201
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Li X, Ponomarev SY, Sa Q, Sigalovsky DL, Kaminski GA. Polarizable simulations with second order interaction model (POSSIM) force field: developing parameters for protein side-chain analogues. J Comput Chem 2013; 34:1241-50. [PMID: 23420678 PMCID: PMC3633718 DOI: 10.1002/jcc.23248] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 01/20/2013] [Indexed: 12/16/2022]
Abstract
A previously introduced polarizable simulations with second-order interaction model (POSSIM) force field has been extended to include parameters for small molecules serving as models for peptide and protein side-chains. Parameters have been fitted to permit reproducing many-body energies, gas-phase dimerization energies, and geometries and liquid-phase heats of vaporization and densities. Quantum mechanical and experimental data have been used as the target for the fitting. The POSSIM framework combines accuracy of a polarizable force field and computational efficiency of the second-order approximation of the full-scale induced point dipole polarization formalism. The resulting parameters can be used for simulations of the parameterized molecules themselves or their analogues. In addition to this, these force field parameters are currently being used in further development of the POSSIM fast polarizable force field for proteins.
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202
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Dahlgren MK, Schyman P, Tirado-Rives J, Jorgensen WL. Characterization of biaryl torsional energetics and its treatment in OPLS all-atom force fields. J Chem Inf Model 2013; 53:1191-9. [PMID: 23621692 DOI: 10.1021/ci4001597] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The frequency of biaryl substructures in a database of approved oral drugs has been analyzed. This led to designation of 20 prototypical biaryls plus 10 arylpyridinones for parametrization in the OPLS all-atom force fields. Bond stretching, angle-bending, and torsional parameters were developed to reproduce the MP2 geometries and torsional energy profiles. The transferability of the new parameters was tested through their application to three additional biaryls. The torsional energetics for the 33 biaryl molecules are analyzed and factors leading to preferences for planar and nonplanar geometries are identified. For liquid biphenyl, the computed density and heat of vaporization at the boiling point (255 °C) are also reported.
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Affiliation(s)
- Markus K Dahlgren
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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203
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Bollini M, Gallardo-Macias R, Spasov KA, Tirado-Rives J, Anderson KS, Jorgensen WL. Optimization of benzyloxazoles as non-nucleoside inhibitors of HIV-1 reverse transcriptase to enhance Y181C potency. Bioorg Med Chem Lett 2013; 23:1110-3. [PMID: 23298809 PMCID: PMC3561933 DOI: 10.1016/j.bmcl.2012.11.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 11/27/2012] [Indexed: 01/06/2023]
Abstract
Design of non-nucleoside inhibitors of HIV-1 reverse transcriptase with improved activity towards Tyr181Cys containing variants was pursued with the assistance of free energy perturbation (FEP) calculations. Optimization of the 4-R substituent in 1 led to ethyl and isopropyl analogs 1e and 1f with 1-7 nM potency towards both the wild-type virus and a Tyr181C variant.
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Affiliation(s)
- Mariela Bollini
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
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204
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Schyman P, Jorgensen WL. Exploring Adsorption of Water and Ions on Carbon Surfaces using a Polarizable Force Field. J Phys Chem Lett 2013; 4:468-474. [PMID: 23440601 PMCID: PMC3579643 DOI: 10.1021/jz302085c] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Graphene, carbon nanotubes, and fullerenes are of great interest due to their unique properties and diverse applications in biology, molecular electronics, and materials science. Therefore, there is demand for methods that can accurately model the interface between carbon surfaces and their environment. In this letter we compare results for complexes of water, potassium ion, and chloride ion with graphene, carbon nanotube, and fullerene surfaces using a standard non-polarizable force field (OPLS-AA), a polarizable force field (OPLS-AAP), DFT, and ab initio theory. For interactions with water, OPLS-AA with the TIP3P or TIP4P water models describes the interactions with benzene (C(6)H(6)) and coronene (C(24)H(12)) well; however, for acenes larger than circumcoronene (C(54)H(18)) and especially for C(60), the interaction energies are somewhat too weak and polarization is needed. For ions interacting with carbon surfaces, inclusion of polarization is essential, and OPLS-AAP is found to perform well in comparison to the highest-level quantum mechanical methods. Overall, OPLS-AAP provides an accurate and computationally efficient force field for modeling condensed-phase systems featuring carbon surfaces.
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205
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Allen C, Sambasivarao SV, Acevedo O. An ionic liquid dependent mechanism for base catalyzed β-elimination reactions from QM/MM simulations. J Am Chem Soc 2013; 135:1065-72. [PMID: 23273322 DOI: 10.1021/ja3098614] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Ionic liquids have been proposed to induce a mechanistic change in the reaction pathway for the fundamentally important base-induced β-elimination class compared to conventional solvents. The role of the reaction medium in the elimination of 1,1,1-tribromo-2,2-bis(3,4-dimethoxyphenyl)ethane via two bases, piperidine and pyrrolidine, has been computationally investigated using methanol and the ionic liquids 1-butyl-3-methylimidazolium tetrafluoroborate and hexafluorophosphate [BMIM][BF(4)] and [BMIM][PF(6)], respectively. QM/MM Monte Carlo simulations utilizing free-energy perturbation theory found the ionic liquids did produce a reaction pathway change from an E1cB-like mechanism in methanol to a pure E2 route that is consistent with experimental observations. The origin of the ionic liquid effect has been found as: (1) a combination of favorable electrostatic interactions, for example, bromine-imidazolium ion, and (2) π-π interactions that enhance the coplanarity between aromatic rings maximizing the electronic effects exerted on the reaction route. Solute-solvent interaction energies have been analyzed and show that liquid clathrate solvation of the transition state is primarily responsible for the observed mechanistic changes. This work provides the first theoretical evidence of an ionic liquid dependent mechanism and elucidates the interplay between sterics and electrostatics crucial to understanding the effect of these unique solvents upon chemical reactions.
