1
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Panda S, Rout M, Mishra S, Turuk J, Pati S, Dehury B. Molecular docking and MD simulations reveal protease inhibitors block the catalytic residues in Prp8 intein of Aspergillus fumigatus: a potential target for antimycotics. J Biomol Struct Dyn 2023:1-16. [PMID: 38149850 DOI: 10.1080/07391102.2023.2298735] [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: 10/03/2023] [Accepted: 12/18/2023] [Indexed: 12/28/2023]
Abstract
Resistance to azoles and amphotericin B especially in Aspergillus fumigatus is a growing concern towards the treatment of invasive fungal infection. At this critical juncture, intein splicing would be a productive, and innovative target to establish therapies against resistant strains. Intein splicing is the central event for the activation of host protein, essential for the growth and survival of various microorganisms including A. fumigatus. The splicing process is a four-step protease-like nucleophilic cascade. Thus, we hypothesise that protease inhibitors would successfully halt intein splicing and potentially restrict the growth of the aforementioned pathogen. Using Rosetta Fold and molecular dynamics simulations, we modelled Prp8 intein structure; resembling classic intein fold with horse shoe shaped splicing domain. To fully comprehend the active site of Afu Prp8 intein, C1, T62, H65, H818, N819 from intein sequences and S820, the first C-extein residue are selected. Molecular docking shows that two FDA-approved drugs, i.e. Lufotrelvir and Remdesivir triphosphate efficiently interact with Prp8 intein from the assortment of 212 protease inhibitors. MD simulation portrayed that Prp8 undergoes conformational change upon ligand binding, and inferred the molecular recognition and stability of the docked complexes. Per-residue decomposition analysis confirms the importance of F: block R802, V803, and Q807 binding pocket in intein splicing domain towards recognition of inhibitors, along with active site residues through strong hydrogen bonds and hydrophobic contacts. However, in vitro and in vivo assays are required to confirm the inhibitory action on Prp8 intein splicing; which may pave the way for the development of new antifungals for A. fumigatus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sunita Panda
- Mycology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Jyotirmayee Turuk
- Mycology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Sanghamitra Pati
- Mycology Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, India
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2
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Rout M, Mishra S, Dey S, Singh MK, Dehury B, Pati S. Exploiting the potential of natural polyphenols as antivirals against monkeypox envelope protein F13 using machine learning and all-atoms MD simulations. Comput Biol Med 2023; 162:107116. [PMID: 37302336 PMCID: PMC10239311 DOI: 10.1016/j.compbiomed.2023.107116] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/12/2023] [Accepted: 05/30/2023] [Indexed: 06/13/2023]
Abstract
The re-emergence of monkeypox (MPX), in the era of COVID-19 pandemic is a new global menace. Regardless of its leniency, there are chances of MPX expediting severe health deterioration. The role of envelope protein, F13 as a critical component for production of extracellular viral particles makes it a crucial drug target. Polyphenols, exhibiting antiviral properties have been acclaimed as an effective alternative to the traditional treatment methods for management of viral diseases. To facilitate the development of potent MPX specific therapeutics, herein, we have employed state-of-the-art machine learning techniques to predict a highly accurate 3-dimensional structure of F13 as well as identify binding hotspots on the protein surface. Additionally, we have effectuated high-throughput virtual screening methodology on 57 potent natural polyphenols having antiviral activities followed by all-atoms molecular dynamics (MD) simulations, to substantiate the mode of interaction of F13 protein and polyphenol complexes. The structure-based virtual screening based on Glide SP, XP and MM/GBSA scores enables the selection of six potent polyphenols having higher binding affinity towards F13. Non-bonded contact analysis, of pre- and post- MD complexes propound the critical role of Glu143, Asp134, Asn345, Ser321 and Tyr320 residues in polyphenol recognition, which is well supported by per-residue decomposition analysis. Close-observation of the structural ensembles from MD suggests that the binding groove of F13 is mostly hydrophobic in nature. Taken together, this structure-based analysis from our study provides a lead on Myricetin, and Demethoxycurcumin, which may act as potent inhibitors of F13. In conclusion, our study provides new insights into the molecular recognition and dynamics of F13-polyphenol bound states, offering new promises for development of antivirals to combat monkeypox. However, further in vitro and in vivo experiments are necessary to validate these results.
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Affiliation(s)
- Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India
| | - Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India
| | - Suchanda Dey
- Biomics and Biodiversity Lab, Siksha 'O' Anusandhan (deemed to be) University, Kalinga Nagar, Ghatikia, Bhubaneswar, 751003, Odisha, India
| | - Mahender Kumar Singh
- Data Science Laboratory, National Brain Research Centre, Gurgaon, Haryana, 122052, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India.
