1
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Case DA. MD simulations of macromolecular crystals: Implications for the analysis of Bragg and diffuse scattering. Methods Enzymol 2023; 688:145-168. [PMID: 37748825 DOI: 10.1016/bs.mie.2023.06.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Some of our most detailed information about structure and dynamics of macromolecules comes from X-ray-diffraction studies in crystalline environments. More than 170,000 atomic models have been deposited in the Protein Data Bank, and the number of observations (typically of intensities of Bragg diffraction peaks) is generally quite large, when compared to other experimental methods. Nevertheless, the general agreement between calculated and observed intensities is far outside the experimental precision, and the majority of scattered photons fall between the sharp Bragg peaks, and are rarely taken into account. This chapter considers how molecular dynamics simulations can be used to explore the connections between microscopic behavior in a crystalline lattice and observed scattering intensities, and point the way to new atomic models that could more faithfully recapitulate Bragg intensities and extract useful information from the diffuse scattering that lies between those peaks.
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Affiliation(s)
- David A Case
- Dept. of Chemistry & Chemical Biology, Rutgers University, Piscataway, NJ, United States.
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2
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Csizi K, Reiher M. Universal
QM
/
MM
approaches for general nanoscale applications. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Markus Reiher
- Laboratorium für Physikalische Chemie ETH Zürich Zürich Switzerland
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3
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Jain AN, Brueckner AC, Cleves AE, Reibarkh M, Sherer EC. A Distributional Model of Bound Ligand Conformational Strain: From Small Molecules up to Large Peptidic Macrocycles. J Med Chem 2023; 66:1955-1971. [PMID: 36701387 PMCID: PMC9923749 DOI: 10.1021/acs.jmedchem.2c01744] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The internal conformational strain incurred by ligands upon binding a target site has a critical impact on binding affinity, and expectations about the magnitude of ligand strain guide conformational search protocols. Estimates for bound ligand strain begin with modeled ligand atomic coordinates from X-ray co-crystal structures. By deriving low-energy conformational ensembles to fit X-ray diffraction data, calculated strain energies are substantially reduced compared with prior approaches. We show that the distribution of expected global strain energy values is dependent on molecular size in a superlinear manner. The distribution of strain energy follows a rectified normal distribution whose mean and variance are related to conformational complexity. The modeled strain distribution closely matches calculated strain values from experimental data comprising over 3000 protein-ligand complexes. The distributional model has direct implications for conformational search protocols as well as for directions in molecular design.
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Affiliation(s)
- Ajay N. Jain
- Research
& Development, BioPharmics LLC, Sonoma County, California95404, United States,
| | - Alexander C. Brueckner
- Molecular
Structure & Design, Bristol Myers Squibb, Princeton, New Jersey08543, United States
| | - Ann E. Cleves
- Research
& Development, BioPharmics LLC, Sonoma County, California95404, United States
| | - Mikhail Reibarkh
- Analytical
Research and Development, Merck & Co.
Inc., Rahway, New Jersey07065, United States
| | - Edward C. Sherer
- Analytical
Research and Development, Merck & Co.
Inc., Rahway, New Jersey07065, United States,
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4
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Abstract
Atomic models for nucleic acids derived from X-ray diffraction data at low resolution provide much useful information, but the observed scattering intensities can be fit with models that can differ in structural detail. Tradtional geometric restraints favor models that have bond length and angle terms derived from small molecule crystal structures. Here we explore replacing these restraints with energy gradients derived from force fields, including recently developed integral equation models to account for the effects of water molecules and ions that are not part of the explicit model. We compare conventional and force-field based refinements for 22 RNA crystals, ranging in resolution from 1.1 to 3.6 Å. As expected, it can be important to account for solvent screening of charge–charge interactions, especially in the crowded environment of a nucleic acid crystal. The newly refined models can show improvements in torsion angles and hydrogen-bonding interactions, and can significantly reduce unfavorable atomic clashes, while maintaining or improving agreement with observed scattering intensities.
