151
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BONAKALA SATYANARAYANA, BALASUBRAMANIAN SUNDARAM. Modelling Gas Adsorption in Porous Solids: Roles of Surface Chemistry and Pore Architecture. J CHEM SCI 2015. [DOI: 10.1007/s12039-015-0939-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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152
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Vilseck JZ, Kostal J, Tirado-Rives J, Jorgensen WL. Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions. J Comput Chem 2015; 36:2064-74. [PMID: 26311531 PMCID: PMC4575649 DOI: 10.1002/jcc.24045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 01/06/2023]
Abstract
Hybrid quantum mechanics and molecular mechanics (QM/MM) computer simulations have become an indispensable tool for studying chemical and biological phenomena for systems too large to treat with QM alone. For several decades, semiempirical QM methods have been used in QM/MM simulations. However, with increased computational resources, the introduction of ab initio and density function methods into on-the-fly QM/MM simulations is being increasingly preferred. This adaptation can be accomplished with a program interface that tethers independent QM and MM software packages. This report introduces such an interface for the BOSS and Gaussian programs, featuring modification of BOSS to request QM energies and partial atomic charges from Gaussian. A customizable C-shell linker script facilitates the interprogram communication. The BOSS-Gaussian interface also provides convenient access to Charge Model 5 (CM5) partial atomic charges for multiple purposes including QM/MM studies of reactions. In this report, the BOSS-Gaussian interface is applied to a nitroaldol (Henry) reaction and two methyl transfer reactions in aqueous solution. Improved agreement with experiment is found by determining free-energy surfaces with MP2/CM5 QM/MM simulations than previously reported investigations using semiempirical methods.
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Affiliation(s)
- Jonah Z. Vilseck
- Department of Chemistry, Yale University, New Haven, CT 06520-8107USA
| | - Jakub Kostal
- Department of Chemistry, Yale University, New Haven, CT 06520-8107USA
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153
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Ligeour C, Dupin L, Angeli A, Vergoten G, Vidal S, Meyer A, Souteyrand E, Vasseur JJ, Chevolot Y, Morvan F. Importance of topology for glycocluster binding to Pseudomonas aeruginosa and Burkholderia ambifaria bacterial lectins. Org Biomol Chem 2015; 13:11244-54. [PMID: 26412676 DOI: 10.1039/c5ob01445j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Pseudomonas aeruginosa (PA) and Burkholderia ambifaria (BA) are two opportunistic Gram negative bacteria and major infectious agents involved in lung infection of cystic fibrosis patients. Both bacteria can develop resistance to conventional antibiotherapies. An alternative strategy consists of targeting virulence factors in particular lectins with high affinity ligands such as multivalent glycoclusters. LecA (PA-IL) and LecB (PA-IIL) are two tetravalent lectins from PA that recognise galactose and fucose respectively. BambL lectin from BA is trimeric with 2 binding sites per monomer and is also specific for fucose. These three lectins are potential therapeutic targets in an anti-adhesive anti-bacterial approach. Herein, we report the synthesis of 18 oligonucleotide pentofuranose-centered or mannitol-centered glycoclusters leading to tri-, penta- or decavalent clusters with different topologies. The linker arm length between the core and the carbohydrate epitope was also varied leading to 9 galactoclusters targeting LecA and 9 fucoclusters targeting both LecB and BambL. Their dissociation constants (Kd) were determined using a DNA-based carbohydrate microarray technology. The trivalent xylo-centered galactocluster and the ribo-centered fucocluster exhibited the best affinity for LecA and LecB respectively while the mannitol-centered decafucocluster displayed the best affinity to BambL. These data demonstrated that the topology and nature of linkers were the predominant factors for achieving high affinity rather than valency.
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Affiliation(s)
- Caroline Ligeour
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université de Montpellier, ENSCM, place Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France.
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154
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Lovering F, Aevazelis C, Chang J, Dehnhardt C, Fitz L, Han S, Janz K, Lee J, Kaila N, McDonald J, Moore W, Moretto A, Papaioannou N, Richard D, Ryan MS, Wan ZK, Thorarensen A. Imidazotriazines: Spleen Tyrosine Kinase (Syk) Inhibitors Identified by Free-Energy Perturbation (FEP). ChemMedChem 2015; 11:217-33. [DOI: 10.1002/cmdc.201500333] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Frank Lovering
- Worldwide Medicinal Chemistry; Pfizer Worldwide R&D; 610 Main Street Cambridge MA 02139 USA
| | - Cristina Aevazelis
- Inflammation and Immunity; Pfizer Worldwide R&D; 610 Main Street Cambridge MA 02139 USA
| | - Jeanne Chang
- Worldwide Medicinal Chemistry; Pfizer Worldwide R&D; Eastern Point Road Groton CT 06340 USA
| | - Christoph Dehnhardt
- Worldwide Medicinal Chemistry; Pfizer Worldwide R&D; 610 Main Street Cambridge MA 02139 USA
| | - Lori Fitz
- Inflammation and Immunity; Pfizer Worldwide R&D; 610 Main Street Cambridge MA 02139 USA
| | - Seungil Han
- Worldwide Medicinal Chemistry; Pfizer Worldwide R&D; Eastern Point Road Groton CT 06340 USA
| | - Kristin Janz
- Worldwide Medicinal Chemistry; Pfizer Worldwide R&D; 610 Main Street Cambridge MA 02139 USA
| | - Julie Lee
- Inflammation and Immunity; Pfizer Worldwide R&D; 610 Main Street Cambridge MA 02139 USA
| | - Neelu Kaila
- Worldwide Medicinal Chemistry; Pfizer Worldwide R&D; 610 Main Street Cambridge MA 02139 USA
| | - Joseph McDonald
- Worldwide Medicinal Chemistry; Pfizer Worldwide R&D; 610 Main Street Cambridge MA 02139 USA
| | - William Moore
- Worldwide Medicinal Chemistry; Pfizer Worldwide R&D; 610 Main Street Cambridge MA 02139 USA
| | - Alessandro Moretto
- Worldwide Medicinal Chemistry; Pfizer Worldwide R&D; 610 Main Street Cambridge MA 02139 USA
| | - Nikolaos Papaioannou
- Worldwide Medicinal Chemistry; Pfizer Worldwide R&D; 610 Main Street Cambridge MA 02139 USA
| | - David Richard
- Worldwide Medicinal Chemistry; Pfizer Worldwide R&D; 610 Main Street Cambridge MA 02139 USA
| | - Mark S. Ryan
- Inflammation and Immunity; Pfizer Worldwide R&D; 610 Main Street Cambridge MA 02139 USA
| | - Zhao-Kui Wan
- Worldwide Medicinal Chemistry; Pfizer Worldwide R&D; 610 Main Street Cambridge MA 02139 USA
| | - Atli Thorarensen
- Worldwide Medicinal Chemistry; Pfizer Worldwide R&D; 610 Main Street Cambridge MA 02139 USA
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155
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Dodda LS, Vilseck JZ, Cutrona KJ, Jorgensen WL. Evaluation of CM5 Charges for Nonaqueous Condensed-Phase Modeling. J Chem Theory Comput 2015; 11:4273-82. [PMID: 26575922 PMCID: PMC4857764 DOI: 10.1021/acs.jctc.5b00414] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Partial atomic charges for neutral molecules from quantum mechanical calculations are typically scaled for use in molecular modeling of liquid-phase systems. Optimal scale factors of 1.14 for CM1A and 1.27 for CM5 charges were previously determined for minimizing errors in free energies of hydration. The adequacy of the 1.14*CM1A and 1.27*CM5 models are evaluated here in pure liquid simulations in combination with the OPLS-AA force field. For 22 organic liquids, the 1.14*CM1A and 1.27*CM5 models yield mean unsigned errors (MUEs) of ca. 1.40 kcal/mol for heats of vaporization. Not surprisingly, this reflects overpolarization with the scale factors derived for aqueous media. Prediction of pure liquid properties using CM5 charges is optimized using a scale factor of 1.14, which reduces the MUE for heats of vaporization to 0.89 kcal/mol. However, due to the impracticality of using different scale factors in different explicit-solvent condensed-phase simulations, a universal scale factor of 1.20 emerged for CM5 charges. This provides a balance between errors in computed pure liquid properties and free energies of hydration. Computation of free energies of hydration by the GB/SA method further found that 1.20 is equally suited for use in explicit or implicit treatments of aqueous solvation. With 1.20*CM5 charges, a variety of condensed-phase simulations can be pursued while maintaining average errors of 1.0 kcal/mol in key thermodynamic properties.
