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Liu X, Zheng L, Cong Y, Gong Z, Yin Z, Zhang JZH, Liu Z, Sun Z. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant. J Comput Aided Mol Des 2022; 36:879-894. [PMID: 36394776 DOI: 10.1007/s10822-022-00487-w] [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: 08/26/2022] [Accepted: 10/29/2022] [Indexed: 11/18/2022]
Abstract
End-point free energy calculations as a powerful tool have been widely applied in protein-ligand and protein-protein interactions. It is often recognized that these end-point techniques serve as an option of intermediate accuracy and computational cost compared with more rigorous statistical mechanic models (e.g., alchemical transformation) and coarser molecular docking. However, it is observed that this intermediate level of accuracy does not hold in relatively simple and prototypical host-guest systems. Specifically, in our previous work investigating a set of carboxylated-pillar[6]arene host-guest complexes, end-point methods provide free energy estimates deviating significantly from the experimental reference, and the rank of binding affinities is also incorrectly computed. These observations suggest the unsuitability and inapplicability of standard end-point free energy techniques in host-guest systems, and alteration and development are required to make them practically usable. In this work, we consider two ways to improve the performance of end-point techniques. The first one is the PBSA_E regression that varies the weights of different free energy terms in the end-point calculation procedure, while the second one is considering the interior dielectric constant as an additional variable in the end-point equation. By detailed investigation of the calculation procedure and the simulation outcome, we prove that these two treatments (i.e., regression and dielectric constant) are manipulating the end-point equation in a somehow similar way, i.e., weakening the electrostatic contribution and strengthening the non-polar terms, although there are still many detailed differences between these two methods. With the trained end-point scheme, the RMSE of the computed affinities is improved from the standard ~ 12 kcal/mol to ~ 2.4 kcal/mol, which is comparable to another altered end-point method (ELIE) trained with system-specific data. By tuning PBSA_E weighting factors with the host-specific data, it is possible to further decrease the prediction error to ~ 2.1 kcal/mol. These observations along with the extremely efficient optimized-structure computation procedure suggest the regression (i.e., PBSA_E as well as its GBSA_E extension) as a practically applicable solution that brings end-point methods back into the library of usable tools for host-guest binding. However, the dielectric-constant-variable scheme cannot effectively minimize the experiment-calculation discrepancy for absolute binding affinities, but is able to improve the calculation of affinity ranks. This phenomenon is somehow different from the protein-ligand case and suggests the difference between host-guest and biomacromolecular (protein-ligand and protein-protein) systems. Therefore, the spectrum of tools usable for protein-ligand complexes could be unsuitable for host-guest binding, and numerical validations are necessary to screen out really workable solutions in these 'prototypical' situations.
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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
| | - Yalong Cong
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China
| | - Zhihao Gong
- School of Micro-Nano Electronics, Zhejiang University, Hangzhou, 310027, China.,Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China
| | - Zhixiang Yin
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai, 201620, China
| | - John Z H Zhang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China. .,School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China. .,Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China. .,Department of Chemistry, New York University, NY, NY, 10003, USA.
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Zhaoxi Sun
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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Liu X, Zheng L, Qin C, Zhang JZH, Sun Z. Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: I. Standard procedure. J Comput Aided Mol Des 2022; 36:735-752. [PMID: 36136209 DOI: 10.1007/s10822-022-00475-0] [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: 07/06/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
Despite the massive application of end-point free energy methods in protein-ligand and protein-protein interactions, computational understandings about their performance in relatively simple and prototypical host-guest systems are limited. In this work, we present a comprehensive benchmark calculation with standard end-point free energy techniques in a recent host-guest dataset containing 13 host-guest pairs involving the carboxylated-pillar[6]arene host. We first assess the charge schemes for solutes by comparing the charge-produced electrostatics with many ab initio references, in order to obtain a preliminary albeit detailed view of the charge quality. Then, we focus on four modelling details of end-point free energy calculations, including the docking procedure for the generation of initial condition, the charge scheme for host and guest molecules, the water model used in explicit-solvent sampling, and the end-point methods for free energy estimation. The binding thermodynamics obtained with different modelling schemes are compared with experimental references, and some practical guidelines on maximizing the performance of end-point methods in practical host-guest systems are summarized. Further, we compare our simulation outcome with predictions in the grand challenge and discuss further developments to improve the prediction quality of end-point free energy methods. Overall, unlike the widely acknowledged applicability in protein-ligand binding, the standard end-point calculations cannot produce useful outcomes in host-guest binding and thus are not recommended unless alterations are performed.
