Predicting anti-HIV activity of 1,3,4-thiazolidinone derivatives: 3D-QSAR approach

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.

Corrosion Mitigation Performance of N80 Steel in 5% Sulfamic Acid Medium by Applying Novel Tetrahydro-1,2,4-triazines Including Triazene Moieties: Electrochemical and Theoretical Approaches

We observed our newly developed tetrahydro-1,2,4-triazines, including triazene moieties (THTA), namely, 6-((1E)-1-((2E)-(4-(((Z)-1-(2,4-diphenyl-2,3,4,5-tetrahydro-1,2,4-triazin-5-yl) ethylidene) triaz-1-en-1-yl)piperazin-1-yl) triaz-2-en-1-ylidene) ethyl)-2,4-diphenyl-2,3,4,5-tetrahydro-1,2,4-triazine (THTA-I), and 1-((E)-((E)-1-(2,4-diphenyl-2,3,4,5-tetrahydro-1,2,4-triazin-6-yl) ethylidene) triaz-1-en-1-yl) naphthalen-2-ol (THTA-II), as effective inhibitors for the corrosion protection of N80 carbon steel metal in 5% sulfamic acid as the corrosive medium via electrochemical approaches such as potentiodynamic polarization and electrochemical impedance spectroscopy. Furthermore, the tested steel exterior was monitored using X-ray photoelectron spectroscopy after the treatment with the investigated components to verify the establishment of the adsorbed shielding film. The investigated compounds acted as mixed-type inhibitors, as shown by Tafel diagrams. The compounds considered obey the Langmuir adsorption isotherm, and their adsorption on the steel surface was chemisorption. When the tested inhibitors were added, the double-layer capacitances, which can be determined by the adsorption of the tested inhibitors on N80 steel specimens, decreased compared with that of the blank solution. At 10^-4 M, the inhibitory efficacy of THTA-I and THTA-II achieved maximum values of 88.5 and 86.5%, respectively. Density-functional theory computations and Monte-Carlo simulation were applied to determine the adsorption attributes and inhibition mechanism through the studied components. Furthermore, the investigated inhibitors were considered to adsorb on the Fe (1 1 0) surface. The adsorption energy was then measured on steel specimens.

One-Pot Synthesis of Novel Hydrazono 1,3-Thiazolidin-4-One Derivatives: Molecular Modelling, ADMET And Biological Evaluation of Anti-HIV And Anti-Tubercular Agents

BACKGROUND

The necessity for newer anti-HIV and anti-tubercular medications has arisen as a result of the prevalence of opportunistic infections caused by HIV (human immunodeficiency virus).

OBJECTIVE

A series of ten new hydrazono 1,3-thiazolidin-4-one derivatives were synthesized in one-pot and evaluated for anti-HIV and anti-tubercular activities. Molecular Docking was perormed with HIV-1 reverse transcriptase protein (PDB ID: 1REV) and Mycobacterium Tuberculosis (M. tuberculosis) H37Rv protein (PDB ID: 2YES) receptors along with drug-likeness and ADMET properties.

METHODS

One-pot synthesis of hydrazono 1,3-thiazolidin-4-one derivatives was carried out by ketones, thiosemicarbazide and ethylchloroacetate with the catalyst of anhydrous sodium acetate. All the synthesized compounds were characterized, and evaluated for their in-vitro anti-HIV and also evaluated for their in-vitro anti-tubercular activity against M. tuberculosis H37Rv. In-silico predicted physicochemical parameters were done by MedChem DesignerTM software version 5.5 and ADMET parameters by pkCSM online tool. Furthermore, molecular docking was performed with pyrx 0.8 by autodock vina software.

RESULTS

All the synthesized compounds were characterized and evaluated for their in-vitro anti-HIV activity for inhibition of syncytia formation, which shows KTE1 with EC5¬0 47.95 µM and Selectivity Index (SI) of >4.17 and for inhibition of p24 antigen production EC5¬0 was found to be 80.02 µM and SI of >2.49. The compounds were also evaluated for their in-vitro anti-tubercular activity against M. tuberculosis H37Rv, in which KTE1 MIC values of 12.5µg/ml with SI of >4.0 and cytotoxicity against Vero cell lines. In-silico predicted physicochemical parameters for synthesized compounds which were found to be drug-like. Furthermore, docking has shown a good dock score and binding energy with anti-HIV and anti-tubercular receptors.

