First report on exploration of structural features of natural compounds (NPACT database) for anti-breast cancer activity (MCF-7): QSAR-based virtual screening, molecular docking, ADMET, MD simulation, and DFT studies

Due to the high toxicity, poor efficacy and resistance associated with current anti-breast cancer drugs, there's growing interest in natural products (NPs) for their potential anti-cancer properties. Computational modelling of NPs to identify key structural features can aid in developing novel natural inhibitors. In this study, we developed statistically significant QSAR models based on NPs from the NPACT database, which have shown potential anticancer activity against the MCF-7 cancer cell lines. All the developed QSAR models were statistically robust, meeting both internal (R 2  = 0.666-0.669, R 2 adj  = 0.657-0.660, Q 2 Loo  = 0.636-0.638) and external (Q 2 F n  = 0.686-0.714, CCC ext = 0.830-0.847) validation criteria. Consequently, they were utilized to virtually screen a series of NPs from the COCONUT database in the search for novel natural inhibitors. Molecular docking studies were conducted on the identified compounds against the human HER2 protein (PDB ID: 3PP0), which is a crucial target in breast cancer. Molecular docking analysis demonstrated that compounds 4608 and 2710 achieved the highest docking scores, with CDOCKER interaction energies of -72.67 kcal/mol and - 72.63 kcal/mol respectively. Compounds 4608 and 2710 were identified as the most promising candidates upon performing triplicate 100 ns MD simulation study using the CHARMM36 force field. DFT studies was performed to evaluate their stability and reactivity as potential drug molecules. This research contributes to the development of new natural inhibitors for breast cancer.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00266-5.

Exploring the 3,5-Dibromo-4,6-dimethoxychalcones and Their Flavone Derivatives as Dual α-Glucosidase and α-Amylase Inhibitors with Antioxidant and Anticancer Potential

The rising levels of type 2 diabetes mellitus (T2DM) and the poor medical effects of the commercially available antidiabetic drugs necessitate the development of potent analogs to treat this multifactorial metabolic disorder. It has been demonstrated that targeting two or more biochemical targets associated with the onset and progression of diabetes along with oxidative stress and/or cancer could be a significant strategy for treating complications related to this metabolic disorder. The 3,5-dibromo-4,6-dimethoxychalcones (2a-f) and the corresponding flavone derivatives (3a-f) were synthesized and characterized using spectroscopic (NMR, HR-MS and FT-IR) techniques. The inhibitory effect of both series of compounds against α-glucosidase and α-amylase was evaluated in vitro through enzymatic assays. Selected compounds were also evaluated for potential to activate or inhibit superoxide dismutase. Compound 3c was selected as a representative model for the flavone series and evaluated spectrophotometrically for potential to coordinate Cu(II) and/or Zn(II) ions implicated in the metal-catalyzed free radical generation. A plausible mechanism for metal-chelation of the test compounds is presented. Furthermore, the most active compounds from each series against the test carbohydrate-hydrolyzing enzymes were selected and evaluated for their antigrowth effect on the human breast (MCF-7) and lung (A549) cancer cell lines and for cytotoxicity against the African Green Monkey kidney (Vero) cell line. The parent chalcone 2a and flavone derivatives 3a, 3c and 3e exhibited relatively high inhibitory activity against the MCF-7 cells with IC50 values of 4.12 ± 0.55, 8.50 ± 0.82, 5.10 ± 0.61 and 6.96 ± 0.66 μM, respectively. The chalcones 2a and 2c exhibited significant cytotoxicity against the A549 cells with IC50 values of 7.40 ± 0.67 and 9.68 ± 0.80 μM, respectively. Only flavone 3c exhibited relatively strong and comparable cytotoxicity against the MCF-7 and A549 cell lines with IC50 values of 6.96 ± 0.66 and 6.42 ± 0.79 μM, respectively. Both series of compounds exhibited strong activity against the MCF-7 and A549 cell lines compared to the analogous quercetin (IC50 = 35.40 ± 1.78 and 35.38 ± 1.78 μM, respectively) though moderate compared to nintedanib (IC50 = 0.53 ± 0.11 and 0.74 ± 0.15 μM, respectively). The test compounds generally exhibited reduced cytotoxicity against the Vero cells compared to this anticancer drug. Molecular docking revealed strong alignment of the test compounds with the enzyme backbone to engage in hydrogen bonding interaction/s and hydrophobic contacts with the residues in the active sites of α-glucosidase and α-amylase. The test compounds possess favorable drug-likeness properties, supporting their potential as therapeutic candidates against T2DM.

Synthesis and conformational analysis of pyran inter-halide analogues of ᴅ-talose

In this work, we describe the synthesis of halogenated pyran analogues of ᴅ-talose using a halo-divergent strategy from known 1,6-anhydro-2,3-dideoxy-2,3-difluoro-β-ᴅ-mannopyranose. In solution and in the solid-state, all analogues adopt standard 4 C 1-like conformations despite 1,3-diaxial repulsion between the F2 and the C4 halogen. Moreover, the solid-state conformational analysis of halogenated pyrans reveals deviation in the intra-annular torsion angles arising from repulsion between the axial fluorine at C2 and the axial halogen at C4, which increases with the size of the halogen at C4 (F < Cl < Br < I). Crystal packing arrangements of pyran inter-halides show hydrogen bond acceptor and nonbonding interactions for the halogen at C4. Finally, density functional theory (DFT) calculations corroborate the preference of talose analogues to adopt a 4 C 1-like conformation and a natural bonding orbital (NBO) analysis demonstrates the effects of hyperconjugation from C-F antibonding orbitals.

Unconventional Radical and Radical-Hole Site-Based Interactions in Halogen-Bearing Dimers and Trimers: A Comparative Study

Radical (R•) and R•-hole site-based interactions are comparatively studied, for the first time, using ab initio methods. In this regard, R•-bearing molecules •XO3 (where X = Cl, Br, and I) were subjected to direct interaction with NH3 within dimeric and trimeric forms in the form of NH3···•XO3/•XO3···NH3 and NH3···•XO3···NH3 complexes, respectively. As confirmed by electrostatic potential analysis, the studied R•-bearing molecules •XO3 had the outstanding potentiality to interact as Lewis acid centers via two positive sites dubbed as R• and R•-hole sites. Such an observation proposed the potentiality of the considered •XO3 molecules to engage in unconventional R• and well-established R•-hole site-based interactions with Lewis bases. This was confirmed by negative interaction (E int) energies, ranging from -4.93 to -19.89 kcal/mol, with higher favorability for R• site-based interactions over the R•-hole site-based ones. MP2 energetic features furnished higher preferability for the R• site-based interactions than the R•-hole site-based ones in the case of chlorine- and bromine-bearing complexes, and the reverse was true for the iodine-bearing complexes. Moreover, elevated E int values were recorded for the NH3···•XO3···NH3 trimers over the NH3···•XO3 and •XO3···NH3 dimers, outlining the higher preference of the •XO3 molecules to engage in R• and R•-hole site-based interactions in the trimeric form over the dimeric one. These results might be considered a requisite linchpin for numerous forthcoming supramolecular chemistry and crystal engineering studies.