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India.
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3
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Dongmo Foumthuim CJ, Giacometti A. Solvent quality and solvent polarity in polypeptides. Phys Chem Chem Phys 2023; 25:4839-4853. [PMID: 36692363 DOI: 10.1039/d2cp05214h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Using molecular dynamics and thermodynamic integration, we report on the solvation process of seven polypeptides (GLY, ALA, ILE, ASN, LYS, ARG, GLU) in water and in cyclohexane. The polypeptides are selected to cover the full hydrophobic scale while varying their chain length from tri- to undeca-homopeptides, providing indications on possible non-additivity effects as well as the role of the peptide backbone in the overall stability of the polypeptides. The use of different solvents and different polypeptides allows us to investigate the relation between solvent quality - the capacity of a given solvent to fold/unfold a given biopolymer often described on a scale ranging from "good" to "poor"; and solvent polarity - related to the specific interactions of any solvent with respect to a reference solvent. Undeca-glycine is found to be the only polypeptide to have a stable collapse in water (polar solvent), with the other hydrophobic polypeptides displaying repeated folding and unfolding events in water, with polar polypeptides presenting even more complex behavior. By contrast, all polypeptides are found to keep an extended conformation in cyclohexane, irrespective of their polarity. All considered polypeptides are also found to have favorable solvation free energy independent of the solvent polarity and their intrinsic hydrophobicity, clearly highlighting the prominent stabilizing role of the peptide backbone - with the solvation process largely enthalpically dominated in polar polypeptides and partially entropically driven for hydrophobic polypeptides. Our study thus reveals the complexity of the solvation process of polypeptides defying the common view "like dissolves like", with the solute polarity playing the most prominent role. The absence of mirror symmetry upon the inversion of polarities of both the solvent and the polypeptides is confirmed.
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Affiliation(s)
- Cedrix J Dongmo Foumthuim
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30172 Venezia Mestre, Italy.
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30172 Venezia Mestre, Italy. .,European Centre for Living Technology (ECLT) Ca Bottacin, Dorsoduro 3911, Calle Crosera 30123 Venice, Italy
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4
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Galantamine Based Novel Acetylcholinesterase Enzyme Inhibitors: A Molecular Modeling Design Approach. Molecules 2023; 28:molecules28031035. [PMID: 36770702 PMCID: PMC9919016 DOI: 10.3390/molecules28031035] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/31/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
Acetylcholinesterase (AChE) enzymes play an essential role in the development of Alzheimer's disease (AD). Its excessive activity causes several neuronal problems, particularly psychopathies and neuronal cell death. A bioactive pose on the hAChE B site of the human acetylcholinesterase (hAChE) enzyme employed in this investigation, which was obtained from the Protein Data Bank (PDB ID 4EY6), allowed for the prediction of the binding affinity and free binding energy between the protein and the ligand. Virtual screening was performed to obtain structures similar to Galantamine (GNT) with potential hAChE activity. The top 200 hit compounds were prioritized through the use of filters in ZincPharmer, with special features related to the pharmacophore. Critical analyses were carried out, such as hierarchical clustering analysis (HCA), ADME/Tox predictions, molecular docking, molecular simulation studies, synthetic accessibility (SA), lipophilicity, water solubility, and hot spots to confirm the stable binding of the two promising molecules (ZINC16951574-LMQC2, and ZINC08342556-LMQC5). The metabolism prediction, with metabolites M3-2, which is formed by Glutathionation reaction (Phase II), M1-2, and M2-2 formed from the reaction of S-oxidation and Aliphatic hydroxylation (Phase I), were both reactive but with no side effects. Theoretical synthetic routes and prediction of synthetic accessibility for the most promising compounds are also proposed. In conclusion, this study shows that in silico modeling can be used to create new drug candidate inhibitors for hAChE. The compounds ZINC16951574-LMQC2, and ZINC08342556-LMQC5 are particularly promising for oral administration because they have a favorable drug-likeness profile, excellent lipid solubility, high bioavailability, and adequate pharmacokinetics.
