Chemical constituents from Limonium tubiflorum and their in silico evaluation as potential antiviral agents against SARS-CoV-2

Wild plants growing in the Egyptian deserts are facing abiotic stress, which can lead to interesting & safe natural products possessing potential chemical profiles. Consequently, our study was designed to assess the phytochemical composition of the aerial parts of Limonium tubiflorum (family Plumbaginaceae) growing wild in Egypt for the first time. In addition, in silico screening and molecular dynamic simulation of all isolated phytoconstituents were run against the main protease (M^pro) and spike glycoprotein SARS-CoV-2 targets which displayed a crucial role in the replication of this virus. Our findings showed that the phytochemical investigation of 70% ethanol extract of L. tubiflorum aerial parts afforded six known flavonoids; myricetin 3-O-(2′′-galloyl)-β-d-galactopyranoside (1), myricetin 3-O-(2′′-galloyl)-α-l-rhamnopyranoside (2), myricetin 3-O-(3′′-galloyl)-α-l-rhamnopyranoside (3), myricetin 3-O-β-d-galactopyranoside (5), apigenin (6), myricetin (7), along with two known phenolic acid derivatives; gallic acid (4) and ethyl gallate (8). Docking studies revealed that compounds (1) & (2) were the most effective compounds with binding energies of −17.9664 & −18.6652 kcal mol⁻¹ against main protease and −18.9244 & −18.9272 kcal mol⁻¹ towards spike glycoprotein receptors, respectively. The molecular dynamics simulation experiment agreed with the docking study and reported stability of compounds (1) and (2) against the selected targets which was proved by low RMSD for the tested components. Moreover, the structure–activity relationship revealed that the presence of the galloyl moiety is necessary for enhancement of the activity. Overall, the galloyl substructure of myricetin 3-O-glycoside derivatives (1 and 2) isolated from L. tubiflorum may be a possible lead for developing COVID-19 drugs. Further, in vitro and in vivo assays are recommended to support our in silico studies.

Wild plants growing in the Egyptian deserts are facing abiotic stress, which can lead to interesting & safe natural products possessing potential chemical profiles.     

Synthesis,acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) activities,and molecular docking studies of a novel compound based on combination of flurbiprofen and isoniazide

Synthesis of a compound with balanced bioactivities against a specific target is always a challenging task. In this study, a novel compound (1) has been synthesized by combination of flurbiprofen and isoniazide and shows ∼2.5 times enhanced acetylcholinesterase (AChE) inhibition activity and ∼1.7 times improved butyrylcholinesterase (BuChE) inhibition activity compared to flurbiprofen and a standard drug (i.e. physostigmine). A comparative AutoDock study has been performed, based on the optimized structure, by the DFT/B3LYP method, which confirmed that compound (1) is more active against AChE and BuChE, with calculated binding energies of −12.9 kcal mol⁻¹ and −9.8 kcal mol⁻¹ respectively as compared to flurbiprofen and an eserine (physostigmine) standard for which the binding energy was calculated to be −10.1 kcal mol⁻¹ and −8.9 kcal mol⁻¹, respectively. A mixed mode of inhibition of AChE and BuChE with compound 1 was confirmed by Lineweaver–Burk plots. AChE and BuChE inhibition activity alongside docking results suggests that compound (1) could be used for treatment of Alzheimer''s disease. Moreover, compound (1) also exhibit better α-chymotrypsin activity compared to flurbiprofen. Furthermore, in vitro and in vivo analysis confirmed that compound (1) exhibit more activity and less toxicity than the parent compounds.

A novel compound (1) shows ∼2.5 and ∼1.7 times enhanced AChE inhibition activity and BuChE inhibition activity respectively compared to flurbiprofen and standard drug (i.e. physostigmine). It has also been confirmed by comparative AutoDock studies.     

Structure characterization and anticoagulant activity of a novel polysaccharide from Leonurus artemisia (Laur.) S. Y. Hu F

