1
|
Devantier K, Kjær VMS, Griffin S, Kragelund BB, Rosenkilde MM. Advancing the field of viroporins-Structure, function and pharmacology: IUPHAR Review X. Br J Pharmacol 2024. [PMID: 39224966 DOI: 10.1111/bph.17317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/28/2024] [Accepted: 07/07/2024] [Indexed: 09/04/2024] Open
Abstract
Viroporins possess important potential as antiviral targets due to their critical roles during virus life cycles, spanning from virus entry to egress. Although the antiviral amantadine targets the M2 viroporin of influenza A virus, successful progression of other viroporin inhibitors into clinical use remains challenging. These challenges relate in varying proportions to a lack of reliable full-length 3D-structures, difficulties in functionally characterising individual viroporins, and absence of verifiable direct binding between inhibitor and viroporin. This review offers perspectives to help overcome these challenges. We provide a comprehensive overview of the viroporin family, including their structural and functional features, highlighting the moldability of their energy landscapes and actions. To advance the field, we suggest a list of best practices to aspire towards unambiguous viroporin identification and characterisation, along with considerations of potential pitfalls. Finally, we present current and future scenarios of, and prospects for, viroporin targeting drugs.
Collapse
Affiliation(s)
- Kira Devantier
- Molecular and Translational Pharmacology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Viktoria M S Kjær
- Molecular and Translational Pharmacology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stephen Griffin
- Leeds Institute of Medical Research, St James' University Hospital, School of Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mette M Rosenkilde
- Molecular and Translational Pharmacology, Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
2
|
Szél V, Zsidó BZ, Hetényi C. Enthalpic Classification of Water Molecules in Target-Ligand Binding. J Chem Inf Model 2024; 64:6583-6595. [PMID: 39135312 DOI: 10.1021/acs.jcim.4c00794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Water molecules play various roles in target-ligand binding. For example, they can be replaced by the ligand and leave the surface of the binding pocket or stay conserved in the interface and form bridges with the target. While experimental techniques supply target-ligand complex structures at an increasing rate, they often have limitations in the measurement of a detailed water structure. Moreover, measurements of binding thermodynamics cannot distinguish between the different roles of individual water molecules. However, such a distinction and classification of the role of individual water molecules would be key to their application in drug design at atomic resolution. In this study, we investigate a quantitative approach for the description of the role of water molecules during ligand binding. Starting from complete hydration structures of the free and ligand-bound target molecules, binding enthalpy scores are calculated for each water molecule using quantum mechanical calculations. A statistical evaluation showed that the scores can distinguish between conserved and displaced classes of water molecules. The classification system was calibrated and tested on more than 1000 individual water positions. The practical tests of the enthalpic classification included important cases of antiviral drug research on HIV-1 protease inhibitors and the Influenza A ion channel. The methodology of classification is based on open source program packages, Gromacs, Mopac, and MobyWat, freely available to the scientific community.
Collapse
Affiliation(s)
- Viktor Szél
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, Pécs 7624, Hungary
| | - Balázs Zoltán Zsidó
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, Pécs 7624, Hungary
| | - Csaba Hetényi
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, Pécs 7624, Hungary
| |
Collapse
|
3
|
Jaros SW, Florek M, Bażanów B, Panek J, Krogul-Sobczak A, Oliveira MC, Król J, Śliwińska-Hill U, Nesterov DS, Kirillov AM, Smoleński P. Silver Coordination Polymers Driven by Adamantoid Blocks for Advanced Antiviral and Antibacterial Biomaterials. ACS APPLIED MATERIALS & INTERFACES 2024; 16:13411-13421. [PMID: 38456838 PMCID: PMC10958451 DOI: 10.1021/acsami.3c15606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/31/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024]
Abstract
The development of sustainable biomaterials and surfaces to prevent the accumulation and proliferation of viruses and bacteria is highly demanded in healthcare areas. This study describes the assembly and full characterization of two new bioactive silver(I) coordination polymers (CPs) formulated as [Ag(aca)(μ-PTA)]n·5nH2O (1) and [Ag2(μ-ada)(μ3-PTA)2]n·4nH2O (2). These products were generated by exploiting a heteroleptic approach based on the use of two different adamantoid building blocks, namely 1,3,5-triaza-7-phosphaadamantane (PTA) and 1-adamantanecarboxylic (Haca) or 1,3-adamantanedicarboxylic (H2ada) acids, resulting in the assembly of 1D (1) and 3D (2). Antiviral, antibacterial, and antifungal properties of the obtained compounds were investigated in detail, followed by their incorporation as bioactive dopants (1 wt %) into hybrid biopolymers based on acid-hydrolyzed starch polymer (AHSP). The resulting materials, formulated as 1@AHSP and 2@AHSP, also featured (i) an exceptional antiviral activity against herpes simplex virus type 1 and human adenovirus (HAd-5) and (ii) a remarkable antibacterial activity against Gram-negative bacteria. Docking experiments, interaction with human serum albumin, mass spectrometry, and antioxidation studies provided insights into the mechanism of antimicrobial action. By reporting these new silver CPs driven by adamantoid building blocks and the derived starch-based materials, this study endows a facile approach to access biopolymers and interfaces capable of preventing and reducing the proliferation of a broad spectrum of different microorganisms, including bacteria, fungi, and viruses.
Collapse
Affiliation(s)
- Sabina W. Jaros
- Faculty
of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Magdalena Florek
- Department
of Veterinary Microbiology, Wrocław
University of Environmental and Life Sciences, Norwida 31, 50-375 Wrocław, Poland
| | - Barbara Bażanów
- Department
of Veterinary Microbiology, Wrocław
University of Environmental and Life Sciences, Norwida 31, 50-375 Wrocław, Poland
| | - Jarosław Panek
- Faculty
of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | | | - M. Conceição Oliveira
- Centro
de Química Estrutural, Institute of Molecular Sciences, Departamento
de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Jarosław Król
- Department
of Veterinary Microbiology, Wrocław
University of Environmental and Life Sciences, Norwida 31, 50-375 Wrocław, Poland
| | - Urszula Śliwińska-Hill
- Faculty
of Pharmacy, Department of Basic Chemical Sciences, Wrocław Medical University, Borowska 211, 50-566 Wrocław, Poland
| | - Dmytro S. Nesterov
- Centro
de Química Estrutural, Institute of Molecular Sciences, Departamento
de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Alexander M. Kirillov
- Centro
de Química Estrutural, Institute of Molecular Sciences, Departamento
de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Piotr Smoleński
- Faculty
of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| |
Collapse
|
4
|
Georgiou K, Konstantinidi A, Hutterer J, Freudenberger K, Kolarov F, Lambrinidis G, Stylianakis I, Stampelou M, Gauglitz G, Kolocouris A. Accurate calculation of affinity changes to the close state of influenza A M2 transmembrane domain in response to subtle structural changes of adamantyl amines using free energy perturbation methods in different lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184258. [PMID: 37995846 DOI: 10.1016/j.bbamem.2023.184258] [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: 06/06/2023] [Revised: 10/18/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
Experimental binding free energies of 27 adamantyl amines against the influenza M2(22-46) WT tetramer, in its closed form at pH 8, were measured by ITC in DPC micelles. The measured Kd's range is ~44 while the antiviral potencies (IC50) range is ~750 with a good correlation between binding free energies computed with Kd and IC50 values (r = 0.76). We explored with MD simulations (ff19sb, CHARMM36m) the binding profile of complexes with strong, moderate and weak binders embedded in DMPC, DPPC, POPC or a viral mimetic membrane and using different experimental starting structures of M2. To predict accurately differences in binding free energy in response to subtle changes in the structure of the ligands, we performed 18 alchemical perturbative single topology FEP/MD NPT simulations (OPLS2005) using the BAR estimator (Desmond software) and 20 dual topology calculations TI/MD NVT simulations (ff19sb) using the MBAR estimator (Amber software) for adamantyl amines in complex with M2(22-46) WT in DMPC, DPPC, POPC. We observed that both methods with all lipids show a very good correlation between the experimental and calculated relative binding free energies (r = 0.77-0.87, mue = 0.36-0.92 kcal mol-1) with the highest performance achieved with TI/MBAR and lowest performance with FEP/BAR in DMPC bilayers. When antiviral potencies are used instead of the Kd values for computing the experimental binding free energies we obtained also good performance with both FEP/BAR (r = 0.83, mue = 0.75 kcal mol-1) and TI/MBAR (r = 0.69, mue = 0.77 kcal mol-1).
Collapse
Affiliation(s)
- Kyriakos Georgiou
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Athina Konstantinidi
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Johanna Hutterer
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Kathrin Freudenberger
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Felix Kolarov
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany; Roche, Penzberg, Bavaria, Germany
| | - George Lambrinidis
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Ioannis Stylianakis
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Margarita Stampelou
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Günter Gauglitz
- Institut für Physikalische und Theoretische Chemie, Eberhard-Karls-Universität, D-72076 Tübingen, Germany
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens (NKUA), Panepistimiopolis-Zografou, 15771 Athens, Greece.
| |
Collapse
|
5
|
Kariev AM, Green ME. Water, Protons, and the Gating of Voltage-Gated Potassium Channels. MEMBRANES 2024; 14:37. [PMID: 38392664 PMCID: PMC10890431 DOI: 10.3390/membranes14020037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Ion channels are ubiquitous throughout all forms of life. Potassium channels are even found in viruses. Every cell must communicate with its surroundings, so all cells have them, and excitable cells, in particular, especially nerve cells, depend on the behavior of these channels. Every channel must be open at the appropriate time, and only then, so that each channel opens in response to the stimulus that tells that channel to open. One set of channels, including those in nerve cells, responds to voltage. There is a standard model for the gating of these channels that has a section of the protein moving in response to the voltage. However, there is evidence that protons are moving, rather than protein. Water is critical as part of the gating process, although it is hard to see how this works in the standard model. Here, we review the extensive evidence of the importance of the role of water and protons in gating these channels. Our principal example, but by no means the only example, will be the Kv1.2 channel. Evidence comes from the effects of D2O, from mutations in the voltage sensing domain, as well as in the linker between that domain and the gate, and at the gate itself. There is additional evidence from computations, especially quantum calculations. Structural evidence comes from X-ray studies. The hydration of ions is critical in the transfer of ions in constricted spaces, such as the gate region and the pore of a channel; we will see how the structure of the hydrated ion fits with the structure of the channel. In addition, there is macroscopic evidence from osmotic experiments and streaming current measurements. The combined evidence is discussed in the context of a model that emphasizes the role of protons and water in gating these channels.
