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Prabha S, Chauhan P, Warkare S, Pandey KM. A computational investigation of potential plant-based bioactive compounds against drug-resistant Staphylococcus aureus of multiple target proteins. J Biomol Struct Dyn 2023:1-19. [PMID: 38133950 DOI: 10.1080/07391102.2023.2297009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023]
Abstract
Drug-resistant Staphylococcus aureus (DRSA) poses a significant global health threat, like bacteremia, endocarditis, skin, soft tissue, bone, and joint infections. Nowadays, the resistance against conventional drugs has been a prompt and focused medical concern. The present study aimed to explore the inhibitory potential of plant-based bioactive compounds (PBBCs) against effective target proteins using a computational approach. We retrieved and verified 22 target proteins associated with DRSA and conducted a screening process that involved testing 87 PBBCs. Molecular docking was performed between screened PBBCs and reference drugs with selected target proteins via AutoDock. Subsequently, we filtered the target proteins and top PBBCs based on their binding affinity scores. Furthermore, molecular dynamic simulation was carried out through GROMACS for a duration of 100 ns, and the binding free energy was calculated using the gmx_MMPBSA. The result showed consistent hydrogen bonding interactions among the amino acid residues Ser 149, Arg 151, Thr 165, Thr 216, Glu 239, Ser 240, Ile 14, as well as Asn 18, Gln 19, Lys 45, Thr 46, Tyr 109, with their respective target proteins of the penicillin-binding protein and dihydrofolate reductase complex. Additionally, we assessed the pharmacokinetic properties of screened PBBCs via SwissADME and AdmetSAR. The findings suggest that β-amyrin, oleanolic acid, kaempferol, quercetin, and friedelin have the potential to inhibit the selected target proteins. In future research, both in vitro and in vivo, experiments will be needed to establish these PBBCs as potent antimicrobial drugs for DRSA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sarit Prabha
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | | | - Sudeesh Warkare
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, India
| | - Khushhali M Pandey
- Department of Biological Science and Engineering, Maulana Azad National Institute of Technology, Bhopal, India
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2
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Gao S, Wang L, Bai F, Xu S. In silico discovery of food-derived phytochemicals against asialoglycoprotein receptor 1 for treatment of hypercholesterolemia: Pharmacophore modeling, molecular docking and molecular dynamics simulation approach. J Mol Graph Model 2023; 125:108614. [PMID: 37651861 DOI: 10.1016/j.jmgm.2023.108614] [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: 07/06/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023]
Abstract
Hypercholesterolemia is a significant risk factor for atherosclerotic cardiovascular disease (ASCVD). Successful management of cholesterol metabolism disorders can prevent these ASCVD effectively. Asialoglycoprotein receptor 1 (ASGR1) is the main subtype of sialoglycoprotein receptor, which is specifically expressed in the liver and mediates the endocytosis of blood asialoglycoprotein to lysosome degradation. Recently, ASGR1 has been reported as a new therapeutic target for the treatment of hypercholesterolemia. In this study, the main aim was to identify natural ASGR1 inhibitors from plant food chemicals library through pharmacophore and docking based virtual screening. Total 14 phytochemicals of potential ASGR1 inhibitors were identified, which presented docking affinity higher than control compound through docking based virtual screening. The docking pose showed the top three hits interacted residues were located at active pocket of ASGR1 with hydrogen bonds, hydrophobic interactions and electrostatic interactions. The top three hits (ZINC85664954, ZINC169372863, and ZINC195764535) were then subjected to 200 ns molecular dynamics simulation to evaluate the stability of docked complexes. These results showed that selected phytochemicals bound to ASGR1 with higher stability than control compound. Binding free energy of each docked complex was calculated by the Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) method. The binding free energy of ZINC85664954, ZINC169372863, ZINC195764535, and control-ASGR1 docked complexes were -18.359, -13.303, -14.389, and -6.229 kcal/mol, respectively. This indicated that selected hits bound to ASGR1 with higher affinity than control compound. Network pharmacology analysis shows that these phytochemicals have obvious multiple-effects and can regulate various biochemical pathways related to hypercholesterolemia. Besides, selected phytochemicals have suitable pharmacokinetics properties, suggesting that these compounds may be potential drug candidates. This study may be contributed to rational design of novel ASGR1 inhibitors for treatment of hypercholesterolemia.
