QSAR Evaluations to Unravel the Structural Features in Lysine-Specific Histone Demethylase 1A Inhibitors for Novel Anticancer Lead Development Supported by Molecular Docking,MD Simulation and MMGBSA

Using 84 structurally diverse and experimentally validated LSD1/KDM1A inhibitors, quantitative structure–activity relationship (QSAR) models were built by OECD requirements. In the QSAR analysis, certainly significant and understated pharmacophoric features were identified as critical for LSD1 inhibition, such as a ring Carbon atom with exactly six bonds from a Nitrogen atom, partial charges of lipophilic atoms within eight bonds from a ring Sulphur atom, a non-ring Oxygen atom exactly nine bonds from the amide Nitrogen, etc. The genetic algorithm–multi-linear regression (GA-MLR) and double cross-validation criteria were used to create robust QSAR models with high predictability. In this study, two QSAR models were developed, with fitting parameters like R² = 0.83–0.81, F = 61.22–67.96, internal validation parameters such as Q²_LOO = 0.79–0.77, Q²_LMO = 0.78–0.76, CCC_cv = 0.89–0.88, and external validation parameters such as, R2ext = 0.82 and CCCex = 0.90. In terms of mechanistic interpretation and statistical analysis, both QSAR models are well-balanced. Furthermore, utilizing the pharmacophoric features revealed by QSAR modelling, molecular docking experiments corroborated with the most active compound’s binding to the LSD1 receptor. The docking results are then refined using Molecular dynamic simulation and MMGBSA analysis. As a consequence, the findings of the study can be used to produce LSD1/KDM1A inhibitors as anticancer leads.     

Discovery of New Coumarin-Based Lead with Potential Anticancer,CDK4 Inhibition and Selective Radiotheranostic Effect: Synthesis, 2D & 3D QSAR,Molecular Dynamics,In Vitro Cytotoxicity,Radioiodination, and Biodistribution Studies

Novel 6-bromo-coumarin-ethylidene-hydrazonyl-thiazolyl and 6-bromo-coumarin-thiazolyl-based derivatives were synthesized. A quantitative structure activity relationship (QSAR) model with high predictive power r² = 0.92, and RMSE = 0.44 predicted five compounds; 2b, 3b, 5a, 9a and 9i to have potential anticancer activities. Compound 2b achieved the best ΔG of –15.34 kcal/mol with an affinity of 40.05 pki. In a molecular dynamic study 2b showed an equilibrium at 0.8 Å after 3.5 ns, while flavopiridol did so at 0.5 Å after the same time (3.5 ns). 2b showed an IC₅₀ of 0.0136 µM, 0.015 µM, and 0.054 µM against MCF-7, A-549, and CHO-K1 cell lines, respectively. The CDK4 enzyme assay revealed the significant CDK4 inhibitory activity of compound 2b with IC₅₀ of 0.036 µM. The selectivity of the newly discovered lead compound 2b toward localization in tumor cells was confirmed by a radioiodination biological assay that was done via electrophilic substitution reaction utilizing the oxidative effect of chloramine-t. ¹³¹I-2b showed good in vitro stability up to 4 h. In solid tumor bearing mice, the values of tumor uptake reached a height of 5.97 ± 0.82%ID/g at 60 min p.i. ¹³¹I-2b can be considered as a selective radiotheranostic agent for solid tumors with promising anticancer activity.     

QSAR Modeling,Molecular Docking and Cytotoxic Evaluation for Novel Oxidovanadium(IV) Complexes as Colon Anticancer Agents

Four new drug-based oxidovanadium (IV) complexes were synthesized and characterized by various spectral techniques, including molar conductance, magnetic measurements, and thermogravimetric analysis. Moreover, optimal structures geometry for all syntheses was obtained by the Gaussian09 program via the DFT/B3LYP method and showed that all of the metal complexes adopted a square-pyramidal structure. The essential parameters, electrophilicity (ω) value and expression for the maximum charge that an electrophile molecule may accept (ΔN_max) showed the practical biological potency of [VO(CTZ)₂] 2H₂O. The complexes were also evaluated for their propensity to bind to DNA through UV–vis absorption titration. The result revealed a high binding ability of the [VO(CTZ)₂] 2H₂O complex with K_b = 1.40 × 10⁶ M⁻¹. Furthermore, molecular docking was carried out to study the behavior of the VO (II) complexes towards colon cancer cell (3IG7) protein. A quantitative structure–activity relationship (QSAR) study was also implemented for the newly synthesized compounds. The results of validation indicate that the generated QSAR model possessed a high predictive power (R² = 0.97). Within the investigated series, the [VO(CTZ)₂] 2H₂O complex showed the greatest potential the most selective compound comparing to the stander chemotherapy drug.     