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5
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Bergmann J, Oksanen E, Ryde U. Combining crystallography with quantum mechanics. Curr Opin Struct Biol 2021; 72:18-26. [PMID: 34392061 DOI: 10.1016/j.sbi.2021.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 11/19/2022]
Abstract
In standard crystallographic refinement of biomacromolecules, the crystallographic raw data are supplemented by empirical restraints that ensure that the structure makes chemical sense. These restraints are typically accurate for amino acids and nucleic acids, but less so for cofactors, substrates, inhibitors, ligands and metal sites. In quantum refinement, this potential is replaced by more accurate quantum mechanical (QM) calculations. Several implementations have been presented, differing in the level of QM and whether it is used for the entire structure or only for a site of particular interest. It has been shown that the method can improve and correct errors in crystal structures and that it can be used to determine protonation and tautomeric states of various ligands and to decide what is really seen in the structure by refining different interpretations and using standard crystallographic and QM quality measures to decide which fits the structure best.
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Affiliation(s)
- Justin Bergmann
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- European Spallation Source ESS ERIC, P. O. Box 176, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
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6
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van Zundert GCP, Moriarty NW, Sobolev OV, Adams PD, Borrelli KW. Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality. Structure 2021; 29:913-921.e4. [PMID: 33823127 DOI: 10.1016/j.str.2021.03.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 01/21/2021] [Accepted: 03/12/2021] [Indexed: 11/30/2022]
Abstract
With the advent of the resolution revolution in cryoelectron microscopy (cryo-EM), low-resolution refinement is common, and likewise increases the need for a reliable force field. Here, we report on the incorporation of the OPLS3e force field with the VSGB2.1 solvation model in the structure determination package Phenix. Our results show significantly improved structure quality and reduced ligand strain at lower resolution for X-ray refinement. For refinement of cryo-EM-based structures, we find comparable quality structures, goodness-of-fit, and reduced ligand strain. We also show how structure quality and ligand strain are related to the map-model cross-correlation as a function of data weight, and how that can detect overfitting. Signs of overfitting are found in over half of our cryo-EM dataset, which can be remedied by a re-refinement at a lower data weight. Finally, a start-to-end script for refining structures with Phenix/OPLS3e is available in the Schrödinger 2020-3 distribution.
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Affiliation(s)
| | - Nigel W Moriarty
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Oleg V Sobolev
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paul D Adams
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Bioengineering, University of California at Berkeley, Berkeley, CA 94720, USA
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7
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Tong J, Zhao S. Large-Scale Analysis of Bioactive Ligand Conformational Strain Energy by Ab Initio Calculation. J Chem Inf Model 2021; 61:1180-1192. [PMID: 33630603 DOI: 10.1021/acs.jcim.0c01197] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Ligand conformational strain energy (LCSE) plays an important role in virtual screening and lead optimization. While various studies have provided insights into LCSE for small-molecule ligands in the Protein Data Bank (PDB), conclusions are inconsistent mainly due to small datasets, poor quality control of crystal structures, and molecular mechanics (MM) or low-level quantum mechanics (QM) calculations. Here, we built a high-quality dataset (LigBoundConf) of 8145 ligand-bound conformations from PDB crystal structures and calculated LCSE at the M062X-D3/ma-TZVPP (SMD)//M062X-D3/def2-SVP(SMD) level for each case in the dataset. The mean/median LCSE is 4.6/3.7 kcal/mol for 6672 successfully calculated cases, which is significantly lower than the estimates based on molecular mechanics in many previous analyses. Especially, when removing ligands with nonaromatic ring(s) that are prone to have large LCSEs due to electron density overfitting, the mean/median LCSE was reduced to 3.3/2.5 kcal/mol. We further reveal that LCSE is correlated with several ligand properties, including formal atomic charge, molecular weight, number of rotatable bonds, and number of hydrogen-bond donors and acceptors. In addition, our results show that although summation of torsion strains is a good approximation of LCSE for most cases, for a small fraction (about 6%) of our dataset, it underestimates LCSEs if ligands could form nonlocal intramolecular interactions in the unbound state. Taken together, our work provides a comprehensive profile of LCSE for ligands in PDB, which could help ligand conformation generation, ligand docking pose evaluation, and lead optimization.
