Technique for energy decomposition in the study of "receptor-ligand" complexes

The Influence of the Functional Group on the Physicochemical and Biological Properties of New Phenanthro[9,10-d]-Imidazole Derivatives

The search for safe, cheap, and repeatable diagnostic methods is a fundamental research goal. Currently, great hope is placed on fluorescence imaging. However, the development of this method mainly depends on efficient fluorescent probes. Designing and obtaining new probes with potential applications in fluorescence imaging is very difficult because compounds of this type must meet several requirements related to their properties. Therefore, this article attempted to obtain and study new phenanthro[9,10-d]-imidazole derivatives (PK1-PK3) with potential application as fluorescent probes for fluorescence imaging. The main goal of the work was to assess the effect of two functional groups (such as the formyl group (PK2) and rhodanine-3-acetic acid (PK3)) on selected physicochemical properties and possibilities of practical application of the considered compounds. The conducted studies proved that the influence of the functional group is significant, as it causes a bathochromic shift in both absorption and emission results (by the order PK1 < PK2 < PK3). Moreover, all compounds could stain live cells cultured in vitro. The staining efficiency was not affected by the cell line, thanks to which we obtained the correct staining of both mouse and human cell lines. PK3 was the most attractive of the tested compounds due to its staining potential of live cells and retention after fixation. Our results also showed some antibacterial and antifungal activity of the newly synthesized compounds (PK1-PK3). Among them, PK3 showed the highest antimicrobial effect, especially against Gram-positive bacteria.

Can a Small Change in the Heterocyclic Substituent Significantly Impact the Physicochemical and Biological Properties of (Z)-2-(5-Benzylidene-4-oxo-2-thioxothiazolidin-3-yl)acetic Acid Derivatives?

Rhodanine-3-acetic acid derivatives are attractive compounds with versatile effects. What is very important is that compounds of this type have many biological properties. They are tested, among others, as fluorescent probes for bioimaging and aldose reductase inhibitors. Rhodanine-3-acetic acid derivatives also have antibacterial, antifungal and anticancer activity. The presented work demonstrates that a slight change in the five-membered heterocyclic substituent significantly affects the properties of the compounds under consideration. Three rhodanine-3-acetic acid derivatives (A-1-A-3) were obtained in the Knoevenagel condensation reaction with good yields, ranging from 54% to 71%. High thermal stability of the tested compounds was also demonstrated above 240 °C. The absorption and emission maxima in polar and non-polar solvents were determined. Then, the possibility of using the considered derivatives for fluorescence bioimaging was checked. Compounds A-1 and A-2 were successfully used as fluorescent dyes of fixed cells of mammalian origin. In addition, biological activity tests against bacteria and fungi were carried out. Our results showed that A-1 and A-2 showed the most excellent antimicrobial activity among the newly synthesized compounds, especially against Gram-positive bacteria.

The design of compounds with desirable properties - The anti-HIV case study

Efficacy and safety are among the most desirable characteristics of an ideal drug. The tremendous increase in computing power and the entry of artificial intelligence into the field of computational drug design are accelerating the process of identifying, developing, and optimizing potential drugs. Here, we present novel approach to design new molecules with desired properties. We combined various neural networks and linear regression algorithms to build models for cytotoxicity and anti-HIV activity based on Continual Molecular Interior analysis (CoMIn) and Cinderella's Shoe (CiS) derived molecular descriptors. After validating the reliability of the models, a genetic algorithm was coupled with the Des-Pot Grid algorithm to generate new molecules from a predefined pool of molecular fragments and predict their bioactivity and cytotoxicity. This combination led to the proposal of 16 hit molecules with high anti-HIV activity and low cytotoxicity. The anti-SARS-CoV-2 activity of the hits was predicted.

Platinum(IV) compounds as potential drugs: a quantitative structure-activity relationship study

Introduction

Machine learning methods, coupled with a tremendous increase in computer power in recent years, are promising tools in modern drug design and drug repurposing.

Methods

Machine learning predictive models, publicly available at chemosophia.com, were used to predict the bioactivity of recently synthesized platinum(IV) complexes against different kinds of diseases and medical conditions. Two novel QSAR models based on the BiS algorithm are developed and validated, capable to predict activities against the SARS-CoV virus and its RNA dependent RNA polymerase.