An acidic polysaccharide, named LAP-1, was extracted and isolated from Leonurus artemisia (Laur.), and was further purified with ion exchange chromatography and gel chromatography. The extraction conditions of the crude polysaccharides were optimized by single-factor experiments and response surface methodology. The primary structure of the purified polysaccharide was measured by FT-IR, GC-MS, and NMR. The results showed that LAP-1 was mainly composed of galacturonic acid (GalA), mannose (Man), xylose (Xyl), rhamnose (Rha), arabinose (Ara), glucose (Glc), galactose (Gal), fucose (Fuc), ribose (Rib), and glucuronic acid (GlcA) in the molar ratio of 8.74 : 3.45 : 1.02 : 1 : 2.11 : 5.60 : 4.73 : 1.08 : 1.09 : 1.47. Primary structure analysis results indicated that LAP-1 contained characteristic glycosyl linkages such as →1)-α-d-Manp, →1)-α-d-Glcp, →1)-α-d-Arap-(2→, →1)-β-d-Galp-(3→, →1)-β-d-Manp-(4→, →1)-β-d-Galp-(4→, →1)-β-d-Glcp-(4→, →1)-β-d-GalAp-(4→, →1)-β-d-GlcAp-(4→, →1)-β-d-Manp-(4,6→, →1)-β-d-Manp-(3,4→. The M_w/M_n (PDI), M_n, M_z and M_w of LAP-1 were determined to be 1.423, 6.979 × 10³ g mol⁻¹, 1.409 × 10⁴ g mol⁻¹, and 9.930 × 10³ g mol⁻¹ by HPSEC-MALLS-RID and DLS. SEM, TEM and AFM results indicated that LAP-1 was a highly branched structure. LAP-1 showed mild anticoagulant activity, low toxicity, and less spontaneous bleeding compared with heparin sodium. These results demonstrated the effective coagulation activity of Leonurus artemisia polysaccharides. Thus, the purified LAP-1 could be explored as a promising anticoagulant agent for the treatment of coagulation disorders.

An acidic polysaccharide, denoted LAP-1 was extracted, isolated and purified from Leonurus artemisia (Laur.), in addition to its structure and anticoagulant activity were explored.     

In vitro and in silico studies of SARS-CoV-2 main protease Mpro inhibitors isolated from Helichrysum bracteatum

Discovering SARS-CoV-2 inhibitors from natural sources is still a target that has captured the interest of many researchers. In this study, the compounds (1–18) present in the methanolic extract of Helichrysum bracteatum were isolated, identified, and their in vitro inhibitory activities against SARS-CoV-2 main protease (M^pro) was evaluated using fluorescence resonance energy transfer assay (FRET-based assay). Based on 1D and 2D spectroscopic techniques, compounds (1–18) were identified as 24-β-ethyl-cholesta-5(6),22(23),25(26)-triene-3-ol (1), α-amyrin (2), linoleic acid (3), 24-β-ethyl-cholesta-5(6),22(23),25(26)-triene-3-O-β-d-glucoside (4), 1,3-propanediol-2-amino-1-(3′,4′-methylenedioxyphenyl) (5), (−)-(7R,8R,8′R)-acuminatolide (6), (+)-piperitol (7), 5,7,4′-trihydroxy-8,3′-dimethoxy flavanone (8), 5,7,4′-trihydroxy-6-methoxy flavanone (9), 4′,5-dihydroxy-3′,7,8-trimethoxyflavone (10), 5,7-dihydroxy-3′,4′,5′,8-tetramethoxy flavone (11), 1,3-propanediol-2-amino-1-(4′-hydroxy-3′-methoxyphenyl) (12), 3′,5′,5,7-tetrahydroxy-6-methoxyflavanone (13), simplexoside (piperitol-O-β-d-glucoside) (14), pinoresinol monomethyl ether-β-d-glucoside (15), orientin (16), luteolin-3′-O-β-d-glucoside (17), and 3,5-dicaffeoylquinic acid (18). Compounds 6, 12, and 14 showed comparable inhibitory activities against SARS-CoV-2 M^pro with IC₅₀ values of 0.917 ± 0.05, 0.476 ± 0.02, and 0.610 ± 0.03 μM, respectively, compared with the control lopinavir with an IC₅₀ value of 0.225 ± 0.01 μM. The other tested compounds showed considerable inhibitory activities. The molecular docking study for the tested compounds was carried out to correlate their binding modes and affinities for the SARS-CoV-2 M^pro enzyme with the in vitro results. Analyzing the results of the in vitro assay together with the obtained in silico results led to the conclusion that phenylpropanoids, lignans, and flavonoids could be considered suitable drug leads for developing anti-COVID-19 therapeutics. Moreover, the phenylpropanoid skeleton oxygenated at C3, C4 of the phenyl moiety and at C1, C3 of the propane parts constitute an essential core of the SARS-CoV-2 M^pro inhibitors, and thus could be proposed as a scaffold for the design of new anti-COVID-19 drugs.

Compounds isolated and identified from Helichrysum bracteatum leaves showed promising in vitro inhibitory activities against SARS-CoV-2 main protease (M^pro). Thus, could be considered suitable drug leads for developing anti-COVID-19 therapeutics.     

