π-π Noncovalent Interaction Involving 1,2,4- and 1,3,4-Oxadiazole Systems: The Combined Experimental, Theoretical, and Database Study

Discovery of Novel and Selective Schiff Base Inhibitors as a Key for Drug Synthesis, Molecular Docking, and Pharmacological Evaluation

Diabetes mellitus (DM) is a chronic disorder and still a challenge throughout the world, and therefore the search for safe and effective inhibitors for α-amylase and α-glucosidase is increasing day by day. In this work, we try to carry out the synthesis, modification, and computer-aided results of and biological research on thiadiazole-based Schiff base derivatives and evaluate their in vitro α-amylase and α-glucosidase inhibitory potential (1-15). In the current series, all of the synthesized analogues were shown to have potential inhibitory effects on targeted enzymes. The IC50 values for α-amylase values ranged from 20.10 ± 0.40 to 0.80 ± 0.05 μM, compared with the standard drug acarbose having an IC50 value of 10.30 ± 0.20 μM, while for α-glucosidase, the IC50 values ranged from 20.10 ± 0.50 to 1.20 ± 0.10 μM, compared to acarbose with an IC50 value of 9.80 ± 0.20 μM. For better understanding, a SAR investigation was undertaken. In this series, nine scaffolds (1, 2, 3, 6, 9, 10, 11, 13, and 15) were more active than the reference drug and the docking parameter RMSD values for α-glucosidase and α-amylase were 1.766, 2.7746, 1.6025, 2.2112, 3.5860, 2.3360, 1.6178, 2.0254, and 2.0797 and 2.6020, 1.9509, 3.1642, 1.7547, 2.2130, 1.4221, and 1.1087, respectively. The toxicity of the selected analogues was calculated by using the OSIRIS tool, and the TPSA values were found to be lower than 140 to represent the drug-like properties; those from Molinspiration were studied as well. The following properties were studied and found to have better biological properties. The remaining analogues (4, 5, 7, 8, 12, and 14) were also identified as potential inhibitors of both enzymes, but they were less active than the reference due to the substituents attached to the aromatic parts. The structures of synthesized compounds were confirmed through different spectroscopic analyses.

Hybrid 2D Supramolecular Organic Frameworks (SOFs) Assembled by the Cooperative Action of Hydrogen and Halogen Bonding and π⋯π Stacking Interactions

The cis- and trans-isomers of 6-(3-(3,4-dichlorophenyl)-1,2,4-oxadiazol-5-yl)cyclohex-3-ene-1-carboxylic acid (cis-A and trans-A) were obtained by the reaction of 3,4-dichloro-N'-hydroxybenzimidamide and cis-1,2,3,6-tetrahydrophthalic anhydride. Cocrystals of cis-A with appropriate solvents (cis-A‧½(1,2-DCE), cis-A‧½(1,2-DBE), and cis-A‧½C6H14) were grown from 1,2-dichloroethane (1,2-DCE), 1,2-dibromoethane (1,2-DBE), and a n-hexane/CHCl3 mixture and then characterized by X-ray crystallography. In their structures, cis-A is self-assembled to give a hybrid 2D supramolecular organic framework (SOF) formed by the cooperative action of O-H⋯O hydrogen bonding, Cl⋯O halogen bonding, and π⋯π stacking. The self-assembled cis-A divides the space between the 2D SOF layers into infinite hollow tunnels incorporating solvent molecules. The energy contribution of each noncovalent interaction to the occurrence of the 2D SOF was verified by several theoretical approaches, including MEP and combined QTAIM and NCIplot analyses. The consideration of the theoretical data proved that hydrogen bonding (approx. -15.2 kcal/mol) is the most important interaction, followed by π⋯π stacking (approx. -11.1 kcal/mol); meanwhile, the contribution of halogen bonding (approx. -3.6 kcal/mol) is the smallest among these interactions. The structure of the isomeric compound trans-A does not exhibit a 2D SOF architecture. It is assembled by the combined action of hydrogen bonding and π⋯π stacking, without the involvement of halogen bonds. A comparison of the cis-A structures with that of trans-A indicated that halogen bonding, although it has the lowest energy in cis-A-based cocrystals, plays a significant role in the crystal design of the hybrid 2D SOF. The majority of the reported porous halogen-bonded organic frameworks were assembled via iodine and bromine-based contacts, while chlorine-based systems-which, in our case, are structure-directing-were unknown before this study.