Results

The internal predictive power of the QSAR models was tested by 10-fold cross-validation, giving cross-R2 from 0.863 to 0.903. 38 different activities, ranging from antioxidant, antibacterial, and antiviral activities, to potential anti-inflammatory, anti-arrhythmic and anti-malarial activity were predicted for a series of eighteen platinum(IV) complexes.

Conclusion

Complexes 1, 3 and 13 have high generalized optimality criteria and are predicted as potential SARS-CoV RNA dependent RNA polymerase inhibitors.

Debelalactone Prevents Hepatic Cancer via Diminishing the Inflammatory Response and Oxidative Stress on Male Wistar Rats

The current study was conducted to exemplify the effect of debelalactone on tissue protection, chronic hepatic inflammation, hepatic protection and oxidative stress induced by diethyl nitrosamine in Wistar rats. Therefore, DEN (200 mg/kg) was used for the induction the hepatocellular carcinoma (HCC) and the level of serum alpha fetoprotein was used for the estimation and confirmation of HCC. The study illustrated that debelalactone (DL) significantly downregulated the hepatic, non-hepatic parameters such as aspartate aminotransferase, alanine aminotransferase, alpha fetoprotein, NO levels, total protein, albumin, blood urea nitrogen, total bilirubin, and direct bilirubin in dose dependent manner, as well as noticeably improving the body weight, of treated animals. The macroscopically observation of DEN-induced rat liver showed the formation of informalities in liver tissue, which was reduced with treatment of DL at dose dependent manner. However, antioxidant markers and inflammatory mediators such as lipid peroxidation, catalase, superoxide dismutase, glutathione peroxidase and transferase, TNF-α, IL-1β, IL-6, and NF-kB restored up to the normal level by DL. The histopathology studies showed that the treated group of animals returned to a normal status. Collectively, it can be concluded that debelalactone mediated chemoprevention in the DEN-induced rats via an increase in the activities of endogenous enzymes and/or inhibition the precancerous cells.

Repurposing Based Identification of Novel Inhibitors against MmpS5-MmpL5 Efflux Pump of Mycobacterium smegmatis: A Combined In Silico and In Vitro Study

In the current era of a pandemic, infections of COVID-19 and Tuberculosis (TB) enhance the detrimental effects of both diseases in suffering individuals. The resistance mechanisms evolving in Mycobacterium tuberculosis are limiting the efficiency of current therapeutic measures and pressurizing the stressed medical infrastructures. The bacterial efflux pumps enable the development of resistance against recently approved drugs such as bedaquiline and clofazimine. Consequently, the MmpS5-MmpL5 protein system was selected because of its role in efflux pumping of anti-TB drugs. The MmpS5-MmpL5 systems of Mycobacterium smegmatis were modelled and the virtual screening was performed using an ASINEX library of 5968 anti-bacterial compounds. The inhibitors with the highest binding affinities and QSAR based highest predicted inhibitory concentration were selected. The MmpS5-MmpL5 associated systems with BDE_26593610 and BDD_27860195 showed highest inhibitory parameters. These were subjected to 100 ns Molecular Dynamics simulations and provided the validation regarding the interaction studies. The in vitro studies demonstrated that the BDE_26593610 and BDD_27860195 can be considered as active inhibitors for M. smegmatis MmpS5-MmpL5. The outcomes of this study can be utilized in other experimentation aimed at drug design and discovery against the drug resistance strains of M. tuberculosis.

A new glimpse on the active site of SARS-CoV-2 3CLpro, coupled with drug repurposing study

Coronavirus disease 2019 (COVID-19) is caused by novel severe acute respiratory syndrome coronavirus (SARS-CoV-2). Its main protease, 3C-like protease (3CLpro), is an attractive target for drug design, due to its importance in virus replication. The analysis of the radial distribution function of 159 3CLpro structures reveals a high similarity index. A study of the catalytic pocket of 3CLpro with bound inhibitors reveals that the influence of the inhibitors is local, perturbing dominantly only residues in the active pocket. A machine learning based model with high predictive ability against SARS-CoV-2 3CLpro is designed and validated. The model is used to perform a drug-repurposing study, with the main aim to identify existing drugs with the highest 3CLpro inhibition power. Among antiviral agents, lopinavir, idoxuridine, paritaprevir, and favipiravir showed the highest inhibition potential. Enzyme - ligand interactions as a key ingredient for successful drug design.

