Investigation of anticancer activity of macrocyclic Schiff bases by means of 4D-QSAR based on simplex representation of molecular structure

Simplex representation of molecular structure as universal QSAR/QSPR tool

We review the development and application of the Simplex approach for the solution of various QSAR/QSPR problems. The general concept of the simplex method and its varieties are described. The advantages of utilizing this methodology, especially for the interpretation of QSAR/QSPR models, are presented in comparison to other fragmentary methods of molecular structure representation. The utility of SiRMS is demonstrated not only in the standard QSAR/QSPR applications, but also for mixtures, polymers, materials, and other complex systems. In addition to many different types of biological activity (antiviral, antimicrobial, antitumor, psychotropic, analgesic, etc.), toxicity and bioavailability, the review examines the simulation of important properties, such as water solubility, lipophilicity, as well as luminescence, and thermodynamic properties (melting and boiling temperatures, critical parameters, etc.). This review focuses on the stereochemical description of molecules within the simplex approach and details the possibilities of universal molecular stereo-analysis and stereochemical configuration description, along with stereo-isomerization mechanism and molecular fragment "topography" identification.

Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback?

A key question confronting computational chemists concerns the preferable ligand geometry that fits complementarily into the receptor pocket. Typically, the postulated ‘bioactive’ 3D ligand conformation is constructed as a ‘sophisticated guess’ (unnecessarily geometry-optimized) mirroring the pharmacophore hypothesis—sometimes based on an erroneous prerequisite. Hence, 4D-QSAR scheme and its ‘dialects’ have been practically implemented as higher level of model abstraction that allows the examination of the multiple molecular conformation, orientation and protonation representation, respectively. Nearly a quarter of a century has passed since the eminent work of Hopfinger appeared on the stage; therefore the natural question occurs whether 4D-QSAR approach is still appealing to the scientific community? With no intention to be comprehensive, a review of the current state of art in the field of receptor-independent (RI) and receptor-dependent (RD) 4D-QSAR methodology is provided with a brief examination of the ‘mainstream’ algorithms. In fact, a myriad of 4D-QSAR methods have been implemented and applied practically for a diverse range of molecules. It seems that, 4D-QSAR approach has been experiencing a promising renaissance of interests that might be fuelled by the rising power of the graphics processing unit (GPU) clusters applied to full-atom MD-based simulations of the protein-ligand complexes.

Cinnamaldehyde Analogs: Docking Based Optimization, COX-2 Inhibitory In Vivo and In Vitro Studies

BACKGROUND

In the past decade CADD has emerged as a rational approach in drug development so with the help molecular docking approach we planned to perform virtual screening of the designed data set of Schiff bases of cinnamaldehyde. The research work will be helpful to put some light on the drug receptor interactions required for anti-inflammatory activity.

METHODS

For carrying out virtual screening of the developed cinnamaldehyde Schiff base data set, AutoDock 4.0 was used. The active hits identified through in silico screening were synthesized. Anti-inflammatory evaluation was carried out using Carrageenan-induced paw oedema method.

RESULTS

Compounds V2A44, V2A55, V2A76, V2A82, V2A119, V2A141 and V2A142 has shown highest binding energy (-4.84, -4.76, -4.59, -4.78, -4.74, -4.85 and -4.72 kcal/mol, respectively) and the binding interactions with amino acids namely, Phe478, Glu479, Lys492, Ala493, Asp497 and Ile498. Some of the analogs have shown significant activity and were comparable to Indomethacin (standard drug).

CONCLUSION

Five new compounds have shown significant activity and the results obtained from in silico studies are parallel to those of in vivo studies.

Synthetic Musks: A Class of Commercial Fragrance Additives in Personal Care Products (PCPs) Causing Concern as Emerging Contaminants

Synthetic musks (SMs) are promising fragrance additives used in personal care products (PCPs). The widespread presence of SMs in environmental media remains a serious risk because of their harmful effects. Recently, the environmental hazards of SMs have been widely reported in various environmental samples including those from coastal and marine regions. This paper provides a systematic review of SMs, including their classification, synthetic routes, analysis and occurrence in environmental samples, fate and toxicity in the environment, as well as the associated risk assessment and pollution control. Research gaps and future opportunities were also identified with the hope of raising interest in this topic.