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5
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Zhao M, Lachowski KJ, Zhang S, Alamdari S, Sampath J, Mu P, Mundy CJ, Pfaendtner J, De Yoreo JJ, Chen CL, Pozzo LD, Ferguson AL. Hierarchical Self-Assembly Pathways of Peptoid Helices and Sheets. Biomacromolecules 2022; 23:992-1008. [PMID: 35020390 DOI: 10.1021/acs.biomac.1c01385] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Peptoids (N-substituted glycines) are a class of tailorable synthetic peptidomic polymers. Amphiphilic diblock peptoids have been engineered to assemble 2D crystalline lattices with applications in catalysis and molecular separations. Assembly is induced in an organic solvent/water mixture by evaporating the organic phase, but the assembly pathways remain uncharacterized. We conduct all-atom molecular dynamics simulations of Nbrpe6Nc6 as a prototypical amphiphilic diblock peptoid comprising an NH2-capped block of six hydrophobic N-((4-bromophenyl)ethyl)glycine residues conjugated to a polar NH3(CH2)5CO tail. We identify a thermodynamically controlled assembly mechanism by which monomers assemble into disordered aggregates that self-order into 1D chiral helical rods then 2D achiral crystalline sheets. We support our computational predictions with experimental observations of 1D rods using small-angle X-ray scattering, circular dichroism, and atomic force microscopy and 2D crystalline sheets using X-ray diffraction and atomic force microscopy. This work establishes a new understanding of hierarchical peptoid assembly and principles for the design of peptoid-based nanomaterials.
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Affiliation(s)
- Mingfei Zhao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Kacper J Lachowski
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Molecular Engineering and Sciences Institute, University of Washington, Seattle, Washington 98195, United States
| | - Shuai Zhang
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States.,Physical Sciences Division, Pacific Northwest National Laboratory, Richmond, Washington 99354, United States
| | - Sarah Alamdari
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Janani Sampath
- Physical Sciences Division, Pacific Northwest National Laboratory, Richmond, Washington 99354, United States
| | - Peng Mu
- Physical Sciences Division, Pacific Northwest National Laboratory, Richmond, Washington 99354, United States.,Department of Mechanical Engineering and Materials Science and Engineering Program, State University of New York, Binghamton, New York 13902, United States
| | - Christopher J Mundy
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Physical Sciences Division, Pacific Northwest National Laboratory, Richmond, Washington 99354, United States
| | - Jim Pfaendtner
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Physical Sciences Division, Pacific Northwest National Laboratory, Richmond, Washington 99354, United States
| | - James J De Yoreo
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Physical Sciences Division, Pacific Northwest National Laboratory, Richmond, Washington 99354, United States
| | - Chun-Long Chen
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Physical Sciences Division, Pacific Northwest National Laboratory, Richmond, Washington 99354, United States
| | - Lilo D Pozzo
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States.,Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Andrew L Ferguson
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
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6
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Ge Y, Hahn DF, Mobley DL. A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations. J Chem Inf Model 2021; 61:1048-1052. [PMID: 33686853 DOI: 10.1021/acs.jcim.0c01424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Relative free energy calculations are fast becoming a critical part of early stage pharmaceutical design, making it important to know how to obtain the best performance with these calculations in applications that could span hundreds of calculations and molecules. In this work, we compared two different treatments of long-range electrostatics, Particle Mesh Ewald (PME) and Reaction Field (RF), in relative binding free energy calculations using a nonequilibrium switching protocol. We found simulations using RF achieve comparable results to those using PME but gain more efficiency when using CPU and similar performance using GPU. The results from this work encourage more use of RF in molecular simulations.