Collapse
Affiliation(s)
- Alisher M Kariev
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| | - Michael E Green
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| |
Collapse
|
6
|
Liu A, Zhang H, Zheng Q, Wang S. The Potential of Cyclodextrins as Inhibitors for the BM2 Protein: An In Silico Investigation. Molecules 2024; 29:620. [PMID: 38338365 PMCID: PMC10856705 DOI: 10.3390/molecules29030620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/23/2024] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
The influenza BM2 transmembrane domain (BM2TM), an acid-activated proton channel, is an attractive antiviral target due to its essential roles during influenza virus replication, whereas no effective inhibitors have been reported for BM2. In this study, we draw inspiration from the properties of cyclodextrins (CDs) and hypothesize that CDs of appropriate sizes may possess the potential to act as inhibitors of the BM2TM proton channel. To explore this possibility, molecular dynamics simulations were employed to assess their inhibitory capabilities. Our findings reveal that CD4, CD5, and CD6 are capable of binding to the BM2TM proton channel, resulting in disrupted water networks and reduced hydrogen bond occupancy between H19 and the solvent within the BM2TM channel necessary for proton conduction. Notably, CD4 completely obstructs the BM2TM water channel. Based on these observations, we propose that CD4, CD5, and CD6 individually contribute to diminishing the proton transfer efficiency of the BM2 protein, and CD4 demonstrates promising potential as an inhibitor for the BM2 proton channel.
Collapse
Affiliation(s)
- Aijun Liu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China; (A.L.); (H.Z.)
| | - Hao Zhang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China; (A.L.); (H.Z.)
| | - Qingchuan Zheng
- School of Pharmaceutical Sciences, Jilin University, Changchun, 130021, China
| | - Song Wang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China; (A.L.); (H.Z.)
| |
Collapse
|
7
|
Tekwani Movellan K, Wegstroth M, Overkamp K, Leonov A, Becker S, Andreas LB. Real-time tracking of drug binding to influenza A M2 reveals a high energy barrier. J Struct Biol X 2023; 8:100090. [PMID: 37363040 PMCID: PMC10285276 DOI: 10.1016/j.yjsbx.2023.100090] [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: 08/17/2022] [Revised: 05/18/2023] [Accepted: 06/02/2023] [Indexed: 06/28/2023] Open
Abstract
The drug Rimantadine binds to two different sites in the M2 protein from influenza A, a peripheral site and a pore site that is the primary site of efficacy. It remained enigmatic that pore binding did not occur in certain detergent micelles, and in particular incomplete binding was observed in a mixture of lipids selected to match the viral membrane. Here we show that two effects are responsible, namely changes in the protein upon pore binding that prevented detergent solubilization, and slow binding kinetics in the lipid samples. Using 55-100 kHz magic-angle spinning NMR, we characterize kinetics of drug binding in three different lipid environments: DPhPC, DPhPC with cholesterol and viral mimetic membrane lipid bilayers. Slow pharmacological binding kinetics allowed the characterization of spectral changes associated with non-specific binding to the protein periphery in the kinetically trapped pore-apo state. Resonance assignments were determined from a set of proton-detected 3D spectra. Chemical shift changes associated with functional binding in the pore of M2 were tracked in real time in order to estimate the activation energy. The binding kinetics are affected by pH and the lipid environment and in particular cholesterol. We found that the imidazole-imidazole hydrogen bond at residue histidine 37 is a stable feature of the protein across several lipid compositions. Pore binding breaks the imidazole-imidazole hydrogen bond and limits solubilization in DHPC detergent.
Collapse
|
8
|
Paschke RR, Mohr S, Lange S, Lange A, Kozuch J. In Situ Spectroscopic Detection of Large-Scale Reorientations of Transmembrane Helices During Influenza A M2 Channel Opening. Angew Chem Int Ed Engl 2023; 62:e202309069. [PMID: 37733579 DOI: 10.1002/anie.202309069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 09/23/2023]
Abstract
Viroporins are small ion channels in membranes of enveloped viruses that play key roles during viral life cycles. To use viroporins as drug targets against viral infection requires in-depth mechanistic understanding and, with that, methods that enable investigations under in situ conditions. Here, we apply surface-enhanced infrared absorption (SEIRA) spectroscopy to Influenza A M2 reconstituted within a solid-supported membrane, to shed light on the mechanics of its viroporin function. M2 is a paradigm of pH-activated proton channels and controls the proton flux into the viral interior during viral infection. We use SEIRA to track the large-scale reorientation of M2's transmembrane α-helices in situ during pH-activated channel opening. We quantify this event as a helical tilt from 26° to 40° by correlating the experimental results with solid-state nuclear magnetic resonance-informed computational spectroscopy. This mechanical motion is impeded upon addition of the inhibitor rimantadine, giving a direct spectroscopic marker to test antiviral activity. The presented approach provides a spectroscopic tool to quantify large-scale structural changes and to track the function and inhibition of the growing number of viroporins from pathogenic viruses in future studies.
Collapse
Affiliation(s)
- Ronja Rabea Paschke
- Physics Department, Freie Universität Berlin, Experimental Molecular Biophysics, Arnimallee 14, 14195, Berlin, Germany
- Research Building SupraFAB, Freie Universität Berlin, Altensteinstr. 23a, 14195, Berlin, Germany
| | - Swantje Mohr
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Sascha Lange
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125, Berlin, Germany
| | - Adam Lange
- Research Unit Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Straße 10, 13125, Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115, Berlin, Germany
| | - Jacek Kozuch
- Physics Department, Freie Universität Berlin, Experimental Molecular Biophysics, Arnimallee 14, 14195, Berlin, Germany
- Research Building SupraFAB, Freie Universität Berlin, Altensteinstr. 23a, 14195, Berlin, Germany
| |
Collapse
|
9
|
Townsend JA, Marty MT. What's the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry. Methods 2023; 218:1-13. [PMID: 37482149 PMCID: PMC10529358 DOI: 10.1016/j.ymeth.2023.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
Many membrane proteins form functional complexes that are either homo- or hetero-oligomeric. However, it is challenging to characterize membrane protein oligomerization in intact lipid bilayers, especially for polydisperse mixtures. Native mass spectrometry of membrane proteins and peptides inserted in lipid nanodiscs provides a unique method to study the oligomeric state distribution and lipid preferences of oligomeric assemblies. To interpret these complex spectra, we developed novel data analysis methods using macromolecular mass defect analysis. Here, we provide an overview of how mass defect analysis can be used to study oligomerization in nanodiscs, discuss potential limitations in interpretation, and explore strategies to resolve these ambiguities. Finally, we review recent work applying this technique to studying formation of antimicrobial peptide, amyloid protein, and viroporin complexes with lipid membranes.
Collapse
Affiliation(s)
- Julia A Townsend
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA.
| |
Collapse
|
10
|
Zeba A, Sekar K, Ganjiwale A. M Protein from Dengue virus oligomerizes to pentameric channel protein: in silico analysis study. Genomics Inform 2023; 21:e41. [PMID: 37813637 PMCID: PMC10584644 DOI: 10.5808/gi.23035] [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: 04/25/2023] [Revised: 06/12/2023] [Accepted: 07/11/2023] [Indexed: 10/11/2023] Open
Abstract
The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics (MD) simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis (RIN) for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.
Collapse
Affiliation(s)
- Ayesha Zeba
- Department of Life Sciences, Bangalore University, Bangalore, Karnataka 560056, India
| | - Kanagaraj Sekar
- Laboratory for Structural Biology and Bio-computing, Computational and Data Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Anjali Ganjiwale
- Department of Life Sciences, Bangalore University, Bangalore, Karnataka 560056, India
| |
Collapse
|
11
|
Stampolaki Μ, Hoffmann A, Tekwani K, Georgiou K, Tzitzoglaki C, Ma C, Becker S, Schmerer P, Döring K, Stylianakis I, Turcu AL, Wang J, Vázquez S, Andreas LB, Schmidtke M, Kolocouris A. A Study of the Activity of Adamantyl Amines against Mutant Influenza A M2 Channels Identified a Polycyclic Cage Amine Triple Blocker, Explored by Molecular Dynamics Simulations and Solid-State NMR. ChemMedChem 2023; 18:e202300182. [PMID: 37377066 DOI: 10.1002/cmdc.202300182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 06/29/2023]
Abstract
We compared the anti-influenza potencies of 57 adamantyl amines and analogs against influenza A virus with serine-31 M2 proton channel, usually termed as WT M2 channel, which is amantadine sensitive. We also tested a subset of these compounds against viruses with the amantadine-resistant L26F, V27A, A30T, G34E M2 mutant channels. Four compounds inhibited WT M2 virus in vitro with mid-nanomolar potency, with 27 compounds showing sub-micromolar to low micromolar potency. Several compounds inhibited L26F M2 virus in vitro with sub-micromolar to low micromolar potency, but only three compounds blocked L26F M2-mediated proton current as determined by electrophysiology (EP). One compound was found to be a triple blocker of WT, L26F, V27A M2 channels by EP assays, but did not inhibit V27A M2 virus in vitro, and one compound inhibited WT, L26F, V27A M2 in vitro without blocking V27A M2 channel. One compound blocked only L26F M2 channel by EP, but did not inhibit virus replication. The triple blocker compound is as long as rimantadine, but could bind and block V27A M2 channel due to its larger girth as revealed by molecular dynamics simulations, while MAS NMR informed on the interaction of the compound with M2(18-60) WT or L26F or V27A.