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Affiliation(s)
- Caley Allen
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
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206
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McCann BW, Acevedo O. Pairwise Alternatives to Ewald Summation for Calculating Long-Range Electrostatics in Ionic Liquids. J Chem Theory Comput 2013; 9:944-50. [DOI: 10.1021/ct300961e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Billy W. McCann
- Department of Chemistry and Biochemistry,
Auburn University,
Auburn, Alabama 36849, United States
| | - Orlando Acevedo
- Department of Chemistry and Biochemistry,
Auburn University,
Auburn, Alabama 36849, United States
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207
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Recent Progress in Density Functional Methodology for Biomolecular Modeling. STRUCTURE AND BONDING 2013. [DOI: 10.1007/978-3-642-32750-6_1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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208
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Gathiaka S, Nanayakkara G, Boncher T, Acevedo O, Wyble J, Patel S, Patel A, Shane ME, Bonkowski B, Wieczorek J, Rong Y, Huggins K, Smith F, Amin RH. Design, development and evaluation of novel dual PPARδ/PPARγ agonists. Bioorg Med Chem Lett 2012; 23:873-9. [PMID: 23273519 DOI: 10.1016/j.bmcl.2012.11.060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 11/07/2012] [Accepted: 11/12/2012] [Indexed: 11/29/2022]
Abstract
Type 2 diabetes is at epidemic proportions and thus development of novel pharmaceutical therapies for improving insulin sensitivity has become of paramount importance. The objectives of the current study were to develop novel dual PPARγ/δ agonists without the deleterious side effects associated with full PPARγ agonists. Docking simulations of 23 novel compounds within the ligand binding domain of PPARγ/δ were performed using AutoDock Vina which consistently reproduced experimental binding poses from known PPAR agonists. Comparisons were made and described with other docking programs AutoDock and Surflex-Dock (from SYBYL-X). Biological evaluation of compounds was accomplished by transcriptional promoter activity assays, quantitative PCR gene analysis for known PPARγ/δ targets as well as in vitro assays for lipid accumulation and mitochondrial biogenesis verses known PPAR agonists. We found one (compound 9) out of the 23 compounds evaluated, to be the most potent and selective dual PPARγ/δ agonist which did not display the deleterious side effects associated with full PPARγ agonists.
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Affiliation(s)
- Symon Gathiaka
- Dept. of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849, USA
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209
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Vanommeslaeghe K, Raman EP, MacKerell AD. Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges. J Chem Inf Model 2012; 52:3155-68. [PMID: 23145473 DOI: 10.1021/ci3003649] [Citation(s) in RCA: 1089] [Impact Index Per Article: 90.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Molecular mechanics force fields are widely used in computer-aided drug design for the study of drug candidates interacting with biological systems. In these simulations, the biological part is typically represented by a specialized biomolecular force field, while the drug is represented by a matching general (organic) force field. In order to apply these general force fields to an arbitrary drug-like molecule, functionality for assignment of atom types, parameters, and partial atomic charges is required. In the present article, algorithms for the assignment of parameters and charges for the CHARMM General Force Field (CGenFF) are presented. These algorithms rely on the existing parameters and charges that were determined as part of the parametrization of the force field. Bonded parameters are assigned based on the similarity between the atom types that define said parameters, while charges are determined using an extended bond-charge increment scheme. Charge increments were optimized to reproduce the charges on model compounds that were part of the parametrization of the force field. A "penalty score" is returned for every bonded parameter and charge, allowing the user to quickly and conveniently assess the quality of the force field representation of different parts of the compound of interest. Case studies are presented to clarify the functioning of the algorithms and the significance of their output data.
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Affiliation(s)
- K Vanommeslaeghe
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, USA
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210
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Sharma I, Kaminski GA. Calculating pKa values for substituted phenols and hydration energies for other compounds with the first-order Fuzzy-Border continuum solvation model. J Comput Chem 2012; 33:2388-99. [PMID: 22815192 PMCID: PMC3472159 DOI: 10.1002/jcc.23074] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Revised: 05/14/2012] [Accepted: 07/01/2012] [Indexed: 02/06/2023]
Abstract
We have computed pK(a) values for 11 substituted phenol compounds using the continuum Fuzzy-Border (FB) solvation model. Hydration energies for 40 other compounds, including alkanes, alkenes, alkynes, ketones, amines, alcohols, ethers, aromatics, amides, heterocycles, thiols, sulfides, and acids have been calculated. The overall average unsigned error in the calculated acidity constant values was equal to 0.41 pH units and the average error in the solvation energies was 0.076 kcal/mol. We have also reproduced pK(a) values of propanoic and butanoic acids within about 0.1 pH units from the experimental values by fitting the solvation parameters for carboxylate ion carbon and oxygen atoms. The FB model combines two distinguishing features. First, it limits the amount of noise which is common in numerical treatment of continuum solvation models by using fixed-position grid points. Second, it uses either second- or first-order approximation for the solvent polarization, depending on a particular implementation. These approximations are similar to those used for solute and explicit solvent fast polarization treatment which we developed previously. This article describes results of using the first-order technique. This approximation places the presented methodology between the Generalized Born and Poisson-Boltzmann continuum solvation models with respect to their accuracy of reproducing the many-body effects in modeling a continuum solvent.
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Affiliation(s)
- Ity Sharma
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA 01609
| | - George A. Kaminski
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA 01609
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211
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Schmidt NW, Lis M, Zhao K, Lai GH, Alexandrova AN, Tew GN, Wong GCL. Molecular basis for nanoscopic membrane curvature generation from quantum mechanical models and synthetic transporter sequences. J Am Chem Soc 2012; 134:19207-16. [PMID: 23061419 DOI: 10.1021/ja308459j] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We investigate the physical origin of peptide-induced membrane curvature by contrasting differences between H-bonding interactions of prototypical cationic amino acids, arginine (Arg) and lysine (Lys), with phosphate groups of phospholipid heads using quantum mechanical (QM) calculations of a minimum model and test the results via synthetic oxaorbornene-based transporter sequences without the geometric constraints of polypeptide backbones. QM calculations suggest that although individual Lys can in principle coordinate two phosphates, they are not able to do so at small inter-Lys distances without drastic energetic penalties. In contrast, Arg can coordinate two phosphates down to less than 5 Å, where guanidinium groups can stack "face to face". In agreement with these observations, poly-Lys cannot generate the nanoscale positive curvature necessary for inducing negative Gaussian membrane curvature, in contrast to poly-Arg. Also consistent with QM calculations, polyguanidine-oxanorbornene homopolymers (PGONs) showed that curvature generation is exquisitely sensitive to the guanidinium group spacing when the phosphate groups are near close packing. Addition of phenyl or butyl hydrophobic groups into guanidine-oxanorbornene polymers increased the amount of induced saddle-splay membrane curvature and broadened the range of lipid compositions where saddle-splay curvature was induced. The enhancement of saddle-splay curvature generation and relaxation of lipid composition requirements via addition of hydrophobicity is consistent with membrane activity profiles. While PGON polymers displayed selective antimicrobial activity against prototypical (Gram positive and negative) bacteria, polymers with phenyl and butyl groups were also active against red blood cells. Our results suggest that it is possible to achieve deterministic molecular design of pore-forming peptides.
