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Abstract
Drug discovery is one of the most complicated processes and establishment of a single drug may require multidisciplinary attempts to design efficient and commercially viable drugs. The main purpose of drug design is to identify a chemical compound or inhibitor that can bind to an active site of a specific cavity on a target protein. The traditional drug design methods involved various experimental based approaches including random screening of chemicals found in nature or can be synthesized directly in chemical laboratories. Except for the long cycle design and time, high cost is also the major issue of concern. Modernized computer-based algorithm including structure-based drug design has accelerated the drug design and discovery process adequately. Surprisingly from the past decade remarkable progress has been made concerned with all area of drug design and discovery. CADD (Computer Aided Drug Designing) based tools shorten the conventional cycle size and also generate chemically more stable and worthy compounds and hence reduce the drug discovery cost. This special edition of editorial comprises the combination of seven research and review articles set emphasis especially on the computational approaches along with the experimental approaches using a chemical synthesizing for the binding affinity in chemical biology and discovery as a salient used in de-novo drug designing. This set of articles exfoliates the role that systems biology and the evaluation of ligand affinity in drug design and discovery for the future.
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Affiliation(s)
- Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Mahalakshmi Nagar, Indore - 452010, Madhya Pradesh, India
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2
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Abstract
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Alchemical
free energy methods have gained much importance recently
from several reports of improved ligand–protein binding affinity
predictions based on their implementation using molecular dynamics
simulations. A large number of variants of such methods implementing
different accelerated sampling techniques and free energy estimators
are available, each claimed to be better than the others in its own
way. However, the key features of reproducibility and quantification
of associated uncertainties in such methods have barely been discussed.
Here, we apply a systematic protocol for uncertainty quantification
to a number of popular alchemical free energy methods, covering both
absolute and relative free energy predictions. We show that a reliable
measure of error estimation is provided by ensemble simulation—an
ensemble of independent MD simulations—which applies irrespective
of the free energy method. The need to use ensemble methods is fundamental
and holds regardless of the duration of time of the molecular dynamics
simulations performed.
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Affiliation(s)
- Agastya P Bhati
- Centre for Computational Science, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom
| | - Shunzhou Wan
- Centre for Computational Science, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom
| | - Yuan Hu
- Modeling and Informatics , Merck & Co., Inc. , 2000 Galloping Hill Road , Kenilworth , New Jersey 07033 , United States
| | - Brad Sherborne
- Modeling and Informatics , Merck & Co., Inc. , 2000 Galloping Hill Road , Kenilworth , New Jersey 07033 , United States
| | - Peter V Coveney
- Centre for Computational Science, Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , United Kingdom
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3
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Wang X, Tu X, Zhang JZH, Sun Z. BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification. Phys Chem Chem Phys 2018; 20:2009-2021. [PMID: 29299568 DOI: 10.1039/c7cp07573a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Following the previously proposed equilibrate-state sampling based adaptive sampling regime Optimum Bennett Acceptance Ratio (OBAR), we introduce its nonequilibrium extension, the Optimum Crooks' Equation (OCE) in the current work. The efficiency of the NonEquilibrium Work (NEW) stratification is improved by adaptively manipulating the significance of each nonequilibrium realization followed by importance sampling. As is exhibited in the equilibrium case, the nonequilibrium extension outperforms the simple equal time rule used in nonequilibrium stratification in the sense of minimizing the total variance of the free energy estimate. The speedup of this non-equal time rule is more than 1-fold. The Time Derivative of total Variance (TDV) proposed for the OBAR criterion is extended to determine the importance of each nonequilibrium transformation, which is linearly dependent on the variance. The TDV in the nonequilibrium case gives a totally different importance rank from the standard errors of the free energy differences and OBAR TDV due to the duration of nonequilibrium pulling being added into the OCE equation. The performance of the OCE workflow is demonstrated in the solvation of several small molecules with a series of lambda increments and relaxation times between successive perturbations. To the best of our knowledge, such a nonequilibrium adaptive sampling regime in alchemical transformation is unprecedented.