Antiproliferative activity of new pentacyclic triterpene and a saponin from Gladiolus segetum Ker-Gawl corms supported by molecular docking study

A new triterpenoidal saponin identified as 3-O-[β-d-glucopyranosyl-(1 → 2)-β-d-glucopyranosyl-(1 → 4)-β-d-xylopyranosyl]-2β,3β,16α-trihydroxyolean-12-en-23,28-dioic acid-28-O-α-l-rhamnopyranosyl-(1 → 4)-α-l-rhamnopyranosyl-(1 → 2)-β-d-glucopyranosyl-(1 → 2)-α-l-arabinopyranoside 1 together with a new oleanane triterpene identified as 2β,3β,13α,22α-tetrahydroxy olean-23,28-dioic acid 2 and 6 known compounds (3–8) have been isolated from Gladiolus segetum Ker-Gawl corms. The structural elucidation of the isolated compounds was confirmed using different chemical and spectroscopic methods, including 1D and 2D NMR experiments as well as HR-ESI-MS. Moreover, the in vitro cytotoxic activity of the fractions and that of the isolated compounds 1–8 were investigated against five human cancer cell lines (PC-3, A-549, HePG-2, MCF-7 and HCT-116) using doxorubicin as a reference drug. The results showed that the saponin fraction exhibited potent in vitro cytotoxic activity against the five human cancer cell lines, whereas the maximum activity was exhibited against the PC-3 and A-549 cell lines with the IC₅₀ values of 1.13 and 1.98 μg mL⁻¹, respectively. In addition, compound 1 exhibited potent activity against A-549 and PC-3 with the IC₅₀ values of 2.41 μg mL⁻¹ and 3.45 μg mL⁻¹, respectively. Interestingly, compound 2 showed the maximum activity against PC-3 with an IC₅₀ of 2.01 μg mL⁻¹. These biological results were in harmony with that of the molecular modeling study, which showed that the cytotoxic activity of compound 2 might occur through the inhibition of the HER-2 enzyme.

A new triterpenoidal saponin 1, a new oleanane triterpene 2, and 6 known compounds (3–8) have been isolated from Gladiolus segetum Ker-Gawl corms.     

Structure-based approach: molecular insight of pyranocumarins against α-glucosidase through computational studies

α-glucosidase is an enzyme that catalyzes the release of α-glucose molecules through hydrolysis reactions. Regulation of this enzyme can increase sugar levels in type-2 diabetes mellitus (DM) patients. Pyranocoumarin derivatives have been identified as α-glucosidase inhibitors. Through an in silico approach, this work studied the inhibition of three pyranocoumarin compounds against the α-glucosidase at the molecular level. Molecular docking and molecular dynamics simulation were performed to understand the dynamics behavior of pyranocoumarin derivatives against α-glucosidase. The prediction of free binding energy (ΔG_bind) using the Quantum Mechanics/Molecular Mechanics-Generalized Born (QM/MM-GBSA) approach for each system had the following results, PC1-α-Glu: −13.97 kcal mol⁻¹, PC2-α-Glu: −3.69 kcal mol⁻¹, and PC3-α-Glu: −13.68 kcal mol⁻¹. The interaction energy of each system shows that the grid score, ΔG_bind, and ΔG_exp values had a similar correlation, that was PC1-α-Glu > PC3-α-Glu > PC2-α-Glu. Additionally, the decomposition energy analysis (ΔG^residue_bind) was carried out to find out the contribution of the key binding residue. The results showed that there were 15 key binding residues responsible for stabilizing pyranocumarin binding with criteria of ΔG^residue_bind < −1.00 kcal mol⁻¹. The evaluation presented in this work could provide information on the molecular level about the inhibitory efficiency of pyranocoumarin derivatives against a-glucosidase enzyme based on computational studies.

We presented the structure-based approach (molecular docking and MD simulation) to understand the dynamics behavior and inhibitory efficiency of pyranocoumarin derivatives against α-glucosidase at the molecular level.     

Inhibition of SARS-CoV-2 main protease by phenolic compounds from Manilkara hexandra (Roxb.) Dubard assisted by metabolite profiling and in silico virtual screening

SARS-CoV-2 is a novel coronavirus that was first identified during the outbreak in Wuhan, China in 2019. It is an acute respiratory illness that can transfer among human beings. Natural products can provide a rich resource for novel antiviral drugs. They can interfere with viral proteins such as viral proteases, polymerases, and entry proteins. Several naturally occurring flavonoids were reported to have antiviral activity against different types of RNA and DNA viruses. A methanolic extract of Manilkara hexandra (Roxb.) Dubard leaves is rich in phenolic compounds, mainly flavonoids. Metabolic profiling of the secondary metabolites of Manilkara hexandra (Roxb.) Dubard leaves methanolic extract (MLME), and bark ethyl acetate (MBEE) extract using LC-HRESIMS resulted in the isolation of 18 compounds belonging to a variety of constituents, among which phenolic compounds, flavones, flavonol glycosides and triterpenes were predominant. Besides, four compounds (I–IV) were isolated and identified as myricetin I, myricitrin II, mearnsitrin III, and mearnsetin-3-O-β-d-rutinoside IV (compound IV is isolated for the first time from genus Manilkara) and dereplicated in a metabolomic study as compounds 3, 5, 6, and 12, respectively. The molecular docking study showed that rutin, myricitrin, mearnsitrin, and quercetin 3-O-β-d-glucoside have strong interaction with SARS-CoV-2 protease with high binding energy of −8.2072, −7.1973, −7.5855, and −7.6750, respectively. Interestingly, the results proved that rutin which is a citrus flavonoid glycoside exhibits the strongest inhibition effect to the SARS-CoV-2 protease enzyme. Consequently, it can contribute to developing an effective antiviral drug lead against the SARS-CoV-2 pandemic.

