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Li D, Minkara MS. Elucidating the enhanced binding affinity of a double mutant SP-D with trimannose on the influenza A virus using molecular dynamics. Comput Struct Biotechnol J 2022; 20:4984-5000. [PMID: 36097510 DOI: 10.1016/j.csbj.2022.08.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 12/02/2022] Open
Abstract
The Asp325Ala mutation in SP-D promotes a trimannose conformational change to a more stable state. The Arg343Val mutation in SP-D reduces its interaction with Glu333 to increase the binding affinity with trimannose. The Arg343Val mutation contributes more to the increase of SP-D’s binding affinity with trimannose than Asp325Ala.
Surfactant protein D (SP-D) is an essential component of the human pulmonary surfactant system, which is crucial in the innate immune response against glycan-containing pathogens, including Influenza A viruses (IAV) and SARS-CoV-2. Previous studies have shown that wild-type (WT) SP-D can bind IAV but exhibits poor antiviral activities. However, a double mutant (DM) SP-D consisting of two point mutations (Asp325Ala and Arg343Val) inhibits IAV more potently. Presently, the structural mechanisms behind the point mutations’ effects on SP-D’s binding affinity with viral surface glycans are not fully understood. Here we use microsecond-scale, full-atomistic molecular dynamics (MD) simulations to understand the molecular mechanism of mutation-induced SP-D’s higher antiviral activity. We find that the Asp325Ala mutation promotes a trimannose conformational change to a more stable state. Arg343Val increases the binding with trimannose by increasing the hydrogen bonding interaction with Glu333. Free energy perturbation (FEP) binding free energy calculations indicate that the Arg343Val mutation contributes more to the increase of SP-D’s binding affinity with trimannose than Asp325Ala. This study provides a molecular-level exploration of how the two mutations increase SP-D binding affinity with trimannose, which is vital for further developing preventative strategies for related diseases.
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Key Words
- CRD, Carbohydrate Recognition Domain
- DM, Double mutant
- FEP, Free Energy Perturbation
- Free Energy Perturbation
- HA, Hemagglutinin
- IAV, Influenza A Viruses
- MD, Molecular Dynamics
- Molecular Dynamics Simulation
- PAP, Pulmonary Alveolar Proteinosis
- PME, Particle Mesh Ewald
- PS, Pulmonary Surfactant
- Protein-Glycan Complexes
- RMSD, Root Mean Square Deviation
- RMSF, Root Mean Square Fluctuation
- SP-A, Surfactant Protein A
- SP-B, Surfactant Protein B
- SP-C, Surfactant Protein C
- SP-D, Surfactant Protein D
- Surfactant Protein D
- WT, Wild-type
- λ-REMD, λ-Replica-Exchange Molecular Dynamics
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Paoletti F, Merzel F, Cassetta A, Ogris I, Covaceuszach S, Grdadolnik J, Lamba D, Golič Grdadolnik S. Endogenous modulators of neurotrophin signaling: Landscape of the transient ATP-NGF interactions. Comput Struct Biotechnol J 2021; 19:2938-2949. [PMID: 34136093 PMCID: PMC8164016 DOI: 10.1016/j.csbj.2021.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/29/2021] [Accepted: 05/02/2021] [Indexed: 12/02/2022] Open
Abstract
High-resolution solution NMR structure of rhNGF has been determined. Quinary interactions characterize ATP binding to rhNGF. SPR, ITC and STD-NMR reveal ATP binding to rhNGF with mM affinity. NMR and MD analysis pinpoint to the presence of two binding sites of ATP on rhNGF. Stoichiometry of ATP-Mg2+ or Zn2+-rhNGF mixtures affects KD affinity to TrkA/p75NTR.
The Nerve Growth Factor (NGF) neurotrophin acts in the maintenance and growth of neuronal populations. Despite the detailed knowledge of NGF’s role in neuron physiology, the structural and mechanistic determinants of NGF bioactivity modulated by essential endogenous ligands are still lacking. We present the results of an integrated structural and advanced computational approach to characterize the extracellular ATP-NGF interaction. We mapped by NMR the interacting surface and ATP orientation on NGF and revealed the functional role of this interaction in the binding to TrkA and p75NTR receptors by SPR. The role of divalent ions was explored in conjunction with ATP. Our results pinpoint ATP as a likely transient molecular modulator of NGF signaling, in health and disease states.
