ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was e... more ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Page 1. 192 Letters in Drug Design & Discovery, 2007, 4, 192-200 Rapid Classification... more Page 1. 192 Letters in Drug Design & Discovery, 2007, 4, 192-200 Rapid Classification of CYP3A4 Inhibition Potential Using Support Vector Machine Approach Diansong Zhou*,1,3, Ruifeng Liu*,2, Sara A. Otmani1, Scott W. Grimm1, Randy J. Zauhar3 and Ismael Zamora4,5 ...
A new technique is presented for incorporating hydration forces into molecular mechanics simulati... more A new technique is presented for incorporating hydration forces into molecular mechanics simulations. The method assumes the classical continuum approximation, where a solvated molecule is represented as a low-dielectric cavity of arbitrary shape embedded in a continuous region of high dielectric constant. Electrostatic effects are computed by first calculating the distribution of polarization charge (induced by the configuration of solute fixed charges) at the molecular surface. The hydration force at a particular atom is then found as the sum of the coulombic interaction with the induced surface charge, plus a purely mechanical contribution that arises from the pressure of the polarized solvent as it is pulled toward the solute. A procedure is developed to use the computed hydration forces in conjunction with the CHARMM molecular mechanics package to carry out energy minimizations in which the effects of solvation are explicitly included. This new technique also allows a detailed analysis of the relative balance of coulombic, hydration, and steric energies as a function of molecular conformation. The method is applied to the test case of a zwitterionic tripeptide (LYS-GLY-GLU), and the computational results suggest that hydration effects can play a significant role in determining a stable conformation for a solvated polar molecule. The future application to larger molecules is discussed.
The effects of minor differences in the amino acid sequences between a vertebrate (bovine testes)... more The effects of minor differences in the amino acid sequences between a vertebrate (bovine testes) and an invertebrate (octopus) calmodulin on metal ion binding were investigated via laser-induced Eu3+ and Tb3+ luminescence. Amino acid substitutions at residues which are coordinated to the metal ion do not produce any detectable changes in the 7F0----5D0 excitation spectrum of the Eu3+ ion bound to octopus calmodulin relative to bovine testes calmodulin; only minor differences in the excited-state lifetime values in D2O solution are observed. The dissociation constants for Eu3+ (1.0 +/- 0.2 microM) and Tb3+ (5 +/- 1 microM) from the weak lanthanide binding sites (III and IV, numbered from the amino terminus) of octopus calmodulin were measured using luminescence techniques. Both values agree well with those reported previously for bovine testes calmodulin [Mulqueen, P. M., Tingey, J. M., & Horrocks, W. D., Jr. (1985) Biochemistry 24, 6639-6645]. The measured dissociation constant of Eu3+ bound in the tight lanthanide binding sites (I and II) is 6 +/- 2 nM for octopus calmodulin and 12 +/- 2 nM for bovine testes calmodulin. The distances between sites I and II (12.4 +/- 0.5 A) and sites III and IV (11.7 +/- 0.8 A) were determined from Förster-type energy transfer in D2O solutions of octopus calmodulin containing bound Eu3+ donor and Nd3+ acceptor ions. Förster theory parameters for nonradiative energy transfer between Tyr138 and Tb3+ ions bound at sites III and IV of octopus calmodulin were comprehensively evaluated, including a dynamics simulation of the orientation factor kappa 2. This theory is found to account quantitatively for the observed energy-transfer efficiency as evaluated from the observed sensitized Tb3+ emission.
Purpose In this study, two unreported estrogen antagonists were identified using a combination of... more Purpose In this study, two unreported estrogen antagonists were identified using a combination of computational screening and a simple bacterial estrogen sensor. Methods Molecules here presented were initially part of a group obtained from a library of over a half million chemical compounds, using the Shape Signatures method. The structures within this group were then clustered and compared to known antagonists based on their physico-chemical parameters, and possible binding modes of the compounds to the Estrogen Receptor α (ERα) were analyzed. Finally, thirteen candidate compounds were purchased, and two of them were shown to behave as potential subtype-selective estrogen antagonists using a set of bacterial estrogen biosensors, which included sensors for ERα, ERβ, and a negative control thyroid hormone β biosensor. These activities were then analyzed using an ELISA assay against activated ERα in human MCF-7 cell extract. Results Two new estrogen receptor antagonists were detected using in silico Shape Signatures method with an engineered subtype-selective bacterial estrogen biosensor and commercially available ELISA assay. Additional thyroid biosensor control experiments confirmed no compounds interacted with human thyroid receptor β. Conclusions This work demonstrates an effective combination of computational analysis and simple bacterial screens for rapid identification of potential hormone-like therapeutics.
