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Zeng Y, Pavlova A, Nelson PM, Glick ZL, Yang L, Pang YT, Spivak M, Licari G, Tajkhorshid E, Sherrill CD, Gumbart JC. Broadening access to small-molecule parameterization with the force field toolkit. J Chem Phys 2024; 160:242501. [PMID: 38916266 DOI: 10.1063/5.0196848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Access to accurate force-field parameters for small molecules is crucial for computational studies of their interactions with proteins. Although a number of general force fields for small molecules exist, e.g., CGenFF, GAFF, and OPLS, they do not cover all common chemical groups and their combinations. The Force Field Toolkit (ffTK) provides a comprehensive graphical interface that streamlines the development of classical parameters for small molecules directly from quantum mechanical (QM) calculations, allowing for force-field generation for almost any chemical group and validation of the fit relative to the target data. ffTK relies on supported external software for the QM calculations, but it can generate the necessary QM input files and parse and analyze the QM output. In previous ffTK versions, support for Gaussian and ORCA QM packages was implemented. Here, we add support for Psi4, an open-source QM package free for all users, thereby broadening user access to ffTK. We also compare the parameter sets obtained with the new ffTK version using Gaussian, ORCA, and Psi4 for three molecules: pyrrolidine, n-propylammonium cation, and chlorobenzene. Despite minor differences between the resulting parameter sets for each compound, most prominently in the dihedral and improper terms, we show that conformational distributions sampled in molecular dynamics simulations using these parameter sets are quite comparable.
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Affiliation(s)
- Yunlin Zeng
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Philip M Nelson
- Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zachary L Glick
- Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Lan Yang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Mariano Spivak
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Giuseppe Licari
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Resource for Macromolecular Modeling and Visualization, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Biochemistry and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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2
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Nalıncı Barbak N, Kıbrıs E, Demirci FC, Elmacı Irmak N. Molecular dynamics simulation of ssDNA and cationic polythiophene. J Mol Graph Model 2023; 123:108501. [PMID: 37182506 DOI: 10.1016/j.jmgm.2023.108501] [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: 12/13/2022] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/16/2023]
Abstract
In this work, molecular dynamics simulations of complexes composed of single strand DNA (ssDNA) sequences and cationic oligothiophenes are performed to understand experimental findings and the sensing ability of polythiophene electrolytes toward ssDNA. The simulation results exhibit no significant structural effect for replacing the cationic amine moiety with imidazole derivative on the side group of the oligomer. Adding a homopurine strand elongates the oligomer backbone; on the contrary, mixing up the homopyrimidine strand causes compression. On the other hand, these ssDNAs do not notably affect the compactness of the oligomer backbones. The anion-cation interactions play an essential role in the structural and spectroscopic change of cationic polythiophenes (CPTs) upon complexation with ssDNAs. The red shift of CPTs in the UV-VIS spectra with the addition of homopurine strands might be explained by the strong anion-cation, weak π -cation interactions, and high binding affinities. Nonpolar interactions (vdW and SA) and complex solvation energies dominate binding free energies. Hydrogen interaction analyses show that oligomers most likely approach the ssDNAs from their backbone upon complexation except for the duplex containing homopyrimidine strand and oligothiophene possessing imidazole derivative side chain.
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Affiliation(s)
- Nehir Nalıncı Barbak
- Faculty of Science, Department of Chemistry, Izmir Institute of Technology, 35430, Urla, Izmir, Turkiye
| | - Erman Kıbrıs
- Faculty of Science, Department of Chemistry, Izmir Institute of Technology, 35430, Urla, Izmir, Turkiye
| | - Fethi Can Demirci
- Faculty of Science, Department of Chemistry, Izmir Institute of Technology, 35430, Urla, Izmir, Turkiye
| | - Nuran Elmacı Irmak
- Faculty of Science, Department of Chemistry, Izmir Institute of Technology, 35430, Urla, Izmir, Turkiye.
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3
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Walesch S, Birkelbach J, Jézéquel G, Haeckl FPJ, Hegemann JD, Hesterkamp T, Hirsch AKH, Hammann P, Müller R. Fighting antibiotic resistance-strategies and (pre)clinical developments to find new antibacterials. EMBO Rep 2022; 24:e56033. [PMID: 36533629 PMCID: PMC9827564 DOI: 10.15252/embr.202256033] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Antibacterial resistance is one of the greatest threats to human health. The development of new therapeutics against bacterial pathogens has slowed drastically since the approvals of the first antibiotics in the early and mid-20th century. Most of the currently investigated drug leads are modifications of approved antibacterials, many of which are derived from natural products. In this review, we highlight the challenges, advancements and current standing of the clinical and preclinical antibacterial research pipeline. Additionally, we present novel strategies for rejuvenating the discovery process and advocate for renewed and enthusiastic investment in the antibacterial discovery pipeline.
