1
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Martí-Centelles V, Piskorz TK, Duarte F. CageCavityCalc ( C3): A Computational Tool for Calculating and Visualizing Cavities in Molecular Cages. J Chem Inf Model 2024; 64:5604-5616. [PMID: 38980812 PMCID: PMC11267575 DOI: 10.1021/acs.jcim.4c00355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/05/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024]
Abstract
Organic(porous) and metal-organic cages are promising biomimetic platforms with diverse applications spanning recognition, sensing, and catalysis. The key to the emergence of these functions is the presence of well-defined inner cavities capable of binding a wide range of guest molecules and modulating their properties. However, despite the myriad cage architectures currently available, the rational design of structurally diverse and functional cages with specific host-guest properties remains challenging. Efficiently predicting such properties is critical for accelerating the discovery of novel functional cages. Herein, we introduce CageCavityCalc (C3), a Python-based tool for calculating the cavity size of molecular cages. The code is available on GitHub at https://github.com/VicenteMartiCentelles/CageCavityCalc. C3 utilizes a novel algorithm that enables the rapid calculation of cavity sizes for a wide range of molecular structures and porous systems. Moreover, C3 facilitates easy visualization of the computed cavity size alongside hydrophobic and electrostatic potentials, providing insights into host-guest interactions within the cage. Furthermore, the calculated cavity can be visualized using widely available visualization software, such as PyMol, VMD, or ChimeraX. To enhance user accessibility, a PyMol plugin has been created, allowing nonspecialists to use this tool without requiring computer programming expertise. We anticipate that the deployment of this computational tool will significantly streamline cage cavity calculations, thereby accelerating the discovery of functional cages.
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Affiliation(s)
- Vicente Martí-Centelles
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Camino de Vera s/n, Valencia 46022, Spain
- CIBER
de Bioingeniería Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid 28029, Spain
- Departamento
de Química, Universitat Politècnica
de València, Camino de Vera
s/n, Valencia 46022, Spain
| | - Tomasz K. Piskorz
- Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Fernanda Duarte
- Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
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2
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Amezcua M, Setiadi J, Ge Y, Mobley DL. An overview of the SAMPL8 host-guest binding challenge. J Comput Aided Mol Des 2022; 36:707-734. [PMID: 36229622 PMCID: PMC9596595 DOI: 10.1007/s10822-022-00462-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022]
Abstract
The SAMPL series of challenges aim to focus the community on specific modeling challenges, while testing and hopefully driving progress of computational methods to help guide pharmaceutical drug discovery. In this study, we report on the results of the SAMPL8 host–guest blind challenge for predicting absolute binding affinities. SAMPL8 focused on two host–guest datasets, one involving the cucurbituril CB8 (with a series of common drugs of abuse) and another involving two different Gibb deep-cavity cavitands. The latter dataset involved a previously featured deep cavity cavitand (TEMOA) as well as a new variant (TEETOA), both binding to a series of relatively rigid fragment-like guests. Challenge participants employed a reasonably wide variety of methods, though many of these were based on molecular simulations, and predictive accuracy was mixed. As in some previous SAMPL iterations (SAMPL6 and SAMPL7), we found that one approach to achieve greater accuracy was to apply empirical corrections to the binding free energy predictions, taking advantage of prior data on binding to these hosts. Another approach which performed well was a hybrid MD-based approach with reweighting to a force matched QM potential. In the cavitand challenge, an alchemical method using the AMOEBA-polarizable force field achieved the best success with RMSE less than 1 kcal/mol, while another alchemical approach (ATM/GAFF2-AM1BCC/TIP3P/HREM) had RMSE less than 1.75 kcal/mol. The work discussed here also highlights several important lessons; for example, retrospective studies of reference calculations demonstrate the sensitivity of predicted binding free energies to ethyl group sampling and/or guest starting pose, providing guidance to help improve future studies on these systems.
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Affiliation(s)
- Martin Amezcua
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Jeffry Setiadi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yunhui Ge
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA. .,Department of Chemistry, University of California, Irvine, CA, 92697, USA.
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3
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González D, Macaya L, Castillo-Orellana C, Verstraelen T, Vogt-Geisse S, Vöhringer-Martinez E. Nonbonded Force Field Parameters from Minimal Basis Iterative Stockholder Partitioning of the Molecular Electron Density Improve CB7 Host-Guest Affinity Predictions. J Chem Inf Model 2022; 62:4162-4174. [PMID: 35959540 DOI: 10.1021/acs.jcim.2c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Binding affinity prediction by means of computer simulation has been increasingly incorporated in drug discovery projects. Its wide application, however, is limited by the prediction accuracy of the free energy calculations. The main error sources are force fields used to describe molecular interactions and incomplete sampling of the configurational space. Organic host-guest systems have been used to address force field quality because they share similar interactions found in ligands and receptors, and their rigidity facilitates configurational sampling. Here, we test the binding free energy prediction accuracy for 14 guests with an aromatic or adamantane core and the CB7 host using molecular electron density derived nonbonded force field parameters. We developed a computational workflow written in Python to derive atomic charges and Lennard-Jones parameters with the Minimal Basis Iterative Stockholder method using the polarized electron density of several configurations of each guest in the bound and unbound states. The resulting nonbonded force field parameters improve binding affinity prediction, especially for guests with an adamantane core in which repulsive exchange and dispersion interactions to the host dominate.
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Affiliation(s)
- Duván González
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
| | - Luis Macaya
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
| | - Carlos Castillo-Orellana
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
| | - Toon Verstraelen
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark-Zwijnnarde 46, B-9052 Ghent, Belgium
| | - Stefan Vogt-Geisse
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070386 Concepción, Chile
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4
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Grimm LM, Spicher S, Tkachenko B, Schreiner PR, Grimme S, Biedermann F. The Role of Packing, Dispersion, Electrostatics, and Solvation in High-Affinity Complexes of Cucurbit[n]urils with Uncharged Polar Guests. Chemistry 2022; 28:e202200529. [PMID: 35612260 PMCID: PMC9401061 DOI: 10.1002/chem.202200529] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Indexed: 12/21/2022]
Abstract
The rationalization of non-covalent binding trends is both of fundamental interest and provides new design concepts for biomimetic molecular systems. Cucurbit[n]urils (CBn) are known for a long time as the strongest synthetic binders for a wide range of (bio)organic compounds in water. However, their host-guest binding mechanism remains ambiguous despite their symmetric and simple macrocyclic structure and the wealth of literature reports. We herein report experimental thermodynamic binding parameters (ΔG, ΔH, TΔS) for CB7 and CB8 with a set of hydroxylated adamantanes, di-, and triamantanes as uncharged, rigid, and spherical/ellipsoidal guests. Binding geometries and binding energy decomposition were obtained from high-level theory computations. This study reveals that neither London dispersion interactions, nor electronic energies or entropic factors are decisive, selectivity-controlling factors for CBn complexes. In contrast, peculiar host-related solvation effects were identified as the major factor for rationalizing the unique behavior and record-affinity characteristics of cucurbit[n]urils.
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Affiliation(s)
- Laura M. Grimm
- Institute of NanotechnologyKarlsruhe Institute of TechnologyHermann-von-Helmholtz Platz 176344Eggenstein-LeopoldshafenGermany
| | - Sebastian Spicher
- Mulliken Center for Theoretical ChemistryInstitute of Physical and Theoretical ChemistryUniversity of BonnBeringstraße 453115BonnGermany
| | - Boryslav Tkachenko
- Institute of Organic ChemistryJustus Liebig UniversityHeinrich-Buff-Ring 1735392GiessenGermany
| | - Peter R. Schreiner
- Institute of Organic ChemistryJustus Liebig UniversityHeinrich-Buff-Ring 1735392GiessenGermany
| | - Stefan Grimme
- Mulliken Center for Theoretical ChemistryInstitute of Physical and Theoretical ChemistryUniversity of BonnBeringstraße 453115BonnGermany
| | - Frank Biedermann
- Institute of NanotechnologyKarlsruhe Institute of TechnologyHermann-von-Helmholtz Platz 176344Eggenstein-LeopoldshafenGermany
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5
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Zhou S, Zhang Y, Cheng LT, Li B. Prediction of multiple dry-wet transition pathways with a mesoscale variational approach. J Chem Phys 2021; 155:124110. [PMID: 34598586 DOI: 10.1063/5.0061773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water fluctuates in a hydrophobic confinement, forming multiple dry and wet hydration states through evaporation and condensation. Transitions between such states are critical to both thermodynamics and kinetics of solute molecular processes, such as protein folding and protein-ligand binding and unbinding. To efficiently predict such dry-wet transition paths, we develop a hybrid approach that combines a variational implicit solvation model, a generalized string method for minimum free-energy paths, and the level-set numerical implementation. This approach is applied to three molecular systems: two hydrophobic plates, a carbon nanotube, and a synthetic host molecule Cucurbit[7]uril. Without an explicit description of individual water molecules, our mesoscale approach effectively captures multiple dry and wet hydration states, multiple dry-wet transition paths, such as those geometrically symmetric and asymmetric paths, and transition states, providing activation energy barriers between different states. Further analysis shows that energy barriers depend on mesoscopic lengths, such as the separation distance between the two plates and the cross section diameter of the nanotube, and that the electrostatic interactions strongly influence the dry-wet transitions. With the inclusion of solute atomic motion, general collective variables as reaction coordinates, and the finite-temperature string method, together with an improved treatment of continuum electrostatics, our approach can be further developed to sample an ensemble of transition paths, providing more accurate predictions of the transition kinetics.
