Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-guest Binding: I. Standard Procedure

Liu, Xiao; Zheng, Lei; Qin, Chu; Zhang, John Z. H.; Sun, Zhaoxi

doi:10.26434/chemrxiv-2022-6zfjj

Cited by 2 publications

(11 citation statements)

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“…The system construction follows exactly the same protocol used in our previous work. 53 Briefly, the 3D chemical structures of all molecules shown in Fig. 1 are grabbed from the GitHub site of the SAMPL9 challenge.…”

Section: Model Constructionmentioning

confidence: 99%

“…Possible reasons causing the underperformance of end-point calculations in host-guest complex along with further directions for developments have been discussed extensively in our previous work. 53 In the current work, building on previous observations of the standard end-point procedure, we expect to extend the evaluation by considering two altered regimes that could lead to improved performance. Specifically, we consider the regression and dielectric-constant-variable alterations that change the weights of free energy terms in the end-point calculation.…”

mentioning

confidence: 99%

“…In a recent work, we report a thorough evaluation of end-point methods with the standard (popular) procedure in a set of WP6 host-guest systems. 53 Specifically, we consider four modelling details including the scoring function used in docking (two scoring functions), the charge scheme for solutes (three charge sets), the water model for solvation (two water models), and the end-point method used in free energy estimation (two endpoint schemes). The resulting calculation regimes include 24 combinations, covering almost all popular selections in modern researches.…”

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confidence: 99%

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Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant

Liu

Zheng

Cong

et al. 2022

J Comput Aided Mol Des

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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 2 / 41 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. This phenomenon along with the extremely efficient optimized-structure computation procedure suggests 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 proteinprotein) cases. Therefore, the spectrum of tools usable in protein-ligand cases could be unsuitable for hostguest binding, and numerical validations are necessary to screen out really workable solutions in these 'prototypical' situations.

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Section: Model Constructionmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant

Liu

Zheng

Cong

et al. 2022

J Comput Aided Mol Des

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“…The bound structure of each host-guest complex remains unknown, which is often solved via molecular docking. Following our previous work, 53 we use the Autodock Vina 72 program to generate the initial guess, i.e., picking the top-1 (the most stable) structure provided by docking. As the starting configuration could have a significant impact on the simulation outcome, especially when the simulation is performed in an unbiased way.…”

Section: Model Constructionmentioning

confidence: 99%

“…72,74,75 Also, according to the analysis of binding modes produced by the two scoring functions reported in the first paper of this WP6 end-point series, for many host-guest pairs there are obvious structural differences. 53 6 / 41…”

Section: Model Constructionmentioning

confidence: 99%

Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-guest Binding: II. Regression and Dielectric Constant

Liu

Zheng

Cong

et al. 2022

Preprint

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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. This phenomenon along with the extremely efficient optimized-structure computation procedure suggests 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) cases. Therefore, the spectrum of tools usable in protein-ligand cases could be unsuitable for host-guest binding, and numerical validations are necessary to screen out really workable solutions in these ‘prototypical’ situations.

show abstract

Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-guest Binding: I. Standard Procedure

Cited by 2 publications

References 77 publications

Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant

Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant

Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host-guest Binding: II. Regression and Dielectric Constant

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