K, Pliushcheuskaya P, Meiler J, Künze G. Targeting ion channels with ultra-large library screening for hit discovery. Front Mol Neurosci 2024; 16:1336004. [PMID: 38249296 PMCID: PMC10796734 DOI: 10.3389/fnmol.2023.1336004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/05/2023] [Indexed: 01/23/2024] Open
Abstract
Ion channels play a crucial role in a variety of physiological and pathological processes, making them attractive targets for drug development in diseases such as diabetes, epilepsy, hypertension, cancer, and chronic pain. Despite the importance of ion channels in drug discovery, the vastness of chemical space and the complexity of ion channels pose significant challenges for identifying drug candidates. The use of in silico methods in drug discovery has dramatically reduced the time and cost of drug development and has the potential to revolutionize the field of medicine. Recent advances in computer hardware and software have enabled the screening of ultra-large compound libraries. Integration of different methods at various scales and dimensions is becoming an inevitable trend in drug development. In this review, we provide an overview of current state-of-the-art computational chemistry methodologies for ultra-large compound library screening and their application to ion channel drug discovery research. We discuss the advantages and limitations of various in silico techniques, including virtual screening, molecular mechanics/dynamics simulations, and machine learning-based approaches. We also highlight several successful applications of computational chemistry methodologies in ion channel drug discovery and provide insights into future directions and challenges in this field.
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Affiliation(s)
- Kortney Melancon
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | | | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
- Medical Faculty, Institute for Drug Discovery, Leipzig University, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence, Leipzig University, Leipzig, Germany
| | - Georg Künze
- Medical Faculty, Institute for Drug Discovery, Leipzig University, Leipzig, Germany
- Center for Scalable Data Analytics and Artificial Intelligence, Leipzig University, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, Leipzig University, Leipzig, Germany
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14
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Jiang W, Wijerathne TD, Zhang H, Lin YC, Jo S, Im W, Lacroix JJ, Luo YL. Structural and thermodynamic framework for PIEZO1 modulation by small molecules. Proc Natl Acad Sci U S A 2023; 120:e2310933120. [PMID: 38060566 PMCID: PMC10723123 DOI: 10.1073/pnas.2310933120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/12/2023] [Indexed: 12/17/2023] Open
Abstract
Mechanosensitive PIEZO channels constitute potential pharmacological targets for multiple clinical conditions, spurring the search for potent chemical PIEZO modulators. Among them is Yoda1, a widely used synthetic small molecule PIEZO1 activator discovered through cell-based high-throughput screening. Yoda1 is thought to bind to PIEZO1's mechanosensory arm domain, sandwiched between two transmembrane regions near the channel pore. However, how the binding of Yoda1 to this region promotes channel activation remains elusive. Here, we first demonstrate that cross-linking PIEZO1 repeats A and B with disulfide bridges reduces the effects of Yoda1 in a redox-dependent manner, suggesting that Yoda1 acts by perturbing the contact between these repeats. Using molecular dynamics-based absolute binding free energy simulations, we next show that Yoda1 preferentially occupies a deeper, amphipathic binding site with higher affinity in PIEZO1 open state. Using Yoda1's binding poses in open and closed states, relative binding free energy simulations were conducted in the membrane environment, recapitulating structure-activity relationships of known Yoda1 analogs. Through virtual screening of an 8 million-compound library using computed fragment maps of the Yoda1 binding site, we subsequently identified two chemical scaffolds with agonist activity toward PIEZO1. This study supports a pharmacological model in which Yoda1 activates PIEZO1 by wedging repeats A and B, providing a structural and thermodynamic framework for the rational design of PIEZO1 modulators. Beyond PIEZO channels, the three orthogonal computational approaches employed here represent a promising path toward drug discovery in highly heterogeneous membrane protein systems.
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Affiliation(s)
- Wenjuan Jiang
- Department of Biotechnology and Pharmaceutical Sciences, Western University of Health Sciences, Pomona, CA91766
| | - Tharaka D. Wijerathne
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA91766
| | - Han Zhang
- Department of Biological Sciences, Lehigh University, Bethlehem, PA18015
- Department of Chemistry, Lehigh University, Bethlehem, PA18015
- Department of Bioengineering, Lehigh University, Bethlehem, PA18015
- Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA18015
| | - Yi-Chun Lin
- Department of Biotechnology and Pharmaceutical Sciences, Western University of Health Sciences, Pomona, CA91766
| | - Sunhwan Jo
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD21201
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, PA18015
- Department of Chemistry, Lehigh University, Bethlehem, PA18015
- Department of Bioengineering, Lehigh University, Bethlehem, PA18015
- Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA18015
| | - Jerome J. Lacroix
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA91766
| | - Yun L. Luo
- Department of Biotechnology and Pharmaceutical Sciences, Western University of Health Sciences, Pomona, CA91766
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15
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Wang Y, Jiao Q, Wang J, Cai X, Zhao W, Cui X. Prediction of protein-ligand binding affinity with deep learning. Comput Struct Biotechnol J 2023; 21:5796-5806. [PMID: 38213884 PMCID: PMC10782002 DOI: 10.1016/j.csbj.2023.11.009] [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: 08/24/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 01/13/2024] Open
Abstract
The prediction of binding affinities between target proteins and small molecule drugs is essential for speeding up the drug research and design process. To attain precise and effective affinity prediction, computer-aided methods are employed in the drug discovery pipeline. In the last decade, a variety of computational methods has been developed, with deep learning being the most commonly used approach. We have gathered several deep learning methods and classified them into convolutional neural networks (CNNs), graph neural networks (GNNs), and Transformers for analysis and discussion. Initially, we conducted an analysis of the different deep learning methods, focusing on their feature construction and model architecture. We discussed the advantages and disadvantages of each model. Subsequently, we conducted experiments using four deep learning methods on the PDBbind v.2016 core set. We evaluated their prediction capabilities in various affinity intervals and statistically and visually analyzed the samples of correct and incorrect predictions for each model. Through visual analysis, we attempted to combine the strengths of the four models to improve the Root Mean Square Error (RMSE) of predicted affinities by 1.6% (reducing the absolute value to 1.101) and the Pearson Correlation Coefficient (R) by 2.9% (increasing the absolute value to 0.894) compared to the current state-of-the-art method. Lastly, we discussed the challenges faced by current deep learning methods in affinity prediction and proposed potential solutions to address these issues.
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Affiliation(s)
- Yuxiao Wang
- School of Computer Science and Technology, Shandong University, Qingdao 266237, Shandong, China
| | - Qihong Jiao
- School of Computer Science and Technology, Shandong University, Qingdao 266237, Shandong, China
| | - Jingxuan Wang
- School of Computer Science and Technology, Shandong University, Qingdao 266237, Shandong, China
| | - Xiaojun Cai
- School of Computer Science and Technology, Shandong University, Qingdao 266237, Shandong, China
| | - Wei Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, Shandong, China
| | - Xuefeng Cui
- School of Computer Science and Technology, Shandong University, Qingdao 266237, Shandong, China
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16
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Wu K, Karapetyan E, Schloss J, Vadgama J, Wu Y. Advancements in small molecule drug design: A structural perspective. Drug Discov Today 2023; 28:103730. [PMID: 37536390 PMCID: PMC10543554 DOI: 10.1016/j.drudis.2023.103730] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023]
Abstract
In this review, we outline recent advancements in small molecule drug design from a structural perspective. We compare protein structure prediction methods and explore the role of the ligand binding pocket in structure-based drug design. We examine various structural features used to optimize drug candidates, including functional groups, stereochemistry, and molecular weight. Computational tools such as molecular docking and virtual screening are discussed for predicting and optimizing drug candidate structures. We present examples of drug candidates designed based on their molecular structure and discuss future directions in the field. By effectively integrating structural information with other valuable data sources, we can improve the drug discovery process, leading to the identification of novel therapeutics with improved efficacy, specificity, and safety profiles.
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Affiliation(s)
- Ke Wu
- Division of Cancer Research and Training, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA
| | - Eduard Karapetyan
- Division of Cancer Research and Training, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA
| | - John Schloss
- Division of Cancer Research and Training, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA; School of Pharmacy, American University of Health Sciences, Signal Hill, CA 90755, USA
| | - Jaydutt Vadgama
- Division of Cancer Research and Training, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA; School of Pharmacy, American University of Health Sciences, Signal Hill, CA 90755, USA.
| | - Yong Wu
- Division of Cancer Research and Training, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, David Geffen UCLA School of Medicine and UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA 90095, USA.