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Affiliation(s)
- Sebastian Walesch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Joy Birkelbach
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Gwenaëlle Jézéquel
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany
| | - F P Jake Haeckl
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Julian D Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Thomas Hesterkamp
- Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany,Helmholtz International Lab for Anti‐InfectivesSaarbrückenGermany
| | - Peter Hammann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)SaarbrückenGermany,Department of PharmacySaarland UniversitySaarbrückenGermany,Helmholtz Centre for Infection research (HZI)BraunschweigGermany,German Center for infection research (DZIF)BraunschweigGermany,Helmholtz International Lab for Anti‐InfectivesSaarbrückenGermany
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4
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Terteci-Popescu AE, Beu TA. Branched polyethyleneimine: CHARMM force field and molecular dynamics simulations. J Comput Chem 2022; 43:2072-2083. [PMID: 36169240 DOI: 10.1002/jcc.27005] [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: 05/10/2022] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 11/11/2022]
Abstract
Polyethyleneimine (PEI), one of the non-viral vectors of great interest for gene delivery, was investigated at all-atom level, with particular emphasis on its branched form. We report the extension of our previously published CHARMM force field (FF) for linear PEI, with parameters optimized specifically for branched configurations. A new residue type for the branch connector is introduced and the charges and bonded parameters are derived from ab initio calculations based on a model polymer. The new FF is validated by extensive molecular dynamics simulations of solvated branched PEIs of various protonation fractions and branch lengths. The gyration radii, end-to-end distances, and diffusion coefficients are compared with results for linear PEIs of similar molecular weights and protonation patterns. Solvated complexes of DNA with (linear/branched) PEI were also investigated to determine favorable attachment conformations. The parametrized atomistic force field is suitable for simulations of PEI with arbitrary branching pattern, protonation, and size, and is expected to provide relevant insights regarding optimal conditions for DNA-PEI complex formation.
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Affiliation(s)
| | - Titus Adrian Beu
- Faculty of Physics, Department of Biomolecular Physics, University Babeş-Bolyai, Cluj-Napoca, Romania
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5
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On the force field optimisation of [Formula: see text]-lactam cores using the force field Toolkit. J Comput Aided Mol Des 2022; 36:537-547. [PMID: 35819650 PMCID: PMC9399072 DOI: 10.1007/s10822-022-00464-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022]
Abstract
When employing molecular dynamics (MD) simulations for computer-aided drug design, the quality of the used force fields is highly important. Here we present reparametrisations of the force fields for the core molecules from 9 different \documentclass[12pt]{minimal}
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\begin{document}$$\beta$$\end{document}β-lactam classes, for which we utilized the force field Toolkit and Gaussian calculations. We focus on the parametrisation of the dihedral angles, with the goal of reproducing the optimised quantum geometry in MD simulations. Parameters taken from CGenFF turn out to be a good initial guess for the multiplicity of each dihedral angle, but the key to a successful parametrisation is found to lie in the phase shifts. Based on the optimised quantum geometry, we come up with a strategy for predicting the phase shifts prior to the dihedral potential fitting. This allows us to successfully parameterise 8 out of the 11 molecules studied here, while the remaining 3 molecules can also be parameterised with small adjustments. Our work highlights the importance of predicting the dihedral phase shifts in the ligand parametrisation protocol, and provides a simple yet valuable strategy for improving the process of parameterising force fields of drug-like molecules.
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6
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Pavlova A, Bassit L, Cox BD, Korablyov M, Chipot C, Patel D, Lynch DL, Amblard F, Schinazi RF, Gumbart JC. The Mechanism of Action of Hepatitis B Virus Capsid Assembly Modulators Can Be Predicted from Binding to Early Assembly Intermediates. J Med Chem 2022; 65:4854-4864. [PMID: 35290049 PMCID: PMC9026740 DOI: 10.1021/acs.jmedchem.1c02040] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Interfering with the self-assembly of virus nucleocapsids is a promising approach for the development of novel antiviral agents. Applied to hepatitis B virus (HBV), this approach has led to several classes of capsid assembly modulators (CAMs) that target the virus by either accelerating nucleocapsid assembly or misdirecting it into noncapsid-like particles, thereby inhibiting the HBV replication cycle. Here, we have assessed the structures of early nucleocapsid assembly intermediates, bound with and without CAMs, using molecular dynamics simulations. We find that distinct conformations of the intermediates are induced depending on whether the bound CAM accelerates or misdirects assembly. Specifically, the assembly intermediates with bound misdirecting CAMs appear to be flattened relative to those with bound accelerators. Finally, the potency of CAMs within the same class was studied. We find that an increased number of contacts with the capsid protein and favorable binding energies inferred from free energy perturbation calculations are indicative of increased potency.