Redox-Responsive Halogen Bonding as a Highly Selective Interaction for Electrochemical Separations

Leveraging specific noncovalent interactions can broaden the mechanims for selective electrochemical separations beyond solely electrostatic interactions. Here, we explore redox-responsive halogen bonding (XB) for selective electrosorption in nonaqueous media, by taking advantage of directional interactions of XB alongisde a cooperative and synergistic ferrocene redox-center. We designed and evaluated a new redox-active XB donor polymer, poly(5-iodo-4-ferrocenyl-1-(4-vinylbenzyl)-1H-1,2,3-triazole) (P(FcTS-I)), for the electrochemically switchable binding and release of target organic and inorganic ions at a heterogeneous interface. Under applied potential, the oxidized ferrocene amplifies the halogen binding site, leading to significantly enhanced uptake and selectivity towards key inorganic and organic species, including chloride, bisulfate, and benzenesulfonate, compared to the open-circuit potential or the hydrogen bonding donor analog. Density functional theory calculations, as well as spectroscopic analysis, offer mechanistic insight into the degree of amplification of σ-holes at a molecular level, with selectivity modulated by charge transfer and dispersion interactions. Our work highlights the potential of XB in selective electrosorption by uniquely leveraging noncovalent interactions for redox-mediated electrochemical separations.

σ-Hole, lone-pair-hole, and π-hole site-based interactions in aerogen-comprising complexes: a comparative study

Herein, the potential of ZO3 and ZF2 aerogen-comprising molecules (where Z = Ar, Kr, and Xe) to engage in σ-, lp-, and π-hole site-based interactions was comparatively studied using various ab initio computations. For the first time, a premier in-depth elucidation of the external electric field (EEF) influence on the strength of the σ-, lp-, and π-hole site-based interactions within the ZO3/ZF2⋯NH3 and ⋯NCH complexes was addressed using oriented EEF with disparate magnitude. Upon the energetic features, σ-hole site-based interactions were noticed with the most prominent preferability in comparison to lp- and π-hole analogs. This finding was ensured by the negative interaction energy values of -11.65, -3.50, and -2.74 kcal mol-1 in the case of σ-, lp-, and π-hole site-based interactions within the XeO3⋯ and XeF2⋯NH3 complexes, respectively. Detailedly, the strength of the σ- and lp-hole site-based interactions directly correlated with the atomic size of the aerogen atoms and the magnitude of the positively oriented EEF. Unexpectedly, an irregular correlation was noticed for the interaction energies of the π-hole site-based interactions with the size of the π-hole. Interestingly, the π-hole site-based interactions within Kr-comprising complexes exhibited higher negative interaction energies than the Ar- and Xe-comprising counterparts. Notwithstanding, a direct proportion between the interaction energies of the π-hole site-based interactions and π-hole size was obtained by employing EEF along the positive orientation with high strength. The present outcomes would be a fundamental basis for forthcoming progress in studying the σ-, lp-, and π-hole site-based interactions within aerogen-comprising complexes and their pertinent applications in materials science and crystal engineering.

Synthesis of novel benzylamine antimycotics and evaluation of their antimycotic potency

A series of 23 novel benzylamines was synthesized by reductive amination from halogen-substituted 3- and 4-benzyloxybenzaldehyde derivatives and 6-methylhept-2-yl amine or n-octylamine. The antimycotic activity of the resulting amines was evaluated in a microdilution assay against the apathogenic yeast Yarrowia lipolytica as test microorganism. Promising compounds were also tested against human pathogenic Candida species. The influence of halogen substituents at the benzyl ether side chain was studied in this screening, as well as the influence of the branched side chain of (±)-6-methylhept-2-yl amine in comparison with the n-octyl side chain.

Weakly Bound Complexes of γ-Butyrolactone with Water as Observed in Matrix Isolation FTIR and Theoretical Calculations

A computational and spectroscopic analysis of weakly bound complexes of 1:1 γ-butyrolactone with water has been completed. In this work, multiple density-functional theories and perturbation theory were used to explore the energy-landscape of the complex. Four unique structures were identified in this analysis. One structure was characterized by the formation of a water to carbonyl hydrogen bond and the other three were formed from water to ester hydrogen bonds. The carbonyl-bound conformation was found to be the global minimum across a comprehensive panel of calculations. A wave function analysis demonstrated that the structures were additionally stabilized by weak van der Waals interactions. FTIR spectroscopy of matrix-isolated samples indicated the presence of at least two of the calculated geometries. The structures were identified to be a carbonyl-bound and at least one ester-bound structure. The transitions identified for the carbonyl-bound complex were noted to be significantly more intense than those of the ester bound, indicating greater prevalence in the matrix.

Investigation of the molecular basis of halogenated Schiff base derivative by combined crystallographic and computational studies

Halogenated Schiff base derivatives are gaining more popularity in supramolecular chemistry due to the synergistic effect of hydrogen and halogen-based noncovalent interactions, which helps to design novel therapeutic materials. In this work, we have examined the nature of molecular interactions to investigate the structure-functional relationship of a halogen-based derivative. The FTIR, HRMS and NMR spectroscopic techniques confirmed the formation of the desired novel Schiff base compound. Further, crystal structure studies showed an infinite 1D supramolecular chain formed by type-I halogen…halogen interaction. The Hirshfeld surface and enrichment ratio analyses were performed to visualize and assess the role of diverse interactions involved in crystal packing. The QTAIM, NCI, LOL and ELF studies were conducted extensively to comprehend the strength of interaction constructed based on electron density distribution. The global and local reactive indices were determined using DFT studies to analyze the molecular properties of the compound. Antibacterial activity against MRSA bacteria was performed and showed a good zone of inhibition. The docking analysis was performed for 1mwt protein and validated. The in silico molecular docking studies of the halogenated Schiff base structure with the penicillin-binding protein showed a good docking affinity of -7.5 kcal/mol and supported by in vitro studies. The ligand binding stability within the protein's active site was further demonstrated by molecular dynamics (MD) simulation studies for the Schiff base molecule.Communicated by Ramaswamy H. Sarma.

In Vitro α-Glucosidase and α-Amylase Inhibition, Cytotoxicity and Free Radical Scavenging Profiling of the 6-Halogeno and Mixed 6,8-Dihalogenated 2-Aryl-4-methyl-1,2-dihydroquinazoline 3-Oxides

