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Ginex T, Vázquez J, Estarellas C, Luque FJ. Quantum mechanical-based strategies in drug discovery: Finding the pace to new challenges in drug design. Curr Opin Struct Biol 2024; 87:102870. [PMID: 38914031 DOI: 10.1016/j.sbi.2024.102870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/02/2024] [Accepted: 06/04/2024] [Indexed: 06/26/2024]
Abstract
The expansion of the chemical space to tangible libraries containing billions of synthesizable molecules opens exciting opportunities for drug discovery, but also challenges the power of computer-aided drug design to prioritize the best candidates. This directly hits quantum mechanics (QM) methods, which provide chemically accurate properties, but subject to small-sized systems. Preserving accuracy while optimizing the computational cost is at the heart of many efforts to develop high-quality, efficient QM-based strategies, reflected in refined algorithms and computational approaches. The design of QM-tailored physics-based force fields and the coupling of QM with machine learning, in conjunction with the computing performance of supercomputing resources, will enhance the ability to use these methods in drug discovery. The challenge is formidable, but we will undoubtedly see impressive advances that will define a new era.
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Affiliation(s)
- Tiziana Ginex
- Pharmacelera, Parc Científic de Barcelona (PCB), Baldiri Reixac 4-8, 08028 Barcelona, Spain
| | - Javier Vázquez
- Pharmacelera, Parc Científic de Barcelona (PCB), Baldiri Reixac 4-8, 08028 Barcelona, Spain; Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Universitat de Barcelona, Institut de Biomedicina (IBUB), 08921 Santa Coloma de Gramenet, Spain; Institut de Biomedicina (IBUB), 08921 Santa Coloma de Gramenet, Spain
| | - Carolina Estarellas
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Universitat de Barcelona, Institut de Biomedicina (IBUB), 08921 Santa Coloma de Gramenet, Spain; Institut de Química Teòrica i Computacional (IQTCUB), 08921 Santa Coloma de Gramenet, Spain
| | - F Javier Luque
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Universitat de Barcelona, Institut de Biomedicina (IBUB), 08921 Santa Coloma de Gramenet, Spain; Institut de Biomedicina (IBUB), 08921 Santa Coloma de Gramenet, Spain; Institut de Química Teòrica i Computacional (IQTCUB), 08921 Santa Coloma de Gramenet, Spain.
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2
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Rossetti G, Mandelli D. How exascale computing can shape drug design: A perspective from multiscale QM/MM molecular dynamics simulations and machine learning-aided enhanced sampling algorithms. Curr Opin Struct Biol 2024; 86:102814. [PMID: 38631106 DOI: 10.1016/j.sbi.2024.102814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/11/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024]
Abstract
Molecular simulations are an essential asset in the first steps of drug design campaigns. However, the requirement of high-throughput limits applications mainly to qualitative approaches with low computational cost, but also low accuracy. Unlocking the potential of more rigorous quantum mechanical/molecular mechanics (QM/MM) models combined with molecular dynamics-based free energy techniques could have a tremendous impact. Indeed, these two relatively old techniques are emerging as promising methods in the field. This has been favored by the exponential growth of computer power and the proliferation of powerful data-driven methods. Here, we briefly review recent advances and applications, and give our perspective on the impact that QM/MM and free-energy methods combined with machine learning-aided algorithms can have on drug design.
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Affiliation(s)
- Giulia Rossetti
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany; Department of Neurology, University Hospital Aachen (UKA), RWTH Aachen University, Aachen, Germany; Jülich Supercomputing Centre (JSC), Forschungszentrum Jülich GmbH, Jülich 52428, Germany. https://twitter.com/G_Rossetti_
| | - Davide Mandelli
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany.
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3
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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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4
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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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5
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Bharatam PV, Valanju OR, Wani AA, Dhaked DK. Importance of tautomerism in drugs. Drug Discov Today 2023; 28:103494. [PMID: 36681235 DOI: 10.1016/j.drudis.2023.103494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/08/2022] [Accepted: 01/13/2023] [Indexed: 01/20/2023]
Abstract
Tautomerism is an important phenomenon exhibited by many drugs. As we discuss in this review, identifying the different tautomers of drugs and exploring their importance in the mechanisms of drug action are integral components of current drug discovery. Nuclear magnetic resonance (NMR), infrared (IR), ultraviolet (UV), Raman, and terahertz spectroscopic techniques, as well as X-ray diffraction, are useful for exploring drug tautomerism. Quantum chemical methods, in association with pharmacoinformatics tools, are being used to evaluate tautomeric preferences in terms of energy effects. Desmotropy (i.e., tautomeric polymorphism) of the drugs is particularly important in drug delivery studies.