Interplay of the Ring and Steric Strains in the Highly Substituted Cyclopropanes

Using the concept of a complete set of homodesmotic reactions for the analysis of molecular energetics of polysubstituted methyl- and fluorocyclopropanes allows assessing the strain energy SE of cyclopropanes, free from interfering effects, in full accordance with the IUPAC definition ("relative to a reference ... hypothetical 'strainless' structure"). The correct SE calculation requires quantifying nonvalence interactions in the products of formal homodesmotic reactions (HDRs) using a routine multiregression analysis. The complete HDR set provides the information necessary for the analysis, namely, the heat effects of HDRs calculated by the G4 composite method and the wide set of reference compounds with various combinations of nonvalence effects. We have found that the SE value for methylcyclopropanes lies in the range from 117.0 (1.1-dimethylcyclopropane) to 146.1 kJ/mol (hexamethylcyclopropane). It is the sum of the ring strain energy RSE = 117.9 ± 0.3 kJ mol, which does not depend on the number of methyl substituents, and the Pitzer strain energy of 4.4±0.1 kJ/mol per one contact (the standard deviation is shown as an error of determination). In the series of fluorocyclopropanes, SE varies from 137.9 (monosubstituted cyclopropane) to 260.0 kJ/mol (hexafluorocyclopropane) and well correlates with the ∑DBCP parameter deduced from the QTAIM analysis of the electron density of the compound, representing the total deviation of bond critical points from geometrical C-C bond lines of CC bonds. The ∑DBCP parameter characterizes the curvature of banana-like bonds in cyclopropanes.

Effect of the Chloro-Substitution on Electrochemical and Optical Properties of New Carbazole Dyes

Carbazole derivatives are the structural key of many biologically active substances, including naturally occurring and synthetic ones. Three novel (E)-2-(2-(4-9H-carbazol-9-yl)benzylidene)hydrazinyl)triazole dyes were synthesized with different numbers of chlorine substituents attached at different locations. The presented research has shown the influence of the number and position of attachment of chlorine substituents on electrochemical, optical, nonlinear, and biological properties. The study also included the analysis of the use of the presented derivatives as potential fluorescent probes for in vivo and in vitro tests. Quantum-chemical calculations complement the conducted experiments.

Design, synthesis, antibacterial evaluation, and computational studies of hybrid oxothiazolidin-1,2,4-triazole scaffolds

Bacterial infections are a serious threat to human health due to the development of resistance against the presently used antibiotics. The problem of growing and widespread antibiotic resistance is only getting worse with the shortage of new classes of antibiotics, creating a substantial unmet medical need in the treatment of serious bacterial infections. Therefore, in the present work, we report 18 novel hybrid thiazolidine-1,2,4-triazole derivatives as DNA gyrase inhibitors. The derivatives were synthesized by multistep organic synthesis and characterized by spectroscopic methods (¹ H and ¹³ C nuclear magnetic resonance and mass spectroscopy). The derivatives were tested for DNA gyrase inhibition, and the result emphasized that the synthesized derivatives have a tendency to inhibit the function of DNA gyrase. Furthermore, the compounds were also tested for antibacterial activity against three Gram-positive (Bacillus subtilis [NCIM 2063], Bacillus cereus [NCIM 2156], Staphylococcus aureus [NCIM 2079]) and two Gram-negative (Escherichia coli [NCIM 2065], Proteus vulgaris [NCIM 2027]) bacteria. The derivatives showed a significant-to-moderate antibacterial activity with noticeable antibiofilm efficacy. Quantitative structure-activity relationship (QSAR), ADME (absorption, distribution, metabolism, elimination) calculation, molecular docking, radial distribution function, and 2D fingerprinting were also performed to elucidate fundamental structural fragments essential for their bioactivity. These studies suggest that the derivatives 10b and 10n have lead antibacterial properties with significant DNA gyrase inhibitory efficacy, and they can serve as a starting scaffold for the further development of new broad-spectrum antibacterial agents.