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Key Words
- ARIA, Ambiguous Restraints for Iterative Assignment
- ATP modulation
- BDNF, Brain Derived Neurotrophic Factor
- CARA, Computer Aided Resonance Assignment
- CS-E, Chrondroitin Sulfate E
- CSP, Chemical Shift Perturbation
- DSF, Differential Scanning Fluorimetry
- EI-MS, Electron Ionization Mass Spectrometry
- Endogenous ligands
- FGF2, Fibroblast Growth Factor 2
- FT-IR, Fourier Transform Infrared Spectroscopy
- HBD, Heparin Binding Domain
- HSQC, Heteronuclear Single Quantum Coherence
- ITC, Isothermal Titration Calorimetry
- MALDI-TOF MS, Matrix Assisted Laser Desorption Ionization-Time Of Flight Mass Spectrometry
- MD, Molecular Dynamics
- MS, Mass Spectrometry
- NGF interactions
- NGF, Nerve Growth Factor
- NMR, Nuclear Magnetic Resonance
- NOE, Nuclear Overhouser Effect
- NOESY, Nuclear Overhauser Effect Spectroscopy
- NT, NeuroTrophin
- Neurotrophins
- P20, Polysorbate 20
- PME, Particle Mesh Ewald
- RMSD, Root Mean Square Deviation
- SAR, Structure-Activity Relationship
- SPR, Surface Plasmon Resonance
- STD, Saturation-Transfer Difference
- TrkA, Tyrosine Kinase Receptor A
- TrkA, p75NTR receptors
- p75NTR, p75 NeuroTrophin Receptor
- proNGF, proNGF – NGF precursor
- rh-proNGF, recombinant human proNGF – NGF precursor
- rhNGF, recombinant human NGF
- rmNGF, recombinant mouse NGF
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Affiliation(s)
- Francesca Paoletti
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Franci Merzel
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Alberto Cassetta
- Institute of Crystallography - C.N.R.- Trieste Outstation. Area Science Park - Basovizza, S.S.14 - Km. 163.5, I-34149 Trieste, Italy
| | - Iza Ogris
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Sonia Covaceuszach
- Institute of Crystallography - C.N.R.- Trieste Outstation. Area Science Park - Basovizza, S.S.14 - Km. 163.5, I-34149 Trieste, Italy
| | - Jože Grdadolnik
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Doriano Lamba
- Institute of Crystallography - C.N.R.- Trieste Outstation. Area Science Park - Basovizza, S.S.14 - Km. 163.5, I-34149 Trieste, Italy.,Interuniversity Consortium "Biostructures and Biosystems National Institute", Viale delle Medaglie d'Oro 305, I-00136 Roma, Italy
| | - Simona Golič Grdadolnik
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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Alexandris N, Lagoumintzis G, Chasapis CT, Leonidas DD, Papadopoulos GE, Tzartos SJ, Tsatsakis A, Eliopoulos E, Poulas K, Farsalinos K. Nicotinic cholinergic system and COVID-19: In silico evaluation of nicotinic acetylcholine receptor agonists as potential therapeutic interventions. Toxicol Rep 2020; 8:73-83. [PMID: 33425684 PMCID: PMC7776751 DOI: 10.1016/j.toxrep.2020.12.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/01/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 infection was announced as a pandemic in March 2020. Since then, several scientists have focused on the low prevalence of smokers among hospitalized COVID-19 patients. These findings led to our hypothesis that the Nicotinic Cholinergic System (NCS) plays a crucial role in the manifestation of COVID-19 and its severe symptoms. Molecular modeling revealed that the SARS-CoV-2 Spike glycoprotein might bind to nicotinic acetylcholine receptors (nAChRs) through a cryptic epitope homologous to snake toxins, substrates well documented and known for their affinity to the nAChRs. This binding model could provide logical explanations for the acute inflammatory disorder in patients with COVID-19, which may be linked to severe dysregulation of NCS. In this study, we present a series of complexes with cholinergic agonists that can potentially prevent SARS-CoV-2 Spike glycoprotein from binding to nAChRs, avoiding dysregulation of the NCS and moderating the symptoms and clinical manifestations of COVID-19. If our hypothesis is verified by in vitro and in vivo studies, repurposing agents currently approved for smoking cessation and neurological conditions could provide the scientific community with a therapeutic option in severe COVID-19.