Sodium Carbonate-Promoted Formation of 5-Amino-1,2,4-thiadiazoles and 5-Amino-1,2,4-selenadiazoles with Elemental Sulfur and Selenium

Sodium carbonate-promoted facile synthesis of 5-amino-1,2,4-thiadiazoles and 5-amino-1,2,4-selenadiazoles with elemental sulfur and selenium, respectively, was developed. This method was carried out with O2 in the air as the green oxidant, and it has several advantages, including low cost, low toxicity, and stable sulfur and selenium sources, good to excellent yields with water as the sole byproduct, simple operation, and a broad substrate scope. Preliminary mechanistic studies indicate that the formation of the 1,2,4-thiadiazole ring and the 1,2,4-selenadiazole ring undergoes different processes.

Noncovalent Dualism in Perylene-Diimide-Based Keggin Anion Complexes: Theoretical and Experimental studies

We report the synthesis and comprehensive characterization of organic-inorganic hybrid salts formed by bis-cationic N,N'-bis(2-(trimethylammonium)ethylene)perylene-3,4,9,10-tetracarboxylic acid bisimide (PTCD2+) and Keggin-type [XW12O40]n- (X = Si, n = 4; X = P, n = 3) polyoxometalates. (PTCD)3[PW12O40]2·3DMSO·2H2O (2) and (PTCD)2[SiW12O40]·DMSO·2H2O (3) were structurally characterized by single crystal X-ray diffraction. The cations in both structures exhibited infinite chainlike arrangements through π-π interactions, contrasting with the previously reported cation-anion stacking observed in naphthalene diimide derivatives. A detailed theoretical study employing topological analysis of the electron density distribution within the quantum theory of atoms in molecules approach provided further insights into this structural dualism. Atomic force microscopy analyses revealed the formation of self-assembled supramolecular structures on graphite from molecular monolayers (3 nm of thick) to submicrometer aggregates for 2. Hyperspectral Raman spectroscopy imaging revealed that such heterostructures are likely formed by an enhanced π-π interactions. Both complexes demonstrated interesting electrochemical behavior, photoluminescence and X-ray-induced luminescence. Electron spin resonance analysis confirmed charge separation in both compounds, with enhanced efficiency observed in compound 2. Our findings of these perylene-based organic-inorganic hybrid salts offer the potential for their application in optoelectronic devices and functional materials.

Novel Route to Cationic Palladium(II)-Cyclopentadienyl Complexes Containing Phosphine Ligands and Their Catalytic Activities

The Pd(II) complexes [Pd(Cp)(L)_n]_m[BF₄]_m were synthesized via the reaction of cationic acetylacetonate complexes with cyclopentadiene in the presence of BF₃∙OEt₂ (n = 2, m = 1: L = PPh₃ (1), P(p-Tol)₃, tris(ortho-methoxyphenyl)phosphine (TOMPP), tri-2-furylphosphine, tri-2-thienylphosphine; n = 1, m = 1: L = dppf, dppp (2), dppb (3), 1,5-bis(diphenylphosphino)pentane; n = 1, m = 2 or 3: 1,6-bis(diphenylphosphino)hexane). Complexes 1-3 were characterized using X-ray diffractometry. The inspection of the crystal structures of the complexes enabled the recognition of (Cp^-)⋯(Ph-group) and (Cp^-)⋯(CH₂-group) interactions, which are of C-H…π nature. The presence of these interactions was confirmed theoretically via DFT calculations using QTAIM analysis. The intermolecular interactions in the X-ray structures are non-covalent in origin with an estimated energy of 0.3-1.6 kcal/mol. The cationic palladium catalyst precursors with monophosphines were found to be active catalysts for the telomerization of 1,3-butadiene with methanol (TON up to 2.4∙10⁴ mol 1,3-butadiene per mol Pd with chemoselectivity of 82%). Complex [Pd(Cp)(TOMPP)₂]BF₄ was found to be an efficient catalyst for the polymerization of phenylacetylene (PA) (catalyst activities up to 8.9 × 10³ g_PA·(mol_Pd·h)^-1 were observed).

