Composition and Antimicrobial Activity of <Emphasis Type="Italic">Helichrysum italicum</Emphasis> Essential Oil and Its Terpene and Terpenoid Fractions

The essential oil of Helichrysum italicum (Roth) G. Don from Croatia has been fractionated into terpene and terpenoid fractions and analyzed using GC/MS. Fifty-two compounds were identified. The main hydrocarbons of the oil were α-pinene (10.2%), α-cedrene (9.6%) aromadendrene (4.4%), β-caryophyllene (4.2%), and limonene (3.8%), while the main oxygen-containing compounds were neryl acetate (11.5%), 2-methylcyclohexyl pentanoate (8.3%), 2-methylcyclohexyl octanoate (4.8%), and geranyl acetate (4.7%). The essential oil and its terpene and terpenoid fractions were evaluated for antibacterial and antifungal activities. The screening of antimicrobial activity was conducted by a disc diffusion test and the minimum inhibitory concentration was determined against Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa, and Candida albicans. The essential oil and its terpenoid fraction exhibited higher antimicrobial activity with respect to the terpene fraction. The antimicrobial activities of the oil and its terpenoid fraction were more pronounced against Staphylococcus aureus and Candida albicans.__________Published in Khimiya Prirodnykh Soedinenii, No. 1, pp. 29–32, January–February, 2005.     

On Chloralose-Cyclodextrin Complexes by <Emphasis Type="Italic">ESI</Emphasis>-Mass Spectrometry

α-Chloralose is a useful mild anaesthetic, providing stable but not deep anaesthesia. Host–guest complexes of α-chloralose with α-, β- and γ-cyclodextrin (CD) were studied using electrospray ionisation (ESI-MS) mass spectrometry and molecular modelling (MD). As it is currently administered, chloralose is transported in a convenient water-soluble complex, and released to react on a physiological level with the reactor sites. It is believed that the chloraloses (α and its isomer β) are encapsulated within the CD cavity. However, the ESI spectra did not reveal such the presence of inclusion compounds. Searching of alternative mechanisms of transportation of these anaesthetic agents, we found that outer-cavity complexes of inserted chloraloses, as found from MD calculations, do have a reasonable stability.This revised version was published online in July 2005 with a corrected issue number.     

Ligand and Structure-Based In Silico Determination of the Most Promising SARS-CoV-2 nsp16-nsp10 2′-o-Methyltransferase Complex Inhibitors among 3009 FDA Approved Drugs

As a continuation of our earlier work against SARS-CoV-2, seven FDA-approved drugs were designated as the best SARS-CoV-2 nsp16-nsp10 2′-o-methyltransferase (2′OMTase) inhibitors through 3009 compounds. The in silico inhibitory potential of the examined compounds against SARS-CoV-2 nsp16-nsp10 2′-o-methyltransferase (PDB ID: (6W4H) was conducted through a multi-step screening approach. At the beginning, molecular fingerprints experiment with SAM (S-Adenosylmethionine), the co-crystallized ligand of the targeted enzyme, unveiled the resemblance of 147 drugs. Then, a structural similarity experiment recommended 26 compounds. Therefore, the 26 compounds were docked against 2′OMTase to reveal the potential inhibitory effect of seven promising compounds (Protirelin, (1187), Calcium folinate (1913), Raltegravir (1995), Regadenoson (2176), Ertapenem (2396), Methylergometrine (2532), and Thiamine pyrophosphate hydrochloride (2612)). Out of the docked ligands, Ertapenem (2396) showed an ideal binding mode like that of the co-crystallized ligand (SAM). It occupied all sub-pockets of the active site and bound the crucial amino acids. Accordingly, some MD simulation experiments (RMSD, RMSF, R_g, SASA, and H-bonding) have been conducted for the 2′OMTase—Ertapenem complex over 100 ns. The performed MD experiments verified the correct binding mode of Ertapenem against 2′OMTase exhibiting low energy and optimal dynamics. Finally, MM-PBSA studies indicated that Ertapenem bonded advantageously to the targeted protein with a free energy value of −43 KJ/mol. Furthermore, the binding free energy analysis revealed the essential amino acids of 2′OMTase that served positively to the binding. The achieved results bring hope to find a treatment for COVID-19 via in vitro and in vivo studies for the pointed compounds.     