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Affiliation(s)
- Shenggao Zhou
- School of Mathematical Sciences and MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanan Zhang
- School of Mathematical Sciences, Soochow University, Suzhou 215006, China
| | - Li-Tien Cheng
- Department of Mathematics, University of California San Diego, La Jolla, California 92093-0112, USA
| | - Bo Li
- Department of Mathematics, University of California San Diego, La Jolla, California 92093-0112, USA
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6
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Prediction of local thermodynamics of water in and around endo-functionalized molecular tube receptors: An approach using grid inhomogeneous solvation theory. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Abstract
The fast and accurate calculation of standard binding free energy has many important applications. Existing methodologies struggle at balancing accuracy and efficiency. We introduce a new method to compute binding free energy using deep generative models and the Bennett acceptance ratio method (DeepBAR). Compared to the rigorous potential of mean force (PMF) approach that requires sampling from intermediate states, DeepBAR is an order-of-magnitude more efficient as demonstrated in a series of host-guest systems. Notably, DeepBAR is exact and does not suffer from approximations for entropic contributions used in methods such as the molecular mechanics energy combined with the generalized Born and surface area continuum solvation (MM/GBSA). We anticipate DeepBAR to be a valuable tool for computing standard binding free energy used in drug design.
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Affiliation(s)
- Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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8
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Çınaroğlu SS, Biggin PC. Evaluating the Performance of Water Models with Host-Guest Force Fields in Binding Enthalpy Calculations for Cucurbit[7]uril-Guest Systems. J Phys Chem B 2021; 125:1558-1567. [PMID: 33538161 DOI: 10.1021/acs.jpcb.0c11383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computational prediction of thermodynamic components with computational methods has become increasingly routine in computer-aided drug design. Although there has been significant recent effort and improvements in the calculation of free energy, the prediction of enthalpy (and entropy) remains underexplored. Furthermore, there has been relatively little work reported so far that attempts to comparatively assess how well different force fields and water models perform in conjunction with each other. Here, we report a comprehensive assessment of force fields and water models using host-guest systems that mimic many features of protein-ligand systems. These systems are computationally inexpensive, possibly because of their small size compared to protein-ligand systems. We present absolute enthalpy calculations using the multibox approach on a set of 25 cucurbit[7]uril-guest pairs. Eight water models were considered (TIP3P, TIP4P, TIP4P-Ew, SPC, SPC/E, OPC, TIP5P, Bind3P), along with five force fields commonly used in the literature (GAFFv1, GAFFv2, CGenFF, Parsley, and SwissParam). We observe that host-guest binding enthalpies are strongly sensitive to the selection of force field and water model. In terms of water models, we find that TIP3P and its derivative Bind3P are the best performing models for this particular host-guest system. The performance is generally better for aliphatic compounds than for aromatic ones, suggesting that aromaticity remains a difficult property to include accurately in these simple force fields.
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Affiliation(s)
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
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9
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Fianchini M, Llorens L, Pericàs MA. Separating Enthalpic, Configurational, and Solvation Entropic Components in Host-Guest Binding: Application to Cucurbit[7]uril Complexes through a Full In Silico Approach via Water Nanodroplets. J Phys Chem B 2020; 124:10486-10499. [PMID: 33166142 DOI: 10.1021/acs.jpcb.0c08507] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cucurbiturils are a family of supramolecular hosts obtained by condensation of glycoluril and formaldehyde. Cucurbit[7]uril, CB[7], is the most prominent member of the family for its biomolecular interest, arising from its mild solubility in water and for its strong binding with a large variety of guests containing nonpolar fragments such as adamantanes and ferrocene. For instance, CB[7] encapsulates diamantane diammonium iodide with an attomolar dissociation constant, a value unmatched even in natural encapsulation processes. Computational chemistry has been extensively employed to describe the enthalpic-entropic compensation principle of the molecular recognition process of cucurbituril hosts, but the synergistic contribution of experimental data is required for accurate results to be obtained. This paper proposes the first fully theoretical model able to reconcile the calculated thermodynamics of the complexation process with the experimental data obtained by calorimetry (ITC) for cucurbit[7]uril. The model allows the isolation and estimation of all of the enthalpic and entropic contributions coming from solute and solvent alike to the whole host-guest binding event and enables the straightforward calculation of the contribution of the solvation entropy to the binding.
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Affiliation(s)
- Mauro Fianchini
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avgda Països Catalans, 16, 43007 Tarragona, Catalonia, Spain
| | - Lluis Llorens
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avgda Països Catalans, 16, 43007 Tarragona, Catalonia, Spain.,Departament de Química Inorgànica i Orgànica, Universitat de Barcelona (UB), 08028 Barcelona, Catalonia, Spain
| | - Miquel A Pericàs
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Avgda Països Catalans, 16, 43007 Tarragona, Catalonia, Spain.,Departament de Química Inorgànica i Orgànica, Universitat de Barcelona (UB), 08028 Barcelona, Catalonia, Spain
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10
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Tosstorff A, Cole JC, Taylor R, Harris SF, Kuhn B. Identification of Noncompetitive Protein–Ligand Interactions for Structural Optimization. J Chem Inf Model 2020; 60:6595-6611. [DOI: 10.1021/acs.jcim.0c00858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Andreas Tosstorff
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Jason C. Cole
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Robin Taylor
- Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, U.K
| | - Seth F. Harris
- Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Bernd Kuhn
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
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11
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Wang E, Liu H, Wang J, Weng G, Sun H, Wang Z, Kang Y, Hou T. Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein–Ligand Binding Affinities. J Chem Inf Model 2020; 60:5353-5365. [DOI: 10.1021/acs.jcim.0c00024] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Hui Liu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Gaoqi Weng
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Yu Kang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
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12
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Sulimov VB, Kutov DC, Sulimov AV. Advances in Docking. Curr Med Chem 2020; 26:7555-7580. [PMID: 30182836 DOI: 10.2174/0929867325666180904115000] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 07/04/2018] [Accepted: 07/06/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Design of small molecules which are able to bind to the protein responsible for a disease is the key step of the entire process of the new medicine discovery. Atomistic computer modeling can significantly improve effectiveness of such design. The accurate calculation of the free energy of binding a small molecule (a ligand) to the target protein is the most important problem of such modeling. Docking is one of the most popular molecular modeling methods for finding ligand binding poses in the target protein and calculating the protein-ligand binding energy. This energy is used for finding the most active compounds for the given target protein. This short review aims to give a concise description of distinctive features of docking programs focusing on computation methods and approximations influencing their accuracy. METHODS This review is based on the peer-reviewed research literature including author's own publications. The main features of several representative docking programs are briefly described focusing on their characteristics influencing docking accuracy: force fields, energy calculations, solvent models, algorithms of the best ligand pose search, global and local optimizations, ligand and target protein flexibility, and the simplifications made for the docking accelerating. Apart from other recent reviews focused mainly on the performance of different docking programs, in this work, an attempt is made to extract the most important functional characteristics defining the docking accuracy. Also a roadmap for increasing the docking accuracy is proposed. This is based on the new generation of docking programs which have been realized recently. These programs and respective new global optimization algorithms are described shortly. RESULTS Several popular conventional docking programs are considered. Their search of the best ligand pose is based explicitly or implicitly on the global optimization problem. Several algorithms are used to solve this problem, and among them, the heuristic genetic algorithm is distinguished by its popularity and an elaborate design. All conventional docking programs for their acceleration use the preliminary calculated grids of protein-ligand interaction potentials or preferable points of protein and ligand conjugation. These approaches and commonly used fitting parameters restrict strongly the docking accuracy. Solvent is considered in exceedingly simplified approaches in the course of the global optimization and the search for the best ligand poses. More accurate approaches on the base of implicit solvent models are used frequently for more careful binding energy calculations after docking. The new generation of docking programs are developed recently. They find the spectrum of low energy minima of a protein-ligand complex including the global minimum. These programs should be more accurate because they do not use a preliminary calculated grid of protein-ligand interaction potentials and other simplifications, the energy of any conformation of the molecular system is calculated in the frame of a given force field and there are no fitting parameters. A new docking algorithm is developed and fulfilled specially for the new docking programs. This algorithm allows docking a flexible ligand into a flexible protein with several dozen mobile atoms on the base of the global energy minimum search. Such docking results in improving the accuracy of ligand positioning in the docking process. The adequate choice of the method of molecular energy calculations also results in the better docking positioning accuracy. An advancement in the application of quantum chemistry methods to docking and scoring is revealed. CONCLUSION The findings of this review confirm the great demand in docking programs for discovery of new medicine substances with the help of molecular modeling. New trends in docking programs design are revealed. These trends are focused on the increase of the docking accuracy at the expense of more accurate molecular energy calculations without any fitting parameters, including quantum-chemical methods and implicit solvent models, and by using new global optimization algorithms which make it possible to treat flexibility of ligands and mobility of protein atoms simultaneously. Finally, it is shown that all the necessary prerequisites for increasing the docking accuracy can be accomplished in practice.