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Affiliation(s)
- Nathan W Schmidt
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
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212
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Cisneros GA. Application of Gaussian Electrostatic Model (GEM) Distributed Multipoles in the AMOEBA Force Field. J Chem Theory Comput 2012; 8:5072-80. [DOI: 10.1021/ct300630u] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- G. Andrés Cisneros
- Department
of Chemistry, Wayne State University, Detroit,
Michigan 48202, United States
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213
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Acevedo O, Ambrose Z, Flaherty PT, Aamer H, Jain P, Sambasivarao SV. Identification of HIV inhibitors guided by free energy perturbation calculations. Curr Pharm Des 2012; 18:1199-216. [PMID: 22316150 DOI: 10.2174/138161212799436421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 12/06/2011] [Indexed: 01/14/2023]
Abstract
Free energy perturbation (FEP) theory coupled to molecular dynamics (MD) or Monte Carlo (MC) statistical mechanics offers a theoretically precise method for determining the free energy differences of related biological inhibitors. Traditionally requiring extensive computational resources and expertise, it is only recently that its impact is being felt in drug discovery. A review of computer-aided anti-HIV efforts employing FEP calculations is provided here that describes early and recent successes in the design of human immunodeficiency virus type 1 (HIV-1) protease and non-nucleoside reverse transcriptase inhibitors. In addition, our ongoing work developing and optimizing leads for small molecule inhibitors of cyclophilin A (CypA) is highlighted as an update on the current capabilities of the field. CypA has been shown to aid HIV-1 replication by catalyzing the cis/trans isomerization of a conserved Gly-Pro motif in the Nterminal domain of HIV-1 capsid (CA) protein. In the absence of a functional CypA, e.g., by the addition of an inhibitor such as cyclosporine A (CsA), HIV-1 has reduced infectivity. Our simulations of acylurea-based and 1-indanylketone-based CypA inhibitors have determined that their nanomolar and micromolar binding affinities, respectively, are tied to their ability to stabilize Arg55 and Asn102. A structurally novel 1-(2,6-dichlorobenzamido) indole core was proposed to maximize these interactions. FEP-guided optimization, experimental synthesis, and biological testing of lead compounds for toxicity and inhibition of wild-type HIV-1 and CA mutants have demonstrated a dose-dependent inhibition of HIV-1 infection in two cell lines. While the inhibition is modest compared to CsA, the results are encouraging.
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Affiliation(s)
- Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA.
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214
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Baggett AW, Cournia Z, Han MS, Patargias G, Glass AC, Liu SY, Nolen BJ. Structural characterization and computer-aided optimization of a small-molecule inhibitor of the Arp2/3 complex, a key regulator of the actin cytoskeleton. ChemMedChem 2012; 7:1286-94. [PMID: 22623398 PMCID: PMC3531959 DOI: 10.1002/cmdc.201200104] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 05/02/2012] [Indexed: 11/06/2022]
Abstract
CK-666 (1) is a recently discovered small-molecule inhibitor of the actin-related protein 2/3 (Arp2/3) complex, a key actin cytoskeleton regulator with roles in bacterial pathogenesis and cancer cell motility. Although 1 is commercially available, the crystal structure of Arp2/3 complex with 1 bound has not been reported, making its mechanism of action uncertain. Furthermore, its relatively low potency increases its potential for off-target effects in vivo, complicating interpretation of its influence in cell biological studies and precluding its clinical use. Herein we report the crystal structure of 1 bound to Arp2/3 complex, which reveals that 1 binds between the Arp2 and Arp3 subunits to stabilize the inactive conformation of the complex. Based on the crystal structure, we used computational docking and free-energy perturbation calculations of monosubstituted derivatives of 1 to guide optimization efforts. Biochemical assays of ten newly synthesized compounds led to the identification of compound 2, which exhibits a threefold increase in inhibitory activity in vitro relative to 1. In addition, our computational analyses unveiled a surface groove at the interface of the Arp2 and Arp3 subunits that can be exploited for additional structure-based optimization.
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Affiliation(s)
- Andrew W. Baggett
- Department of Chemistry, University of Oregon, Eugene, OR 97403-1253, United States Tel. 541-346-7412, Fax 541-346-5891
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 115 27 Athens, Greece
| | - Min Suk Han
- Department of Chemistry, University of Oregon, Eugene, OR 97403-1253, United States Tel. 541-346-7412, Fax 541-346-5891
| | - George Patargias
- Biomedical Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 115 27 Athens, Greece
| | - Adam C. Glass
- Department of Chemistry, University of Oregon, Eugene, OR 97403-1253, United States Tel. 541-346-7412, Fax 541-346-5891
| | - Shih-Yuan Liu
- Department of Chemistry, University of Oregon, Eugene, OR 97403-1253, United States Tel. 541-346-7412, Fax 541-346-5891
| | - Brad J. Nolen
- Department of Chemistry, University of Oregon, Eugene, OR 97403-1253, United States Tel. 541-346-7412, Fax 541-346-5891
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215
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Carlsson J, Persson B. Investigating protein variants using structural calculation techniques. Methods Mol Biol 2012; 857:313-30. [PMID: 22323228 DOI: 10.1007/978-1-61779-588-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Structure calculation techniques can be very useful to bridge the gap between available sequence information and structural knowledge. In order to understand the molecular mechanisms behind diseases caused by residue exchanges, knowledge about the modified structure is needed. In this chapter, we describe how energy minimizations and molecular dynamics can be useful tools in order to study the structural effects of sequence variation. With these techniques, together with investigation of other properties, it is often possible to obtain a complete picture of the effect and mechanism behind disease-causing mutations. To take this information one step further, we also describe prediction methods that can be used to judge the effects of mutations and how to evaluate these and the interplay between the protein properties.