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Affiliation(s)
- Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160062, India.
| | - Omkar R Valanju
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160062, India
| | - Aabid A Wani
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S.A.S. Nagar, Punjab 160062, India
| | - Devendra K Dhaked
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Chunilal Bhawan, 168 Maniktala Main Road, Kolkata, West Bengal 700054, India
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6
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Kar RK. Benefits of hybrid QM/MM over traditional classical mechanics in pharmaceutical systems. Drug Discov Today 2023; 28:103374. [PMID: 36174967 DOI: 10.1016/j.drudis.2022.103374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/27/2022] [Accepted: 09/22/2022] [Indexed: 02/02/2023]
Abstract
Hybrid quantum mechanics/molecular mechanics (QM/MM) is one of the most reliable approaches for accurately modeling and studying the complex pharmaceutical discovery system. Classical mechanics has significantly accelerated the drug discovery process in the past decade. However, the current challenge is the large pool of false positives, which require extensive validation. Hybrid QM/MM is an effective solution for accurately studying ligand binding, structural mechanisms, free energy evaluation, and spectroscopic characterization. This article highlights the methodological details relevant to cost-effective hybrid QM/MM methods. This approach, combined with traditional pharmacoinformatics methods, could be a reliable strategy to balance the cost and accuracy of the calculations.
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Affiliation(s)
- Rajiv K Kar
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
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7
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Deneva V, Slavova S, Kumanova A, Vassilev N, Nedeltcheva-Antonova D, Antonov L. Favipiravir-Tautomeric and Complexation Properties in Solution. Pharmaceuticals (Basel) 2022; 16:ph16010045. [PMID: 36678542 PMCID: PMC9864296 DOI: 10.3390/ph16010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/16/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
The tautomeric properties of favipiravir were investigated experimentally for the first time by using molecular spectroscopy (UV-Vis absorption, fluorescence and NMR), as well as DFT quantum-chemical calculations. According to the obtained results, the enol tautomer is substantially more stable in most of the organic solvents. In the presence of water, a keto form appears to be favored due to the specific solute-solvent interactions. Upon the addition of alkaline-earth-metal ions, deprotonation and complexation occurred simultaneously, giving the formation of 2 : 1 ligand : metal complexes. According to the theoretical simulations, the metal ion is captured between the carbonyl groups as a result of the size-fit effect.
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Affiliation(s)
- Vera Deneva
- Institute of Electronics, Bulgarian Academy of Sciences, 1784 Sofia, Bulgaria
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
- Correspondence: (V.D.); (L.A.)
| | - Sofia Slavova
- Institute of Electronics, Bulgarian Academy of Sciences, 1784 Sofia, Bulgaria
- Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Alina Kumanova
- Institute of Electronics, Bulgarian Academy of Sciences, 1784 Sofia, Bulgaria
| | - Nikolay Vassilev
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Daniela Nedeltcheva-Antonova
- Institute of Electronics, Bulgarian Academy of Sciences, 1784 Sofia, Bulgaria
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Luidmil Antonov
- Institute of Electronics, Bulgarian Academy of Sciences, 1784 Sofia, Bulgaria
- Correspondence: (V.D.); (L.A.)
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Dushanan R, Weerasinghe S, Dissanayake DP, Senthilinithy R. Implication of Ab Initio, QM/MM, and molecular dynamics calculations on the prediction of the therapeutic potential of some selected HDAC inhibitors. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2097672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Ramachandren Dushanan
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka
| | - Samantha Weerasinghe
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | | | - Rajendram Senthilinithy
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka
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9
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Manathunga M, Götz AW, Merz KM. Computer-aided drug design, quantum-mechanical methods for biological problems. Curr Opin Struct Biol 2022; 75:102417. [PMID: 35779437 DOI: 10.1016/j.sbi.2022.102417] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 11/28/2022]
Abstract
Quantum chemistry enables to study systems with chemical accuracy (<1 kcal/mol from experiment) but is restricted to a handful of atoms due to its computational expense. This has led to ongoing interest to optimize and simplify these methods while retaining accuracy. Implementing quantum mechanical (QM) methods on modern hardware such as multiple-GPUs is one example of how the field is optimizing performance. Multiscale approaches like the so-called QM/molecular mechanical method are gaining popularity in drug discovery because they focus the application of QM methods on the region of choice (e.g., the binding site), while using efficient MM models to represent less relevant areas. The creation of simplified QM methods is another example, including the use of machine learning to create ultra-fast and accurate QM models. Herein, we summarize recent advancements in the development of optimized QM methods that enhance our ability to use these methods in computer aided drug discovery.