SARS-CoV-2 is a novel coronavirus that was first identified during the outbreak in Wuhan, China in 2019.     

An in silico perception for newly isolated flavonoids from peach fruit as privileged avenue for a countermeasure outbreak of COVID-19

3′-Hydroxy-4′-methoxy-chroman-7-O-β-d-glucopyranoside 4 was first isolated from a natural source, together with three known compounds, the ferulic acid heptyl ester 1, naringenin 2, and 4,2′,4′-trihydroxy-6′-methoxychalcone-4′-O-β-d-glucopyranoside 3, which were isolated from peach [Prunus persica (L.) Batsch] fruits. These compounds were subjected to different virtual screening strategies in order to examine their activity to combat the COVID-19 outbreak. The study design composed of some major aspects: (a) docking with main protease (M^pro), (b) docking with spike protein, (c) 3D shape similarity study (Rapid Overlay Chemical Similarity-ROCS) to the clinically used drugs in COVID-19 patients, and finally, (d) the rule of five and the estimated pre-ADMT properties of the separated flavonoids. Docking study with M^pro of SARS-CoV-2 (PDB ID:6LU7, and 6Y2F) showed that compound 3, its aglycone part, and compound 4 have a strong binding mode to a protease receptor with key amino acids, especially Gln:166AA, and having a similar docking pose to co-crystalized ligands. Docking with the spike protein of SARS-CoV-2 illustrated that compounds 3 and 4 have a good binding affinity to PDB ID:6VSB through the formation of HBs with Asp:467A and Asn:422A. According to ROCS analysis, compounds 1, 3, and 4 displayed high similarities to drugs that prevent SARS-Co2 entry to the lung cells or block the inflammatory storm causing lung injury. Compounds 3 and 4 are good candidates for drug development especially because they showed predicted activity against SARS-CoV-2 through different mechanisms either by preventing genome replication or by blocking inflammatory storm that trigger lung injury. These compounds were isolated from peach fruit, and the study supports data and continues with the recommendation of peach fruits in controlling and managing COVID-19 cases.

3′-Hydroxy-4′-methoxy-chroman-7-O-β-d-glucopyranoside 4, together with three known compounds, ferulic acid heptyl ester 1, naringenin 2, and 4,2′,4′-trihydroxy-6′-methoxychalcone-4′-O-β-d-glucopyranoside 3, was isolated from peach fruits.     

Structural analysis and antioxidant activity of an arabinoxylan from Malvastrum coromandelianum L. (Garcke)

Malvastrum coromandelianum L. (Garcke) is extensively used in traditional medicinal systems to treat various ailments. In the present study, an alkali-soluble polysaccharide (MAP) was isolated from the leaves of M. coromandelianum in 1.15% (w/w) yield. MAP was composed of l-rhamnose, l-arabinose, d-xylose, d-glucose and d-galactose in a 1.00 : 6.04 : 19.88 : 1.07 : 3.03 molar ratio along with d-glucuronic acid (1.95). Methylation/linkage analysis revealed a backbone of →4)-β-d-Xylp(1→ (30.09 mol%) with a side chain of →3)-α-l-Araf(1→ (15.21 mol%) residues. The structure of MAP was elucidated by a combination of degradative and derivatization techniques, including hydrolysis, alditol acetate derivatization, methylation, GC-MS, partial hydrolysis, ESI-MS and NMR (1D, 2D) spectral analysis. Based on correlation analysis, MAP was found to be an arabinoxylan comprising a backbone of →4)-β-d-linked Xylp(1→ with branching at O-2 by a →3)-α-l-Araf(1→ and →3)-β-d-Xylp(1→ chain. MAP also exhibited ferric ion reducing activity, with a reducing power of 0.914 ± 0.01 (R² = 0.972) at 1 mg mL⁻¹ concentration, which showed dose-dependent behavior. MAP can be utilized as a potential antioxidant.