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Affiliation(s)
- Leela S. Dodda
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Jonah Z. Vilseck
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Kara J. Cutrona
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L. Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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156
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Robertson M, Tirado-Rives J, Jorgensen WL. Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field. J Chem Theory Comput 2015; 11:3499-509. [PMID: 26190950 PMCID: PMC4504185 DOI: 10.1021/acs.jctc.5b00356] [Citation(s) in RCA: 491] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Indexed: 11/28/2022]
Abstract
The development and validation of new peptide dihedral parameters are reported for the OPLS-AA force field. High accuracy quantum chemical methods were used to scan φ, ψ, χ1, and χ2 potential energy surfaces for blocked dipeptides. New Fourier coefficients for the dihedral angle terms of the OPLS-AA force field were fit to these surfaces, utilizing a Boltzmann-weighted error function and systematically examining the effects of weighting temperature. To prevent overfitting to the available data, a minimal number of new residue-specific and peptide-specific torsion terms were developed. Extensive experimental solution-phase and quantum chemical gas-phase benchmarks were used to assess the quality of the new parameters, named OPLS-AA/M, demonstrating significant improvement over previous OPLS-AA force fields. A Boltzmann weighting temperature of 2000 K was determined to be optimal for fitting the new Fourier coefficients for dihedral angle parameters. Conclusions are drawn from the results for best practices for developing new torsion parameters for protein force fields.
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Affiliation(s)
- Michael
J. Robertson
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L. Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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157
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Lionta E, Spyrou G, Vassilatis DK, Cournia Z. Structure-based virtual screening for drug discovery: principles, applications and recent advances. Curr Top Med Chem 2015; 14:1923-38. [PMID: 25262799 PMCID: PMC4443793 DOI: 10.2174/1568026614666140929124445] [Citation(s) in RCA: 526] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 01/01/2014] [Accepted: 02/18/2014] [Indexed: 02/06/2023]
Abstract
Structure-based drug discovery (SBDD) is becoming an essential tool in assisting fast and cost-efficient lead
discovery and optimization. The application of rational, structure-based drug design is proven to be more efficient than the
traditional way of drug discovery since it aims to understand the molecular basis of a disease and utilizes the knowledge
of the three-dimensional structure of the biological target in the process. In this review, we focus on the principles and applications
of Virtual Screening (VS) within the context of SBDD and examine different procedures ranging from the initial
stages of the process that include receptor and library pre-processing, to docking, scoring and post-processing of topscoring
hits. Recent improvements in structure-based virtual screening (SBVS) efficiency through ensemble docking, induced
fit and consensus docking are also discussed. The review highlights advances in the field within the framework of
several success studies that have led to nM inhibition directly from VS and provides recent trends in library design as well
as discusses limitations of the method. Applications of SBVS in the design of substrates for engineered proteins that enable
the discovery of new metabolic and signal transduction pathways and the design of inhibitors of multifunctional proteins
are also reviewed. Finally, we contribute two promising VS protocols recently developed by us that aim to increase
inhibitor selectivity. In the first protocol, we describe the discovery of micromolar inhibitors through SBVS designed to
inhibit the mutant H1047R PI3Kα kinase. Second, we discuss a strategy for the identification of selective binders for the
RXRα nuclear receptor. In this protocol, a set of target structures is constructed for ensemble docking based on binding
site shape characterization and clustering, aiming to enhance the hit rate of selective inhibitors for the desired protein target
through the SBVS process.
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Affiliation(s)
| | | | | | - Zoe Cournia
- Biomedical Research Foundation of the Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece.
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158
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Kostal J, Voutchkova-Kostal A, Anastas PT, Zimmerman JB. Identifying and designing chemicals with minimal acute aquatic toxicity. Proc Natl Acad Sci U S A 2015; 112:6289-94. [PMID: 24639521 PMCID: PMC4443366 DOI: 10.1073/pnas.1314991111] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Industrial ecology has revolutionized our understanding of material stocks and flows in our economy and society. For this important discipline to have even deeper impact, we must understand the inherent nature of these materials in terms of human health and the environment. This paper focuses on methods to design synthetic chemicals to reduce their intrinsic ability to cause adverse consequence to the biosphere. Advances in the fields of computational chemistry and molecular toxicology in recent decades allow the development of predictive models that inform the design of molecules with reduced potential to be toxic to humans or the environment. The approach presented herein builds on the important work in quantitative structure-activity relationships by linking toxicological and chemical mechanistic insights to the identification of critical physical-chemical properties needed to be modified. This in silico approach yields design guidelines using boundary values for physiochemical properties. Acute aquatic toxicity serves as a model endpoint in this study. Defining value ranges for properties related to bioavailability and reactivity eliminates 99% of the chemicals in the highest concern for acute aquatic toxicity category. This approach and its future implementations are expected to yield very powerful tools for life cycle assessment practitioners and molecular designers that allow rapid assessment of multiple environmental and human health endpoints and inform modifications to minimize hazard.
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Affiliation(s)
- Jakub Kostal
- Sustainability A to Z, LLC, Guilford, CT 06437; and
| | | | | | - Julie Beth Zimmerman
- School of Forestry and Environmental Studies and Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06511
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159
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Somani S, Okamoto Y, Ballard AJ, Wales DJ. Equilibrium molecular thermodynamics from Kirkwood sampling. J Phys Chem B 2015; 119:6155-69. [PMID: 25915525 PMCID: PMC4500650 DOI: 10.1021/acs.jpcb.5b01800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
We
present two methods for barrierless equilibrium sampling of
molecular systems based on the recently proposed Kirkwood method (J. Chem. Phys.2009, 130,
134102). Kirkwood sampling employs low-order correlations among internal
coordinates of a molecule for random (or non-Markovian) sampling of
the high dimensional conformational space. This is a geometrical sampling
method independent of the potential energy surface. The first method
is a variant of biased Monte Carlo, where Kirkwood sampling is used
for generating trial Monte Carlo moves. Using this method, equilibrium
distributions corresponding to different temperatures and potential
energy functions can be generated from a given set of low-order correlations.
Since Kirkwood samples are generated independently, this method is
ideally suited for massively parallel distributed computing. The second
approach is a variant of reservoir replica exchange, where Kirkwood
sampling is used to construct a reservoir of conformations, which
exchanges conformations with the replicas performing equilibrium sampling
corresponding to different thermodynamic states. Coupling with the
Kirkwood reservoir enhances sampling by facilitating global jumps
in the conformational space. The efficiency of both methods depends
on the overlap of the Kirkwood distribution with the target equilibrium
distribution. We present proof-of-concept results for a model nine-atom
linear molecule and alanine dipeptide.
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Affiliation(s)
- Sandeep Somani
- †University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Yuko Okamoto
- ‡Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.,§Structural Biology Research Center, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.,∥Center for Computational Science, Graduate School of Engineering, Nagoya University, Nagoya, Aichi 464-8603, Japan.,⊥Information Technology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Andrew J Ballard
- †University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - David J Wales
- †University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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160
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Vilseck JZ, Tirado-Rives J, Jorgensen WL. Determination of partial molar volumes from free energy perturbation theory. Phys Chem Chem Phys 2015; 17:8407-15. [PMID: 25589343 PMCID: PMC4872387 DOI: 10.1039/c4cp05304d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood-Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm(3) mol(-1). The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute-solvent interactions.