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Affiliation(s)
- Yunhui Ge
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - David F Hahn
- Computational Chemistry, Janssen Research & Development, Turnhoutseweg 30, Beerse B-2340, Belgium
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States.,Department of Chemistry, University of California, Irvine, California 92697, United States
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7
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Matricon P, Suresh RR, Gao ZG, Panel N, Jacobson KA, Carlsson J. Ligand design by targeting a binding site water. Chem Sci 2020; 12:960-968. [PMID: 34163862 PMCID: PMC8179138 DOI: 10.1039/d0sc04938g] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood. We investigated how altered interactions with a water network can influence ligand binding to a receptor. A series of ligands of the A2A adenosine receptor, which either interacted with or displaced an ordered binding site water, were studied experimentally and by molecular dynamics simulations. An analog of the endogenous ligand that was unable to hydrogen bond to the ordered water lost affinity and this activity cliff was captured by molecular dynamics simulations. Two compounds designed to displace the ordered water from the binding site were then synthesized and evaluated experimentally, leading to the discovery of an A2A agonist with nanomolar activity. Calculation of the thermodynamic profiles resulting from introducing substituents that interacted with or displaced the ordered water showed that the gain of binding affinity was enthalpy driven. Detailed analysis of the energetics and binding site hydration networks revealed that the enthalpy change was governed by contributions that are commonly neglected in structure-based drug optimization. In particular, simulations suggested that displacement of water from a binding site to the bulk solvent can lead to large energy contributions. Our findings provide insights into the molecular driving forces of protein–ligand binding and strategies for rational drug design. Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood.![]()
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Affiliation(s)
- Pierre Matricon
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University SE-75124 Uppsala Sweden
| | - R Rama Suresh
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health Bethesda Maryland 20892 USA
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health Bethesda Maryland 20892 USA
| | - Nicolas Panel
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University SE-75124 Uppsala Sweden
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health Bethesda Maryland 20892 USA
| | - Jens Carlsson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University SE-75124 Uppsala Sweden
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8
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Kellett K, Slochower DR, Schauperl M, Duggan BM, Gilson MK. Experimental characterization of the association of β-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds. J Comput Aided Mol Des 2020; 35:95-104. [PMID: 33037548 DOI: 10.1007/s10822-020-00350-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/30/2020] [Indexed: 12/19/2022]
Abstract
We investigate the binding of native β-cyclodextrin (β-CD) and eight novel β-CD derivatives with two different guest compounds, using isothermal calorimetry and 2D NOESY NMR. In all cases, the stoichiometry is 1:1 and binding is exothermic. Overall, modifications at the 3' position of β-CD, which is at the secondary face, weaken binding by several kJ/mol relative to native β-CD, while modifications at the 6' position (primary face) maintain or somewhat reduce the binding affinity. The variations in binding enthalpy are larger than the variations in binding free energy, so entropy-enthalpy compensation is observed. Characterization of the bound conformations with NOESY NMR shows that the polar groups of the guests may be situated at either face, depending on the host molecule, and, in some cases, both orientations are populated. The present results were used in the SAMPL7 blinded prediction challenge whose results are detailed in the same special issue of JCAMD.
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Affiliation(s)
- K Kellett
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA
| | - D R Slochower
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA
| | - M Schauperl
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA
| | - B M Duggan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA
| | - M K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0751, USA.
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9
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Gao D, Penno C, Wünsch B. Rigid Scaffolds: Synthesis of 2,6-Bridged Piperazines with Functional Groups in all three Bridges. ChemistryOpen 2020; 9:874-889. [PMID: 32884883 PMCID: PMC7450790 DOI: 10.1002/open.202000188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/06/2020] [Indexed: 11/10/2022] Open
Abstract
The activity of pharmacologically active compounds can be increased by presenting a drug in a defined conformation, which fits exactly into the binding pocket of its target. Herein, the piperazine scaffold was conformationally restricted by substituted C2- or C3-bridges across the 2- and 6-position. At first, a three-step, one-pot procedure was developed to obtain reproducibly piperazine-2,6-diones with various substituents at the N-atoms in high yields. Three strategies for bridging of piperazine-2,6-diones were pursued: 1. The bicyclic mixed ketals 8-benzyl-6-ethoxy-3-(4-methoxybenzyl)-6-(trimethylsilyloxy)-3,8-diazabicyclo[3.2.1]octane-2,4-diones were prepared by Dieckmann analogous cyclization of 2-(3,5-dioxopiperazin-2-yl)acetates. 2. Stepwise allylation, hydroboration and oxidation of piperazine-2,6-diones led to 3-(3,5-dioxopiperazin-2-yl)propionaldehydes. Whereas reaction of such an aldehyde with base provided the bicyclic alcohol 9-benzyl-6-hydroxy-3-(4-methoxybenzyl)-3,9-diazabicyclo[3.3.1]nonane-2,4-dione in only 10 % yield, the corresponding sulfinylimines reacted with base to give N-(2,4-dioxo-3,9-diazabicyclo[3.3.1]nonan-6-yl)-2-methylpropane-2-sulfinamides in >66 % yield. 3. Transformation of a piperazine-2,6-dione with 1,4-dibromobut-2-ene and 3-halo-2-halomethylprop-1-enes provided 3,8-diazabicyclo[3.2.1]octane-2,4-dione and 3,9-diazabicyclo[3.3.1]nonane-2,4-dione with a vinyl group at the C2- or a methylene group at the C3-bridge, respectively. Since bridging via sulfinylimines and the one-pot bridging with 3-bromo-2-bromomethylprop-1-ene gave promising yields, these strategies will be exploited for the synthesis of novel receptor ligands bearing various substituents in a defined orientation at the carbon bridge.