Electronic properties investigation of human dihydrofolate reductase complexes with ligands

Despite the fact that there are already drugs for cancer, they still show strong toxicity to the human organism. That is why it is necessary to establish the factors affecting activity in order to develop new, more effective drugs aimed at tumor cells, minimizing harm to healthy cells. The present research is based on electronic properties calculation of the complexes using AlteQ approach. In the focus of this study are complexes of human dihydrofolate reductase (hDHFR) with a series of known inhibitors bound in the active site. Further, a statistical analysis was performed to establish the relationships between a myriad electronic characteristics and IC₅₀. The change in total volume and the change of own electrons number of hydrogen atoms in their atomic basins are identified as the descriptors correlating the most with the hDHFR inhibition potency. Additionally, two lipophilic parts of protein (Thr56, Ser59, Ile60 and Ile7, Val8, Ala9) were found, which act as a key factor in decreasing bioactivity. The depth analysis of intermolecular interactions showed that the interactions between water molecules and ligand play a crucial role in hDHFR inhibition. Furthermore, the molecular dynamics simulations were used for deeper understanding of the structural inhibition, each for 50 ns time scale in explicit water conditions. Thus, the AlteQ approach made it possible to determine the factors influencing the activity and evaluate them not only qualitatively, but also quantitatively.Communicated by Ramaswamy H. Sarma.

Modulation of benzofuran structure as a fluorescent probe to optimize linear and nonlinear optical properties and biological activities

The study presents the influence of structure modulation by introducing selected donor and acceptor substituents on optical properties of benzofuran used in biological imaging. As the starting form, 2-(5-formylbenzofuran-2-yl)acetamide described experimentally was used. This molecule contains an aldehyde group as reactive site, through which conjugation with protein occurs. Structure modulation was carried out by attaching additional electron-donating and electron-withdrawing substituents to the amino group, namely -NH2, -NHCH3, -NO2, -OH, and -OCH3. Studies have shown that the -NH2, -NHCH3, -OH, and -OCH3 substituents do not induce a significant change in the position of maximum absorption and fluorescence relative to each other. They also do not change the parameters describing the nonlinear response. Only the presence of the -NO2 substituent results in significant solvatochromic shifts. Changing substituents also does not significantly affect the LD50 value, and all tested fluorescent probes should not be considered toxic to humans. Modulation of the benzofuran derivative structure also does not change the active center in which the biocomplex with the protein is formed. In each case, the conjugation takes place via LYS114. In addition, the study was prompted to analyze the linear and nonlinear optical properties of conjugates formed after the reaction with Concanavalin A.Graphical abstract.

The study of EGFR-ligand complex electron property relationship with biological activity

The present investigation grounded on estimation of electron properties of the structures of EGFR proteins-ligand complexes using our laboratory-developed methodology AlteQ approach, which describes the molecular electron density of the complex in space for a certain point in three-dimensional coordinates. Briefly, the system embodies molecular electron density as a sum of Slater's type atomic increments of the molecular system. Further, using this methodology, we calculated different electron characteristics of selected EGFR protein-ligand complexes and established the relationship between different electron properties with their experimental pharmacological activity value (pIC₅₀). The study suggested that EGFR inhibitory activity has higher correlation with intermolecular contacts of H with pi-system of aromatic ring between protein and ligands. Therefore, this created model has impact to identify and design potential ligands against EGFR in anticancer drug discovery.Communicated by Ramaswamy H. Sarma.

Topological Analysis of Electron Density in Large Biomolecular Systems

BACKGROUND

A great step toward describing the structure of the molecular electron was made in the era of quantum chemical methods. Methods play a very important role in the prediction of molecular properties and in the description of the reactivity of compounds, which cannot be overestimated. There are many works, books, and articles on quantum methods, their applications, and comparisons. At the same time, quantum methods of a high level of theory, which give the most accurate results, are time-consuming, which makes them almost impossible to describe large complex molecular systems, such as macromolecules, enzymes, supramolecular compounds, crystal fragments, and so on.

OBJECTIVES

To propose an approach that allows real-time estimation of electron density in large systems, such as macromolecules, nanosystems, proteins.