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Affiliation(s)
- Jonas Carlsson
- IFM Bioinformatics and SeRC (Swedish e-Science Research Centre), Linköping University, Linköping, Sweden
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216
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Larionov E, Mahesh M, Spivey AC, Wei Y, Zipse H. Theoretical Prediction of Selectivity in Kinetic Resolution of Secondary Alcohols Catalyzed by Chiral DMAP Derivatives. J Am Chem Soc 2012; 134:9390-9. [DOI: 10.1021/ja302420g] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Evgeny Larionov
- Department of Chemistry, LMU München, Butenandtstrasse 5-13, D-81377
München, Germany
| | - Mohan Mahesh
- Department of Chemistry, South
Kensington Campus, Imperial College, London,
SW7 2AZ, United Kingdom
| | - Alan C. Spivey
- Department of Chemistry, South
Kensington Campus, Imperial College, London,
SW7 2AZ, United Kingdom
| | - Yin Wei
- Department of Chemistry, LMU München, Butenandtstrasse 5-13, D-81377
München, Germany
| | - Hendrik Zipse
- Department of Chemistry, LMU München, Butenandtstrasse 5-13, D-81377
München, Germany
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217
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Leung CS, Leung SSF, Tirado-Rives J, Jorgensen WL. Methyl effects on protein-ligand binding. J Med Chem 2012; 55:4489-500. [PMID: 22500930 DOI: 10.1021/jm3003697] [Citation(s) in RCA: 280] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effects of addition of a methyl group to a lead compound on biological activity are examined. A literature analysis of >2000 cases reveals that an activity boost of a factor of 10 or more is found with an 8% frequency, and a 100-fold boost is a 1 in 200 event. Four cases in the latter category are analyzed in depth to elucidate any unusual aspects of the protein-ligand binding, distribution of water molecules, and changes in conformational energetics. The analyses include Monte Carlo/free-energy perturbation (MC/FEP) calculations for methyl replacements in inhibitor series for p38α MAP kinase, ACK1, PTP1B, and thrombin. Methyl substitutions ortho to an aryl ring can be particularly effective at improving activity by inducing a propitious conformational change. The greatest improvements in activity arise from coupling the conformational gain with the burial of the methyl group in a hydrophobic region of the protein.
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Affiliation(s)
- Cheryl S Leung
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
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218
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Jorgensen WL, Schyman P. Treatment of Halogen Bonding in the OPLS-AA Force Field; Application to Potent Anti-HIV Agents. J Chem Theory Comput 2012; 8:3895-3801. [PMID: 23329896 DOI: 10.1021/ct300180w] [Citation(s) in RCA: 197] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The representation of chlorine, bromine, and iodine in aryl halides has been modified in the OPLS-AA and OPLS/CM1A force fields in order to incorporate halogen bonding. The enhanced force fields, OPLS-AAx and OPLS/CM1Ax, have been tested in calculations on gas-phase complexes of halobenzenes with Lewis bases, and for free energies of hydration, densities, and heats of vaporization of halobenzenes. Comparisons with results of MP2/aug-cc-pVDZ(-PP) calculations for the complexes are included. Implementation in the MCPRO software also allowed computation of relative free energies of binding for a series of HIV reverse transcriptase inhibitors via Monte Carlo/free-energy perturbation calculations. The results support the notion that the activity of an unusually potent chloro analog likely benefits from halogen bonding with the carbonyl group of a proline residue.
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219
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Janowski T, Wolinski K, Pulay P. Ultrafast Quantum Mechanics/Molecular Mechanics Monte Carlo simulations using generalized multipole polarizabilities. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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220
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Ekkati AR, Bollini M, Domaoal RA, Spasov KA, Anderson KS, Jorgensen WL. Discovery of dimeric inhibitors by extension into the entrance channel of HIV-1 reverse transcriptase. Bioorg Med Chem Lett 2012; 22:1565-8. [PMID: 22269110 PMCID: PMC3278212 DOI: 10.1016/j.bmcl.2011.12.132] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 12/27/2011] [Accepted: 12/29/2011] [Indexed: 12/01/2022]
Abstract
Design of non-nucleoside inhibitors of HIV-1 reverse transcriptase is being pursued with computational guidance. Extension of azine-containing inhibitors into the entrance channel between Lys103 and Glu138 has led to the discovery of potent and structurally novel derivatives including dimeric inhibitors in an NNRTI-linker-NNRTI motif.
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Affiliation(s)
- Anil R Ekkati
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
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221
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Theoretical studies on the chemical decomposition of 5-aza-2′-deoxycytidine: DFT study and Monte Carlo simulation. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1108-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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222
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Enjalbert Q, Racaud A, Lemoine J, Redon S, Ayhan MM, Andraud C, Chambert S, Bretonnière Y, Loison C, Antoine R, Dugourd P. Optical Properties of a Visible Push–Pull Chromophore Covalently Bound to Carbohydrates: Solution and Gas-Phase Spectroscopy Combined to Theoretical Investigations. J Phys Chem B 2012; 116:841-51. [DOI: 10.1021/jp2099015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Quentin Enjalbert
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579, CNRS, Université Lyon 1, France
- Laboratoire de Sciences Analytiques, UMR5180, CNRS, Université Lyon 1, France
| | - Amandine Racaud
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579, CNRS, Université Lyon 1, France
- Laboratoire de Sciences Analytiques, UMR5180, CNRS, Université Lyon 1, France
| | - Jérôme Lemoine
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Sciences Analytiques, UMR5180, CNRS, Université Lyon 1, France
| | - Sébastien Redon
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Chimie Organique et Bioorganique, INSA de Lyon, Lyon, France
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR5246, CNRS, Université Lyon 1, INSA de Lyon, CPE-Lyon, Lyon, France
| | - Mehmet Menaf Ayhan
- Université de Lyon, F-69622, Lyon, France
- Laboratoire de Chimie de l’ENS Lyon, UMR5182, CNRS, ENS Lyon, 46 allée d’Italie, F-69364 Lyon, France
| | - Chantal Andraud
- Université de Lyon, F-69622, Lyon, France
- Laboratoire de Chimie de l’ENS Lyon, UMR5182, CNRS, ENS Lyon, 46 allée d’Italie, F-69364 Lyon, France
| | - Stéphane Chambert
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Chimie Organique et Bioorganique, INSA de Lyon, Lyon, France
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR5246, CNRS, Université Lyon 1, INSA de Lyon, CPE-Lyon, Lyon, France
| | - Yann Bretonnière
- Université de Lyon, F-69622, Lyon, France
- Laboratoire de Chimie de l’ENS Lyon, UMR5182, CNRS, ENS Lyon, 46 allée d’Italie, F-69364 Lyon, France
| | - Claire Loison
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579, CNRS, Université Lyon 1, France
| | - Rodolphe Antoine
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579, CNRS, Université Lyon 1, France
| | - Philippe Dugourd
- Université de Lyon, F-69622, Lyon, France
- Université Lyon 1, 43, Bld du 11 Novembre 1918, F-69622 Villeurbanne, France
- Laboratoire de Spectrométrie Ionique et Moléculaire, UMR5579, CNRS, Université Lyon 1, France
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223
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Molecular Design using Three-Dimensional Signature Descriptors. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/b978-0-444-59507-2.50037-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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224
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Kale S, Herzfeld J, Dai S, Blank M. Lewis-inspired representation of dissociable water in clusters and Grotthuss chains. J Biol Phys 2012; 38:49-59. [PMID: 23277669 PMCID: PMC3285721 DOI: 10.1007/s10867-011-9229-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 05/08/2011] [Indexed: 10/18/2022] Open
Abstract
Proton transfer to and from water is critical to the function of water in many settings. However, it has been challenging to model. Here, we present proof-of-principle for an efficient yet robust model based on Lewis-inspired submolecular particles with interactions that deviate from Coulombic at short distances to take quantum effects into account. This "LEWIS" model provides excellent correspondence with experimental structures for water molecules and water clusters in their neutral, protonated and deprotonated forms; reasonable values for the proton affinities of water and hydroxide; a good value for the strength of the hydrogen bond in the water dimer; the correct order of magnitude for the stretch and bend force constants of water; and the expected time course for Grotthuss transport in water chains.