Computer-Aided Discovery and Characterization of Novel Ebola Virus Inhibitors

The Ebola virus (EBOV) causes severe human infection that lacks effective treatment. A recent screen identified a series of compounds that block EBOV-like particle entry into human cells. Using data from this screen, quantitative structure-activity relationship models were built and employed for virtual screening of a ∼17 million compound library. Experimental testing of 102 hits yielded 14 compounds with IC₅₀ values under 10 μM, including several sub-micromolar inhibitors, and more than 10-fold selectivity against host cytotoxicity. These confirmed hits include FDA-approved drugs and clinical candidates with non-antiviral indications, as well as compounds with novel scaffolds and no previously known bioactivity. Five selected hits inhibited BSL-4 live-EBOV infection in a dose-dependent manner, including vindesine (0.34 μM). Additional studies of these novel anti-EBOV compounds revealed their mechanisms of action, including the inhibition of NPC1 protein, cathepsin B/L, and lysosomal function. Compounds identified in this study are among the most potent and well-characterized anti-EBOV inhibitors reported to date.

In vitro cytotoxicity activity of novel Schiff base ligand-lanthanide complexes

A Schiff base ligand (SBL), N², N³-bis (anthracen-9-ylmethylene) pyridine-2, 3-diamine, was synthesized through the condensation of 2,6-diaminopyridine and anthracene-9-carbaldehyde using a 1:2 ratio. ¹H NMR spectra confirmed the observation of non-involvement aromatic carboxylic proton in SBL. A novel series of lanthanide (i.e., praseodymium (Pr), erbium (Er), and ytterbium (Yb))-based SBL metal complexes was successfully synthesized, and their functional groups were elaborately demonstrated using UV–visible, Fourier transform infrared (FT-IR), and fluorescence spectroscopy analyses. FT-IR spectral studies revealed that SBL behaved as a bidentate ligand and it was structured with metal ions by the two azomethine nitrogens. The synthesized SBL-based metal complexes were elaborately performed for cytotoxicity activity versus Vero, human breast cancer (MCF7), and cervical (HeLa) anticancer cell lines.

xMaP-An Interpretable Alignment-Free Four-Dimensional Quantitative Structure-Activity Relationship Technique Based on Molecular Surface Properties and Conformer Ensembles

A novel alignment-free molecular descriptor called xMaP (flexible MaP descriptor) is introduced. The descriptor is the advancement of the previously published translationally and rotationally invariant three-dimensional (3D) descriptor MaP (mapping property distributions onto the molecular surface) to the fourth dimension (4D). In addition to MaP, xMaP is independent of the chosen starting conformation of the encoded molecules and is therefore entirely alignment-free. This is achieved by using ensembles of conformers, which are generated by conformational searches. This step of the procedure is similar to Hopfinger's 4D quantitative structure-activity relationship (QSAR). A five-step procedure is used to compute the xMaP descriptor. First, a conformational search for each molecule is carried out. Next, for each of the conformers an approximation to the molecular surface with equally distributed surface points is computed. Third, molecular properties are projected onto this surface. Fourth, areas of identical properties are clustered to so-called patches. Fifth, the spatial distribution of the patches is converted into an alignment-free descriptor that is based on the entire conformer ensemble. The resulting descriptor can be interpreted by superimposing the most important descriptor variables and the molecules of the data set. The most important descriptor variables are identified with chemometric regression tools. The novel descriptor was applied to several benchmark data sets and was compared to other descriptors and QSAR techniques comprising a binary fingerprint, a topological pharmacophore descriptor (Cats2D), and the field-based 3D-QSAR technique GRID/PLS which is alignment-dependent. The use of conformer ensembles renders xMaP very robust. It turns out that xMaP performs very well on (almost) all data sets and that the statistical results are comparable to GRID/PLS. In addition to that, xMaP can also be used to efficiently visualize the derived quantitative structure-activity relationships.

Databases and QSAR for Cancer Research

In this review, we take a survey of bioinformatics databases and quantitative structure-activity relationship studies reported in published literature. Databases from the most general to special cancer-related ones have been included. Most commonly used methods of structure-based analysis of molecules have been reviewed, along with some case studies where they have been used in cancer research. This article is expected to be of use for general bioinformatics researchers interested in cancer and will also provide an update to those who have been actively pursuing this field of research.