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Affiliation(s)
- Jonah Z Vilseck
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA.
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161
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Li M, Cao H, Han D, Li X, He M. Kinetics and mechanism of the reactions of OH radicals with p-nitroaniline in gas-phase and aqueous solution. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.12.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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162
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Dziedzic P, Cisneros JA, Robertson MJ, Hare AA, Danford NE, Baxter RHG, Jorgensen WL. Design, synthesis, and protein crystallography of biaryltriazoles as potent tautomerase inhibitors of macrophage migration inhibitory factor. J Am Chem Soc 2015; 137:2996-3003. [PMID: 25697265 DOI: 10.1021/ja512112j] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Optimization is reported for biaryltriazoles as inhibitors of the tautomerase activity of human macrophage migration inhibitory factor (MIF), a proinflammatory cytokine associated with numerous inflammatory diseases and cancer. A combined approach was taken featuring organic synthesis, enzymatic assaying, crystallography, and modeling including free-energy perturbation (FEP) calculations. X-ray crystal structures for 3a and 3b bound to MIF are reported and provided a basis for the modeling efforts. The accommodation of the inhibitors in the binding site is striking with multiple hydrogen bonds and aryl-aryl interactions. Additional modeling encouraged pursuit of 5-phenoxyquinolinyl analogues, which led to the very potent compound 3s. Activity was further enhanced by addition of a fluorine atom adjacent to the phenolic hydroxyl group as in 3w, 3z, 3aa, and 3bb to strengthen a key hydrogen bond. It is also shown that physical properties of the compounds can be modulated by variation of solvent-exposed substituents. Several of the compounds are likely the most potent known MIF tautomerase inhibitors; the most active ones are more than 1000-fold more active than the well-studied (R)-ISO-1 and more than 200-fold more active than the chromen-4-one Orita-13.
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Affiliation(s)
- Pawel Dziedzic
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
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163
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Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL, Masse C, Knight JL, Steinbrecher T, Beuming T, Damm W, Harder E, Sherman W, Brewer M, Wester R, Murcko M, Frye L, Farid R, Lin T, Mobley DL, Jorgensen WL, Berne BJ, Friesner RA, Abel R. Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. J Am Chem Soc 2015; 137:2695-703. [PMID: 25625324 DOI: 10.1021/ja512751q] [Citation(s) in RCA: 801] [Impact Index Per Article: 89.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Designing tight-binding ligands is a primary objective of small-molecule drug discovery. Over the past few decades, free-energy calculations have benefited from improved force fields and sampling algorithms, as well as the advent of low-cost parallel computing. However, it has proven to be challenging to reliably achieve the level of accuracy that would be needed to guide lead optimization (∼5× in binding affinity) for a wide range of ligands and protein targets. Not surprisingly, widespread commercial application of free-energy simulations has been limited due to the lack of large-scale validation coupled with the technical challenges traditionally associated with running these types of calculations. Here, we report an approach that achieves an unprecedented level of accuracy across a broad range of target classes and ligands, with retrospective results encompassing 200 ligands and a wide variety of chemical perturbations, many of which involve significant changes in ligand chemical structures. In addition, we have applied the method in prospective drug discovery projects and found a significant improvement in the quality of the compounds synthesized that have been predicted to be potent. Compounds predicted to be potent by this approach have a substantial reduction in false positives relative to compounds synthesized on the basis of other computational or medicinal chemistry approaches. Furthermore, the results are consistent with those obtained from our retrospective studies, demonstrating the robustness and broad range of applicability of this approach, which can be used to drive decisions in lead optimization.
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Affiliation(s)
- Lingle Wang
- Schrödinger, Inc. , 120 West 45th Street, New York, New York 10036, United States
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164
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Jorgensen WL. Autobiography of William L. Jorgensen: Scientific History and Recollections. J Phys Chem B 2015; 119:624-32. [DOI: 10.1021/jp510442j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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165
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Tintori C, Fallacara AL, Radi M, Zamperini C, Dreassi E, Crespan E, Maga G, Schenone S, Musumeci F, Brullo C, Richters A, Gasparrini F, Angelucci A, Festuccia C, Delle Monache S, Rauh D, Botta M. Combining X-ray Crystallography and Molecular Modeling toward the Optimization of Pyrazolo[3,4-d]pyrimidines as Potent c-Src Inhibitors Active in Vivo against Neuroblastoma. J Med Chem 2014; 58:347-61. [DOI: 10.1021/jm5013159] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Cristina Tintori
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena Via Aldo Moro 2, 53100 Siena, Italy
| | - Anna Lucia Fallacara
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena Via Aldo Moro 2, 53100 Siena, Italy
- Dipartimento
di Chimica e Tecnologie Farmaceutiche, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Marco Radi
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena Via Aldo Moro 2, 53100 Siena, Italy
| | - Claudio Zamperini
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena Via Aldo Moro 2, 53100 Siena, Italy
| | - Elena Dreassi
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena Via Aldo Moro 2, 53100 Siena, Italy
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Silvia Schenone
- Dipartimento
di Farmacia, Università degli Studi di Genova, Viale Benedetto
XV, 3, 16132 Genova, Italy
| | - Francesca Musumeci
- Dipartimento
di Farmacia, Università degli Studi di Genova, Viale Benedetto
XV, 3, 16132 Genova, Italy
| | - Chiara Brullo
- Dipartimento
di Farmacia, Università degli Studi di Genova, Viale Benedetto
XV, 3, 16132 Genova, Italy
| | - André Richters
- Department
of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Francesca Gasparrini
- Dipartimento
di Medicina Molecolare, Sapienza Università di Roma, Piazzale Aldo
Moro 5, 00185 Roma, Italy
| | - Adriano Angelucci
- Dipartimento
di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell’Aquila, Via Vetoio, 67100 Coppito, L’Aquila, Italy
| | - Claudio Festuccia
- Dipartimento
di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell’Aquila, Via Vetoio, 67100 Coppito, L’Aquila, Italy
| | - Simona Delle Monache
- Dipartimento
di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi dell’Aquila, Via Vetoio, 67100 Coppito, L’Aquila, Italy
| | - Daniel Rauh
- Department
of Chemistry and Chemical Biology, Technical University of Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Maurizio Botta
- Dipartimento
di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena Via Aldo Moro 2, 53100 Siena, Italy
- Sbarro
Institute for Cancer Research and Molecular Medicine, Center for Biotechnology,
College of Science and Technology, Temple University, BioLife Science
Building, Suite 333, 1900 North 12th Street, Philadelphia, Pennsylvania 19122, United States
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166
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Three-dimensional protein structure prediction: Methods and computational strategies. Comput Biol Chem 2014; 53PB:251-276. [DOI: 10.1016/j.compbiolchem.2014.10.001] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 10/03/2014] [Accepted: 10/07/2014] [Indexed: 01/01/2023]
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167
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Doron D, Stojković V, Gakhar L, Vardi-Kilshtain A, Kohen A, Major DT. Free energy simulations of active-site mutants of dihydrofolate reductase. J Phys Chem B 2014; 119:906-16. [PMID: 25382260 DOI: 10.1021/jp5059963] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This study employs hybrid quantum mechanics-molecular mechanics (QM/MM) simulations to investigate the effect of mutations of the active-site residue I14 of E. coli dihydrofolate reductase (DHFR) on the hydride transfer. Recent kinetic measurements of the I14X mutants (X = V, A, and G) indicated slower hydride transfer rates and increasingly temperature-dependent kinetic isotope effects (KIEs) with systematic reduction of the I14 side chain. The QM/MM simulations show that when the original isoleucine residue is substituted in silico by valine, alanine, or glycine (I14V, I14A, and I14G DHFR, respectively), the free energy barrier height of the hydride transfer reaction increases relative to the wild-type enzyme. These trends are in line with the single-turnover rate measurements reported for these systems. In addition, extended dynamics simulations of the reactive Michaelis complex reveal enhanced flexibility in the mutants, and in particular for the I14G mutant, including considerable fluctuations of the donor-acceptor distance (DAD) and the active-site hydrogen bonding network compared with those detected in the native enzyme. These observations suggest that the perturbations induced by the mutations partly impair the active-site environment in the reactant state. On the other hand, the average DADs at the transition state of all DHFR variants are similar. Crystal structures of I14 mutants (V, A, and G) confirmed the trend of increased flexibility of the M20 and other loops.