De novo design based identification of potential HIV-1 integrase inhibitors: A pharmacoinformatics study

In the present study, pharmacoinformatics paradigms include receptor-based de novo design, virtual screening through molecular docking and molecular dynamics (MD) simulation are implemented to identify novel and promising HIV-1 integrase inhibitors. The de novodrug/ligand/molecule design is a powerful and effective approach to design a large number of novel and structurally diverse compounds with the required pharmacological profiles. A crystal structure of HIV-1 integrase bound with standard inhibitor BI-224436 is used and a set of 80,000 compounds through the de novo approach in LigBuilder is designed. Initially, a number of criteria including molecular docking, in-silico toxicity and pharmacokinetics profile assessments are implied to reduce the chemical space. Finally, four de novo designed molecules are proposed as potential HIV-1 integrase inhibitors based on comparative analyses. Notably, strong binding interactions have been identified between a few newly identified catalytic amino acid residues and proposed HIV-1 integrase inhibitors. For evaluation of the dynamic stability of the protein-ligand complexes, a number of parameters are explored from the 100 ns MD simulation study. The MD simulation study suggested that proposed molecules efficiently retained their molecular interaction and structural integrity inside the HIV-1 integrase. The binding free energy is calculated through the Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) approach for all complexes and it also explains their thermodynamic stability. Hence, proposed molecules through de novo design might be critical to inhibiting the HIV-1 integrase.     

Triterpene Glycosides from <Emphasis Type="Italic">Kalopanax septemlobum</Emphasis>. II. Glycosides E,K, and L from Leaves of <Emphasis Type="Italic">Kalopanax septemlobum</Emphasis> var. <Emphasis Type="Italic">maximowiczii</Emphasis> Introduced to Crimea

The known hederagenin 3-O-β-D-glucopyranosyl-(1→4)-O-β-D-xylopyranosyl-(1→ 3)-O-α-L-rhamnopyranosyl-(1→2)-O-α-L-arabinopyranoside (sapindoside C) and its 28-O-α-L-rhamnopyranosyl-(1→4)-β-D-glucopyranosyl-(1→6)-O-β-D-glucopyranosyl and 28-O-α-L-rhamnopyranosyl-(1→4)-O-6-O-acetyl-β-D-glucopyranosyl-(1→6)-O-β-D-glucopyranosyl esters, new triterpene glycosides, were isolated from leaves of Kalopanax septemlobum var. maximowiczii introduced to Crimea. The structures of these compounds were established using chemical methods and two-dimensional NMR spectroscopy.__________Translated from Khimiya Prirodnykh Soedinenii, No. 3, pp. 260–262, May–June, 2005.     

Conformational dependence of the intrinsic acidity of the aspartic acid residue sidechain in N-acetyl- -aspartic acid-N′-methylamide

The sidechain conformational potential energy hypersurfaces (PEHS) for the γ_L, β_L, α_L, and α_D backbone conformations of N-acetyl- -aspartate-N′-methylamide were generated. Of the 81 possible conformers initially expected for the aspartate residue, only seven were found after geometric optimizations at the B3LYP/6-31G(d) level of theory. No stable conformers could be located in the δ_L, _L, γ_D, δ_D, and _D backbone conformations. The ‘adiabatic’ deprotonation energies for the endo and exo forms of N-acetyl- -aspartic acid-N′-methylamide were calculated by comparing their optimized relative energies against those found for the seven stable conformers of N-acetyl- -aspartate-N′-methylamide. Sidechain conformational PEHSs were also generated for the estimation of ‘vertical’ deprotonation energies for both endo and exo forms of N-acetyl- -aspartic acid-N′-methylamide. All backbone–sidechain (N–H⁻O–C) and backbone–backbone (N–HO=C) hydrogen bond interactions were analyzed. A total of two backbone–backbone and four backbone–sidechain interactions were found for N-acetyl- -aspartate-N′-methylamide. The deprotonated sidechain of N-acetyl- -aspartate-N′-methylamide may allow the aspartyl residue to form strong hydrogen bond interactions (since it is negatively charged) which may be significant in such processes as protein–ligand recognition and ligand binding. As a primary example, the molecular geometry of the aspartyl residue may be important in peptide folding, such as that in the RGD tripeptide.     