Synthesis and molecular modelling studies of phenyl linked oxadiazole-phenylhydrazone hybrids as potent antileishmanial agents

Molecular hybridization yielded phenyl linked oxadiazole-benzohydrazones hybrids 6-35 and were evaluated for their antileishmanial potentials. Compound 10, a 3,4-dihydroxy analog with IC₅₀ value of 0.95 ± 0.01 μM, was found to be the most potent antileishmanial agent (7 times more active) than the standard drug pentamidine (IC₅₀ = 7.02 ± 0.09 μM). The current series 6-35 conceded in the identification of thirteen (13) potent antileishmanial compounds with the IC₅₀ values ranging between 0.95 ± 0.01-78.6 ± 1.78 μM. Molecular docking analysis against pteridine reductase (PTR1) were also performed to probe the mode of action. Selectivity index showed that compounds with higher number of hydroxyl groups have low selectivity index. Theoretical stereochemical assignment was also done for certain derivatives by using density functional calculations.

Alarms about structural alerts

Structural alerts are widely accepted in chemical toxicology and regulatory decision support as a simple and transparent means to flag potential chemical hazards or group compounds into categories for read-across. However, there has been a growing concern that alerts disproportionally flag too many chemicals as toxic, which questions their reliability as toxicity markers. Conversely, the rigorously developed and properly validated statistical QSAR models can accurately and reliably predict the toxicity of a chemical; however, their use in regulatory toxicology has been hampered by the lack of transparency and interpretability. We demonstrate that contrary to the common perception of QSAR models as "black boxes" they can be used to identify statistically significant chemical substructures (QSAR-based alerts) that influence toxicity. We show through several case studies, however, that the mere presence of structural alerts in a chemical, irrespective of the derivation method (expert-based or QSAR-based), should be perceived only as hypotheses of possible toxicological effect. We propose a new approach that synergistically integrates structural alerts and rigorously validated QSAR models for a more transparent and accurate safety assessment of new chemicals.

Crystal structures, spectroscopic and theoretical study of novel Schiff bases of 2-(methylthiomethyl)anilines

New Schiff bases derived from p-methoxysalicylaldehyde and 2-(methylthiomethyl)anilines (substituted with methyl, methoxy, nitro) were synthesized and characterized by elemental analyses, FT-IR, NMR, electronic spectra and quantum chemical calculations. X-ray crystallography of two compounds showed the solid structures are stabilized by intramolecular and intermolecular H-bonds. The effect of OH⋯N interaction between the phenolic hydrogen and imine nitrogen on the proton and carbon NMR shifts, and the role of CH⋯O and CH⋯S contacts are discussed. The bond lengths and angles, (1)H and (13)C NMR data, E(LUMO-HOMO), dipole moments and polarizability of the compounds were predicted by density functional theory, DFT (B3LYP/6-31G∗∗) method. The experimental geometric parameters and the NMR shifts were compared with the calculated values, which gave good correlations. The electronic effects of aryl ring substituents (methyl, methoxy and nitro) on the properties of the resulting compounds, such as the color, NMR shifts, electronic spectra and the calculated energy band gaps, dipole moments and polarizability are discussed. Increase in electron density shifted the phenolic proton resonance to lower fields. The methoxy-substituted compound has a small dipole moment and subsequent large polarizability value. Highest polarity was indicated by the nitro compound which also showed high polarizability due to its larger size. The energy gaps obtained from E(LUMO-HOMO) calculations suggest these compounds may have applications as organic semiconducting materials.

QSAR modeling: where have you been? Where are you going to?

Quantitative structure-activity relationship modeling is one of the major computational tools employed in medicinal chemistry. However, throughout its entire history it has drawn both praise and criticism concerning its reliability, limitations, successes, and failures. In this paper, we discuss (i) the development and evolution of QSAR; (ii) the current trends, unsolved problems, and pressing challenges; and (iii) several novel and emerging applications of QSAR modeling. Throughout this discussion, we provide guidelines for QSAR development, validation, and application, which are summarized in best practices for building rigorously validated and externally predictive QSAR models. We hope that this Perspective will help communications between computational and experimental chemists toward collaborative development and use of QSAR models. We also believe that the guidelines presented here will help journal editors and reviewers apply more stringent scientific standards to manuscripts reporting new QSAR studies, as well as encourage the use of high quality, validated QSARs for regulatory decision making.