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Affiliation(s)
- Jiahui Tong
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China.,University of Chinese Academy of Sciences, No. 19A, Yuquan Road, Beijing 100049, China.,Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
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8
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Borbulevych OY, Martin RI, Westerhoff LM. The critical role of QM/MM X-ray refinement and accurate tautomer/protomer determination in structure-based drug design. J Comput Aided Mol Des 2020; 35:433-451. [PMID: 33108589 PMCID: PMC8018927 DOI: 10.1007/s10822-020-00354-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/12/2020] [Indexed: 12/29/2022]
Abstract
Conventional protein:ligand crystallographic refinement uses stereochemistry restraints coupled with a rudimentary energy functional to ensure the correct geometry of the model of the macromolecule—along with any bound ligand(s)—within the context of the experimental, X-ray density. These methods generally lack explicit terms for electrostatics, polarization, dispersion, hydrogen bonds, and other key interactions, and instead they use pre-determined parameters (e.g. bond lengths, angles, and torsions) to drive structural refinement. In order to address this deficiency and obtain a more complete and ultimately more accurate structure, we have developed an automated approach for macromolecular refinement based on a two layer, QM/MM (ONIOM) scheme as implemented within our DivCon Discovery Suite and "plugged in" to two mainstream crystallographic packages: PHENIX and BUSTER. This implementation is able to use one or more region layer(s), which is(are) characterized using linear-scaling, semi-empirical quantum mechanics, followed by a system layer which includes the balance of the model and which is described using a molecular mechanics functional. In this work, we applied our Phenix/DivCon refinement method—coupled with our XModeScore method for experimental tautomer/protomer state determination—to the characterization of structure sets relevant to structure-based drug design (SBDD). We then use these newly refined structures to show the impact of QM/MM X-ray refined structure on our understanding of function by exploring the influence of these improved structures on protein:ligand binding affinity prediction (and we likewise show how we use post-refinement scoring outliers to inform subsequent X-ray crystallographic efforts). Through this endeavor, we demonstrate a computational chemistry ↔ structural biology (X-ray crystallography) "feedback loop" which has utility in industrial and academic pharmaceutical research as well as other allied fields.
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Affiliation(s)
- Oleg Y Borbulevych
- QuantumBio Inc, 2790 West College Ave, Suite 900, State College, PA, 16801, USA
| | - Roger I Martin
- QuantumBio Inc, 2790 West College Ave, Suite 900, State College, PA, 16801, USA
| | - Lance M Westerhoff
- QuantumBio Inc, 2790 West College Ave, Suite 900, State College, PA, 16801, USA.
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9
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Zheng Z, Borbulevych OY, Liu H, Deng J, Martin RI, Westerhoff LM. MovableType Software for Fast Free Energy-Based Virtual Screening: Protocol Development, Deployment, Validation, and Assessment. J Chem Inf Model 2020; 60:5437-5456. [PMID: 32791826 PMCID: PMC7781189 DOI: 10.1021/acs.jcim.0c00618] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
For decades, the
complicated energy surfaces found in macromolecular
protein:ligand structures, which require large amounts of computational
time and resources for energy state sampling, have been an inherent
obstacle to fast, routine free energy estimation in industrial drug
discovery efforts. Beginning in 2013, the Merz research group addressed
this cost with the introduction of a novel sampling methodology termed
“Movable Type” (MT). Using numerical integration methods,
the MT method reduces the computational expense for energy state sampling
by independently calculating each atomic partition function from an
initial molecular conformation in order to estimate the molecular
free energy using ensembles of the atomic partition functions. In
this work, we report a software package, the DivCon Discovery Suite
with the MovableType module from QuantumBio Inc., that performs this
MT free energy estimation protocol in a fast, fully encapsulated manner.
We discuss the computational procedures and improvements to the original
work, and we detail the corresponding settings for this software package.