Stalis: A Computational Method for Template-Based Ab Initio Ligand Design

Proteins interact with small molecules through specific molecular recognition, which is central to essential biological functions in living systems. Therefore, understanding such interactions is crucial for basic sciences and drug discovery. Here, we present S tructure t emplate-based a b initio li gand design s olution (Stalis), a knowledge-based approach that uses structure templates from the Protein Data Bank libraries of whole ligands and their fragments and generates a set of molecules (virtual ligands) whose structures represent the pocket shape and chemical features of a given target binding site. Our benchmark performance evaluation shows that ligand structure-based virtual screening using virtual ligands from Stalis outperforms a receptor structure-based virtual screening using AutoDock Vina, demonstrating reliable overall screening performance applicable to computational high-throughput screening. However, virtual ligands from Stalis are worse in recognizing active compounds at the small fraction of a rank-ordered list of screened library compounds than crystal ligands, due to the low resolution of the virtual ligand structures. In conclusion, Stalis can facilitate drug discovery research by designing virtual ligands that can be used for fast ligand structure-based virtual screening. Moreover, Stalis provides actual three-dimensional ligand structures that likely bind to a target protein, enabling to gain structural insight into potential ligands. Stalis can be an efficient computational platform for high-throughput ligand design for fundamental biological study and drug discovery research at the proteomic level. © 2019 Wiley Periodicals, Inc.     

β-Lactam antibiotics. Spectroscopy and molecular orbital (MO) calculations: Part I: IR studies of complexation in penicillin-transition metal ion systems and semi-empirical PM3 calculations on simple model compounds

IR studies were preformed to determine possible transition metal ion binding sites of penicillin. the observed changes in spectral position and shape of characteristic IR bands of cloxacillin in the presence of transition metal ions (both in solutions and in the solid state) indicate formation of M–L complexes with engagement of –COO⁻ and/or –CONH– functional groups. The small shift of ν_C=O towards higher frequencies rules out direct M–L interaction via β-lactam carbonyl. PM3 calculations on simple model compounds (substituted formamide, cyclic ketones, lactams and substituted monocyclic β-lactams) have been performed. All structures were fully optimized and the calculated bond lengths, angles, heats of formation and C=O stretching frequencies were discussed to determine the β-lactam binding sites and to explain its susceptibility towards nucleophilic attack (hydrolysis in vitro) and biological activity. The relative changes of calculated values were critically compared with available experimental data and same correlation between structural parameters and in vivo activity was shown.     

Arjunolic Acid Derivative Glycoside from the Stems of <Emphasis Type="Italic">Hedera colchica</Emphasis>

Five triterpenoid saponins were isolated from the stems of Hedera colchica K. Koch (Araliaceae). Two of them are new natural substances. HCS-A (1): 3-O-α-L-arabinopyranoside, 28-O-α-L-rhamnopyranosyl-(1→ 4)-O-β-D-glucopyranosyl-(1→6)-O-β-D-glucopyranosyl-arjunolic acid. HCSt-B (2):3-O-β-D-xylopyranoside, 28-O-α-L-rhamnopyranosyl-(1→4)-O-β-D-glucopyranosyl-(1→6)-O-β-D-glucopyranosyl-hederagenin. A derivative of arjunolic acid is described for the first time in the Araliaceae family. The chemical structures of isolated compounds were established on the basis of chemical and 1D and 2D NMR experiments.__________Published in Khimiya Prirodnykh Soedinenii, No. 1, pp. 39–41, January–February, 2005.     