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Affiliation(s)
- Shengyun Gao
- Chest Pain Center, Department of Cardiovascular Medicine, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, 733000, China
| | - Lei Wang
- Chest Pain Center, Department of Cardiovascular Medicine, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, 733000, China
| | - Feng Bai
- Drug Clinical Trial Center, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, 733000, China
| | - Shaohua Xu
- Drug Clinical Trial Center, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, 733000, China.
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3
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Kong J, Li L, Yuan H, Bai F, Yang K, Zhao L, Xu S. In silico discovery of potential sodium-glucose cotransporter-2 inhibitors from natural products for treatment of heart failure via molecular docking and molecular dynamics simulation approach. J Biomol Struct Dyn 2023; 41:8109-8120. [PMID: 36200619 DOI: 10.1080/07391102.2022.2130983] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/24/2022] [Indexed: 10/10/2022]
Abstract
Heart failure (HF) is the end stage of cardiovascular disease. Because of its complex condition and poor prognosis, HF has become an important public health problem in the world. Sodium-glucose cotransporter-2 (SGLT2) is a member of the glucose transporter family. Recently, SGLT2 inhibitors have been applied to treat HF. In this study, the main aim was to discover natural SGLT2 inhibitor from Chinese herbs through docking-based virtual screening. Totally 113 natural compounds of potential SGLT2 inhibitor were identified, which displayed docking affinity higher than six approved inhibitors (dapagliflozin (IC50 = 4.9 nM), canagliflozin (IC50 = 4.4 nM 6.7), ipragliflozin (IC50 = 7.4 nM), empagliflozin (IC50 = 3.1 nM), tofogliflozin (IC50 = 4 nM) and luseogliflozin (IC50 = 2.3 nM)) through docking-based virtual screening. Then, the top three hits (ZINC70455591, ZINC85594065 and ZINC14588133) and six known inhibitors were selected for molecular dynamics simulation and the binding free energy calculation using molecular mechanics Poisson-Boltzmann surface area to demonstrate the stability and affinity of docked complexes. These results pointed out that the three docked complexes were stabilized and the chosen compounds were tightly adhering to the binding site of SGLT2. Besides, pharmacokinetic properties of the selected compounds showed those natural compounds may be potential drug candidates. This study may be contributed to further in vitro and in vivo validation and the development of novel SGLT2 inhibitor for treating HF.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jiwu Kong
- Drug Clinical Trial Center, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, China
| | - Ling Li
- Drug Clinical Trial Center, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, China
| | - Huicheng Yuan
- Drug Clinical Trial Center, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, China
| | - Feng Bai
- Drug Clinical Trial Center, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, China
| | - Kai Yang
- Drug Clinical Trial Center, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, China
| | - Liangcun Zhao
- Drug Clinical Trial Center, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, China
| | - Shaohua Xu
- Drug Clinical Trial Center, Gansu Wuwei Tumor Hospital, Wuwei, Gansu, China
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4
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Ortiz de Luzuriaga I, Elleuchi S, Jarraya K, Artacho E, Lopez X, Gil A. Semi-empirical and Linear-Scaling DFT Methods to Characterize duplex DNA and G-quadruplexes in Presence of Interacting Small Molecules. Phys Chem Chem Phys 2022; 24:11510-11519. [DOI: 10.1039/d2cp00214k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The computational study of DNA and its interaction with ligands is a highly relevant area of research, with significant consequences for developing new therapeutic strategies. However, the computational description of...
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Bannwarth C, Caldeweyher E, Ehlert S, Hansen A, Pracht P, Seibert J, Spicher S, Grimme S. Extended
tight‐binding
quantum chemistry methods. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1493] [Citation(s) in RCA: 218] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Christoph Bannwarth
- Department of Chemistry and The PULSE Institute Stanford University Stanford California USA
| | - Eike Caldeweyher
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Philipp Pracht
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Jakob Seibert
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Sebastian Spicher
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry Rheinische Friedrich‐Wilhelms‐Universität Bonn Bonn Germany
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7
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Walters ET, Mohebifar M, Johnson ER, Rowley CN. Evaluating the London Dispersion Coefficients of Protein Force Fields Using the Exchange-Hole Dipole Moment Model. J Phys Chem B 2018; 122:6690-6701. [DOI: 10.1021/acs.jpcb.8b02814] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Evan T. Walters
- Department of Chemistry, Memorial University of Newfoundland, St. John’s A1C 5S7, Newfoundland and Labrador, Canada
| | - Mohamad Mohebifar
- Department of Chemistry, Memorial University of Newfoundland, St. John’s A1C 5S7, Newfoundland and Labrador, Canada
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University, Halifax B3H 4R2, Nova Scotia, Canada
| | - Christopher N. Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John’s A1C 5S7, Newfoundland and Labrador, Canada
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8
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Chen WL, Lin ST. Explicit consideration of spatial hydrogen bonding direction for activity coefficient prediction based on implicit solvation calculations. Phys Chem Chem Phys 2017; 19:20367-20376. [DOI: 10.1039/c7cp02317k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Directional hydrogen bonding is introduced to implicit solvation calculations for improved prediction of solvation properties and phase equilibria of associating fluids.