Collapse
Affiliation(s)
- Μarianna Stampolaki
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Anja Hoffmann
- Department of Medical Microbiology, Jena University Hospital, CMB Building, R. 443, Hans Knoell Str. 2, 07745, Jena (Germany), Germany
| | - Kumar Tekwani
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Kyriakos Georgiou
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece
| | - Christina Tzitzoglaki
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece
| | - Chunlong Ma
- Department of Medicinal Chemistry, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Patrick Schmerer
- Department of Medical Microbiology, Jena University Hospital, CMB Building, R. 443, Hans Knoell Str. 2, 07745, Jena (Germany), Germany
| | - Kristin Döring
- Department of Medical Microbiology, Jena University Hospital, CMB Building, R. 443, Hans Knoell Str. 2, 07745, Jena (Germany), Germany
| | - Ioannis Stylianakis
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece
| | - Andreea L Turcu
- Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, Barcelona, 08028, Spain
| | - Jun Wang
- Department of Medicinal Chemistry, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854-8020, USA
| | - Santiago Vázquez
- Facultat de Farmàcia i Ciències de l'Alimentació, and Institute of Biomedicine (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, Barcelona, 08028, Spain
| | - Loren B Andreas
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen, Germany
| | - Michaela Schmidtke
- Department of Medical Microbiology, Jena University Hospital, CMB Building, R. 443, Hans Knoell Str. 2, 07745, Jena (Germany), Germany
| | - Antonios Kolocouris
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece
| |
Collapse
|
12
|
Zsidó BZ, Bayarsaikhan B, Börzsei R, Szél V, Mohos V, Hetényi C. The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering. Int J Mol Sci 2023; 24:11784. [PMID: 37511543 PMCID: PMC10381018 DOI: 10.3390/ijms241411784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Water is a key actor of various processes of nature and, therefore, molecular engineering has to take the structural and energetic consequences of hydration into account. While the present review focuses on the target-ligand interactions in drug design, with a focus on biomolecules, these methods and applications can be easily adapted to other fields of the molecular engineering of molecular complexes, including solid hydrates. The review starts with the problems and solutions of the determination of water structures. The experimental approaches and theoretical calculations are summarized, including conceptual classifications. The implementations and applications of water models are featured for the calculation of the binding thermodynamics and computational ligand docking. It is concluded that theoretical approaches not only reproduce or complete experimental water structures, but also provide key information on the contribution of individual water molecules and are indispensable tools in molecular engineering.
Collapse
Affiliation(s)
- Balázs Zoltán Zsidó
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Bayartsetseg Bayarsaikhan
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Rita Börzsei
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Viktor Szél
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Violetta Mohos
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Csaba Hetényi
- Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| |
Collapse
|
13
|
Kyaw A, Roepke K, Arthur T, Howard KP. Conformation of influenza AM2 membrane protein in nanodiscs and liposomes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184152. [PMID: 36948480 PMCID: PMC10175228 DOI: 10.1016/j.bbamem.2023.184152] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/15/2023] [Accepted: 03/14/2023] [Indexed: 03/24/2023]
Abstract
The influenza A M2 protein (AM2) is a multifunctional membrane-associated homotetramer that orchestrates several essential events in the viral infection cycle including viral assembly and budding. An atomic-level conformational understanding of this key player in the influenza life cycle could inform new antiviral strategies. For conformational studies of complex systems like the AM2 membrane protein, a multipronged approach using different biophysical methods and different model membranes is a powerful way to incorporate complementary data and achieve a fuller, more robust understanding of the system. However, one must be aware of how the sample composition required for a particular method impacts the data collected and how conclusions are drawn. In that spirit, we systematically compared the properties of AM2 in two different model membranes: nanodiscs and liposomes. Electron paramagnetic spectroscopy of spin-labeled AM2 showed that the conformation and dynamics were strikingly similar in both AM2-nanodiscs and AM2-liposomes consistent with similar conformations in both model membranes. Analysis of spin labeled lipids embedded in both model membranes revealed that the bilayer in AM2-liposomes was more fluid and permeable to oxygen than AM2-nanodiscs with the same lipid composition. Once the difference in the partitioning of the paramagnetic oxygen relaxation agent was taken into account, the membrane topology of AM2 appeared to be the same in both liposomes and nanodiscs. Finally, functionally relevant AM2 conformational shifts previously seen in liposomes due to the addition of cholesterol were also observed in nanodiscs.
Collapse
Affiliation(s)
- Aye Kyaw
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States of America
| | - Kyra Roepke
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States of America
| | - Tyrique Arthur
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States of America
| | - Kathleen P Howard
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, United States of America.
| |
Collapse
|
14
|
Eberhardt J, Forli S. WaterKit: Thermodynamic Profiling of Protein Hydration Sites. J Chem Theory Comput 2023; 19:2535-2556. [PMID: 37094087 PMCID: PMC10732097 DOI: 10.1021/acs.jctc.2c01087] [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] [Indexed: 04/26/2023]
Abstract
Water desolvation is one of the key components of the free energy of binding of small molecules to their receptors. Thus, understanding the energetic balance of solvation and desolvation resulting from individual water molecules can be crucial when estimating ligand binding, especially when evaluating different molecules and poses as done in High-Throughput Virtual Screening (HTVS). Over the most recent decades, several methods were developed to tackle this problem, ranging from fast approximate methods (usually empirical functions using either discrete atom-atom pairwise interactions or continuum solvent models) to more computationally expensive and accurate ones, mostly based on Molecular Dynamics (MD) simulations, such as Grid Inhomogeneous Solvation Theory (GIST) or Double Decoupling. On one hand, MD-based methods are prohibitive to use in HTVS to estimate the role of waters on the fly for each ligand. On the other hand, fast and approximate methods show an unsatisfactory level of accuracy, with low agreement with results obtained with the more expensive methods. Here we introduce WaterKit, a new grid-based sampling method with explicit water molecules to calculate thermodynamic properties using the GIST method. Our results show that the discrete placement of water molecules is successful in reproducing the position of crystallographic waters with very high accuracy, as well as providing thermodynamic estimates with accuracy comparable to more expensive MD simulations. Unlike these methods, WaterKit can be used to analyze specific regions on the protein surface, (such as the binding site of a receptor), without having to hydrate and simulate the whole receptor structure. The results show the feasibility of a general and fast method to compute thermodynamic properties of water molecules, making it well-suited to be integrated in high-throughput pipelines such as molecular docking.
Collapse
Affiliation(s)
- Jerome Eberhardt
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California 92037, United States
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California 92037, United States
| |
Collapse
|
15
|
Qian Y, Wu Y, Qiu S, He X, Liu Y, Kong X, Tian W, Jiang L, Wen L. A Bioinspired Free‐Standing 2D Crown‐Ether‐Based Polyimine Membrane for Selective Proton Transport. Angew Chem Int Ed Engl 2023. [DOI: 10.1002/ange.202300167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
|
16
|
Kumari R, Sharma SD, Kumar A, Ende Z, Mishina M, Wang Y, Falls Z, Samudrala R, Pohl J, Knight PR, Sambhara S. Antiviral Approaches against Influenza Virus. Clin Microbiol Rev 2023; 36:e0004022. [PMID: 36645300 PMCID: PMC10035319 DOI: 10.1128/cmr.00040-22] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Preventing and controlling influenza virus infection remains a global public health challenge, as it causes seasonal epidemics to unexpected pandemics. These infections are responsible for high morbidity, mortality, and substantial economic impact. Vaccines are the prophylaxis mainstay in the fight against influenza. However, vaccination fails to confer complete protection due to inadequate vaccination coverages, vaccine shortages, and mismatches with circulating strains. Antivirals represent an important prophylactic and therapeutic measure to reduce influenza-associated morbidity and mortality, particularly in high-risk populations. Here, we review current FDA-approved influenza antivirals with their mechanisms of action, and different viral- and host-directed influenza antiviral approaches, including immunomodulatory interventions in clinical development. Furthermore, we also illustrate the potential utility of machine learning in developing next-generation antivirals against influenza.
Collapse
Affiliation(s)
- Rashmi Kumari
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Department of Anesthesiology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Suresh D. Sharma
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amrita Kumar
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Zachary Ende
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education (ORISE), CDC Fellowship Program, Oak Ridge, Tennessee, USA
| | - Margarita Mishina
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yuanyuan Wang
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Association of Public Health Laboratories, Silver Spring, Maryland, USA
| | - Zackary Falls
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Ram Samudrala
- Department of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Jan Pohl
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Paul R. Knight
- Department of Anesthesiology, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, New York, USA
| | - Suryaprakash Sambhara
- Immunology and Pathogenesis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| |
Collapse
|
17
|
Xue YW, Miura K, Itoh H, Inoue M. C-Terminal modification of polytheonamide B uncouples its dual functions in MCF-7 cancer cells. Chem Commun (Camb) 2023; 59:3914-3917. [PMID: 36919651 DOI: 10.1039/d2cc05915k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Polytheonamide B (1) is an exceptionally large peptide that forms a transmembrane ion channel. The potent cytotoxicity of 1 against MCF-7 cancer cells originates from its two ion transport functions. Compound 1 depolarizes the plasma membrane and neutralizes acidic lysosomes. Here, we describe how we uncoupled these functions by designing and synthesizing new analogues of 1.
Collapse
Affiliation(s)
- Yun-Wei Xue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Kensuke Miura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Hiroaki Itoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| |
Collapse
|
18
|
Hegazy A, Mahmoud SH, Elshaier YAMM, Shama NMA, Nasr NF, Ali MA, El-Shazly AM, Mostafa I, Mostafa A. Antiviral activities of plant-derived indole and β-carboline alkaloids against human and avian influenza viruses. Sci Rep 2023; 13:1612. [PMID: 36709362 PMCID: PMC9883826 DOI: 10.1038/s41598-023-27954-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/10/2023] [Indexed: 01/29/2023] Open
Abstract
The persistent evolution of drug-resistant influenza strains represents a global concern. The innovation of new treatment approaches through drug screening strategies and investigating the antiviral potential of bioactive natural-based chemicals may address the issue. Herein, we screened the anti-influenza efficacy of some biologically active indole and β-carboline (βC) indole alkaloids against two different influenza A viruses (IAV) with varied host range ranges; seasonal influenza A/Egypt/NRC098/2019(H1N1) and avian influenza A/chicken/Egypt/N12640A/2016(H5N1). All compounds were first assessed for their half-maximal cytotoxic concentration (CC50) in MDCK cells and half-maximal inhibitory concentrations (IC50) against influenza A/H5N1. Intriguingly, Strychnine sulfate, Harmalol, Harmane, and Harmaline showed robust anti-H5N1 activities with IC50 values of 11.85, 0.02, 0.023, and 3.42 µg/ml, respectively, as compared to zanamivir and amantadine as control drugs (IC50 = 0.079 µg/ml and 17.59 µg/ml, respectively). The efficacy of the predefined phytochemicals was further confirmed against influenza A/H1N1 and they displayed potent anti-H1N1 activities compared to reference drugs. Based on SI values, the highly promising compounds were then evaluated for antiviral efficacy through plaque reduction assay and consistently they revealed high viral inhibition percentages at non-toxic concentrations. By studying the modes of antiviral action, Harmane and Harmalol could suppress viral infection via interfering mainly with the viral replication of the influenza A/H5N1 virus, whilst Harmaline exhibited a viricidal effect against the influenza A/H5N1 virus. Whereas, Strychnine sulfate elucidated its anti-influenza potency by interfering with viral adsorption into MDCK cells. Consistently, chemoinformatic studies showed that all studied phytochemicals illustrated HB formations with essential peptide cleft through the NH of indole moiety. Among active alkaloids, harmalol displayed the best lipophilicity metrics including ligand efficiency (LE) and ligand lipophilic efficiency (LLE) for both viruses. Compounds geometry and their ability to participate in HB formation are very crucial.