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Key Words
- ACh, Acetylcholine
- AChBP, Acetylcholine-binding protein
- ARDS, acute respiratory distress syndrome
- BLAST, Basic Local Alignment Search Tool
- CHARMM, Chemistry at Harvard Macromolecular Mechanics
- CNS, Central Nervous System
- COVID-19
- Cholinergic agonists
- CoV, coronavirus
- DCD, single precision binary FORTRAN
- ECD, extracellular domain
- HADDOCK, High Ambiguity Driven protein-protein DOCKing
- HMGB1, High-mobility group protein 1
- IL, Interleukin
- Jak2, Janus kinases 2
- LBD, Ligand Binding Domain
- MD, Molecular Dynamics
- MDS, Molecular Dynamics Simulations
- MERS, Middle East Respiratory Syndrome
- NAMD, Nanoscale Molecular Dynamics
- NCBI, National Center for Biotechnology Information
- NCS, Nicotinic Cholinergic System
- NF-kB, nuclear factor kappa-light-chain-enhancer of activated B cells
- NPT, constant number, pressure, energy
- NVT, constant number, volume, energy
- Nicotinic acetylcholine receptors
- PDB, Protein Data Bank
- PME, Particle Mesh Ewald
- PRODIGY, PROtein binDIng enerGY prediction
- PyMOL, Python Molecule
- RBD, Receptor Binding Domain
- RMSD, Root-mean-square deviation
- SARS, Severe Acute Respiratory Syndrome
- SARS-CoV-2
- SARS-CoV-2 S1, SARS - 2 Spike Subunit 1 protein
- STAT3, signal transducer and activator of transcription 3
- STD NMR, Saturation Transfer Difference Nuclear Magnetic Resonance
- Spike glycoprotein
- TNF, Tumor Necrosis Factor
- VMD, Visual Molecular Dynamics
- lig, ligand
- nAChRs, nicotinic acetylcholine receptors
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Affiliation(s)
- Nikolaos Alexandris
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece
| | - George Lagoumintzis
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece
- Institute of Research and Innovation - IRIS, Patras Science Park SA, 26500 Patras, Greece
| | - Christos T. Chasapis
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece
| | - Demetres D. Leonidas
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Georgios E. Papadopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | | | | | - Elias Eliopoulos
- Department of Biotechnology, Laboratory of Genetics, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Konstantinos Poulas
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece
- Institute of Research and Innovation - IRIS, Patras Science Park SA, 26500 Patras, Greece
| | - Konstantinos Farsalinos
- Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, 26500, Rio-Patras, Greece
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Yang W, Sun X, Zhang C, Lai L. Discovery of novel helix binding sites at protein-protein interfaces. Comput Struct Biotechnol J 2019; 17:1396-1403. [PMID: 31768230 PMCID: PMC6872852 DOI: 10.1016/j.csbj.2019.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 10/29/2019] [Accepted: 11/01/2019] [Indexed: 01/09/2023] Open
Abstract
Protein-protein interactions (PPIs) play a key role in numerous biological processes. Many efforts have been undertaken to develop PPI modulators for therapeutic applications; however, to date, most of the peptide binders designed to target PPIs are derived from native binding helices or using the native helix binding site, which has limited the applications of protein-protein interface binding peptide design. Here, we developed a general computational algorithm, HPer (Helix Positioner), that locates single-helix binding sites at protein-protein interfaces based on the structure of protein targets. HPer performed well on known single-helix-mediated PPIs and recaptured the key interactions and hot-spot residues of native helical binders. We also screened non-helical-mediated PPIs in the PDBbind database and identified 17 PPIs that were suitable for helical peptide binding, and the helical binding sites in these PPIs were also predicted for designing novel peptide ligands. The L2 domain of EGFR, which was the top ranked, was selected as an example to show the protocol and results of designing novel helical peptide ligands on the searched binding site. The binding stability of the designed sequences were further investigated using molecular dynamics simulations.