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17
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Somberg NH, Medeiros‐Silva J, Jo H, Wang J, DeGrado WF, Hong M. Hexamethylene amiloride binds the SARS-CoV-2 envelope protein at the protein-lipid interface. Protein Sci 2023; 32:e4755. [PMID: 37632140 PMCID: PMC10503410 DOI: 10.1002/pro.4755] [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: 07/17/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023]
Abstract
The SARS-CoV-2 envelope (E) protein forms a five-helix bundle in lipid bilayers whose cation-conducting activity is associated with the inflammatory response and respiratory distress symptoms of COVID-19. E channel activity is inhibited by the drug 5-(N,N-hexamethylene) amiloride (HMA). However, the binding site of HMA in E has not been determined. Here we use solid-state NMR to measure distances between HMA and the E transmembrane domain (ETM) in lipid bilayers. 13 C, 15 N-labeled HMA is combined with fluorinated or 13 C-labeled ETM. Conversely, fluorinated HMA is combined with 13 C, 15 N-labeled ETM. These orthogonal isotopic labeling patterns allow us to conduct dipolar recoupling NMR experiments to determine the HMA binding stoichiometry to ETM as well as HMA-protein distances. We find that HMA binds ETM with a stoichiometry of one drug per pentamer. Unexpectedly, the bound HMA is not centrally located within the channel pore, but lies on the lipid-facing surface in the middle of the TM domain. This result suggests that HMA may inhibit the E channel activity by interfering with the gating function of an aromatic network. These distance data are obtained under much lower drug concentrations than in previous chemical shift perturbation data, which showed the largest perturbation for N-terminal residues. This difference suggests that HMA has higher affinity for the protein-lipid interface than the channel pore. These results give insight into the inhibition mechanism of HMA for SARS-CoV-2 E.
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Affiliation(s)
- Noah H. Somberg
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - João Medeiros‐Silva
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Hyunil Jo
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgersthe State University of New JerseyPiscatawayNew JerseyUSA
| | - William F. DeGrado
- Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Mei Hong
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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18
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Morstein J, Shrestha R, Van QN, López CA, Arora N, Tonelli M, Liang H, Chen D, Zhou Y, Hancock JF, Stephen AG, Turbyville TJ, Shokat KM. Direct Modulators of K-Ras-Membrane Interactions. ACS Chem Biol 2023; 18:2082-2093. [PMID: 37579045 PMCID: PMC10510109 DOI: 10.1021/acschembio.3c00413] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 07/31/2023] [Indexed: 08/16/2023]
Abstract
Protein-membrane interactions (PMIs) are ubiquitous in cellular signaling. Initial steps of signal transduction cascades often rely on transient and dynamic interactions with the inner plasma membrane leaflet to populate and regulate signaling hotspots. Methods to target and modulate these interactions could yield attractive tool compounds and drug candidates. Here, we demonstrate that the conjugation of a medium-chain lipid tail to the covalent K-Ras(G12C) binder MRTX849 at a solvent-exposed site enables such direct modulation of PMIs. The conjugated lipid tail interacts with the tethered membrane and changes the relative membrane orientation and conformation of K-Ras(G12C), as shown by molecular dynamics (MD) simulation-supported NMR studies. In cells, this PMI modulation restricts the lateral mobility of K-Ras(G12C) and disrupts nanoclusters. The described strategy could be broadly applicable to selectively modulate transient PMIs.
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Affiliation(s)
- Johannes Morstein
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
| | - Rebika Shrestha
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Que N. Van
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - César A. López
- Theoretical
Biology and Biophysics Group, Los Alamos
National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Neha Arora
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Marco Tonelli
- National
Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Hong Liang
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - De Chen
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Yong Zhou
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - John F. Hancock
- Department
of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, Texas 77030, United States
| | - Andrew G. Stephen
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Thomas J. Turbyville
- NCI
RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Kevan M. Shokat
- Department
of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
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19
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Hu G, Lv M, Guo B, Huang Y, Su Z, Qian Y, Xue X, Liu HK. Immunostimulation with chemotherapy of a ruthenium-arene complex via blockading CD47 signal in chronic myelogenous leukemia cells. J Inorg Biochem 2023; 243:112195. [PMID: 36996696 DOI: 10.1016/j.jinorgbio.2023.112195] [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: 01/19/2023] [Revised: 02/26/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
Abstract
Combination of novel immunomodulation and traditional chemotherapy has become a new tendency in cancer treatment. Increasing evidence suggests that blocking the "don't eat me" signal transmitted by the CD47 can promote the phagocytic ability of macrophages to cancer cells, which might be promising for improved cancer chemoimmunotherapy. In this work, we conjugated CPI-alkyne modified by Devimistat (CPI-613) with ruthenium-arene azide precursor Ru-N3 by copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction to construct Ru complex CPI-Ru. CPI-Ru exhibited satisfactory cytotoxicity towards the K562 cells while nearly non-toxic towards the normal HLF cells. CPI-Ru has been demonstrated to cause severe damage to mitochondria and DNA, ultimately inducing cancer cell death through the autophagic pathway. Moreover, CPI-Ru could significantly downregulate the expression of CD47 on the surface of K562 accompanied by the enhanced immune response by targeting the blockade of CD47. This work provides a new strategy for utilizing metal-based anticancer agents to block CD47 signal to achieve chemoimmunotherapy in chronic myeloid leukemia treatment.
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Affiliation(s)
- Guojing Hu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Mengdi Lv
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Binglian Guo
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Yuanlei Huang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Zhi Su
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Yong Qian
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Xuling Xue
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.
| | - Hong-Ke Liu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.
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20
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Kumari P, Inoue A, Chapman K, Lian P, Rosenbaum DM. Molecular mechanism of fatty acid activation of FFAR1. Proc Natl Acad Sci U S A 2023; 120:e2219569120. [PMID: 37216523 PMCID: PMC10235965 DOI: 10.1073/pnas.2219569120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/03/2023] [Indexed: 05/24/2023] Open
Abstract
FFAR1 is a G-protein-coupled receptor (GPCR) that responds to circulating free fatty acids to enhance glucose-stimulated insulin secretion and release of incretin hormones. Due to the glucose-lowering effect of FFAR1 activation, potent agonists for this receptor have been developed for the treatment of diabetes. Previous structural and biochemical studies of FFAR1 showed multiple sites of ligand binding to the inactive state but left the mechanism of fatty acid interaction and receptor activation unknown. We used cryo-electron microscopy to elucidate structures of activated FFAR1 bound to a Gq mimetic, which were induced either by the endogenous FFA ligand docosahexaenoic acid or γ-linolenic acid and the agonist drug TAK-875. Our data identify the orthosteric pocket for fatty acids and show how both endogenous hormones and synthetic agonists induce changes in helical packing along the outside of the receptor that propagate to exposure of the G-protein-coupling site. These structures show how FFAR1 functions without the highly conserved "DRY" and "NPXXY" motifs of class A GPCRs and also illustrate how the orthosteric site of a receptor can be bypassed by membrane-embedded drugs to confer full activation of G protein signaling.
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Affiliation(s)
- Punita Kumari
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Asuka Inoue
- Department of Pharmaceutical Sciences, Tohoku University, Sendai980-8578, Japan
| | - Karen Chapman
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Peng Lian
- BioHPC at the Lyda Hill Department of Bioinformatics, The University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Daniel M. Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX75390
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21
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Gavutis M, Schulze-Niemand E, Lee HH, Liedberg B, Stein M, Valiokas R. Bilayer lipid membrane formation on surface assemblies with sparsely distributed tethers. NANOSCALE 2023. [PMID: 37128711 DOI: 10.1039/d2nr07069c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A combined computational and experimental study of small unilamellar vesicle (SUV) fusion on mixed self-assembled monolayers (SAMs) terminated with different deuterated tether moieties (-(CD2)7CD3 or -(CD2)15CD3) is reported. Tethered bilayer lipid membrane (tBLM) formation of synthetic 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine was initially probed on SAMs with controlled tether (d-alkyl tail) surface densities and lateral molecular packing using quartz crystal microbalance with dissipation monitoring (QCM-D). Long time-scale coarse-grained molecular dynamics (MD) simulations were then employed to elucidate the mechanisms behind the interaction between the SUVs and the different phases formed by the -(CD2)7CD3 and -(CD2)15CD3 tethers. Furthermore, a series of real time kinetics was recorded under different osmotic conditions using QCM-D to determine the accumulated lipid mass and for probing the fusion process. It is shown that the key factors driving the SUV fusion and tBLM formation on this type of surfaces involve tether insertion into the SUVs along with vesicle deformation. It is also evident that surface densities of the tethers as small as a few mol% are sufficient to obtain stable tBLMs with a high reproducibility. The described "sparsely tethered" tBLM system can be advantageous in studying different biophysical phenomena, such as membrane protein insertion, effects of receptor clustering, and raft formation.