Series of the 6-bromo/iodo substituted 2-aryl-4-methyl-1,2-dihydroquinazoline-3-oxides and their mixed 6,8-dihalogenated (Br/I and I/Br) derivatives were evaluated for inhibitory properties against α-glucosidase and/or α-amylase activities and for cytotoxicity against breast (MCF-7) and lung (A549) cancer cell lines. The 6-bromo-2-phenyl substituted 3a and its corresponding 6-bromo-8-iodo-2-phenyl-substituted derivative 3i exhibited dual activity against α-glucosidase (IC50 = 1.08 ± 0.02 μM and 1.01 ± 0.05 μM, respectively) and α-amylase (IC50 = 5.33 ± 0.01 μM and 1.18 ± 0.06 μM, respectively) compared to acarbose (IC50 = 4.40 ± 0.05 μM and 2.92 ± 0.02 μM, respectively). The 6-iodo-2-(4-fluorophenyl)-substituted derivative 3f, on the other hand, exhibited strong activity against α-amylase and significant inhibitory effect against α-glucosidase with IC50 values of 0.64 ± 0.01 μM and 9.27 ± 0.02 μM, respectively. Compounds 3c, 3l and 3p exhibited the highest activity against α-glucosidase with IC50 values of 1.04 ± 0.03, 0.92 ± 0.01 and 0.78 ± 0.05 μM, respectively. Moderate cytotoxicity against the MCF-7 and A549 cell lines was observed for these compounds compared to the anticancer drugs doxorubicin (IC50 = 0.25 ± 0.05 μM and 0.36 ± 0.07 μM, respectively) and gefitinib (IC50 = 0.19 ± 0.04 μM and 0.25 ± 0.03 μM, respectively), and their IC50 values are in the range of 10.38 ± 0.08-25.48 ± 0.08 μM and 11.39 ± 0.12-20.00 ± 0.05 μM, respectively. The test compounds generally exhibited moderate to strong antioxidant capabilities, as demonstrated via robust free radical scavenging activity assays, viz., DPPH and NO. The potential of selected derivatives to inhibit superoxide dismutase (SOD) was also investigated via enzymatic assay in vitro. Molecular docking revealed the N-O moiety as essential to facilitate electrostatic interactions of the test compounds with the protein residues in the active site of α-glucosidase and α-amylase. The presence of bromine and/or iodine atoms resulted in increased hydrophobic (alkyl and/or π-alkyl) interactions and therefore increased inhibitory effect against both enzymes.

Creating an Amyloid 'Kaleidoscope' Using Short Iodinated Peptides

Amyloid fibrils formed by peptides with different sequences exhibit diversified morphologies, material properties and activities, making them valuable for developing functional bionanomaterials. However, the molecular understanding underlying the structural diversity of peptide fibrillar assembly at atomic level is still lacking. In this study, by using cryogenic electron microscopy, we first revealed the structural basis underlying the highly reversible assembly of 1 GFGGNDNFG9 (referred to as hnRAC1) peptide fibril. Furthermore, by installing iodine at different sites of hnRAC1, we generated a collection of peptide fibrils with distinct thermostability. By determining the atomic structures of the iodinated fibrils, we discovered that iodination at different sites of the peptide facilitates the formation of diverse halogen bonds and triggers the assembly of entirely different structures of iodinated fibrils. Finally, based on this structural knowledge, we designed an iodinated peptide that assembles into new atomic structures of fibrils, exhibiting superior thermostability, that aligned with our design. Our work provides an in-depth understanding of the atomic-level processes underlying the formation of diverse peptide fibril structures, and paves the way for creating an amyloid "kaleidoscope" by employing various modifications and peptide sequences to fine-tune the atomic structure and properties of fibrillar nanostructures.

Sigma-Hole and Lone-Pair-Hole Site-Based Interactions of Seesaw Tetravalent Chalcogen-Bearing Molecules with Lewis Bases

For the first time, sigma (σ)- and lone-pair (lp)-hole site-based interactions of SF4 and SeF4 molecules in seesaw geometry with NH3 and FH Lewis bases were herein comparatively investigated. The obtained findings from the electrostatic potential analysis outlined the emergence of sundry holes on the molecular entity of the SF4 and SeF4 molecules, dubbed the σ- and lp-holes. The energetic viewpoint announced splendid negative binding energy values for σ-hole site-based interactions succeeded by lp-hole analogues, which were found to be -9.21 and -0.50 kcal/mol, respectively, for SeF4···NH3 complex as a case study. Conspicuously, a proper concurrence between the strength of chalcogen σ-hole site-based interactions and the chalcogen's atomic size was obtained, whereas a reverse pattern was proclaimed for the lp-hole counterparts. Further, a higher preference for the YF4···NH3 complexes with elevated negative binding energy was promulgated over the YF4···FH ones, indicating the eminent role of Lewis basicity. The indications of the quantum theory of atoms in molecules generally asserted the closed-shell nature of all the considered interactions. The observation of symmetry-adapted perturbation theory revealed the substantial contributing role of the electrostatic forces beyond the occurrence of σ-hole site-based interactions. In comparison, the dispersion forces were specified to govern the lp-hole counterparts. Such emerging findings would be a gate for the fruitful forthcoming applications of chalcogen bonding interactions in crystal engineering and biological systems.

Exploring the role of halogen bonding in iodonium ylides: insights into unexpected reactivity and reaction control

Halogen bonding is commonly found with iodine-containing molecules, and it arises when Lewis bases interact with iodine's σ-holes. Halogen bonding and σ-holes have been encountered in numerous monovalent and hypervalent iodine-containing compounds, and in 2022 σ-holes were computationally confirmed and quantified in the iodonium ylide subset of hypervalent iodine compounds. In light of this new discovery, this article provides an overview of the reactions of iodonium ylides in which halogen bonding has been invoked. Herein, we summarize key discoveries and mechanistic proposals from the early iodonium ylide literature that invoked halogen bonding-type mechanisms, as well as recent reports of reactions between iodonium ylides and Lewis basic nucleophiles in which halogen bonding has been specifically invoked. The reactions discussed herein are organized to enable the reader to build an understanding of how halogen bonding might impact yield and chemoselectivity outcomes in reactions of iodonium ylides. Areas of focus include nucleophile σ-hole selectivity, and how ylide structural modifications and intramolecular halogen bonding (e.g., the ortho-effect) can improve ylide stability or solubility, and alter reaction outcomes.

Structural and Computational Analyses of the Unique Interactions of Opicapone in the Binding Pocket of Catechol O-Methyltransferase: A Crystallographic Study and Fragment Molecular Orbital Analyses

A third-generation inhibitor of catechol O-methyltransferase (COMT), opicapone (1), has the 3-nitrocatechol scaffold as do the second-generation inhibitors such as entacapone (2) and tolcapone (3), but only 1 can sustainably inhibit COMT activity making it suitable for a once-daily regimen. These improvements should be attributed to the optimized sidechain moiety (oxidopyridyloxadiazolyl group) of 1 substituted at the 5-position of the 3-nitrocatechol ring. We analyzed the role of the sidechain moiety by solving the crystal structures of COMT/S-adenosylmethionine (SAM)/Mg/1 and COMT/S-adenosylhomocysteine (SAH)/Mg/1 complexes. Fragment molecular orbital (FMO) calculations elucidated that the dispersion interaction between the sidechains of Leu 198 and Met 201 on the β6β7-loop and the oxidopyridine ring of 1 were unique and important in both complexes. In contrast, the catechol binding site made a remarkable difference in the sidechain conformation of Lys 144. The ε-amino group of Lys 144 was outside of the catalytic pocket and was replaced by a water molecule in the COMT/SAH/Mg/1 complex. No nitrocatechol inhibitor has ever been reported to make a complex with COMT and SAH. Thus, the conformational change of Lys 144 found in the COMT/SAH/Mg/1 complex is the first crystallographic evidence that supports the role of Lys 144 as a catalytic base to take out a proton ion from the reaction site to the outside of the enzyme. The fact that 1 generated a complex with SAH and COMT also suggests that 1 could inhibit COMT twofold, as a typical substrate mimic competitive inhibitor and as a product-inhibition enhancer.