The structure of MAP was studied by degradative, derivatization and spectroscopic methods, and it was found to be an arabinoxylan comprising a backbone of →4)-β-d-linked Xylp(1→ with branching at O-2 by →3)-α-l-Araf(1→ and →3)-β-d-Xylp(1→ chains.     

Antioxidant and UV-radiation absorption activity of aaptamine derivatives – potential application for natural organic sunscreens

Antioxidant and UV absorption activities of three aaptamine derivatives including piperidine[3,2-b]demethyl(oxy)aaptamine (C1), 9-amino-2-ethoxy-8-methoxy-3H-benzo[de][1,6]naphthyridine-3-one (C2), and 2-(sec-butyl)-7,8-dimethoxybenzo[de]imidazo[4,5,1-ij][1,6]-naphthyridin-10(9H)-one (C3) were theoretically studied by density functional theory (DFT). Direct antioxidant activities of C1–C3 were firstly evaluated via their intrinsic thermochemical properties and the radical scavenging activity of the potential antioxidants with the HOO˙/HO˙ radicals via four mechanisms, including: hydrogen atom transfer (HAT), single electron transfer (SET), proton loss (PL) and radical adduct formation (RAF). Kinetic calculation reveals that HOO˙ scavenging in water occurs via HAT mechanism with C1 (k_app, 7.13 × 10⁶ M⁻¹ s⁻¹) while RAF is more dominant with C2 (k_app, 1.40 × 10⁵ M⁻¹ s⁻¹) and C3 (k_app, 2.90 × 10⁵ M⁻¹ s⁻¹). Antioxidant activity of aaptamine derivatives can be classified as C1 > C3 > C2. Indirect antioxidant properties based on Cu(i) and Cu(ii) ions chelating activity were also investigated in aqueous phase. All three studied compounds show spontaneous and favorable Cu(i) ion chelating activity with ΔG⁰ being −15.4, −13.7, and −15.7 kcal mol⁻¹, whereas ΔG⁰ for Cu(ii) chelation are −10.4, −10.8, and −2.2 kcal mol⁻¹ for C1, C2 and C3, respectively. In addition, all compounds show UVA and UVB absorption; in which the excitations are determined mostly as π–π* transition. Overall, the results suggest the potential applications of the aaptamines in pharmaceutics and cosmetics, i.e. as a sunscreen and antioxidant ingredient.

Antioxidant and UV absorption activities of three aaptamine derivatives were theoretically studied by density functional theory (DFT) and time-dependent density functional theory (TD-DFT).     

Rapid prediction of possible inhibitors for SARS-CoV-2 main protease using docking and FPL simulations

Originating for the first time in Wuhan, China, the outbreak of SARS-CoV-2 has caused a serious global health issue. An effective treatment for SARS-CoV-2 is still unavailable. Therefore, in this study, we have tried to predict a list of potential inhibitors for SARS-CoV-2 main protease (Mpro) using a combination of molecular docking and fast pulling of ligand (FPL) simulations. The approaches were initially validated over a set of eleven available inhibitors. Both Autodock Vina and FPL calculations produced consistent results with the experiments with correlation coefficients of R_Dock = 0.72 ± 0.14 and R_W = −0.76 ± 0.10, respectively. The combined approaches were then utilized to predict possible inhibitors that were selected from a ZINC15 sub-database for SARS-CoV-2 Mpro. Twenty compounds were suggested to be able to bind well to SARS-CoV-2 Mpro. Among them, five top-leads are periandrin V, penimocycline, cis-p-Coumaroylcorosolic acid, glycyrrhizin, and uralsaponin B. The obtained results could probably lead to enhance the COVID-19 therapy.

A combination of Autodock Vina and FPL calculations suggested that periandrin V, penimocycline, cis-p-Coumaroylcorosolic acid, glycyrrhizin, and uralsaponin B are able to bind well to SARS-CoV-2 Mpro.     

Synthesis of BINOL–xylose-conjugates as “Turn-off” fluorescent receptors for Fe3+ and secondary recognition of cysteine by their complexes

A novel chiral fluorescence “turn-off” sensor was synthesised using the click reaction. The sensor was a BINOL–xylose derivative, modified at the 2-position and linked by 1,2,3-triazole. It was structurally characterized by ¹HNMR, ¹³CNMR, ESI-MS and IR analysis. The selectivity of R-β-d-2 in methanol solution has been studied. Among the 19 transition metal ions, alkaline metal ions and alkaline earth metal ions studied, R-β-d-2 had a selective fluorescence quenching reaction for Fe³⁺. The detection limit of R-β-d-2 for Fe³⁺ was 0.91 μmol L⁻¹. Complexation between R-β-d-2 and Fe³⁺ was investigated by ESI-MS and ¹HNMR. The stoichiometric ratio of R-β-d-2 was 1 : 1. In addition, the R-β-d-2–Fe³⁺ complex was titrated with 20 naturally occurring amino acids and Hcy with GSH. It was found that the complex R-β-d-2–Fe³⁺ had a secondary recognition effect on Cys by switching to fluorescence.