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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
| | - Chu Qin
- School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai, 201620, China
| | - John Z H Zhang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China.,School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.,Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China.,Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Zhaoxi Sun
- College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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Theoretical prediction of structures and inclusion properties of heteroatom-bridged pillar[n]arenes. Struct Chem 2019. [DOI: 10.1007/s11224-019-01409-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Understanding the structure, reactivity and absorption spectra of borazine doped pillar[5]arene: A DFT study. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Structure, electronic, inclusion complex formation behavior and spectral properties of pillarplex. J INCL PHENOM MACRO 2017. [DOI: 10.1007/s10847-017-0711-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Xiao XD, Shi L, Guo LH, Wang JW, Zhang X. Determination of dopamine hydrochloride by host-guest interaction based on water-soluble pillar[5]arene. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:6-12. [PMID: 27588725 DOI: 10.1016/j.saa.2016.08.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/23/2016] [Accepted: 08/25/2016] [Indexed: 06/06/2023]
Abstract
The supramolecular interaction between the water-soluble pillar[5]arene (WP[5]) as host and dopamine hydrochloride (DH) as guest was studied by spectrofluorometry. The fluorescence intensity of DH gradually decreased with increasing WP[5] concentration, and the possible interaction mechanism between WP[5] and DH was confirmed by 1H NMR, 2D NOESY, and molecular modelling. Based on significant DH fluorescence, a highly sensitive and selective method for DH determination was developed for the first time. The fluorescence intensity was measured at 312nm, with excitation at 285nm. The effects of pH, temperature, and reaction time on the fluorescence spectra of the WP[5]-DH complex were investigated. A linear relationship between fluorescence intensity and DH concentration in the range of 0.07-6.2μgmL-1 was obtained. The corresponding linear regression equation is ΔF=25.76 C+13.56 (where C denotes the concentration in μgmL-1), with the limit of detection equal to 0.03μgmL-1 and the correlation coefficient equal to 0.9996. This method can be used for the determination of dopamine in injection and urine samples. In addition, the WP[5]-DH complex has potential applications in fluorescent sensing and pharmacokinetics studies of DH.
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Affiliation(s)
- Xue-Dong Xiao
- Department of Chemistry, Shanxi Normal University, Linfen 041004, China
| | - Lin Shi
- Department of Chemistry, Shanxi Normal University, Linfen 041004, China
| | - Li-Hui Guo
- Department of Chemistry, Shanxi Normal University, Linfen 041004, China
| | - Jun-Wen Wang
- Department of Chemistry, Shanxi Normal University, Linfen 041004, China.
| | - Xiang Zhang
- Department of Chemistry, Shanxi Normal University, Linfen 041004, China.
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Sahu D, Jana K, Ganguly B. The role of non-covalent interaction for the adsorption of CO2 and hydrocarbons with per-hydroxylated pillar[6]arene: a computational study. NEW J CHEM 2017. [DOI: 10.1039/c7nj01744h] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A systematic study has been performed with DFT calculations for the physisorption of CO2, CH4, and n-butane gases by pillar[6]arene (PA[6]) in gas phase.
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Affiliation(s)
- Debashis Sahu
- Computation and Simulation Unit
- Analytical Discipline & Centralized Instrument Facility, and Academy of Scientific and Innovative Research
- CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar
- India
| | - Kalyanashis Jana
- Computation and Simulation Unit
- Analytical Discipline & Centralized Instrument Facility, and Academy of Scientific and Innovative Research
- CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar
- India
| | - Bishwajit Ganguly
- Computation and Simulation Unit
- Analytical Discipline & Centralized Instrument Facility, and Academy of Scientific and Innovative Research
- CSIR-Central Salt and Marine Chemicals Research Institute
- Bhavnagar
- India
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Bhadane SA, Lande DN, Gejji SP. Understanding Binding of Cyano-Adamantyl Derivatives to Pillar[6]arene Macrocycle from Density Functional Theory. J Phys Chem A 2016; 120:8738-8749. [DOI: 10.1021/acs.jpca.6b08512] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Smita A. Bhadane
- Department of Chemistry, Savitribai Phule Pune University, Pune 411 007, India
| | - Dipali N. Lande
- Department of Chemistry, Savitribai Phule Pune University, Pune 411 007, India
| | - Shridhar P. Gejji
- Department of Chemistry, Savitribai Phule Pune University, Pune 411 007, India
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Xie J, Zuo T, Huang Z, Huan L, Gu Q, Gao C, Shao J. Theoretical study of a novel imino bridged pillar[5]arene derivative. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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DFT/TDDFT investigation on the chemical reactivities, aromatic properties, and UV–Vis absorption spectra of 1-butoxy-4-methoxybenzenepillar[5]arene constitutional isomers. J Mol Model 2016; 22:209. [DOI: 10.1007/s00894-016-3076-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 08/03/2016] [Indexed: 11/25/2022]
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Bhattacharyya PK. Reactivity, aromaticity and absorption spectra of pillar[5]arene conformers: A DFT study. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.05.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Peerannawar SR, Gejji SP. Characterization of structure and 1H NMR of methyl viologen encapsulated noria and substituted noria hosts from density functional theory. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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