CONCLUSION

From the novel synthesized molecules none of the molecule is as effective as standards for anti-HIV and anti-tubercular drugs and hence can be further explored for its potential activities. Furthermore, derivatization was made to achieve more potent compounds for anti-HIV and anti-tubercular drugs.

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.

Molecular structure and vibrational spectra of 2-(4-bromophenyl)-3-(4-hydroxyphenyl) 1,3-thiazolidin-4-one and its selenium analogue: Insights using HF and DFT methods

2-(4-Bromophenyl)-3-(4-hydroxyphenyl)-1,3-thiazolidin-4-one and its selenium analogue were studied in the gas phase using HF and DFT methods. The functionals considered were B3LYP, BP86 and M06. The basis set for all the atoms was 6-311++ G(d,p). Molecular parameters such as bond lengths, bond angles, rotational constants, dipole moments, electronic energies, and vibrational parameters namely harmonic vibrational frequencies and relative intensities were computed for these compounds. Atomization energies, HOMO-LUMO gaps and natural charges on the atoms were also calculated. The molecular parameters and the vibrational spectra of sulfur compound are in good agreement with the experimental data. Therefore, the data for the selenium analogue should be helpful in its future characterization.

Retracted: Novel spiro-thiazolidin-4-one and thioether derivatives of benzylidene flavanones: New leads in cancer and microbial chemotherapy

The above article from Archiv der Pharmazie, published online on 12 March 2018 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the authors, the journal Editor-in-Chief, Prof. Holger Stark, and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. The retraction has been agreed due to errors in the spectroscopic data of the investigated new compounds.

REFERENCE TO RETRACTION

S. Mukhtar, M. A. Alsharif, M. I. Alahmdi, H. Parveen, A. U. Khan, Arch. Pharm. Chem. Life Sci. 2018;1-12. DOI: 10.1002/ardp.201700397.

Design, Synthesis and DFT/DNP Modeling Study of New 2-Amino-5-arylazothiazole Derivatives as Potential Antibacterial Agents

A new series of 2-amino-5-arylazothiazole derivatives has been designed and synthesized in 61–78% yields and screened as potential antibacterial drug candidates against the Gram negative bacterium Escherichia coli. The geometry of the title compounds were being studied using the Material Studio package and semi-core pseudopods calculations (dspp) were performed with the double numerica basis sets plus polarization functional (DNP) to predict the properties of materials using the hybrid FT/B3LYP method. Modeling calculations, especially the (E_H-E_L) difference and the energetic parameters revealed that some of the title compounds may be promising tools for further research work and the activity is structure dependent.

Design, synthesis and biological evaluation of novel pyridine-thiazolidinone derivatives as anticancer agents: Targeting human carbonic anhydrase IX

In order to obtain novel Human carbonic anhydrase IX (CAIX) inhibitors, a series of pyridine-thiazolidinone derivatives was synthesized and characterized by various spectroscopic techniques. The binding affinity of the compounds was measured by fluorescence binding studies and enzyme inhibition activity using esterase assay of CAIX. It was observed that compound 8 and 11 significantly inhibit the CAIX activity with the IC₅₀ value, 1.61 μM and 1.84 μM, respectively. The binding-affinity of compound 8 and 11 for CAIX was significantly high with their K_D values 11.21 μM and 2.32 μM, respectively. Docking studies revealed that compound 8 and 11 efficiently binds in the active site cavity of CA IX by forming sufficient numbers of H-bonds and van der Waals interactions with active side residues. All the compounds were further screened in vitro for anticancer activity and found that compound 8 and 11 exhibit considerable anticancer activity against MCF-7 and HepG-2 cell lines. All these findings suggest that compound 8 and 11 may be further exploited as a novel pharmacophore model for the development of anticancer agents.