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Affiliation(s)
- Dvir Doron
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University , Ramat-Gan 5290002, Israel
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168
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Lee LP, Limas NG, Cole DJ, Payne MC, Skylaris CK, Manz TA. Expanding the Scope of Density Derived Electrostatic and Chemical Charge Partitioning to Thousands of Atoms. J Chem Theory Comput 2014; 10:5377-90. [DOI: 10.1021/ct500766v] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Louis P. Lee
- TCM Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom
| | - Nidia Gabaldon Limas
- Chemical & Materials Engineering Department, New Mexico State University, Las Cruces, New Mexico 88003-8001, United States
| | - Daniel J. Cole
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Mike C. Payne
- TCM Group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, United Kingdom
| | - Chris-Kriton Skylaris
- School
of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Thomas A. Manz
- Chemical & Materials Engineering Department, New Mexico State University, Las Cruces, New Mexico 88003-8001, United States
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169
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Kaminski GA. Computational Studies of the Effect of Shock Waves on the Binding of Model Complexes. J Chem Theory Comput 2014; 10:4972-4981. [PMID: 25400519 PMCID: PMC4230379 DOI: 10.1021/ct500461s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 01/03/2023]
Abstract
We have simulated effects of a shock wave in water that would result from the collapse of a cavitation bubble on binding in model complexes. We have considered a benzene dimer, a pair of uracil molecules, a complex of fragments of the X-linked inhibitor of apoptosis and caspase-9, and a fragment of c-Myc oncoprotein in binding with its dimerization partner Max. The effect of the shock waves was simulated by adding a momentum to a slab of solvent water molecules and observing the system as the slab moved and caused changes. In the cases of the small molecular pairs, the passage of the shock waves lead to dissociation of the complexes. The behavior of the protein systems was more complex, yet significant disruption of the binding and geometry was also observed. In all the cases, the effects did not occur during the immediate impact of the high-momentum solvent molecules, but rather during the expansion of the compressed system that followed the passage of the waves. The rationale of the studies was in attempting to understand the strong effects that irradiation with a low-intensity ultrasound can have on biomolecular systems, because such ultrasound irradiation can cause cavitation bubbles to be produced and collapse, thus leading to local shock wave generation. The long-term objective is to contribute to future design of synergetic ultrasound and chemical drug strategy of protein inhibition.
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Affiliation(s)
- George A. Kaminski
- Department of Chemistry and
Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, United States
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170
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Nomme J, Li Z, Gipson RM, Wang J, Armijo AL, Le T, Poddar S, Smith T, Santarsiero BD, Nguyen HA, Czernin J, Alexandrova AN, Jung ME, Radu CG, Lavie A. Structure-guided development of deoxycytidine kinase inhibitors with nanomolar affinity and improved metabolic stability. J Med Chem 2014; 57:9480-94. [PMID: 25341194 PMCID: PMC4255734 DOI: 10.1021/jm501124j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Recently,
we have shown that small molecule dCK inhibitors in combination
with pharmacological perturbations of de novo dNTP biosynthetic pathways
could eliminate acute lymphoblastic leukemia cells in animal models.
However, our previous lead compound had a short half-life in vivo. Therefore, we set out to develop dCK inhibitors with favorable pharmacokinetic
properties. We delineated the sites of the inhibitor for modification,
guided by crystal structures of dCK in complex with the lead compound
and with derivatives. Crystal structure of the complex between dCK
and the racemic mixture of our new lead compound indicated that the R-isomer is responsible for kinase inhibition. This was
corroborated by kinetic analysis of the purified enantiomers, which
showed that the R-isomer has >60-fold higher affinity
than the S-isomer for dCK. This new lead compound
has significantly improved metabolic stability, making it a prime
candidate for dCK-inhibitor based therapies against hematological
malignancies and, potentially, other cancers.
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Affiliation(s)
- Julian Nomme
- Department of Biochemistry and Molecular Genetics, and ‡Center for Pharmaceutical Biotechnology, University of Illinois at Chicago , Chicago, Illinois 60607, United States
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171
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Acevedo O. Simulating chemical reactions in ionic liquids using QM/MM methodology. J Phys Chem A 2014; 118:11653-66. [PMID: 25329366 DOI: 10.1021/jp507967z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The use of ionic liquids as a reaction medium for chemical reactions has dramatically increased in recent years due in large part to the numerous reported advances in catalysis and organic synthesis. In some extreme cases, ionic liquids have been shown to induce mechanistic changes relative to conventional solvents. Despite the large interest in the solvents, a clear understanding of the molecular factors behind their chemical impact is largely unknown. This feature article reviews our efforts developing and applying mixed quantum and molecular mechanical (QM/MM) methodology to elucidate the microscopic details of how these solvents operate to enhance rates and alter mechanisms for industrially and academically important reactions, e.g., Diels-Alder, Kemp eliminations, nucleophilic aromatic substitutions, and β-eliminations. Explicit solvent representation provided the medium dependence of the activation barriers and atomic-level characterization of the solute-solvent interactions responsible for the experimentally observed "ionic liquid effects". Technical advances are also discussed, including a linear-scaling pairwise electrostatic interaction alternative to Ewald sums, an efficient polynomial fitting method for modeling proton transfers, and the development of a custom ionic liquid OPLS-AA force field.
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Affiliation(s)
- Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849, United States
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172
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Carvalho ATP, Barrozo A, Doron D, Kilshtain AV, Major DT, Kamerlin SCL. Challenges in computational studies of enzyme structure, function and dynamics. J Mol Graph Model 2014; 54:62-79. [PMID: 25306098 DOI: 10.1016/j.jmgm.2014.09.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 09/13/2014] [Accepted: 09/16/2014] [Indexed: 01/23/2023]
Abstract
In this review we give an overview of the field of Computational enzymology. We start by describing the birth of the field, with emphasis on the work of the 2013 chemistry Nobel Laureates. We then present key features of the state-of-the-art in the field, showing what theory, accompanied by experiments, has taught us so far about enzymes. We also briefly describe computational methods, such as quantum mechanics-molecular mechanics approaches, reaction coordinate treatment, and free energy simulation approaches. We finalize by discussing open questions and challenges.