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Affiliation(s)
- Donglin Gao
- Institut für Pharmazeutische und Medizinische Chemie der WestfälischenWilhelms-Universität MünsterCorrensstraße 4848149MünsterGermany
| | - Christian Penno
- Institut für Pharmazeutische und Medizinische Chemie der WestfälischenWilhelms-Universität MünsterCorrensstraße 4848149MünsterGermany
| | - Bernhard Wünsch
- Institut für Pharmazeutische und Medizinische Chemie der WestfälischenWilhelms-Universität MünsterCorrensstraße 4848149MünsterGermany
- Cells-in-Motion Cluster of Excellence (EXC 1003 – CiM)Westfälische Wilhelms-Universität Münster48149MünsterGermany
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10
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Barria-Urenda M, Garate JA. Entropy deepens loading chemical potentials of small alcohols by narrow carbon nanotubes. Phys Chem Chem Phys 2020; 22:22369-22379. [DOI: 10.1039/d0cp03426f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small alcohol confinement within narrow carbon nanotubes has been extensively and systematically studied via rigorous free-energy calculations.
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11
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Maurer M, Oostenbrink C. Water in protein hydration and ligand recognition. J Mol Recognit 2019; 32:e2810. [PMID: 31456282 PMCID: PMC6899928 DOI: 10.1002/jmr.2810] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/16/2022]
Abstract
This review describes selected basics of water in biomolecular recognition. We focus on a qualitative understanding of the most important physical aspects, how these change in magnitude between bulk water and protein environment, and how the roles that water plays for proteins arise from them. These roles include mechanical support, thermal coupling, dielectric screening, mass and charge transport, and the competition with a ligand for the occupation of a binding site. The presence or absence of water has ramifications that range from the thermodynamic binding signature of a single ligand up to cellular survival. The large inhomogeneity in water density, polarity and mobility around a solute is hard to assess in experiment. This is a source of many difficulties in the solvation of protein models and computational studies that attempt to elucidate or predict ligand recognition. The influence of water in a protein binding site on the experimental enthalpic and entropic signature of ligand binding is still a point of much debate. The strong water‐water interaction in enthalpic terms is counteracted by a water molecule's high mobility in entropic terms. The complete arrest of a water molecule's mobility sets a limit on the entropic contribution of a water displacement process, while the solvent environment sets limits on ligand reactivity.
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Affiliation(s)
- Manuela Maurer
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
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12
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Free-Energy Calculations for Bioisosteric Modifications of A 3 Adenosine Receptor Antagonists. Int J Mol Sci 2019; 20:ijms20143499. [PMID: 31315296 PMCID: PMC6679372 DOI: 10.3390/ijms20143499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/12/2019] [Accepted: 07/14/2019] [Indexed: 11/16/2022] Open
Abstract
Adenosine receptors are a family of G protein-coupled receptors with increased attention as drug targets on different indications. We investigate the thermodynamics of ligand binding to the A3 adenosine receptor subtype, focusing on a recently reported series of diarylacetamidopyridine inhibitors via molecular dynamics simulations. With a combined approach of thermodynamic integration and one-step perturbation, we characterize the impact of the charge distribution in a central heteroaromatic ring on the binding affinity prediction. Standard charge distributions according to the GROMOS force field yield values in good agreement with the experimental data and previous free energy calculations. Subsequently, we examine the thermodynamics of inhibitor binding in terms of the energetic and entropic contributions. The highest entropy penalties are found for inhibitors with methoxy substituents in meta position of the aryl groups. This bulky group restricts rotation of aromatic rings attached to the pyrimidine core which leads to two distinct poses of the ligand. Our predictions support the previously proposed binding pose for the o-methoxy ligand, yielding in this case a very good correlation with the experimentally measured affinities with deviations below 4 kJ/mol.