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Affiliation(s)
- Wei Yang
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Center for Quantitative Biology, AAIS, Peking University, Beijing 100871, China
| | - Xiangyu Sun
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Changsheng Zhang
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Luhua Lai
- BNLMS, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, AAIS, Peking University, Beijing 100084, China
- Center for Quantitative Biology, AAIS, Peking University, Beijing 100871, China
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Kumar R, Jade D, Gupta D. A novel identification approach for discovery of 5-HydroxyTriptamine 2A antagonists: combination of 2D/3D similarity screening, molecular docking and molecular dynamics. J Biomol Struct Dyn 2018; 37:931-943. [PMID: 29468945 DOI: 10.1080/07391102.2018.1444509] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
5-HydroxyTriptamine 2A antagonists are potential targets for treatment of various cerebrovascular and cardiovascular disorders. In this study, we have developed and performed a unique screening pipeline for filtering ZINC database compounds on the basis of similarities to known antagonists to determine novel small molecule antagonists of 5-HydroxyTriptamine 2A. The screening pipeline is based on 2D similarity, 3D dissimilarity and a combination of 2D/3D similarity. The shortlisted compounds were docked to a 5-HydroxyTriptamine 2A homology-based model, and complexes with low binding energies (287 complexes) were selected for molecular dynamics (MD) simulations in a lipid bilayer. The MD simulations of the shortlisted compounds in complex with 5-HydroxyTriptamine 2A confirmed the stability of the complexes and revealed novel interaction insights. The receptor residues S239, N343, S242, S159, Y370 and D155 predominantly participate in hydrogen bonding. π-π stacking is observed in F339, F340, F234, W151 and W336, whereas hydrophobic interactions are observed amongst V156, F339, F234, V362, V366, F340, V235, I152 and W151. The known and potential antagonists shortlisted by us have similar overlapping molecular interaction patterns. The 287 potential 5-HydroxyTriptamine 2A antagonists may be experimentally verified.
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Key Words
- , tanimoto coefficient
- 2D similarity
- 2D, two-dimensional space
- 2D/3D screening
- 3D similarity
- 3D, three-dimensional space
- 5HT
- 5HT, 5-HydroxyTryptamine
- ADHD, attention deficit hyperactivity disorders
- BLAST, basic local alignment search tool
- CNS, central nervous system
- Cl ions, chloride ions
- DOPE, discrete optimized protein energy
- G-protein coupled receptor
- GPCRs, G protein-coupled receptors
- HB, hydrogen bond
- HBA, hydrogen bond acceptors
- HBD, hydrogen bond donors
- JC virus, John Cunningham virus
- Ki, equilibrium dissociation constant for the ligand
- LBVS, ligand-based virtual screening
- MD, molecular dynamic
- MSD, mean square displacement
- MW, molecular weight
- NHB, number of hydrogen bonds
- OCD, obsessive compulsive disorder
- P5/P95, percentile calculation
- PAINS, Pan assay interference compounds
- PDB, protein data bank
- PLIP, protein–ligand interaction profiler
- PME, Particle Mesh Ewald
- PNS, peripheral nervous system
- POPC, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
- RMSD, root mean square deviation
- RMSF, root mean square fluctuations
- Rg, radius of gyration
- SASA, solvent accessible surface area
- SCA, stochastic clustering algorithm
- SD, steepest descent
- SDF, structure data file
- SPC, single point charge
- SPD, simple point charge
- SSE, secondary structure elements
- Sn-1/sn-2, Stereospecific number
- TM, Transmembrane
- TPSA, topological polar surface area
- drug discovery
- fs, femtosecond
- kJ/mol, kilo Joule per mol
- kcal/mol, kilocalorie per mole sn-1
- ligand-based virtual screening
- nm, nanomolar
- ns, nanosecond
- Å Ångström
- β2-AR, β2 adrenergic receptor
- μM, micromolar
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Affiliation(s)
- Rakesh Kumar
- a Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) , Aruna Asaf Ali Marg, New Delhi 110067 , India
| | - Dhananjay Jade
- a Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) , Aruna Asaf Ali Marg, New Delhi 110067 , India
| | - Dinesh Gupta
- a Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB) , Aruna Asaf Ali Marg, New Delhi 110067 , India
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