Preferred microenvironments of halogen bonds and hydrogen bonds revealed using statistics and QM/MM calculation studies

Hydrogen bonds (HBs) and halogen bonds (XBs) are two essential non-covalent interactions for molecular recognition and drug design. As proteins are heterogeneous in structure, the microenvironments of protein structures should have effects on the formation of HBs and XBs with ligands. However, there are no systematic studies reported on this effect to date. For quantitatively describing protein microenvironments, we defined the local hydrophobicities (LHs) and local dielectric constants (LDCs) in this study. With the defined parameters, we conducted an elaborate database survey on the basis of 22 011 ligand-protein structures to explore the microenvironmental preference of HBs (91 966 in total) and XBs (1436 in total). The statistics show that XBs prefer hydrophobic microenvironments compared to HBs. The polar residues like ASP are more likely to form HBs with ligands, while nonpolar residues such as PHE and MET prefer XBs. Both the LHs and LDCs (10.69 ± 4.36 for HBs; 8.86 ± 4.00 for XBs) demonstrate that XBs are prone to hydrophobic microenvironments compared with HBs with significant differences (p < 0.001), indicating that evaluating their strengths in the corresponding environments should be necessary. Quantum Mechanics-Molecular Mechanics (QM/MM) calculations reveal that in comparison with vacuum environments, the interaction energies of HBs and XBs are decreased to varying degrees given different microenvironments. In addition, the strengths of HBs are impaired more than those of XBs when the local dielectric constant's difference between the XB microenvironments and the HB microenvironments is large.

Force field-inspired molecular representation learning for property prediction

Molecular representation learning is a crucial task to accelerate drug discovery and materials design. Graph neural networks (GNNs) have emerged as a promising approach to tackle this task. However, most of them do not fully consider the intramolecular interactions, i.e. bond stretching, angle bending, torsion, and nonbonded interactions, which are critical for determining molecular property. Recently, a growing number of 3D-aware GNNs have been proposed to cope with the issue, while these models usually need large datasets and accurate spatial information. In this work, we aim to design a GNN which is less dependent on the quantity and quality of datasets. To this end, we propose a force field-inspired neural network (FFiNet), which can include all the interactions by incorporating the functional form of the potential energy of molecules. Experiments show that FFiNet achieves state-of-the-art performance on various molecular property datasets including both small molecules and large protein-ligand complexes, even on those datasets which are relatively small and without accurate spatial information. Moreover, the visualization for FFiNet indicates that it automatically learns the relationship between property and structure, which can promote an in-depth understanding of molecular structure.

Substituent Effect and Its Halogen-Atom Dependence of Halogen Bonding Viewed through Electron Density Changes

Elucidating how the halogen-bonding ability and strength are controlled by the substituent effect and how this control depends on halogen atom will be essential for finely-tuned design of functionally important molecules. Here, this problem is tackled by analyzing the electron density differences/changes for variously substituted halobenzenes. It is shown that the anisotropy of the electron distribution around the halogen atom, which is an important factor for halogen-bonding ability, is not much affected by the substituent effect and rather simply depends on the halogen atom, while the partial charge on the halogen atom, which is related to the bond dipole of the C-X bond, is significantly modulated by the substituent effect and gives rise to enhancement of the electrostatic potential on the line extended from the C-X bond. The properties related to the polarization effect are also discussed.

Structural analysis of an anthrol reductase inspires enantioselective synthesis of enantiopure hydroxycycloketones and β-halohydrins

Asymmetric reduction of prochiral ketones, particularly, reductive desymmetrization of 2,2-disubstituted prochiral 1,3-cyclodiketones to produce enantiopure chiral alcohols is challenging. Herein, an anthrol reductase CbAR with the ability to accommodate diverse bulky substrates, like emodin, for asymmetric reduction is identified. We firstly solve crystal structures of CbAR and CbAR-Emodin complex. It reveals that Tyr210 is critical for emodin recognition and binding, as it forms a hydrogen-bond interaction with His162 and π-π stacking interactions with emodin. This ensures the correct orientation for the stereoselectivity. Then, through structure-guided engineering, variant CbAR-H162F can convert various 2,2-disubstituted 1,3-cyclodiketones and α-haloacetophenones to optically pure (2S, 3S)-ketols and (R)-β-halohydrins, respectively. More importantly, their stereoselectivity mechanisms are also well explained by the respective crystal structures of CbAR-H162F-substrate complex. Therefore, this study demonstrates that an in-depth understanding of catalytic mechanism is valuable for exploiting the promiscuity of anthrol reductases to prepare diverse enantiopure chiral alcohols.

Copper(II) complexes with 3,5-dihalogeno-salicylaldehydes: Synthesis, structure and interaction with DNA and albumins

Eight copper(II) complexes of 3,5-dichloro-salicyladehyde or 3,5-dibromo-salicyladehyde (3,5-diX-saloH, X = Br or Cl) were synthesized in the absence or presence of a N,N'-donor co-ligand such as 2,2'-bipyridylamine, 1,10-phenanthroline, or 2,2'-bipyridine. The resultant compounds were formulated as [Cu(3,5-diX-salo)₂(MeOH)₂] (1-2) and [Cu(3,5-diX-salo)(N,N'-donor)Cl] (3-8) and were characterized by diverse techniques. The crystal structures of three complexes were determined by single-crystal X-ray crystallography. Diverse techniques were employed in order to investigate the interaction of the complexes with calf-thymus DNA which showed intercalation as the most possible mode of their interaction. The affinity of the complexes for bovine serum albumin and human serum albumin was evaluated by fluorescence emission spectroscopy in order to calculate the binding constants which suggested a tight and reversible binding. SYNOPSIS: A series of copper(II) complexes with 3,5-dihalogen-substituted salicylaldehydes as ligands were isolated and characterized. In vitro biological studies showed the intercalation of the compounds with calf-thymus DNA and their tight and reversible binding with serum albumins.

QSAR Studies, Molecular Docking, Molecular Dynamics, Synthesis, and Biological Evaluation of Novel Quinolinone-Based Thiosemicarbazones against Mycobacterium tuberculosis

In this study, a series of novel quinolinone-based thiosemicarbazones were designed in silico and their activities tested in vitro against Mycobacterium tuberculosis (M. tuberculosis). Quantitative structure-activity relationship (QSAR) studies were performed using quinolinone and thiosemicarbazide as pharmacophoric nuclei; the best model showed statistical parameters of R² = 0.83; F = 47.96; s = 0.31, and was validated by several different methods. The van der Waals volume, electron density, and electronegativity model results suggested a pivotal role in antituberculosis (anti-TB) activity. Subsequently, from this model a new series of quinolinone-thiosemicarbazone 11a-e was designed and docked against two tuberculosis protein targets: enoyl-acyl carrier protein reductase (InhA) and decaprenylphosphoryl-β-D-ribose-2'-oxidase (DprE1). Molecular dynamics simulation over 200 ns showed a binding energy of -71.3 to -12.7 Kcal/mol, suggesting likely inhibition. In vitro antimycobacterial activity of quinolinone-thiosemicarbazone for 11a-e was evaluated against M. bovis, M. tuberculosis H37Rv, and six different strains of drug-resistant M. tuberculosis. All compounds exhibited good to excellent activity against all the families of M. tuberculosis. Several of the here synthesized compounds were more effective than the standard drugs (isoniazid, oxafloxacin), 11d and 11e being the most active products. The results suggest that these compounds may contribute as lead compounds in the research of new potential antimycobacterial agents.

