A graph theoretical approach to structure-property and structure-activity correlations

The structure similarity and dissimilarity implied in many structure-property and structure-activity relationships has been examined from the graph theoretical point of view. The approach outlined is fundamentally different from generally used schemes in that, rather than seeking a new parametrization which will quantitatively fit observed data and trends,similarities among the skeletal forms and connectivities of the compounds of interest are studied quantitatively. The basis of the method is the assumption that skeletal forms of apparent similarity will yield similar enumerations for a number of graph theoretical invariants. In particular, allpaths within molecular skeletons are enumerated and sequences of path numbers (i.e., the number of paths of different length) are compared. The degree of similarity between molecules is proportional to the distance between points in the corresponding structure space obtained by interpreting the entries in molecular path sequences as coordinates inn-dimensional space. As anexample of the use of the concept of structural similarity, structure-activity data relating cerebral dopamine agonist properties for a series of N-substituted 2-aminotetralins are considered. The analysis suggests that the method may find wide application in the field of structure-activity correlations and structure-property studies. The data could be mass spectra, the fingerprint regions of infrared spectra, optical rotation and circular dichroism measurements, or any of many not fullyunderstood complex experimental findings suspected of having an inherent structural basis.On leave from Ames Laboratory - DOE, Iowa State University, Ames, Iowa 50011     

Computational strategy for intrinsically disordered protein ligand design leads to the discovery of p53 transactivation domain I binding compounds that activate the p53 pathway

Intrinsically disordered proteins or intrinsically disordered regions (IDPs) have gained much attention in recent years due to their vital roles in biology and prevalence in various human diseases. Although IDPs are perceived as attractive therapeutic targets, rational drug design targeting IDPs remains challenging because of their conformational heterogeneity. Here, we propose a hierarchical computational strategy for IDP drug virtual screening (IDPDVS) and applied it in the discovery of p53 transactivation domain I (TAD1) binding compounds. IDPDVS starts from conformation sampling of the IDP target, then it combines stepwise conformational clustering with druggability evaluation to identify potential ligand binding pockets, followed by multiple docking screening runs and selection of compounds that can bind multi-conformations. p53 is an important tumor suppressor and restoration of its function provides an opportunity to inhibit cancer cell growth. TAD1 locates at the N-terminus of p53 and plays key roles in regulating p53 function. No compounds that directly bind to TAD1 have been reported due to its highly disordered structure. We successfully used IDPDVS to identify two compounds that bind p53 TAD1 and restore wild-type p53 function in cancer cells. Our study demonstrates that IDPDVS is an efficient strategy for IDP drug discovery and p53 TAD1 can be directly targeted by small molecules.

A hierarchical computational strategy for IDP drug virtual screening (IDPDVS) was proposed and successfully applied to identify compounds that bind p53 TAD1 and restore wild-type p53 function in cancer cells.     

Use of vibrational spectroscopy to study protein and DNA structure,hydration, and binding of biomolecules: A combined theoretical and experimental approach

We report on our work with vibrational absorption, vibrational circular dichroism, Raman scattering, Raman optical activity, and surface‐enhanced Raman spectroscopy to study protein and DNA structure, hydration, and the binding of ligands, drugs, pesticides, or herbicides via a combined theoretical and experimental approach. The systems we have studied systematically are the amino acids (L ‐alanine, L ‐tryptophan, and L ‐histidine), peptides (N‐4271 acetyl L ‐alanine N′‐methyl amide, N‐acetyl L ‐tryptophan N′‐methyl amide, N‐acetyl L ‐histidine N′‐methyl amide, L ‐alanyl L ‐alanine, tri‐L ‐serine, N‐acetyl L ‐alanine L ‐proline L ‐tyrosine N′‐methyl amide, Leu‐enkephalin, cyclo‐(gly‐L ‐pro)₃, N‐acetyl (L ‐alanine)_n N′‐methyl amide), 3‐methyl indole, and a variety of small molecules (dichlobenil and 2,6‐dochlorobenzamide) of relevance to the protein systems under study. We have used molecular mechanics, the SCC‐DFTB, SCC‐DFTB+disp, RHF, MP2, and DFT methodologies for the modeling studies with the goal of interpreting the experimentally measured vibrational spectra for these molecules to the greatest extent possible and to use this combined approach to understand the structure, function, and electronic properties of these molecules in their various environments. The application of these spectroscopies to biophysical and environmental assays is expanding, and therefore a thorough understanding of the phenomenon from a rigorous theoretical basis is required. In addition, we give some exciting and new preliminary results which allow us to extend our methods to even larger and more complex systems. The work presented here is the current state of the art to this ever and fast changing field of theoretical spectroscopic interpretation and use of VA, VCD, Raman, ROA, EA, and ECD spectroscopies. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Exploring the structure,binding mode,flexibility and toxicity nature for Sinefungin molecule: a theoretical approach