Lithiated γ-O-functionalized propyl phenyl sulfides and sulfones of the type Li[CH(SOxPh)CH2CH2OR] (x = 0, 2). [Li{CH(SPh)CH2CH2Ot-Bu}(tmeda)] – A structurally characterized organolithium inner complex

Lithiation of O-functionalized alkyl phenyl sulfides PhSCH₂CH₂CH₂OR (R = Me, 1a; i-Pr, 1b; t-Bu, 1c; CPh₃, 1d) with n-BuLi/tmeda in n-pentane resulted in the formation of α- and ortho-lithiated compounds [Li{CH(SPh)CH₂CH₂OR}(tmeda)] (α-2a–d) and [Li{o-C₆H₄SCH₂CH₂CH₂OR)(tmeda)] (o-2a–d), respectively, which has been proved by subsequent reaction with n-Bu₃SnCl yielding the requisite stannylated γ-OR-functionalized propyl phenyl sulfides n-Bu₃SnCH(SPh)CH₂CH₂OR (α-3a–d) and n-Bu₃Sn(o-C₆H₄SCH₂CH₂CH₂OR) (o-3a–d). The α/ortho ratios were found to be dependent on the sterical demand of the substituent R. Stannylated alkyl phenyl sulfides α-3a–c were found to react with n-BuLi/tmeda and n-BuLi yielding the pure α-lithiated compounds α-2a–c and [Li{CH(SPh)CH₂CH₂OR}] (α-4a–b), respectively, as white to yellowish powders. Single-crystal X-ray diffraction analysis of [Li{CH(SPh)CH₂CH₂Ot-Bu}(tmeda)] (α-2c) exhibited a distorted tetrahedral coordination of lithium having a chelating tmeda ligand and a C,O coordinated organyl ligand. Thus, α-2c is a typical organolithium inner complex.Lithiation of O-functionalized alkyl phenyl sulfones PhSO₂CH₂CH₂CH₂OR (R = Me, 5a; i-Pr, 5b; CPh₃, 5c) with n-BuLi resulted in the exclusive formation of the α-lithiated products Li[CH(SO₂Ph)CH₂CH₂OR] (6a–c) that were found to react with n-Bu₃SnCl yielding the requisite α-stannylated compounds n-Bu₃SnCH(SO₂Ph)CH₂CH₂OR (7a–c). The identities of all lithium and tin compounds have been unambiguously proved by NMR spectroscopy (¹H, ¹³C, ¹¹⁹Sn).     

Driving forces in substitution reactions of octahedral complexes: The influence of the competitive effect

The reaction of cis-[RuCl₂(P–P)(N–N)] type complexes (P–P = 1,4-bis(diphenylphosphino)butane or (1,1′-diphenylphosphino)ferrocene; N–N = 2,2′-bipyridine or 1,10-phenantroline) with monodentate ligands (L), such as 4-methylpyridine, 4-phenylpyridine and benzonitrile forms [RuCl(L)(P–P)(N–N)]⁺ species. Upon characterization of the isolated compounds by elemental analysis, ³¹P{¹H} NMR and X-ray crystallography it was found out that the type of the L ligand determines its position in relation to the phosphorus atom. While pyridine derivatives like 4-methylpyridine and 4-phenylpyridine coordinate trans to the phosphorus atom, the benzonitrile ligand (bzCN), a good π acceptor, coordinates trans to the nitrogen atom. A ³¹P{¹H} NMR experiment following the reaction of the precursor cis-[RuCl₂(dppb)(phen)] with the benzonitrile ligand shows that the final position of the entering ligand in the complex is better defined as a consequence of the competitive effect between the phosphorus atom and the cyano-group from the benzonitrile moiety and not by the trans effect. In this case, the benzonitrile group is stabilized trans to one of the nitrogen atoms of the N–N ligand. A differential pulse voltammetry experiment confirms this statement. In both experiments the [RuCl(bzCN)(dppb)(phen)]PF₆ species with the bzCN ligand positioned trans to a phosphorus atom of the dppb ligand was detected as an intermediate complex.     

Terpenes,Coumarins, and Flavones from <Emphasis Type="Italic">Acacia pennatula</Emphasis>

The chemical analysis of the acetone extract of the dried leaves from Acacia pennatula yielded triacontanol, β-sitosterol palmitate, β-sitosterol, squalene, nonaprenol, norphytane, lupenone, lupeol, daphnetin and catechin, while from the methanol extract were isolated catechin, epigallocatechin, eriodictyol, β-sitosteryl-β-D-glucopyranoside, and stigmasteryl-β-D-glucopyranoside. The structures of all these natural products were established based on their IR, ¹H, and ¹³C NMR and MS data.__________Published in Khimiya Prirodnykh Soedinenii, No. 3, pp. 240–241, May–June, 2005.     