Nano-colloidal silica-tethered polyhedral oligomeric silsesquioxanes with eight branches of 3-aminopropyltriethoxysilane as high-performance catalyst for the preparation of bis-thiazolidinones under ultrasonic conditions

We report a class of organic–inorganic hybrid material based on nano-colloidal silica-tethered polyhedral oligomeric silsesquioxanes with eight branches of 3-aminopropyltriethoxysilane [nano-colloidal silica@APTPOSS (a series of polyhedral oligomeric silsesquioxanes with eight branches of 3-aminopropyltriethoxysilane)]. It was characterized by 1H NMR spectroscopy, dynamic light scattering, scanning electron microscope, energy dispersive spectroscopy and thermogravimetric analysis. An easy and rapid method for the synthesis of bis-thiazolidinones has been presented by one-pot pseudo-five-component reaction of benzaldehydes, ethylenediamine and 2-mercaptoacetic acid using nano-colloidal silica@APTPOSS. The reusability of the catalyst and little catalyst loading, excellent yields, short reaction times, using the sonochemical procedure as a green process and an alternative energy source are some benefits of this method.

Recent Developments in 3D QSAR and Molecular Docking Studies of Organic and Nanostructures

The development of quantitative structure–activity relationship (QSAR) methods is going very fast for the last decades. OSAR approach already plays an important role in lead structure optimization, and nowadays, with development of big data approaches and computer power, it can even handle a huge amount of data associated with combinatorial chemistry. One of the recent developments is a three-dimensional QSAR, i.e., 3D QSAR. For the last two decades, 3D-OSAR has already been successfully applied to many datasets, especially of enzyme and receptor ligands. Moreover, quite often 3D QSAR investigations are going together with protein–ligand docking studies and this combination works synergistically. In this review, we outline recent advances in development and applications of 3D QSAR and protein–ligand docking approaches, as well as combined approaches for conventional organic compounds and for nanostructured materials, such as fullerenes and carbon nanotubes.

Crystal structures of 3-(2H-1,3-benzodioxol-5-ylmethyl)-2-(m- and p-nitrophenyl)-1,3-thiazolidin-4-ones: different roles of the oxygen atoms

The crystal structures of two isomeric 3-(2H-1,3-benzodioxol-5-ylmethyl)-2-(aryl)-1,3-thiazolidin-4-one compounds (1: aryl=4-O2NC6H4; 2: aryl=3-O2NC6H4) are reported. In both these nonplanar, compounds, the carbonyl oxygen is involved in intramolecular C–H···O hydrogen bonds. However, there are significant differences in the sets of intermolecular interactions, in particular the roles of the oxygen atoms, exhibited by the two compounds. Thus in 1, a dioxolyl oxygen and the two nitro group oxygen atoms are each involved in different chain forming C–H···O intermolecular hydrogen bonds, while the carbonyl oxygen atom is not involved in any intermolecular interaction. In 2, the dioxolyl oxygen atom is involved in the formation of centrosymmetric dimers, the carbonyl oxygen in three different C–H···O hydrogen bonds and the nitro group oxygens in two N–O···π(aryl) interactions. Compound 2 exhibits also C–H···π(phenyl), π(phenyl)···π(phenyl) and π(benzodioxolyl)···π(benzodioxolyl) interactions, while in 1 only the latter interaction is present. Compound 1 crystallizes in the monoclinic space group, P21/a with Z=4, while compound 2 crystallizes in the triclinic space group, P1̅, with Z=2.

One-pot synthesis of 2-hydrazonyl-4-phenylthiazoles via [PDBMDIm]Br-catalyzed reaction under solvent-free conditions

A clean and environmentally benign route for the preparation of substituted thiazoles

Highly selective fluorimetric sensor for Cu2+and Hg2+using a benzothiazole-based receptor in semi-aqueous media and molecular docking studies

A new chemosensor (Z)-ethyl 2-((Z)-2-(benzo[d]thiazol-2-ylimino)-4-oxo-3-phenylthiazolidin-5-ylidene)acetate (receptor1) was designed and synthesized under catalyst-free conditions.