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Affiliation(s)
- Vladimir B Sulimov
- Dimonta, Ltd., Nagornaya Street 15, Building 8, 117186 Moscow, Russian Federation.,Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, 119991 Moscow, Russian Federation
| | - Danil C Kutov
- Dimonta, Ltd., Nagornaya Street 15, Building 8, 117186 Moscow, Russian Federation.,Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, 119991 Moscow, Russian Federation
| | - Alexey V Sulimov
- Dimonta, Ltd., Nagornaya Street 15, Building 8, 117186 Moscow, Russian Federation.,Research Computer Center, Moscow State University, Leninskie Gory 1, Building 4, 119991 Moscow, Russian Federation
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13
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Lübtow MM, Haider MS, Kirsch M, Klisch S, Luxenhofer R. Like Dissolves Like? A Comprehensive Evaluation of Partial Solubility Parameters to Predict Polymer-Drug Compatibility in Ultrahigh Drug-Loaded Polymer Micelles. Biomacromolecules 2019; 20:3041-3056. [PMID: 31318531 DOI: 10.1021/acs.biomac.9b00618] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Despite decades of research, our understanding of the molecular interactions between drugs and polymers in drug-loaded polymer micelles does not extend much beyond concepts such as "like-dissolves-like" or hydrophilic/hydrophobic. However, polymer-drug compatibility strongly affects formulation properties and therefore the translation of a formulation into the clinics. Specific interactions such as hydrogen-bonding, π-π stacking, or coordination interactions can be utilized to increase drug loading. This is commonly based on trial and error and eventually leads to an optimized drug carrier. Unfortunately, due to the unique characteristics of each drug, the deduction of advanced general concepts remains challenging. Furthermore, the introduction of complex moieties or specifically modified polymers hampers systematic investigations regarding polymer-drug compatibility as well as clinical translation. In this study, we reduced the complexity to isolate the crucial factors determining drug loading. Therefore, the compatibility of 18 different amphiphilic polymers for five different hydrophobic drugs was determined empirically. Subsequently, the obtained specificities were compared to theoretical compatibilities derived from either the Flory-Huggins interaction parameters or the Hansen solubility parameters. In general, the Flory-Huggins interaction parameters were less suited to correctly estimate the experimental drug solubilization compared to the Hansen solubility parameters. The latter were able to correctly predict some trend regarding good and poor solubilizers, yet the overall predictive strength of Hansen solubility parameters is clearly unsatisfactory.
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Affiliation(s)
- Michael M Lübtow
- Functional Polymer Materials, Chair for Advanced Materials Synthesis, Department of Chemistry and Pharmacy and Bavarian Polymer Institute , University of Würzburg , Röntgenring 11 , 97070 Würzburg , Germany
| | - Malik Salman Haider
- Functional Polymer Materials, Chair for Advanced Materials Synthesis, Department of Chemistry and Pharmacy and Bavarian Polymer Institute , University of Würzburg , Röntgenring 11 , 97070 Würzburg , Germany
| | - Marius Kirsch
- Functional Polymer Materials, Chair for Advanced Materials Synthesis, Department of Chemistry and Pharmacy and Bavarian Polymer Institute , University of Würzburg , Röntgenring 11 , 97070 Würzburg , Germany
| | - Stefanie Klisch
- Functional Polymer Materials, Chair for Advanced Materials Synthesis, Department of Chemistry and Pharmacy and Bavarian Polymer Institute , University of Würzburg , Röntgenring 11 , 97070 Würzburg , Germany
| | - Robert Luxenhofer
- Functional Polymer Materials, Chair for Advanced Materials Synthesis, Department of Chemistry and Pharmacy and Bavarian Polymer Institute , University of Würzburg , Röntgenring 11 , 97070 Würzburg , Germany
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14
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Venkataramanan NS, Suvitha A, Sahara R. Structure, stability, and nature of bonding between high energy water clusters confined inside cucurbituril: A computational study. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2018.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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15
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Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD. Overview of the SAMPL6 host-guest binding affinity prediction challenge. J Comput Aided Mol Des 2018; 32:937-963. [PMID: 30415285 PMCID: PMC6301044 DOI: 10.1007/s10822-018-0170-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/07/2018] [Indexed: 10/27/2022]
Abstract
Accurately predicting the binding affinities of small organic molecules to biological macromolecules can greatly accelerate drug discovery by reducing the number of compounds that must be synthesized to realize desired potency and selectivity goals. Unfortunately, the process of assessing the accuracy of current computational approaches to affinity prediction against binding data to biological macromolecules is frustrated by several challenges, such as slow conformational dynamics, multiple titratable groups, and the lack of high-quality blinded datasets. Over the last several SAMPL blind challenge exercises, host-guest systems have emerged as a practical and effective way to circumvent these challenges in assessing the predictive performance of current-generation quantitative modeling tools, while still providing systems capable of possessing tight binding affinities. Here, we present an overview of the SAMPL6 host-guest binding affinity prediction challenge, which featured three supramolecular hosts: octa-acid (OA), the closely related tetra-endo-methyl-octa-acid (TEMOA), and cucurbit[8]uril (CB8), along with 21 small organic guest molecules. A total of 119 entries were received from ten participating groups employing a variety of methods that spanned from electronic structure and movable type calculations in implicit solvent to alchemical and potential of mean force strategies using empirical force fields with explicit solvent models. While empirical models tended to obtain better performance than first-principle methods, it was not possible to identify a single approach that consistently provided superior results across all host-guest systems and statistical metrics. Moreover, the accuracy of the methodologies generally displayed a substantial dependence on the system considered, emphasizing the need for host diversity in blind evaluations. Several entries exploited previous experimental measurements of similar host-guest systems in an effort to improve their physical-based predictions via some manner of rudimentary machine learning; while this strategy succeeded in reducing systematic errors, it did not correspond to an improvement in statistical correlation. Comparison to previous rounds of the host-guest binding free energy challenge highlights an overall improvement in the correlation obtained by the affinity predictions for OA and TEMOA systems, but a surprising lack of improvement regarding root mean square error over the past several challenge rounds. The data suggests that further refinement of force field parameters, as well as improved treatment of chemical effects (e.g., buffer salt conditions, protonation states), may be required to further enhance predictive accuracy.
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Affiliation(s)
- Andrea Rizzi
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, 10065, USA
| | - Steven Murkli
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - John N McNeill
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Wei Yao
- Department of Chemistry, Tulane University, Louisiana, LA, 70118, USA
| | - Matthew Sullivan
- Department of Chemistry, Tulane University, Louisiana, LA, 70118, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Michael W Chiu
- Qualcomm Institute, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Bruce C Gibb
- Department of Chemistry, Tulane University, Louisiana, LA, 70118, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, California, 92697, USA.
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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16
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Caldararu O, Olsson MA, Misini Ignjatović M, Wang M, Ryde U. Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods. J Comput Aided Mol Des 2018; 32:1027-1046. [PMID: 30203229 DOI: 10.1007/s10822-018-0158-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 08/31/2018] [Indexed: 01/15/2023]
Abstract
We have estimated free energies for the binding of eight carboxylate ligands to two variants of the octa-acid deep-cavity host in the SAMPL6 blind-test challenge (with or without endo methyl groups on the four upper-rim benzoate groups, OAM and OAH, respectively). We employed free-energy perturbation (FEP) for relative binding energies at the molecular mechanics (MM) and the combined quantum mechanical (QM) and MM (QM/MM) levels, the latter obtained with the reference-potential approach with QM/MM sampling for the MM → QM/MM FEP. The semiempirical QM method PM6-DH+ was employed for the ligand in the latter calculations. Moreover, binding free energies were also estimated from QM/MM optimised structures, combined with COSMO-RS estimates of the solvation energy and thermostatistical corrections from MM frequencies. They were performed at the PM6-DH+ level of theory with the full host and guest molecule in the QM system (and also four water molecules in the geometry optimisations) for 10-20 snapshots from molecular dynamics simulations of the complex. Finally, the structure with the lowest free energy was recalculated using the dispersion-corrected density-functional theory method TPSS-D3, for both the structure and the energy. The two FEP approaches gave similar results (PM6-DH+/MM slightly better for OAM), which were among the five submissions with the best performance in the challenge and gave the best results without any fit to data from the SAMPL5 challenge, with mean absolute deviations (MAD) of 2.4-5.2 kJ/mol and a correlation coefficient (R2) of 0.77-0.93. This is the first time QM/MM approaches give binding free energies that are competitive to those obtained with MM for the octa-acid host. The QM/MM-optimised structures gave somewhat worse performance (MAD = 3-8 kJ/mol and R2 = 0.1-0.9), but the results were improved compared to previous studies of this system with similar methods.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden
| | - Martin A Olsson
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden
| | - Majda Misini Ignjatović
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden
| | - Meiting Wang
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, 221 00, Lund, Sweden.