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Affiliation(s)
- Martynas Gavutis
- Department of Nanoengineering, Center for Physical Sciences and Technology, Savanorių 231, 02300 Vilnius, Lithuania.
| | - Eric Schulze-Niemand
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical System, Magdeburg, Germany
- Institute of Experimental Internal Medicine, Medical Faculty, Otto von Guericke University, 39120 Magdeburg, Germany
| | - Hung-Hsun Lee
- Division of Molecular Physics, Department of Physics, Chemistry and Biology, Linköping University, 58183 Linköping, Sweden
| | - Bo Liedberg
- Division of Molecular Physics, Department of Physics, Chemistry and Biology, Linköping University, 58183 Linköping, Sweden
| | - Matthias Stein
- Molecular Simulations and Design Group, Max Planck Institute for Dynamics of Complex Technical System, Magdeburg, Germany
| | - Ramūnas Valiokas
- Department of Nanoengineering, Center for Physical Sciences and Technology, Savanorių 231, 02300 Vilnius, Lithuania.
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22
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Peyear TA, Andersen OS. Screening for bilayer-active and likely cytotoxic molecules reveals bilayer-mediated regulation of cell function. J Gen Physiol 2023; 155:e202213247. [PMID: 36763053 PMCID: PMC9948646 DOI: 10.1085/jgp.202213247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 12/06/2022] [Accepted: 01/13/2023] [Indexed: 02/11/2023] Open
Abstract
A perennial problem encountered when using small molecules (drugs) to manipulate cell or protein function is to assess whether observed changes in function result from specific interactions with a desired target or from less specific off-target mechanisms. This is important in laboratory research as well as in drug development, where the goal is to identify molecules that are unlikely to be successful therapeutics early in the process, thereby avoiding costly mistakes. We pursued this challenge from the perspective that many bioactive molecules (drugs) are amphiphiles that alter lipid bilayer elastic properties, which may cause indiscriminate changes in membrane protein (and cell) function and, in turn, cytotoxicity. Such drug-induced changes in bilayer properties can be quantified as changes in the monomer↔dimer equilibrium for bilayer-spanning gramicidin channels. Using this approach, we tested whether molecules in the Pathogen Box (a library of 400 drugs and drug-like molecules with confirmed activity against tropical diseases released by Medicines for Malaria Venture to encourage the development of therapies for neglected tropical diseases) are bilayer modifiers. 32% of the molecules in the Pathogen Box were bilayer modifiers, defined as molecules that at 10 µM shifted the monomer↔dimer equilibrium toward the conducting dimers by at least 50%. Correlation analysis of the molecules' reported HepG2 cell cytotoxicity to bilayer-modifying potency, quantified as the shift in the gramicidin monomer↔dimer equilibrium, revealed that molecules producing <25% change in the equilibrium had significantly lower probability of being cytotoxic than molecules producing >50% change. Neither cytotoxicity nor bilayer-modifying potency (quantified as the shift in the gramicidin monomer↔dimer equilibrium) was well predicted by conventional physico-chemical descriptors (hydrophobicity, polar surface area, etc.). We conclude that drug-induced changes in lipid bilayer properties are robust predictors of the likelihood of membrane-mediated off-target effects, including cytotoxicity.
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Affiliation(s)
- Thasin A. Peyear
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences. New York, NY, USA
| | - Olaf S. Andersen
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
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23
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Zhang D, Lape R, Shaikh SA, Kohegyi BK, Watson JF, Cais O, Nakagawa T, Greger IH. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. Nat Commun 2023; 14:1659. [PMID: 36966141 PMCID: PMC10039940 DOI: 10.1038/s41467-023-37259-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 03/09/2023] [Indexed: 03/27/2023] Open
Abstract
AMPA glutamate receptors (AMPARs) mediate excitatory neurotransmission throughout the brain. Their signalling is uniquely diversified by brain region-specific auxiliary subunits, providing an opportunity for the development of selective therapeutics. AMPARs associated with TARP γ8 are enriched in the hippocampus, and are targets of emerging anti-epileptic drugs. To understand their therapeutic activity, we determined cryo-EM structures of the GluA1/2-γ8 receptor associated with three potent, chemically diverse ligands. We find that despite sharing a lipid-exposed and water-accessible binding pocket, drug action is differentially affected by binding-site mutants. Together with patch-clamp recordings and MD simulations we also demonstrate that ligand-triggered reorganisation of the AMPAR-TARP interface contributes to modulation. Unexpectedly, one ligand (JNJ-61432059) acts bifunctionally, negatively affecting GluA1 but exerting positive modulatory action on GluA2-containing AMPARs, in a TARP stoichiometry-dependent manner. These results further illuminate the action of TARPs, demonstrate the sensitive balance between positive and negative modulatory action, and provide a mechanistic platform for development of both positive and negative selective AMPAR modulators.
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Affiliation(s)
- Danyang Zhang
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Remigijus Lape
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Saher A Shaikh
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Bianka K Kohegyi
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Jake F Watson
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
- IST Austria, Klosterneuburg, Austria
| | - Ondrej Cais
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Terunaga Nakagawa
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, USA
| | - Ingo H Greger
- Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
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24
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Gc JB, Szlenk CT, Diyaolu A, Obi P, Wei H, Shi X, Gibson KM, Natesan S, Roullet JB. Allosteric modulation of α1β3γ2 GABA A receptors by farnesol through the neurosteroid sites. Biophys J 2023; 122:849-867. [PMID: 36721367 PMCID: PMC10027449 DOI: 10.1016/j.bpj.2023.01.032] [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: 07/25/2022] [Revised: 12/13/2022] [Accepted: 01/23/2023] [Indexed: 02/02/2023] Open
Abstract
In mammalian cells, all-trans farnesol, a 15-carbon isoprenol, is a product of the mevalonate pathway. It is the natural substrate of alcohol dehydrogenase and a substrate for CYP2E1, two enzymes implicated in ethanol metabolism. Studies have shown that farnesol is present in the human brain and inhibits voltage-gated Ca2+ channels at much lower concentrations than ethanol. Here we show that farnesol modulates the activity of γ-aminobutyric acid type A receptors (GABAARs), some of which also mediate the sedative activity of ethanol. Electrophysiology experiments performed in HEK cells expressing human α1β3γ2 or α6β3γ2 GABAARs revealed that farnesol increased chloride currents through positive allosteric modulation of these receptors and showed dependence on both the alcoholic functional group of farnesol and the length of the alkyl chain for activity. In silico studies using long-timescale unbiased all-atom molecular dynamics (MD) simulations of the human α1β3γ2 GABAA receptors revealed that farnesol modulates the channel by directly binding to the transmembrane neurosteroid-binding site, after partitioning into the surrounding membrane and reaching the receptor by lateral diffusion. Channel activation by farnesol was further characterized by several structural and dynamic variables, such as global twisting of the receptor's extracellular domain, tilting of the transmembrane M2 helices, radius, cross-sectional area, hydration status, and electrostatic potential of the channel pore. Our results expand the pharmacological activities of farnesol to yet another class of ion channels implicated in neurotransmission, thus providing a novel path for understanding and treatment of diseases involving GABAA receptor dysfunction.
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Affiliation(s)
- Jeevan B Gc
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Christopher T Szlenk
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Ayobami Diyaolu
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Peter Obi
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Haiyang Wei
- Eurofins Panlabs, Inc., St. Charles, Missouri
| | - Xutong Shi
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - K Michael Gibson
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Senthil Natesan
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington.
| | - Jean-Baptiste Roullet
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington.
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25
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Zohairi F, Khandelia H, Hakami Zanjani AA. Interaction of psychedelic tryptamine derivatives with a lipid bilayer. Chem Phys Lipids 2023; 251:105279. [PMID: 36627076 DOI: 10.1016/j.chemphyslip.2023.105279] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
Naturally occurring psychedelics have been used for a long time as remedies or in religious ceremonies and recreational activities. Recent studies have proven the therapeutic potential of some psychedelic compounds to safely treat a wide range of diseases such as anxiety, depression, migraine, and addiction. It is hypothesized that psychedelic compounds like tryptamines can exert their effects by two possible mechanisms: binding to the transmembrane serotonin receptor and/or modifying the properties of the neuronal membrane that can alter the conformational equilibrium and desensitize receptors. The impact of three different tryptamine class compounds with a tertiary amine (dimethyltryptamine, bufotenine, and 5-MeO-DMT) in both neutral and charged forms on a model bilayer lipid membrane are studied using all-atom MD simulations. All compounds partition into the bilayer, and change membrane properties, but to different extents. We determine the tendency of compounds to partition into the membrane by free energy calculations. Neutral tryptamines partition into the bilayer almost completely. Dimethyltryptamine and 5-MeO-DMT cross the membrane spontaneously during the simulation time, but bufotenine does not, although it has the maximum effect on the structural properties of the membrane. However, protonated compounds partition partially into the bilayer and cannot pass through the middle of the membrane during the simulation time. In this way, subtle alteration of chemical structure can play a significant role in the improvement or deterioration of partitioning of these compounds into the bilayer and their passage across the membrane.
