Computational approaches for the design of peptides with anti-breast cancer properties

Background: Breast cancer is the most common cancer among women. Tamoxifen is the preferred drug for estrogen receptor-positive breast cancer treatment, yet many of these cancers are intrinsically resistant to tamoxifen or acquire resistance during treatment. Therefore, scientists are searching for breast cancer drugs that have different molecular targets. Methodology: Recently, a computational approach was used to successfully design peptides that are new lead compounds against breast cancer. We used replica exchange molecular dynamics to predict the structure and dynamics of active peptides, leading to the discovery of smaller bioactive peptides. Conclusions: These analogs inhibit estrogen-dependent cell growth in a mouse uterine growth assay, a test showing reliable correlation with human breast cancer inhibition. We outline the computational methods that were tried and used along with the experimental information that led to the successful completion of this research.

Quantum Mechanical Study of Sulfuric Acid Hydration: Atmospheric Implications

The role of the binary nucleation of sulfuric acid in aerosol formation and its implications for global warming is one of the fundamental unsettled questions in atmospheric chemistry. We have investigated the thermodynamics of sulfuric acid hydration using ab initio quantum mechanical methods. For H2SO4(H2O)n where n = 1–6, we used a scheme combining molecular dynamics configurational sampling with high-level ab initio calculations to locate the global and many low lying local minima for each cluster size. For each isomer, we extrapolated the Møller–Plesset perturbation theory (MP2) energies to their complete basis set (CBS) limit and added finite temperature corrections within the rigid-rotor-harmonic-oscillator (RRHO) model using scaled harmonic vibrational frequencies. We found that ionic pair (HSO4–·H3O+)(H2O)n−1 clusters are competitive with the neutral (H2SO4)(H2O)n clusters for n ≥ 3 and are more stable than neutral clusters for n ≥ 4 depending on the temperature. The Boltzmann averaged Gibbs free energies for the formation of H2SO4(H2O)n clusters are favorable in colder regions of the troposphere (T = 216.65–273.15 K) for n = 1–6, but the formation of clusters with n ≥ 5 is not favorable at higher (T > 273.15 K) temperatures. Our results suggest the critical cluster of a binary H2SO4–H2O system must contain more than one H2SO4 and are in concert with recent findings(1) that the role of binary nucleation is small at ambient conditions, but significant at colder regions of the troposphere. Overall, the results support the idea that binary nucleation of sulfuric acid and water cannot account for nucleation of sulfuric acid in the lower troposphere.

Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections

For (H2O)n where n = 1–10, we used a scheme combining molecular dynamics sampling with high level ab initio calculations to locate the global and many low lying local minima for each cluster. For each isomer, we extrapolated the RI-MP2 energies to their complete basis set limit, included a CCSD(T) correction using a smaller basis set and added finite temperature corrections within the rigid-rotor-harmonic-oscillator (RRHO) model using scaled and unscaled harmonic vibrational frequencies. The vibrational scaling factors were determined specifically for water clusters by comparing harmonic frequencies with VPT2 fundamental frequencies. We find the CCSD(T) correction to the RI-MP2 binding energy to be small (

Hydration of the Bisulfate Ion: Atmospheric Implications

Using molecular dynamics configurational sampling combined with ab initio energy calculations, we determined the low energy isomers of the bisulfate hydrates. We calculated the CCSD(T) complete basis set (CBS) binding electronic and Gibbs free energies for 53 low energy isomers of HSO4–(H2O)n=1–6 and derived the thermodynamics of adding waters sequentially to the bisulfate ion and its hydrates. Comparing the HSO4–/H2O system to the neutral H2SO4/H2O cluster, water binds more strongly to the anion than it does to the neutral molecules. The difference in the binding thermodynamics of HSO4–/H2O and H2SO4/H2O systems decreases with increasing number of waters. The thermodynamics for the formation of HSO4–(H2O)n=1–5 is favorable at 298.15 K, and that of HSO4–(H2O)n=1–6 is favorable for T < 273.15 K. The HSO4– ion is almost always hydrated at temperatures and relative humidity values encountered in the troposphere. Because the bisulfate ion binds more strongly to sulfuric acid than it does to water, it is expected to play a role in ion-induced nucleation by forming a strong complex with sulfuric acid and water, thus facilitating the formation of a critical nucleus.

Atmospheric Implications for Formation of Clusters of Ammonium and 1−10 Water Molecules

A mixed molecular dynamics/quantum mechanics model has been applied to the ammonium/water clustering system. The use of the high level MP2 calculation method and correlated basis sets, such as aug-cc-pVDZ and aug-cc-pVTZ, lends confidence in the accuracy of the extrapolated energies. These calculations provide electronic and free energies for the formation of clusters of ammonium and 1−10 water molecules at two different temperatures. Structures and thermodynamic values are in good agreement with previous experimental and theoretical results. The estimated concentration of these clusters in the troposphere was calculated using atmospheric amounts of ammonium and water. Results show the favorability of forming these clusters and implications for ion-induced nucleation in the atmosphere.