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17
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Mehranfar A, Izadyar M. Theoretical evaluation of symmetrical α,α′,δ,δ′-tetramethyl cucurbit[6]uril for haloalkane 1-(3-chlorophenyl)-4-(3-chloropropyl)-piperazinium and chloroform encapsulation. J INCL PHENOM MACRO 2018. [DOI: 10.1007/s10847-018-0820-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Sager CP, Fiege B, Zihlmann P, Vannam R, Rabbani S, Jakob RP, Preston RC, Zalewski A, Maier T, Peczuh MW, Ernst B. The price of flexibility - a case study on septanoses as pyranose mimetics. Chem Sci 2017; 9:646-654. [PMID: 29629131 PMCID: PMC5868388 DOI: 10.1039/c7sc04289b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/07/2017] [Indexed: 12/22/2022] Open
Abstract
Seven-membered ring mimetics of mannose were studied as ligands for the mannose-specific bacterial lectin FimH, which plays an essential role in the first step of urinary tract infections (UTI). A competitive binding assay and isothermal titration calorimetry (ITC) experiments indicated an approximately ten-fold lower affinity for the seven-membered ring mannose mimetic 2-O-n-heptyl-1,6-anhydro-d-glycero-d-galactitol (7) compared to n-heptyl α-d-mannopyranoside (2), resulting exclusively from a loss of conformational entropy. Investigations by solution NMR, X-ray crystallography, and molecular modeling revealed that 7 establishes a superimposable H-bond network compared to mannoside 2, but at the price of a high entropic penalty due to the loss of its pronounced conformational flexibility. These results underscore the importance of having access to the complete thermodynamic profile of a molecular interaction to "rescue" ligands from entropic penalties with an otherwise perfect fit to the protein binding site.
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Affiliation(s)
- Christoph P Sager
- University of Basel , Institute of Molecular Pharmacy , Pharmacenter of the University of Basel , Klingelbergstrasse 50 , 4056 , Basel , Switzerland .
| | - Brigitte Fiege
- University of Basel , Institute of Molecular Pharmacy , Pharmacenter of the University of Basel , Klingelbergstrasse 50 , 4056 , Basel , Switzerland .
| | - Pascal Zihlmann
- University of Basel , Institute of Molecular Pharmacy , Pharmacenter of the University of Basel , Klingelbergstrasse 50 , 4056 , Basel , Switzerland .
| | - Raghu Vannam
- Department of Chemistry , University of Connecticut , 55 N. Eagleville Road U3060, Storrs , CT , 06279 USA .
| | - Said Rabbani
- University of Basel , Institute of Molecular Pharmacy , Pharmacenter of the University of Basel , Klingelbergstrasse 50 , 4056 , Basel , Switzerland .
| | - Roman P Jakob
- University of Basel , Biozentrum: Focal Area Structural Biology , Klingelbergstrasse 70 , 4056 Basel , Switzerland
| | - Roland C Preston
- University of Basel , Institute of Molecular Pharmacy , Pharmacenter of the University of Basel , Klingelbergstrasse 50 , 4056 , Basel , Switzerland .
| | - Adam Zalewski
- University of Basel , Institute of Molecular Pharmacy , Pharmacenter of the University of Basel , Klingelbergstrasse 50 , 4056 , Basel , Switzerland .
| | - Timm Maier
- University of Basel , Biozentrum: Focal Area Structural Biology , Klingelbergstrasse 70 , 4056 Basel , Switzerland
| | - Mark W Peczuh
- Department of Chemistry , University of Connecticut , 55 N. Eagleville Road U3060, Storrs , CT , 06279 USA .
| | - Beat Ernst
- University of Basel , Institute of Molecular Pharmacy , Pharmacenter of the University of Basel , Klingelbergstrasse 50 , 4056 , Basel , Switzerland .
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19
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Sommer F, Marcus Y, Kubik S. Effects of Solvent Properties on the Anion Binding of Neutral Water-Soluble Bis(cyclopeptides) in Water and Aqueous Solvent Mixtures. ACS OMEGA 2017; 2:3669-3680. [PMID: 31457681 PMCID: PMC6641638 DOI: 10.1021/acsomega.7b00867] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/03/2017] [Indexed: 05/31/2023]
Abstract
In this study, the anion-binding bis(cyclopeptide) 2 is introduced, which dissolves freely in water, affording up to 10 mM concentrations, thanks to triethylene glycol-derived substituents in the cyclopeptide subunits and the linker connecting them. Binding studies provided evidence that the anion affinity previously demonstrated for less-soluble analogs of this compound is retained under highly competitive aqueous conditions. The highest affinity in water was observed for iodide, closely followed by sulfate anions, whereas binding of soft and weakly coordinating anions could not be observed. The anion selectivity of 2 thus differs from that of other recently described receptors, which also do not require electrostatic or coordinative interactions for anion binding in water but typically fail to bind strongly coordinating sulfate anions. The ability of 2 to overcome sulfate hydration is attributed to the special mode of binding, combining direct N-H···A- interactions with the release of water molecules from the receptor cavity. The characterization of the anion binding of 2 and a related bis(cyclopeptide) in a variety of different solvents and aqueous solvent mixtures furthermore allowed the correlation of the binding properties with solvent parameters. These analyses provided qualitative and even quantitative insights into the solvent properties and solvation phenomena that mainly affect anion complexation.
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Affiliation(s)
- Fabian Sommer
- Fachbereich
Chemie—Organische Chemie, Technische
Universität Kaiserslautern, Erwin-Schrödinger-Straße, 67663 Kaiserslautern, Germany
| | - Yizhak Marcus
- Institute
of Chemistry, The Hebrew University, Edmund Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Stefan Kubik
- Fachbereich
Chemie—Organische Chemie, Technische
Universität Kaiserslautern, Erwin-Schrödinger-Straße, 67663 Kaiserslautern, Germany
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20
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Abstract
Binding free energy calculations based on molecular simulations provide predicted affinities for biomolecular complexes. These calculations begin with a detailed description of a system, including its chemical composition and the interactions among its components. Simulations of the system are then used to compute thermodynamic information, such as binding affinities. Because of their promise for guiding molecular design, these calculations have recently begun to see widespread applications in early-stage drug discovery. However, many hurdles remain in making them a robust and reliable tool. In this review, we highlight key challenges of these calculations, discuss some examples of these challenges, and call for the designation of standard community benchmark test systems that will help the research community generate and evaluate progress. In our view, progress will require careful assessment and evaluation of new methods, force fields, and modeling innovations on well-characterized benchmark systems, and we lay out our vision for how this can be achieved.
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Affiliation(s)
- David L Mobley
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, California 92697;
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences and Center for Drug Discovery Innovation, University of California, San Diego, La Jolla, California 92093;
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21
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Caldararu O, Olsson MA, Riplinger C, Neese F, Ryde U. Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T). J Comput Aided Mol Des 2017; 31:87-106. [PMID: 27600554 PMCID: PMC5239813 DOI: 10.1007/s10822-016-9957-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/25/2016] [Indexed: 10/27/2022]
Abstract
We have tried to calculate the free energy for the binding of six small ligands to two variants of the octa-acid deep cavitand host in the SAMPL5 blind challenge. We employed structures minimised with dispersion-corrected density-functional theory with small basis sets and energies were calculated using large basis sets. Solvation energies were calculated with continuum methods and thermostatistical corrections were obtained from frequencies calculated at the HF-3c level. Care was taken to minimise the effects of the flexibility of the host by keeping the complexes as symmetric and similar as possible. In some calculations, the large net charge of the host was reduced by removing the propionate and benzoate groups. In addition, the effect of a restricted molecular dynamics sampling of structures was tested. Finally, we tried to improve the energies by using the DLPNO-CCSD(T) approach. Unfortunately, results of quite poor quality were obtained, with no correlation to the experimental data, systematically too positive affinities (by ~50 kJ/mol) and a mean absolute error (after removal of the systematic error) of 11-16 kJ/mol. DLPNO-CCSD(T) did not improve the results, so the accuracy is not limited by the energy function. Instead, four likely sources of errors were identified: first, the minimised structures were often incorrect, owing to the omission of explicit solvent. They could be partly improved by performing the minimisations in a continuum solvent with four water molecules around the charged groups of the ligands. Second, some ligands could bind in several different conformations, requiring sampling of reasonable structures. Third, there is an indication the continuum-solvation model has problems to accurately describe the binding of both the negatively and positively charged guest molecules. Fourth, different methods to calculate the thermostatistical corrections gave results that differed by up to 30 kJ/mol and there is an indication that HF-3c overestimates the entropy term. In conclusion, it is a challenge to calculate binding affinities for this octa-acid system with quantum-mechanical methods.
