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Liu X, Zheng L, Qin C, Li Y, Zhang JZH, Sun Z. Screening Power of End-Point Free-Energy Calculations in Cucurbituril Host-Guest Systems. J Chem Inf Model 2023; 63:6938-6946. [PMID: 37908066 DOI: 10.1021/acs.jcim.3c01356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
End-point free-energy methods as an indispensable component in virtual screening are commonly recognized as a tool with a certain level of screening power in pharmaceutical research. While a huge number of records could be found for end-point applications in protein-ligand, protein-protein, and protein-DNA complexes from academic and industrial reports, up to now, there is no large-scale benchmark in host-guest complexes supporting the screening power of end-point free-energy techniques. A good benchmark requires a data set of sufficient coverage of pharmaceutically relevant chemical space, a long-time sampling length supporting the trajectory approximation of the ensemble average, and a sufficient sample size of receptor-acceptor pairs to stabilize the performance statistics. In this work, selecting a popular family of macrocyclic hosts named cucurbiturils, we construct a large data set containing 154 host-guest pairs, perform extensive end-point sampling of several hundred nanosecond lengths for each system, and extract the free-energy estimates with a variety of end-point free-energy techniques, including the advanced three-trajectory dielectric-constant-variable regime proposed in our recent work. The best-performing end-point protocol employs GAFF2 for solute descriptions, the three-trajectory end-point sampling regime, and the MM/GBSA Hamiltonian in free-energy extraction, achieving a high ranking metrics of Kendall τ > 0.6, a Pearlman predictive index of ∼0.8, and a high scoring power of Pearson r > 0.8. The current project as the first large-scale systematic benchmark of end-point methods in host-guest complexes in academic publications provides solid evidence of the applicability of end-point techniques and direct guidance of computational setups in practical host-guest systems.
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Affiliation(s)
- Xiao Liu
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Lei Zheng
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Chu Qin
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Yang Li
- College of Information Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - John Z H Zhang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Department of Chemistry, New York University, New York, New York 10003, United States
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- Faculty of Synthetic Biology and Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen Guangdong 518055, China
| | - Zhaoxi Sun
- Changping Laboratory, Beijing 102206, China
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Unimuke TO, Louis H, Ikenyirimba OJ, Mathias GE, Adeyinka AS, Nasr CB. High throughput computations of the effective removal of liquified gases by novel perchlorate hybrid material. Sci Rep 2023; 13:10837. [PMID: 37407702 DOI: 10.1038/s41598-023-38091-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 07/03/2023] [Indexed: 07/07/2023] Open
Abstract
The utilization of hybrid materials in separation technology, sorbents, direct air capture (DAC) technology, sensors, adsorbents, and chiral material recognition has increased in the past decade due to the recognized impact of atmospheric pollutants and hazardous industrial gases on climate change. A novel hybrid material, perchlorate hybrid (PClH), has been proposed in this study for the effective sensory detection and trapping of atmospheric pollutants and industrial hazardous gases. The study evaluated the structural properties, adsorption mechanism, electronic sensitivity, and topological analysis of PClH using highly accurate computational methods (M062X-D3BJ/def2-ccpVTZ and DSDPBEP86/def2-ccpVTZ). The computational analysis demonstrated that PClH has considerable adsorption energies and favorable interaction with CO2, NO2, SO2, COCl2, and H2S. PClH is more suitable for detecting liquefiable gases such as COCl2, CO2, and SO2, and can be easily recovered under ambient conditions. Developing such materials can contribute to reducing hazardous gases and pollutants in the atmosphere, leading to a cleaner and safer environment.
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Affiliation(s)
- Tomsmith O Unimuke
- Computational and Bio-Simulation Research Group, University of Calabar, P.M.B 1115, Calabar, Nigeria.
- Department of Pure and Applied Chemistry, University of Calabar, P.M.B 1115, Calabar, Nigeria.
| | - Hitler Louis
- Computational and Bio-Simulation Research Group, University of Calabar, P.M.B 1115, Calabar, Nigeria.