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Affiliation(s)
- Anna Pavlova
- School of Physics and School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Leda Bassit
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Bryan D Cox
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Maksym Korablyov
- MIT Media Lab, Massachusetts Institute of Technology, Boston, Massachusetts 02139, United States
| | - Christophe Chipot
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Laboratoire international associé CNRS-UIUC, UMR 7019, Université de Lorraine, B.P. 70239, 54506 Vandæuvre-lès-Nancy, France
| | - Dharmeshkumar Patel
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Diane L Lynch
- School of Physics and School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, United States
| | - James C Gumbart
- School of Physics and School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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7
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Acharya A, Yi D, Pavlova A, Agarwal V, Gumbart JC. Resolving the Hydride Transfer Pathway in Oxidative Conversion of Proline to Pyrrole. Biochemistry 2022; 61:206-215. [DOI: 10.1021/acs.biochem.1c00741] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Atanu Acharya
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Dongqi Yi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - James C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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8
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Teo RD, Tieleman DP. Modulation of Phospholipid Bilayer Properties by Simvastatin. J Phys Chem B 2021; 125:8406-8418. [PMID: 34296883 DOI: 10.1021/acs.jpcb.1c03359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Simvastatin (Zocor) is one of the most prescribed drugs for reducing high cholesterol. Although simvastatin is ingested in its inactive lactone form, it is converted to its active dihydroxyheptanoate form by carboxylesterases in the liver. The dihydroxyheptanoate form can also be converted back to its original lactone form. Unfortunately, some of the side effects associated with the intake of simvastatin and other lipophilic statins at higher doses include statin-associated myopathy (SAM) and, in more severe cases, kidney failure. While the cause of SAM is unknown, it is hypothesized that these side effects are dependent on the localization of statins in lipid bilayers and their impact on bilayer properties. In this work, we carry out all-atom molecular dynamics simulations on both the lactone and dihydroxyheptanoate forms of simvastatin (termed "SN" and "SA", respectively) with a pure 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer and a POPC/cholesterol (30 mol %) binary mixture as membrane models. Additional simulations were carried out with multiple simvastatin molecules to mimic in vitro conditions that produced pleiotropic effects. Both SN and SA spontaneously diffused into the lipid bilayer, and a longer simulation time of 4 μs was needed for the complete incorporation of multiple SAs into the bilayer. By constructing potential mean force and electron density profiles, we find that SN localizes deeper within the hydrophobic interior of the bilayer and that SA has a greater tendency to form hydrogen-bonding interactions with neighboring water molecules and lipid headgroups. For the pure POPC bilayer, both SN and SA increase membrane order, while membrane fluidity increases for the POPC/cholesterol bilayer.
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Affiliation(s)
- Ruijie D Teo
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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9
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Pang YT, Pavlova A, Tajkhorshid E, Gumbart JC. Parameterization of a drug molecule with a halogen σ-hole particle using ffTK: Implementation, testing, and comparison. J Chem Phys 2021; 153:164104. [PMID: 33138412 DOI: 10.1063/5.0022802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Halogen atoms are widely used in drug molecules to improve their binding affinity for the receptor proteins. Many of the examples involve "halogen bonding" between the molecule and the binding site, which is a directional interaction between a halogen atom and a nucleophilic atom. Such an interaction is induced by an electron cloud shift of the halogen atom toward its covalently bonded neighbor to form the σ-bond, leaving a small electrostatic positive region opposite to the bond called the "σ-hole." To mimic the effect of the σ-hole in the CHARMM non-polarizable force field, recently CGenFF added a positively charged massless particle to halogen atoms, positioned at the opposite side of the carbon-halogen bond. This particle is referred to as a lone pair (LP) particle because it uses the lone pair implementation in the CHARMM force field. Here, we have added support for LP particles to ffTK, an automated force field parameterization toolkit widely distributed as a plugin to the molecular visualization software VMD. We demonstrate the updated optimization process using an example halogenated drug molecule, AT130, which is a capsid assembly modulator targeting the hepatitis B virus. Our results indicate that parameterization with the LP particle significantly improves the accuracy of the electrostatic response of the molecule, especially around the halogen atom. Although the inclusion of the LP particle does not produce a prominent effect on the interactions between the molecule and its target protein, the protein-ligand binding performance is greatly improved by optimization of the parameters.