A fluorescence sensor of BINOL–xylose derivative was synthesized, which could only detect Fe³⁺ by 1 + 1 complex with high selectivity and sensitivity. The complex of the derivative with Fe³⁺ was found to perform secondary recognition of cysteine.     

Effect of non-covalent self-dimerization on the spectroscopic and electrochemical properties of mixed Cu(i) complexes

A series of six new Cu(i) complexes with ([Cu(N-{4-R}pyridine-2-yl-methanimine)(PPh₃)Br]) formulation, where R corresponds to a donor or acceptor p-substituent, have been synthesized and were used to study self-association effects on their structural and electrochemical properties. X-ray diffraction results showed that in all complexes the packing is organized from a dimer generated by supramolecular π stacking and hydrogen bonding. ¹H-NMR experiments at several concentrations showed that all complexes undergo a fast-self-association monomer–dimer equilibrium in solution, while changes in resonance frequency towards the high or low field in specific protons of the imine ligand allow establishing that dimers have similar structures to those found in the crystal. The thermodynamic parameters for this self-association process were calculated from dimerization constants determined by VT-¹H-NMR experiments for several concentrations at different temperatures. The values for K_D (4.0 to 70.0 M⁻¹ range), ΔH (−1.4 to −2.6 kcal mol⁻¹ range), ΔS (−0.2 to 2.1 cal mol⁻¹ K⁻¹ range), and ΔG₂₉₈ (−0.8 to −2.0 kcal mol⁻¹ range) are of the same order and indicate that the self-dimerization process is enthalpically driven for all complexes. The electrochemical profile of the complexes shows two redox Cu(ii)/Cu(i) processes whose relative intensities are sensitive to concentration changes, indicating that both species are in chemical equilibrium, with the monomer and the dimer having different electrochemical characteristics. We associate this behaviour with the structural lability of the Cu(i) centre that allows the monomeric molecules to reorder conformationally to achieve a more adequate assembly in the non-covalent dimer. As expected, structural properties in the solid and in solution, as well as their electrochemical properties, are not correlated with the electronic parameters usually used to evaluate R substituent effects. This confirms that the properties of the Cu(i) complexes are usually more influenced by steric effects than by the inductive effects of substituents of the ligands. In fact, the results obtained showed the importance of non-covalent intermolecular interactions in the structuring of the coordination geometry around the Cu centre and in the coordinative stability to avoid dissociative equilibria.

Organized crystal packing from non-covalent dimers and the self-dimerization in solution of Cu(NN′)(PPh₃)Br] were characterized. Differences in Cu(ii)/Cu(i) potentials between the monomer and dimer are modulated by the non-covalent interactions.     

Potential mechanism of action of Ixeris sonchifolia extract injection against cardiovascular diseases revealed by combination of HPLC-Q-TOF-MS,virtual screening and systems pharmacology approach

Ixeris sonchifolia extract injection, a Chinese medicine preparation named as Kudiezi injection (KDZI) in China, has been widely used for the treatment of cardiovascular diseases (CVDs) in recent years. Owing to the component complexity of the preparation, the study on the effect mechanism of the herbal medicine against CVDs is a big challenge. In this research, HPLC-Q-TOF-MS was used to analyze the constituents of the preparation, disclosing that the KDZI mainly consists of 10 ingredients, namely 3-caffeoylquinic acid (KDZI-1), 4-caffeoylquinic acid (KDZI-2), 5-caffeoylquinic acid (KDZI-3), apigenin-7-O-β-d-glucuronide (KDZI-4), caffeic acid (KDZI-5), chicoric acid (KDZI-6), caftaric acid (KDZI-7), luteolin-7-O-β-d-gentiobioside (KDZI-8), luteolin-7-O-β-d-glucopyranoside (KDZI-9) and luteolin-7-O-β-d-glucuronide (KDZI-10). Afterwards, target fishing and an integrated systems pharmacology approach combined with molecular docking (Sybyl 1.3 and AutoDock Vina) were adopted to predict the potential targets and pathways for the main ingredients in KDZI. As results, 39 protein targets and 9 KEGG pathways, possessing high relevance to the therapeutic effects of the ingredients of KDZI against CVDs, were screened out reasonably. The integrated pharmacology analysis suggested that KDZI could exert its therapeutic effects against CVDs possibly via multi-targets including EGFR, MAPK10, and SRC and multi-pathways referring to MAPK, focal adhesion, complement and coagulation cascades, etc. This research provides insights into understanding the comprehensive therapeutic effect and mechanism of the KDZI on CVDs.