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Affiliation(s)
- Wei-Lin Chen
- Department of Chemical Engineering
- National Taiwan University
- Taipei 10617
- Taiwan
| | - Shiang-Tai Lin
- Department of Chemical Engineering
- National Taiwan University
- Taipei 10617
- Taiwan
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9
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Yilmazer ND, Korth M. Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods. Int J Mol Sci 2016; 17:ijms17050742. [PMID: 27196893 PMCID: PMC4881564 DOI: 10.3390/ijms17050742] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/18/2016] [Accepted: 05/03/2016] [Indexed: 11/16/2022] Open
Abstract
We review the first successes and failures of a “new wave” of quantum chemistry-based approaches to the treatment of protein/ligand interactions. These approaches share the use of “enhanced”, dispersion (D), and/or hydrogen-bond (H) corrected density functional theory (DFT) or semi-empirical quantum mechanical (SQM) methods, in combination with ensemble weighting techniques of some form to capture entropic effects. Benchmark and model system calculations in comparison to high-level theoretical as well as experimental references have shown that both DFT-D (dispersion-corrected density functional theory) and SQM-DH (dispersion and hydrogen bond-corrected semi-empirical quantum mechanical) perform much more accurately than older DFT and SQM approaches and also standard docking methods. In addition, DFT-D might soon become and SQM-DH already is fast enough to compute a large number of binding modes of comparably large protein/ligand complexes, thus allowing for a more accurate assessment of entropic effects.
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Affiliation(s)
- Nusret Duygu Yilmazer
- Institute for Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89069 Ulm, Germany.
| | - Martin Korth
- Institute for Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89069 Ulm, Germany.
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10
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Abstract
For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied.
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Affiliation(s)
- Tobias Schwabe
- Center for Bioinformatics and Physical Chemistry Institute, University of Hamburg, Bundesstraße 43, D-20146 Hamburg, Germany
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11
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Yilmazer ND, Heitel P, Schwabe T, Korth M. Benchmark of electronic structure methods for protein–ligand interactions based on high-level reference data. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1142/s0219633615400015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The accurate prediction of the strength of protein–ligand interactions is a very difficult problem despite impressive advances in the field of biomolecular modeling. There are good reasons to believe that quantum mechanical methods can help with this task, but the application of such methods in the context of scoring is still in its infancy. Here we benchmark several wave function theory (WFT), density functional theory (DFT) and semiempirical quantum mechanical (SQM) approaches against high-level theoretical references for realistic test cases. Based on our findings for systematically generated model systems of real protein/ligand complexes from the PDB-bind database, we can recommend SCS-MP2 and B2-PLYP-D3 as reference methods, TPSS-D3+Dabc/def-TZVPP as the best DFT approach and PM6-DH+ as a fast and accurate alternative to full ab initio treatments.
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Affiliation(s)
- Nusret Duygu Yilmazer
- Institute for Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89069 Ulm, Germany
| | - Pascal Heitel
- Institute for Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89069 Ulm, Germany
| | - Tobias Schwabe
- Center for Bioinformatics and Institute of Physical Chemistry, University of Hamburg, Bundesstraße 43, 20146 Hamburg, Germany
| | - Martin Korth
- Institute for Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89069 Ulm, Germany
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12
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Yilmazer ND, Korth M. Enhanced semiempirical QM methods for biomolecular interactions. Comput Struct Biotechnol J 2015; 13:169-75. [PMID: 25848495 PMCID: PMC4372622 DOI: 10.1016/j.csbj.2015.02.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 12/21/2022] Open
Abstract
Recent successes and failures of the application of 'enhanced' semiempirical QM (SQM) methods are reviewed in the light of the benefits and backdraws of adding dispersion (D) and hydrogen-bond (H) correction terms. We find that the accuracy of SQM-DH methods for non-covalent interactions is very often reported to be comparable to dispersion-corrected density functional theory (DFT-D), while computation times are about three orders of magnitude lower. SQM-DH methods thus open up a possibility to simulate realistically large model systems for problems both in life and materials science with comparably high accuracy.
