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Xiao T, Zhou Y, Li B. Energy-Scaled Debye-Hückel Theory for the Electrostatic Solvation Free Energy in Size-Asymmetric Electrolyte Solutions. J Phys Chem B 2024; 128:1029-1039. [PMID: 38235680 DOI: 10.1021/acs.jpcb.3c07233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
In this report, an energy-scaled Debye-Hückel theory is developed for fast and accurate evaluation of the electrostatic solvation free energy in size-asymmetric electrolyte solutions. A size-asymmetric electrolyte solution is mapped to a dielectric continuum medium with Debye-Hückel-like response. Based on the scaling relation of the electrostatic energy of a spherical ion in the small and large size limits, a Padé polynomial is used to interpolate the electrostatic energy at finite size. The Padé polynomial is further interpreted as the electrostatic energy of an effective Debye-Hückel mean field model, depicted by a modified Debye parameter and a surface charge density due to the size asymmetry of the solvent ions. This theory can distinguish the electrostatic energies and the electrostatic solvation free energies of solutes with the same size but opposite charges. Application to charged hard and charged soft spheres demonstrates the accuracy of our approach.
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Affiliation(s)
- Tiejun Xiao
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, Guiyang 550018, People's Republic of China
| | - Yun Zhou
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, Guiyang 550018, People's Republic of China
| | - Bo Li
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, Guiyang 550018, People's Republic of China
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2
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Pitaloka DAE, Arfan A, Ramadhan DSF, Chaidir L. Insights from the molecular mechanism of pyrazinamide to mutated pyrazinamidase linked to the pncA gene in clinical isolates of Mycobacterium tuberculosis. J Biomol Struct Dyn 2024; 42:759-765. [PMID: 37096659 DOI: 10.1080/07391102.2023.2195002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/18/2023] [Indexed: 04/26/2023]
Abstract
This study aims to conduct a comprehensive molecular dynamics strategy to evaluate whether mutations found in pyrazinamide monoresistant (PZAMR) strains of Mycobacterium tuberculosis (MTB) can potentially reduce the effectiveness of pyrazinamide (PZA) for tuberculosis (TB) treatment. Five single point mutations of pyrazinamidase (PZAse), an enzyme which is responsible for the activation of prodrug PZA into pyrazinoic acid, found in MTB clinical isolates, namely His82Arg, Thr87Met, Ser66Pro, Ala171Val, and Pro62Leu, were analyzed by the dynamics simulations both in the apo state (unbound state) and in the PZA bound state. The results showed that the mutation of His82 to Arg, Thr87 to Met, and Ser66 to Pro in PZAse affects the coordination state of the Fe2+ ion, which is a cofactor required for enzyme activity. These mutations change the flexibility, stability, and fluctuation of His51, His57, and ASP49 amino acid residues around the Fe2+ ion, culminating in an unstable complex and dissociation of PZA from the PZAse binding site. However, mutations of Ala171 to Val and Pro62 to Leu were found to have no effect on the complex's stability. Based on the results, PZAse mutations of His82Arg, Thr87Met, and Ser66Pro culminated in weak binding affinity for PZA and caused significant structural deformations that led to PZA resistance. Future structural and functional studies, as well as investigations into other aspects of drug resistance in PZAse, will require experimental clarification.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dian Ayu Eka Pitaloka
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang, Indonesia
- Center for Translational Biomarker Research, Universitas Padjadjaran, Bandung, Indonesia
| | - Arfan Arfan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Universitas Halu Oleo, Kendari, Indonesia
| | - Dwi Syah Fitra Ramadhan
- Department of Pharmaceutical Chemistry, Sekolah Tinggi Ilmu Kesehatan Mandala Waluya, Kendari, Indonesia
| | - Lidya Chaidir
- Center for Translational Biomarker Research, Universitas Padjadjaran, Bandung, Indonesia
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Sumedang, Indonesia
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3
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Djamali E. Thermodynamics and Solubility of Electrolytes in Mixed Solvent Systems at High Temperatures. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.2c02148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Essmaiil Djamali
- Department of Chemistry, Sierra College, 5100 Sierra College Boulevard, Rocklin, California 95677, United States
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4
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Rahimi AM, Jamali S, Bardhan JP, Lustig SR. Solvation Thermodynamics of Solutes in Water and Ionic Liquids Using the Multiscale Solvation-Layer Interface Condition Continuum Model. J Chem Theory Comput 2022; 18:5539-5558. [PMID: 36001344 DOI: 10.1021/acs.jctc.2c00248] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular assembly processes are generally driven by thermodynamic properties in solutions. Atomistic modeling can be very helpful in designing and understanding complex systems, except that bulk solvent is very inefficient to treat explicitly as discrete molecules. In this work, we develop and assess two multiscale solvation models for computing solvation thermodynamic properties. The new SLIC/CDC model combines continuum solvent electrostatics based on the solvent layer interface condition (SLIC) with new statistical thermodynamic models for hydrogen bonding and nonpolar modes: cavity formation, dispersion interactions, combinatorial mixing (CDC). Given the structures of 500 solutes, the SLIC/CDC model predicts Gibbs energies of solvation in water with an average accuracy better than 1 kcal/mol, when compared to experimental measurements, and better than 0.8 kcal/mol, when compared to explicit-solvent molecular dynamics simulations. The individual SLIC/CDC energy mode values agree quantitatively with those computed from explicit-solvent molecular dynamics. The previously published SLIC/SASA multiscale model combines the SLIC continuum electrostatic model with the solvent-accessible surface area (SASA) nonpolar energy mode. With our new, improved parametrization method, the SLIC/SASA model now predicts Gibbs energies of solvation with better than 1.4 kcal/mol average accuracy in aqueous systems, compared to experimental and explicit-solvent molecular dynamics, and better than 1.6 kcal/mol average accuracy in ionic liquids, compared to explicit-solvent molecular dynamics. Both models predict solvation entropies, and are the first implicit-solvation models capable of predicting solvation heat capacities.