METHODS

AlteQ approach was applied to the tolopogical analysis of electron density for "substrate - cytochrome" complexes. The approach is based on the use of Slater's type atomic contributions. Parameters of the atomic contributions were found using high resolution X-ray diffraction data for organic and inorganic molecules. Relationships of the parameters with atomic number, ionization potentials and electronegativities were determined. The sufficient quality of the molecular electron structure representation was shown under comparison of AlteQ predicted and observed electron densities. AlteQ algorithm was applied for evaluation of electron structure of "CYP3A4 - substrate" complexes modeled using BiS/MC restricted docking procedure. Topological analysis (similar to Atoms In Molecules (AIM) theory suggested by Richard F.W. Bader) of the AlteQ molecular electron density was carried out for each complex. The determination of (3,-1) bond, (3,+1) ring, (3,+3) cage critical points of electron density in the intermolecular "CYP3A4 - substrate" space was performed.

RESULTS

Different characteristics such as electron density, Laplacian eigen values, etc. at the critical points were computed. Relationship of pKM (KM is Michaelis constant) with the maximal value of the second Laplacian eigen value of electron density at the critical points and energy of complex formation computed using MM3 force field was determined.

CONCLUSION

It was shown that significant number of (3,-1) bond critical points are located in the intermolecular space between the enzyme site and groups of substrate atoms eliminating during metabolism processes.

Experimental and Computational Studies of Microwave-Assisted, Facile Ring Opening of Epoxide with Less Reactive Aromatic Amines in Nitromethane

Nucleophilic ring opening reactions of epoxides with aromatic amines are in the forefront of the synthetic organic chemistry research to build new bioactive scaffolds. Here, convenient, green, and highly efficient regioselective ring opening reactions of sterically hindered (2R,3S)-3-(N-Boc-amino)-1-oxirane-4-phenylbutane with various poorly reactive aromatic amines are accomplished under microwave irradiation in nitromethane. All the reactions effectively implemented for various aromatic amines involve the reuse of nitromethane that supports its dual role as a solvent and catalyst. The corresponding new β-alcohol analogs of hydroxyethylamine (HEA) are isolated in 41-98% yields. The reactions proceed under mild conditions for a broad range of less reactive and sterically hindered aromatic amines. Proton NMR experiments suggest that the nucleophilicity of amines is influenced by nitromethane, which is substantiated by the extensive computational studies. Overall, this methodology elucidates the first-time use of nitromethane as a solvent for the ring opening reactions under microwave conditions involving an equimolar ratio of epoxide and aromatic amine without any catalyst, facile ring opening of complex epoxide by less reactive aromatic amines, low reaction time, less energy consumption, recycling of the solvent, and simple workup procedures.

Novel radial distribution function approach in the study of point mutations: the HIV-1 protease case study

Background: Mutations are one of the engines of evolution. Under constant stress pressure, mutations can lead to the emergence of unwanted, drug-resistant entities. Methodology: The radial distribution function weighted by the number of valence shell electrons is used to design quantitative structure-activity relationship (QSAR) model relating descriptors with the inhibition constant for a series of wild-type HIV-1 protease inhibitor complexes. The residuals of complexes with mutant HIV-1 protease were correlated with the energy of the highest occupied molecular orbitals of the residues introduced to enzyme via point mutations. Conclusion: Successful identification of residues Ile3, Asp25, Val32 and Ile50 as the one whose substitution influences the inhibition constant the most, demonstrates the potential of the proposed methodology for the study of the effects of point mutations.

4-(4-Chloro-2-oxo-3(1H-phenanthro[9,10-d]imidazol-2-yl)-2H-chromen-6-yl) benzaldehyde as a fluorescent probe for medical imaging: linear and nonlinear optical properties

This study presents the full theoretical optical and biological characteristics of a new fluorescent probe based on the phenanthroimidazole backbone (PB5). The aldehyde group was selected as the active group to bind to the protein during conjugation. The new fluorescent probe is based on the phenanthroimidazole backbone; however, unlike previously presented works, as the chromophore part, it contains the first introduction of the 4-chloro-2H-chromen-2-one part. In order to achieve the best cognitive aspect, the study included not only the dye itself but also the concanavalin A conjugate. The linear and non-linear optical properties and biological activities described in this study clearly indicate that the presented dye is a promising material as a fluorescent probe in medical imaging.