Abnormalities of the Halogen Bonds in the Complexes between Y2CTe (Y = H, F, CH3) and XF (X = F, Cl, Br, I)

In this work, the hydrogen bonds and halogen bonds in the complexes between Y2CTe (Y = H, F, CH3) and XF (X = F, Cl, Br, I) have been studied by quantum chemical calculations. We found three interesting abnormalities regarding the interactions. Firstly, the strength of halogen bonds increases in the order of IF < BrF < ClF < F2. Secondly, the halogen bonds formed by F2 are very strong, with an interaction energy in the range between −199.8 and −233.1 kJ/mol. Thirdly, all the halogen bonds are stronger than the hydrogen bonds in the systems we examined. All these results are against the general understanding of halogen bonds. These apparent abnormal properties are reconciled with the high polarizability of the Te atom and the strong inducing effect of F on the Te atom of Y2CTe. These findings provide a new perspective on halogen bonds. Additionally, we also proposed bonding distance-based methods to compare the strength of halogen/hydrogen bonds formed between different donor atoms and the same acceptor atom.

Three water-soluble acylhydrazone tetranuclear transition metal complexes: Crystal structures, DNA/BSA interactions and cytotoxicity studies

2-acetylpyridine-4-chloropyridine-2‑carbonyl hydrazone (C₁₃H₁₁ClN₄O, HL) and its three water-soluble tetranuclear complexes [Cu₄(NO₃)₂(L)₄]·(NO₃)₂ (1), [Co₄(NO₃)₂(H₂O)(C₂H₅OH)(L)₄]·(NO₃)₂ (2) and [Zn₄(NO₃)₂(H₂O)(C₂H₅OH)(L)₄]·(NO₃)₂ (3) were synthesized and characterized showing that 1-3 were all tetranuclear complexes. The interactions of HL, 1-3 with calf thymus DNA (CT-DNA) and bovine serum albumin (BSA) were explored using ultraviolet-visible (UV-Vis) titration, fluorescence spectroscopy, microcalorimetry and molecular docking techniques. The UV-Vis spectroscopy measurements showed that complexes 1-3 could strongly bind to CT-DNA by the intercalation mode, while HL interacted with CT-DNA through groove binding. From the fluorescence spectroscopy results, the interaction between HL, 1-3 and BSA was a static quenching procedure, in which complexes 1-3 had two binding sites near Trp residues of BSA while HL only had one. The microcalorimetric studies revealed that the interactions of HL and 1-3 to CT-DNA/BSA were all endothermic and the duration of each interaction was all less than 30 min. The in silico molecular docking illustrated intermolecular interactions of 1-3 binding with DNA/BSA included hydrogen bond, halogen bond, hydrophobic and electrostatic interactions. 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay indicated that complex 1 possessed better cytotoxicity against HeLa, A549, MCF7 and HCT-116 than cisplatin and could be used as an alternative anticancer drug.

Combining OSMAC, metabolomic and genomic methods for the production and annotation of halogenated azaphilones and ilicicolins in termite symbiotic fungi

We gathered a collection of termite mutualistic strains from French Guiana to explore the metabolites of symbiotic microorganisms. Molecular networks reconstructed from a metabolomic analysis using LC-ESI-MS/MS methodology led us to identify two families of chlorinated polyketides, i.e., azaphilones from Penicillium sclerotiorum and ilicicolins from Neonectria discophora. To define the biosynthetic pathways related to these two types of scaffolds, we used a whole genome sequencing approach followed by hybrid assembly from short and long reads. We found two biosynthetic gene clusters, including two FAD-dependent halogenases. To exploit the enzymatic promiscuity of the two identified FAD halogenases, we sought to biosynthesize novel halogenated metabolites. An OSMAC strategy was used and resulted in the production of brominated analogs of ilicicolins and azaphilones as well as iodinated analogs of azaphilones.

Discovery of Simple Diacylhydrazine-Functionalized Cinnamic Acid Derivatives as Potential Microtubule Stabilizers

To develop novel microtubule-binding agents for cancer therapy, an array of N-cinnamoyl-N'-(substituted)acryloyl hydrazide derivatives were facilely synthesized through a two-step process. Initially, the antiproliferative activity of these title compounds was explored against A549, 98 PC-3 and HepG2 cancer cell lines. Notably, compound I₂₃ exhibited the best antiproliferative activity against three cancer lines with IC₅₀ values ranging from 3.36 to 5.99 μM and concurrently afforded a lower cytotoxicity towards the NRK-52E cells. Anticancer mechanism investigations suggested that the highly bioactive compound I₂₃ could potentially promote the protofilament assembly of tubulin, thus eventually leading to the stagnation of the G2/M phase cell cycle of HepG2 cells. Moreover, compound I₂₃ also disrupted cancer cell migration and significantly induced HepG2 cells apoptosis in a dosage-dependent manner. Additionally, the in silico analysis indicated that compound I₂₃ exhibited an acceptable pharmacokinetic profile. Overall, these easily prepared N-cinnamoyl-N'-(substituted)acryloyl hydrazide derivatives could serve as potential microtubule-interacting agents, probably as novel microtubule-stabilizers.

Properties and Stabilities of Cyclic and Open Chains of Halogen Bonds

Open and cyclic chains from two to eight units of ICl and IF are constructed and examined by density functional theory (DFT) calculations. These chains contain either I···I or I···X halogen bonds (XBs) where X refers to Cl or F. The closed rings are more stable than the open chains due to the presence of an additional XB and enhanced cooperativity. This pattern is true even for most trimers where there is sizable geometric distortion in the rings. I···F rings are generally more stable than the corresponding I···I cycles as the I···F bond is stronger than I···I even in the simple dimer. However, I···I rings are comparable in energy to I···Cl. It is possible to construct I···I rings of at least as large as eight units, which are held together exclusively by XBs. On the other hand, the maximum possible size of I···X rings is 6. Red shifts are observed in the I-X stretching frequency bands, which magnify as the chain, both cyclic and open, grows longer. The NMR chemical shielding of the I atoms increases for I···I chains but diminishes when I···Cl bonds are present.

Genetic and Biochemical Characterization of Halogenation and Drug Transportation Genes Encoded in the Albofungin Biosynthetic Gene Cluster

Albofungin, a hexacyclic aromatic natural product, exhibits broad-spectrum antimicrobial activity. Its biosynthesis, regulation, and resistance remain elusive. Here, we report the albofungin (abf) biosynthetic gene cluster (BGC) from its producing strain Streptomyces tumemacerans JCM5050. The nascent abf BGC encodes 70 putative genes, including regulators, transporters, type II polyketide synthases (PKSs), oxidoreductase, and tailoring enzymes. To validate the intactness and functionality of the BGC, we developed an Escherichia coli-Streptomyces shuttle bacterial artificial chromosome system, whereby the abf BGC was integrated into the genome of a nonproducing host via heterologous conjugation, wherefrom albofungin can be produced, confirming that the BGC is in effect. We then delimited the boundaries of the BGC by means of in vitro CRISPR-Cas9 DNA editing, concluding a minimal but essential 60-kb abf BGC ranging from orfL to abf58. The orfA gene encoding a reduced flavin adenine dinucleotide (FADH₂)-dependent halogenase was examined and is capable of transforming albofungin to halogen-substituted congeners in vivo and in vitro. The orfL gene encoding a transporter was examined in vivo. The presence/absence of orfA or orfL demonstrated that the MIC of albofungin is subject to alteration when an extracellular polysaccharide intercellular adhesin was formed. Despite that halogenation of albofungin somewhat increases binding affinity to transglycosylase (TGase), albofungin with/without a halogen substituent manifests similar in vitro antimicrobial activity. Halogenation, however, limits overall dissemination and effectiveness given a high secretion rate, weak membrane permeability, and high hydrophobicity of the resulting products, whereby the functions of orfA and orfL are correlated with drug detoxification/resistance for the first time.