Synthesis, characterization, antimicrobial, DNA cleavage, and in vitro cytotoxic studies of some metal complexes of schiff base ligand derived from thiazole and quinoline moiety

A novel Schiff base ligand N-(4-phenylthiazol-2yl)-2-((2-thiaxo-1,2-dihydroquinolin-3-yl)methylene)hydrazinecarboxamide (L) obtained by the condensation of N-(4-phenylthiazol-2-yl)hydrazinecarboxamide with 2-thioxo-1,2-dihydroquinoline-3-carbaldehyde and its newly synthesized Cu(II), Co(II), Ni(II), and Zn(II) complexes have been characterized by elemental analysis and various spectral studies like FT-IR, (1)H NMR, ESI mass, UV-Visible, ESR, TGA/DTA, and powder X-ray diffraction studies. The Schiff base ligand (L) behaves as tridentate ONS donor and forms the complexes of type [ML(Cl)2] with square pyramidal geometry. The Schiff base ligand (L) and its metal complexes have been screened in vitro for their antibacterial and antifungal activities by minimum inhibitory concentration (MIC) method. The DNA cleavage activity of ligand and its metal complexes were studied using plasmid DNA pBR322 as a target molecule by gel electrophoresis method. The brine shrimp bioassay was also carried out to study the in vitro cytotoxicity properties for the ligand and its metal complexes against Artemia salina. The results showed that the biological activities of the ligand were found to be increased on complexation.

Spectroscopic and biological activities studies of bivalent transition metal complexes of Schiff bases derived from condensation of 1,4-phenylenediamine and benzopyrone derivatives

Many tools of analysis such as elemental analyses, infrared, ultraviolet-visible, electron spin resonance (ESR) and thermal analysis, as well as conductivity and magnetic susceptibility measurements were used to elucidate the structures of the newly prepared Co(II), Ni(II) and Cu(II) complexes with Schiff bases derived from the condensation of 1,4-phenylenediamine with 6-formyl-7-hydroxy-5-methoxy-2-methylbenzo-pyran-4-one (H2L) or 5,7-dihydroxy-6-formyl-2-methylbenzopyran-4-one (H4L). The data showed that all formed complexes are 1:1 or 2:2 (M:L) and non-electrolyte chelates. The Co(II) and Cu(II) complexes of the two Schiff bases were screened for antibacterial activities by the disk diffusion method. The antibacterial activity was screened using Escherichia coli and Staphylococcus capitis but the antifungal activity was examined by using Aspergillus flavus and Candida albicans. The Results showed that the tested complexes have antibacterial, except CuH4L, but not antifungal activities.

Synthesis of 5-arylidine amino-1,3,4-thiadiazol-2-[(N-substituted benzyol)]sulphonamides endowed with potent antioxidants and anticancer activity induces growth inhibition in HEK293, BT474 and NCI-H226 cells

Abstract

A series of imines 5-amino-1,3,4-thiadiazol-2-[(N-substituted benzyol)]sulphonamide derivatives were synthesized from various aromatic aldehydes and substituted with benzoyl acetazolamides under different reaction conditions and were evaluated for their antioxidant and free radical scavenging, antimitotic activity by Allium cepa meristem root model and cytotoxicity activity against HEK 293 (human epidermal kidney cell line), BT474 (breast cancer cell line) and NCI-H226 (lung cancer cell line) by MTT assay. Some of the synthesized compounds showed moderately potent cytotoxicity compared to indisulam.

Graphical abstract

A series of imines 5-amino-1,3,4-thiadiazol-2-[(N-substituted benzyol)]sulphonamide derivatives (9a–j); 5-amino-1,3,4-thiadiazol-2-[N-(substituted benzoyl)]sulphonamide (4a–g); 5-(4-acetamido phenyl sulphonamido)-1,3,4-thiadiazol-2-[N-(substituted benzoyl)]sulphonamide (6a–g); and 5-(4-amino phenyl sulphonamido)-1,3,4-thiadiazol-2-[N-(substituted benzoyl)]sulphonamide (7a–g) were synthesized from acetazolamide and were investigated for the in vitro anticancer by MTT assay, free radical scavenging and antimitotic activity by Allium cepa root meristem model. Experimental observations indicate that synthesized compounds were moderately potent anticancer agents.