Collapse
Affiliation(s)
- Akram Hegazy
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Giza District, 12613, Giza, Egypt
| | - Sara H Mahmoud
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, 12622, Egypt
| | - Yaseen A M M Elshaier
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Sadat City, Sadat City, 32897, Menoufia, Egypt
| | - Noura M Abo Shama
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, 12622, Egypt
| | - Nasr Fawzy Nasr
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Giza District, 12613, Giza, Egypt
| | - M A Ali
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Giza District, 12613, Giza, Egypt
| | - Assem Mohamed El-Shazly
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Sharkia, Egypt.,Faculty of Pharmacy, El Saleheya El Gadida University, El Saleheya El Gadida, 44813, Sharkia, Egypt
| | - Islam Mostafa
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig, 44519, Sharkia, Egypt.
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, 12622, Egypt.
| |
Collapse
|
19
|
Antonijevic M, Rochais C, Dallemagne P. C3-Symmetric Ligands in Drug Design: When the Target Controls the Aesthetics of the Drug. Molecules 2023; 28:molecules28020679. [PMID: 36677739 PMCID: PMC9862528 DOI: 10.3390/molecules28020679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
A number of proteins are able to adopt a homotrimeric spatial conformation. Among these structures, this feature appears as crucial for biologic targets, since it facilitates the design of C3-symmetric ligands that are especially suitable for displaying optimized ligand-target interactions and therapeutic benefits. Additionally, DNA as a therapeutic target, even if its conformation into a superhelix does not correspond to a C3-symmetry, can also take advantage of these C3-symmetric ligands for better interactions and therapeutic effects. For the moment, this opportunity appears to be under-exploited, but should become more frequent with the discovery of new homotrimeric targets such as the SARS-CoV2 spike protein. Besides their potential therapeutic interest, the synthetic access to these C3-symmetric ligands often leads to chemical challenges, although drug candidates with an aesthetic structure are generally obtained.
Collapse
|
20
|
Lazaridis T. Molecular origins of asymmetric proton conduction in the influenza M2 channel. Biophys J 2023; 122:90-98. [PMID: 36403086 PMCID: PMC9822799 DOI: 10.1016/j.bpj.2022.11.029] [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: 10/14/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 11/20/2022] Open
Abstract
The M2 proton channel of influenza A is embedded into the viral envelope and allows acidification of the virion when the external pH is lowered. In contrast, no outward proton conductance is observed when the internal pH is lowered, although outward current is observed at positive voltage. Residues Trp41 and Asp44 are known to play a role in preventing pH-driven outward conductance, but the mechanism for this is unclear. We investigate this issue using classical molecular dynamics simulations with periodic proton hops. When all key His37 residues are neutral, inward proton movement is much more facile than outward movement if the His are allowed to shuttle the proton. The preference for inward movement increases further as the charge on the His37 increases. Analysis of the trajectories reveals three factors accounting for this asymmetry. First, in the outward direction, Asp44 traps the hydronium by strong electrostatic interactions. Secondly, Asp44 and Trp41 orient the hydronium with the protons pointing inward, hampering outward Grotthus hopping. As a result, the effective barrier is lower in the inward direction. Trp41 adds to the barrier by weakly H-bonding to potential H+ acceptors. Finally, for charged His, the H3O+ in the inner vestibule tends to get trapped at lipid-lined fenestrations of the cone-shaped channel. Simulations qualitatively reproduce the experimentally observed higher outward conductance of mutants. The ability of positive voltage, unlike proton gradient, to induce an outward current appears to arise from its ability to bias H3O+ and the waters around it toward more H-outward orientations.
Collapse
Affiliation(s)
- Themis Lazaridis
- Department of Chemistry, City College of New York/CUNY, New York, New York; Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, New York.
| |
Collapse
|
21
|
Zhang S, Li Y, Li X, Gu J, Shao H, Huang Q, Cui P, Liu Y, Ran J, Fu CF. Polycations inclusion to simultaneously boost permeation and selectivity of two-dimensional TaS2 membranes for acid recovery. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.122759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
22
|
Kolocouris A, Arkin I, Glykos NM. A proof-of-concept study of the secondary structure of influenza A, B M2 and MERS- and SARS-CoV E transmembrane peptides using folding molecular dynamics simulations in a membrane mimetic solvent. Phys Chem Chem Phys 2022; 24:25391-25402. [PMID: 36239696 DOI: 10.1039/d2cp02881f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Here, we have carried out a proof-of-concept molecular dynamics (MD) simulation with adaptive tempering in a membrane mimetic environment to study the folding of single-pass membrane peptides. We tested the influenza A M2 viroporin, influenza B M2 viroporin, and protein E from coronaviruses MERS-Cov-2 and SARS-CoV-2 peptides with known experimental secondary structures in membrane bilayers. The two influenza-derived peptides are significantly different in the peptide sequence and secondary structure and more polar than the two coronavirus-derived peptides. Through a total of more than 50 μs of simulation time that could be accomplished in trifluoroethanol (TFE), as a membrane model, we characterized comparatively the folding behavior, helical stability, and helical propensity of these transmembrane peptides that match perfectly their experimental secondary structures, and we identified common motifs that reflect their quaternary organization and known (or not) biochemical function. We showed that BM2 is organized into two structurally distinct parts: a significantly more stable N-terminal half, and a fast-converting C-terminal half that continuously folds and unfolds between α-helical structures and non-canonical structures, which are mostly turns. In AM2, both the N-terminal half and C-terminal half are very flexible. In contrast, the two coronavirus-derived transmembrane peptides are much more stable and fast helix-formers when compared with the influenza ones. In particular, the SARS-derived peptide E appears to be the fastest and most stable helix-former of all the four viral peptides studied, with a helical structure that persists almost without disruption for the whole of its 10 μs simulation. By comparing the results with experimental observations, we benchmarked TFE in studying the conformation of membrane and hydrophobic peptides. This work provided accurate results suggesting a methodology to run long MD simulations and predict structural properties of biologically important membrane peptides.
Collapse
Affiliation(s)
- Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Greece.
| | - Isaiah Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, 91904, Israel
| | - Nicholas M Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Alexandroupolis, 68100, Greece.
| |
Collapse
|
23
|
Lazaridis T, Sepehri A. Amino acid deprotonation rates from classical force fields. J Chem Phys 2022; 157:085101. [DOI: 10.1063/5.0101960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Acid ionization constants (pKa's) of titratable amino acid side chains have received a large amount of experimental and theoretical attention. In many situations, however, the rates of protonation and deprotonation, kon & koff, may also be important, for example in understanding the mechanism of action of proton channels or membrane proteins that couple proton transport to other processes. Protonation and deprotonation involve making and breaking of covalent bonds, which cannot be studied by classical force fields. However, environment effects on the rates should be captured by such methods. Here we present an approach for estimating deprotonation rates based on Warshel's extension of Marcus's theory of electron transfer, with input from molecular simulations. The missing bond dissociation energy is represented by a constant term determined by fitting the pKa value in solution. The statistics of the energy gap between protonated and deprotonated states is used to compute free energy curves of the two states and thus free energy barriers, from which the rate can be deduced. The method is applied to Glu, Asp, and His in bulk solution and select membrane proteins: the M2 proton channel, bacteriorhodopsin, and cytochrome c oxidase.
Collapse
Affiliation(s)
- Themis Lazaridis
- Department of Chemistry, City College of New York, United States of America
| | | |
Collapse
|
24
|
Bálint M, Zsidó BZ, van der Spoel D, Hetényi C. Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design. Int J Mol Sci 2022; 23:ijms23137313. [PMID: 35806314 PMCID: PMC9267029 DOI: 10.3390/ijms23137313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 02/01/2023] Open
Abstract
The human genome codes only a few thousand druggable proteins, mainly receptors and enzymes. While this pool of available drug targets is limited, there is an untapped potential for discovering new drug-binding mechanisms and modes. For example, enzymes with long binding cavities offer numerous prerequisite binding sites that may be visited by an inhibitor during migration from a bulk solution to the destination site. Drug design can use these prerequisite sites as new structural targets. However, identifying these ephemeral sites is challenging. Here, we introduce a new method called NetBinder for the systematic identification and classification of prerequisite binding sites at atomic resolution. NetBinder is based on atomistic simulations of the full inhibitor binding process and provides a networking framework on which to select the most important binding modes and uncover the entire binding mechanism, including previously undiscovered events. NetBinder was validated by a study of the binding mechanism of blebbistatin (a potent inhibitor) to myosin 2 (a promising target for cancer chemotherapy). Myosin 2 is a good test enzyme because, like other potential targets, it has a long internal binding cavity that provides blebbistatin with numerous potential prerequisite binding sites. The mechanism proposed by NetBinder of myosin 2 structural changes during blebbistatin binding shows excellent agreement with experimentally determined binding sites and structural changes. While NetBinder was tested on myosin 2, it may easily be adopted to other proteins with long internal cavities, such as G-protein-coupled receptors or ion channels, the most popular current drug targets. NetBinder provides a new paradigm for drug design by a network-based elucidation of binding mechanisms at an atomic resolution.
Collapse
Affiliation(s)
- Mónika Bálint
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12., 7624 Pécs, Hungary; (M.B.); (B.Z.Z.)
| | - Balázs Zoltán Zsidó
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12., 7624 Pécs, Hungary; (M.B.); (B.Z.Z.)
| | - David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden;
| | - Csaba Hetényi
- Pharmacoinformatics Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12., 7624 Pécs, Hungary; (M.B.); (B.Z.Z.)