Sinefungin (SFN) is an antiviral agent of dengue (DENV) and Zika (ZIKV) viruses with IC₅₀ values of 0.63 and 1.18 µM, respectively. The ADMET properties of SFN revealed that the SFN molecule can be used as an oral drug due to its good solubility nature. The molecular docking analysis of SFN molecule with RNA capping site of DENV and ZIKV NS5 MTase was performed. From this, the SFN-DENV MTase was found to be the best, based on binding energy (??7.56 kcal/mol) and intermolecular interactions. The geometrical parameters of the optimized conformation and docked conformations of SFN molecule are compared which indicated that the intermolecular interactions lead to the modifications of SFN conformation in active site. The molecular electrostatic potential map of SFN depicts the possible nucleophilic and electrophilic locations present in the molecule. The HOMO–LUMO based electronic properties such as electron affinity (A), electrophilicity (ω), electronegativity (χ) and global hardness (η) were calculated to determine the stability and toxicity of SFN molecule. Fukui function and NBO analysis of SFN were also computed.

     

A theoretical study on cyclacenes: Analytical tight‐binding approach

We present a theoretical study of cyclacene molecules performed at tight‐binding level. The orbital energies and eigenvectors have been analytically computed, and exact expressions for the axial component of the total position spread and polarizability tensors have been obtained. In absence of dimerization, the system has a D_nh symmetry, where n is the number of hexagonal units. The energy bands present no gap at the Fermi level, and to this fact it corresponds a diverging (per‐electron) polarizability for in the direction of the system symmetry axis. The two (degenerate) components of the polarizability on the σ_h symmetry plane, conversely, remain finite for . The total position spread tensor presents a qualitatively different behavior, since all the three components of the position spread per electron remain finite for . The results are analyzed and discussed for both axial and planar components separately as these are affected differently with respect to the increasing system size. Both dipole polarizability and total position spread have been computed using an ab initio approach for the smallest systems, to compare the analytical tight‐binding expressions with a higher‐level theory.     

NikR repressor: high-affinity nickel binding to the C-terminal domain regulates binding to operator DNA

E. coli NikR repressor binds operator DNA in a nickel-dependent fashion. The pM affinity of NikR for nickel is mediated by its C-terminal 86 residues. Nickel binding induced additional secondary structure, decreased the compactness, and increased the stability of NikR. Tetramer formation by the C-terminal domain and intact NikR did not require nickel. High-affinity nickel binding decreased the NikR concentration needed to half maximally protect operator DNA from undetectable levels to 30 nM. The intracellular concentration of NikR in E. coli is high enough that saturation of the high-affinity nickel sites should lead to substantial occupancy of the nik operator. Nickel binding to a set of low-affinity NikR sites resulted in an additional large increase in operator affinity and substantially increased the size of the NikR footprint on the operator.     

Electrochemical detection of DNA binding by tumor suppressor p53 protein using osmium-labeled oligonucleotide probes and catalytic hydrogen evolution at the mercury electrode

In this paper, we present an electrochemical DNA–protein interaction assay based on a combination of protein-specific immunoprecipitation at magnetic beads (MBIP) with application of oligonucleotide (ON) probes labeled with an electroactive oxoosmium complex (Os,bipy). We show that double-stranded ONs bearing a dT₂₀ tail labeled with Os,bipy are specifically recognized by the tumor suppressor p53 protein according to the presence or absence of a specific binding site (p53CON) in the double-stranded segment. We demonstrate the applicability of the Os,bipy-labeled probes in titration as well as competition MBIP assays to evaluate p53 relative affinity to various sequence-specific or structurally distinct unlabeled DNA substrates upon modulation of the p53-DNA binding by monoclonal antibodies used for the immunoprecipitation. To detect the p53-bound osmium-labeled probes, we took advantage of a catalytic peak yielded by Os,bipy-modified DNA at the mercury-based electrodes, allowing facile determination of subnanogram quantities of the labeled oligonucleotides. Versatility of the electrochemical MBIP technique and its general applicability in studies of any DNA-binding protein is discussed. Figure

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A novel approach to the calculation of the free energy due to molecular flexibility

The contribution of the molecular flexibility to the solvation excess free energy is expressed in terms of probabilities of reaching hard limits on intramolecular coordinates in a series of calculations successively relaxing those limits. Numerical tests on the harmonic oscillator are also presented and used to make suggestion about computational issues.     