Accurate Predictions of Water Cluster Formation, (H2O)n=2−10

An efficient mixed molecular dynamics/quantum mechanics model has been applied to the water cluster system. The use of the MP2 method and correlation consistent basis sets, with appropriate correction for BSSE, allows for the accurate calculation of electronic and free energies for the formation of clusters of 2−10 water molecules. This approach reveals new low energy conformers for (H2O)n=7,9,10. The water heptamer conformers comprise five different structural motifs ranging from a three-dimensional prism to a quasi-planar book structure. A prism-like structure is favored energetically at low temperatures, but a chair-like structure is the global Gibbs free energy minimum past 200 K. The water nonamers exhibit less complexity with all the low energy structures shaped like a prism. The decamer has 30 conformers that are within 2 kcal/mol of the Gibbs free energy minimum structure at 298 K. These structures are categorized into four conformer classes, and a pentagonal prism is the most stable structure from 0 to 320 K. Results can be used as benchmark values for empirical water models and density functionals, and the method can be applied to larger water clusters.

Quantum Mechanical Study of Sulfuric Acid Hydration: Atmospheric Implications

The role of the binary nucleation of sulfuric acid in aerosol formation and its implications for global warming is one of the fundamental unsettled questions in atmospheric chemistry. We have investigated the thermodynamics of sulfuric acid hydration using ab initio quantum mechanical methods. For H2SO4(H2O)n where n = 1–6, we used a scheme combining molecular dynamics configurational sampling with high-level ab initio calculations to locate the global and many low lying local minima for each cluster size. For each isomer, we extrapolated the Møller–Plesset perturbation theory (MP2) energies to their complete basis set (CBS) limit and added finite temperature corrections within the rigid-rotor-harmonic-oscillator (RRHO) model using scaled harmonic vibrational frequencies. We found that ionic pair (HSO4–·H3O+)(H2O)n−1clusters are competitive with the neutral (H2SO4)(H2O)n clusters for n ≥ 3 and are more stable than neutral clusters for n ≥ 4 depending on the temperature. The Boltzmann averaged Gibbs free energies for the formation of H2SO4(H2O)n clusters are favorable in colder regions of the troposphere (T = 216.65–273.15 K) for n = 1–6, but the formation of clusters with n ≥ 5 is not favorable at higher (T > 273.15 K) temperatures. Our results suggest the critical cluster of a binary H2SO4–H2O system must contain more than one H2SO4 and are in concert with recent findings(1) that the role of binary nucleation is small at ambient conditions, but significant at colder regions of the troposphere. Overall, the results support the idea that binary nucleation of sulfuric acid and water cannot account for nucleation of sulfuric acid in the lower troposphere.

Natural variations at position 93 of the invariant Vα24-Jα18 α chain of human iNKT-cell TCRs strongly impact on CD1d binding

Human invariant natural killer T (NKT) cell TCRs bind to CD1d via an "invariant" Vα24-Jα18 chain (iNKTα) paired to semi-invariant Vβ11 chains (iNKTβ). Single-amino acid variations at position 93 (p93) of iNKTα, immediately upstream of the "invariant" CDR3α region, have been reported in a substantial proportion of human iNKT-cell clones (4-30%). Although p93, a serine in most human iNKT-cell TCRs, makes no contact with CD1d, it could affect CD1d binding by altering the conformation of the crucial CDR3α loop. By generating recombinant refolded iNKT-cell TCRs, we show that natural single-nucleotide variations in iNKTα, translating to serine, threonine, asparagine or isoleucine at p93, exert a powerful effect on CD1d binding, with up to 28-fold differences in affinity between these variants. This effect was observed with CD1d loaded with either the artificial α-galactosylceramide antigens KRN7000 or OCH, or the endogenous glycolipid β-galactosylceramide, and its importance for autoreactive recognition of endogenous lipids was demonstrated by the binding of variant iNKT-cell TCR tetramers to cell surface expressed CD1d. The serine-containing variant showed the strongest CD1d binding, offering an explanation for its predominance in vivo. Complementary molecular dynamics modeling studies were consistent with an impact of p93 on the conformation of the CDR3α loop.

Position-dependent effects on stability in tricyclo-DNA modified oligonucleotide duplexes

A series of oligodeoxyribonucleotides and oligoribonucleotides containing single and multiple tricyclo(tc)-nucleosides in various arrangements were prepared and the thermal and thermodynamic transition profiles of duplexes with complementary DNA and RNA evaluated. Tc-residues aligned in a non-continuous fashion in an RNA strand significantly decrease affinity to complementary RNA and DNA, mostly as a consequence of a loss of pairing enthalpy DeltaH. Arranging the tc-residues in a continuous fashion rescues T(m) and leads to higher DNA and RNA affinity. Substitution of oligodeoxyribonucleotides in the same way causes much less differences in T(m) when paired to complementary DNA and leads to substantial increases in T(m) when paired to complementary RNA. CD-spectroscopic investigations in combination with molecular dynamics simulations of duplexes with single modifications show that tc-residues in the RNA backbone distinctly influence the conformation of the neighboring nucleotides forcing them into higher energy conformations, while tc-residues in the DNA backbone seem to have negligible influence on the nearest neighbor conformations. These results rationalize the observed affinity differences and are of relevance for the design of tc-DNA containing oligonucleotides for applications in antisense or RNAi therapy.