Fluorescence Properties and Electrochemical Behavior of Some Schiff Bases Derived from N-Aminopyrimidine

A series of Schiff bases (L 1 , L 2 and L 3) were prepared by refluxing aromatic aldehydes with N-Aminopyrimidine derivatives in methanol and ethanol. The structures of synthesized compounds were characterized by FTIR, (1)H NMR, (13)C NMR and microanalysis. The electrochemical behaviors of the Schiff base ligands were also discussed. Moreover, the evaluation of absorption and emission properties of the structures were carried out in five different solvents. The products show visible absorption maxima in the range of 304-576 nm, and emission maxima from 636 to 736 nm in all solvents tested.

Synthesis, Spectroscopic Characterization and Biological Activities of Transition Metal Complexes Derived from a Tridentate Schiff Base

A new series of Cu (II), Ni (II), Co (II) and Zn (II) complexes have been synthesized from the Schiff base derived from 4-hydroxy-3-methoxybenzylidine-4-aminoantipyrine and 2-aminophenol. The structural features have been determined from their elemental analysis, magnetic susceptibility, molar conductance, Mass, IR, UV-Vis,1H-NMR,13C-NMR and ESR spectral studies. The redox behavior of the copper complex has been studied by cyclic voltammetry. The data confirm that the complexes have composition of ML2type. The electronic absorption spectral data of the complexes propose an octahedral geometry around the central metal ion. All the metal complexes with DNA structure were guided by the presence of inter-molecular C–HO and C–HN hydrogen bonds. The biological activity of the synthesized compounds were tested against the bacterial species such asBacillus subtilis, Staphylococcus aureus, Proteus vulgarisand fungal species such asCandida albicansby thewell-diffusionmethod.

Synthesis, biological evaluation, and molecular docking studies of 2,6-dinitro-4-(trifluoromethyl)phenoxysalicylaldoxime derivatives as novel antitubulin agents

A series of 2,6-dinitro-4-(trifluoromethyl)phenoxysalicylaldoxime derivatives (1h-20h) have been designed and synthesized, and their biological activities were also evaluated as potential antiproliferation and tubulin polymerization inhibitors. Among all the compounds, 2h showed the most potent activity in vitro, which inhibited the growth of MCF-7, Hep-G2 and A549 cell lines with IC(50) values of 0.70 ± 0.05, 0.68 ± 0.02 and 0.86 ± 0.05 μM, respectively. Compound 2h also exhibited significant tubulin polymerization inhibitory activity (IC(50)=3.06 ± 0.05 μM). The result of flow cytometry (FCM) demonstrated that compound 2h induced cell apoptosis. Docking simulation was performed to insert compound 2h into the crystal structure of tubulin at colchicine binding site to determine the probable binding model. Based on the preliminary results, compound 2h with potent inhibitory activity in tumor growth may be a potential anticancer agent.

Existing and Developing Approaches for QSAR Analysis of Mixtures

This review is devoted to the critical analysis of advantages and disadvantages of existing mixture descriptors and their usage in various QSAR/QSPR tasks. We describe good practices for the QSAR modeling of mixtures, data sources for mixtures, a discussion of various mixture descriptors and their application, recommendations about proper external validation specific for mixture QSAR modeling, and future perspectives of this field. The biggest problem in QSAR of mixtures is the lack of reliable data about the mixtures' properties. Various mixture descriptors are used for the modeling of different endpoints. However, these descriptors have certain disadvantages, such as applicability only to 1 : 1 binary mixtures, and additive nature. The field of QSAR of mixtures is still under development, and existing efforts could be considered as a foundation for future approaches and studies. The usage of non-additive mixture descriptors, which are sensitive to interaction effects, in combination with best practices of QSAR model development (e.g., thorough data collection and curation, rigorous external validation, etc.) will significantly improve the quality of QSAR studies of mixtures.