Ion-molecule reactions catalyzed by a single gold atom

We report that Au atoms within van der Waals complexes serve as catalysts for the first time. This was observed in ionization-induced chemistry of 1,6-hexanediol–Au and 1,8-octanediol–Au complexes formed in superfluid helium nanodroplets, where the addition of Au atom(s) made C₂H₄⁺ the sole prominent product in dissociative reactions. Density functional theory (DFT) calculations showed that the Au atom significantly strengthens all of the C–C bonds and weakens the C–O bonds in the meantime, making the C–C bonds stronger than the two C–O bonds in the ionized complexes. This leads to a preferential cleavage of the C–O bonds and thus a strong catalytic effect of the Au atoms in the reactions.

Single Au atoms within van der Waals complexes are found to serve as catalysts in ionisation-induced chemistry for the first time.     

Quantitative structure–activity relationship model for prediction study of corrosion inhibition efficiency using two‐stage sparse multiple linear regression

A new quantitative structure–activity relationship (QSAR) of the inhibition of mild steel corrosion in 1 M hydrochloric acid using furan derivatives was developed by proposing two‐stage sparse multiple linear regression. The sparse multiple linear regression using ridge penalty and sparse multiple linear regression using elastic net (SMLRE) were used to develop the QSAR model. The results show that the SMLRE‐based model possesses high predictive power compared with sparse multiple linear regression using ridge penalty‐based model according to the mean‐squared errors for both training and test datasets, leave‐one‐out internal validation (Q²_int = 0.98), and external validation (Q²_ext = 0.95). In addition, the results of applicability domain assessment using the leverage approach reveal a reliable and robust SMLRE‐based model. In conclusion, the developed QSAR model using SMLRE can be efficiently used in the studies of corrosion inhibition efficiency. Copyright © 2016 John Wiley & Sons, Ltd.     

Visible light driven deuteration of formyl C–H and hydridic C(sp3)–H bonds in feedstock chemicals and pharmaceutical molecules

Deuterium labelled compounds are of significant importance in chemical mechanism investigations, mass spectrometric studies, diagnoses of drug metabolisms, and pharmaceutical discovery. Herein, we report an efficient hydrogen deuterium exchange reaction using deuterium oxide (D₂O) as the deuterium source, enabled by merging a tetra-n-butylammonium decatungstate (TBADT) hydrogen atom transfer photocatalyst and a thiol catalyst under light irradiation at 390 nm. This deuteration protocol is effective with formyl C–H bonds and a wide range of hydridic C(sp³)–H bonds (e.g. α-oxy, α-thioxy, α-amino, benzylic, and unactivated tertiary C(sp³)–H bonds). It has been successfully applied to the high incorporation of deuterium in 38 feedstock chemicals, 15 pharmaceutical compounds, and 6 drug precursors. Sequential deuteration between formyl C–H bonds of aldehydes and other activated hydridic C(sp³)–H bonds can be achieved in a selective manner.

A selective hydrogen deuterium exchange reaction with formyl C–H bonds and a wide range of hydridic C(sp³)–H bonds has been achieved by merging tetra-n-butylammonium decatungstate photocatalyst and a thiol catalyst under 390 nm light irradiation.     

DFT‐based QSAR study and molecular design of AHMA derivatives as potent anticancer agents

A quantitative structure–activity relationship (QSAR) of 3‐(9‐acridinylamino)‐5‐hydroxymethylaniline (AHMA) derivatives and their alkylcarbamates as potent anticancer agents has been studied using density functional theory (DFT), molecular mechanics (MM+), and statistical methods. In the best established QSAR equation, the energy (E_NL) of the next lowest unoccupied molecular orbital (NLUMO) and the net charges (Q_FR) of the first atom of the substituent R, as well as the steric parameter (MR₂) of subsituent R₂ are the main independent factors contributing to the anticancer activity of the compounds. A new scheme determining outliers by “leave‐one‐out” (LOO) cross‐validation coefficient (q) was suggested and successfully used. The fitting correlation coefficient (R²) and the “LOO” cross‐validation coefficient (q²) values for the training set of 25 compounds are 0.881 and 0.829, respectively. The predicted activities of 5 compounds in the test set using this QSAR model are in good agreement with their experimental values, indicating that this model has excellent predictive ability. Based on the established QSAR equation, 10 new compounds with rather high anticancer activity much greater than that of 34 compounds have been designed and await experimental verification. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Magnesium–halobenzene bonding: mapping the halogen sigma-hole with a Lewis-acidic complex