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Affiliation(s)
- Seyit Kale
- Graduate Program in Biophysics and Structural Biology, Brandeis University, Waltham, MA 02454 USA
| | - Judith Herzfeld
- Department of Chemistry, Brandeis University, Waltham, MA 02454 USA
| | - Stacy Dai
- Department of Chemistry, Brandeis University, Waltham, MA 02454 USA
| | - Michael Blank
- Department of Chemistry, Brandeis University, Waltham, MA 02454 USA
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225
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Bollini M, Domaoal RA, Thakur VV, Gallardo-Macias R, Spasov KA, Anderson KS, Jorgensen WL. Computationally-guided optimization of a docking hit to yield catechol diethers as potent anti-HIV agents. J Med Chem 2011; 54:8582-91. [PMID: 22081993 DOI: 10.1021/jm201134m] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A 5-μM docking hit has been optimized to an extraordinarily potent (55 pM) non-nucleoside inhibitor of HIV reverse transcriptase. Use of free energy perturbation (FEP) calculations to predict relative free energies of binding aided the optimizations by identifying optimal substitution patterns for phenyl rings and a linker. The most potent resultant catechol diethers feature terminal uracil and cyanovinylphenyl groups. A halogen bond with Pro95 likely contributes to the extreme potency of compound 42. In addition, several examples are provided illustrating failures of attempted grafting of a substructure from a very active compound onto a seemingly related scaffold to improve its activity.
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Affiliation(s)
- Mariela Bollini
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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226
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Alexandrova AN, Jorgensen WL. On the mechanism and rate of spontaneous decomposition of amino acids. J Phys Chem B 2011; 115:13624-32. [PMID: 21995727 PMCID: PMC3241013 DOI: 10.1021/jp2081808] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spontaneous decarboxylation of amino acids is among the slowest known reactions; it is much less facile than the cleavage of amide bonds in polypeptides. Establishment of the kinetics and mechanisms for this fundamental reaction is important for gauging the proficiency of enzymes. In the present study, multiple mechanisms for glycine decomposition in water are explored using QM/MM Monte Carlo simulations and free energy perturbation theory. Simple CO(2) detachment emerges as the preferred pathway for decarboxylation; it is followed by water-assisted proton transfer to yield the products: CO(2) and methylamine. The computed free energy of activation of 45 kcal/mol, and the resulting rate-constant of 1 × 10(-21) s(-1), can be compared with an extrapolated experimental rate constant of ~2 × 10(-17) s(-1) at 25 °C. The half-life for the reaction is more than 1 billion years. Furthermore, examination of deamination finds simple NH(3)-detachment yielding α-lactone to be the favored route, though it is less facile than decarboxylation by 6 kcal/mol. Ab initio and DFT calculations with the CPCM hydration model were also carried out for the reactions; the computed free energies of activation for glycine decarboxylation agree with the QM/MM result, whereas deamination is predicted to be more favorable. QM/MM calculations were also performed for decarboxylation of alanine; the computed barrier is 2 kcal/mol higher than for glycine in qualitative accord with experiment.
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Affiliation(s)
- Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA.
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227
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Ravindranathan K, Tirado-Rives J, Jorgensen WL, Guimarães CRW. Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model. J Chem Theory Comput 2011; 7:3859-3865. [PMID: 22606071 DOI: 10.1021/ct200565u] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A variable dielectric model based on residue types for better description of protein-ligand electrostatics in MM-GBSA scoring is reported. The variable dielectric approach provides better correlation with binding data and reduces the score dynamic range, typically observed in the standard MM-GB/SA method. The latter supports the view that exaggerated enthalpic separation between weak and potent compounds due to the lack of shielding effects in the model is greatly responsible for the wide scoring spread.
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228
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Leavitt CM, Wolk AB, Kamrath MZ, Garand E, Van Stipdonk MJ, Johnson MA. Characterizing the intramolecular H-bond and secondary structure in methylated GlyGlyH+ with H2 predissociation spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1941-1952. [PMID: 21952771 DOI: 10.1007/s13361-011-0228-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/03/2011] [Accepted: 08/03/2011] [Indexed: 05/31/2023]
Abstract
We report vibrational predissociation spectra of the four protonated dipeptides derived from glycine and sarcosine, GlyGlyH(+)•(H(2))(1,2), GlySarH(+)•(D(2))(2), SarGlyH(+)•(H(2))(2), and SarSarH(+)•(D(2))(2), generated in a cryogenic ion trap. Sharp bands were recovered by monitoring photoevaporation of the weakly bound H(2) (D(2)) molecules in a linear action regime throughout the 700-4200 cm(-1) range using a table-top laser system. The spectral patterns were analyzed in the context of the low energy structures obtained from electronic structure calculations. These results indicate that all four species are protonated on the N-terminus, and feature an intramolecular H-bond involving the amino group. The large blue-shift in the H-bonded N-H fundamental upon incorporation of a methyl group at the N-terminus indicates that this modification significantly lowers the strength of the intramolecular H-bond. Methylation at the amide nitrogen, on the other hand, induces a significant rotation (~110°) about the peptide backbone.