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13
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Redox thermodynamics of B-class dye-decolorizing peroxidases. J Inorg Biochem 2019; 199:110761. [PMID: 31325671 DOI: 10.1016/j.jinorgbio.2019.110761] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/22/2019] [Accepted: 07/08/2019] [Indexed: 11/23/2022]
Abstract
With >5000 annotated genes dye-decolorizing peroxidases (DyPs) represent a heme b peroxidase family of broad functional diversity. Bacterial B-class DyPs are poor peroxidases of unknown physiological function. Hydrogen peroxide efficiently mediates the rapid formation of Compound I in B-class DyPs, which, however, is stable and shows modest reactivity towards organic and inorganic electron donors. To understand these characteristics, we have investigated the redox thermodynamics of the one-electron reduction of the ferric high-spin form of wild-type B-class DyP from the pathogenic bacterium Klebsiella pneumoniae (KpDyP) and the variants D143A, R232A and D143A/R232A. These distal amino acids are fully conserved in all DyPs and play important roles in Compound I formation and maintenance of the heme cavity architecture and substrate access route(s). The E°' values of the respective redox couples Fe(III)/Fe(II) varied from -350 mV (wild-type KpDyP) to -299 mV (D143A/R232A) at pH 7.0. Variable-temperature spectroelectrochemical experiments revealed that the reduction reaction of B-class DyPs is enthalpically unfavored but entropically favored with significant differences in enthalpic and entropic contributions to E°' between the four proteins. Molecular dynamics simulations demonstrated the impact of solvent reorganization on the entropy change during reduction reaction and revealed the dynamics and restriction of substrate access channels. Obtained data are discussed with respect to the poor peroxidase activities of B-class DyPs and compared with heme peroxidases from other (super)families as well as with chlorite dismutases, which do not react with hydrogen peroxide but share a similar fold and heme cavity architecture.
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14
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Hayatshahi HS, Henriksen NM, Cheatham TE. Consensus Conformations of Dinucleoside Monophosphates Described with Well-Converged Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:1456-1470. [PMID: 29323894 DOI: 10.1021/acs.jctc.7b00581] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dinucleoside monophosphates (DNMPs) have been described using various experimental approaches as flexible molecules which generate ensembles populating at least a small set of different conformations in solution. However, due to limitations of each approach in its ability to delineate the ensemble of conformations, an accurate and quantitative description of certain conformational features has not been performed for all DNMPs. Here, we apply a temperature replica-exchange molecular dynamics approach to fully and quickly converge conformational distributions of all RNA DNMPs immersed in the TIP3P water model using the AMBER ff14 force field. For a selection of DNMPs, the conformational ensembles were also generated when immersed in the OPC water model using alternative AMBER and CHARMM force fields. The OPC water model and other force field choices did not introduce new conformational classes but shifted the populations among existing conformations. Except for pyrimidine-pyrimidine dinucleosides, all other DNMPs populated four major conformations (which are defined in the main text and labeled A-form, Ladder, Inverted, and Sheared), in addition to an Extended form. Pyrimidine-pyrimidines did not generate the Sheared conformation. Distinguishing features and stabilizing factors of each conformation were identified and assessed based on the known experimental interpretations. The configuration of the glycosidic bond and the nonbonding interactions of hydrogen bond acceptors with the 2'-hydroxyl group were found to play determining roles in stabilizing particular conformations which could serve as a guide for potential force field modifications to improve the accuracy. Additionally, we computed stacking free energies based on the DNMP conformational distributions and found significant discrepancies with a previous study. Our investigation determined that the AMBER force field was incorrectly implemented in the previous study. In the future, this simulation approach can be used to quickly analyze the effects of new force field modifications in shifting the conformational populations of DNMPs, and can can be further applied to foresee such effects in larger RNA motifs including tetranucleotides and tetraloops.
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Affiliation(s)
- Hamed S Hayatshahi
- Department of Medicinal Chemistry, College of Pharmacy, L. S. Skaggs Pharmacy Research Institute , University of Utah , Salt Lake City , Utah 84112-5820 , United States
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California at San Diego , 9500 Gilman Drive , MC 0736, La Jolla , California 92093 , United States
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, L. S. Skaggs Pharmacy Research Institute , University of Utah , Salt Lake City , Utah 84112-5820 , United States
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15
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van Gunsteren WF, Daura X, Hansen N, Mark AE, Oostenbrink C, Riniker S, Smith LJ. Validation of Molecular Simulation: An Overview of Issues. Angew Chem Int Ed Engl 2017; 57:884-902. [PMID: 28682472 DOI: 10.1002/anie.201702945] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Indexed: 12/14/2022]
Abstract
Computer simulation of molecular systems enables structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic, or supra-molecular level. To interpret results of such simulations appropriately, the quality of the calculated properties must be evaluated. This depends on the way the simulations are performed and on the way they are validated by comparison to values Qexp of experimentally observable quantities Q. One must consider 1) the accuracy of Qexp , 2) the accuracy of the function Q(rN ) used to calculate a Q-value based on a molecular configuration rN of N particles, 3) the sensitivity of the function Q(rN ) to the configuration rN , 4) the relative time scales of the simulation and experiment, 5) the degree to which the calculated and experimental properties are equivalent, and 6) the degree to which the system simulated matches the experimental conditions. Experimental data is limited in scope and generally corresponds to averages over both time and space. A critical analysis of the various factors influencing the apparent degree of (dis)agreement between simulations and experiment is presented and illustrated using examples from the literature. What can be done to enhance the validation of molecular simulation is also discussed.