IMPORTANCE Albofungin, a natural product produced from Streptomycetes, exhibits bioactivities against bacteria, fungi, and tumor cells. The biosynthetic logic, regulations, and resistance of albofungin remain yet to be addressed. Herein, the minimal albofungin (abf) biosynthetic gene cluster (BGC) from the producing strain Streptomyces tumemacerans JCM5050 was precisely delimited using the Escherichia coli-Streptomyces shuttle bacterial artificial chromosome system, of which the gene essentiality was established in vivo and in vitro. Next, we characterized two genes orfA and orfL encoded in the abf BGC, which act as a reduced flavin adenine dinucleotide (FADH₂)-dependent halogenase and an albofungin-congeners transporter, respectively. While each testing microorganism exhibited different sensitivities to albofungins, the MIC values of albofungins against testing strains with/without orfA and/or orfL were subject to considerable changes. Halogen-substituted albofungins mediated by OrfA manifested overall compromised dissemination and effectiveness, revealing for the first time that two functionally distinct proteins OrfA and OrfL are associated together, exerting a novel “belt and braces” mechanism in antimicrobial detoxification/resistance.

Nature of hydrogen-bond-enhanced halogen bonding viewed through electron density changes

Elucidating the mechanism of how we can achieve fine tuning of intermolecular interaction strength will be helpful for designing functionally important molecules. In the present study, a theoretical analysis is conducted, by examining the electron density changes, for two halogen-bonding iodinated systems whose halogen-bond strengths have been considered to be enhanced by the presence of a hydrogen-bond donating group (termed hydrogen-bond-enhanced halogen bonding). It is shown that, contrary to the expectation obtained from the enhancement of electrostatic potential along the line extended from the C-I bond, the anisotropy of electron distribution on the iodine atom remains nearly the same. This means that the hydrogen bond and halogen bond contribute almost independently and additively to the enhancement of electrostatic potential, indicating the nature of this enhancement and, in a more general sense, the relationship between the strength and the extent of directionality of halogen bonding.

Structure, properties of gossypol and its derivatives-from physiological activities to drug discovery and drug design

Covering up to 2022Gossypol is a polyphenolic compound isolated from cottonseed. There are two optical enantiomers of gossypol, (-)-gossypol and (+)-gossypol. Gossypol exists as three different tautomers, aldehyde, ketone and lactol. Gossypol is toxic and provides a protective mechanism for cotton plants against pests. Gossypol was used as a male contraceptive in China in the 1970s. It was eventually abandoned due to noticeable side effects, disruption of potassium uptake and incomplete reversibility. Gossypol has gained considerable research interest due to its attractive biological activities, especially antitumor and antivirus. Gossypol derivatives are prepared by a structural modification to reduce toxicity and improve their therapeutic effect. This review depicts the bioactivity and regulation mechanisms of gossypol and its derivatives as drug lead compounds, with emphasis on its antitumor mechanism. The design and synthesis of pharmacologically active derivatives based on the structure of gossypol, such as gossypol Schiff bases, apogossypol, gossypolone, are thoroughly discussed. This review aims to serve as a reference for gossypol-based drug discovery and drug design.

External Electric Field Effect on the Strength of σ-Hole Interactions: A Theoretical Perspective in Like⋯Like Carbon-Containing Complexes

For the first time, σ-hole interactions within like⋯like carbon-containing complexes were investigated, in both the absence and presence of the external electric field (EEF). The effects of the directionality and strength of the utilized EEF were thoroughly unveiled in the (F-C-F₃)₂, (F-C-H₃)₂, and (H-C-F₃)₂ complexes. In the absence of the EEF, favorable interaction energies, with negative values, are denoted for the (F-C-F₃)₂ and (H-C-F₃)₂ complexes, whereas the (F-C-H₃)₂ complex exhibits unfavorable interactions. Remarkably, the strength of the applied EEF exhibits a prominent role in turning the repulsive forces within the latter complex into attractive ones. The symmetrical nature of the considered like⋯like carbon-containing complexes eradicated the effect of directionality of the EEF. The quantum theory of atoms in molecules (QTAIM), and the noncovalent interaction (NCI) index, ensured the occurrence of the attractive forces, and also outlined the substantial contributions of the three coplanar atoms to the total strength of the studied complexes. Symmetry-adapted perturbation theory (SAPT) results show the dispersion-driven nature of the interactions.

σ-Hole and LP-Hole Interactions of Pnicogen···Pnicogen Homodimers under the External Electric Field Effect: A Quantum Mechanical Study

σ-Hole and lone-pair (lp)-hole interactions within σ-hole···σ-hole, σ-hole···lp-hole, and lp-hole···lp-hole configurations were comparatively investigated on the pnicogen···pnicogen homodimers (PCl3)2, for the first time, under field-free conditions and the influence of the external electric field (EEF). The electrostatic potential calculations emphasized the impressive versatility of the examined PCl3 monomers to participate in σ-hole and lp-hole pnicogen interactions. Crucially, the sizes of σ-hole and lp-hole were enlarged under the influence of the positively directed EEF and decreased in the case of reverse direction. Interestingly, the energetic quantities unveiled more favorability of the σ-hole···lp-hole configuration of the pnicogen···pnicogen homodimers, with significant negative interaction energies, than σ-hole···σ-hole and lp-hole···lp-hole configurations. Quantum theory of atoms in molecules and noncovalent interaction index analyses were adopted to elucidate the nature and origin of the considered interactions, ensuring their closed shell nature and the occurrence of attractive forces within the studied homodimers. Symmetry-adapted perturbation theory-based energy decomposition analysis alluded to the dispersion force as the main physical component beyond the occurrence of the examined interactions. The obtained findings would be considered as a fundamental underpinning for forthcoming studies pertinent to chemistry, materials science, and crystal engineering.