The dependence between the anomeric carbon chemical shift and the glycosidic bond 〈 φ, ψ〉 dihedra... more The dependence between the anomeric carbon chemical shift and the glycosidic bond 〈 φ, ψ〉 dihedral angles in oligosaccharide and glycopeptide model compounds was studied by Gauge-Including Atomic Orbital (GIAO) ab initio calculations. Complete chemical shift surfaces versus φ and ψ for d-Glcp-d-Glcp disaccharides with (1→1), (1→2), (1→3), and (1→4) linkages in both α- and β-configurations were computed using a 3-21G basis set, and scaled to reference results from calculations at the 6-311G** level of theory. Similar surfaces were obtained for GlcNAcThr and GlcNAcSer model glycopeptides in α- and β-configurations, using in this case different conformations for the peptide moiety. The results obtained for both families of model compounds are discussed. We also present the determination of empirical formulas of the form 13Cδ=f(φ,ψ) obtained by fitting the raw ab initio data to trigonometric series expansions suitable for use in molecular mechanics and dynamics simulations. Our investigations are consistent with experimental observations and earlier calculations performed on smaller glycosidic bond models, and show the applicability of chemical shift surfaces in the study of the conformational behavior of oligosaccharides and glycopeptides.
An algorithm is presented for generating a representation of the solvent-accessible molecular sur... more An algorithm is presented for generating a representation of the solvent-accessible molecular surface as a smooth triangulated manifold. The algorithm, called SMART (SMooth moleculAR surface Triangulator), divides the contact and reentrant portions of the solvent-accessible molecular surface into curvilinear three-sided elements. In contrast to the author's earlier implementation of this general approach [Zauhar, R.J. and Morgan, R.S., J. Comput. Chem., 11 (1990) 603], the SMART algorithm defines elements directly on the appropriate geometric surface types (rather than using interpolation over cubic elements), and has special features to handle highly distorted regions which often appear in deep crevices and internal cavities. While the method is designed for use with boundary element techniques in continuum electrostatics, it can also be applied to the accurate computation of molecular surface areas and volumes, and the generation of shaded surfaces for display with interactive computer graphics.
ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was e... more ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Abstract At present, there are two widely used approaches for computing molecular hydration and e... more Abstract At present, there are two widely used approaches for computing molecular hydration and electrostatic effects within the continuum approximation: the finite difference method, in which the electric potential is directly computed on a cubic grid, and the ...
Canadian Journal of Chemistry-revue Canadienne De Chimie, 1993
ABSTRACT Relative stabilities and features of tautomers of N,N-dimethyl-N′-(1-nitro-9-acridinyl)-... more ABSTRACT Relative stabilities and features of tautomers of N,N-dimethyl-N′-(1-nitro-9-acridinyl)-1,3-propanediamine (known as nitracrine by the World Health Organization (WHO) or as Ledakrin in Poland), which exhibits antitumour activity, and its three nitro isomers were examined by AM1 and, in some cases, by PM3 and ab initio (STO-3G) methods. The lowest energy form of three compounds was always an imino tautomer, while the energy of the amino tautomers was a few kcal mol−1 higher and that of the aci forms (in the case of the 2- and 4-nitro isomers) was more than 25 kcal mol−1 higher. Each tautomer can further exist in several structural forms (conformers or stereoisomers). In some of them internal hydrogen bonding interactions are feasible. The barriers to rotation of the -NHR group, as well as to inversion of the -NHR group (in amino tautomers of nitracrine and its 2-nitro isomer) and of the whole molecule (in the case of non-planar imino structures), were also evaluated, as were enthalpies of formation (total energies), entropies, free energies, dipole moments, and energies of HOMO and LUMO orbitals. Molecular electrostatic potential maps reveal that only in nitracrine are both -NO2 and -NHR groups surrounded by a negative electrostatic potential, whereas in other isomers the -NHR fragment is surrounded by a positive electrostatic potential while the -NO2 group remains in the region of a negative electrostatic potential. The possible influence of physicochemical features on the biological activity of the molecules is also considered.
ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was e... more ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Page 1. 192 Letters in Drug Design & Discovery, 2007, 4, 192-200 Rapid Classification... more Page 1. 192 Letters in Drug Design & Discovery, 2007, 4, 192-200 Rapid Classification of CYP3A4 Inhibition Potential Using Support Vector Machine Approach Diansong Zhou*,1,3, Ruifeng Liu*,2, Sara A. Otmani1, Scott W. Grimm1, Randy J. Zauhar3 and Ismael Zamora4,5 ...
A new technique is presented for incorporating hydration forces into molecular mechanics simulati... more A new technique is presented for incorporating hydration forces into molecular mechanics simulations. The method assumes the classical continuum approximation, where a solvated molecule is represented as a low-dielectric cavity of arbitrary shape embedded in a continuous region of high dielectric constant. Electrostatic effects are computed by first calculating the distribution of polarization charge (induced by the configuration of solute fixed charges) at the molecular surface. The hydration force at a particular atom is then found as the sum of the coulombic interaction with the induced surface charge, plus a purely mechanical contribution that arises from the pressure of the polarized solvent as it is pulled toward the solute. A procedure is developed to use the computed hydration forces in conjunction with the CHARMM molecular mechanics package to carry out energy minimizations in which the effects of solvation are explicitly included. This new technique also allows a detailed analysis of the relative balance of coulombic, hydration, and steric energies as a function of molecular conformation. The method is applied to the test case of a zwitterionic tripeptide (LYS-GLY-GLU), and the computational results suggest that hydration effects can play a significant role in determining a stable conformation for a solvated polar molecule. The future application to larger molecules is discussed.
The effects of minor differences in the amino acid sequences between a vertebrate (bovine testes)... more The effects of minor differences in the amino acid sequences between a vertebrate (bovine testes) and an invertebrate (octopus) calmodulin on metal ion binding were investigated via laser-induced Eu3+ and Tb3+ luminescence. Amino acid substitutions at residues which are coordinated to the metal ion do not produce any detectable changes in the 7F0----5D0 excitation spectrum of the Eu3+ ion bound to octopus calmodulin relative to bovine testes calmodulin; only minor differences in the excited-state lifetime values in D2O solution are observed. The dissociation constants for Eu3+ (1.0 +/- 0.2 microM) and Tb3+ (5 +/- 1 microM) from the weak lanthanide binding sites (III and IV, numbered from the amino terminus) of octopus calmodulin were measured using luminescence techniques. Both values agree well with those reported previously for bovine testes calmodulin [Mulqueen, P. M., Tingey, J. M., & Horrocks, W. D., Jr. (1985) Biochemistry 24, 6639-6645]. The measured dissociation constant of Eu3+ bound in the tight lanthanide binding sites (I and II) is 6 +/- 2 nM for octopus calmodulin and 12 +/- 2 nM for bovine testes calmodulin. The distances between sites I and II (12.4 +/- 0.5 A) and sites III and IV (11.7 +/- 0.8 A) were determined from Förster-type energy transfer in D2O solutions of octopus calmodulin containing bound Eu3+ donor and Nd3+ acceptor ions. Förster theory parameters for nonradiative energy transfer between Tyr138 and Tb3+ ions bound at sites III and IV of octopus calmodulin were comprehensively evaluated, including a dynamics simulation of the orientation factor kappa 2. This theory is found to account quantitatively for the observed energy-transfer efficiency as evaluated from the observed sensitized Tb3+ emission.
Purpose In this study, two unreported estrogen antagonists were identified using a combination of... more Purpose In this study, two unreported estrogen antagonists were identified using a combination of computational screening and a simple bacterial estrogen sensor. Methods Molecules here presented were initially part of a group obtained from a library of over a half million chemical compounds, using the Shape Signatures method. The structures within this group were then clustered and compared to known antagonists based on their physico-chemical parameters, and possible binding modes of the compounds to the Estrogen Receptor α (ERα) were analyzed. Finally, thirteen candidate compounds were purchased, and two of them were shown to behave as potential subtype-selective estrogen antagonists using a set of bacterial estrogen biosensors, which included sensors for ERα, ERβ, and a negative control thyroid hormone β biosensor. These activities were then analyzed using an ELISA assay against activated ERα in human MCF-7 cell extract. Results Two new estrogen receptor antagonists were detected using in silico Shape Signatures method with an engineered subtype-selective bacterial estrogen biosensor and commercially available ELISA assay. Additional thyroid biosensor control experiments confirmed no compounds interacted with human thyroid receptor β. Conclusions This work demonstrates an effective combination of computational analysis and simple bacterial screens for rapid identification of potential hormone-like therapeutics.