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Affiliation(s)
- Fateme Zohairi
- Faculty of Science, Technology and Medicine, University of Luxembourg, 2 Av. de l'Universite, 4365 Esch-sur-Alzette, Luxembourg
| | - Himanshu Khandelia
- PHYLIFE: Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
| | - Ali Asghar Hakami Zanjani
- PHYLIFE: Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
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26
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Tzortzini E, Corey RA, Kolocouris A. Comparative Study of Receptor-, Receptor State-, and Membrane-Dependent Cholesterol Binding Sites in A 2A and A 1 Adenosine Receptors Using Coarse-Grained Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:928-949. [PMID: 36637988 DOI: 10.1021/acs.jcim.2c01181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We used coarse-grained molecular dynamics (CG MD) simulations to study protein-cholesterol interactions for different activation states of the A2A adenosine receptor (A2AR) and the A1 adenosine receptor (A1R) and predict new cholesterol binding sites indicating amino acid residues with a high residence time in three biologically relevant membranes. Compared to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)-cholesterol and POPC-phosphatidylinositol-bisphosphate (PIP2)-cholesterol, the plasma mimetic membrane best described the cholesterol binding sites previously detected for the inactive state of A2AR and revealed the binding sites with long-lasting amino acid residues. We observed that using the plasma mimetic membrane and plotting residues with cholesterol residence time ≥2 μs, our CG MD simulations captured most obviously the cholesterol-protein interactions. For the inactive A2AR, we identified one more binding site in which cholesterol is bound to residues with a long residence time compared to the previously detected, for the active A1R, three binding sites, and for the inactive A1R, two binding sites. We calculated that for the active states, cholesterol binds to residues with a much longer residence time compared to the inactive state for both A2AR and A1R. The stability of the identified binding sites to A1R or A2AR with CG MD simulations was additionally investigated with potential of mean force calculations using umbrella sampling. We observed that the binding sites with residues to which cholesterol has a long residence time in A2AR have shallow binding free energy minima compared to the related binding sites in A1R, suggesting a stronger binding for cholesterol to A1R. The differences in binding sites in which cholesterol is stabilized and interacts with residues with a long residence time between active and inactive states of A1R and A2AR can be important for differences in functional activity and orthosteric agonist or antagonist affinity and can be used for the design of allosteric modulators, which can bind through lipid pathways. We observed a stronger binding for cholesterol to A1R (i.e., generally higher association rates) compared to A2AR, which remains to be demonstrated. For the active states, cholesterol binds to residues with much longer residence times compared to the inactive state for both A2AR and A1R. Taken together, binding sites of active A1R may be considered as promising allosteric targets.
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Affiliation(s)
- Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771Athens, Greece
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - 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, 15771Athens, Greece
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27
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Wurm KW, Bartz FM, Schulig L, Bodtke A, Bednarski PJ, Link A. Replacing the oxidation-sensitive triaminoaryl chemotype of problematic K V 7 channel openers: Exploration of a nicotinamide scaffold. Arch Pharm (Weinheim) 2023; 356:e2200473. [PMID: 36395379 DOI: 10.1002/ardp.202200473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022]
Abstract
KV 7 channel openers have proven their therapeutic value in the treatment of pain as well as epilepsy and, moreover, they hold the potential to expand into additional indications with unmet medical needs. However, the clinically validated but meanwhile discontinued KV 7 channel openers flupirtine and retigabine bear an oxidation-sensitive triaminoraryl scaffold, which is suspected of causing adverse drug reactions via the formation of quinoid oxidation products. Here, we report the design and synthesis of nicotinamide analogs and related compounds that remediate the liability in the chemical structure of flupirtine and retigabine. Optimization of a nicotinamide lead structure yielded analogs with excellent KV 7.2/3 opening activity, as evidenced by EC50 values approaching the single-digit nanomolar range. On the other hand, weighted KV 7.2/3 opening activity data including inactive compounds allowed for the establishment of structure-activity relationships and a plausible binding mode hypothesis verified by docking and molecular dynamics simulations.
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Affiliation(s)
- Konrad W Wurm
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Frieda-Marie Bartz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Lukas Schulig
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Anja Bodtke
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Patrick J Bednarski
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Andreas Link
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
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28
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Gastaldi MS, Felsztyna I, Miguel V, Sánchez-Borzone ME, García DA. Theoretical and Experimental Study of Molecular Interactions of Fluralaner with Lipid Membranes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2134-2142. [PMID: 36688903 DOI: 10.1021/acs.jafc.2c06811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Fluralaner is a relatively new insecticide belonging to the isoxazoline group, whose action mechanism involves the blocking of GABAA-receptors in the insect nervous system. Because of its high hydrophobicity, fluralaner could bioaccumulate and reach toxic local concentrations. Since there are no data available about the penetration and persistence of isoxazolines in biological membranes, we intend to evaluate fluralaner permanence as a pollutant by using model membranes. We used experimental and in silico models to characterize the incorporation of fluralaner into the lipid phase at different packing states. We determined its impact in the membrane structure and organization. Our results confirm that fluralaner is capable of penetrating, holding, and accumulating in the lipid membrane and provide details on its precise location and orientation. These properties would allow fluralaner to reach high local concentrations in different membranes and organs, which could be dangerous for vertebrate organisms if its handling is not properly controlled.
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Affiliation(s)
- María Salomé Gastaldi
- Facultad de Ciencias Exactas, Físicas y Naturales, Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba5016, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba5016, Argentina
| | - Iván Felsztyna
- Facultad de Ciencias Exactas, Físicas y Naturales, Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba5016, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba5016, Argentina
| | - Virginia Miguel
- Facultad de Ciencias Exactas, Físicas y Naturales, Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba5016, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba5016, Argentina
| | - Mariela E Sánchez-Borzone
- Facultad de Ciencias Exactas, Físicas y Naturales, Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba5016, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba5016, Argentina
| | - Daniel A García
- Facultad de Ciencias Exactas, Físicas y Naturales, Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba5016, Argentina
- Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba5016, Argentina
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29
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Levental I, Lyman E. Regulation of membrane protein structure and function by their lipid nano-environment. Nat Rev Mol Cell Biol 2023; 24:107-122. [PMID: 36056103 PMCID: PMC9892264 DOI: 10.1038/s41580-022-00524-4] [Citation(s) in RCA: 139] [Impact Index Per Article: 139.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2022] [Indexed: 02/04/2023]
Abstract
Transmembrane proteins comprise ~30% of the mammalian proteome, mediating metabolism, signalling, transport and many other functions required for cellular life. The microenvironment of integral membrane proteins (IMPs) is intrinsically different from that of cytoplasmic proteins, with IMPs solvated by a compositionally and biophysically complex lipid matrix. These solvating lipids affect protein structure and function in a variety of ways, from stereospecific, high-affinity protein-lipid interactions to modulation by bulk membrane properties. Specific examples of functional modulation of IMPs by their solvating membranes have been reported for various transporters, channels and signal receptors; however, generalizable mechanistic principles governing IMP regulation by lipid environments are neither widely appreciated nor completely understood. Here, we review recent insights into the inter-relationships between complex lipidomes of mammalian membranes, the membrane physicochemical properties resulting from such lipid collectives, and the regulation of IMPs by either or both. The recent proliferation of high-resolution methods to study such lipid-protein interactions has led to generalizable insights, which we synthesize into a general framework termed the 'functional paralipidome' to understand the mutual regulation between membrane proteins and their surrounding lipid microenvironments.
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Affiliation(s)
- Ilya Levental
- Department of Molecular Physiology and Biological Physics, Center for Molecular and Cell Physiology, University of Virginia, Charlottesville, VA, USA.
| | - Ed Lyman
- Department of Physics and Astronomy, Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA.
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30
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Lv M, Qian X, Li S, Gong J, Wang Q, Qian Y, Su Z, Xue X, Liu HK. Unlocking the potential of iridium and ruthenium arene complexes as anti-tumor and anti-metastasis chemotherapeutic agents. J Inorg Biochem 2023; 238:112057. [PMID: 36370504 DOI: 10.1016/j.jinorgbio.2022.112057] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
It is a major challenge to design novel multifunctional metal-based chemotherapeutic agents for anti-tumor and anti-metastasis applications. Two complexes (OA-Ir and OA-Ru) were synthesized via CuAAC (copper-catalyzed azide-alkyne cycloaddition) reaction from nontoxic Ir-N3 or Ru-N3 species and low toxic alkynyl precursor OA-Alkyne, and exhibited satisfactory anti-tumor and anti-metastasis pharmacological effects. Conjugation of Oleanolic acid (OA) and metal-arene species significantly enhanced the cytotoxicity in A2780 cells compared to the precursors through mitochondrial-induced autophagy pathway. Moreover, the two complexes could inhibit the cell metastasis and invasion through damage of actin dynamics and down-regulation of MMP2/MMP9 proteins. Combination of two precursors improved the lipophilicity and biocompatibility, simultaneously enhanced the cell uptake and the mitochondrial accumulation of metal-arene complexes, which caused mitochondrial membrane potential damage, oxidative phosphorylation, ATP depletion and autophagy. Besides, OA-Ir and OA-Ru displayed excellent activity to disintegrate the 3D multicellular tumor spheroids, showing potential for the treatment of solid tumors. This work provides a new way for developing novel metal-based complexes via CuAAC reaction for simultaneously inhibiting tumor proliferation and metastasis.