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Affiliation(s)
- Octav Caldararu
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden
| | - Martin A Olsson
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden
| | - Christoph Riplinger
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, 45470, Mülheim an der Ruhr, Germany
| | - Ulf Ryde
- Department of Theoretical Chemistry, Chemical Centre, Lund University, P. O. Box 124, 221 00, Lund, Sweden.
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22
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Katkova EV, Onufriev AV, Aguilar B, Sulimov VB. Accuracy comparison of several common implicit solvent models and their implementations in the context of protein-ligand binding. J Mol Graph Model 2016; 72:70-80. [PMID: 28064081 DOI: 10.1016/j.jmgm.2016.12.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/07/2016] [Accepted: 12/15/2016] [Indexed: 11/18/2022]
Abstract
In this study several commonly used implicit solvent models are compared with respect to their accuracy of estimating solvation energies of small molecules and proteins, as well as desolvation penalty in protein-ligand binding. The test set consists of 19 small proteins, 104 small molecules, and 15 protein-ligand complexes. We compared predicted hydration energies of small molecules with their experimental values; the results of the solvation and desolvation energy calculations for small molecules, proteins and protein-ligand complexes in water were also compared with Thermodynamic Integration calculations based on TIP3P water model and Amber12 force field. The following implicit solvent (water) models considered here are: PCM (Polarized Continuum Model implemented in DISOLV and MCBHSOLV programs), GB (Generalized Born method implemented in DISOLV program, S-GB, and GBNSR6 stand-alone version), COSMO (COnductor-like Screening Model implemented in the DISOLV program and the MOPAC package) and the Poisson-Boltzmann model (implemented in the APBS program). Different parameterizations of the molecules were examined: we compared MMFF94 force field, Amber12 force field and the quantum-chemical semi-empirical PM7 method implemented in the MOPAC package. For small molecules, all of the implicit solvent models tested here yield high correlation coefficients (0.87-0.93) between the calculated solvation energies and the experimental values of hydration energies. For small molecules high correlation (0.82-0.97) with the explicit solvent energies is seen as well. On the other hand, estimated protein solvation energies and protein-ligand binding desolvation energies show substantial discrepancy (up to 10kcal/mol) with the explicit solvent reference. The correlation of polar protein solvation energies and protein-ligand desolvation energies with the corresponding explicit solvent results is 0.65-0.99 and 0.76-0.96 respectively, though this difference in correlations is caused more by different parameterization and less by methods and indicates the need for further improvement of implicit solvent models parameterization. Within the same parameterization, various implicit methods give practically the same correlation with results obtained in explicit solvent model for ligands and proteins: e.g. correlation values of polar ligand solvation energies and the corresponding energies in the frame of explicit solvent were 0.953-0.966 for the APBS program, the GBNSR6 program and all models used in the DISOLV program. The DISOLV program proved to be on a par with the other used programs in the case of proteins and ligands solvation energy calculation. However, the solution of the Poisson-Boltzmann equation (APBS program) and Generalized Born method (implemented in the GBNSR6 program) proved to be the most accurate in calculating the desolvation energies of complexes.
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Affiliation(s)
- E V Katkova
- Dimonta, Ltd., Nagornaya Street 15, Bldg 8, Moscow, 117186, Russia; Research Computer Center, Lomonosov Moscow State University, Leninskie Gory 1,Bldg 4, Moscow, 119992, Russia.
| | - A V Onufriev
- Departments of Computer Science and Physics, Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, VA, USA
| | - B Aguilar
- Institute for Systems Biology, Seattle, WA, USA
| | - V B Sulimov
- Dimonta, Ltd., Nagornaya Street 15, Bldg 8, Moscow, 117186, Russia; Research Computer Center, Lomonosov Moscow State University, Leninskie Gory 1,Bldg 4, Moscow, 119992, Russia
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23
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Pan A, Kar T, Rakshit AK, Moulik SP. Enthalpy–Entropy Compensation (EEC) Effect: Decisive Role of Free Energy. J Phys Chem B 2016; 120:10531-10539. [DOI: 10.1021/acs.jpcb.6b05890] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Animesh Pan
- Centre for Surface Science, Department of Chemistry and ‡Indian Society for Surface Science & Technology, Department of Chemistry, Jadavpur University, Kolkata 700032, India
| | - Tanmoy Kar
- Centre for Surface Science, Department of Chemistry and ‡Indian Society for Surface Science & Technology, Department of Chemistry, Jadavpur University, Kolkata 700032, India
| | - Animesh K. Rakshit
- Centre for Surface Science, Department of Chemistry and ‡Indian Society for Surface Science & Technology, Department of Chemistry, Jadavpur University, Kolkata 700032, India
| | - Satya P. Moulik
- Centre for Surface Science, Department of Chemistry and ‡Indian Society for Surface Science & Technology, Department of Chemistry, Jadavpur University, Kolkata 700032, India
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24
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Wang J, Jang Y, Khedkar JK, Koo JY, Kim Y, Lee CJ, Rhee YM, Kim K. How Does Solvation Affect the Binding of Hydrophilic Amino Saccharides to Cucurbit[7]uril with Exceptional Anomeric Selectivity? Chemistry 2016; 22:15791-15799. [PMID: 27632939 DOI: 10.1002/chem.201602810] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Indexed: 01/06/2023]
Abstract
Cucurbit[7]uril (CB[7]) is known to bind strongly to hydrophilic amino saccharide guests with exceptional α-anomer selectivities under aqueous conditions. Single-crystal X-ray crystallography and computational methods were used to elucidate the reason behind this interesting phenomenon. The crystal structures of protonated galactosamine (GalN) and glucosamine (GluN) complexes confirm the inclusion of α anomers inside CB[7] and disclose the details of the host-guest binding. Whereas computed gas-phase structures agree with these crystal structures, gas-phase binding free energies show preferences for the β-anomer complexes over their α counterparts, in striking contrast to the experimental results under aqueous conditions. However, when the solvation effect is considered, the binding structures drastically change and the preference for the α anomers is recovered. The α anomers also tend to bind more tightly and leave less space in the CB[7] cavity toward inclusion of only one water molecule, whereas loosely bound β anomers leave more space toward accommodating two water molecules, with markedly different hydrogen-bonding natures. Surprisingly, entropy seems to contribute significantly to both anomeric discrimination and binding. This suggests that of all the driving factors for the strong complexation of the hydrophilic amino saccharide guests, water mediation plays a crucial role in the anomer discrimination.
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Affiliation(s)
- Jianping Wang
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea
| | - Yoonjung Jang
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea.,Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea
| | - Jayshree K Khedkar
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea
| | - Jin Young Koo
- Division of Advanced Materials Science, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea
| | - Yonghwi Kim
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea
| | - Chang Jun Lee
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea
| | - Young Min Rhee
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea. .,Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea.
| | - Kimoon Kim
- Center for Self-assembly and Complexity, Institute for Basic Science (IBS), 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea. .,Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea. .,Division of Advanced Materials Science, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, 37673, Republic of Korea.
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25
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El-Nahass MN, Atlam FM. Diarylethylene guest anchored into a cyclodextrin molecular host: optical, quantum chemical studies and biological activity. Supramol Chem 2016. [DOI: 10.1080/10610278.2016.1212054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Marwa N. El-Nahass
- Faculty of Science, Chemistry Department, Tanta University, Tanta, Egypt
| | - Faten M. Atlam
- Faculty of Science, Chemistry Department, Tanta University, Tanta, Egypt
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26
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Zhou S, Sun H, Cheng LT, Dzubiella J, Li B, McCammon JA. Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations. J Chem Phys 2016; 145:054114. [PMID: 27497546 PMCID: PMC4975753 DOI: 10.1063/1.4959971] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 07/05/2016] [Indexed: 12/29/2022] Open
Abstract
Recent years have seen the initial success of a variational implicit-solvent model (VISM), implemented with a robust level-set method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The level-set minimization of the VISM solvation free-energy functional of all possible solute-solvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic level-set method to numerically implement such a theory. We describe the interfacial fluctuation through the "normal velocity" that is the solute-solvent interfacial force, derive the corresponding stochastic level-set equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit[7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the free-energy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the inter-plate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the inclusion of fluctuations into the VISM and understanding the impact of interfacial fluctuations on biomolecular solvation with an implicit-solvent approach.