Ixeris sonchifolia extract injection, a Chinese medicine preparation named as Kudiezi injection (KDZI) in China, has been widely used for the treatment of cardiovascular diseases (CVDs) in recent years.     

The enzyme-like catalytic hydrogen abstraction reaction mechanisms of cyclic hydrocarbons with magnesium-diluted Fe-MOF-74

Enzymatic heme and non-heme Fe(iv)–O species usually play an important role in hydrogen abstraction of biocatalytic reactions, yet duplicating the reactivity in biomimicry remains a great challenge. Based on Xiao et al.''s experimental work [Nat. Chem., 2014, 6(7), 590], we theoretically found that in the presence of the oxidant N₂O, the enzyme-like metal organic framework, i.e., magnesium-diluted Fe-MOF-74 [Fe/(Mg)-MOF-74] can activate the C–H bonds of 1,4-cyclohexadiene (CHD) into benzene with a two-step hydrogen abstraction mechanism based on the density functional theory (DFT) level. It is shown that the first transition state about the cleavage of the N–O bond of N₂O to form the Fe(iv)–O species is the rate-determining step with activation enthalpy of 19.4 kcal mol⁻¹ and the complete reaction is exothermic by 62.8 kcal mol⁻¹ on quintet rather than on triplet PES. In addition, we proposed a rebound mechanism of cyclic cyclohexane (CHA) hydroxylation to cyclohexanol which has not been studied experimentally. Note that the activation enthalpies on the first hydrogen abstraction for both cyclic CHD and cyclohexane are just 8.1 and 3.5 kcal mol⁻¹, respectively, which are less than that of 13.9 kcal mol⁻¹ for chained ethane. Most importantly, for the hydrogen abstraction of methane catalyzed by M/(Mg)-MOF-74 (M = Cu, Ni, Fe, and Co), we found that the activation enthalpies versus the C–H bond length of methane of TSs, NPA charge of the reacting oxyl atom have linear relationships with different slopes, i.e., shorter C–H bond and less absolute value of NPA charge of oxyl atom are associated with lower activation enthalpy; while for the activation of methane, ethane, propane and CHD catalyzed by Fe/(Mg)-MOF-74, there also exists positive correlations between activation enthalpies, bond dissociation energies (BDEs) and C–H bond lengths in TSs, respectively. We hope the present theoretical study may provide the guideline to predict the performance of MOFs in C–H bond activation reactions.

The enzyme-like catalytic hydrogen abstraction reaction of cyclic hydrocarbons.     

Molecular modeling studies and in vitro screening of dihydrorugosaflavonoid and its derivatives against Mycobacterium tuberculosis

Novel drug regimens against tuberculosis (TB) are urgently needed and may be developed by targeting essential enzymes of Mtb that sustain the pathogenicity of tuberculosis. In the present investigation, series of compounds (5a–f and 6a–f) based on a naturally occurring rugosaflavonoid moiety were evaluated by in silico molecular modeling studies against β-ketoacyl-ACP reductase (MabA) (PDB ID: IUZN) and pantothenate kinase (PanK) (PDB ID: 3AF3). Compounds 5a, 5c, 5d, and 6c, which had docking scores of −8.29, −8.36, −8.17 and −7.39 kcal mol⁻¹, respectively, displayed interactions with MabA that were better than those of isoniazid (−6.81 kcal mol⁻¹). Similarly, compounds 5a, 5c, 5d, and 6c, which had docking scores of −7.55, −7.64, −7.40 and −6.7 kcal mol⁻¹, respectively, displayed interactions with PanK that were comparable to those of isoniazid (−7.64 kcal mol⁻¹). Because of their docking scores, these compounds were screened in vitro against Mycobacterium tuberculosis H37Ra (Mtb) using an XRMA protocol. Among the screened compounds, the dihydrorugosaflavonoid derivatives 5a, 5c, and 5d had IC₅₀ values of 12.93, 8.43 and 11.3 μg mL⁻¹, respectively, and exhibited better inhibitory activity than the parent rugosaflavonoid derivatives. The rugosaflavonoid derivative 6c had an IC₅₀ value of 17.57 μg mL⁻¹. The synthesized compounds also displayed inhibitory activity against the Gram-positive bacteria Bacillus subtilis and Staphylococcus aureus. The present study will be helpful for the further development of these molecules into antitubercular lead candidates.

Novel drug regimens against tuberculosis (TB) are urgently needed and may be developed by targeting essential enzymes of Mtb that sustain the pathogenicity of tuberculosis. Dihydrorugosaflavonoid interacted with the active pocket of MabA and PanK.     