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Affiliation(s)
- Mengdi Lv
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Xiaoting Qian
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Shijie Li
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Jie Gong
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Qun Wang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Yong Qian
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Zhi Su
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China
| | - Xuling Xue
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.
| | - Hong-Ke Liu
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, China.
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31
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Shin G, Lim SI. Unveiling the biological interface of protein complexes by mass spectrometry-coupled methods. Proteins 2022; 91:593-607. [PMID: 36573681 DOI: 10.1002/prot.26459] [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: 07/16/2022] [Revised: 11/28/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Most biomolecules become functional and bioactive by forming protein complexes through interaction with ligands that are diverse in size, shape, and physicochemical properties. In the complex biological milieu, the interaction is ligand-specific, driven by molecular sensing, and involves the recognition of a binding interface localized within a protein structure. Mapping interfaces of protein complexes is a highly sought area of research as it delivers fundamental insights into proteomes and pathology and hence strategies for therapeutics. While X-ray crystallography and electron microscopy remain the gold standard for structural elucidation of protein complexes, their artificial and static analytic nature often produces a non-native interface that otherwise might be negligible or non-existent in a biological environment. Recently, the mass spectrometry-coupled approaches, chemical crosslinking (CLMS) and hydrogen-deuterium exchange (HDMS) have become valuable analytic complements to the traditional techniques. These methods explicitly identify hot residues and motifs embedded in binding interfaces, especially when the interaction is predominantly dynamic, transient, and/or caused by an intrinsically disordered domain. Here, we review the principal role of CLMS and HDMS in protein structural biology with a particular emphasis on the contribution of recent examples to exploring biological interfaces. Additionally, we describe recent studies that utilized these methods to expand our understanding of protein complex formation and the related biological processes, to increase the probability of structure-based drug design.
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Affiliation(s)
- Goeun Shin
- Department of Chemical Engineering, Pukyong National University, Busan, South Korea
| | - Sung In Lim
- Department of Chemical Engineering, Pukyong National University, Busan, South Korea
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32
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Morstein J, Capecchi A, Hinnah K, Park B, Petit-Jacques J, Van Lehn RC, Reymond JL, Trauner D. Medium-Chain Lipid Conjugation Facilitates Cell-Permeability and Bioactivity. J Am Chem Soc 2022; 144:18532-18544. [PMID: 36178375 DOI: 10.1021/jacs.2c07833] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The majority of bioactive molecules act on membrane proteins or intracellular targets and therefore needs to partition into or cross biological membranes. Natural products often exhibit lipid modifications to facilitate critical molecule-membrane interactions, and in many cases their bioactivity is markedly reduced upon removal of a lipid group. However, despite its importance in nature, lipid-conjugation of small molecules is not commonly used in chemical biology and medicinal chemistry, and the effect of such conjugation has not been systematically studied. To understand the composition of lipids found in natural products, we carried out a chemoinformatic characterization of the "natural product lipidome". According to this analysis, lipidated natural products predominantly contain saturated medium-chain lipids (MCLs), which are significantly shorter than the long-chain lipids (LCLs) found in membranes and lipidated proteins. To study the usefulness of such modifications in probe design, we systematically explored the effect of lipid conjugation on five different small molecule chemotypes and find that permeability, cellular retention, subcellular localization, and bioactivity can be significantly modulated depending on the type of lipid tail used. We demonstrate that MCL conjugation can render molecules cell-permeable and modulate their bioactivity. With all explored chemotypes, MCL-conjugates consistently exhibited superior uptake or bioactivity compared to LCL-conjugates and either comparable or superior uptake or bioactivity to short-chain lipid (SCL)-conjugates. Together, our findings suggest that conjugation of small molecules with MCLs could be a powerful strategy for the design of probes and drugs.
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Affiliation(s)
- Johannes Morstein
- Department of Cellular and Molecular Pharmacology and Howard Hughes Medical Institute, University of California, San Francisco, California 94158, United States
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Alice Capecchi
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Konstantin Hinnah
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - ByungUk Park
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jerome Petit-Jacques
- Ion Lab, NYU School of Medicine, 435 East 30th Street, New York, New York 10016, United States
| | - Reid C Van Lehn
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry, and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Dirk Trauner
- Department of Chemistry, New York University, New York, New York 10003, United States
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33
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Ding T, Karlov DS, Pino-Angeles A, Tikhonova IG. Intermolecular Interactions in G Protein-Coupled Receptor Allosteric Sites at the Membrane Interface from Molecular Dynamics Simulations and Quantum Chemical Calculations. J Chem Inf Model 2022; 62:4736-4747. [PMID: 36178787 PMCID: PMC9554917 DOI: 10.1021/acs.jcim.2c00788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Allosteric modulators are called promising candidates in G protein-coupled receptor (GPCR) drug development by displaying subtype selectivity and more specific receptor modulation. Among the allosteric sites known to date, cavities at the receptor-lipid interface represent an uncharacteristic binding location that raises many questions about the ligand interactions and stability, the binding site structure, and how all of these are affected by lipid molecules. In this work, we analyze interactions in the allosteric sites of the PAR2, C5aR1, and GCGR receptors in three lipid compositions using molecular dynamics simulations. In addition, we performed quantum chemical calculations involving the symmetry-adapted perturbation theory (SAPT) and the natural population analysis to quantify the strength of intermolecular interactions. We show that besides classical hydrogen bonds, weak polar interactions such as O-HC, O-Br, and long-range electrostatics with the backbone amides contribute to the stability of allosteric modulators at the receptor-lipid interface. The allosteric cavities are detectable in various membrane compositions. The availability of polar atoms for interactions in such cavities can be assessed by water molecules from simulations. Although ligand-lipid interactions are weak, lipid tails play a role in ligand binding pose stability and the size of allosteric cavities. We discuss physicochemical aspects of ligand binding at the receptor-lipid interface and suggest a compound library enriched by weak donor groups for ligand search in such sites.
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Affiliation(s)
- Tianyi Ding
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
| | - Dmitry S Karlov
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
| | - Almudena Pino-Angeles
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
| | - Irina G Tikhonova
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, Northern IrelandBT9 7BL, U.K
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34
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Obi P, Natesan S. Membrane Lipids Are an Integral Part of Transmembrane Allosteric Sites in GPCRs: A Case Study of Cannabinoid CB1 Receptor Bound to a Negative Allosteric Modulator, ORG27569, and Analogs. J Med Chem 2022; 65:12240-12255. [PMID: 36066412 PMCID: PMC9512009 DOI: 10.1021/acs.jmedchem.2c00946] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Indexed: 11/28/2022]
Abstract
A growing number of G-protein-coupled receptor (GPCR) structures reveal novel transmembrane lipid-exposed allosteric sites. Ligands must first partition into the surrounding membrane and take lipid paths to these sites. Remarkably, a significant part of the bound ligands appears exposed to the membrane lipids. The experimental structures do not usually account for the surrounding lipids, and their apparent contribution to ligand access and binding is often overlooked and poorly understood. Using classical and enhanced molecular dynamics simulations, we show that membrane lipids are critical in the access and binding of ORG27569 and its analogs at the transmembrane site of cannabinoid CB1 receptor. The observed differences in the binding affinity and cooperativity arise from the functional groups that interact primarily with lipids. Our results demonstrate the significance of incorporating membrane lipids as an integral component of transmembrane sites for accurate characterization, binding-affinity calculations, and lead optimization in drug discovery.