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Affiliation(s)
- Ali Mehdizadeh Rahimi
- Department of Mechanical and Industrial Engineering, Northeastern University, 360 Huntington Ave., Boston Massachusetts 02115, United States
| | - Safa Jamali
- Department of Mechanical and Industrial Engineering, Northeastern University, 360 Huntington Ave., Boston Massachusetts 02115, United States
| | - Jaydeep P Bardhan
- Pacific Northwest National Laboratory, 902 Battelle Blvd., Richland, Washington 99354, United States
| | - Steven R Lustig
- Department of Chemical Engineering, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115, United States
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Tembe N, Machaba KE, Ndagi U, Kumalo HM, Mhlongo NN. Ursolic acid as a potential inhibitor of Mycobacterium tuberculosis cytochrome bc1 oxidase-a molecular modelling perspective. J Mol Model 2022; 28:35. [PMID: 35022913 DOI: 10.1007/s00894-021-04993-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 11/23/2021] [Indexed: 01/05/2023]
Abstract
The escalating burden of tuberculosis disease and drastic effects of current medicine has stimulated a search for alternative drugs. A medicinal plant Warburgia salutaris has been reported to possess inhibitory properties against M. tuberculosis. In this study, we apply computational methods to investigate the probability of W. salutaris compounds as potential inhibitors of M. tuberculosis QcrB protein. We performed molecular docking, molecular dynamics simulations, radius of gyration, principal component analysis (PCA), and molecular mechanics-generalized born surface area (MM-GBSA) binding-free energy calculations in explicit solvent to achieve our objective. The results suggested that ursolic acid (UA) and ursolic acid acetate (UAA) could serve as preferred potential inhibitors of mycobacterial QcrB compared to lansoprazole sulphide (LSPZ) and telacebec (Q203)-UA and UAA have a higher binding affinity to QcrB compared to LSPZ and Q203 drugs. UA binding affinity is attributed to hydrogen bond formation with Val120, Arg364 and Arg366, and largely resonated from van der Waals forces resulting from UA interactions with hydrophobic amino acids in its vicinity. UAA binds to the porphyrin ring binding site with higher binding affinity compared to LSPZ. The binding affinity results primarily from van der Waals forces between UAA and hydrophobic residues of QcrB in the porphyrin ring binding site where UAA binds competitively. UA and UAA formed stable complexes with the protein with reduced overall residue mobility, consequently supporting the magnitude of binding affinity of the respective ligands. UAA could potentially compete with the porphyrin ring for the binding site and deprive the mycobacterial cell from oxygen, consequently disturbing mycobacterial oxygen-dependent metabolic processes. Therefore, discovery of a compound that competes with porphyrin ring for the binding site may be useful in QcrB pharmocological studies. UA proved to be a superior compound, although its estimated toxicity profile revealed UA to be hepatotoxic within acceptable parameters. Although preliminary findings of this report still warrant experimental validation, they could serve as a baseline for the development of new anti-tubercular drugs from natural resources that target QcrB.