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Affiliation(s)
- Yui Tik Pang
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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10
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Kıbrıs E, Barbak NN, Irmak NE. CHARMM force field generation for a cationic thiophene oligomer with ffTK. J Mol Model 2021; 27:34. [PMID: 33420831 DOI: 10.1007/s00894-020-04610-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
In the present work, CHARMM force field parameters are generated for a cationic oligomer of N, N, N-trimethyl-3-(4-methylthiophen-3-yl) oxy) propan-1-aminium) which has the potential for sensing biological molecules such as nucleic acids, nucleobases. We have used ffTK (force field tool kit) to obtain potential parameters. MD simulations are performed for 20-mer and its complexes with AMP and ATP. The simulation results are analyzed to see the number of phosphates in adenosine nucleotides effects on the structure of the backbone of oligomer. The UV-VIS calculations for the conformers which possess the most probable radius of gyration are carried out and compared to the experimental ones to validate the generated force field. Graphical Abstract Recent studies have shown that, biologically important anions (ATP, AMP, vb.) change the spectroscopic properties of cationic polythiophenes (CPT) in the solutions. This work aims to generate CHARMM compatible force field parameters for a CPT to explain experimental studies. The type of interactions will be investigated deeply to lead new biosensor studies by examining the formation and the structure of complexes that consist of a oligothiophene and biological molecules, ATP, AMP by molecular dynamic simulations.
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Affiliation(s)
- Erman Kıbrıs
- Faculty of Science, Department of Chemistry, İzmir Institute of Technology, 35430, Urla, Izmir, Turkey
| | - Nehir Nalıncı Barbak
- Faculty of Science, Department of Chemistry, İzmir Institute of Technology, 35430, Urla, Izmir, Turkey
| | - Nuran Elmacı Irmak
- Faculty of Science, Department of Chemistry, İzmir Institute of Technology, 35430, Urla, Izmir, Turkey.
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11
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Jednačak T, Mikulandra I, Novak P. Advanced Methods for Studying Structure and Interactions of Macrolide Antibiotics. Int J Mol Sci 2020; 21:E7799. [PMID: 33096889 PMCID: PMC7589898 DOI: 10.3390/ijms21207799] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/09/2020] [Accepted: 10/19/2020] [Indexed: 11/17/2022] Open
Abstract
Macrolide antibiotics are macrocyclic compounds that are clinically used and prescribed for the treatment of upper and lower respiratory tract infections. They inhibit the synthesis of bacterial proteins by reversible binding to the 23S rRNA at or near the peptidyl transferase center. However, their excellent antibacterial profile was largely compromised by the emergence of bacterial resistance. Today, fighting resistance to antibiotics is one of the greatest challenges in medicinal chemistry. Considering various physicochemical properties of macrolides, understanding their structure and interactions with macromolecular targets is crucial for the design of new antibiotics efficient against resistant pathogens. The solid-state structures of some macrolide-ribosome complexes have recently been solved, throwing new light on the macrolide binding mechanisms. On the other hand, a combination of NMR spectroscopy and molecular modeling calculations can be applied to study free and bound conformations in solution. In this article, a description of advanced physicochemical methods for elucidating the structure and interactions of macrolide antibiotics in solid state and solution will be provided, and their principal advantages and drawbacks will be discussed.
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Affiliation(s)
- Tomislav Jednačak
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia;
| | | | - Predrag Novak
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia;
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12
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Pavlova A, Parks JM, Gumbart JC. Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations. J Chem Theory Comput 2018; 14:784-798. [PMID: 29334459 DOI: 10.1021/acs.jctc.7b01236] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Corrinoid cofactors such as cobalamin are used by many enzymes and are essential for most living organisms. Therefore, there is broad interest in investigating cobalamin-protein interactions with molecular dynamics simulations. Previously developed parameters for cobalamins are based mainly on crystal structure data. Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations. We provide parameters for corrinoids in three oxidation states, Co3+, Co2+, and Co1+, and with various axial ligands. Lennard-Jones parameters for the cobalt center in the Co(II) and Co(I) states were optimized using a helium atom probe, and partial atomic charges were obtained with a combination of natural population analysis (NPA) and restrained electrostatic potential (RESP) fitting approaches. The Force Field Toolkit was used to optimize all bonded terms. The resulting parameters, determined solely from calculations of cobalamin alone or in water, were then validated by assessing their agreement with density functional theory geometries and by analyzing molecular dynamics simulation trajectories of several corrinoid proteins for which X-ray crystal structures are available. In each case, we obtained excellent agreement with the reference data. In comparison to previous CHARMM-compatible parameters for cobalamin, we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site. The approach described here is readily adaptable for developing CHARMM-compatible force-field parameters for other corrinoids or large biomolecules.