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Affiliation(s)
- Peter Obi
- College of Pharmacy and Pharmaceutical
Sciences, Washington State University, Spokane, Washington 99202, United States
| | - Senthil Natesan
- College of Pharmacy and Pharmaceutical
Sciences, Washington State University, Spokane, Washington 99202, United States
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35
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Kelley DP, Chaichi A, Duplooy A, Singh D, Gartia MR, Francis J. Labelfree mapping and profiling of altered lipid homeostasis in the rat hippocampus after traumatic stress: Role of oxidative homeostasis. Neurobiol Stress 2022; 20:100476. [PMID: 36032405 PMCID: PMC9403561 DOI: 10.1016/j.ynstr.2022.100476] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022] Open
Abstract
Oxidative and lipid homeostasis are altered by stress and trauma and post-traumatic stress disorder (PTSD) is associated with alterations to lipid species in plasma. Stress-induced alterations to lipid oxidative and homeostasis may exacerbate PTSD pathology, but few preclinical investigations of stress-induced lipidomic changes in the brain exist. Currently available techniques for the quantification of lipid species in biological samples require tissue extraction and are limited in their ability to retrieve spatial information. Raman imaging can overcome this limitation through the quantification of lipid species in situ in minimally processed tissue slices. Here, we utilized a predator exposure and psychosocial stress (PE/PSS) model of traumatic stress to standardize Raman imaging of lipid species in the hippocampus using LC-MS based lipidomics and these data were confirmed with qRT-PCR measures of mRNA expression of relevant enzymes and transporters. Electron Paramagnetic Resonance Spectroscopy (EPR) was used to measure free radical production and an MDA assay to measure oxidized polyunsaturated fatty acids. We observed that PE/PSS is associated with increased cholesterol, altered lipid concentrations, increased free radical production and reduced oxidized polyunsaturated fats (PUFAs) in the hippocampus (HPC), indicating shifts in lipid and oxidative homeostasis in the HPC after traumatic stress.
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Affiliation(s)
- D. Parker Kelley
- Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, 70803, USA
| | - Ardalan Chaichi
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Alexander Duplooy
- Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, 70803, USA
| | - Dhirendra Singh
- Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, 70803, USA
| | - Manas Ranjan Gartia
- Department of Mechanical and Industrial Engineering, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Joseph Francis
- Comparative Biomedical Sciences, Louisiana State University School of Veterinary Medicine, Baton Rouge, LA, 70803, USA
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36
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Nguyen TQT, Lund FW, Zanjani AAH, Khandelia H. Magic mushroom extracts in lipid membranes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183957. [PMID: 35561790 DOI: 10.1016/j.bbamem.2022.183957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
The active hallucinogen of magic mushrooms, psilocin, is being repurposed to treat nicotine addiction and treatment-resistant depression. Psilocin belongs to the tryptamine class of psychedelic compounds which include the hormone serotonin. It is believed that psilocin exerts its effect by binding to the serotonin 5-HT2A receptor. However, recent in-vivo evidence suggests that psilocin may employ a different mechanism to exert its effects. Membrane-mediated receptor desensitization of neurotransmitter receptors is one such mechanism. We compare the impact of the neutral and charged versions of psilocin and serotonin on the properties of zwitterionic and anionic lipid membranes using molecular dynamics simulations and calorimetry. Both compounds partition to the lipid interface and induce membrane thinning. The tertiary amine in psilocin, as opposed to the primary amine in serotonin, limits psilocin's impact on the membrane although more psilocin partitions into the membrane than serotonin. Calorimetry corroborates that both compounds induce a classical melting point depression like anesthetics do. Our results also lend support to a membrane-mediated receptor-binding mechanism for both psilocin and serotonin and provide physical insights into subtle chemical changes that can alter the membrane-binding of psychedelic compounds.
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Affiliation(s)
- Teresa Quynh Tram Nguyen
- Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Frederik Wendelboe Lund
- Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Ali Asghar Hakami Zanjani
- Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
| | - Himanshu Khandelia
- Physical Life Science, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
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37
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Garza DL, Hanashima S, Umegawa Y, Murata M, Kinoshita M, Matsumori N, Greimel P. Behavior of Triterpenoid Saponin Ginsenoside Rh2 in Ordered and Disordered Phases in Model Membranes Consisting of Sphingomyelin, Phosphatidylcholine, and Cholesterol. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:10478-10491. [PMID: 35984899 DOI: 10.1021/acs.langmuir.2c01261] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The ginsenoside Rh2 (Rh2) is a saponin of medicinal ginseng, and it has attracted much attention for its pharmacological activities. In this study, we investigated the interaction of Rh2 with biological membranes using model membranes. We examined the effects of various lipids on the membrane-disrupting activity of Rh2 and found that cholesterol and sphingomyelin (SM) had no significant effect. Furthermore, the effects of Rh2 on acyl chain packing (DPH anisotropy) and water molecule permeability (GP340 values) did not differ significantly between bilayers containing SM and saturated phosphatidylcholine. These results suggest that the formation of the liquid-ordered (Lo) phase affects the behavior of Rh2 in the membrane rather than a specific interaction of Rh2 with a particular lipid. We investigated the effects of Rh2 on the Lo and liquid-disordered (Ld) phases using surface tension measurements and fluorescence experiments. In the surface tension-area isotherms, we compared the monolayers of the Ld and Lo lipid compositions and found that Rh2 is abundantly bound to both monolayers, with the amount being greater in the Ld phase than in the Lo phase. In addition, the hydration state of the bilayers, mainly consisting of the Lo or Ld phase, showed that Rh2 tends to bind to the surface of the bilayer in both phases. At higher concentrations, Rh2 tends to bind more abundantly to the relatively shallow interior of the Ld phase than the Lo phase. The phase-dependent membrane behavior of Rh2 is probably due to the phase-selective affinity and binding mode of Rh2.
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Affiliation(s)
- Darcy Lacanilao Garza
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Shinya Hanashima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yuichi Umegawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Michio Murata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Masanao Kinoshita
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Peter Greimel
- Laboratory for Cell Function Dynamics, RIKEN Center for Brain Science, Wako, Saitama 351-0198 Japan
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38
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Liu W, Jiang J, Lin Y, You Q, Wang L. Insight into Thermodynamic and Kinetic Profiles in Small-Molecule Optimization. J Med Chem 2022; 65:10809-10847. [PMID: 35969687 DOI: 10.1021/acs.jmedchem.2c00682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-activity relationships (SARs) and structure-property relationships (SPRs) have been considered the most important factors during the drug optimization process. For medicinal chemists, improvements in the potencies and druglike properties of small molecules are regarded as their major goals. Among them, the binding affinity and selectivity of small molecules on their targets are the most important indicators. In recent years, there has been growing interest in using thermodynamic and kinetic profiles to analyze ligand-receptor interactions, which could provide not only binding affinities but also detailed binding parameters for small-molecule optimization. In this perspective, we are trying to provide an insight into thermodynamic and kinetic profiles in small-molecule optimization. Through a highlight of strategies on the small-molecule optimization with specific cases, we aim to put forward the importance of structure-thermodynamic relationships (STRs) and structure-kinetic relationships (SKRs), which could provide more guidance to find safe and effective small-molecule drugs.
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Affiliation(s)
- Wei Liu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jingsheng Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yating Lin
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.,Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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39
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Zhou W, Richmond-Buccola D, Wang Q, Kranzusch PJ. Structural basis of human TREX1 DNA degradation and autoimmune disease. Nat Commun 2022; 13:4277. [PMID: 35879334 PMCID: PMC9314330 DOI: 10.1038/s41467-022-32055-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/11/2022] [Indexed: 01/13/2023] Open
Abstract
TREX1 is a cytosolic DNA nuclease essential for regulation of cGAS-STING immune signaling. Existing structures of mouse TREX1 establish a mechanism of DNA degradation and provide a key model to explain autoimmune disease, but these structures incompletely explain human disease-associated mutations and have limited ability to guide development of small-molecule therapeutics. Here we determine crystal structures of human TREX1 in apo and DNA-bound conformations that provide high-resolution detail of all human-specific features. A 1.25 Å structure of human TREX1 establishes a complete model of solvation of the exonuclease active site and a 2.2 Å structure of the human TREX1-DNA complex enables identification of specific substitutions involved in DNA recognition. We map each TREX1 mutation associated with autoimmune disease and establish distinct categories of substitutions predicted to impact enzymatic function, protein stability, and interaction with cGAS-DNA liquid droplets. Our results explain how human-specific substitutions regulate TREX1 function and provide a foundation for structure-guided design of TREX1 therapeutics.
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Affiliation(s)
- Wen Zhou
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China.
| | - Desmond Richmond-Buccola
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Qiannan Wang
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Philip J Kranzusch
- Department of Microbiology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
- Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
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40
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Liddle I, Glass M, Tyndall JDA, Vernall AJ. Covalent cannabinoid receptor ligands - structural insight and selectivity challenges. RSC Med Chem 2022; 13:497-510. [PMID: 35694688 PMCID: PMC9132230 DOI: 10.1039/d2md00006g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/31/2022] [Indexed: 11/21/2022] Open
Abstract
X-ray crystallography and cryogenic electronic microscopy have provided significant advancement in the knowledge of GPCR structure and have allowed the rational design of GPCR ligands. The class A GPCRs cannabinoid receptor type 1 and type 2 are implicated in many pathophysiological processes and thus rational design of drug and tool compounds is of great interest. Recent structural insight into cannabinoid receptors has already led to a greater understanding of ligand binding sites and receptor residues that likely contribute to ligand selectivity. Herein, classes of heterocyclic covalent cannabinoid receptor ligands are reviewed in light of the recent advances in structural knowledge of cannabinoid receptors, with particular discussion regarding covalent ligand selectivity and rationale design.