Finally, we introduce two validation benchmarks to evaluate the overall
robustness of the method against a broad range of protein:ligand structural
cases. With these publicly available benchmarks, we show that the
method can use a variety of input types and parameters and exhibits
comparable predictability whether the method is presented with “expensive”
X-ray structures or “inexpensively docked” theoretical
models. We also explore some next steps for the method. The MovableType
software is available at http://www.quantumbioinc.com/
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Affiliation(s)
- Zheng Zheng
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States.,School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Oleg Y Borbulevych
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States
| | - Hao Liu
- School of Mechanical and Electronic Engineering, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Jianpeng Deng
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, P. R. China
| | - Roger I Martin
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States
| | - Lance M Westerhoff
- QuantumBio Inc., 2790 West College Avenue, Suite 900, State College, Pennsylvania 16801, United States
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10
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Jain AN, Cleves AE, Brueckner AC, Lesburg CA, Deng Q, Sherer EC, Reibarkh MY. XGen: Real-Space Fitting of Complex Ligand Conformational Ensembles to X-ray Electron Density Maps. J Med Chem 2020; 63:10509-10528. [DOI: 10.1021/acs.jmedchem.0c01373] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ajay N. Jain
- Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94143 United States
| | - Ann E. Cleves
- BioPharmics LLC, Santa Rosa, California 95404 United States
| | | | | | - Qiaolin Deng
- Merck and Co., Inc., Kenilworth, New Jersey 07033 United States
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11
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Abstract
Quantum mechanics (QM) methods provide a fine description of receptor-ligand interactions and of chemical reactions. Their use in drug design and drug discovery is increasing, especially for complex systems including metal ions in the binding sites, for the design of highly selective inhibitors, for the optimization of bi-specific compounds, to understand enzymatic reactions, and for the study of covalent ligands and prodrugs. They are also used for generating molecular descriptors for predictive QSAR/QSPR models and for the parameterization of force fields. Thanks to the continuous increase of computational power offered by GPUs and to the development of sophisticated algorithms, QM methods are becoming part of the standard tools used in computer-aided drug design (CADD). We present the most used QM methods and software packages, and we discuss recent representative applications in drug design and drug discovery.
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Affiliation(s)
- Martin Kotev
- Global Research Informatics/Cheminformatics and Drug Design, Evotec (France) SAS, Toulouse, France
| | - Laurie Sarrat
- Global Research Informatics/Cheminformatics and Drug Design, Evotec (France) SAS, Toulouse, France
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12
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Rai BK, Sresht V, Yang Q, Unwalla R, Tu M, Mathiowetz AM, Bakken GA. Comprehensive Assessment of Torsional Strain in Crystal Structures of Small Molecules and Protein–Ligand Complexes using ab Initio Calculations. J Chem Inf Model 2019; 59:4195-4208. [DOI: 10.1021/acs.jcim.9b00373] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | | | | | | | | | | | - Gregory A. Bakken
- Simulation and Modeling Sciences, Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
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13
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Cachau RE, Zhu J, Nicklaus MC. The upcoming subatomic resolution revolution. Curr Opin Struct Biol 2019; 58:53-58. [PMID: 31233975 DOI: 10.1016/j.sbi.2019.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/12/2019] [Accepted: 05/13/2019] [Indexed: 10/26/2022]
Abstract
Subatomic resolution macromolecular crystallography has been revealing the most fascinating details of macromolecular structures for many years. This most extreme form of macromolecular crystallography is going through rapid changes. A new generation of superbrilliant X-ray sources and detectors is facilitating the rapid acquisition of high-quality datasets. Equally important, a new breed of methods and highly integrated advanced computational tools for structure refinement and analysis is poised to change the way we use subatomic resolution data and reposition high-resolution macromolecular crystallography in medicinal chemistry studies. Subatomic resolution macromolecular crystallography may soon be a routine source of detailed molecular information besides precise geometries, including binding energies and other chemical descriptors, opening new possibilities of application.
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Affiliation(s)
- Raul E Cachau
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Inc., Frederick, MD 21702, USA.
| | - Jianghai Zhu
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Inc., Frederick, MD 21702, USA
| | - Marc C Nicklaus
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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