- Correspondence:
| |
Collapse
|
25
|
Correy GJ, Kneller DW, Phillips G, Pant S, Russi S, Cohen AE, Meigs G, Holton JM, Gahbauer S, Thompson MC, Ashworth A, Coates L, Kovalevsky A, Meilleur F, Fraser JS. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature. SCIENCE ADVANCES 2022; 8:eabo5083. [PMID: 35622909 PMCID: PMC9140965 DOI: 10.1126/sciadv.abo5083] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 05/04/2023]
Abstract
The nonstructural protein 3 (NSP3) macrodomain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Mac1) removes adenosine diphosphate (ADP) ribosylation posttranslational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the coronavirus disease 2019 pandemic. Here, we determined neutron and x-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose-bound states. We characterize extensive solvation in the Mac1 active site and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase the potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a reevaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.
Collapse
Affiliation(s)
- Galen J. Correy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Swati Pant
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - George Meigs
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James M. Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael C. Thompson
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA 95343, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Leighton Coates
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Flora Meilleur
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|
26
|
Yu D, Wang L, Wang Y. Recent Advances in Application of Computer-Aided Drug Design in Anti-Influenza A Virus Drug Discovery. Int J Mol Sci 2022; 23:ijms23094738. [PMID: 35563129 PMCID: PMC9105300 DOI: 10.3390/ijms23094738] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 02/06/2023] Open
Abstract
Influenza A is an acute respiratory infectious disease caused by the influenza A virus, which seriously threatens global human health and causes substantial economic losses every year. With the emergence of new viral strains, anti-influenza drugs remain the most effective treatment for influenza A. Research on traditional, innovative small-molecule drugs faces many challenges, while computer-aided drug design (CADD) offers opportunities for the rapid and effective development of innovative drugs. This literature review describes the general process of CADD, the viral proteins that play an essential role in the life cycle of the influenza A virus and can be used as therapeutic targets for anti-influenza drugs, and examples of drug screening of viral target proteins by applying the CADD approach. Finally, the main limitations of current CADD strategies in anti-influenza drug discovery and the field's future directions are discussed.
Collapse
Affiliation(s)
| | | | - Ye Wang
- Correspondence: ; Tel.: +86-431-8515-5249
| |
Collapse
|
27
|
Antiviral Effects of ABMA and DABMA against Influenza Virus In Vitro and In Vivo via Regulating the Endolysosomal Pathway and Autophagy. Int J Mol Sci 2022; 23:ijms23073940. [PMID: 35409297 PMCID: PMC8999625 DOI: 10.3390/ijms23073940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 03/27/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023] Open
Abstract
Influenza virus is an acute and highly contagious respiratory pathogen that causes great concern to public health and for which there is a need for extensive drug discovery. The small chemical compound ABMA and its analog DABMA, containing an adamantane or a dimethyl-adamantane group, respectively, have been demonstrated to inhibit multiple toxins (diphtheria toxin, Clostridium difficile toxin B, Clostridium sordellii lethal toxin) and viruses (Ebola, rabies virus, HSV-2) by acting on the host’s vesicle trafficking. Here, we showed that ABMA and DABMA have antiviral effects against both amantadine-sensitive influenza virus subtypes (H1N1 and H3N2), amantadine-resistant subtypes (H3N2), and influenza B virus with EC50 values ranging from 2.83 to 7.36 µM (ABMA) and 1.82 to 6.73 µM (DABMA), respectively. ABMA and DABMA inhibited the replication of influenza virus genomic RNA and protein synthesis by interfering with the entry stage of the virus. Molecular docking evaluation together with activity against amantadine-resistant influenza virus strains suggested that ABMA and DABMA were not acting as M2 ion channel blockers. Subsequently, we found that early internalized H1N1 virions were retained in accumulated late endosome compartments after ABMA treatment. Additionally, ABMA disrupted the early stages of the H1N1 life cycle or viral RNA synthesis by interfering with autophagy. ABMA and DABMA protected mice from an intranasal H1N1 challenge with an improved survival rate of 67%. The present study suggests that ABMA and DABMA are potential antiviral leads for the development of a host-directed treatment against influenza virus infection.
Collapse
|
28
|
Shelley KL, Garman EF. Quantifying and comparing radiation damage in the Protein Data Bank. Nat Commun 2022; 13:1314. [PMID: 35288575 PMCID: PMC8921271 DOI: 10.1038/s41467-022-28934-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 02/18/2022] [Indexed: 11/09/2022] Open
Abstract
Radiation damage remains one of the major bottlenecks to accurate structure solution in protein crystallography. It can induce structural and chemical changes in protein crystals, and is hence an important consideration when assessing the quality and biological veracity of crystal structures in repositories like the Protein Data Bank (PDB). However, detection of radiation damage artefacts has traditionally proved very challenging. To address this, here we introduce the Bnet metric. Bnet summarises in a single value the extent of damage suffered by a crystal structure by comparing the B-factor values of damage-prone and non-damage-prone atoms in a similar local environment. After validating that Bnet successfully detects damage in 23 different crystal structures previously characterised as damaged, we calculate Bnet values for 93,978 PDB crystal structures. Our metric highlights a range of damage features, many of which would remain unidentified by the other summary statistics typically calculated for PDB structures.
Collapse
Affiliation(s)
- Kathryn L Shelley
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom.
| | - Elspeth F Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.
| |
Collapse
|
29
|
Correy GJ, Kneller DW, Phillips G, Pant S, Russi S, Cohen AE, Meigs G, Holton JM, Gahbauer S, Thompson MC, Ashworth A, Coates L, Kovalevsky A, Meilleur F, Fraser JS. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.07.479477. [PMID: 35169801 PMCID: PMC8845425 DOI: 10.1101/2022.02.07.479477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The NSP3 macrodomain of SARS CoV 2 (Mac1) removes ADP-ribosylation post-translational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the COVID-19 pandemic. Here, we determined neutron and X-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose-bound states. We characterize extensive solvation in the Mac1 active site, and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a re-evaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.
Collapse
Affiliation(s)
- Galen J Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Daniel W Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Swati Pant
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - George Meigs
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94158, USA
| | - James M Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94158, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michael C Thompson
- Department of Chemistry and Chemical Biology, University of California Merced, CA 95343, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, CA 94158, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Flora Meilleur
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|
30
|
Avdeeva VV, Garaev TM, Malinina EA, Zhizhin KY, Kuznetsov NT. Physiologically Active Compounds Based on Membranotropic Cage Carriers–Derivatives of Adamantane and Polyhedral Boron Clusters (Review). RUSS J INORG CHEM+ 2022. [PMCID: PMC8824546 DOI: 10.1134/s0036023622010028] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Data on compounds based on cage structures―boron clusters (polyhedral boron hydrides, carboranes, metallacarboranes) and compounds of the adamantane series, which possess physiological activity, have been generalized. The main emphasis is placed on the antiviral activity of the compounds. The mechanism of the possible action of the replication inhibitors of influenza A virus strains is considered, the molecular model of viroporin inhibitors is discussed. The proposed model consists of a cage hydrophobic core that performs the function of a membranotropic carrier (a boron cluster or adamantane fragment), into which physiologically active functional groups are introduced. The relationship between the structure of the cage compound with the introduced substitute and the biologically active properties of this molecular structure has been analyzed.
Collapse
Affiliation(s)
- V. V. Avdeeva
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - T. M. Garaev
- Gamaleya Federal Research Center for Epidemiology and Microbiology, Ministry of Health of Russian Federation, 123098 Moscow, Russia
| | - E. A. Malinina
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - K. Yu. Zhizhin
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - N. T. Kuznetsov
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| |
Collapse
|
31
|
Aledavood E, Selmi B, Estarellas C, Masetti M, Luque FJ. From Acid Activation Mechanisms of Proton Conduction to Design of Inhibitors of the M2 Proton Channel of Influenza A Virus. Front Mol Biosci 2022; 8:796229. [PMID: 35096969 PMCID: PMC8795881 DOI: 10.3389/fmolb.2021.796229] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/24/2021] [Indexed: 11/26/2022] Open
Abstract
With an estimated 1 billion people affected across the globe, influenza is one of the most serious health concerns worldwide. Therapeutic treatments have encompassed a number of key functional viral proteins, mainly focused on the M2 proton channel and neuraminidase. This review highlights the efforts spent in targeting the M2 proton channel, which mediates the proton transport toward the interior of the viral particle as a preliminary step leading to the release of the fusion peptide in hemagglutinin and the fusion of the viral and endosomal membranes. Besides the structural and mechanistic aspects of the M2 proton channel, attention is paid to the challenges posed by the development of efficient small molecule inhibitors and the evolution toward novel ligands and scaffolds motivated by the emergence of resistant strains.
Collapse
Affiliation(s)
- Elnaz Aledavood
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Institut de Biomedicina and Institut de Química Teòrica i Computacional, University of Barcelona, Barcelona, Spain
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
| | - Beatrice Selmi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
| | - Carolina Estarellas
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Institut de Biomedicina and Institut de Química Teòrica i Computacional, University of Barcelona, Barcelona, Spain
- *Correspondence: Carolina Estarellas, ; Matteo Masetti, ; F. Javier Luque,
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
- *Correspondence: Carolina Estarellas, ; Matteo Masetti, ; F. Javier Luque,
| | - F. Javier Luque
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Institut de Biomedicina and Institut de Química Teòrica i Computacional, University of Barcelona, Barcelona, Spain
- *Correspondence: Carolina Estarellas, ; Matteo Masetti, ; F. Javier Luque,
| |
Collapse
|
32
|
Li X, Lv B, Zhang X, Jin X, Guo K, Zhou D, Bian H, Zhang W, Apfel U, Cao R. Introducing Water‐Network‐Assisted Proton Transfer for Boosted Electrocatalytic Hydrogen Evolution with Cobalt Corrole. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Xialiang Li
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Bin Lv
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Xue‐Peng Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Xiaotong Jin
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Kai Guo
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Dexia Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Hongtao Bian
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Wei Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| | - Ulf‐Peter Apfel
- Ruhr-Universität Bochum Fakultät für Chemie und Biochemie Anorganische Chemie I Universitätsstrasse 150 44801 Bochum Germany
- Fraunhofer UMSICHT Osterfelder Strasse 3 46047 Oberhausen Germany
| | - Rui Cao
- Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education School of Chemistry and Chemical Engineering Shaanxi Normal University Xi'an 710119 China
| |
Collapse
|
33
|
Kratochvil HT, Newberry RW, Mensa B, Mravic M, DeGrado WF. Spiers Memorial Lecture: Analysis and de novo design of membrane-interactive peptides. Faraday Discuss 2021; 232:9-48. [PMID: 34693965 PMCID: PMC8979563 DOI: 10.1039/d1fd00061f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Membrane-peptide interactions play critical roles in many cellular and organismic functions, including protection from infection, remodeling of membranes, signaling, and ion transport. Peptides interact with membranes in a variety of ways: some associate with membrane surfaces in either intrinsically disordered conformations or well-defined secondary structures. Peptides with sufficient hydrophobicity can also insert vertically as transmembrane monomers, and many associate further into membrane-spanning helical bundles. Indeed, some peptides progress through each of these stages in the process of forming oligomeric bundles. In each case, the structure of the peptide and the membrane represent a delicate balance between peptide-membrane and peptide-peptide interactions. We will review this literature from the perspective of several biologically important systems, including antimicrobial peptides and their mimics, α-synuclein, receptor tyrosine kinases, and ion channels. We also discuss the use of de novo design to construct models to test our understanding of the underlying principles and to provide useful leads for pharmaceutical intervention of diseases.