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Affiliation(s)
- Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
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4
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Abstract
A series of computational methods for pKa shift prediction are extensively tested on a set of benchmark protein systems, aiming at identifying pitfalls and evaluating their performance on high variants. Including 19 ASP residues in 10 protein systems, the benchmark set consists of both residues with highly shifted pKa values as well as those varying little from the reference value, with an experimental RMS free energy differences of 2.49 kcal/mol with respect to blocked amino acid, namely the RMS pKa shift being 1.82 pKa units. The constant pH molecular dynamics (MD), alchemical methods, PROPKA3.1, and multiconformation continuum electrostatics give RMSDs of 1.52, 2.58, 1.37, and 3.52 pKa units, respectively, on the benchmark set. The empirical scoring method is the most accurate one with extremely low computational cost, and the pH-dependent model is also able to provide accurate results, while the accuracy of MD sampling incorporating alchemical free energy simulation is prohibited by convergence achievement and the performance of conformational search incorporating multiconformation continuum electrostatics is bad. Former research works did not define statistical uncertainty with care and yielded the questionable conclusion that alchemical methods perform well in most benchmarks. In this work the traditional alchemical methods are thoroughly tested for high variants. We also performed the first application of nonequilibrium alchemical methods to the pKa cases.
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Affiliation(s)
- Zhaoxi Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Material Science, East China Normal University , Shanghai 200062, China
| | - Xiaohui Wang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Material Science, East China Normal University , Shanghai 200062, China
| | - Jianing Song
- NYU-ECNU Center for Computational Chemistry, NYU Shanghai , Shanghai 200062, China.,School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200062, China
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5
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Sun ZX, Wang XH, Zhang JZH. BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation. Phys Chem Chem Phys 2017; 19:15005-15020. [DOI: 10.1039/c7cp01561e] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The efficiency of alchemical free energy simulations with a staging strategy is improved by adaptively manipulating the significance of each ensemble followed by importance sampling.
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Affiliation(s)
- Zhao X. Sun
- State Key Laboratory of Precision Spectroscopy
- Institute of Theoretical and Computational Science
- East China Normal University
- Shanghai 200062
- China
| | - Xiao H. Wang
- State Key Laboratory of Precision Spectroscopy
- Institute of Theoretical and Computational Science
- East China Normal University
- Shanghai 200062
- China
| | - John Z. H. Zhang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai
- Shanghai 200062
- China
- School of Chemistry and Molecular Engineering
- East China Normal University
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6
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Abstract
The quasiharmonic approximation (QH) allows the configurational entropy of a molecule to be estimated on the basis of a molecular dynamics simulation, through construction of a Gaussian probability distribution of conformations with variances equal to those provided by the simulation. At its introduction in 1981, the QH method was successfully applied to simple molecular systems with only one highly occupied energy well, and fluctuations were analyzed in a system of internal bond-angle-torsion coordinates. However, more recent studies have applied the QH method to complex biomolecular systems and have relied upon Cartesian coordinates. The present study evaluates the accuracy of the QH method through comparisons with more detailed methods. The chief findings are that the QH method can markedly overestimate the configurational entropy for systems with multiple occupied energy wells and that such errors tend to be magnified by the use of Cartesian coordinates instead of bond-angle-torsion coordinates.
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Affiliation(s)
- Chia-En Chang
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, and Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, Maryland 20850
| | - Wei Chen
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, and Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, Maryland 20850
| | - Michael K Gilson
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California, and Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, Maryland 20850
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7
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Zhou R, Friesner RA, Ghosh A, Rizzo RC, Jorgensen WL, Levy RM. New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model. J Phys Chem B 2001. [DOI: 10.1021/jp011480z] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Abstract
The past few years have seen an exponential growth in the calculations of electrostatic energies of macromolecules and an increased recognition of the crucial role of electrostatic effects. This review considers the current state of the field. Focus is placed on calculations of pKas, redox potentials and binding energies in macromolecules and clarification of the fact that the value of the dielectric 'constant' of a protein depends on its definition and that small dielectric constants should not be used in describing charge-charge interactions by current continuum models.