2'-(1H-phenanthro[9,10-d]imidazol-2-yl)-phenyl-4-carboxylic acid N-hydroxysuccinimide ester: A new phenanthroimidazole derivative as a fluorescent probe for medical imaging applications

In this study a new probe (2'-(1H-phenanthro[9,10-d]imidazol-2-yl)-phenyl-4-carboxylic acid N-hydroxysuccinimide ester, PB1-1) was synthesized and presented, containing the ester group as reactive group for medical imaging applications. The tests included a comparison to the PB1 probe with the aldehyde group described earlier. Also, the photophysics of PB1 and PB1-1 when conjugated to albumin (HSA) and concanavalin A (Con A) was studied. The fluorescence anisotropy measurements and the method of fluorescence quenching of protein were used to examine these interactions. The results showed that both dyes are highly bound to the studied proteins, especially PB1-1. In the present study we also compared the stability of prepared conjugates. The in vitro study have shown that all tested compounds presented to be usable in the case of fixated cell staining. PB1-1-ConA and PB1-1-HSA were characterized with the lowest cytotoxicity during the MTT assay, and thus should be more suitable for live imaging applications than PB1-ConA and PB1-HSA. The results obtained in this work confirmed the theses presented in in silico studies as to the correctness of the choice of ester group as actively binding to the protein. At the same time, we have experimentally demonstrated the significant influence of a probe-protein linker on the spectral properties of conjugates used in medical imaging. We have clearly indicated that a detailed analysis of derivatives with different reactive group allows for proper probe selection. We also pointed out that based on the geometric skeleton of one dye, a whole range of fluorescent probes with different absorption and fluorescence spectra can be obtained for in vitro tests in medical imaging.

Performance of radial distribution function-based descriptors in the chemoinformatic studies of HIV-1 protease

Aim: This letter investigates the role of radial distribution function-based descriptors for in silico design of new drugs. Methodology: The multiple linear regression models for HIV-1 protease and its complexes with a series of inhibitors were constructed. A detailed analysis of major atomic contributions to the radial distribution function descriptor weighted by the number of valence shell electrons identified residues Arg8, Asp29 and residues of the catalytic triad as crucial for the correlation with the inhibition constant, together with residues Asp30 and Ile50, whose mutations are known to cause an emergence of drug resistant variants. Conclusion: This study demonstrates an easy and fast assessment of the activity of potential drugs and the derivation of structural information of their complexes with the receptor or enzyme.

The Influence of Hydrogen Atoms on the Performance of Radial Distribution Function-Based Descriptors in the Chemoinformatic Studies of HIV-1 Protease Complexes with Inhibitors

AIMS

The aim of this letter is to explore the influence of adding hydrogen atoms to the crystallographic structures of HIV-1 protease complexes with a series of inhibitors on the performance of radial distribution function based descriptors recently introduced in chemoinformatic studies.

BACKGROUND

Quite recently the successful application of molecular descriptors based on a radial distribution function to correlate it with biologically interesting properties of a ligand - enzyme complex was demonstrated. Except its predictive power, the analysis of atoms with dominant contributions to the RDFs can be used to identify relevant atoms and interactions. Since original paper was published on dataset consisting of the X-ray structures of complexes without hydrogen atoms, we wonder weather addition of light atoms can provide us new piece of information.

OBJECTIVE

The primarily objective is to create the model correlating the RDF based descriptors and physicochemical properties of the HIV-1 protease complexes with inhibitors with hydrogen atoms. Then, we will compare the performance of new model with previous one, where the hydrogen atoms were discarded. Information about interactions between the enzyme and the inhibitors will be extracted from the analysis of the RDF.

METHODS

The radial distribution function descriptor weighted by the number of valence shell electrons has proven to be sensitive to the changes in the structure of the enzyme and enzyme-ligand complexes. For each structure in our data set, RDF will be calculated and using multiple linear regression method the mathematical model will be designed correlating RDF based descriptors and the physicochemical properties. Statistical analysis of the atom's contribution to the total RDF will reveal relevant interactions.