QSAR analysis of [(biphenyloxy)propyl]isoxazoles: agents against coxsackievirus B3

BACKGROUND

Antiviral drugs are urgently needed for the treatment of acute and chronic diseases caused by enteroviruses such as coxsackievirus B3 (CVB3). The main goal of this study is quantitative structure-activity relationship (QSAR) analysis of anti-CVB3 activity (clinical CVB3 isolate 97927 [log IC50, µM]) and investigation of the selectivity of 25 ([biphenyloxy]propyl)isoxazoles, followed by computer-aided design and virtual screening of novel active compounds.

DISCUSSION

The 2D QSAR obtained models are quite satisfactory (R(2) = 0.84-0.99, Q(2) = 0.76-0.92, R(2)(ext) = 0.62-0.79). Compounds with high antiviral activity and selectivity have to contain 5-trifluoromethyl-[1,2,4]oxadiazole or 2,4-difluorophenyl fragments. Insertion of 2,5-dimethylbenzene, napthyl and especially biphenyl substituents into investigated compounds substantially decreases both their antiviral activity and selectivity. Several compounds were proposed as a result of design and virtual screening. A high level of activity of 2-methoxy-1-phenyl-1H-imidazo[4,5-c]pyridine (sm428) was confirmed experimentally.

CONCLUSION

Simplex representation of molecular structure allows successful QSAR analysis of anti-CVB3 activity of ([biphenyloxy]propyl)isoxazole derivatives. Two possible ways of battling CVB3 are considered as a future perspective.

QSAR analysis of the toxicity of nitroaromatics in Tetrahymena pyriformis: structural factors and possible modes of action

The Hierarchical Technology for Quantitative Structure-Activity Relationships (HiT QSAR) was applied to 95 diverse nitroaromatic compounds (including some widely known explosives) tested for their toxicity (50% inhibition growth concentration, IGC₅₀) against the ciliate Tetrahymena pyriformis. The dataset was divided into subsets according to putative mechanisms of toxicity. The Classification and Regression Trees (CART) approach implemented within HiT QSAR has been used for prediction of mechanism of toxicity for new compounds. The resulting models were shown to have ~80% accuracy for external datasets indicating that the mechanistic dataset division was sensible. The Partial Least Squares (PLS) statistical approach was then used to develop 2D QSAR models. Validated PLS models were explored to: (1) elucidate the effects of different substituents in nitroaromatic compounds on toxicity; (2) differentiate compounds by probable mechanisms of toxicity based on their structural descriptors; and (3) analyse the role of various physical-chemical factors responsible for compounds' toxicity. Models were interpreted in terms of molecular fragments promoting or interfering with toxicity. It was also shown that mutual influence of substituents in benzene ring plays the determining role in toxicity variation. Although chemical mechanism based models were statistically significant and externally predictive (r²(ext) = 0.64 for the external set of 63 nitroaromatics identified after all calculations have been completed), they were also shown to have limited coverage (57% for modelling and 76% for external set).

Per aspera ad astra: application of Simplex QSAR approach in antiviral research

This review explores the application of the Simplex representation of molecular structure (SiRMS) QSAR approach in antiviral research. We provide an introduction to and description of SiRMS, its application in antiviral research and future directions of development of the Simplex approach and the whole QSAR field. In the Simplex approach every molecule is represented as a system of different simplexes (tetratomic fragments with fixed composition, structure, chirality and symmetry). The main advantages of SiRMS are consideration of the different physical–chemical properties of atoms, high adequacy and good interpretability of models obtained and clear procedures for molecular design. The reliability of developed QSAR models as predictive virtual screening tools and their ability to serve as the basis of directed drug design was validated by subsequent synthetic and biological experiments. The SiRMS approach is realized as the complex of the computer program ‘HiT QSAR’, which is available on request.

New QSPR equations for prediction of aqueous solubility for military compounds

The development of a new quantitative structure-property relationship (QSPR) model to predict aqueous solubility (S(w)) accurately for compounds of military interest is presented. The ability of the new model to predict solubility is assessed and compared to available experimental data. A large set of structurally diverse organic compounds was used in this analysis. SiRMS methodology was employed to develop PLS models based on 135 training compounds and predictive accuracy was tested for 155 compounds selected for that purpose. The use of descriptors calculated only from the 2D level of representation of molecular structure produces a well-fitted and robust QSPR model (R(2)=0.90; Q(2)=0.87). Predictive ability for the model produced in this study on external test set (R(test)(2)=0.81) is comparable to the predictive ability of EPI Suite 4.0. Consensus solubility predictions using SiRMS and EPI models for 25 compounds of military interest (not included into the training set) have been completed.