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Affiliation(s)
| | - Martin Korth
- Institute of Theoretical Chemistry, Ulm University, D-89069 Ulm, Germany
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13
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Husch T, Yilmazer ND, Balducci A, Korth M. Large-scale virtual high-throughput screening for the identification of new battery electrolyte solvents: computing infrastructure and collective properties. Phys Chem Chem Phys 2015; 17:3394-401. [DOI: 10.1039/c4cp04338c] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A volunteer computing approach is presented for the purpose of screening a large number of molecular structures with respect to their suitability as new battery electrolyte solvents.
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Affiliation(s)
- Tamara Husch
- Institute for Theoretical Chemistry
- Ulm University
- 89069 Ulm
- Germany
| | | | | | - Martin Korth
- Institute for Theoretical Chemistry
- Ulm University
- 89069 Ulm
- Germany
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14
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Grimme S. A General Quantum Mechanically Derived Force Field (QMDFF) for Molecules and Condensed Phase Simulations. J Chem Theory Comput 2014; 10:4497-514. [DOI: 10.1021/ct500573f] [Citation(s) in RCA: 134] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
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15
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Kromann JC, Christensen AS, Steinmann C, Korth M, Jensen JH. A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+. PeerJ 2014; 2:e449. [PMID: 25024918 PMCID: PMC4081274 DOI: 10.7717/peerj.449] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/04/2014] [Indexed: 02/05/2023] Open
Abstract
We present new dispersion and hydrogen bond corrections to the PM6 method, PM6-D3H+, and its implementation in the GAMESS program. The method combines the DFT-D3 dispersion correction by Grimme et al. with a modified version of the H+ hydrogen bond correction by Korth. Overall, the interaction energy of PM6-D3H+ is very similar to PM6-DH2 and PM6-DH+, with RMSD and MAD values within 0.02 kcal/mol of one another. The main difference is that the geometry optimizations of 88 complexes result in 82, 6, 0, and 0 geometries with 0, 1, 2, and 3 or more imaginary frequencies using PM6-D3H+ implemented in GAMESS, while the corresponding numbers for PM6-DH+ implemented in MOPAC are 54, 17, 15, and 2. The PM6-D3H+ method as implemented in GAMESS offers an attractive alternative to PM6-DH+ in MOPAC in cases where the LBFGS optimizer must be used and a vibrational analysis is needed, e.g., when computing vibrational free energies. While the GAMESS implementation is up to 10 times slower for geometry optimizations of proteins in bulk solvent, compared to MOPAC, it is sufficiently fast to make geometry optimizations of small proteins practically feasible.
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Affiliation(s)
| | | | - Casper Steinmann
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , Denmark
| | - Martin Korth
- Institute of Theoretical Chemistry, Ulm University , Germany
| | - Jan H Jensen
- Department of Chemistry, University of Copenhagen , Denmark
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16
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Brandenburg JG, Grimme S. Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB). J Phys Chem Lett 2014; 5:1785-1789. [PMID: 26273854 DOI: 10.1021/jz500755u] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The ambitious goal of organic crystal structure prediction challenges theoretical methods regarding their accuracy and efficiency. Dispersion-corrected density functional theory (DFT-D) in principle is applicable, but the computational demands, for example, to compute a huge number of polymorphs, are too high. Here, we demonstrate that this task can be carried out by a dispersion-corrected density functional tight binding (DFTB) method. The semiempirical Hamiltonian with the D3 correction can accurately and efficiently model both solid- and gas-phase inter- and intramolecular interactions at a speed up of 2 orders of magnitude compared to DFT-D. The mean absolute deviations for interaction (lattice) energies for various databases are typically 2-3 kcal/mol (10-20%), that is, only about two times larger than those for DFT-D. For zero-point phonon energies, small deviations of <0.5 kcal/mol compared to DFT-D are obtained.