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Affiliation(s)
- Alexandra T P Carvalho
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Alexandre Barrozo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Dvir Doron
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Alexandra Vardi Kilshtain
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and the Lise Meitner-Minerva Center of Computational Quantum Chemistry Bar-Ilan University, Ramat-Gan 52900, Israel.
| | - Shina Caroline Lynn Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
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173
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Casoni F, Dupin L, Vergoten G, Meyer A, Ligeour C, Géhin T, Vidal O, Souteyrand E, Vasseur JJ, Chevolot Y, Morvan F. The influence of the aromatic aglycon of galactoclusters on the binding of LecA: a case study with O-phenyl, S-phenyl, O-benzyl, S-benzyl, O-biphenyl and O-naphthyl aglycons. Org Biomol Chem 2014; 12:9166-79. [DOI: 10.1039/c4ob01599a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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174
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Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design. Biochim Biophys Acta Gen Subj 2014; 1850:966-971. [PMID: 25196360 DOI: 10.1016/j.bbagen.2014.08.018] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 08/26/2014] [Accepted: 08/28/2014] [Indexed: 11/24/2022]
Abstract
BACKGROUND Non-nucleoside inhibitors of HIV reverse transcriptase are an important component of treatment against HIV infection. Novel inhibitors are sought that increase potency against variants that contain the Tyr181Cys mutation. METHODS Molecular dynamics based free energy perturbation simulations have been run to study factors that contribute to protein-ligand binding, and the results are compared with those from previous Monte Carlo based simulations and activity data. RESULTS Predictions of protein-ligand binding modes are very consistent for the two simulation methods; the accord is attributed to the use of an enhanced sampling protocol. The Tyr181Cys binding pocket supports large, hydrophobic substituents, which is in good agreement with experiment. CONCLUSIONS Although some discrepancies exist between the results of the two simulation methods and experiment, free energy perturbation simulations can be used to rapidly test small molecules for gains in binding affinity. GENERAL SIGNIFICANCE Free energy perturbation methods show promise in providing fast, reliable and accurate data that can be used to complement experiment in lead optimization projects. This article is part of a Special Issue entitled "Recent developments of molecular dynamics".
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175
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Lexa KW, Goh GB, Carlson HA. Parameter choice matters: validating probe parameters for use in mixed-solvent simulations. J Chem Inf Model 2014; 54:2190-9. [PMID: 25058662 PMCID: PMC4144759 DOI: 10.1021/ci400741u] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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Probe mapping is a common approach
for identifying potential binding
sites in structure-based drug design; however, it typically relies
on energy minimizations of probes in the gas phase and a static protein
structure. The mixed-solvent molecular dynamics (MixMD) approach was
recently developed to account for full protein flexibility and solvation
effects in hot-spot mapping. Our first study used only acetonitrile
as a probe, and here, we have augmented the set of functional group
probes through careful testing and parameter validation. A diverse
range of probes are needed in order to map complex binding interactions.
A small variation in probe parameters can adversely effect mixed-solvent
behavior, which we highlight with isopropanol. We tested 11 solvents
to identify six with appropriate behavior in TIP3P water to use as
organic probes in the MixMD method. In addition to acetonitrile and
isopropanol, we have identified acetone, N-methylacetamide,
imidazole, and pyrimidine. These probe solvents will enable MixMD
studies to recover hydrogen-bonding sites, hydrophobic pockets, protein–protein
interactions, and aromatic hotspots. Also, we show that ternary-solvent
systems can be incorporated within a single simulation. Importantly,
these binary and ternary solvents do not require artificial repulsion
terms like other methods. Within merely 5 ns, layered solvent boxes
become evenly mixed for soluble probes. We used radial distribution
functions to evaluate solvent behavior, determine adequate mixing,
and confirm the absence of phase separation. We recommend that radial
distribution functions should be used to assess adequate sampling
in all mixed-solvent techniques rather than the current practice of
examining the solvent ratios at the edges of the solvent box.
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Affiliation(s)
- Katrina W Lexa
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor , 428 Church St., Ann Arbor, Michigan 48109-1065, United States
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176
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Vilseck J, Tirado-Rives J, Jorgensen WL. Evaluation of CM5 Charges for Condensed-Phase Modeling. J Chem Theory Comput 2014; 10:2802-2812. [PMID: 25061445 PMCID: PMC4095915 DOI: 10.1021/ct500016d] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Indexed: 11/30/2022]
Abstract
The recently developed Charge Model 5 (CM5) is tested for its utility in condensed-phase simulations. The CM5 approach, which derives partial atomic charges from Hirshfeld population analyses, provides excellent results for gas-phase dipole moments and is applicable to all elements of the periodic table. Herein, the adequacy of scaled CM5 charges for use in modeling aqueous solutions has been evaluated by computing free energies of hydration (ΔGhyd) for 42 neutral organic molecules via Monte Carlo statistical mechanics. An optimal scaling factor for the CM5 charges was determined to be 1.27, resulting in a mean unsigned error (MUE) of 1.1 kcal/mol for the free energies of hydration. Testing for an additional 20 molecules gave an MUE of 1.3 kcal/mol. The high precision of the results is confirmed by free energy calculations using both sequential perturbations and complete molecular annihilation. Performance for specific functional groups is discussed; sulfur-containing molecules yield the largest errors. In addition, the scaling factor of 1.27 is shown to be appropriate for CM5 charges derived from a variety of density functional methods and basis sets. Though the average errors from the 1.27*CM5 results are only slightly lower than those using 1.14*CM1A charges, the broader applicability and easier access to CM5 charges via the Gaussian program are additional attractive features. The 1.27*CM5 charge model can be used for an enormous variety of applications in conjunction with many fixed-charge force fields and molecular modeling programs.
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Affiliation(s)
- Jonah
Z. Vilseck
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L. Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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177
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Yang X, Xue Y. Medium Effects on the 1,3-Dipolar Cycloaddition of Pyridazinium Dicyanomethanide with Ethyl Vinyl Ketone in Pure and Mixed Solvents from QM/MM Simulations. J Org Chem 2014; 79:4863-70. [DOI: 10.1021/jo500184f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xin Yang
- College of Chemistry, Key
Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Ying Xue
- College of Chemistry, Key
Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People’s Republic of China
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178
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Abstract
Proteins are fascinating supramolecular structures, which are able to recognize ligands transforming binding information into chemical signals. They can transfer information across the cell, can catalyse complex chemical reactions, and are able to transform energy into work with much more efficiency than any human engine. The unique abilities of proteins are tightly coupled with their dynamic properties, which are coded in a complex way in the sequence and carefully refined by evolution. Despite its importance, our experimental knowledge of protein dynamics is still rather limited, and mostly derived from theoretical calculations. I will review here, in a systematic way, the current state-of-the-art theoretical approaches to the study of protein dynamics, emphasizing the most recent advances, examples of use and the expected lines of development in the near future.
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Affiliation(s)
- Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri i Reixac 8, Barcelona 08028, Spain.
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179
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Duke RE, Starovoytov ON, Piquemal JP, Cisneros GA. GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations. J Chem Theory Comput 2014; 10:1361-5. [PMID: 26580355 PMCID: PMC5207213 DOI: 10.1021/ct500050p] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
GEM*, a force field that combines Coulomb and Exchange terms calculated with Hermite Gaussians with the polarization, bonded, and modified van der Waals terms from AMOEBA is presented. GEM* is tested on an initial water model fitted at the same level as AMOEBA. The integrals required for the evaluation of the intermolecular Coulomb interactions are efficiently evaluated by means of reciprocal space methods. The GEM* water model is tested by comparing energies and forces for a series of water oligomers and MD simulations. Timings for GEM* compared to AMOEBA are presented and discussed.
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Affiliation(s)
- Robert E. Duke
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Oleg N. Starovoytov
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Jean-Philip Piquemal
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7616 Laboratoire de Chimie Théorique case courrier 137, 4 place Jussieu 75005, Paris, France
- CNRS, UMR 7616 Laboratoire de Chimie Théorique case courrier 137, 4 place Jussieu 75005, Paris, France
| | - G. Andrés Cisneros
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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180
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Yan XC, Schyman P, Jorgensen WL. Cooperative effects and optimal halogen bonding motifs for self-assembling systems. J Phys Chem A 2014; 118:2820-6. [PMID: 24678636 PMCID: PMC3993918 DOI: 10.1021/jp501553j] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
Halogen bonding, due to its directionality
and tunable strength,
is being increasingly utilized in self-assembling materials and crystal
engineering. Using density functional theory (DFT) and molecular mechanics
(OPLS/CM1Ax) calculations, multiply halogen bonded complexes of brominated
imidazole and pyridine are investigated along with their potential
in construction of self-assembling architectures. Dimers with 1–10
halogen bonds are considered and reveal maximal binding energies of
3–36 kcal/mol. Cooperative (nonadditive) effects are found
in complexes that extend both along and perpendicular to the halogen
bonding axes, with interaction energies depending on polarization,
secondary interactions, and ring spacers. Four structural motifs were
identified to yield optimal halogen bonding. For the largest systems,
the excellent agreement found between the DFT and OPLS/CM1Ax results
supports the utility of the latter approach for analysis and design
of self-assembling supramolecular structures.