The dependence between the anomeric carbon chemical shift and the glycosidic bond 〈 φ, ψ〉 dihedra... more The dependence between the anomeric carbon chemical shift and the glycosidic bond 〈 φ, ψ〉 dihedral angles in oligosaccharide and glycopeptide model compounds was studied by Gauge-Including Atomic Orbital (GIAO) ab initio calculations. Complete chemical shift surfaces versus φ and ψ for d-Glcp-d-Glcp disaccharides with (1→1), (1→2), (1→3), and (1→4) linkages in both α- and β-configurations were computed using a 3-21G basis set, and scaled to reference results from calculations at the 6-311G** level of theory. Similar surfaces were obtained for GlcNAcThr and GlcNAcSer model glycopeptides in α- and β-configurations, using in this case different conformations for the peptide moiety. The results obtained for both families of model compounds are discussed. We also present the determination of empirical formulas of the form 13Cδ=f(φ,ψ) obtained by fitting the raw ab initio data to trigonometric series expansions suitable for use in molecular mechanics and dynamics simulations. Our investigations are consistent with experimental observations and earlier calculations performed on smaller glycosidic bond models, and show the applicability of chemical shift surfaces in the study of the conformational behavior of oligosaccharides and glycopeptides.
An algorithm is presented for generating a representation of the solvent-accessible molecular sur... more An algorithm is presented for generating a representation of the solvent-accessible molecular surface as a smooth triangulated manifold. The algorithm, called SMART (SMooth moleculAR surface Triangulator), divides the contact and reentrant portions of the solvent-accessible molecular surface into curvilinear three-sided elements. In contrast to the author's earlier implementation of this general approach [Zauhar, R.J. and Morgan, R.S., J. Comput. Chem., 11 (1990) 603], the SMART algorithm defines elements directly on the appropriate geometric surface types (rather than using interpolation over cubic elements), and has special features to handle highly distorted regions which often appear in deep crevices and internal cavities. While the method is designed for use with boundary element techniques in continuum electrostatics, it can also be applied to the accurate computation of molecular surface areas and volumes, and the generation of shaded surfaces for display with interactive computer graphics.
ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was e... more ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Abstract At present, there are two widely used approaches for computing molecular hydration and e... more Abstract At present, there are two widely used approaches for computing molecular hydration and electrostatic effects within the continuum approximation: the finite difference method, in which the electric potential is directly computed on a cubic grid, and the ...
Canadian Journal of Chemistry-revue Canadienne De Chimie, 1993
ABSTRACT Relative stabilities and features of tautomers of N,N-dimethyl-N′-(1-nitro-9-acridinyl)-... more ABSTRACT Relative stabilities and features of tautomers of N,N-dimethyl-N′-(1-nitro-9-acridinyl)-1,3-propanediamine (known as nitracrine by the World Health Organization (WHO) or as Ledakrin in Poland), which exhibits antitumour activity, and its three nitro isomers were examined by AM1 and, in some cases, by PM3 and ab initio (STO-3G) methods. The lowest energy form of three compounds was always an imino tautomer, while the energy of the amino tautomers was a few kcal mol−1 higher and that of the aci forms (in the case of the 2- and 4-nitro isomers) was more than 25 kcal mol−1 higher. Each tautomer can further exist in several structural forms (conformers or stereoisomers). In some of them internal hydrogen bonding interactions are feasible. The barriers to rotation of the -NHR group, as well as to inversion of the -NHR group (in amino tautomers of nitracrine and its 2-nitro isomer) and of the whole molecule (in the case of non-planar imino structures), were also evaluated, as were enthalpies of formation (total energies), entropies, free energies, dipole moments, and energies of HOMO and LUMO orbitals. Molecular electrostatic potential maps reveal that only in nitracrine are both -NO2 and -NHR groups surrounded by a negative electrostatic potential, whereas in other isomers the -NHR fragment is surrounded by a positive electrostatic potential while the -NO2 group remains in the region of a negative electrostatic potential. The possible influence of physicochemical features on the biological activity of the molecules is also considered.
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