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Affiliation(s)
- Ian Liddle
- Department of Chemistry, University of Otago Dunedin New Zealand +64 3 479 5214
| | - Michelle Glass
- Department of Pharmacology and Toxicology, University of Otago Dunedin New Zealand
| | | | - Andrea J Vernall
- Department of Chemistry, University of Otago Dunedin New Zealand +64 3 479 5214
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41
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An overview on the exploring the interaction of inorganic nanoparticles with microtubules for the advancement of cancer therapeutics. Int J Biol Macromol 2022; 212:358-369. [PMID: 35618086 DOI: 10.1016/j.ijbiomac.2022.05.150] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/17/2022] [Accepted: 05/21/2022] [Indexed: 01/01/2023]
Abstract
Targeting microtubules (MTs), dynamic and stable proteins in cells, by different ligands have been reported to be a potential strategy to combat cancer cells. Inorganic nanoparticles (NPs) have been widely used as anticancer, antibacterial, and free radical scavenging agents, where the come in contact with biological macromolecules. The interaction between the NPs and biological macromolecules like MTs frequently occurs through different mechanisms. A prerequisite for a detailed exploration of MT structures and functions for biomedical applications like cancer therapy is to investigate profoundly the mechanisms involved in MT-NP interactions, for which the full explanation and characterization of the parameters that are responsible for the formation of a NP-protein complex are crucial. Therefore, in view of the fact that the goal of the rational NP-based future drug design and new therapies is to rely on the information of the structural details and protein-NPs binding mechanisms to manipulate the process of developing new potential drugs, a comprehensive investigation of the essence of the molecular recognition/interaction is also of considerable importance. In the present review, first, the microtubule (MT) structure and its binding sites upon interaction with MT stabilizing agents (MSAs) and MT destabilizing agents (MDAs) are introduced and rationalized. Next, MT targeting in cancer therapy and interaction of NPs with MTs are discussed. Furthermore, interaction of NPs with proteins and the manipulation of protein corona (PC), experimental techniques, and direct interaction of NPs with MTs, are discussed, and finally the challenges and future perspective of the field are introduced. We envision this review can provide useful information on the manipulation of the MT lattice for the progress of cancer nanomedicine.
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42
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Lim SA, Su W, Chapman NM, Chi H. Lipid metabolism in T cell signaling and function. Nat Chem Biol 2022; 18:470-481. [PMID: 35484263 PMCID: PMC11103273 DOI: 10.1038/s41589-022-01017-3] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/17/2022] [Indexed: 12/19/2022]
Abstract
T cells orchestrate adaptive immunity against pathogens and other immune challenges, but their dysfunction can also mediate the pathogenesis of cancer and autoimmunity. Metabolic adaptation in response to immunological and microenvironmental signals contributes to T cell function and fate decision. Lipid metabolism has emerged as a key regulator of T cell responses, with selective lipid metabolites serving as metabolic rheostats to integrate environmental cues and interplay with intracellular signaling processes. Here, we discuss how extracellular, de novo synthesized and membrane lipids orchestrate T cell biology. We also describe the roles of lipids as regulators of intracellular signaling at the levels of transcriptional, epigenetic and post-translational regulation in T cells. Finally, we summarize therapeutic targeting of lipid metabolism and signaling, and conclude with a discussion of important future directions. Understanding the molecular and functional interplay between lipid metabolism and T cell biology will ultimately inform therapeutic intervention for human disease.
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Affiliation(s)
- Seon Ah Lim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wei Su
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nicole M Chapman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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43
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Markowicz-Piasecka M, Markiewicz A, Darłak P, Sikora J, Adla SK, Bagina S, Huttunen KM. Current Chemical, Biological, and Physiological Views in the Development of Successful Brain-Targeted Pharmaceutics. Neurotherapeutics 2022; 19:942-976. [PMID: 35391662 PMCID: PMC9294128 DOI: 10.1007/s13311-022-01228-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2022] [Indexed: 12/13/2022] Open
Abstract
One of the greatest challenges with successful pharmaceutical treatments of central nervous system (CNS) diseases is the delivery of drugs into their target sites with appropriate concentrations. For example, the physically tight blood-brain barrier (BBB) effectively blocks compounds from penetrating into the brain, also by the action of metabolizing enzymes and efflux transport mechanisms. However, many endogenous compounds, including both smaller compounds and macromolecules, like amino acids, sugars, vitamins, nucleosides, hormones, steroids, and electrolytes, have their peculiar internalization routes across the BBB. These delivery mechanisms, namely carrier-mediated transport and receptor-mediated transcytosis have been utilized to some extent in brain-targeted drug development. The incomplete knowledge of the BBB and the smaller than a desirable number of chemical tools have hindered the development of successful brain-targeted pharmaceutics. This review discusses the recent advancements achieved in the field from the point of medicinal chemistry view and discusses how brain drug delivery can be improved in the future.
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Affiliation(s)
- Magdalena Markowicz-Piasecka
- Laboratory of Bioanalysis, Department of Pharmaceutical Chemistry, Drug Analysis and Radiopharmacy, Medical University of Lodz, ul. Muszyńskiego1, 90-151 Lodz, Poland
| | - Agata Markiewicz
- Students Research Group, Laboratory of Bioanalysis, Department of Pharmaceutical Chemistry, Drug Analysis and Radiopharmacy, Medical University of Lodz, ul. Muszyńskiego 1, 90-151 Lodz, Poland
| | - Patrycja Darłak
- Students Research Group, Laboratory of Bioanalysis, Department of Pharmaceutical Chemistry, Drug Analysis and Radiopharmacy, Medical University of Lodz, ul. Muszyńskiego 1, 90-151 Lodz, Poland
| | - Joanna Sikora
- Department of Bioinorganic Chemistry, Medical University of Lodz, Medical University of Lodz, ul. Muszyńskiego1, 90-151 Lodz, Poland
| | - Santosh Kumar Adla
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1C, POB 1627, 70211 Kuopio, Finland
- Institute of Organic Chemistry and Biochemistry (IOCB), Czech Academy of Sciences, Flemingovo Namesti 542/2, 160 00 Prague, Czech Republic
| | - Sreelatha Bagina
- Charles River Discovery Research Services Finland Oy, Neulaniementie 4, 70210 Kuopio, Finland
| | - Kristiina M. Huttunen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1C, POB 1627, 70211 Kuopio, Finland
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44
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Verma VA, Wang L, Labadie SS, Liang J, Sellers BD, Wang J, Dong L, Wang Q, Zhang S, Xu Z, Zhang Y, Niu Y, Wang X, Wai J, Koehler MFT, Hu H, Alexander MK, Nishiyama M, Miu A, Xu Y, Pang J, Katakam AK, Reichelt M, Austin CD, Ho H, Payandeh J, Koth CM. Discovery of Inhibitors of the Lipopolysaccharide Transporter MsbA: From a Screening Hit to Potent Wild-Type Gram-Negative Activity. J Med Chem 2022; 65:4085-4120. [DOI: 10.1021/acs.jmedchem.1c01909] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vishal A. Verma
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Lan Wang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sharada S. Labadie
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jun Liang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Benjamin D. Sellers
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jian Wang
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Liting Dong
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Qiuyue Wang
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Shuang Zhang
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Zhongya Xu
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Yexia Zhang
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Yanan Niu
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Xinxin Wang
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - John Wai
- WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s Republic of China
| | | | - Huiyong Hu
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Mary Kate Alexander
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Mireille Nishiyama
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Anh Miu
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Yiming Xu
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jodie Pang
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Anand K. Katakam
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Michael Reichelt
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Cary D. Austin
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Hoangdung Ho
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jian Payandeh
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher M. Koth
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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45
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Szymaszek P, Fiedor P, Chachaj-Brekiesz A, Tyszka-Czochara M, Świergosz T, Ortyl J. Molecular interactions of bovine serum albumin (BSA) with pyridine derivatives as candidates for non-covalent protein probes: a spectroscopic investigation. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118262] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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46
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Cheng WWL, Arcario MJ, Petroff JT. Druggable Lipid Binding Sites in Pentameric Ligand-Gated Ion Channels and Transient Receptor Potential Channels. Front Physiol 2022; 12:798102. [PMID: 35069257 PMCID: PMC8777383 DOI: 10.3389/fphys.2021.798102] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/02/2021] [Indexed: 12/17/2022] Open
Abstract
Lipids modulate the function of many ion channels, possibly through direct lipid-protein interactions. The recent outpouring of ion channel structures by cryo-EM has revealed many lipid binding sites. Whether these sites mediate lipid modulation of ion channel function is not firmly established in most cases. However, it is intriguing that many of these lipid binding sites are also known sites for other allosteric modulators or drugs, supporting the notion that lipids act as endogenous allosteric modulators through these sites. Here, we review such lipid-drug binding sites, focusing on pentameric ligand-gated ion channels and transient receptor potential channels. Notable examples include sites for phospholipids and sterols that are shared by anesthetics and vanilloids. We discuss some implications of lipid binding at these sites including the possibility that lipids can alter drug potency or that understanding protein-lipid interactions can guide drug design. Structures are only the first step toward understanding the mechanism of lipid modulation at these sites. Looking forward, we identify knowledge gaps in the field and approaches to address them. These include defining the effects of lipids on channel function in reconstituted systems using asymmetric membranes and measuring lipid binding affinities at specific sites using native mass spectrometry, fluorescence binding assays, and computational approaches.