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Affiliation(s)
- Xin Cindy Yan
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
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181
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Gao JY, Xue Y, Kim CK. Mechanism for the decomposition of 5-aza-2′-deoxycytidine: a theoretical study using Monte Carlo simulation plus local microhydration model. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1462-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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182
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Porzio F, Levert E, Vadnais R, Soldera A. New Insights into the Thermal Stability of the Smectic C Phase. J Phys Chem B 2014; 118:4037-43. [DOI: 10.1021/jp5011605] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- François Porzio
- Centre Québécois des Matériaux Fonctionnels (CQMF), Département de Chimie, Université de Sherbrooke , Sherbrooke (Québec) J1K 2R1, Canada
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183
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HarmonyDOCK: The Structural Analysis of Poses in Protein-Ligand Docking. J Comput Biol 2014; 21:247-56. [DOI: 10.1089/cmb.2009.0111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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184
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Acevedo O, Jorgensen WL. Quantum and Molecular Mechanical (QM/MM) Monte Carlo Techniques for Modeling Condensed-Phase Reactions. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014; 4:422-435. [PMID: 25431625 DOI: 10.1002/wcms.1180] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A recent review (Acc. Chem. Res. 2010, 43:142-151) examined our use and development of a combined quantum and molecular mechanical (QM/MM) technique for modelling organic and enzymatic reactions. Advances included the PDDG/PM3 semiempirical QM (SQM) method, computation of multi-dimensional potentials of mean force (PMF), incorporation of on-the-fly QM in Monte Carlo simulations, and a polynomial quadrature method for rapidly treating proton-transfer reactions. The current article serves as a follow up on our progress. Highlights include new reactions, alternative SQM methods, a polarizable OPLS force field, and novel solvent environments, e.g., "on water" and room temperature ionic liquids. The methodology is strikingly accurate across a wide range of condensed-phase and antibody-catalyzed reactions including substitution, decarboxylation, elimination, isomerization, and pericyclic classes. Comparisons are made to systems treated with continuum-based solvents and ab initio or density functional theory (DFT) methods. Overall, the QM/MM methodology provides detailed characterization of reaction paths, proper configurational sampling, several advantages over implicit solvent models, and a reasonable computational cost.
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Affiliation(s)
- Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | - Wiliiam L Jorgensen
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520-8107
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185
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Yang KR, Xu X, Truhlar DG. Anchor Points Reactive Potential for Bond-Breaking Reactions. J Chem Theory Comput 2014; 10:924-33. [DOI: 10.1021/ct401074s] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ke R. Yang
- Department of Chemistry,
Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431 United States
| | - Xuefei Xu
- Department of Chemistry,
Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431 United States
| | - Donald G. Truhlar
- Department of Chemistry,
Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431 United States
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186
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Ali ST, Antonov L, Fabian WMF. Phenol-quinone tautomerism in (arylazo)naphthols and the analogous Schiff bases: benchmark calculations. J Phys Chem A 2014; 118:778-89. [PMID: 24417622 DOI: 10.1021/jp411502u] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tautomerization energies of a series of isomeric [(4-R-phenyl)azo]naphthols and the analogous Schiff bases (R = N(CH3)2, OCH3, H, CN, NO2) are calculated by LPNO-CEPA/1-CBS using the def2-TZVPP and def2-QZVPP basis sets for extrapolation. The performance of various density functionals (B3LYP, M06-2X, PW6B95, B2PLYP, mPW2PLYP, PWPB95) as well as MP2 and SCS-MP2 is evaluated against these results. M06-2X and SCS-MP2 yield results close to the LPNO-CEPA/1-CBS values. Solvent effects (CCl4, CHCl3, CH3CN, and CH3OH) are treated by a variety of bulk solvation models (SM8, IEFPCM, COSMO, PBF, and SMD) as well as explicit solvation (Monte Carlo free energy perturbation using the OPLSAA force field).
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Affiliation(s)
- S Tahir Ali
- Department of Chemistry, Federal Urdu University of Arts, Science & Technology , Karachi, Sindh, Pakistan
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187
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Cole DJ, Tirado-Rives J, Jorgensen WL. Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering. J Chem Theory Comput 2014; 10:565-571. [PMID: 24803853 PMCID: PMC3985685 DOI: 10.1021/ct400989x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Indexed: 11/30/2022]
Abstract
![]()
With
a view to improving the consistency of free energy perturbation calculations
in Monte Carlo simulations of protein–ligand complexes, we
have implemented the replica exchange with solute tempering (REST)
method in the MCPRO software. By augmenting the standard
REST approach with regular attempted jumps in selected dihedral angles,
our combined method facilitates sampling of ligand binding modes that
are separated by high free energy barriers and ensures that computed
free energy changes are considerably less dependent on the starting
conditions and the chosen mutation pathway than those calculated with
standard Monte Carlo sampling. We have applied the enhanced sampling
method to the calculation of the activities of seven non-nucleoside
inhibitors of HIV-1 reverse transcriptase, and its Tyr181Cys variant,
and have shown that a range of binding orientations is possible depending
on the nature of the ligand and the presence of mutations at the binding
site.
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Affiliation(s)
- Daniel J Cole
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
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188
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Armacost K, Acevedo O. Exploring the Aldol Reaction using Catalytic Antibodies and “On Water” Organocatalysts from QM/MM Calculations. J Am Chem Soc 2013; 136:147-56. [DOI: 10.1021/ja405614p] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Kira Armacost
- Department
of Chemistry,
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Orlando Acevedo
- Department
of Chemistry,
Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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189
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Candotti M, Pérez A, Ferrer-Costa C, Rueda M, Meyer T, Gelpí JL, Orozco M. Exploring early stages of the chemical unfolding of proteins at the proteome scale. PLoS Comput Biol 2013; 9:e1003393. [PMID: 24348236 PMCID: PMC3861036 DOI: 10.1371/journal.pcbi.1003393] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/29/2013] [Indexed: 11/18/2022] Open
Abstract
After decades of using urea as denaturant, the kinetic role of this molecule in the unfolding process is still undefined: does urea actively induce protein unfolding or passively stabilize the unfolded state? By analyzing a set of 30 proteins (representative of all native folds) through extensive molecular dynamics simulations in denaturant (using a range of force-fields), we derived robust rules for urea unfolding that are valid at the proteome level. Irrespective of the protein fold, presence or absence of disulphide bridges, and secondary structure composition, urea concentrates in the first solvation shell of quasi-native proteins, but with a density lower than that of the fully unfolded state. The presence of urea does not alter the spontaneous vibration pattern of proteins. In fact, it reduces the magnitude of such vibrations, leading to a counterintuitive slow down of the atomic-motions that opposes unfolding. Urea stickiness and slow diffusion is, however, crucial for unfolding. Long residence urea molecules placed around the hydrophobic core are crucial to stabilize partially open structures generated by thermal fluctuations. Our simulations indicate that although urea does not favor the formation of partially open microstates, it is not a mere spectator of unfolding that simply displaces to the right of the folded←→unfolded equilibrium. On the contrary, urea actively favors unfolding: it selects and stabilizes partially unfolded microstates, slowly driving the protein conformational ensemble far from the native one and also from the conformations sampled during thermal unfolding. The delicate equilibrium between the folded and functional structure of a protein and its unfolded state is highly dependent on environmental variables such as the solvent. For example the co-solvent urea is a well-known protein denaturant that displaces the equilibrium towards unstructured and non-functional conformations of proteins. However the molecular mechanism behind its ability remains an enigma and the interpretation of the experimental data is still ambiguous. By analyzing a set of representative proteins through extensive molecular dynamics simulations in urea, we provide a robust and consensus picture of the first stages of urea-driven protein unfolding and elucidate the role of urea in accelerating protein unfolding. Our results suggest that urea, thanks to its stickiness and slow diffusion, benefits from the intrinsic flexibility of proteins and stabilizes partially open-states, slowly driving the protein toward unfolding.