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Affiliation(s)
- Christopher M Leavitt
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520, USA
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229
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Jorgensen WL, Bollini M, Thakur VV, Domaoal RA, Spasov KA, Anderson KS. Efficient discovery of potent anti-HIV agents targeting the Tyr181Cys variant of HIV reverse transcriptase. J Am Chem Soc 2011; 133:15686-96. [PMID: 21853995 PMCID: PMC3183387 DOI: 10.1021/ja2058583] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) that interfere with the replication of human immunodeficiency virus (HIV) are being pursued with guidance from molecular modeling including free-energy perturbation (FEP) calculations for protein-inhibitor binding affinities. The previously reported pyrimidinylphenylamine 1 and its chloro analogue 2 are potent anti-HIV agents; they inhibit replication of wild-type HIV-1 in infected human T-cells with EC(50) values of 2 and 10 nM, respectively. However, they show no activity against viral strains containing the Tyr181Cys (Y181C) mutation in HIV-RT. Modeling indicates that the problem is likely associated with extensive interaction between the dimethylallyloxy substituent and Tyr181. As an alternative, a phenoxy group is computed to be oriented in a manner diminishing the contact with Tyr181. However, this replacement leads to a roughly 1000-fold loss of activity for 3 (2.5 μM). The present report details the efficient, computationally driven evolution of 3 to novel NNRTIs with sub-10 nM potency toward both wild-type HIV-1 and Y181C-containing variants. The critical contributors were FEP substituent scans for the phenoxy and pyrimidine rings and recognition of potential benefits of addition of a cyanovinyl group to the phenoxy ring.
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230
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Garrido NM, Economou IG, Queimada AJ, Jorge M, Macedo EA. Prediction of then-hexane/water and 1-octanol/water partition coefficients for environmentally relevant compounds using molecular simulation. AIChE J 2011. [DOI: 10.1002/aic.12718] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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231
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Ponomarev SY, Click TH, Kaminski GA. Electrostatic polarization is crucial in reproducing Cu(I) interaction energies and hydration. J Phys Chem B 2011; 115:10079-85. [PMID: 21761909 DOI: 10.1021/jp2051933] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have explored the suitability of fixed-charges and polarizable force fields for modeling interactions of the monovalent Cu(I) ion. Parameters for this ion have been tested and refitted within the fixed-charges OPLS-AA and polarizable force field (PFF) frameworks. While this ion plays an important role in many protein interactions, the attention to it in developing empirical force fields is limited. Our PFF parameters for the copper ion worked very well for the Cu(I) interactions with water, while both the original OPLS2005 and our refitted OPLS versions moderately underestimated the copper-water interaction energy. However, the greatest problem in using the nonpolarizable fixed-charges OPLS force field was observed while calculating interaction energies and distances for Cu(I)-benzene complexes. The OPLS2005 model underestimates the interaction energy by a factor of 4. Refitting the OPLS parameters reduced this underestimation to a factor of 2.2-2.4, but only at a cost of distorting the complex geometry. At the same time, the polarizable calculations had an error of about 4%. Moreover, we then used the PFF and nonpolarizable refitted OPLS models for finding free energy of hydration for copper ion via molecular dynamics simulations. While the OPLS calculations lead to a 22% error in the solvation energy, the PFF result was off by only 1.8%. This was achieved with no refitting of the parameters but simply by employing the model developed for the Cu(I) interaction with a single water molecule. We believe that the presented results not only lead to a conclusion about a qualitatively greater suitability of polarizable force fields for simulating molecular interactions with ions but also attest to the excellent level of transferability of PFF parameters.
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Affiliation(s)
- Sergei Y Ponomarev
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, USA
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232
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Vilseck JZ, Sambasivarao SV, Acevedo O. Optimal scaling factors for CM1 and CM3 atomic charges in RM1‐based aqueous simulations. J Comput Chem 2011; 32:2836-42. [DOI: 10.1002/jcc.21863] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 05/04/2011] [Accepted: 05/15/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Jonah Z. Vilseck
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
| | | | - Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849
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233
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Jorgensen WL, Trofimov A, Du X, Hare AA, Leng L, Bucala R. Benzisothiazolones as modulators of macrophage migration inhibitory factor. Bioorg Med Chem Lett 2011; 21:4545-9. [PMID: 21719283 DOI: 10.1016/j.bmcl.2011.05.127] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 05/27/2011] [Accepted: 05/31/2011] [Indexed: 02/02/2023]
Abstract
Substituted N-phenylbenzisothiazolones have been investigated as inhibitors of the tautomerase activity of the proinflammatory cytokine MIF (macrophage migration inhibitory factor). Numerous compounds were found to possess antagonist activity in the low micromolar range with the most potent being the 6-hydroxy analog 1w. Compound 1w and the p-cyano analog 1c were also shown to exhibit significant inhibition of the binding of MIF to its transmembrane receptor CD74. Consistently, both compounds were also found to retard the MIF-dependent phosphorylation of ERK1/2 in human synovial fibroblasts.