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Affiliation(s)
- Wayland W L Cheng
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, United States
| | - Mark J Arcario
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, United States
| | - John T Petroff
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO, United States
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47
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Dickson CJ, Hornak V, Duca JS. Relative Binding Free-Energy Calculations at Lipid-Exposed Sites: Deciphering Hot Spots. J Chem Inf Model 2021; 61:5923-5930. [PMID: 34843243 DOI: 10.1021/acs.jcim.1c01147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Relative binding free-energy (RBFE) calculations are experiencing resurgence in the computer-aided drug design of novel small molecules due to performance gains allowed by cutting-edge molecular mechanic force fields and computer hardware. Application of RBFE to soluble proteins is becoming a routine, while recent studies outline necessary steps to successfully apply RBFE at the orthosteric site of membrane-embedded G-protein-coupled receptors (GPCRs). In this work, we apply RBFE to a congeneric series of antagonists that bind to a lipid-exposed, extra-helical site of the P2Y1 receptor. We find promising performance of RBFE, such that it may be applied in a predictive manner on drug discovery programs targeting lipid-exposed sites. Further, by the application of the microkinetic model, binding at a lipid-exposed site can be split into (1) membrane partitioning of the drug molecule followed by (2) binding at the extra-helical site. We find that RBFE can be applied to calculate the free energy of each step, allowing the uncoupling of observed binding free energy from the influence of membrane affinity. This protocol may be used to identify binding hot spots at extra-helical sites and guide drug discovery programs toward optimizing intrinsic activity at the target.
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Affiliation(s)
- Callum J Dickson
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jose S Duca
- Computer-Aided Drug Discovery, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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48
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Bottalico L, Charitos IA, Potenza MA, Montagnani M, Santacroce L. The war against bacteria, from the past to present and beyond. Expert Rev Anti Infect Ther 2021; 20:681-706. [PMID: 34874223 DOI: 10.1080/14787210.2022.2013809] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
INTRODUCTION The human defense against microorganisms dates back to the ancient civilizations, with attempts to use substances from vegetal, animal, or inorganic origin to fight infections. Today, the emerging threat of multidrug-resistant bacteria highlights the consequences of antibiotics inappropriate use, and the urgent need for novel effective molecules. METHODS AND MATERIALS We extensively researched on more recent data within PubMed, Medline, Web of Science, Elsevier's EMBASE, Cochrane Review for the modern pharmacology in between 1987 - 2021. The historical evolution included a detailed analysis of past studies on the significance of medical applications in the ancient therapeutic field. AREAS COVERED We examined the history of antibiotics development and discovery, the most relevant biochemical aspects of their mode of action, and the biomolecular mechanisms conferring bacterial resistance to antibiotics. EXPERT OPINION The list of pathogens showing low sensitivity or full resistance to most currently available antibiotics is growing worldwide. Long after the 'golden age' of antibiotic discovery, the most novel molecules should be carefully reserved to treat serious bacterial infections of susceptible bacteria. A correct diagnostic and therapeutic procedure can slow down the spreading of nosocomial and community infections sustained by multidrug-resistant bacterial strains.
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Affiliation(s)
- Lucrezia Bottalico
- Interdepartmental Research Center for Pre-Latin, Latin and Oriental Rights and Culture Studies (Cediclo), University of Bari, Bari, Italy
| | - Ioannis Alexandros Charitos
- Interdepartmental Research Center for Pre-Latin, Latin and Oriental Rights and Culture Studies (Cediclo), University of Bari, Bari, Italy.,Emergency/Urgent Department, National Poisoning Center, Riuniti University Hospital of Foggia, Foggia, Italy
| | - Maria Assunta Potenza
- Department of Biomedical Sciences and Human Oncology - Section of Pharmacology, School of Medicine, University of Bari "Aldo Moro," Policlinico University Hospital of Bari, Bari, Italy
| | - Monica Montagnani
- Department of Biomedical Sciences and Human Oncology - Section of Pharmacology, School of Medicine, University of Bari "Aldo Moro," Policlinico University Hospital of Bari, Bari, Italy
| | - Luigi Santacroce
- Department of Interdisciplinary Medicine, Microbiology and Virology Unit, School of Medicine,University of Bari "Aldo Moro", Bari, Italy
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49
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Elisi GM, Scalvini L, Lodola A, Mor M, Rivara S. Free-Energy Simulations Support a Lipophilic Binding Route for Melatonin Receptors. J Chem Inf Model 2021; 62:210-222. [PMID: 34932329 PMCID: PMC8757440 DOI: 10.1021/acs.jcim.1c01183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
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The effects of the
neurohormone melatonin are mediated by the activation
of the GPCRs MT1 and MT2 in a variety of tissues.
Crystal structures suggest ligand access to the orthosteric binding
site of MT1 and MT2 receptors through a lateral
channel between transmembrane (TM) helices IV and V. We investigated
the feasibility of this lipophilic entry route for 2-iodomelatonin,
a nonselective agonist with a slower dissociation rate from the MT2 receptor, applying enhanced sampling simulations and free-energy
calculations. 2-Iodomelatonin unbinding was investigated with steered
molecular dynamics simulations which revealed different trajectories
passing through the gap between TM helices IV and V for both receptors.
For one of these unbinding trajectories from the MT1 receptor,
an umbrella-sampling protocol with path-collective variables provided
a calculated energy barrier consistent with the experimental dissociation
rate. The side-chain flexibility of Tyr5.38 was significantly different
in the two receptor subtypes, as assessed by metadynamics simulations,
and during ligand unbinding it frequently assumes an open conformation
in the MT1 but not in the MT2 receptor, favoring
2-iodomelatonin egress. Taken together, our simulations are consistent
with the possibility that the gap between TM IV and V is a way of
connecting the orthosteric binding site and the membrane core for
lipophilic melatonin receptor ligands. Our simulations also suggest
that the open state of Tyr5.38 generates a small pocket on the surface
of MT1 receptor, which could participate in the recognition
of MT1-selective ligands and may be exploited in the design
of new selective compounds.
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Affiliation(s)
- Gian Marco Elisi
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Laura Scalvini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
| | - Marco Mor
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy.,Microbiome Research Hub, University of Parma, I-43124 Parma, Italy
| | - Silvia Rivara
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università degli Studi di Parma, Parco Area delle Scienze 27/A, I-43124 Parma, Italy
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50
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Smithers L, Olatunji S, Caffrey M. Bacterial Lipoprotein Posttranslational Modifications. New Insights and Opportunities for Antibiotic and Vaccine Development. Front Microbiol 2021; 12:788445. [PMID: 34950121 PMCID: PMC8689077 DOI: 10.3389/fmicb.2021.788445] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022] Open
Abstract
Lipoproteins are some of the most abundant proteins in bacteria. With a lipid anchor to the cell membrane, they function as enzymes, inhibitors, transporters, structural proteins, and as virulence factors. Lipoproteins activate the innate immune system and have biotechnological applications. The first lipoprotein was described by Braun and Rehn in 1969. Up until recently, however, work on lipoproteins has been sluggish, in part due to the challenges of handling proteins that are anchored to membranes by covalently linked lipids or are membrane integral. Activity in the area has quickened of late. In the past 5 years, high-resolution structures of the membrane enzymes of the canonical lipoprotein synthesis pathway have been determined, new lipoprotein types have been discovered and the enzymes responsible for their synthesis have been characterized biochemically. This has led to a flurry of activity aimed at developing novel antibiotics targeting these enzymes. In addition, surface exposed bacterial lipoproteins have been utilized as candidate vaccine antigens, and their potential to act as self-adjuvanting antigens is increasingly recognized. A summary of the latest developments in lipoproteins and their synthesis, as well as how this information is being exploited for therapeutic purposes is presented here.
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Affiliation(s)
- Luke Smithers
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Samir Olatunji
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Martin Caffrey
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
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