Type I-IV Halogen⋯Halogen Interactions: A Comparative Theoretical Study in Halobenzene⋯Halobenzene Homodimers

In the current study, unexplored type IV halogen⋯halogen interaction was thoroughly elucidated, for the first time, and compared to the well-established types I−III interactions by means of the second-order Møller−Plesset (MP2) method. For this aim, the halobenzene⋯halobenzene homodimers (where halogen = Cl, Br, and I) were designed into four different types, parodying the considered interactions. From the energetic perspective, the preference of scouted homodimers was ascribed to type II interactions (i.e., highest binding energy), whereas the lowest binding energies were discerned in type III interactions. Generally, binding energies of the studied interactions were observed to decline with the decrease in the σ-hole size in the order, C6H5I⋯IC6H5 > C6H5Br⋯BrC6H5 > C6H5Cl⋯ClC6H5 homodimers and the reverse was noticed in the case of type IV interactions. Such peculiar observations were relevant to the ample contributions of negative-belt⋯negative-belt interactions within the C6H5Cl⋯ClC6H5 homodimer. Further, type IV torsional trans → cis interconversion of C6H5X⋯XC6H5 homodimers was investigated to quantify the π⋯π contributions into the total binding energies. Evidently, the energetic features illustrated the amelioration of the considered homodimers (i.e., more negative binding energy) along the prolonged scope of torsional trans → cis interconversion. In turn, these findings outlined the efficiency of the cis configuration over the trans analog. Generally, symmetry-adapted perturbation theory-based energy decomposition analysis (SAPT-EDA) demonstrated the predominance of all the scouted homodimers by the dispersion forces. The obtained results would be beneficial for the omnipresent studies relevant to the applications of halogen bonds in the fields of materials science and crystal engineering.

Halogen Bonds Exist between Noncovalent Ligands and Natural Nucleic Acids

Because of their strong electron-rich properties, nucleic acids (NAs) can theoretically serve as halogen bond (XB) acceptors. From a PDB database survey, Kolář found that no XBs are formed between noncovalent ligands and NAs. Through statistical database analysis, quantum-mechanics/molecular-mechanics (QM/MM) optimizations, and energy calculations, we find that XBs formed between natural NAs and noncovalent ligands are primarily underestimated and that NAs can serve as XB acceptors to interact with noncovalent halogen ligands. Finally, through energy calculations, natural bond orbital analysis, and noncovalent interaction analysis, XBs are confirmed in 13 systems, among which two systems (445D and 4Q9Q) have relatively strong XBs. In addition, on the basis of energy scanning of four model systems, we explore the geometric rule for XB formation in NAs. This work will inspire researchers to utilize XBs in rational drug design targeting NAs.

Disruption of DYRK1A-induced hyperphosphorylation of amyloid-beta and tau protein in Alzheimer's disease: An integrative molecular modeling approach

Alzheimer's disease (AD) is a neurological disorder caused by the abnormal accumulation of hyperphosphorylated proteins. Dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) is a dual phosphorylation enzyme which phosphorylates the amyloid-β (Aβ) and neurofibrillary tangles (NFTs). A high throughput virtual screening approach was applied to screen a library of 98,071 compounds against DYRK1A using different programs including AutoDock Vina, Smina, and idock. Based on the binding affinities, we selected 330 compounds for absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis. Various pharmacokinetics parameters were predicted using the admetSAR server, and based on the pharmacokinetics results, 14 compounds were selected for cross-docking analysis using AutoDock. Cross-docking analysis revealed four compounds, namely, ZINC3843365 (-11.07 kcal/mol^-1), ZINC2123081 (-10.93 kcal/mol^-1), ZINC5220992 (-10.63 kcal/mol^-1), and ZINC68569602 (-10.35 kcal/mol^-1), which had the highest negative affinity scores compared to the 10 other molecules analyzed. Density functional theory (DFT) analysis was conducted for all the four top-ranked compounds. The molecular interaction stability of these four compounds with DYRK1A has been evaluated using molecular dynamics (MD) simulations on 100 nanoseconds followed by principal component analysis (PCA) and binding free energy calculations. The Gibbs free energy landscape analysis suggested the metastable state and folding pattern of selected docking complexes. Based on the present study outcome, we propose four antagonists, viz., ZINC3843365, ZINC2123081, ZINC5220992, and ZINC68569602 as potential inhibitors against DYRK1A and to reduce the amyloid-β and neurofibrillary tangle burden. These screened molecules can be further investigated using a number of in vitro and in vivo experiments.

Computational details of molecular structure, spectroscopic properties, topological studies and SARS-Cov-2 enzyme molecular docking simulation of substituted triazolo pyrimidine thione heterocycles

Investigation the molecular structure of the system requires a detailed experience in dealing with theoretical computational guides to highlight its important role. Molecular structure of three heterocyclic compounds 8,10-diphenylpyrido[3,2-e][1,2,4]triazolo[4,3-c]pyrimidine-3(2H)-thione (HL), 8-phenyl-10-(p-tolyl)pyrido[3,2-e][1,2,4]triazolo[4,3-c]pyrimidine-3(2H)-thione (CH3L) and10-(4-nitrophenyl)-8-phenylpyrido[3,2-e][1,2,4]triazolo[4,3-c]pyrimidine-3(2H)-thione (NO2L) was studied at DFT/B3LYP/6-31G (d,p) level in ethanol solvent. Spectroscopic properties such Infrared (IR, 1H NMR and 13C NMR) and ultraviolet-visible (UV-VIS) analyses were computed. Some quantum and reactivity parameters (HOMO energy, LUMO energy, energy gap, ionization potential, electron affinity, chemical potential, global softness, lipophelicity) were studied, also molecular electrostatic potential (MEP) was performed to indicate the reactive nucleophilic and electrophilic sites. The effects of H-, CH3- and NO2- substituents on heterocyclic ligands were studied and it was found that the electron donation sites concerned with hydrogen and methyl substituents over nitro substituent. Topological analysis using reduced density gradient (RDG) was discussed in details. To predict the relevant antiviral activity of the reported heterocyclic compounds, molecular docking simulation was applied to the crystal structure of SARS-Cov-2 viral Mpro enzyme with 6WTT code and PLpro with 7JRN code. The enzymatic viral protein gives an image about the binding affinity between the target protein receptor and the heterocyclic ligands entitled. The hydrogen bonding interactions were evaluated from molecular docking with different strength for each ligand compound to discuss the efficiency of heterocyclic ligands toward viral inhibition.

Design, Synthesis, and Mechanism of Antiviral Acylurea Derivatives Containing a Trifluoromethylpyridine Moiety

Novel acylurea derivatives 7a-7ab were designed and synthesized by linking the active substructures trifluoromethylpyridine and anthranilic diamide via an acylurea bridge. Most of the title compounds exhibited good activity against tobacco mosaic virus (TMV), particularly compound 7x (EC₅₀ of 211.8 μg/mL), which showed much higher curative activity than ningnanmycin (EC₅₀ of 389.8 μg/mL), and compound 7ab, which showed excellent inactivation activity (EC₅₀ of 36.1 μg/mL), similar to ningnanmycin (EC₅₀ of 23.2 μg/mL). The preliminary mechanism of these derivatives was investigated. Autodocking analysis revealed that compounds 7x and 7ab had good affinity for TMV coat protein (TMV CP), with low binding energies (-7.86 and -8.59 kcal/mol) comparable to ningnanmycin (-8.75 kcal/mol). Molecular dynamics simulation showed that compound 7x had a stable system structure with a better binding free energy (-32.94 kcal/mol) than ningnanmycin (-25.62 kcal/mol). Microscale thermophoresis showed that compound 7x bound more strongly to TMV CP (K_d of 19.8 ± 7.3 μM) than ningnanmycin (K_d of 21.2 ± 7.3 μM). Transmission electron microscopy and self-assembly experiments demonstrated that compounds 7x and 7ab significantly obstructed the self-assembly of TMV RNA and TMV CP. This new acylurea derivative has excellent antiviral activity by targeting TMV CP and inhibiting TMV self-assembly and can be considered a candidate for antiviral applications.