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Affiliation(s)
- Shenggao Zhou
- Department of Mathematics and Mathematical Center for Interdiscipline Research, Soochow University, 1 Shizi Street, Jiangsu, Suzhou 215006, China
| | - Hui Sun
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, USA
| | - Li-Tien Cheng
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, USA
| | - Joachim Dzubiella
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, 14109 Berlin, Germany and Institut für Physik, Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Bo Li
- Department of Mathematics and Quantitative Biology Graduate Program, University of California, San Diego, La Jolla, California 92093-0112, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, Department of Pharmacology, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0365, USA
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27
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Study on the inclusion behaviour and solid inclusion complex of lomustine with cyclodextrins. J INCL PHENOM MACRO 2016. [DOI: 10.1007/s10847-016-0640-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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28
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Study on the inclusion behavior and solid inclusion complex of 5-amino-6-methyl-2-benzimidazolone with cyclodextrins. CHINESE CHEM LETT 2016. [DOI: 10.1016/j.cclet.2016.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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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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30
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Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chem Rev 2016; 116:5520-66. [DOI: 10.1021/acs.chemrev.5b00630] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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31
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Pan A, Rakshit AK, Moulik SP. Micellization thermodynamics and the nature of enthalpy–entropy compensation. Colloids Surf A Physicochem Eng Asp 2016. [DOI: 10.1016/j.colsurfa.2016.02.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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Parrish RM, Parker TM, Sherrill CD. Chemical Assignment of Symmetry-Adapted Perturbation Theory Interaction Energy Components: The Functional-Group SAPT Partition. J Chem Theory Comput 2015; 10:4417-31. [PMID: 26588139 DOI: 10.1021/ct500724p] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Recently, we introduced an effective atom-pairwise partition of the many-body symmetry-adapted perturbation theory (SAPT) interaction energy decomposition, producing a method known as atomic SAPT (A-SAPT) [Parrish, R. M.; Sherrill, C. D. J. Chem. Phys. 2014, 141, 044115]. A-SAPT provides ab initio atom-pair potentials for force field development and also automatic visualizations of the spatial contributions of noncovalent interactions, but often has difficulty producing chemically useful partitions of the electrostatic energy, due to the buildup of oscillating partial charges on adjacent functional groups. In this work, we substitute chemical functional groups in place of atoms as the relevant local quasiparticles in the partition, resulting in a functional-group-pairwise partition denoted as functional-group SAPT (F-SAPT). F-SAPT assigns integral sets of local occupied electronic orbitals and protons to chemical functional groups and linking σ bonds. Link-bond contributions can be further assigned to chemical functional groups to simplify the analysis. This approach yields a SAPT partition between pairs of functional groups with integral charge (usually neutral), preventing oscillations in the electrostatic partition. F-SAPT qualitatively matches chemical intuition and the cut-and-cap fragmentation technique but additionally yields the quantitative many-body SAPT interaction energy. The conceptual simplicity, chemical utility, and computational efficiency of F-SAPT is demonstrated in the context of phenol dimer, proflavine(+)-DNA intercalation, and a cucurbituril host-guest inclusion complex.
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Affiliation(s)
- Robert M Parrish
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Trent M Parker
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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33
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Shetty D, Khedkar JK, Park KM, Kim K. Can we beat the biotin-avidin pair?: cucurbit[7]uril-based ultrahigh affinity host-guest complexes and their applications. Chem Soc Rev 2015; 44:8747-61. [PMID: 26434388 DOI: 10.1039/c5cs00631g] [Citation(s) in RCA: 296] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The design of synthetic, monovalent host-guest molecular recognition pairs is still challenging and of particular interest to inquire into the limits of the affinity that can be achieved with designed systems. In this regard, cucurbit[7]uril (CB[7]), an important member of the host family cucurbit[n]uril (CB[n], n = 5-8, 10, 14), has attracted much attention because of its ability to form ultra-stable complexes with multiple guests. The strong hydrophobic effect between the host cavity and guests, ion-dipole and dipole-dipole interactions of guests with CB portals helps in cooperative and multiple noncovalent interactions that are essential for realizing such strong complexations. These highly selective, strong yet dynamic interactions can be exploited in many applications including affinity chromatography, biomolecule immobilization, protein isolation, biological catalysis, and sensor technologies. In this review, we summarize the progress in the development of high affinity guests for CB[7], factors affecting the stability of complexes, theoretical insights, and the utility of these high affinity pairs in different challenging applications.
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Affiliation(s)
- Dinesh Shetty
- Center for Self-assembly and Complexity (CSC), Institute for Basic Science (IBS), Pohang 37673, Republic of Korea.
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34
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Gao K, Yin J, Henriksen NM, Fenley AT, Gilson MK. Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models. J Chem Theory Comput 2015; 11:4555-64. [PMID: 26574247 DOI: 10.1021/acs.jctc.5b00676] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Dissolved salts are a part of the physiological milieu and can significantly influence the kinetics and thermodynamics of various biomolecular processes, such as binding and catalysis; thus, it is important for molecular simulations to reliably describe their effects. The present study uses a simple, nonionized host-guest model system to study the sensitivity of computed binding enthalpies to the choice of water and salt models. Molecular dynamics simulations of a cucurbit[7]uril host with a neutral guest molecule show striking differences in the salt dependency of the binding enthalpy across four water models, TIP3P, SPC/E, TIP4P-Ew, and OPC, with additional sensitivity to the choice of parameters for sodium and chloride. In particular, although all of the models predict that binding will be less exothermic with increasing NaCl concentration, the strength of this effect varies by 7 kcal/mol across models. The differences appear to result primarily from differences in the number of sodium ions displaced from the host upon binding the guest rather than from differences in the enthalpy associated with this displacement, and it is the electrostatic energy that contributes most to the changes in enthalpy with increasing salt concentration. That a high sensitivity of salt affecting the choice of water model, as observed for the present host-guest system despite it being nonionized, raises issues regarding the selection and adjustment of water models for use with biological macromolecules, especially as these typically possess multiple ionized groups that can interact relatively strongly with ions in solution.
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Affiliation(s)
- Kaifu Gao
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Jian Yin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Andrew T Fenley
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093-0736, United States
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35
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Izadi S, Aguilar B, Onufriev AV. Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation. J Chem Theory Comput 2015; 11:4450-9. [PMID: 26575935 PMCID: PMC5217485 DOI: 10.1021/acs.jctc.5b00483] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Accurate yet efficient computational models of solvent environment are central for most calculations that rely on atomistic modeling, such as prediction of protein-ligand binding affinities. In this study, we evaluate the accuracy of a recently developed generalized Born implicit solvent model, GBNSR6 (Aguilar et al. J. Chem. Theory Comput. 2010, 6, 3613-3639), in estimating the electrostatic solvation free energies (ΔG(pol)) and binding free energies (ΔΔG(pol)) for small protein-ligand complexes. We also compare estimates based on three different explicit solvent models (TIP3P, TIP4PEw, and OPC). The two main findings are as follows. First, the deviation (RMSD = 7.04 kcal/mol) of GBNSR6 binding affinities from commonly used TIP3P reference values is comparable to the deviations between explicit models themselves, e.g. TIP4PEw vs TIP3P (RMSD = 5.30 kcal/mol). A simple uniform adjustment of the atomic radii by a single scaling factor reduces the RMS deviation of GBNSR6 from TIP3P to within the above "error margin" - differences between ΔΔG(pol) estimated by different common explicit solvent models. The simple radii scaling virtually eliminates the systematic deviation (ΔΔG(pol)) between GBNSR6 and two out of the three explicit water models and significantly reduces the deviation from the third explicit model. Second, the differences between electrostatic binding energy estimates from different explicit models is disturbingly large; for example, the deviation between TIP4PEw and TIP3P estimates of ΔΔG(pol) values can be up to ∼50% or ∼9 kcal/mol, which is significantly larger than the "chemical accuracy" goal of ∼1 kcal/mol. The absolute ΔG(pol) calculated with different explicit models could differ by tens of kcal/mol. These discrepancies point to unacceptably high sensitivity of binding affinity estimates to the choice of common explicit water models. The absence of a clear "gold standard" among these models strengthens the case for the use of accurate implicit solvation models for binding energetics, which may be orders of magnitude faster.