Collapse
Affiliation(s)
- Huong T Kratochvil
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Robert W Newberry
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Bruk Mensa
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| | - Marco Mravic
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA 92037, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California - San Francisco, San Francisco, CA 94158, USA.
| |
Collapse
|
34
|
Li X, Lv B, Zhang XP, Jin X, Guo K, Zhou D, Bian H, Zhang W, Apfel UP, Cao R. Introducing Water-Network-Assisted Proton Transfer for Boosted Electrocatalytic Hydrogen Evolution with Cobalt Corrole. Angew Chem Int Ed Engl 2021; 61:e202114310. [PMID: 34913230 DOI: 10.1002/anie.202114310] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Indexed: 11/10/2022]
Abstract
Proton transfer is vital for many biological and chemical reactions. Hydrogen-bonded water-containing networks are often found in enzymes to assist proton transfer, but similar strategy has been rarely presented by synthetic catalysts. We herein report the Co corrole 1 with an appended crown ether unit and its boosted activity for the hydrogen evolution reaction (HER). Crystallographic and 1H NMR studies proved that the crown ether of 1 can grab water via hydrogen bonds. By using protic acids as proton sources, the HER activity of 1 was largely boosted with added water, while the activity of crown-ether-free analogues showed very small enhancement. Inhibition studies by adding (1) external 18-crown-6-ether to extract water molecules and (2) potassium ion or N-benzyl-n-butylamine to block the crown ether of 1 further confirmed its critical role in assisting proton transfer via grabbed water molecules. This work presents a synthetic example to boost HER through water-containing networks.
Collapse
Affiliation(s)
- Xialiang Li
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, CHINA
| | - Bin Lv
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, CHINA
| | - Xue-Peng Zhang
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, CHINA
| | - Xiaotong Jin
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, CHINA
| | - Kai Guo
- shaanxi normal university, School of Chemistry and Chemical Engineering, CHINA
| | - Dexia Zhou
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, CHINA
| | - Hongtao Bian
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, CHINA
| | - Wei Zhang
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, CHINA
| | - Ulf-Peter Apfel
- Ruhr-Universität Bochum: Ruhr-Universitat Bochum, Fakultät fur Chemie und Biochemie, GERMANY
| | - Rui Cao
- Shaanxi Normal University, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Chang'an Campus, Number 620 West Chang'an Avenue, Chang'an District, 710119, Xi'an, CHINA
| |
Collapse
|
35
|
Townsend JA, Sanders HM, Rolland AD, Park CK, Horton NC, Prell JS, Wang J, Marty MT. Influenza AM2 Channel Oligomerization Is Sensitive to Its Chemical Environment. Anal Chem 2021; 93:16273-16281. [PMID: 34813702 DOI: 10.1021/acs.analchem.1c04660] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Viroporins are small viral ion channels that play important roles in the viral infection cycle and are proven antiviral drug targets. Matrix protein 2 from influenza A (AM2) is the best-characterized viroporin, and the current paradigm is that AM2 forms monodisperse tetramers. Here, we used native mass spectrometry and other techniques to characterize the oligomeric state of both the full-length and transmembrane (TM) domain of AM2 in a variety of different pH and detergent conditions. Unexpectedly, we discovered that AM2 formed a range of different oligomeric complexes that were strongly influenced by the local chemical environment. Native mass spectrometry of AM2 in nanodiscs with different lipids showed that lipids also affected the oligomeric states of AM2. Finally, nanodiscs uniquely enabled the measurement of amantadine binding stoichiometries to AM2 in the intact lipid bilayer. These unexpected results reveal that AM2 can form a wider range of oligomeric states than previously thought possible, which may provide new potential mechanisms of influenza pathology and pharmacology.
Collapse
Affiliation(s)
- Julia A Townsend
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Henry M Sanders
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States.,Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Chad K Park
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403, United States
| | - Jun Wang
- Department of Pharmacology and Toxicology, The University of Arizona, Tucson, Arizona 85721, United States.,Bio5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
| | - Michael T Marty
- Department of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States.,Bio5 Institute, The University of Arizona, Tucson, Arizona 85721, United States
| |
Collapse
|
36
|
Toft-Bertelsen TL, Jeppesen MG, Tzortzini E, Xue K, Giller K, Becker S, Mujezinovic A, Bentzen BH, B Andreas L, Kolocouris A, Kledal TN, Rosenkilde MM. Amantadine has potential for the treatment of COVID-19 because it inhibits known and novel ion channels encoded by SARS-CoV-2. Commun Biol 2021; 4:1347. [PMID: 34853399 PMCID: PMC8636635 DOI: 10.1038/s42003-021-02866-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 11/02/2021] [Indexed: 12/16/2022] Open
Abstract
The dire need for COVID-19 treatments has inspired strategies of repurposing approved drugs. Amantadine has been suggested as a candidate, and cellular as well as clinical studies have indicated beneficial effects of this drug. We demonstrate that amantadine and hexamethylene-amiloride (HMA), but not rimantadine, block the ion channel activity of Protein E from SARS-CoV-2, a conserved viroporin among coronaviruses. These findings agree with their binding to Protein E as evaluated by solution NMR and molecular dynamics simulations. Moreover, we identify two novel viroporins of SARS-CoV-2; ORF7b and ORF10, by showing ion channel activity in a X. laevis oocyte expression system. Notably, amantadine also blocks the ion channel activity of ORF10, thereby providing two ion channel targets in SARS-CoV-2 for amantadine treatment in COVID-19 patients. A screen of known viroporin inhibitors on Protein E, ORF7b, ORF10 and Protein 3a from SARS-CoV-2 revealed inhibition of Protein E and ORF7b by emodin and xanthene, the latter also blocking Protein 3a. This illustrates a general potential of well-known ion channel blockers against SARS-CoV-2 and specifically a dual molecular basis for the promising effects of amantadine in COVID-19 treatment. We therefore propose amantadine as a novel, cheap, readily available and effective way to treat COVID-19.
Collapse
Affiliation(s)
- Trine Lisberg Toft-Bertelsen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mads Gravers Jeppesen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Synklino ApS, Charlottenlund, Denmark
| | - Eva Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis-Zografou, Athens, Greece
| | - Kai Xue
- Department of NMR-based structural biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Karin Giller
- Department of NMR-based structural biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-based structural biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Amer Mujezinovic
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bo Hjorth Bentzen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Loren B Andreas
- Department of NMR-based structural biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis-Zografou, Athens, Greece
| | | | - Mette Marie Rosenkilde
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
37
|
Sette-DE-Souza PH, Costa MJF, Araújo FAC, Alencar EN, Amaral-Machado L. Two phytocompounds from Schinopsis brasiliensis show promising antiviral activity with multiples targets in Influenza A virus. AN ACAD BRAS CIENC 2021; 93:e20210964. [PMID: 34817041 DOI: 10.1590/0001-3765202120210964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/24/2021] [Indexed: 01/02/2023] Open
Abstract
Influenza A virus, the main flu agent, affects billions of people worldwide. Conventional treatments still present limitations related to drug-resistance and severe side effects. As a result, natural product-derived molecules have been increasingly investigated as prospect drug candidates. Therefore, the aim of this study was to investigate the possible anti-flu activity and to evaluate the toxicity and pharmacokinetic parameters, by in silico approaches, of the Schinopsis brasiliensis Engl. phytochemical compounds. Nine phytocompounds and six antiviral drugs (Amantadine, Umifenovir, Favipiravir, Nitazoxanide, Oseltamivir, Zanamivir) were selected for the analyses against four Influenza A proteins: neuraminidase, polymerase basic protein 2, hemagglutinin and M2 ion channel protein. The molecular docking, the predicted antiviral activity, the predicted toxicity and the pharmacokinetics investigations were conducted. The obtained results demonstrated that Syringaresinol and Cycloartenone display promising in silico antiviral activity (binding energy < 5.0 and ≥ 9.0 kcal/mol) and safety (low toxicity than commercial anti-flu drugs). Overall, this study corroborated the hypothesis that S. brasiliensis barks extract has a biological activity against Influenza A virus. Additionally, Syringaresinol and Cycloartenone have multiple targets in Influenza A virus and showed themselves as the most promising phytocompounds to be isolated and considered for the therapeutic arsenal against the flu.