Structural characterization,anti-inflammatory and glycosidase inhibitory activities of two new polysaccharides from the root of Pueraria lobata

Diabetes seriously endangers public health and brings a heavy economic burden to the country. Inflammation is one of the main inducing factors of type-2 diabetes (T2D) and may cause some complications of diabetes, such as diabetic encephalopathy and peripheral neuropathy. In-depth research and development of drugs to cure diabetes and complications are of great significance. Pueraria lobate is a medicinal herb used in several countries to treat many diseases. Here, two new polysaccharides (PLB-1-1 and PLB-1-2) were isolated and purified from the root of Pueraria lobata with molecular weights of 9.1 × 10³ Da and 3.8 × 10³ Da, respectively. The structure was evaluated by monosaccharide composition, GC-MS and NMR spectroscopy. It was determined that PLB-1-1 comprised →4)-α-d-Glcp-(1→, α-d-Glcp-(1→, →6)-β-d-Galp-(1→, →3)-α-l-Araf-(1→, →3,6)-β-d-Manp-(1→ and →4,6)-β-d-Manp-(1→, and PLB-1-2 consisted of →4)-α-d-Glcp-(1→, β-d-Glcp-(1→, →4,6)-β-d-Glcp-(1→, →3,6)-β-d-Manp-(1→ and α-l-Fucp-(1→. Furthermore, both PLB-1-1 and PLB-1-2 showed anti-inflammatory and inhibitory activities of α-glucosidase and α-amylase in vitro. Therefore, the new polysaccharides, i.e., PLB-1-1 and PLB-1-2, may be considered candidates for the treatment of diabetes and its related complications.

Through the extraction, isolation and purification of Pueraria lobata, we identified two new polysaccharides with molecular weights of 9.1 × 10³ Da and 3.8 × 10³ Da, and found that they have excellent anti-inflammatory and glycosidase inhibitory effects.     

Identifying the specific-targeted marine cerebrosides against SARS-CoV-2: an integrated computational approach

Cerebrosides are a group of metabolites belonging to the glycosphingolipids class of natural products. So far, 167 cerebrosides, compounds 1–167, have been isolated from diverse marine organisms or microorganisms. The as yet smaller number of compounds that have been studied more in depth proves a potential against challenging diseases, such as cancer, a range of viral and bacterial diseases, as well as inflammation. This review provides a comprehensive summary on this so far under-explored class of compounds, their chemical structures, bioactivities, and their marine sources, with a full coverage to the end of 2020. Today, the global pandemic concern, COVID-19, has claimed millions of death cases around the world, making the development of anti-SARS-CoV-2 drugs urgently needed for such a battle. Accordingly, selected examples from all subclasses of cerebrosides were virtually screened for potential inhibition of SARS-CoV-2 proteins that are crucially involved in the viral–host interaction, viral replication, or in disease progression. The results highlight five cerebrosides that could preferentially bind to the hACE2 protein, with binding scores between −7.1 and −7.6 kcal mol⁻¹ and with the docking poses determined underneath the first α₁-helix of the protein. Moreover, the molecular interaction determined by molecular dynamic (MD) simulation revealed that renieroside C1 (60) is more conveniently involved in key hydrophobic interactions with the best stability, least deviation, least ΔG (−6.9 kcal mol⁻¹) and an RMSD value of 3.6 Å. Thus, the structural insights assure better binding affinity and favorable molecular interaction of renieroside C1 (60) towards the hACE2 protein, which plays a crucial role in the biology and pathogenesis of SARS-CoV-2.

Cerebrosides are a group of metabolites belonging to the glycosphingolipids class of natural products.     

Molecular design of anticancer drugs from marine fungi derivatives

Heat shock protein 90 (Hsp90) is one of the most potential targets in cancer therapy. We have demonstrated using a combination of molecular docking and fast pulling of ligand (FPL) simulations that marine fungi derivatives can be possible inhibitors, preventing the biological activity of Hsp90. The computational approaches were validated and compared with previous experiments. Based on the benchmark of available inhibitors of Hsp90, the GOLD docking package using the ChemPLP scoring function was found to be superior over both Autodock Vina and Autodock4 in the preliminary estimation of the ligand-binding affinity and binding pose with the Pearson correlation, R = −0.62. Moreover, FPL calculations were also indicated as a suitable approach to refine docking simulations with a correlation coefficient with the experimental data of R = −0.81. Therefore, the binding affinity of marine fungi derivatives to Hsp90 was evaluated. Docking and FPL calculations suggest that five compounds including 23, 40, 46, 48, and 52 are highly potent inhibitors for Hsp90. The obtained results enhance cancer therapy research.

Five compounds originating from marine fungi species Aspergillus sp. and Penicillium sp. were found to be highly potent inhibitors of cancer therapy target, Hsp90, using molecular docking and FPL calculations.