Antileishmanial, antimicrobial and antifungal activities of some new aryl azomethines

A series of eighteen azomethines has been synthesized by the reaction of appropriate primary aromatic amines with aryl and/or heteroaryl carboxaldehydes. The synthesized azomethines have been evaluated for their in vitro antileishmanial, antibacterial and antifungal activities. The results revealed some antifungal activity of most of the synthesized compounds, whereas the antileishmaniasis activity results highlighted that all synthesized azomethines inhibited parasite growth and most of them showed highly potent action towards Leishmania major promastigotes. No remarkable bactericidal activities were observed.

QSPR Analysis of Peroxidase Substrates Reactivity

Quantitative structure-property relationship (QSPR) analysis of phenol derivatives reactivity in the horseradish peroxidase catalyzed oxidative reactions was carried out. The statistic models, which describe the substituted phenols reactivity (Кm-1, Vmax) quite adequately, were obtained by multiple linear regression and partial least squares (PLS) methods. The electronic parameters of molecules, their lipophylicity, molecular refraction, and form parameters were used as descriptors for molecular structure. The obtained models allow to predict the reactivity of the new phenolic substrates with satisfactory reliability.

Virtual Screening and Molecular Design Based on Hierarchical Qsar Technology

This chapter is devoted to the hierarchical QSAR technology (HiT QSAR) based on simplex representation of molecular structure (SiRMS) and its application to different QSAR/QSPR tasks. The essence of this technology is a sequential solution (with the use of the information obtained on the previous steps) of the QSAR paradigm by a series of enhanced models based on molecular structure description (in a specific order from 1D to 4D). Actually, it’s a system of permanently improved solutions. Different approaches for domain applicability estimation are implemented in HiT QSAR. In the SiRMS approach every molecule is represented as a system of different simplexes (tetratomic fragments with fixed composition, structure, chirality, and symmetry). The level of simplex descriptors detailed increases consecutively from the 1D to 4D representation of the molecular structure. The advantages of the approach presented are an ability to solve QSAR/QSPR tasks for mixtures of compounds, the absence of the “molecular alignment” problem, consideration of different physical–chemical properties of atoms (e.g., charge, lipophilicity), and the high adequacy and good interpretability of obtained models and clear ways for molecular design. The efficiency of HiT QSAR was demonstrated by its comparison with the most popular modern QSAR approaches on two representative examination sets. The examples of successful application of the HiT QSAR for various QSAR/QSPR investigations on the different levels (1D–4D) of the molecular structure description are also highlighted. The reliability of developed QSAR models as the predictive virtual screening tools and their ability to serve as the basis of directed drug design was validated by subsequent synthetic, biological, etc. experiments. The HiT QSAR is realized as the suite of computer programs termed the “HiT QSAR” software that so includes powerful statistical capabilities and a number of useful utilities.

[Artificial ribonucleases: quantitative analysis of the structure-activity relationship and new insight into the strategy of design of highly efficient RNase mimetics]

The dependence of hydrolytic activity of artificial ribonucleases toward an HIV-I RNA fragment, a 21-mer oligonucleotide, and tRNA Asp on the structure of the RNase mimetic was analyzed. The quantitative structure-activity relationship (QSAR task) was determined by the method of simplex representation of the molecular structure where the amounts of four-atom fragments (simplexes) of fixed structure, symmetry, and chirality served as descriptors. Not only the types of atoms participating in simplexes but also their physicochemical properties (e.g., partial charges, lipophilicities, etc.) were taken into account. This allowed the estimation of the relative role of various factors affecting the interaction of molecules under study with the corresponding biological target. The 2D QSAR models obtained by the method of projection to latent structures have quite satisfactory statistical indices (R2 = 0.82-0.96; Q2 = 0.73-0.89), which help predict the activities of new compounds. The electrostatic properties of ribonuclease atoms were shown to contribute significantly to the manifestation of the hydrolytic activity of ribonucleases in the case of the 21-mer oligonucleotide and tRNA. In addition, the structural fragments that most greatly contribute to the alteration of the hydrolytic activity of RNases were identified. The models obtained were used for the virtual screening and molecular design of new highly efficient RNase mimetics.