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Affiliation(s)
- Wilfred F van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autonoma de Barcelona, UAB, 08193, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies, ICREA, 08010, Barcelona, Spain
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569, Stuttgart, Germany
| | - Alan E Mark
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Sereina Riniker
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland
| | - Lorna J Smith
- Department of Chemistry, Inorganic Chemistry, Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
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16
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van Gunsteren WF, Daura X, Hansen N, Mark AE, Oostenbrink C, Riniker S, Smith LJ. Validierung von molekularen Simulationen: eine Übersicht verschiedener Aspekte. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702945] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Wilfred F. van Gunsteren
- Laboratorium für Physikalische Chemie; Eidgenössische Technische Hochschule Zürich; 8093 Zürich Schweiz
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine; Universitat Autònoma de Barcelona; Spanien
- Catalan Institution for Research and Advanced Studies, ICREA; Barcelona Spanien
| | - Niels Hansen
- Institut für Technische Thermodynamik und Thermische Verfahrenstechnik; Universität Stuttgart; Deutschland
| | - Alan E. Mark
- School of Chemistry and Molecular Biosciences; University of Queensland; St. Lucia Australien
| | - Chris Oostenbrink
- Institut für Molekulare Modellierung und Simulation; Universität für Bodenkultur Wien; Österreich
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie; Eidgenössische Technische Hochschule Zürich; 8093 Zürich Schweiz
| | - Lorna J. Smith
- Inorganic Chemistry Laboratory; Department of Chemistry; University of Oxford; Großbritannien
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17
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Reif MM, Zacharias M. Rapid approximate calculation of water binding free energies in the whole hydration domain of (bio)macromolecules. J Comput Chem 2016; 37:1711-24. [DOI: 10.1002/jcc.24390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/22/2016] [Accepted: 03/22/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Maria M. Reif
- Physics Department (T38); Technische Universität München; James-Franck-Str. 1 85748 Garching Germany
| | - Martin Zacharias
- Physics Department (T38); Technische Universität München; James-Franck-Str. 1 85748 Garching Germany
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18
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Henriksen NM, Fenley A, Gilson MK. Computational Calorimetry: High-Precision Calculation of Host-Guest Binding Thermodynamics. J Chem Theory Comput 2015; 11:4377-94. [PMID: 26523125 PMCID: PMC4614838 DOI: 10.1021/acs.jctc.5b00405] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Indexed: 11/29/2022]
Abstract
We present a strategy for carrying out high-precision calculations of binding free energy and binding enthalpy values from molecular dynamics simulations with explicit solvent. The approach is used to calculate the thermodynamic profiles for binding of nine small molecule guests to either the cucurbit[7]uril (CB7) or β-cyclodextrin (βCD) host. For these systems, calculations using commodity hardware can yield binding free energy and binding enthalpy values with a precision of ∼0.5 kcal/mol (95% CI) in a matter of days. Crucially, the self-consistency of the approach is established by calculating the binding enthalpy directly, via end point potential energy calculations, and indirectly, via the temperature dependence of the binding free energy, i.e., by the van't Hoff equation. Excellent agreement between the direct and van't Hoff methods is demonstrated for both host-guest systems and an ion-pair model system for which particularly well-converged results are attainable. Additionally, we find that hydrogen mass repartitioning allows marked acceleration of the calculations with no discernible cost in precision or accuracy. Finally, we provide guidance for accurately assessing numerical uncertainty of the results in settings where complex correlations in the time series can pose challenges to statistical analysis. The routine nature and high precision of these binding calculations opens the possibility of including measured binding thermodynamics as target data in force field optimization so that simulations may be used to reliably interpret experimental data and guide molecular design.