RESULTS

The applicability of RDF based descriptor for the correlation with pKi and EC50 values is demonstrated, while simple models containing only two or three parameters are able to explain 78 and 86 % of the variance, respectively. The models with explicitly included hydrogens are of comparable quality with the previous models without hydrogens. The analysis of the atom's dominant contributions highlighted the importance of the hydroxyl groups of the inhibitor near the Asp25 and Asp25' residues when it is bounded to the protease.

CONCLUSION

Models based on the RDF weighted by the number of valence shell electrons for correlating small number of molecular descriptors and physicocehmical properties for structures with and without hydrogens are of comparable quality and both can be used for identification of relevant functional groups and interactions. Other: Our approach can be integrated to the next generation virtual screening methods, because is fast, reliable with high predictability potential.

Theoretical study of the surface structure of anatase nanoparticles: effect on dye adsorption and photovoltaic properties

The properties of TiO₂ can vary greatly, depending on the size and morphology of the particles used.

Optimizing the optical and biological properties of 6-(1H-benzimidazole)-2-naphthalenol as a fluorescent probe for the detection of thiophenols: a theoretical study

The study presents the influence of structure modulation by introduction of selected donor and acceptor substituents on the properties of 6-(1H-benzimidazole)-2(2,4-dinitrobenzenesulfonate)naphthalene used in thiophenol identification. The presence of –OH and –OR groups enhances the non-linear optics (NLO) response of the marker. The –NO₂ substituent maximizes the non-linear response and increases the amount of transferred charge and the charge-transfer distance. The introduction of the –OH, –NO₂ and –CN groups into the marker structure significantly improves the solubility and optical availability. The –NO₂ group however contributes to mutagenicity and carcinogenicity. The –OH and –OR groups can be successfully used in bioimaging to detect specific molecules containing the –SH group in their structure. At the same time, the –OR group minimizes the energy barrier necessary to break the bond between the chromophore and the linker. The paper also includes a comparison of optical and biological properties of structures before and after identification of thiophenols.

The study presents the influence of structure modulation by introduction of selected donor and acceptor substituents on the properties of 6-(1H-bezimidazole)-2(2,4-dinitrobenzenesulfonate)naphthalene used in thiophenol identification.

Nonparametric chemical descriptors for the calculation of ligand-biopolymer affinities with machine-learning scoring functions

The computational prediction of ligand-biopolymer affinities is a crucial endeavor in modern drug discovery and one that still poses major challenges. The choice of the appropriate computational method often reveals itself as a trade-off between accuracy and speed, with mathematical devices referred to as scoring functions being the fastest. Among the many shortcomings of scoring functions there is the lack of universal applicability to every molecular system. This is so largely due to their reliance on atom type perception and/or parametrization. This article proposes the use of nonparametric Model of Effective Radii of Atoms descriptors that can be readily computed for the entire Periodic Table and demonstrate that, in combination with machine learning algorithms, they can yield competitive performances and chemically meaningful insights.

Reactive group effects on the photophysical and biological properties of 2-phenyl-1H-phenanthro[9,10-d]imidazole derivatives as fluorescent markers

The presented research focuses on the theoretical design and procedures for preparing protein conjugates with markers. For this purpose a series of phenanthroimidazole (PhI) analogous compounds was designed and investigated by means of first principle methods. Through the judicious choice of cross-linking reagents and the selection of reactive groups, five target fluorescent probes were selected, one of which was previously described using in vitro tests. For the best cognitive purpose and understanding of the nature of the protein conjugation, the studies describe the impact of the reactive group on the solvatochromism, the polarity of the charge transfer of the excited states, the Stokes' shift, ECD spectra and two-photon cross sections. The research is also extended to an analysis of PhI-Concanavalin A biocomplexes and changes in photophysical properties after conjugation. In order to identify valuable alternatives to commercial probes designed for cellular labelling in biological and biomedical imaging, biological properties were described such as ecotoxicity, log P and log BCF, and dye-protein binding was quantified by means of AutoDock and molecular dynamics simulations. The study showed that for phenanthroimidazole derivatives the factor which limits the possibility of their use in medical imaging is the presence of a pyridyl disulfide group, while the introduction of an N-hydroxysuccinimide ester may be used to create stable and valuable fluorescent probes with a wide spectrum for applications in biomedical imaging.