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Affiliation(s)
- Saeed Izadi
- Department of Biomedical Engineering and Mechanics, Department of Computer Science, and Departments of Computer Science and Physics, Virginia Tech , Blacksburg, Virginia 24060, United States
| | - Boris Aguilar
- Department of Biomedical Engineering and Mechanics, Department of Computer Science, and Departments of Computer Science and Physics, Virginia Tech , Blacksburg, Virginia 24060, United States
| | - Alexey V Onufriev
- Department of Biomedical Engineering and Mechanics, Department of Computer Science, and Departments of Computer Science and Physics, Virginia Tech , Blacksburg, Virginia 24060, United States
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36
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Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data. J Mol Recognit 2015; 29:10-21. [PMID: 26256816 DOI: 10.1002/jmr.2489] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/06/2015] [Accepted: 06/07/2015] [Indexed: 12/13/2022]
Abstract
Force field accuracy is still one of the "stalemates" in biomolecular modeling. Model systems with high quality experimental data are valuable instruments for the validation and improvement of effective potentials. With respect to protein-ligand binding, organic host-guest complexes have long served as models for both experimental and computational studies because of the abundance of binding affinity data available for such systems. Binding affinity data collected for cyclodextrin (CD) inclusion complexes, a popular model for molecular recognition, is potentially a more reliable resource for tuning energy parameters than hydration free energy measurements. Convergence of binding free energy calculations on CD host-guest systems can also be obtained rapidly, thus offering the opportunity to assess the robustness of these parameters. In this work, we demonstrate how implicit solvent parameters can be developed using binding affinity experimental data and the binding energy distribution analysis method (BEDAM) and validated using the Grid Inhomogeneous Solvation Theory analysis. These new solvation parameters were used to study protein-ligand binding in two drug targets against the HIV-1 virus and improved the agreement between the calculated and the experimental binding affinities. This work illustrates how benchmark sets of high quality experimental binding affinity data and physics-based binding free energy models can be used to evaluate and optimize force fields for protein-ligand systems. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Lauren Wickstrom
- Borough of Manhattan Community College, Department of Science, The City University of New York, New York, NY, 10007, USA
| | - Nanjie Deng
- Center for Biophysics and Computational Biology/ICMS, Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| | - Peng He
- Center for Biophysics and Computational Biology/ICMS, Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| | - Ahmet Mentes
- Center for Biophysics and Computational Biology/ICMS, Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| | - Crystal Nguyen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093-0736, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093-0736, USA
| | - Tom Kurtzman
- Department of Chemistry, Lehman College, The City University of New York, Bronx, NY, 10468, USA
| | - Emilio Gallicchio
- Department of Chemistry, Brooklyn College, The City University of New York, Brooklyn, NY, 11210, USA
| | - Ronald M Levy
- Center for Biophysics and Computational Biology/ICMS, Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
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37
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Yin J, Fenley AT, Henriksen NM, Gilson MK. Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics. J Phys Chem B 2015; 119:10145-55. [PMID: 26181208 DOI: 10.1021/acs.jpcb.5b04262] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Improving the capability of atomistic computer models to predict the thermodynamics of noncovalent binding is critical for successful structure-based drug design, and the accuracy of such calculations remains limited by nonoptimal force field parameters. Ideally, one would incorporate protein-ligand affinity data into force field parametrization, but this would be inefficient and costly. We now demonstrate that sensitivity analysis can be used to efficiently tune Lennard-Jones parameters of aqueous host-guest systems for increasingly accurate calculations of binding enthalpy. These results highlight the promise of a comprehensive use of calorimetric host-guest binding data, along with existing validation data sets, to improve force field parameters for the simulation of noncovalent binding, with the ultimate goal of making protein-ligand modeling more accurate and hence speeding drug discovery.
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Affiliation(s)
- Jian Yin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0736, United States
| | - Andrew T Fenley
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0736, United States
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0736, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093-0736, United States
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38
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Zhou S, Cheng LT, Sun H, Che J, Dzubiella J, Li B, McCammon JA. LS-VISM: A software package for analysis of biomolecular solvation. J Comput Chem 2015; 36:1047-59. [PMID: 25766844 PMCID: PMC4412808 DOI: 10.1002/jcc.23890] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/08/2015] [Indexed: 12/30/2022]
Abstract
We introduce a software package for the analysis of biomolecular solvation. The package collects computer codes that implement numerical methods for a variational implicit-solvent model (VISM). The input of the package includes the atomic data of biomolecules under consideration and the macroscopic parameters such as solute-solvent surface tension, bulk solvent density and ionic concentrations, and the dielectric coefficients. The output includes estimated solvation free energies and optimal macroscopic solute-solvent interfaces that are obtained by minimizing the VISM solvation free-energy functional among all possible solute-solvent interfaces enclosing the solute atoms. We review the VISM with various descriptions of electrostatics. We also review our numerical methods that consist mainly of the level-set method for relaxing the VISM free-energy functional and a compact coupling interface method for the dielectric Poisson-Boltzmann equation. Such numerical methods and algorithms constitute the central modules of the software package. We detail the structure of the package, format of input and output files, workflow of the codes, and the postprocessing of output data. Our demo application to a host-guest system illustrates how to use the package to perform solvation analysis for biomolecules, including ligand-receptor binding systems. The package is simple and flexible with respect to minimum adjustable parameters and a wide range of applications. Future extensions of the package use can include the efficient identification of ligand binding pockets on protein surfaces.
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Affiliation(s)
- Shenggao Zhou
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Li-Tien Cheng
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Hui Sun
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Jianwei Che
- Parallel Computing Labs, 3525 Del Mar Heights Road, No. 288, San Diego, CA 92130
| | - Joachim Dzubiella
- Soft Matter and Functional Materials, Helmholtz-Center Berlin, 14109 Berlin, Germany, and Physics Department, Humboldt-University of Berlin, 12489 Berlin, Germany
| | - Bo Li
- Department of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - J. Andrew McCammon
- Department of Chemistry and Biochemistry, Department of Pharmacology, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0365, United States
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39
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Lee JW, Lee HHL, Ko YH, Kim K, Kim HI. Deciphering the Specific High-Affinity Binding of Cucurbit[7]uril to Amino Acids in Water. J Phys Chem B 2015; 119:4628-36. [DOI: 10.1021/acs.jpcb.5b00743] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
| | | | - Young Ho Ko
- Center
for Self-Assembly and Complexity, Institute for Basic Science, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Republic of Korea
| | - Kimoon Kim
- Center
for Self-Assembly and Complexity, Institute for Basic Science, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Republic of Korea
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40
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Goehry C, Besora M, Maseras F. Computational Study on the Mechanism of the Acceleration of 1,3-Dipolar Cycloaddition inside Cucurbit[6]uril. ACS Catal 2015. [DOI: 10.1021/cs501703t] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Charles Goehry
- Institute of Chemical Research of Catalonia (ICIQ), Avgda. Paı̈sos Catalans, 16, 43007 Tarragona, Catalonia, Spain
| | - Maria Besora
- Institute of Chemical Research of Catalonia (ICIQ), Avgda. Paı̈sos Catalans, 16, 43007 Tarragona, Catalonia, Spain
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ), Avgda. Paı̈sos Catalans, 16, 43007 Tarragona, Catalonia, Spain
- Departament
de Quı́mica, Universitat Autònoma de Barcelona, 08193 Bellaterra, Catalonia, Spain
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41
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Kim Y, Lee M. Supramolecular Capsules from Bilayer Membrane Scission Driven by Corannulene. Chemistry 2015; 21:5736-40. [DOI: 10.1002/chem.201500101] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Indexed: 01/07/2023]
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42
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Wang Y, Huang Z, Kim Y, He Y, Lee M. Guest-Driven Inflation of Self-Assembled Nanofibers through Hollow Channel Formation. J Am Chem Soc 2014; 136:16152-5. [DOI: 10.1021/ja510182x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yanqiu Wang
- State
Key Lab for Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Zhegang Huang
- Department
of Chemistry, Harbin Institute of Technology, Harbin150001, China
| | - Yongju Kim
- State
Key Lab for Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Ying He
- State
Key Lab for Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Myongsoo Lee
- State
Key Lab for Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
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43
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Robinson EL, Zavalij PY, Isaacs L. Synthesis of a Disulfonated Derivative of Cucurbit[7]uril and Investigations of its Ability to Solubilize Insoluble Drugs. Supramol Chem 2014; 27:288-297. [PMID: 25937787 DOI: 10.1080/10610278.2014.940952] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cucurbit[7]uril (CB[7]) is currently being investigated as a solubilizing agent for insoluble drugs. We recently found that acyclic CB[n]-type receptors that bear sulfonate solubilizing groups are well suited for this application. Herein, we report cucurbit[7]uril derivative (1) that bears two sulfonate groups on its convex face that we hypothesized would be a superior solubilizing excipient for insoluble drugs. Before using 1 for drug solubilization experiments we showed that 1 does not self-associate and that it retained its ability to bind to diammonium compounds as common guests for CB[7] sized cavities. X-ray crystallography shows that 1 maintains the key structural features of CB[7] with only minor ellipsoidal deformations at the equator and carbonyl portals of 1. Unfortunately, the aqueous solubility of 1 (20 mM) is slightly lower than CB[7] (20-30 mM) which limits its potential as a solubilizing excipient for insoluble drugs. We created phase solubility diagrams for the solubilization of three drugs (camptothecin, albendazole, cinnarizine) with two different containers (1 and CB[7]). CB[7] and 1 exhibit comparable solubilization abilities (e.g. Ka and maximum solubility) toward camptothecin and albendazole but 1 is an inferior solubilizing agent for cinnarizine because of the low solubility exhibited by the 1•cinnarizine complex.