Synthesis of 3-(Pyridin-2-yl)quinazolin-2,4(1H,3H)-diones via Annulation of Anthranilic Esters with N-pyridyl Ureas

A new route for the synthesis of quinazolin-2,4(1H,3H)-diones and thieno [2,3-d]pyrimidine-2,4(1H,3H)-diones substituted by pyridyl/quinolinyl moiety in position 3 has been developed. The proposed method concluded in an annulation of substituted anthranilic esters or 2-aminothiophene-3-carboxylates with 1,1-dimethyl-3-(pyridin-2-yl) ureas. The process consists of the formation of N-aryl-N'-pyridyl ureas followed by their cyclocondensation into the corresponding fused heterocycles. The reaction does not require the use of metal catalysts and proceeds with moderate to good yields (up to 89%). The scope of the method is more than 30 examples, including compounds with both electron-withdrawing and electron-donating groups, as well as diverse functionalities. At the same time, strong electron-acceptor substituents in the pyridine ring of the starting ureas reduce the product yield or even prevent the cyclocondensation step. The reaction can be easily scaled to gram quantities.

Palladium(II) and Platinum(II) Deprotonated Diaminocarbene Complexes Based on N-(2-Pyridyl)ureas with Oxadiazole Periphery

Metal mediated coupling of isocyanides with substituted N-(pyridine-2-yl) ureas was first used to incorporate privileged biological motifs into platinum metal complexes. We synthesized two palladium(II) and two platinum(II) cyclometallated species with oxadiazole cores. The compounds were isolated in good yields (61–73%) and characterized by high-resolution mass spectrometry and 1H, 13C, and 195Pt NMR spectroscopies. The structures of three complexes were additionally elucidated by X-ray diffraction analysis. These complexes indeed showed cytotoxic activity. The species bearing the 1,3,4-oxadiazole moiety exhibit more potency than the ones with the 1,2,4-oxadiazole ring. Particularly, the cytotoxic effect of both 1,3,4-oxadiazole-based complexes towards T98G cells significantly exceeds the common antitumor metal-drug cisplatin.

Thiazolidin-4-Ones as Potential Antimicrobial Agents: Experimental and In Silico Evaluation

Herein, we report computational and experimental evaluations of the antimicrobial activity of twenty one 2,3-diaryl-thiazolidin-4-ones. All synthesized compounds exhibited an antibacterial activity against six Gram-positive and Gram-negative bacteria to different extents. Thus, the MIC was in the range of 0.008-0.24 mg/mL, while the MBC was 0.0016-0.48 mg/mL. The most sensitive bacterium was S. Typhimurium, whereas S. aureus was the most resistant. The best antibacterial activity was observed for compound 5 (MIC at 0.008-0.06 mg/mL). The three most active compounds 5, 8, and 15, as well as compound 6, which were evaluated against three resistant strains, MRSA, P. aeruginosa, and E. coli, were more potent against all bacterial strains used than ampicillin. The antifungal activity of some compounds exceeded or were equipotent with those of the reference antifungal agents bifonazole and ketoconazole. The best activity was expressed by compound 5. All compounds exhibited moderate to good drug-likeness scores ranging from -0.39 to 0.39. The docking studies indicated a probable involvement of E. coli Mur B inhibition in the antibacterial action, while CYP51 inhibition is likely responsible for the antifungal activity of the tested compounds. Finally, the assessment of cellular cytotoxicity of the compounds in normal human MRC-5 cells revealed that the compounds were not toxic.

Multi-Phase In Silico Discovery of Potential SARS-CoV-2 RNA-Dependent RNA Polymerase Inhibitors among 3009 Clinical and FDA-Approved Related Drugs

Proceeding our prior studies of SARS-CoV-2, the inhibitory potential against SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) has been investigated for a collection of 3009 clinical and FDA-approved drugs. A multi-phase in silico approach has been employed in this study. Initially, a molecular fingerprint experiment of Remdesivir (RTP), the co-crystallized ligand of the examined protein, revealed the most similar 150 compounds. Among them, 30 compounds were selected after a structure similarity experiment. Subsequently, the most similar 30 compounds were docked against SARS-CoV-2 RNA-dependent RNA polymerase (PDB ID: 7BV2). Aloin 359, Baicalin 456, Cefadroxil 1273, Sophoricoside 1459, Hyperoside 2109, and Vitexin 2286 exhibited the most precise binding modes, as well as the best binding energies. To confirm the obtained results, MD simulations experiments have been conducted for Hyperoside 2109, the natural flavonoid glycoside that exhibited the best docking scores, against RdRp (PDB ID: 7BV2) for 100 ns. The achieved results authenticated the correct binding of 2109, showing low energy and optimum dynamics. Our team presents these outcomes for scientists all over the world to advance in vitro and in vivo examinations against COVID-19 for the promising compounds.