Toward <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> DXR inhibitor design: homology modeling and molecular dynamics simulations

Mycobacterium tuberculosis 1-deoxy-d-xylulose-5-phosphate reductoisomerase (MtDXR) is a potential target for antitubercular chemotherapy. In the absence of its crystallographic structure, our aim was to develop a structural model of MtDXR. This will allow us to gain early insight into the structure and function of the enzyme and its likely binding to ligands and cofactors and thus, facilitate structure-based inhibitor design. To achieve this goal, initial models of MtDXR were generated using MODELER. The best quality model was refined using a series of minimizations and molecular dynamics simulations. A protein–ligand complex was also developed from the initial homology model of the target protein by including information about the known ligand as spatial restraints and optimizing the mutual interactions between the ligand and the binding site. The final model was evaluated on the basis of its ability to explain several site-directed mutagenesis data. Furthermore, a comparison of the homology model with the X-ray structure published in the final stages of the project shows excellent agreement and validates the approach. The knowledge gained from the current study should prove useful in the design and development of inhibitors as potential novel therapeutic agents against tuberculosis by either de novo drug design or virtual screening of large chemical databases. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Chemical Constituents from the Hulls of <Emphasis Type="Italic">Oryza sativa</Emphasis> with Cytotoxic Activity

Five new compounds, orizaterpenol (1), orizaterpenoid (2), orizaterpenyl benzoate (3), orizanor-diterpenyl benzoate (4), and orizaditerpenyl benzoate (5), along with nine known compounds, were isolated and identified from the rice hulls of Oryza sativa. Their structures were elucidated with the help of different spectroscopic techniques. Orizaterpenol (1) and the known momilactone A (6) and B (7) were found to have cytotoxic effects against P388 murine leukaemia cells, while the other new and known compounds exhibited weak cytotoxicity.__________Published in Khimiya Prirodnykh Soedinenii, No. 2, pp. 146–151, March–April, 2005.     

Localized Mixed‐Valence and Redox Activity within a Triazole‐Bridged Dinucleating Ligand upon Coordination to Palladium

The new dinucleating redox‐active ligand ( L^H4 ), bearing two redox‐active NNO‐binding pockets linked by a 1,2,3‐triazole unit, is synthetically readily accessible. Coordination to two equivalents of Pd^II resulted in the formation of paramagnetic (S= ) dinuclear Pd complexes with a κ²‐N,N′‐bridging triazole and a single bridging chlorido or azido ligand. A combined spectroscopic, spectroelectrochemical, and computational study confirmed Robin–Day Class II mixed‐valence within the redox‐active ligand, with little influence of the secondary bridging anionic ligand. Intervalence charge transfer was observed between the two ligand binding pockets. Selective one‐electron oxidation allowed for isolation of the corresponding cationic ligand‐based diradical species. SQUID (super‐conducting quantum interference device) measurements of these compounds revealed weak anti‐ferromagnetic spin coupling between the two ligand‐centered radicals and an overall singlet ground state in the solid state, which is supported by DFT calculations. The rigid and conjugated dinucleating redox‐active ligand framework thus allows for efficient electronic communication between the two binding pockets.     

Essential Oil Composition and Antibacterial Activity of the Leaves of <Emphasis Type="Italic">Stachys schtschegleevii</Emphasis> from Iran

The composition of the essential oil obtained by hydrodistillation from the leaves of Stachys schtschegleevii Sosn. before the flowering stage was analyzed by GC and GC-MS. Forty-five compounds representing 98.7% of the total oil were identified, of which α-pinene (36.4%), germacrene-D (18.6%), limonene (8.2%), and piperitone (6.2%) were the major constituents. Furthermore, antibacterial activity of the entire oil and its two main monoterpenes was evaluated against six Gram-positive and Gram-negative bacteria. The oil exhibited moderate activity against the tested bacteria.__________Published in Khimiya Prirodnykh Soedinenii, No. 2, pp. 138–140, March–April, 2005.     