A theoretical approach to the solvent extraction of metal chelates

A simplified theory for the solvent extraction of metal chelates is presented. Factors which are taken into account include the metal ion, the chelating reagent, aqueous complexing agents, adduct-forming substances, the organic solvent, temperature, rates of extraction, and other effects. Equations are developed for estimating the stoichiometries and the association constants of the involved species.     

A meanfield approach to the thermodynamics of a protein-solvent system with application to the oligomerization of the tumor suppressor p53

The thermodynamic stability and oligomerization status of the tumor suppressor p53 tetramerization domain have been studied experimentally and theoretically. A series of hydrophilic mutations at Met-340 and Leu-344 of human p53 were designed to disrupt the hydrophobic dimer-dimer interface of the tetrameric oligomerization domain of p53. Meanfield calculations of the free energy of the solvated mutants as a function of interdimer distance were compared with experimental data on the thermal stability and oligomeric state [tetramer, dimer, or equilibrium mixture of both] of each mutant. The calculations predicted a decreasing stability and oligomeric state for the following amino acids at residue 340: Met [tetramer] > Ser Asp, His, Gin, > Glu, Lys [dimer], whereas the experimental results showed the following order: Met [tetramer] > Ser > Gln > His, Lys > Asp, Glu [dimers]. For residue 344, the calculated trend was Leu [tetramer] > Ala > Arg, Gln, Lys [dimer], and the experimental trend was Leu [tetramer] > Ala, Arg, Gln, Lys [dimer]. The discrepancy for the lysine side chain at residue 340 is attributed to the dual nature of lysine, both hydrophobic and charged. The incorrect prediction of stability of the mutant with Asp at residue 340 is attributed to the fact that within the meanfield approach, we use the wild-type backbone configuration for all mutants, but low melting temperatures suggest a softening of the α-helices at the dimer-dimer interface. This initial application of meanfield theory toward a protein-solvent system is encouraging for the application of the theoretical model to more complex systems.     

A pH‐dependent computational approach to the effect of mutations on protein stability

This article describes a novel software implementation for high‐throughput scanning mutagenesis with a focus on protein stability. The approach combines molecular mechanics calculations with calculations of protein ionization and a Gaussian‐chain model of electrostatic interactions in unfolded state. Comprehensive testing demonstrates a state‐of‐the‐art accuracy for predicted free energy differences on single, double, and triple mutations with a correlation coefficient R above 0.7, which takes about 1.5 min per mutation on a single CPU. Unlike most of existing in silico methods for fast mutagenesis, the stability changes are reported as a continuous function of solution pH for wide pH intervals. We also propose a novel in silico strategy for searching stabilized protein variants that is based on combinatorial scanning mutagenesis using representative amino acid types. Our in silico predictions are in excellent agreement with the hyper‐stabilized variants of mesophilic cold shock protein found using the Proside method of direct evolution. © 2016 Wiley Periodicals, Inc.     

Fluorescence turn-on detection of a protein through the displaced single-stranded DNA binding protein binding to a molecular beacon

A new approach has been developed for the highly sensitive and selective sensing of a protein. Lysozyme binding to its aptamer prevents SSB protein binding, and the subsequent binding of the free SSB protein to a molecular beacon results in a turn-on fluorescence signal, which can be used for lysozyme quantification.     

Spermine binding to Parkinson's protein alpha-synuclein and its disease-related A30P and A53T mutants

Aggregation of alpha-synuclein (alpha-syn), a protein implicated in Parkinson's disease (PD), is believed to progress through formation of a partially folded intermediate. Using nanoelectrospray ionization (nano-ESI) mass spectrometry combined with ion mobility measurements we found evidence for a highly compact partially folded family of structures for alpha-syn and its disease-related A53T mutant with net charges of -6, -7, and -8. For the other early onset PD mutant, A30P, this highly compact population was only evident when the protein had a net charge of -6. When bound to spermine near physiologic pH, all three proteins underwent a charge reduction from the favored solution charge state of -10 to a net charge of -6. This charge reduction is accompanied by a dramatic size reduction of about a factor of 2 (cross section of 2600 A2 (-10 charge state) down to 1430 A2 (-6 charge state)). We conclude that spermine increases the aggregation rate of alpha-syn by inducing a collapsed conformation, which then proceeds to form aggregates.