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Affiliation(s)
- Madushanka Manathunga
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States. https://twitter.com/@MaduManathunga
| | - Andreas W Götz
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, United States. https://twitter.com/@awgoetz
| | - Kenneth M Merz
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, United States.
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Behboodyzad F, Mohseniabbasabadi T, Ghanemnia N, Balali E. Structural analysis of dexrazoxane: Exploring tautomeric conformations. MAIN GROUP CHEMISTRY 2021. [DOI: 10.3233/mgc-210158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Structural analysis of dexrazoxane, as a cardioprotective agent, was done in this work by exploring formations of tautomeric conformations and investigating the corresponding effects. Density functional theory (DFT) calculations were performed to optimize the structures to evaluate their molecular and atomic descriptors. In addition to the original structure of dexrazoxane, eight tautomers were obtained with lower stability than the original compound. Movements of two hydrogen atoms in between nitrogen and oxygen atoms of heterocyclic ring put such significant effects. Moreover, electronic molecular orbital features showed effects of such tautomerism processes on distribution patterns and surfaces, in which evaluating the quadrupole coupling constants helped to show the role of atomic sites for resulting the features. As a consequence, the results indicated that the tautomeric formations could significantly change the features of dexrazoxane reminding the importance of carful medication of this drug for patients.
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Affiliation(s)
- Farnoosh Behboodyzad
- Department of Organic Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Tahereh Mohseniabbasabadi
- Department of Organic Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Nahal Ghanemnia
- Department of Molecular Sciences and Nanosystems, Faculty of Science and Technology of Bio and Nanomaterials, University of Ca’ Foscari, Venice, Italy
| | - Ebrahim Balali
- Department of Organic Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
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11
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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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12
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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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Brueckner AC, Deng Q, Cleves AE, Lesburg CA, Alvarez JC, Reibarkh MY, Sherer EC, Jain AN. Conformational Strain of Macrocyclic Peptides in Ligand-Receptor Complexes Based on Advanced Refinement of Bound-State Conformers. J Med Chem 2021; 64:3282-3298. [PMID: 33724820 DOI: 10.1021/acs.jmedchem.0c02159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Macrocyclic peptides are an important modality in drug discovery, but molecular design is limited due to the complexity of their conformational landscape. To better understand conformational propensities, global strain energies were estimated for 156 protein-macrocyclic peptide cocrystal structures. Unexpectedly large strain energies were observed when the bound-state conformations were modeled with positional restraints. Instead, low-energy conformer ensembles were generated using xGen that fit experimental X-ray electron density maps and gave reasonable strain energy estimates. The ensembles featured significant conformational adjustments while still fitting the electron density as well or better than the original coordinates. Strain estimates suggest the interaction energy in protein-ligand complexes can offset a greater amount of strain for macrocyclic peptides than for small molecules and non-peptidic macrocycles. Across all molecular classes, the approximate upper bound on global strain energies had the same relationship with molecular size, and bound-state ensembles from xGen yielded favorable binding energy estimates.
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Affiliation(s)
- Alexander C Brueckner
- Computational & Structural Chemistry, Merck & Co Inc, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Qiaolin Deng
- Computational & Structural Chemistry, Merck & Co Inc, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Ann E Cleves
- Bioengineering and Therapeutic Sciences, University of California San Francisco, Box 0128, San Francisco, California 94158, United States
| | - Charles A Lesburg
- Computational and Structural Chemistry, Merck and Co Inc, 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Juan C Alvarez
- Computational and Structural Chemistry, Merck and Co Inc, 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Mikhail Y Reibarkh
- Analytical Research and Development, Merck & Co Inc, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Edward C Sherer
- Analytical Research and Development, Merck & Co Inc, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Ajay N Jain
- Bioengineering and Therapeutic Sciences, University of California San Francisco, Box 0128, San Francisco, California 94158, United States
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