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Affiliation(s)
- Anna Pavlova
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology , Atlanta, Georgia 30332, United States.,School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology , Atlanta, Georgia 30332, United States
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13
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Dinos GP. The macrolide antibiotic renaissance. Br J Pharmacol 2017; 174:2967-2983. [PMID: 28664582 DOI: 10.1111/bph.13936] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/29/2017] [Accepted: 06/20/2017] [Indexed: 12/19/2022] Open
Abstract
Macrolides represent a large family of protein synthesis inhibitors of great clinical interest due to their applicability to human medicine. Macrolides are composed of a macrocyclic lactone of different ring sizes, to which one or more deoxy-sugar or amino sugar residues are attached. Macrolides act as antibiotics by binding to bacterial 50S ribosomal subunit and interfering with protein synthesis. The high affinity of macrolides for bacterial ribosomes, together with the highly conserved structure of ribosomes across virtually all of the bacterial species, is consistent with their broad-spectrum activity. Since the discovery of the progenitor macrolide, erythromycin, in 1950, many derivatives have been synthesised, leading to compounds with better bioavailability and acid stability and improved pharmacokinetics. These efforts led to the second generation of macrolides, including well-known members such as azithromycin and clarithromycin. Subsequently, in order to address increasing antibiotic resistance, a third generation of macrolides displaying improved activity against many macrolide resistant strains was developed. However, these improvements were accompanied with serious side effects, leading to disappointment and causing many researchers to stop working on macrolide derivatives, assuming that this procedure had reached the end. In contrast, a recent published breakthrough introduced a new chemical platform for synthesis and discovery of a wide range of diverse macrolide antibiotics. This chemical synthesis revolution, in combination with reduction in the side effects, namely, 'Ketek effects', has led to a macrolide renaissance, increasing the hope for novel and safe therapeutic agents to combat serious human infectious diseases.
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Affiliation(s)
- George P Dinos
- Department of Biochemistry, School of Medicine, University of Patras, Patras, Greece
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Pavlova A, Parks JM, Oyelere AK, Gumbart JC. Toward the rational design of macrolide antibiotics to combat resistance. Chem Biol Drug Des 2017; 90:641-652. [DOI: 10.1111/cbdd.13004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/03/2017] [Accepted: 04/08/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Anna Pavlova
- School of Physics Georgia Institute of Technology Atlanta GA USA
| | - Jerry M. Parks
- Biosciences Division Oak Ridge National Laboratory Oak Ridge TN USA
| | - Adegboyega K. Oyelere
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology Atlanta GA USA
| | - James C. Gumbart
- School of Physics Georgia Institute of Technology Atlanta GA USA
- School of Chemistry and Biochemistry Parker H. Petit Institute for Bioengineering and Bioscience Georgia Institute of Technology Atlanta GA USA
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15
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Pothula KR, Solano CJF, Kleinekathöfer U. Simulations of outer membrane channels and their permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1760-71. [PMID: 26721326 DOI: 10.1016/j.bbamem.2015.12.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/25/2022]
Abstract
Channels in the outer membrane of Gram-negative bacteria provide essential pathways for the controlled and unidirectional transport of ions, nutrients and metabolites into the cell. At the same time the outer membrane serves as a physical barrier for the penetration of noxious substances such as antibiotics into the bacteria. Most antibiotics have to pass through these membrane channels to either reach cytoplasmic bound targets or to further cross the hydrophobic inner membrane. Considering the pharmaceutical significance of antibiotics, understanding the functional role and mechanism of these channels is of fundamental importance in developing strategies to design new drugs with enhanced permeation abilities. Due to the biological complexity of membrane channels and experimental limitations, computer simulations have proven to be a powerful tool to investigate the structure, dynamics and interactions of membrane channels. Considerable progress has been made in computer simulations of membrane channels during the last decade. The goal of this review is to provide an overview of the computational techniques and their roles in modeling the transport across outer membrane channels. A special emphasis is put on all-atom molecular dynamics simulations employed to better understand the transport of molecules. Moreover, recent molecular simulations of ion, substrate and antibiotics translocation through membrane pores are briefly summarized. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Karunakar R Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Carlos J F Solano
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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