Complexes of the Lewis base-free cations (^MeBDI)Mg⁺ and (^tBuBDI)Mg⁺ with Ph–X ligands (X = F, Cl, Br, I) have been studied (^MeBDI = HC[C(Me)N-DIPP]₂ and ^tBuBDI = HC[C(tBu)N-DIPP]₂; DIPP = 2,6-diisopropylphenyl). For the smaller β-diketiminate ligand (^MeBDI) only complexes with PhF could be isolated. Heavier Ph–X ligands could not compete with bonding of Mg to the weakly coordinating anion B(C₆F₅)₄⁻. For the cations with the bulkier ^tBuBDI ligand, the full series of halobenzene complexes was structurally characterized. Crystal structures show that the Mg⋯X–Ph angle strongly decreases with the size of X: F 139.1°, Cl 101.4°, Br 97.7°, I 95.1°. This trend, which is supported by DFT calculations, can be explained with the σ-hole which increases from F to I. Charge calculation and Atoms-In-Molecules analyses show that Mg⋯F–Ph bonding originates from electrostatic attraction between Mg²⁺ and the very polar C^δ+–F^δ− bond. For the heavier halobenzenes, polarization of the halogen atom becomes increasingly important (Cl < Br < I). Complexation with Mg leads in all cases to significant Ph–X bond activation and elongation. This unusual coordination of halogenated species to early main group metals is therefore relevant to C–X bond breaking.

Complexes of a highly Lewis acidic Mg cation and the full series of Ph–X (X = F, Cl, Br, I) have been structurally characterized. The Mg⋯X–Ph angle decreases with halogen size on account of the growing halogen σ-hole.     

Iron-catalyzed remote functionalization of inert C(sp3)–H bonds of alkenes via 1,n-hydrogen-atom-transfer by C-centered radical relay

As an alternative approach to traditional C–H activation that often involved harsh conditions, and vicinal or primary C–H functionalization, radical relay offers a solution to these long-held problems. Enabled by 1,n (n = 5, 6)-hydrogen atom transfer (HAT), we use a most prevalent moiety, alkene, as the precursor to an sp³ C-centered radical to promote selective cleavage of inert C(sp³)–H bonds for the generation of azidotrifluoromethylated molecules. Mild conditions, broad scope and excellent regioselective control (>20 : 1) are observed in the reactions. Deuterium labelling studies disclose the kinetic characteristics of the transformations and verify a direct 1,n-HAT pathway. The key to this C-centered radical relay is that iron plays a dual role as a radical initiator and terminator to incorporate the azide functionality through radical oxidation via azido–ligand-transfer. The methods and the later derivatization promise expeditious synthesis of CF₃-containing organic azides, γ-lactam and triazoles that are widely used in designing new fluorescent tags and functional materials.

Remote functionalization of inert C(sp³)–H bonds is described via iron-catalyzed sp³ C-centered radical relay.     

Computational Studies of Coinage Metal Anion M− + CH3X (X = F,Cl, Br,I) Reactions in Gas Phase

We characterized the stationary points along the nucleophilic substitution (S_N2), oxidative insertion (OI), halogen abstraction (XA), and proton transfer (PT) product channels of M⁻ + CH₃X (M = Cu, Ag, Au; X = F, Cl, Br, I) reactions using the CCSD(T)/aug-cc-pVTZ level of theory. In general, the reaction energies follow the order of PT > XA > S_N2 > OI. The OI channel that results in oxidative insertion complex [CH₃–M–X]⁻ is most exothermic, and can be formed through a front-side attack of M on the C-X bond via a high transition state OxTS or through a S_N2-mediated halogen rearrangement path via a much lower transition state invTS. The order of OxTS > invTS is inverted when changing M⁻ to Pd, a d¹⁰ metal, because the symmetry of their HOMO orbital is different. The back-side attack S_N2 pathway proceeds via typical Walden-inversion transition state that connects to pre- and post-reaction complexes. For X = Cl/Br/I, the invS_N2-TS’s are, in general, submerged. The shape of this M⁻ + CH₃X S_N2 PES is flatter as compared to that of a main-group base like F⁻ + CH₃X, whose PES has a double-well shape. When X = Br/I, a linear halogen-bonded complex [CH₃−X∙··M]⁻ can be formed as an intermediate upon the front-side attachment of M on the halogen atom X, and it either dissociates to CH₃ + MX⁻ through halogen abstraction or bends the C-X-M angle to continue the back-side S_N2 path. Natural bond orbital analysis shows a polar covalent M−X bond is formed within oxidative insertion complex [CH₃–M–X]⁻, whereas a noncovalent M–X halogen-bond interaction exists for the [CH₃–X∙··M]⁻ complex. This work explores competing channels of the M⁻ + CH₃X reaction in the gas phase and the potential energy surface is useful in understanding the dynamic behavior of the title and analogous reactions.