Synthesis, photophysical and biological properties of a new oxazolone fluorescent probe for bioimaging: an experimental and theoretical study

In this study, a new oxazolone derivative 4-{N,N-bis[2-phenyl-4-benzylidene-1,3-oxazol-5(4H)-one]amino}benzaldehyde (PB3) was synthesized and investigated as a fluorescent dye. The spectroscopic properties in different solvents were thoroughly studied. The experimental data were supported by quantum-chemical calculations using density functional theory. Measurements and theoretical calculations showed that the PB3 dye is characterized by non-monotonic solvatochromism, a strongly polar charge transfer excited state, a large Stokes' shift, a high fluorescence quantum yield and a high fluorescence lifetime. Bioconjugate complexes (PB3-concanavalin A) were studied by circular dichroism (CD) spectroscopy. The results showed that the secondary structure of concanavalin A was not significantly influenced by the PB3-fluorophore. Conventional fluorescence microscopy imaging of Candida albicans cells, incubated with the PB3-concanavalin A, was demonstrated. The results from cytochemistry experiments demonstrate that the PB3 dye has valuable advantages compared to the other long-wavelength dyes in typical fluorescence-based cell labeling applications. In vitro tolerance was evaluated by the MTT method in the human colon adenocarcinoma cell line HT29. The PB3 and bioconjugate complexes (PB3-concanavalin A), in the range of concentrations tested, were not considerably toxic. The AutoDock simulations showed LYS46 as the most likely active site for covalent bond formation during PB3-concanavalin A conjugation. In addition, theoretical studies have shown that PB3 is characterized by good bioavailability and absorption/transmission across the cell membrane. This molecule will not bioaccumulate in living organisms and should be excreted in urine without interacting with other drugs. This work provided promising results for the red fluorescent probe (PB3) as a valuable alternative to commercial probes designed for cellular labeling in biological and biomedical research.

Enhancement of biocompatibility and photoacoustic contrast activity of metal clusters

Organometallic carbonyl clusters (OMCC) of group VIII elements are water soluble, bio-compatible and stable high-contrast photoacoustic agents for live cell imaging. But, they have limited application due to weak absorption within 700-1000nm wavelength which is known as the biological window of absorption. In this article, we report that hexa-nuclear iron (Fe₆) carbonyl cluster derivatized with sodium thio-propanoate has very good absorption within 700-1600nm wave length. This modeled compound is water soluble and bio-compatible. The bio-compatibility of this compound is tested through cytotoxicity, LogP and metabolic probability at CYP450-2D6 enzyme.

From descriptors to predicted properties: experimental design by using applicability domain estimation

The importance of reliable methods for representative sub-sampling in terms of experimental design and risk assessment within the European Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) system is crucial. We developed experimental design approaches, by utilising predicted properties and the 'distance to model' parameter, to estimate the benefits of certain compounds to the quality of a resulting model. A statistical evaluation of four regression data sets and one classification data set showed that the adaptive concept of iteratively refining the representation of the chemical space contributes to a more efficient and more reliable selection in comparison to traditional approaches. The evaluation of compounds with regard to the uncertainty and the correlation of prediction is beneficial, and in particular, for regression data sets of sufficient size, whereas the use of predicted properties to define the chemical space is beneficial for classification models.

Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information

The Online Chemical Modeling Environment is a web-based platform that aims to automate and simplify the typical steps required for QSAR modeling. The platform consists of two major subsystems: the database of experimental measurements and the modeling framework. A user-contributed database contains a set of tools for easy input, search and modification of thousands of records. The OCHEM database is based on the wiki principle and focuses primarily on the quality and verifiability of the data. The database is tightly integrated with the modeling framework, which supports all the steps required to create a predictive model: data search, calculation and selection of a vast variety of molecular descriptors, application of machine learning methods, validation, analysis of the model and assessment of the applicability domain. As compared to other similar systems, OCHEM is not intended to re-implement the existing tools or models but rather to invite the original authors to contribute their results, make them publicly available, share them with other users and to become members of the growing research community. Our intention is to make OCHEM a widely used platform to perform the QSPR/QSAR studies online and share it with other users on the Web. The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://www.ochem.eu.