Synthesis, Structure, and Antiproliferative Action of 2-Pyridyl Urea-Based Cu(II) Complexes

Relying on a recently suggested protocol that furnishes convenient access to variously substituted 2-pyridyl ureas, twelve hitherto unknown Cu(II) complexes have been synthesized in the present work and their structures were evaluated by elemental analysis, HRMS, IR spectroscopy, and X-ray diffraction study. Two structural motifs ([Cu(L)2Cl]+[Cl]− or (Cu(L)2Cl2) depending on the substitution pattern on the 2-pyridine fragment were revealed. In addition, antiproliferative action of the obtained compounds have been investigated against lung cancer cell lines (A549, NCI-H460, NCI-H1975), and healthy WI-26 VA4 cells were used to monitor non-specific cytotoxicity. Two nitro-group substituted complexes Cu(U3)2Cl2 (IC50 = 39.6 ± 4.5 μM) and Cu(U11)2Cl2 (IC50 = 33.4 ± 3.8 μM) demonstrate enhanced activity against the drug resistant NCI-H1975 cells with moderate selectivity toward normal WI-26 VA4 cells. The antiproliferative mechanism of cell death underlying the growth inhibitory effect of the synthesized complexes was studied via additional experiments, including the cell cycle analysis and the apoptosis induction test. Reassuringly, certain 2-pyridyl urea-based Cu(II) complexes exerted cell line-specific antiproliferative effect which renders them valuable starting points for further unveiling the anticancer potential of this class of coordination compounds.

Non-Covalent Interactions in Organic, Organometallic, and Inorganic Supramolecular Systems Relevant for Medicine, Materials Science, and Catalysis

The structure, fundamental properties, and reactivity of chemical systems at various hierarchical levels of organization of matter is the paradigm of chemistry. A qualitative and quantitative description of various intermolecular and intramolecular non-covalent interactions in chemical systems is the main tool for supramolecular design and the driving force of smart prediction of kinetic and thermodynamic parameters of chemical reactions. This perspective is dedicated to highlighting the recent progress of our research group in the investigation of various non-covalent contacts in organic, organometallic, and inorganic chemical systems relevant for medicine, materials science, and catalysis. This research is interdisciplinary in nature and lies at the intersection of computer modeling with such natural science disciplines as chemistry, physics, crystallography, biology, and medicine, as well as directly related to materials science and nanotechnology.

Theoretical Investigation on Non-Covalent Interactions

This editorial is dedicated to announcing the Special Issue “Theoretical investigation on non-covalent interactions” of Crystals. The Special Issue covers the most recent progress in the rapidly growing fields of data science, artificial intelligence, and quantum and computational chemistry in topics relevant to the problem of theoretical investigation on non-covalent interactions (including, but not limited to, hydrogen, halogen, chalcogen, pnictogen, tetrel, and semi-coordination bonds; agosic and anagosic interactions; stacking, anion-/cation–π interactions; metallophilic interactions, etc.). The main successes of my colleagues and I in the field of fundamental theoretical studies of non-covalent interactions in various chemical compounds over the past year are briefly highlighted.

Oxadiazol-based mTOR inhibitors with potent antiproliferative activities: synthetic and computational modeling

Series of N-aryl-1,3,4-oxadiazole-2-amines and 3-aryl-1,2,4-oxadiazole-5-carboxamides derivatives were synthesized as novel chemotherapeutic agents. Synthesized compounds were evaluated for their anticancer activities against several cancer cell lines. Many analogues of 1,3,4-oxadiazole scaffold showed potent antiproliferative activities against breast cancer cell lines, with higher activities toward the metastatic breast cancer cell line (MDA-MB-231). Active analogues were profiled using in-house pharmacophore database in search for molecular target. Active analogues (2j and 2k) were found to fit the pharmacophoric map of ATP-competitive inhibitors of mTOR. The mTOR inhibitory activities of the most active compounds were confirmed with IC₅₀ values in nanomolar range. The N-aryl-1,3,4-oxadiazole-2-amines linked to a basic head is a novel ATP-competitive inhibitors of mTOR with potential activities for treatment of different types of cancer.

Experimental and computational evidence for stabilising parallel, offset π[C(O)N(H)NC]⋯π(phenyl) interactions in acetohydrazide derivatives

Stabilising π[C(O)N(H)NC]⋯π(phenyl) interactions are described.