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Affiliation(s)
- Michela Candotti
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Joint Research Program in Computational Biology, Institute for Research in Biomedicine and Barcelona Supercomputing Center, Barcelona, Spain
| | - Alberto Pérez
- Laufer Center, Stony Brook University, Stony Brook, New York, United States of America
| | - Carles Ferrer-Costa
- Joint Research Program in Computational Biology, Institute for Research in Biomedicine and Barcelona Supercomputing Center, Barcelona, Spain
| | - Manuel Rueda
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Tim Meyer
- Theoretische und Computergestützte Biophysik, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
| | - Josep Lluís Gelpí
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Joint Research Program in Computational Biology, Institute for Research in Biomedicine and Barcelona Supercomputing Center, Barcelona, Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain
- * E-mail:
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190
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La Pietra V, La Regina G, Coluccia A, Famiglini V, Pelliccia S, Plotkin B, Eldar-Finkelman H, Brancale A, Ballatore C, Crowe A, Brunden KR, Marinelli L, Novellino E, Silvestri R. Design, synthesis, and biological evaluation of 1-phenylpyrazolo[3,4-e]pyrrolo[3,4-g]indolizine-4,6(1H,5H)-diones as new glycogen synthase kinase-3β inhibitors. J Med Chem 2013; 56:10066-78. [PMID: 24295046 DOI: 10.1021/jm401466v] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Compound 5 was selected from our in-house library as a suitable starting point for the rational design of new GSK-3β inhibitors. MC/FEP calculations of 5 led to the identification of a structural class of new GSK-3β inhibitors. Compound 18 inhibited GSK-3β with an IC50 of 0.24 μM and inhibited tau phosphorylation in a cell-based assay. It proved to be a selective inhibitor of GSK-3 against a panel of 17 kinases and showed >10-fold selectivity against CDK2. Calculated physicochemical properties and Volsurf predictions suggested that compound 18 has the potential to diffuse passively across the blood-brain barrier.
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Affiliation(s)
- Valeria La Pietra
- Dipartimento di Farmacia, Università di Napoli Federico II , Via Domenico Montesano 49, I-80131 Napoli, Italy
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191
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Chempath S, Düren T, Sarkisov L, Snurr RQ. Experiences with the publicly available multipurpose simulation code, Music. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.819103] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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192
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Poelking C, Andrienko D. Effect of Polymorphism, Regioregularity and Paracrystallinity on Charge Transport in Poly(3-hexylthiophene) [P3HT] Nanofibers. Macromolecules 2013. [DOI: 10.1021/ma4015966] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Carl Poelking
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Denis Andrienko
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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193
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Lee WG, Gallardo-Macias R, Frey KM, Spasov KA, Bollini M, Anderson KS, Jorgensen WL. Picomolar inhibitors of HIV reverse transcriptase featuring bicyclic replacement of a cyanovinylphenyl group. J Am Chem Soc 2013; 135:16705-13. [PMID: 24151856 PMCID: PMC3877923 DOI: 10.1021/ja408917n] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Members of the catechol diether class are highly potent non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs). The most active compounds yield EC50 values below 0.5 nM in assays using human T-cells infected by wild-type HIV-1. However, these compounds such as rilpivirine, the most recently FDA-approved NNRTI, bear a cyanovinylphenyl (CVP) group. This is an uncommon substructure in drugs that gives reactivity concerns. In the present work, computer simulations were used to design bicyclic replacements for the CVP group. The predicted viability of a 2-cyanoindolizinyl alternative was confirmed experimentally and provided compounds with 0.4 nM activity against the wild-type virus. The compounds also performed well with EC50 values of 10 nM against the challenging HIV-1 variant that contains the Lys103Asn/Tyr181Cys double mutation in the RT enzyme. Indolyl and benzofuranyl analogues were also investigated; the most potent compounds in these cases have EC50 values toward wild-type HIV-1 near 10 nM and high-nanomolar activities toward the double-variant. The structural expectations from the modeling were much enhanced by obtaining an X-ray crystal structure at 2.88 Å resolution for the complex of the parent 2-cyanoindolizine 10b and HIV-1 RT. The aqueous solubilities of the most potent indolizine analogues were also measured to be ~40 μg/mL, which is similar to that for the approved drug efavirenz and ~1000-fold greater than for rilpivirine.
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Affiliation(s)
- Won-Gil Lee
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
| | | | - Kathleen M. Frey
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066
| | - Krasimir A. Spasov
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066
| | - Mariela Bollini
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
| | - Karen S. Anderson
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520-8066
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194
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Sancineto L, Iraci N, Massari S, Attanasio V, Corazza G, Barreca ML, Sabatini S, Manfroni G, Avanzi NR, Cecchetti V, Pannecouque C, Marcello A, Tabarrini O. Computer-Aided Design, Synthesis and Validation of 2-Phenylquinazolinone Fragments as CDK9 Inhibitors with Anti-HIV-1 Tat-Mediated Transcription Activity. ChemMedChem 2013; 8:1941-53. [DOI: 10.1002/cmdc.201300287] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Indexed: 12/20/2022]
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195
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Denton EV, Craig CJ, Pongratz RL, Appelbaum JS, Doerner AE, Narayanan A, Shulman GI, Cline GW, Schepartz A. A β-peptide agonist of the GLP-1 receptor, a class B GPCR. Org Lett 2013; 15:5318-21. [PMID: 24087900 DOI: 10.1021/ol402568j] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Previous work has shown that certain β(3)-peptides can effectively mimic the side chain display of an α-helix and inhibit interactions between proteins, both in vitro and in cultured cells. Here we describe a β(3)-peptide analog of GLP-1, CC-3(Act), that interacts with the GLP-1R extracellular domain (nGLP-1R) in vitro in a manner that competes with exendin-4 and induces GLP-1R-dependent cAMP signaling in cultured CHO-K1 cells expressing GLP-1R.
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Affiliation(s)
- Elizabeth V Denton
- Department of Chemistry, Yale University , New Haven, Connecticut 06511, United States, Department of Internal Medicine, Yale University School of Medicine , New Haven, Connecticut 06536, United States, Department of Cell Biology, Yale University School of Medicine , New Haven, Connecticut 06520, United States, Department of Cellular and Molecular Physiology, Yale University School of Medicine , New Haven, Connecticut 06520, United States, Howard Hughes Medical Institute, Yale University School of Medicine , New Haven, Connecticut 06520, United States, and Department of Molecular, Cellular and Developmental Biology, Yale University , New Haven, Connecticut 06520, United States
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196
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Thellamurege NM, Si D, Cui F, Zhu H, Lai R, Li H. QuanPol: a full spectrum and seamless QM/MM program. J Comput Chem 2013; 34:2816-33. [PMID: 24122765 DOI: 10.1002/jcc.23435] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 08/07/2013] [Accepted: 08/10/2013] [Indexed: 12/29/2022]
Abstract
The quantum chemistry polarizable force field program (QuanPol) is implemented to perform combined quantum mechanical and molecular mechanical (QM/MM) calculations with induced dipole polarizable force fields and induced surface charge continuum solvation models. The QM methods include Hartree-Fock method, density functional theory method (DFT), generalized valence bond theory method, multiconfiguration self-consistent field method, Møller-Plesset perturbation theory method, and time-dependent DFT method. The induced dipoles of the MM atoms and the induced surface charges of the continuum solvation model are self-consistently and variationally determined together with the QM wavefunction. The MM force field methods can be user specified, or a standard force field such as MMFF94, Chemistry at Harvard Molecular Mechanics (CHARMM), Assisted Model Building with Energy Refinement (AMBER), and Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA). Analytic gradients for all of these methods are implemented so geometry optimization and molecular dynamics (MD) simulation can be performed. MD free energy perturbation and umbrella sampling methods are also implemented.