Synthesis of novel dibenzo-2,6,9-triazabicyclo[3.3.1]nonanes from <Emphasis Type="Italic">o</Emphasis>-tosylamino- and <Emphasis Type="Italic">o</Emphasis>-mesylaminobenzaldehydes

Condensation of o-tosylaminobenzaldehyde with γ-aminobutyric, 4-aminophenylthioacetic, and p-aminobenzoic acids and β-alanine gave 6,12-epimino-5,11-ditosyl-5,6,11,12-tetrahydrodibenzo[b, f]-1,5-diazocines with carboxyl-containing substituents at the bridging N atoms. The structures of three products were examined by X-ray diffraction analysis. Condensation of o-mesylaminobenzaldehyde (prepared by the McFadyen-Stevens reaction) with NH₄OAc and primary amines afforded 6,12-epimino-5,11-dimesyl-5,6,11,12-tetrahydrodibenzo[b, f]-1,5-diazocine derivatives.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 2165–2171, October, 2004.     

Targeting programmed cell death 4 (PDCD4) with biogenic compounds in ARDS by Gaussian process‐based QSAR virtual screening

The programmed cell death 4 (PDCD4) has recently been recognized as a new and attractive target of acute respiratory distress syndrome. Here, we attempted to discover new and potent PDCD4 mediator ligands from biogenic compounds using a synthetic strategy of statistical virtual screening and experimental affinity assay. In the procedure, a Gaussian process‐based quantitative structure‐activity relationship regression predictor was developed and validated statistically based on a curated panel of structure‐based protein‐ligand affinity data. The predictor was integrated with pharmacokinetics analysis, chemical redundancy reduction, and flexible molecular docking to perform high‐throughput virtual screening against a distinct library of chemically diverse, drug‐like biogenic compounds. Consequently, 6 hits with top scores were selected, and their binding affinities to the recumbent protein of human PDCD4 were identified, 3 out of which were determined to have high or moderate affinity with K_d at micromolar level. Structural analysis of protein‐ligand complexes revealed that hydrophobic interactions and van der Waals contacts are the primary chemical forces to stabilize the complex architecture of PDCD4 with these mediator ligands, while few hydrogen bonds, salt bridges, and/or π‐π stacking at the complex interfaces confer selectivity and specificity for the protein‐ligand recognition. It is suggested that the statistical Gaussian process‐based quantitative structure‐activity relationship screening strategy can be successfully applied to rational discovery of biologically active compounds. The newly identified molecular entities targeting PDCD4 are considered as promising lead scaffolds to develop novel chemical therapeutics for acute respiratory distress syndrome.     

GPCR structure-based virtual screening approach for CB2 antagonist search

The potential for therapeutic specificity in regulating diseases has made cannabinoid (CB) receptors one of the most important G-protein-coupled receptor (GPCR) targets in search for new drugs. Considering the lack of related 3D experimental structures, we have established a structure-based virtual screening protocol to search for CB2 bioactive antagonists based on the 3D CB2 homology structure model. However, the existing homology-predicted 3D models often deviate from the native structure and therefore may incorrectly bias the in silico design. To overcome this problem, we have developed a 3D testing database query algorithm to examine the constructed 3D CB2 receptor structure model as well as the predicted binding pocket. In the present study, an antagonist-bound CB2 receptor complex model was initially generated using flexible docking simulation and then further optimized by molecular dynamic and mechanical (MD/MM) calculations. The refined 3D structural model of the CB2-ligand complex was then inspected by exploring the interactions between the receptor and ligands in order to predict the potential CB2 binding pocket for its antagonist. The ligand-receptor complex model and the predicted antagonist binding pockets were further processed and validated by FlexX-Pharm docking against a testing compound database that contains known antagonists. Furthermore, a consensus scoring (CScore) function algorithm was established to rank the binding interaction modes of a ligand on the CB2 receptor. Our results indicated that the known antagonists seeded in the testing database can be distinguished from a significant amount of randomly chosen molecules. Our studies demonstrated that the established GPCR structure-based virtual screening approach provided a new strategy with a high potential for in silico identifying novel CB2 antagonist leads based on the homology-generated 3D CB2 structure model.