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234
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Sparta M, Alexandrova AN. Computational design and characterisation of artificial enzymes for Kemp elimination. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.565760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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235
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Sergiievskyi VP. Model for calculating the free energy of hydration of bioactive compounds based on integral equation theory of liquids. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2011. [DOI: 10.1134/s1990793111020382] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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236
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Persson R, Nordholm S, Perlovich G, Lindfors L. Monte Carlo Studies of Drug Nucleation 1: Formation of Crystalline Clusters of Bicalutamide in Water. J Phys Chem B 2011; 115:3062-72. [DOI: 10.1021/jp111817h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rasmus Persson
- Department of Chemistry, University of Gothenburg, Sweden
| | - Sture Nordholm
- Department of Chemistry, University of Gothenburg, Sweden
| | - German Perlovich
- Institute of Solution Chemistry, Russian Academy of Science, Ivanovo, Russia
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237
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Chen ZQ, Zhang CH, Kim CK, Xue Y. Quantum mechanics study and Monte Carlo simulation on the hydrolytic deamination of 5-methylcytosine glycol. Phys Chem Chem Phys 2011; 13:6471-83. [PMID: 21380473 DOI: 10.1039/c0cp02783a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The efficient formation of 5-methylcytosine glycol (mCg) and its facile deamination to thymine glycol (Tg) may account for the prevalent C → T transition mutation found at methylated CpG site (mCpG) in human p53 gene, a hallmark for many types of human tumors. In this work, the hydrolytic deamination of mCg was investigated at the MP2 and B3LYP levels of theory using the 6-311G(d,p) basis set. In the gas phase, three pathways were explored, paths A-C, and it indicates that the direct deamination of mCg with H(2)O by either pathway is unlikely because of the high activation free energies involved in the rate-determining steps, the formation of the tetrahedral intermediate for paths A and B as well as the formation of the Tg tautomer for path C. In aqueous solution, the role of the water molecules in the deamination of mCg with H(2)O was analyzed in two separate parts: the direct participation of one water molecule in the reaction pathway, called the water-assisted mechanism; and the complementary participation of the aqueous solvation. The water-assisted mechanism was carried out for mCg and the cluster of two water molecules by quantum mechanical calculations in the gas phase. This indicates that the presence of the auxiliary water molecule significantly contributes to decreasing all the activation free energies. The bulk solution effect on the water-assisted mechanism was included by free energy perturbation implemented on Monte Carlo simulations, which is found to be substantial and decisive in the deamination mechanism of mCg. In this case, the water-assisted path A is the most plausible mechanism reported for the deamination of mCg, where the calculated activation free energy (22.6 kcal mol(-1) at B3LYP level of theory) agrees well with the experimentally determined activation free energy (24.8 kcal mol(-1)). The main striking results of the present DFT computational study which is in agreement with previous experimental data is the higher rate of deamination displayed by mCg residues with respect to 5-methylcytosine (mC) bases, which supports that the deamination of mCg contributes significantly to the C → T transition mutation at mCpG dinucleotide site.
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Affiliation(s)
- Ze Qin Chen
- College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People's Republic of China
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238
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Orozco M, Orellana L, Hospital A, Naganathan AN, Emperador A, Carrillo O, Gelpí JL. Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2011; 85:183-215. [PMID: 21920324 DOI: 10.1016/b978-0-12-386485-7.00005-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Flexibility is the key magnitude to understand the variety of functions of proteins. Unfortunately, its experimental study is quite difficult, and in fact, most experimental procedures are designed to reduce flexibility and allow a better definition of the structure. Theoretical approaches have become then the alternative but face serious timescale problems, since many biologically relevant deformation movements happen in a timescale that is far beyond the possibility of current atomistic models. In this complex scenario, coarse-grained simulation methods have emerged as a powerful and inexpensive alternative. Along this chapter, we will review these coarse-grained methods, and explain their physical foundations and their range of applicability.
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Affiliation(s)
- Modesto Orozco
- Joint IRB-BSC Program on Computational Biology, Barcelona Supercomputing Center and Institute of Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain
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239
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Zakrzewski VG, Dolgounitcheva O, Zakjevskii AV, Ortiz J. Ab initio Electron Propagator Calculations on Electron Detachment Energies of Fullerenes, Macrocyclic Molecules, and Nucleotide Fragments. ADVANCES IN QUANTUM CHEMISTRY 2011. [DOI: 10.1016/b978-0-12-386477-2.00009-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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240
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Thermodynamic Properties for Applications in Chemical Industry via Classical Force Fields. MULTISCALE MOLECULAR METHODS IN APPLIED CHEMISTRY 2011; 307:201-49. [DOI: 10.1007/128_2011_164] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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241
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Sambasivarao SV, Acevedo O. Computational insight into small molecule inhibition of cyclophilins. J Chem Inf Model 2010; 51:475-82. [PMID: 21194235 DOI: 10.1021/ci1004114] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cyclophilins (Cyp) are a family of cellular enzymes possessing peptidyl-prolyl isomerase activity, which catalyze the cis-trans interconversion of proline-containing peptide bonds. The two most abundant family members, CypA and CypB, have been identified as valid drug targets for a wide range of diseases, including HCV, HIV, and multiple cancers. However, the development of small molecule inhibitors that possess nM potency and high specificity for a particular Cyp is difficult given the complete conservation of all active site residues between the enzymes. Monte Carlo statistical sampling coupled to free energy perturbation theory (MC/FEP) calculations have been carried out to elucidate the origin of the experimentally observed nM inhibition of CypA by acylurea-based derivatives and the >200-fold in vitro selectivity between CypA and CypB from aryl 1-indanylketone-based μM inhibitors. The computed free-energies of binding were in close accord with those derived from experiments. Binding affinity values for the inhibitors were determined to be dependent upon the stabilization strength of the nonbonded interactions provided toward two catalytic residues: Arg55 and Asn102 in CypA and the analogous Arg63 and Asn110 residues in CypB. Fine-tuning of the hydrophobic interactions allowed for enhanced potency among derivatives. The aryl 1-indanylketones are predicted to differentiate between the cyclophilins by using distinct binding motifs that exploit subtle differences in the active site arrangements. Ideas for the development of new selective compounds with the potential for advancement to low-nanomolar inhibition are presented.
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242
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Chen I, Foloppe N. Is conformational sampling of drug‐like molecules a solved problem? Drug Dev Res 2010. [DOI: 10.1002/ddr.20405] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- I‐Jen Chen
- Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB21 6GB, United Kingdom
| | - Nicolas Foloppe
- Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge CB21 6GB, United Kingdom
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243
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Luccarelli J, Michel J, Tirado-Rives J, Jorgensen WL. Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors. J Chem Theory Comput 2010; 6:3850-3856. [PMID: 21278915 DOI: 10.1021/ct100504h] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Monte Carlo free energy perturbation (MC/FEP) calculations have been applied to compute the relative binding affinities of 17 congeneric pyridazo-pyrimidinone inhibitors of the protein p38α MAP kinase. Overall correlation with experiment was found to be modest when the complexes were hydrated using a traditional procedure with a stored solvent box. Significant improvements in accuracy were obtained when the MC/FEP calculations were repeated using initial solvent distributions optimized by the water placement algorithm JAWS. The results underscore the importance of accurate placement of water molecules in a ligand binding site for the reliable prediction of relative free energies of binding.