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Affiliation(s)
- Elizabeth L Robinson
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Peter Y Zavalij
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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44
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Zhou S, Cheng LT, Dzubiella J, Li B, McCammon JA. Variational Implicit Solvation with Poisson-Boltzmann Theory. J Chem Theory Comput 2014; 10:1454-1467. [PMID: 24803864 PMCID: PMC3985794 DOI: 10.1021/ct401058w] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Indexed: 12/26/2022]
Abstract
We incorporate the Poisson-Boltzmann (PB) theory of electrostatics into our variational implicit-solvent model (VISM) for the solvation of charged molecules in an aqueous solvent. In order to numerically relax the VISM free-energy functional by our level-set method, we develop highly accurate methods for solving the dielectric PB equation and for computing the dielectric boundary force. We also apply our VISM-PB theory to analyze the solvent potentials of mean force and the effect of charges on the hydrophobic hydration for some selected molecular systems. These include some single ions, two charged particles, two charged plates, and the host-guest system Cucurbit[7]uril and Bicyclo[2.2.2]octane. Our computational results show that VISM with PB theory can capture well the sensitive response of capillary evaporation to the charge in hydrophobic confinement and the polymodal hydration behavior and can provide accurate estimates of binding affinity of the host-guest system. We finally discuss several issues for further improvement of VISM.
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Affiliation(s)
- Shenggao Zhou
- Department
of Mathematics and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Li-Tien Cheng
- Department
of Mathematics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - Joachim Dzubiella
- Soft
Matter and Functional Materials, Helmholtz-Center Berlin, 14109 Berlin,
Germany, and Physics Department, Humboldt-University
of Berlin, 12489 Berlin, Germany
| | - Bo Li
- Department
of Mathematics and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093-0112, United States
| | - J. Andrew McCammon
- Department
of Chemistry and Biochemistry, Department of Pharmacology, Center
for Theoretical Biological Physics, and Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California 92093-0365, United States
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De Filippo CC, Tang H, Ravotto L, Bergamini G, Salice P, Mba M, Ceroni P, Galoppini E, Maggini M. Synthesis and Electronic Properties of 1,2‐Hemisquarimines and Their Encapsulation in a Cucurbit[7]uril Host. Chemistry 2014; 20:6412-20. [DOI: 10.1002/chem.201400039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Indexed: 01/15/2023]
Affiliation(s)
- Christian C. De Filippo
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova (Italy), Fax: (+) 30 0498275050
| | - Hao Tang
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ ‐ 07102 (USA)
| | - Luca Ravotto
- Department of Chemistry “G. Ciamician”, Via Selmi 2, 40126 Bologna (Italy)
| | - Giacomo Bergamini
- Department of Chemistry “G. Ciamician”, Via Selmi 2, 40126 Bologna (Italy)
| | - Patrizio Salice
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova (Italy), Fax: (+) 30 0498275050
| | - Miriam Mba
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova (Italy), Fax: (+) 30 0498275050
| | - Paola Ceroni
- Department of Chemistry “G. Ciamician”, Via Selmi 2, 40126 Bologna (Italy)
| | - Elena Galoppini
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ ‐ 07102 (USA)
| | - Michele Maggini
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova (Italy), Fax: (+) 30 0498275050
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Muddana HS, Yin J, Sapra NV, Fenley AT, Gilson MK. Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method. J Comput Aided Mol Des 2014; 28:463-74. [PMID: 24510191 PMCID: PMC4053532 DOI: 10.1007/s10822-014-9726-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 01/31/2014] [Indexed: 12/14/2022]
Abstract
Accurate methods for predicting protein-ligand binding affinities are of central interest to computer-aided drug design for hit identification and lead optimization. Here, we used the mining minima (M2) method to predict cucurbit[7]uril binding affinities from the SAMPL4 blind prediction challenge. We tested two different energy models, an empirical classical force field, CHARMm with VCharge charges, and the Poisson-Boltzmann surface area solvation model; and a semiempirical quantum mechanical (QM) Hamiltonian, PM6-DH+, coupled with the COSMO solvation model and a surface area term for nonpolar solvation free energy. Binding affinities based on the classical force field correlated strongly with the experiments with a correlation coefficient (R(2)) of 0.74. On the other hand, binding affinities based on the QM energy model correlated poorly with experiments (R(2) = 0.24), due largely to two major outliers. As we used extensive conformational search methods, these results point to possible inaccuracies in the PM6-DH+ energy model or the COSMO solvation model. Furthermore, the different binding free energy components, solute energy, solvation free energy, and configurational entropy showed significant deviations between the classical M2 and quantum M2 calculations. Comparison of different classical M2 free energy components to experiments show that the change in the total energy, i.e. the solute energy plus the solvation free energy, is the key driving force for binding, with a reasonable correlation to experiment (R(2) = 0.56); however, accounting for configurational entropy further improves the correlation.
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Affiliation(s)
- Hari S Muddana
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, Room# 3224, La Jolla, CA, 92093-0736, USA
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47
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Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations. J Comput Aided Mol Des 2014; 28:401-15. [PMID: 24610238 DOI: 10.1007/s10822-014-9716-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/21/2014] [Indexed: 10/25/2022]
Abstract
Molecular containers such as cucurbit[7]uril (CB7) and the octa-acid (OA) host are ideal simplified model test systems for optimizing and analyzing methods for computing free energies of binding intended for use with biologically relevant protein-ligand complexes. To this end, we have performed initially blind free energy calculations to determine the free energies of binding for ligands of both the CB7 and OA hosts. A subset of the selected guest molecules were those included in the SAMPL4 prediction challenge. Using expanded ensemble simulations in the dimension of coupling host-guest intermolecular interactions, we are able to show that our estimates in most cases can be demonstrated to fully converge and that the errors in our estimates are due almost entirely to the assigned force field parameters and the choice of environmental conditions used to model experiment. We confirm the convergence through the use of alternative simulation methodologies and thermodynamic pathways, analyzing sampled conformations, and directly observing changes of the free energy with respect to simulation time. Our results demonstrate the benefits of enhanced sampling of multiple local free energy minima made possible by the use of expanded ensemble molecular dynamics and may indicate the presence of significant problems with current transferable force fields for organic molecules when used for calculating binding affinities, especially in non-protein chemistries.
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48
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Exhaustive docking and solvated interaction energy scoring: lessons learned from the SAMPL4 challenge. J Comput Aided Mol Des 2014; 28:417-27. [PMID: 24474162 DOI: 10.1007/s10822-014-9715-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 01/16/2014] [Indexed: 10/25/2022]
Abstract
We continued prospective assessments of the Wilma-solvated interaction energy (SIE) platform for pose prediction, binding affinity prediction, and virtual screening on the challenging SAMPL4 data sets including the HIV-integrase inhibitor and two host-guest systems. New features of the docking algorithm and scoring function are tested here prospectively for the first time. Wilma-SIE provides good correlations with actual binding affinities over a wide range of binding affinities that includes strong binders as in the case of SAMPL4 host-guest systems. Absolute binding affinities are also reproduced with appropriate training of the scoring function on available data sets or from comparative estimation of the change in target's vibrational entropy. Even when binding modes are known, SIE predictions lack correlation with experimental affinities within dynamic ranges below 2 kcal/mol as in the case of HIV-integrase ligands, but they correctly signaled the narrowness of the dynamic range. Using a common protein structure for all ligands can reduce the noise, while incorporating a more sophisticated solvation treatment improves absolute predictions. The HIV-integrase virtual screening data set consists of promiscuous weak binders with relatively high flexibility and thus it falls outside of the applicability domain of the Wilma-SIE docking platform. Despite these difficulties, unbiased docking around three known binding sites of the enzyme resulted in over a third of ligands being docked within 2 Å from their actual poses and over half of the ligands docked in the correct site, leading to better-than-random virtual screening results.
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49
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Cao L, Šekutor M, Zavalij PY, Mlinarić-Majerski K, Glaser R, Isaacs L. Cucurbit[7]uril⋅Guest Pair with an Attomolar Dissociation Constant. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309635] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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50
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Cao L, Šekutor M, Zavalij PY, Mlinarić-Majerski K, Glaser R, Isaacs L. Cucurbit[7]uril⋅Guest Pair with an Attomolar Dissociation Constant. Angew Chem Int Ed Engl 2014; 53:988-93. [DOI: 10.1002/anie.201309635] [Citation(s) in RCA: 305] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Indexed: 11/11/2022]
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