Collapse
Affiliation(s)
- Pedro Henrique Sette-DE-Souza
- Universidade de Pernambuco, Faculdade de Odontologia, Rua Cicero Monteiro de Melo, s/n, São Cristóvão, 56503-146 Arcoverde, PE, Brazil.,Universidade de Pernambuco, Programa de Pós-Graduação em Saúde e Desenvolvimento Socioambiental (PPGSDS), Rua Capitão Pedro Rodrigues, 105, São José, 55294-902 Garanhuns, PE, Brazil.,Universidade de Pernambuco, Programa de Pós-Graduação em Odontologia, Av. General, Newton Cavalcanti, 1650, Tabatinga, 54756-220 Camaragibe, PE, Brazil
| | - Moan J F Costa
- Universidade de Pernambuco, Faculdade de Odontologia, Rua Cicero Monteiro de Melo, s/n, São Cristóvão, 56503-146 Arcoverde, PE, Brazil
| | - Fábio A C Araújo
- Universidade de Pernambuco, Faculdade de Odontologia, Rua Cicero Monteiro de Melo, s/n, São Cristóvão, 56503-146 Arcoverde, PE, Brazil.,Universidade de Pernambuco, Programa de Pós-Graduação em Odontologia, Av. General, Newton Cavalcanti, 1650, Tabatinga, 54756-220 Camaragibe, PE, Brazil
| | - Everton N Alencar
- Universidade Federal do Rio Grande do Norte, Departamento de Farmácia, Rua General Gustavo Cordeiro de Faria, s/n, Petrópolis, 59012-570 Natal, RN, Brazil
| | - Lucas Amaral-Machado
- Universidade Federal do Rio Grande do Norte, Departamento de Farmácia, Rua General Gustavo Cordeiro de Faria, s/n, Petrópolis, 59012-570 Natal, RN, Brazil
| |
Collapse
|
38
|
Li L, Li Q, Li X, Wang S, Zheng K, Zuo M, Zu X, Zhao Y, Yan W, Zhu J, Sun Y, Xie Y. Constructing artificial mimic-enzyme catalysts for carbon dioxide electroreduction. Sci China Chem 2021. [DOI: 10.1007/s11426-021-1116-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
39
|
Kolokouris D, Kalenderoglou IE, Kolocouris A. Inside and Out of the Pore: Comparing Interactions and Molecular Dynamics of Influenza A M2 Viroporin Complexes in Standard Lipid Bilayers. J Chem Inf Model 2021; 61:5550-5568. [PMID: 34714655 DOI: 10.1021/acs.jcim.1c00264] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ion channels located at viral envelopes (viroporins) have a critical function for the replication of infectious viruses and are important drug targets. Over the last decade, the number and duration of molecular dynamics (MD) simulations of the influenza A M2 ion channel owing to the increased computational efficiency. Here, we aimed to define the system setup and simulation conditions for the correct description of the protein-pore and the protein-lipid interactions for influenza A M2 in comparison with experimental data. We performed numerous MD simulations of the influenza A M2 protein in complex with adamantane blockers in standard lipid bilayers using OPLS2005 and CHARMM36 (C36) force fields. We explored the effect of varying the M2 construct (M2(22-46) and M2(22-62)), the lipid buffer size and type (stiffer DMPC or softer POPC with or without 20% cholesterol), the simulation time, the H37 protonation site (Nδ or Νε), the conformational state of the W41 channel gate, and M2's cholesterol binding sites (BSs). We report that the 200 ns MD with M2(22-62) (having Nε Η37) in the 20 Å lipid buffer with the C36 force field accurately describe: (a) the M2 pore structure and interactions inside the pore, that is, adamantane channel blocker location, water clathrate structure, and water or chloride anion blockage/passage from the M2 pore in the presence of a channel blocker and (b) interactions between M2 and the membrane environment as reflected by the calculation of the M2 bundle tilt, folding of amphipathic helices, and cholesterol BSs. Strikingly, we also observed that the C36 1 μs MD simulations using M2(22-62) embedded in a 20 Å POPC:cholesterol (5:1) scrambled membrane produced frequent interactions with cholesterol, which when combined with computational kinetic analysis, revealed the experimentally observed BSs of cholesterol and suggested three similarly long-interacting positions in the top leaflet that have previously not been observed experimentally. These findings promise to be useful for other viroporin systems.
Collapse
Affiliation(s)
- Dimitrios Kolokouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Iris E Kalenderoglou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, Athens 15771, Greece
| |
Collapse
|
40
|
Movellan KT, Dervişoğlu R, Becker S, Andreas LB. Porengebundenes Wasser an der Schlüsselaminosäure Histidin‐37 in Influenza A M2. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kumar Tekwani Movellan
- NMR-basierte Strukturbiologie Max-Planck-Institut für biophysikalische Chemie Am Faßberg 11 Göttingen 37077 Deutschland
| | - Rıza Dervişoğlu
- NMR-basierte Strukturbiologie Max-Planck-Institut für biophysikalische Chemie Am Faßberg 11 Göttingen 37077 Deutschland
| | - Stefan Becker
- NMR-basierte Strukturbiologie Max-Planck-Institut für biophysikalische Chemie Am Faßberg 11 Göttingen 37077 Deutschland
| | - Loren B. Andreas
- NMR-basierte Strukturbiologie Max-Planck-Institut für biophysikalische Chemie Am Faßberg 11 Göttingen 37077 Deutschland
| |
Collapse
|
41
|
Movellan KT, Dervişoğlu R, Becker S, Andreas LB. Pore-Bound Water at the Key Residue Histidine 37 in Influenza A M2. Angew Chem Int Ed Engl 2021; 60:24075-24079. [PMID: 34477305 PMCID: PMC8597138 DOI: 10.1002/anie.202103955] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 08/02/2021] [Indexed: 01/14/2023]
Abstract
Atomic details of structured water molecules are indispensable to understand the thermodynamics of important biological processes including the proton conduction mechanism of the M2 protein. Despite the expectation of structured water molecules based on crystal structures of Influenza A M2, only two water populations have been observed by NMR in reconstituted lipid bilayer samples. These are the bulk‐ and lipid‐associated water populations typically seen in membrane samples. Here, we detect a bound water molecule at a chemical shift of 11 ppm, located near the functional histidine 37 residue in the M2 conductance domain, which comprises residues 18 to 60. Combining 100 kHz magic‐angle spinning NMR, dynamic nuclear polarization and density functional theory calculations, we show that the bound water forms a hydrogen bond to the δ1 nitrogen of histidine 37.
Collapse
Affiliation(s)
- Kumar Tekwani Movellan
- NMR based Structural Biology, Max Planck Institute for biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
| | - Rıza Dervişoğlu
- NMR based Structural Biology, Max Planck Institute for biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
| | - Stefan Becker
- NMR based Structural Biology, Max Planck Institute for biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
| | - Loren B Andreas
- NMR based Structural Biology, Max Planck Institute for biophysical Chemistry, Am Fassberg 11, Göttingen, 37077, Germany
| |
Collapse
|
42
|
Abstract
Tertiary tetraols of adamantane (C10H16, Tricyclo[3.3.1.1(3,7)]decan) have been widely used for the synthesis of highly symmetric compounds with unique physical and chemical properties. The methods for one-stage simultaneously selective, deep, and cheap oxidation of adamantane to tetraols of different structures have not yet been developed. In this research, chemically simple, cheap, and environmentally friendly reagents are used and that is the first step in this direction. The conditions, under which the impact of a hydrogen peroxide water solution on adamantane dissolved in acetonitrile results in full conversion of adamantane and formation of a total 72% mixture of its tri-, tetra-, and penta-oxygenated products, predominantly poliols, have been found. Conversion and adamantane oxidation depth are shown to depend on the ratio of components of the water-acetonitrile solution and the method of oxidizer solution introduction when using the dimer form of 1:1 dimethylglyoxime and copper dichloride complex as a catalyst. Under the conditions of mass-spectrometry ionization by electrons (70 eV), fragmentation across three C–C bonds of the molecular ions framework of adamantane tertiary alcohols Ad(OH)n in the range n = 0–4 increases linearly with the rise of n.
Collapse
|
43
|
Zsidó B, Börzsei R, Szél V, Hetényi C. Determination of Ligand Binding Modes in Hydrated Viral Ion Channels to Foster Drug Design and Repositioning. J Chem Inf Model 2021; 61:4011-4022. [PMID: 34313421 PMCID: PMC8389532 DOI: 10.1021/acs.jcim.1c00488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Indexed: 12/29/2022]
Abstract
Target-based design and repositioning are mainstream strategies of drug discovery. Numerous drug design and repositioning projects have been launched to fight the ongoing COVID-19 pandemic. The resulting drug candidates have often failed due to the misprediction of their target-bound structures. The determination of water positions of such structures is particularly challenging due to the large number of possible drugs and the diversity of their hydration patterns. To answer this challenge and help correct predictions, we introduce a new protocol HydroDock, which can build hydrated drug-target complexes from scratch. HydroDock requires only the dry target and drug structures and produces their complexes with appropriately positioned water molecules. As a test application of the protocol, we built the structures of amantadine derivatives in complex with the influenza M2 transmembrane ion channel. The repositioning of amantadine derivatives from this influenza target to the SARS-CoV-2 envelope protein was also investigated. Excellent agreement was observed between experiments and the structures determined by HydroDock. The atomic resolution complex structures showed that water plays a similar role in the binding of amphipathic amantadine derivatives to transmembrane ion channels of both influenza A and SARS-CoV-2. While the hydrophobic regions of the channels capture the bulky hydrocarbon group of the ligand, the surrounding waters direct its orientation parallel with the axes of the channels via bridging interactions with the ionic ligand head. As HydroDock supplied otherwise undetermined structural details, it can be recommended to improve the reliability of future design and repositioning of antiviral drug candidates and many other ligands with an influence of water structure on their mechanism of action.