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Affiliation(s)
- Ntombikayise Tembe
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Kgothatso E Machaba
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Umar Ndagi
- Africa Centre of Excellence for Mycotoxin and Food Safety, Federal University of Technology, Minna, Nigeria
| | - Hezekiel M Kumalo
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Ndumiso N Mhlongo
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
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Fakih TM, Kurniawan F, Yusuf M, Mudasir M, Tjahjono DH. Molecular Dynamics of Cobalt Protoporphyrin Antagonism of the Cancer Suppressor REV-ERBβ. Molecules 2021; 26:3251. [PMID: 34071361 PMCID: PMC8198987 DOI: 10.3390/molecules26113251] [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: 04/06/2021] [Revised: 05/15/2021] [Accepted: 05/26/2021] [Indexed: 11/17/2022] Open
Abstract
Nuclear receptor REV-ERBβ is an overexpressed oncoprotein that has been used as a target for cancer treatment. The metal-complex nature of its ligand, iron protoporphyrin IX (Heme), enables the REV-ERBβ to be used for multiple therapeutic modalities as a photonuclease, a photosensitizer, or a fluorescence imaging agent. The replacement of iron with cobalt as the metal center of protoporphyrin IX changes the ligand from an agonist to an antagonist of REV-ERBβ. The mechanism behind that phenomenon is still unclear, despite the availability of crystal structures of REV-ERBβ in complex with Heme and cobalt protoporphyrin IX (CoPP). This study used molecular dynamic simulations to compare the effects of REV-ERBβ binding to Heme and CoPP, respectively. The initial poses of Heme and CoPP in complex with agonist and antagonist forms of REV-ERBβ were predicted using molecular docking. The binding energies of each ligand were calculated using the MM/PBSA method. The computed binding affinity of Heme to REV-ERBβ was stronger than that of CoPP, in agreement with experimental results. CoPP altered the conformation of the ligand-binding site of REV-ERBβ, disrupting the binding site for nuclear receptor corepressor, which is required for REV-ERBβ to regulate the transcription of downstream target genes. Those results suggest that a subtle change in the metal center of porphyrin can change the behavior of porphyrin in cancer cell signaling. Therefore, modification of porphyrin-based agents for cancer therapy should be conducted carefully to avoid triggering unfavorable effects.
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Affiliation(s)
- Taufik Muhammad Fakih
- School of Pharmacy, Bandung Institute of Technology, Jalan Ganesha 10, Bandung 40135, Indonesia; (T.M.F.); (F.K.)
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Islam Bandung, Jalan Rangga Gading 8, Bandung 40116, Indonesia
| | - Fransiska Kurniawan
- School of Pharmacy, Bandung Institute of Technology, Jalan Ganesha 10, Bandung 40135, Indonesia; (T.M.F.); (F.K.)
| | - Muhammad Yusuf
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Sumedang 45363, Indonesia;
| | - Mudasir Mudasir
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara BLS 21, Yogyakarta 55281, Indonesia;
| | - Daryono Hadi Tjahjono
- School of Pharmacy, Bandung Institute of Technology, Jalan Ganesha 10, Bandung 40135, Indonesia; (T.M.F.); (F.K.)
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Docking-Based Virtual Screening and Molecular Dynamics Simulations of Quercetin Analogs as Enoyl-Acyl Carrier Protein Reductase (InhA) Inhibitors of Mycobacterium tuberculosis. Sci Pharm 2021. [DOI: 10.3390/scipharm89020020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The emergence of multidrug-resistant Mycobacterium tuberculosis (MTB) has become a major problem in treating tuberculosis (TB) and shows the need to develop new and efficient drugs for better TB control. This study aimed to use in silico techniques to discover potential inhibitors to the Enoyl-[acyl-carrier-protein] reductase (InhA), which controls mycobacterial cell wall construction. Initially, 391 quercetin analogs present in the KNApSAck_3D database were selected, filters were sequentially applied by docking-based virtual screening. After recategorizing the variables (bond energy prediction and molecular interaction, including hydrogen bond and hydrophobic bond), compounds C00013874, C00006532, and C00013887 were selected as hit ligands. These compounds showed great hydrophobic contributions, and for each hit ligand, 100 ns of molecular dynamic simulations were performed, and the binding free energy was calculated. C00013874 demonstrated the greatest capacity for the InhA enzyme inhibition with ΔGbind = −148.651 kcal/mol compare to NAD (native ligand) presented a ΔGbind = −87.570 kcal/mol. These data are preliminary studies and might be a suitable candidate for further experimental analysis.
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Herbert JM. Dielectric continuum methods for quantum chemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1519] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- John M. Herbert
- Department of Chemistry and Biochemistry The Ohio State University Columbus Ohio USA
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Affiliation(s)
- Matthew Truscott
- Department of Physics, University of North Texas, Denton, Texas 76207, United States
| | - Oliviero Andreussi
- Department of Physics, University of North Texas, Denton, Texas 76207, United States
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Hofer TS, Hünenberger PH. Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration. J Chem Phys 2018; 148:222814. [DOI: 10.1063/1.5000799] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Centre for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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Molavi Tabrizi A, Goossens S, Mehdizadeh Rahimi A, Cooper CD, Knepley MG, Bardhan JP. Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson–Boltzmann Solvent. J Chem Theory Comput 2017; 13:2897-2914. [DOI: 10.1021/acs.jctc.6b00832] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amirhossein Molavi Tabrizi
- Department
of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Spencer Goossens
- Department
of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ali Mehdizadeh Rahimi
- Department
of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Christopher D. Cooper
- Departamento
de Ingeniería Mecánica and Centro Científico
Tecnológico de Valparaíso (CCTVal), Universidad Técnica Federico Santa María, Valparaiso, Chile
| | - Matthew G. Knepley
- Department
of Computational and Applied Mathematics, Rice University, Houston, Texas 77005, United States
| | - Jaydeep P. Bardhan
- Department
of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115, United States
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