Hidden Halogen-Bonding Ability of Fluorine Manifesting in the Hydrogen-Bond Configurations of Hydrogen Fluoride

Elucidating how the intermolecular interactions of a covalently bonded fluorine atom are similar to and different from those of the other halogen atoms will be helpful for a better unified understanding of them. In the present study, the case of hydrogen fluoride is theoretically studied from this viewpoint by using the techniques of electron density analysis, molecular dynamics of liquid, and others. It is shown that the extra-point model, which locates an additional charge site on the line extended from (not within) the covalent bond and has been adopted for halogen-bonding systems as a key to the generation of proper stability and directionality, works well also in this case. A significantly bent hydrogen-bond configuration, which is characteristic of the intermolecular interactions of hydrogen fluoride, is reasonably well reproduced, meaning that it is a manifestation of the latent halogen-bonding ability, which is hidden by the strongly electronegative nature.

Revisiting the covalent nature of halogen bonding: a polarized three-center four-electron bond

As an important intermolecular interaction, halogen bonding has been studied extensively, but its nature still suffers from controversy without one uniform essence. Electrostatics, charge transfer, polarization and dispersion are emphasized, but the covalent nature is usually overlooked except for the strong halogen bonding species I₃⁻, which is widely accepted as a result of a three-center four-electron (3c-4e) interaction. In our study, the potential energy surface of I₃⁻ has been evaluated to explore the dissociation from I₃⁻ to I₂⋯I⁻. We found that different from an equivalent 3c-4e bond in I₃⁻, I₂⋯I⁻ can be rationalized by a polarized one. In addition, when the orbitals are polarized, it is exactly what traditional charge transfer or the popular σ-hole picture describes. I₃⁻ can be described by the Lewis theory model with the middle I⁺ cation serving as the Lewis acid and two terminal I⁻ anions acting as Lewis base. Therefore, we further extended this model to a series of I-containing species with chemical composition of L–I⁺–L, F⁻–I⁺–L and H₃P–I⁺–L (L = OH⁻, F⁻, Cl⁻, Br⁻, I⁻, PH₃, NH₃, H₂S, HI, H₂O, HBr and HCl) to explore the nature of halogen bonding. When the forces of two bases around I⁺ are the same, it corresponds to an equivalent 3c-4e bond, such as I₃⁻. Otherwise, it is a polarized multicenter bond, such as I₂⋯I⁻. This work gives a new insight into the nature of halogen bonding compounds: besides the well-known I₃⁻, the nature of the other species is also a multicenter bond, existing as equivalent and polarized 3c-4e bonds, respectively.

The halogen bond could be described with a polarized 3c-4e bond.

The Influence of Secondary Interactions on the [N-I-N]+ Halogen Bond

[Bis(pyridine)iodine(I)]⁺ complexes offer controlled access to halonium ions under mild conditions. The reactivity of such stabilized halonium ions is primarily determined by their three-center, four-electron [N-I-N]⁺ halogen bond. We studied the importance of chelation, strain, steric hindrance and electrostatic interaction for the structure and reactivity of halogen bonded halonium ions by acquiring their ¹⁵ N NMR coordination shifts and measuring their iodenium release rates, and interpreted the data with the support of DFT computations. A bidentate ligand stabilizes the [N-I-N]⁺ halogen bond, decreasing the halenium transfer rate. Strain weakens the bond and accordingly increases the release rate. Remote modifications in the backbone do not influence the stability as long as the effect is entirely steric. Incorporating an electron-rich moiety close by the [N-I-N]⁺ motif increases the iodenium release rate. The analysis of the iodine(I) transfer mechanism highlights the impact of secondary interactions, and may provide a handle on the induction of stereoselectivity in electrophilic halogenations.

Uracil Derivatives for Halogen-Bonded Cocrystals

Among non-covalent interactions, halogen bonding is emerging as a new powerful tool for supramolecular self-assembly. Here, along with a green and effective method, we report three new halogen-bonded cocrystals containing uracil derivatives and 1,2,4,5-tetrafluoro-3,6-diiodobenzene as X-bond donor coformer. These multicomponent solids were prepared both by solvent-drop grinding and solution methods and further characterized by powder and single-crystal X-ray diffraction, Fourier-transformed infrared spectroscopy, and thermal methods (TGA-DSC). In order to study the relative importance of hydrogen versus halogen bonds in the crystal packing, computational methods were applied.

Discovery of facile amides-functionalized rhodanine-3-acetic acid derivatives as potential anticancer agents by disrupting microtubule dynamics

Microtubule dynamics are crucial for multiple cell functions, and cancer cells are particularly sensitive to microtubule-modulating agents. Here, we describe the design and synthesis of a series of (Z)-2-(5-benzylidene-4-oxo-2-thioxothiazolidin-3-yl)-N-phenylacetamide derivatives and evaluation of their microtubule-modulating and anticancer activities in vitro. Proliferation assays identified I₂₀ as the most potent of the antiproliferative compounds, with 50% inhibitory concentrations ranging from 7.0 to 20.3 µM with A549, PC-3, and HepG2 human cancer cell lines. Compound I₂₀ also disrupted cancer A549 cell migration in a concentration-dependent manner. Immunofluorescence microscopy, transmission electron microscopy, and tubulin polymerisation assays suggested that compound I₂₀ promoted protofilament assembly. In support of this possibility, computational docking studies revealed a strong interaction between compound I₂₀ and tubulin Arg β369, which is also the binding site for the anticancer drug Taxol. Our results suggest that (Z)-2-(5-benzylidene-4-oxo-2-thioxothiazolidin-3-yl)-N-phenylacetamide derivatives could have utility for the development of microtubule-stabilising therapeutic agents.

On the Potentiality of X-T-X3 Compounds (T = C, Si, and Ge, and X = F, Cl, and Br) as Tetrel- and Halogen-Bond Donors

The versatility of the X-T-X3 compounds (where T = C, Si, and Ge, and X = F, Cl, and Br) to participate in tetrel- and halogen-bonding interactions was settled out, at the MP2/aug-cc-pVTZ level of theory, within a series of configurations for (X-T-X3)2 homodimers. The electrostatic potential computations ensured the remarkable ability of the investigated X-T-X3 monomers to participate in σ-hole halogen and tetrel interactions. The energetic findings significantly unveil the favorability of the tetrel···tetrel directional configuration with considerable negative binding energies over tetrel···halogen, type III halogen···halogen, and type II halogen···halogen analogs. Quantum theory of atoms in molecules and noncovalent interaction analyses were accomplished to disclose the nature of the tetrel- and halogen-bonding interactions within designed configurations, giving good correlations between the total electron densities and binding energies. Further insight into the binding energy physical meanings was invoked through using symmetry-adapted perturbation theory-based energy decomposition analysis, featuring the dispersion term as the most prominent force beyond the examined interactions. The theoretical results were supported by versatile crystal structures which were characterized by the same type of interactions. Presumably, the obtained findings would be considered as a solid underpinning for future supramolecular chemistry, materials science, and crystal engineering studies, as well as a fundamental linchpin for a better understanding of the biological activities of chemicals.