- Department of Pure and Applied Chemistry, University of Calabar, P.M.B 1115, Calabar, Nigeria.
| | - Onyinye J Ikenyirimba
- Computational and Bio-Simulation Research Group, University of Calabar, P.M.B 1115, Calabar, Nigeria
| | - Gideon E Mathias
- Computational and Bio-Simulation Research Group, University of Calabar, P.M.B 1115, Calabar, Nigeria
- Department of Pure and Applied Chemistry, University of Calabar, P.M.B 1115, Calabar, Nigeria
| | - Adedapo S Adeyinka
- Department of Chemical Sciences, Research Centre for Synthesis and Catalysis, University of Johannesburg, Johannesburg, 2006, South Africa
| | - Chérif Ben Nasr
- Laboratoire de Chimie des Matériaux, Faculté des Sciences de Bizerte, Université de Carthage, 7021, Zarzouna, Tunisie
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Sun Z, He Q, Gong Z, Kalhor P, Huai Z, Liu Z. A General Picture of Cucurbit[8]uril Host–Guest Binding: Recalibrating Bonded Interactions. Molecules 2023; 28:molecules28073124. [PMID: 37049887 PMCID: PMC10095826 DOI: 10.3390/molecules28073124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/15/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Atomic-level understanding of the dynamic feature of host–guest interactions remains a central challenge in supramolecular chemistry. The remarkable guest binding behavior of the Cucurbiturils family of supramolecular containers makes them promising drug carriers. Among Cucurbit[n]urils, Cucurbit[8]uril (CB8) has an intermediate portal size and cavity volume. It can exploit almost all host–guest recognition motifs formed by this host family. In our previous work, an extensive computational investigation of the binding of seven commonly abused and structurally diverse drugs to the CB8 host was performed, and a general dynamic binding picture of CB8-guest interactions was obtained. Further, two widely used fixed-charge models for drug-like molecules were investigated and compared in great detail, aiming at providing guidelines in choosing an appropriate charge scheme in host-guest modelling. Iterative refitting of atomic charges leads to improved binding thermodynamics and the best root-mean-squared deviation from the experimental reference is 2.6 kcal/mol. In this work, we focus on a thorough evaluation of the remaining parts of classical force fields, i.e., the bonded interactions. The widely used general Amber force fields are assessed and refitted with generalized force-matching to improve the intra-molecular conformational preference, and thus the description of inter-molecular host–guest interactions. The interaction pattern and binding thermodynamics show a significant dependence on the modelling parameters. The refitted system-specific parameter set improves the consistency of the modelling results and the experimental reference significantly. Finally, combining the previous charge-scheme comparison and the current force-field refitting, we provide general guidelines for the theoretical modelling of host–guest binding.
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Xie J, Xi Z, Yang Z, Zhang X, Yuan H, Yang Y, Ni L, He M. Computational Approach to Understanding the Structures, Properties, and Supramolecular Chemistry of Pagoda[n]arenes. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Venkataramanan NS, Suvitha A, Sahara R, Kawazoe Y. Unveiling the gemcitabine drug complexation with cucurbit[n]urils (n = 6–8): a computational analysis. Struct Chem 2023. [DOI: 10.1007/s11224-023-02133-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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The structure, stability, thermochemistry, and bonding in SO3-(H2O)n (n = 1–7) clusters: a computational analysis. Struct Chem 2022. [DOI: 10.1007/s11224-022-02085-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Xie J, Yang Y, Xi Z, Yang Z, Zhang X, Ni L. Cyclized oligomer of tetracyanoquinodimethane-tetrathiafulvalene (TCNQ-TTF): a versatile macrocyclic molecule by DFT calculations. J INCL PHENOM MACRO 2022. [DOI: 10.1007/s10847-022-01156-z] [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]
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Prabhu AAM, Madi F, Leila N, Kumar GSS, Sathiyaseelan K. Structural Aspects and Stability of Interactions between Phenyl-3,3'-Bis(Indolyl)Methanes and β-Cyclodextrin from Density Functional Theory. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2101490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
| | - Fatiha Madi
- Laboratory of Computational Chemistry and Nanostructures, Department of Material Sciences, Faculty of Mathematical, Informatics and Material Sciences, University of 08 Mai 1945, Guelma, Algeria
| | - Nouar Leila
- Laboratory of Computational Chemistry and Nanostructures, Department of Material Sciences, Faculty of Mathematical, Informatics and Material Sciences, University of 08 Mai 1945, Guelma, Algeria
| | - G. S. Suresh Kumar