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Affiliation(s)
- A Warshel
- Department of Chemistry, University of Southern California, Los Angeles 90089, USA.
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10
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Affiliation(s)
- Martha S. Head
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850
| | - James A. Given
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850
| | - Michael K. Gilson
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, Maryland 20850
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11
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Abstract
Models for predicting the binding affinities of molecules in solution are either very detailed, making them computationally intensive and hard to test, or very simple, and thus less informative than one might wish. A new class of models that focus on the predominant states of the binding molecules promise to capture the essential physics of binding at modest computational cost.
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Affiliation(s)
- M K Gilson
- Center for Advanced Research in Biotechnology, National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850 USA.
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12
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Böhm HJ, Klebe G. Was läßt sich aus der molekularen Erkennung in Protein-Ligand-Komplexen für das Design neuer Wirkstoffe lernen? Angew Chem Int Ed Engl 1996. [DOI: 10.1002/ange.19961082205] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Abstract
BACKGROUND p21ras is one of the GTP-binding proteins that act as intercellular molecular switches. The GTP-bound form of p21ras sends a growth-promoting signal that is terminated once the protein is cycled back into its GDP-bound form. The interaction of guanine-nucleotide-exchange factors (GEFs) with p21ras leads to activation of the protein by promoting GDP --> GTP exchange. Oncogenic mutations of p21ras trap the protein in its biological active GTP-bound form. Other mutations interfere with the activity of GEF. Thus, it is important to explore the structural basis for the action of different mutations. RESULTS The crystal structures of p21ras are correlated with the binding affinities of GTP and GDP by calculating the relevant electrostatic energies. It is demonstrated that such calculations can provide a road map to the location of 'hot' residues whose mutations are likely to change functional properties of the protein. Furthermore, calculations of the effect of specific mutations on GTP and GDP binding are consistent with those observed. This helps to analyze and locate functionally important parts of the protein. CONCLUSIONS Our calculations indicate that the protein main chain provides a major contribution to the binding energies of nucleotides and probably plays a key role in relaying the effect of GEF action. Analysis of p21ras mutations in residues that are important for the proper function of GEFs suggests that the region comprising residues 62-67 in p21ras is the major GEF-binding site. This analysis and our computer simulations indicate that the effect of GEF is probably propagated to the P-loop (residues 10-17) through interaction between Gly60 and Gly12. This then reduces the interaction between the main-chain dipoles of the P-loop and the nucleotide. Finally, the results also suggest a possible relationship between the GTP --> GDP structural transition and the catalytic effect of the GTPase-activating protein.
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Affiliation(s)
- I Muegge
- Department of Chemistry, University of Southern California, Los Angeles 90089-1062, USA
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14
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Madura JD, Nakajima Y, Hamilton RM, Wierzbicki A, Warshel A. Calculations of the electrostatic free energy contributions to the binding free energy of sulfonamides to carbonic anhydrase. Struct Chem 1996; 7:131-8. [DOI: 10.1007/bf02278738] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Abstract
Fueled by advances in molecular structure determination, tools for structure-based drug design are proliferating rapidly. Lead discovery through searching of ligand databases with molecular docking techniques represents an attractive alternative to high-throughout random screening. The size of commercial databases imposes severe computational constraints on molecular docking, compromising the level of calculational detail permitted for each putative ligand. We describe alternative philosophies for docking which effectively address this challenge. With respect to the dynamic aspects of molecular recognition, these strategies lie along a spectrum of models bounded by the Lock-and-Key and Induced-Fit theories for ligand binding. We explore the potential of a rigid model in exploiting species specificity and of a tolerant model in predicting absolute ligand binding affinity. Current molecular docking methods are limited primarily by their ability to rank docked complexes; we therefore place particular emphasis on this aspect of the problem throughout our validation of docking strategies.
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Affiliation(s)
- D A Gschwend
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143-0446, USA
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17
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Affiliation(s)
- H J Böhm
- F. Hoffmann-La Roche Ltd., Pharmaceuticals Division, Basel, Switzerland
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