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197
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Bollini M, Cisneros JA, Spasov KA, Anderson KS, Jorgensen WL. Optimization of diarylazines as anti-HIV agents with dramatically enhanced solubility. Bioorg Med Chem Lett 2013; 23:5213-6. [PMID: 23937980 PMCID: PMC3759246 DOI: 10.1016/j.bmcl.2013.06.091] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 06/21/2013] [Accepted: 06/27/2013] [Indexed: 11/24/2022]
Abstract
Non-nucleoside inhibitors of HIV-1 reverse transcriptase are reported that have ca. 100-fold greater solubility than the structurally related drugs etravirine and rilpivirine, while retaining high anti-viral activity. The solubility enhancements come from strategic placement of a morpholinylalkoxy substituent in the entrance channel of the NNRTI binding site. Compound 4d shows low-nanomolar activity similar to etravirine towards wild-type HIV-1 and key viral variants.
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Affiliation(s)
- Mariela Bollini
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
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198
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Murphy JM, Armijo AL, Nomme J, Lee CH, Smith QA, Li Z, Campbell DO, Liao HI, Nathanson DA, Austin WR, Lee JT, Darvish R, Wei L, Wang J, Su Y, Damoiseaux R, Sadeghi S, Phelps ME, Herschman HR, Czernin J, Alexandrova AN, Jung ME, Lavie A, Radu CG. Development of new deoxycytidine kinase inhibitors and noninvasive in vivo evaluation using positron emission tomography. J Med Chem 2013; 56:6696-708. [PMID: 23947754 DOI: 10.1021/jm400457y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Combined inhibition of ribonucleotide reductase and deoxycytidine kinase (dCK) in multiple cancer cell lines depletes deoxycytidine triphosphate pools leading to DNA replication stress, cell cycle arrest, and apoptosis. Evidence implicating dCK in cancer cell proliferation and survival stimulated our interest in developing small molecule dCK inhibitors. Following a high throughput screen of a diverse chemical library, a structure-activity relationship study was carried out. Positron Emission Tomography (PET) using (18)F-L-1-(2'-deoxy-2'-FluoroArabinofuranosyl) Cytosine ((18)F-L-FAC), a dCK-specific substrate, was used to rapidly rank lead compounds based on their ability to inhibit dCK activity in vivo. Evaluation of a subset of the most potent compounds in cell culture (IC50 = ∼1-12 nM) using the (18)F-L-FAC PET pharmacodynamic assay identified compounds demonstrating superior in vivo efficacy.
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Affiliation(s)
- Jennifer M Murphy
- Department of Molecular and Medical Pharmacology, §Ahmanson Translational Imaging Division, ⊥Department of Chemistry and Biochemistry, #California NanoSystems Institute, △Department of Biological Chemistry, University of California, Los Angeles , 650 Charles E. Young Dr. S., Los Angeles, California 90095, United States
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199
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Yang X, Xue Y. QM/MM investigation on 1,3-dipolar cycloadditions of the phthalazinium dicyanomethanide with three different dipolarophiles on water and in solution. Phys Chem Chem Phys 2013; 15:11846-55. [PMID: 23760163 DOI: 10.1039/c3cp51048d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
An "on water" environment, describing the reactions with insoluble reactants in water, has been reported to give high yields of products compared to organic solvents. The 1,3-dipolar cycloadditions of phthalazinium dicyanomethanide 1 with three different dipolarophiles, methyl vinyl ketone (MVK), methyl acrylate (MAC), and styrene (STY), have been investigated using QM/MM calculations in water, acetonitrile, and acetonitrile-water solvent mixtures, as well as at the vacuum-water interface. Monte Carlo statistical mechanics simulations utilizing the free-energy perturbation theory and PDDG/PM3 for the QM method have been used. The transition structures for all three reactions do not show large variations among different solvents. However, the calculated free energies of activation at the interface are found to be higher than those calculated in bulk water. Computed energy pair distributions and radial distribution functions reveal a uniform loss of hydrogen bonds for the reactants and transitions states in progressing from bulk water to the vacuum-water interface. The hydrophobic effects in the reactions of 1 with MVK and MAC are similar for both, and weaker than the effect in the reaction with STY. According to the results in water-acetonitrile mixtures at different molar ratios, it is clear that the special hydrogen bonding effects are the main reason which leads to the rapid rate enhancement in progressing from a water-acetonitrile molar ratio of 0.9 : 0.1 to pure water. New insights into solvent effects for 1,3-dipolar cycloadditions are presented herein.
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Affiliation(s)
- Xin Yang
- College of Chemistry, Key Lab of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People's Republic of China
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200
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Radi M, Tintori C, Musumeci F, Brullo C, Zamperini C, Dreassi E, Fallacara AL, Vignaroli G, Crespan E, Zanoli S, Laurenzana I, Filippi I, Maga G, Schenone S, Angelucci A, Botta M. Design, Synthesis, and Biological Evaluation of Pyrazolo[3,4-d]pyrimidines Active in Vivo on the Bcr-Abl T315I Mutant. J Med Chem 2013; 56:5382-94. [DOI: 10.1021/jm400233w] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Marco Radi
- Dipartimento di Biotecnologie,
Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
- Dipartimento di Farmacia, Università degli Studi di Parma, Viale delle
Scienze 27/A, 43124 Parma, Italy
| | - Cristina Tintori
- Dipartimento di Biotecnologie,
Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Francesca Musumeci
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto
XV 3, 16132 Genova, Italy
| | - Chiara Brullo
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto
XV 3, 16132 Genova, Italy
| | - Claudio Zamperini
- Dipartimento di Biotecnologie,
Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Elena Dreassi
- Dipartimento di Biotecnologie,
Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Anna Lucia Fallacara
- Dipartimento di Biotecnologie,
Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
- Dipartimento di Chimica e Tecnologie
del Farmaco, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Roma, Italy
| | - Giulia Vignaroli
- Dipartimento di Biotecnologie,
Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Emmanuele Crespan
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia,
Italy
| | - Samantha Zanoli
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia,
Italy
| | - Ilaria Laurenzana
- Laboratory of Preclinical
and Translational
Research, IRCCS-Referral Cancer Center of Basilicata (CROB), Rionero in Vulture (PZ), Italy
| | - Irene Filippi
- Dipartimento di Medicina Molecolare
e dello Sviluppo, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Giovanni Maga
- Istituto di Genetica Molecolare, IGM-CNR, Via Abbiategrasso 207, 27100 Pavia,
Italy
| | - Silvia Schenone
- Dipartimento di Farmacia, Università degli Studi di Genova, Viale Benedetto
XV 3, 16132 Genova, Italy
| | - Adriano Angelucci
- Dipartimento di Scienze Cliniche
Applicate e Biotecnologiche, Università dell’Aquila Via Vetoio, 67100 Coppito, L’Aquila, Italy
| | - Maurizio Botta
- Dipartimento di Biotecnologie,
Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100 Siena, Italy
- Sbarro Institute for Cancer
Research and Molecular Medicine, Center for Biotechnology, College
of Science and Technology, Temple University, BioLife Science Building, Suite 333, 1900 North 12th Street, Philadelphia,
Pennsylvania 19122, United States
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