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Affiliation(s)
- Niel M. Henriksen
- Skaggs School of Pharmacy
and Pharmaceutical Sciences, University
of California San Diego, La Jolla, California 92093-0736, United States
| | - Andrew
T. Fenley
- Skaggs School of Pharmacy
and Pharmaceutical Sciences, University
of California San Diego, La Jolla, California 92093-0736, United States
| | - Michael K. Gilson
- Skaggs School of Pharmacy
and Pharmaceutical Sciences, University
of California San Diego, La Jolla, California 92093-0736, United States
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19
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Yin J, Fenley AT, Henriksen NM, Gilson MK. Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics. J Phys Chem B 2015; 119:10145-55. [PMID: 26181208 DOI: 10.1021/acs.jpcb.5b04262] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Improving the capability of atomistic computer models to predict the thermodynamics of noncovalent binding is critical for successful structure-based drug design, and the accuracy of such calculations remains limited by nonoptimal force field parameters. Ideally, one would incorporate protein-ligand affinity data into force field parametrization, but this would be inefficient and costly. We now demonstrate that sensitivity analysis can be used to efficiently tune Lennard-Jones parameters of aqueous host-guest systems for increasingly accurate calculations of binding enthalpy. These results highlight the promise of a comprehensive use of calorimetric host-guest binding data, along with existing validation data sets, to improve force field parameters for the simulation of noncovalent binding, with the ultimate goal of making protein-ligand modeling more accurate and hence speeding drug discovery.
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Affiliation(s)
- Jian Yin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0736, United States
| | - Andrew T Fenley
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0736, United States
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0736, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0736, United States
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20
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Lin Z, van Gunsteren WF. Effects of Polarizable Solvent Models upon the Relative Stability of an α-Helical and a β-Hairpin Structure of an Alanine Decapeptide. J Chem Theory Comput 2015; 11:1983-6. [DOI: 10.1021/acs.jctc.5b00210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zhixiong Lin
- Laboratory of Physical
Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Zürich, Switzerland
| | - Wilfred F. van Gunsteren
- Laboratory of Physical
Chemistry, Swiss Federal Institute of Technology, ETH, 8093 Zürich, Zürich, Switzerland
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21
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Nørholm AB, Francotte P, Goffin E, Botez I, Danober L, Lestage P, Pirotte B, Kastrup JS, Olsen L, Oostenbrink C. Thermodynamic characterization of new positive allosteric modulators binding to the glutamate receptor A2 ligand-binding domain: combining experimental and computational methods unravels differences in driving forces. J Chem Inf Model 2014; 54:3404-16. [PMID: 25420075 DOI: 10.1021/ci500559b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Positive allosteric modulation of the ionotropic glutamate receptor GluA2 presents a potential treatment of cognitive disorders, for example, Alzheimer's disease. In the present study, we describe the synthesis, pharmacology, and thermodynamic studies of a series of monofluoro-substituted 3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxides. Measurements of ligand binding by isothermal titration calorimetry (ITC) showed similar binding affinities for the modulator series at the GluA2 LBD but differences in the thermodynamic driving forces. Binding of 5c (7-F) and 6 (no-F) is enthalpy driven, and 5a (5-F) and 5b (6-F) are entropy driven. For 5d (8-F), both quantities were equal in size. Thermodynamic integration (TI) and one-step perturbation (OSP) were used to calculate the relative binding affinity of the modulators. The OSP calculations had a higher predictive power than those from TI, and combined with the shorter total simulation time, we found the OSP method to be more effective for this setup. Furthermore, from the molecular dynamics simulations, we extracted the enthalpies and entropies, and along with the ITC data, this suggested that the differences in binding free energies are largely explained by the direct ligand-surrounding enthalpies. Furthermore, we used the OSP setup to predict binding affinities for a series of polysubstituted fluorine compounds and monosubstituted methyl compounds and used these predictions to characterize the modulator binding pocket for this scaffold of positive allosteric modulators.
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Affiliation(s)
- Ann-Beth Nørholm
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen , Universitetsparken 2, DK-2100 Copenhagen, Denmark
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22
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Garate JA, Perez-Acle T, Oostenbrink C. On the thermodynamics of carbon nanotube single-file water loading: free energy, energy and entropy calculations. Phys Chem Chem Phys 2014; 16:5119-28. [DOI: 10.1039/c3cp54554g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single-file water chains confined in carbon nanotubes are studied using molecular dynamics simulations and free energy calculations to characterize the pore loading in terms of energy, entropy and free energy.
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Affiliation(s)
- Jose Antonio Garate
- Computational Biology Lab
- Fundación Ciencia & Vida
- Santiago, Chile
- Institute for Molecular Modeling and Simulation
- Vienna, Austria
| | - Tomas Perez-Acle
- Computational Biology Lab
- Fundación Ciencia & Vida
- Santiago, Chile
- Centro Interdisciplinario de Neurociencias de Valparaiíso
- Universidad de Valparaíso
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