Collapse
Affiliation(s)
- Balázs
Zoltán Zsidó
- Pharmacoinformatics
Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Rita Börzsei
- Pharmacoinformatics
Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
- Department
of Pharmacology, Faculty of Pharmacy, University
of Pécs, Szigeti
út 12, 7624 Pécs, Hungary
| | - Viktor Szél
- Pharmacoinformatics
Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| | - Csaba Hetényi
- Pharmacoinformatics
Unit, Department of Pharmacology and Pharmacotherapy, Medical School, University of Pécs, Szigeti út 12, 7624 Pécs, Hungary
| |
Collapse
|
44
|
Thomaston JL, Samways ML, Konstantinidi A, Ma C, Hu Y, Bruce Macdonald HE, Wang J, Essex JW, DeGrado WF, Kolocouris A. Rimantadine Binds to and Inhibits the Influenza A M2 Proton Channel without Enantiomeric Specificity. Biochemistry 2021; 60:10.1021/acs.biochem.1c00437. [PMID: 34342217 PMCID: PMC8810914 DOI: 10.1021/acs.biochem.1c00437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The influenza A M2 wild-type (WT) proton channel is the target of the anti-influenza drug rimantadine. Rimantadine has two enantiomers, though most investigations into drug binding and inhibition have used a racemic mixture. Solid-state NMR experiments using the full length-M2 WT have shown significant spectral differences that were interpreted to indicate tighter binding for (R)- vs (S)-rimantadine. However, it was unclear if this correlates with a functional difference in drug binding and inhibition. Using X-ray crystallography, we have determined that both (R)- and (S)-rimantadine bind to the M2 WT pore with slight differences in the hydration of each enantiomer. However, this does not result in a difference in potency or binding kinetics, as shown by similar values for kon, koff, and Kd in electrophysiological assays and for EC50 values in cellular assays. We concluded that the slight differences in hydration for the (R)- and (S)-rimantadine enantiomers are not relevant to drug binding or channel inhibition. To further explore the effect of the hydration of the M2 pore on binding affinity, the water structure was evaluated by grand canonical ensemble molecular dynamics simulations as a function of the chemical potential of the water. Initially, the two layers of ordered water molecules between the bound drug and the channel's gating His37 residues mask the drug's chirality. As the chemical potential becomes more unfavorable, the drug translocates down to the lower water layer, and the interaction becomes more sensitive to chirality. These studies suggest the feasibility of displacing the upper water layer and specifically recognizing the lower water layers in novel drugs.
Collapse
Affiliation(s)
- Jessica L Thomaston
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, University of California, San Francisco, California 94158, United States
| | - Marley L Samways
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - Athina Konstantinidi
- Department of Pharmaceutical Chemistry, School of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Chunlong Ma
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Yanmei Hu
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Hannah E Bruce Macdonald
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Jun Wang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - William F DeGrado
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, University of California, San Francisco, California 94158, United States
| | - Antonios Kolocouris
- Department of Pharmaceutical Chemistry, School of Pharmacy, National and Kapodistrian University of Athens, 15771 Athens, Greece
| |
Collapse
|
45
|
Kim KH. Outliers in SAR and QSAR: 3. Importance of considering the role of water molecules in protein-ligand interactions and quantitative structure-activity relationship studies. J Comput Aided Mol Des 2021; 35:371-396. [PMID: 33712973 DOI: 10.1007/s10822-021-00377-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/05/2021] [Indexed: 11/30/2022]
Abstract
It is frequently mentioned that QSARs have not generally lived up to expectations, especially in cases where high predictability is expected yet failed to deliver satisfactory results. Even though outliers can provide an increased opportunity in drug discovery research, outliers in SAR and QSAR can contort predictions and affect the accuracy if proper attention is not given. The percentages of outliers in QSARs have not changed appreciably over the last decade. In our previous studies, we suggested two possible sources of outliers in SAR and QSAR. In this paper, we suggest an additional possible source of outliers in QSAR. We presented several literature examples that show one or more water molecules that play a critical role in protein-ligand binding interactions as observed in their crystal structures. These examples illustrate that failing to account for the effects of water molecules in protein-ligand interactions could mislead interpretation and possibly yield outliers in SAR and QSAR. Examples include cases where QSAR, considering the role of water molecules in protein-ligand crystal structures, provided deeper insight into the understanding and interpretation of the developed QSAR.
Collapse
|
46
|
Zhang Y, Zheng QC. In Silico Analysis Revealed a Unique Binding but Ineffective Mode of Amantadine to Influenza Virus B M2 Channel. J Phys Chem Lett 2021; 12:1169-1174. [PMID: 33480694 DOI: 10.1021/acs.jpclett.0c03560] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The M2 proton channel of influenza A (AM2) and B (BM2) have a highly conserved function motif, considered as the effective target. As yet, there is no effective drug against BM2. Research showed that AM2 channel blocker, amantadine (AMT), was able to bind to BM2 channel, but AMT lacked inhibition against BM2. Nevertheless, the study of the binding but ineffective mode of AMT to BM2 is challenging. To resolve the challenge and obtain more information for drug design of inhibitors targeting BM2, multiple molecular dynamics simulations were performed. We discovered AMT mainly adopted up binding mode in BM2, involved in a transition flipping from down mode to up mode. Furthermore, we discovered a new key factor to explain ineffective inhibition of AMT to BM2 because of the unmatched spatial geometry between AMT and BM2. Our work could enrich structural feature information on BM2 and provide a new perspective for rational drug design of anti-influenza B.
Collapse
Affiliation(s)
- Yue Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, College of Chemistry, Jilin University, Changchun 130023, People's Republic of China
| | - Qing-Chuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of Nano-Micro Architecture Chemistry, College of Chemistry, Jilin University, Changchun 130023, People's Republic of China
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130023, People's Republic of China
| |
Collapse
|
47
|
Danysz W, Dekundy A, Scheschonka A, Riederer P. Amantadine: reappraisal of the timeless diamond-target updates and novel therapeutic potentials. J Neural Transm (Vienna) 2021; 128:127-169. [PMID: 33624170 PMCID: PMC7901515 DOI: 10.1007/s00702-021-02306-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/13/2021] [Indexed: 12/30/2022]
Abstract
The aim of the current review was to provide a new, in-depth insight into possible pharmacological targets of amantadine to pave the way to extending its therapeutic use to further indications beyond Parkinson's disease symptoms and viral infections. Considering amantadine's affinities in vitro and the expected concentration at targets at therapeutic doses in humans, the following primary targets seem to be most plausible: aromatic amino acids decarboxylase, glial-cell derived neurotrophic factor, sigma-1 receptors, phosphodiesterases, and nicotinic receptors. Further three targets could play a role to a lesser extent: NMDA receptors, 5-HT3 receptors, and potassium channels. Based on published clinical studies, traumatic brain injury, fatigue [e.g., in multiple sclerosis (MS)], and chorea in Huntington's disease should be regarded potential, encouraging indications. Preclinical investigations suggest amantadine's therapeutic potential in several further indications such as: depression, recovery after spinal cord injury, neuroprotection in MS, and cutaneous pain. Query in the database http://www.clinicaltrials.gov reveals research interest in several further indications: cancer, autism, cocaine abuse, MS, diabetes, attention deficit-hyperactivity disorder, obesity, and schizophrenia.
Collapse
Affiliation(s)
- Wojciech Danysz
- Merz Pharmaceuticals GmbH., Eckenheimer Landstraße 100, 60318, Frankfurt am Main, Germany
| | - Andrzej Dekundy
- Merz Pharmaceuticals GmbH., Eckenheimer Landstraße 100, 60318, Frankfurt am Main, Germany
| | - Astrid Scheschonka
- Merz Pharmaceuticals GmbH., Eckenheimer Landstraße 100, 60318, Frankfurt am Main, Germany
| | - Peter Riederer
- Clinic and Policlinic for Psychiatry, Psychosomatics and Psychotherapy, University Hospital Würzburg, University of Würzburg, Margarete-Höppel-Platz 1, 97080, Würzburg, Germany.
- Department Psychiatry, University of Southern Denmark Odense, Vinslows Vey 18, 5000, Odense, Denmark.
| |
Collapse
|
48
|
Terrier O, Slama-Schwok A. Anti-Influenza Drug Discovery and Development: Targeting the Virus and Its Host by All Possible Means. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:195-218. [PMID: 34258742 DOI: 10.1007/978-981-16-0267-2_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Infections by influenza virus constitute a major and recurrent threat for human health. Together with vaccines, antiviral drugs play a key role in the prevention and treatment of influenza virus infection and disease. Today, the number of antiviral molecules approved for the treatment of influenza is relatively limited, and their use is threatened by the emergence of viral strains with resistance mutations. There is therefore a real need to expand the prophylactic and therapeutic arsenal. This chapter summarizes the state of the art in drug discovery and development for the treatment of influenza virus infections, with a focus on both virus-targeting and host cell-targeting strategies. Novel antiviral strategies targeting other viral proteins or targeting the host cell, some of which are based on drug repurposing, may be used in combination to strengthen our therapeutic arsenal against this major pathogen.
Collapse
Affiliation(s)
- Olivier Terrier
- CIRI, Centre International de Recherche en Infectiologie, (Team VirPath), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Anny Slama-Schwok
- Sorbonne Université, Centre de Recherche Saint-Antoine, INSERM U938, Biologie et Thérapeutique du Cancer, Paris, France.
| |
Collapse
|
49
|
Adhikari N, Amin SA, Jha T. Dissecting the Drug Development Strategies Against SARS-CoV-2 Through Diverse Computational Modeling Techniques. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/7653_2020_46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
50
|
Watkins LC, DeGrado WF, Voth GA. Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics. J Am Chem Soc 2020; 142:17425-17433. [PMID: 32933245 PMCID: PMC7564090 DOI: 10.1021/jacs.0c06419] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Prevalent resistance to inhibitors
that target the influenza A
M2 proton channel has necessitated a continued drug design effort,
supported by a sustained study of the mechanism of channel function
and inhibition. Recent high-resolution X-ray crystal structures present
the first opportunity to see how the adamantyl amine class of inhibitors
bind to M2 and disrupt and interact with the channel’s water
network, providing insight into the critical properties that enable
their effective inhibition in wild-type M2. In this work, we examine
the hypothesis that these drugs act primarily as mechanism-based inhibitors
by comparing hydrated excess proton stabilization during proton transport
in M2 with the interactions revealed in the crystal structures, using
the Multiscale Reactive Molecular Dynamics (MS-RMD) methodology. MS-RMD,
unlike classical molecular dynamics, models the hydrated proton (hydronium-like
cation) as a dynamic excess charge defect and allows bonds to break
and form, capturing the intricate interactions between the hydrated
excess proton, protein atoms, and water. Through this, we show that
the ammonium group of the inhibitors is effectively positioned to
take advantage of the channel’s natural ability to stabilize
an excess protonic charge and act as a hydronium mimic. Additionally,
we show that the channel is especially stable in the drug binding
region, highlighting the importance of this property for binding the
adamantane group. Finally, we characterize an additional hinge point
near Val27, which dynamically responds to charge and inhibitor binding.
Altogether, this work further illuminates a dynamic understanding
of the mechanism of drug inhibition in M2, grounded in the fundamental
properties that enable the channel to transport and stabilize excess
protons, with critical implications for future drug design efforts.
Collapse
Affiliation(s)
- Laura C Watkins
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
| |
Collapse
|