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Affiliation(s)
- James Luccarelli
- Department of Chemistry, Yale University, New Haven, CT 06520-8107
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244
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Hori K, Yamaguchi T, Uezu K, Sumimoto M. A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): Application to highly solvent-dependent reactions. J Comput Chem 2010; 32:778-86. [DOI: 10.1002/jcc.21653] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 07/28/2010] [Accepted: 07/30/2010] [Indexed: 11/09/2022]
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245
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Alexandrova AN. Promiscuous DNA alkyladenine glycosylase dramatically favors a bound lesion over undamaged adenine. Biophys Chem 2010; 152:118-27. [DOI: 10.1016/j.bpc.2010.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 08/14/2010] [Accepted: 08/17/2010] [Indexed: 10/19/2022]
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246
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Hare AA, Leng L, Gandavadi S, Du X, Cournia Z, Bucala R, Jorgensen WL. Optimization of N-benzyl-benzoxazol-2-ones as receptor antagonists of macrophage migration inhibitory factor (MIF). Bioorg Med Chem Lett 2010; 20:5811-4. [PMID: 20728358 PMCID: PMC2939296 DOI: 10.1016/j.bmcl.2010.07.129] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 07/28/2010] [Accepted: 07/29/2010] [Indexed: 11/20/2022]
Abstract
The cytokine MIF is involved in inflammation and cell proliferation via pathways initiated by its binding to the transmembrane receptor CD74. MIF also exhibits keto-enol tautomerase activity, believed to be vestigial in mammals. Starting from a 1 μM hit from virtual screening, substituted benzoxazol-2-ones have been discovered as antagonists with IC(50) values as low as 7.5 nM in a tautomerase assay and 80 nM in a MIF-CD74 binding assay. Additional studies for one of the potent inhibitors demonstrated that it is not a covalent inhibitor of MIF and that it attenuates MIF-dependent ERK1/2 phosphorylation in human synovial fibroblasts.
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Affiliation(s)
- Alissa A. Hare
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Lin Leng
- Department of Medicine, Yale University School of Medicine, New Haven, CT 06520-8066, USA
| | | | - Xin Du
- Department of Medicine, Yale University School of Medicine, New Haven, CT 06520-8066, USA
| | - Zoe Cournia
- Department of Chemistry, Yale University, New Haven, CT 06520-8107, USA
| | - Richard Bucala
- Department of Medicine, Yale University School of Medicine, New Haven, CT 06520-8066, USA
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247
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248
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Zhang AX, Murelli RP, Barinka C, Michel J, Cocleaza A, Jorgensen WL, Lubkowski J, Spiegel DA. A remote arene-binding site on prostate specific membrane antigen revealed by antibody-recruiting small molecules. J Am Chem Soc 2010; 132:12711-6. [PMID: 20726553 PMCID: PMC2965167 DOI: 10.1021/ja104591m] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Prostate specific membrane antigen (PSMA) is a membrane-bound glutamate carboxypeptidase overexpressed in many forms of prostate cancer. Our laboratory has recently disclosed a class of small molecules, called ARM-Ps (antibody-recruiting molecule targeting prostate cancer) that are capable of enhancing antibody-mediated immune recognition of prostate cancer cells. Interestingly, during the course of these studies, we found ARM-Ps to exhibit extraordinarily high potencies toward PSMA, compared to previously reported inhibitors. Here, we report in-depth biochemical, crystallographic, and computational investigations which elucidate the origin of the observed affinity enhancement. These studies reveal a previously unreported arene-binding site on PSMA, which we believe participates in an aromatic stacking interaction with ARMs. Although this site is composed of only a few amino acid residues, it drastically enhances small molecule binding affinity. These results provide critical insights into the design of PSMA-targeted small molecules for prostate cancer diagnosis and treatment; more broadly, the presence of similar arene-binding sites throughout the proteome could prove widely enabling in the optimization of small molecule-protein interactions.
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Affiliation(s)
- Andrew X. Zhang
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06510-8107 USA
| | - Ryan P. Murelli
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06510-8107 USA
| | - Cyril Barinka
- Laboratory of Structural Biology, Institute of Biotechnology AS CR,v.v.i., 14200 Prague 4, Czech Republic
| | - Julien Michel
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06510-8107 USA
| | - Alexandra Cocleaza
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06510-8107 USA
| | - William L. Jorgensen
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06510-8107 USA
| | - Jacek Lubkowski
- Macromolecular Crystallography Laboratory, 539 Boyles Street, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - David A. Spiegel
- Department of Chemistry, Yale University, 225 Prospect Street, PO Box 208107, New Haven, CT 06510-8107 USA
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 USA
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249
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Terhorst JP, Jorgensen WL. E/Z Energetics for Molecular Modeling and Design. J Chem Theory Comput 2010; 6:2762-2769. [PMID: 20871784 DOI: 10.1021/ct1004017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thermochemical data have been obtained from G3B3 quantum mechanical calculations for 18 prototypical organic molecules, which exhibit E/Z conformational equilibria. The results are fundamentally important for molecular design including evaluation of structures from protein-ligand docking. For the 18 E/Z pairs, relative energies, enthalpies, free energies, and dipole moments are reported; the E - Z free-energy differences at 298 K range from +8.2 kcal/mol for 1,3-dimethyl carbamate to -6.4 kcal/mol for acetone oxime. A combination of steric and electronic effects can rationalize the variations. Free energies of hydration were also estimated using the GB/SA continuum solvent model. These results indicate that differential hydration is unlikely to qualitatively change the preferred direction of the E/Z equilibria, though further study with free-energy methods using explicit solvent is desirable.
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Affiliation(s)
- John P Terhorst
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
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250
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Alexandrova AN, Tully JC, Granucci G. Photochemistry of DNA Fragments via Semiclassical Nonadiabatic Dynamics. J Phys Chem B 2010; 114:12116-28. [DOI: 10.1021/jp103322c] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - John C. Tully
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107
| | - Giovanni Granucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, v. Risorgimento 35, I-56126, Pisa, Italy
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