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Affiliation(s)
- Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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17
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McKenzie RH, Bekker C, Athokpam B, Ramesh SG. Effect of quantum nuclear motion on hydrogen bonding. J Chem Phys 2014; 140:174508. [DOI: 10.1063/1.4873352] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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18
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Kruse H, Havrila M, Šponer J. QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin–Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches. J Chem Theory Comput 2014; 10:2615-29. [DOI: 10.1021/ct500183w] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Holger Kruse
- CEITEC
− Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
| | - Marek Havrila
- CEITEC
− Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Jiřı́ Šponer
- CEITEC
− Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
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19
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Thiel W. Semiempirical quantum–chemical methods. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1161] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Walter Thiel
- Max‐Planck‐Institut für KohlenforschungMülheimGermany
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20
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Yilmazer ND, Korth M. Comparison of molecular mechanics, semi-empirical quantum mechanical, and density functional theory methods for scoring protein-ligand interactions. J Phys Chem B 2013; 117:8075-84. [PMID: 23758433 DOI: 10.1021/jp402719k] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Correctly ranking protein-ligand interactions with respect to overall free energy of binding is a grand challenge for virtual drug design. Here we compare the performance of various quantum chemical approaches for tackling this so-called "scoring" problem. Relying on systematically generated benchmark sets of large protein/ligand model complexes based on the PDBbind database, we show that the performance depends first of all on the general level of theory. Comparing classical molecular mechanics (MM), semiempirical quantum mechanical (SQM), and density functional theory (DFT) based methods, we find that enhanced SQM approaches perform very similar to DFT methods and substantially different from MM potentials.
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Affiliation(s)
- Nusret Duygu Yilmazer
- Institute for Theoretical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89069 Ulm, Germany
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21
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Wu X, Thiel W, Pezeshki S, Lin H. Specific Reaction Path Hamiltonian for Proton Transfer in Water: Reparameterized Semiempirical Models. J Chem Theory Comput 2013; 9:2672-86. [PMID: 26583861 DOI: 10.1021/ct400224n] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The semiempirical MNDO-based AM1 and PM3 methods and the orthogonalization-corrected OM1, OM2, and OM3 models were reparameterized to improve their description of bulk water and of proton transfer in water. Reference data included the gas-phase geometries and energies of the water molecule, small water clusters, the hydronium ion, and small hydronium ion-water clusters, as well as the gas-phase potential energy surface for proton transfer between the two water molecules in a Zundel ion, all calculated at the MP2/aug-cc-pVTZ level of theory. Combined QM/MM molecular dynamics simulations were carried out for bulk water and for a proton solvated in water using large cluster models. Both the authentic and reparameterized semiempirical models were employed in the simulations. The reparameterization led to significantly better results in all cases. The new set of OM3 parameters gave the best overall results for the structural and dynamic properties of water and the hydrated proton, with a small but finite barrier of 0.1-0.2 kcal/mol in the potential of mean force for proton transfer, in agreement with ab initio path-integral molecular dynamics simulations. The reparameterized OM3 model is expected to be useful for efficient modeling of proton transfer in aqueous solution.
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Affiliation(s)
- Xin Wu
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Soroosh Pezeshki
- Chemistry Department, University of Colorado, Denver , Denver, Colorado 80217, United States
| | - Hai Lin
- Chemistry Department, University of Colorado, Denver , Denver, Colorado 80217, United States
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Sure R, Grimme S. Corrected small basis set Hartree-Fock method for large systems. J Comput Chem 2013; 34:1672-85. [PMID: 23670872 DOI: 10.1002/jcc.23317] [Citation(s) in RCA: 289] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 03/28/2013] [Accepted: 04/03/2013] [Indexed: 01/23/2023]
Abstract
A quantum chemical method based on a Hartree-Fock calculation with a small Gaussian AO basis set is presented. Its main area of application is the computation of structures, vibrational frequencies, and noncovalent interaction energies in huge molecular systems. The method is suggested as a partial replacement of semiempirical approaches or density functional theory (DFT) in particular when self-interaction errors are acute. In order to get accurate results three physically plausible atom pair-wise correction terms are applied for London dispersion interactions (D3 scheme), basis set superposition error (gCP scheme), and short-ranged basis set incompleteness effects. In total nine global empirical parameters are used. This so-called Hartee-Fock-3c (HF-3c) method is tested for geometries of small organic molecules, interaction energies and geometries of noncovalently bound complexes, for supramolecular systems, and protein structures. In the majority of realistic test cases good results approaching large basis set DFT quality are obtained at a tiny fraction of computational cost.
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Affiliation(s)
- Rebecca Sure
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstr. 4, D-53115, Bonn, Germany
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Korth M. Error estimates for (semi-)empirical dispersion terms and large biomacromolecules. Org Biomol Chem 2013; 11:6515-9. [DOI: 10.1039/c3ob41309h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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