- Photosciences and Photonics Section, Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, India
| | - K. Sathiyaseelan
- Department of PG Chemistry, Aditanar College of Arts and Science, Tiruchendur, India
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Molecular insights into the complex formation between dodecamethylcucurbit[6]uril and phenylenediamine isomers. J INCL PHENOM MACRO 2022. [DOI: 10.1007/s10847-022-01144-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Pradeep Kumar PS, Sunil K, Chethan BS, Lokanath NK, Madan N, Sajith AM. Synthesis, characterisation, biological and theoretical studies of novel pyridine derivatives. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2093283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- P. S. Pradeep Kumar
- Department of Chemistry, Sri Siddhartha Institute of Technology, SSAHE, Tumakuru, India
| | - K. Sunil
- Department of Chemistry, Sri Siddhartha Institute of Technology, SSAHE, Tumakuru, India
| | - B. S. Chethan
- Department of Studies in Physics, Manasagangotri, University of Mysore, Mysuru, India
| | - N. K. Lokanath
- Department of Studies in Physics, Manasagangotri, University of Mysore, Mysuru, India
| | - N. Madan
- Department of Chemistry, Sri Siddhartha Institute of Technology, SSAHE, Tumakuru, India
| | - A. M. Sajith
- Department of Chemistry, Sri Siddhartha Institute of Technology, SSAHE, Tumakuru, India
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Chethan B, Lokanath N. Study of the crystal structure, H-bonding and noncovalent interactions of novel cocrystal by systematic computational search approach. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Cao Y, Farahmand M, Fosshat S, Rezaei S, Pourmomen Arabi L, Liu P. Potential of aluminum nitride nanocone as a chemical sensor for anticancer drug detection. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2021.113537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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Sun Z, Huai Z, He Q, Liu Z. A General Picture of Cucurbit[8]uril Host-Guest Binding. J Chem Inf Model 2021; 61:6107-6134. [PMID: 34818004 DOI: 10.1021/acs.jcim.1c01208] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Describing, understanding, and designing complex interaction networks within macromolecular systems remain challenging in modern chemical research. Host-guest systems, despite their relative simplicity in both the structural feature and interaction patterns, still pose problems in theoretical modeling. The barrel-shaped supramolecular container cucurbit[8]uril (CB8) shows promising functionalities in various areas, e.g., catalysis and molecular recognition. It can stably coordinate a series of structurally diverse guests with high affinities. In this work, we examine the binding of seven commonly abused drugs to the CB8 host, aiming at providing a general picture of CB8-guest binding. Extensive sampling of the configurational space of these host-guest systems is performed, and the binding pathway and interaction patterns of CB8-guest complexes are investigated. A thorough comparison of widely used fixed-charge models for drug-like molecules is presented. Iterative refitting of the atomic charges suggests significant conformation dependence of charge generation. The initial model generated at the original conformation could be inaccurate for new conformations explored during conformational search, and the newly fitted charge set improves the prediction-experiment correlation significantly. Our investigations of the configurational space of CB8-drug complexes suggest that the host-guest interactions are more complex than expected. Despite the structural simplicities of these molecules, the conformational fluctuations of the host and the guest molecules and orientations of functional groups lead to the existence of an ensemble of binding modes. The insights of the binding thermodynamics, performance of fixed-charge models, and binding patterns of the CB8-guest systems are useful for studying and elucidating the binding mechanism of other host-guest complexes.
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Affiliation(s)
- Zhaoxi Sun
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhe Huai
- XtalPi-AI Research Center (XARC), 9F, Tower A, Dongsheng Building, No. 8, Zhongguancun East Road, Haidian District, Beijing 100083, P.R. China
| | - Qiaole He
- AI Department of Enzymaster (Ningbo) Bio-Engineering Co., Ltd., North Century Avenue 333, Ningbo 315100, China
| | - Zhirong Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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A computational study on the complexation of bisbenzimidazolyl derivatives with cucurbituril and cyclohexylcucurbituril. J INCL PHENOM MACRO 2021. [DOI: 10.1007/s10847-021-01078-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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