Synthesis and biological activity evaluation of 5-pyrazoline substituted 4-thiazolidinones

A series of novel 5-pyrazoline substituted 4-thiazolidinones have been synthesized. Target compounds were evaluated for their anticancer activity in vitro within DTP NCI protocol. Among the tested compounds, the derivatives 4d and 4f were found to be the most active, which demonstrated certain sensitivity profile toward the leukemia subpanel cell lines with GI₅₀ value ranges of 2.12–4.58 μM (4d) and 1.64–3.20 μM (4f). The screening of antitrypanosomal and antiviral activities of 5-(3-naphthalen-2-yl-5-aryl-4,5-dihydropyrazol-1-yl)-thiazolidine-2,4-diones was carried out with the promising influence of the mentioned compounds on Trypanosoma brucei, but minimal effect on SARS coronavirus and influenza types A and B viruses.

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Synthesis of novel 5-pyrazoline substituted 4-thiazolidinones was performed.

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Compounds 4d and 4f showed promising activity on the leukemia subpanel cell lines.

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Compounds were evaluated for antitrypanosomal and antiviral properties.

QSAR studies for the computational prediction of HMG-CoA reductase inhibitors by genetic function approximation technique

Two-dimensional quantitative structure−activity relationship (2D-QSAR) models are useful in understanding how chemical structure is related to the biological activity of natural and synthetic chemicals. Also, they could be usefully employed for designing newer and better therapeutics. A 2D-QSAR study was performed for 52 compounds of a series of thiophenyl quinolines and α-asarone derivatives as potential hypocholesterolemic inhibitors using different types of physicochemical descriptors, which correlated significantly with the activity. Linear QSAR models were developed using multiple linear regression, where the genetic algorithm (genetic function approximation technique) was adopted for selecting the most appropriate descriptors. The results are discussed on the basis of regression data and the cross-validation technique. Model A is the best 2D-QSAR model describing the inhibition efficiency of HMG-CoA reductase with cross-validated squared correlation coefficient (Q 2 = 0.700) and the squared correlation coefficient (R 2 = 0.752), which is able to describe 70% of the variance in the experimental activity. The good agreement between the experimental and the predicted values of pIC50 (micromoles per litre) (R = 0.876) confirms the reliability and the predictability of the proposed model. The results obtained from the present QSAR study explained the importance of the electronic, structural, spatial, and electrotopological descriptors in enhancing the biological activity of the investigated inhibitors.

Ultrasonics promoted synthesis of thiazolidinones from 2-aminopyridine and 2-picolilamine

The efficient multicomponent synthesis of thiazolidinones from the reaction of arenealdehydes, mercaptoacetic acid and 2-picolilamine or 2-aminopyridine under ultrasound irradiation are reported. The reaction with 2-aminopyridine needs a Lewis acid catalysis to afford the corresponding 2-aryl-3-(pyridin-2-yl)-1,3-thiazolidin-4-ones. All novel compounds were identified and characterized by (1)H and (13)C NMR spectra. Applying the sonochemical methodology, two series of heterocyclic thiazolidinones were synthesized in good yields after short reaction times.

3-(2H-1,3-Benzodioxol-5-ylmeth-yl)-2-(2-meth-oxy-phen-yl)-1,3-thia-zolidin-4-one

The title mol­ecule, C₁₈H₁₇NO₄S, features a 1,3-thia­zolidine ring that is twisted about the S—C(methyl­ene) bond. With reference to this ring, the 1,3-benzodioxole and benzene rings lie to either side and form dihedral angles of 69.72 (16) and 83.60 (14)°, respectively, with the central ring. Significant twisting in the mol­ecule is confirmed by the dihedral angle of 79.91 (13)° formed between the outer rings. Linear supra­molecular chains along the a-axis direction mediated by C—H⋯O inter­actions feature in the crystal packing.

Designing hypothesis of substituted benzoxazinones as HIV-1 reverse transcriptase inhibitors: QSAR approach

A linear quantitative structure activity relationship (QSAR) model is presented for predicting human immunodeficiency virus-1 (HIV-1) reverse transcriptase enzyme inhibition. The 2D QSAR and 3D-QSAR models were developed by stepwise multiple linear regression, partial least square (PLS) regression and k-nearest neighbor-molecular field analysis, PLS regression, respectively using a database consisting of 33 recently discovered benzoxazinones. The primary findings of this study is that the number of hydrogen atoms, number of (-NH2) group connected with solitary single bond alters the inhibition of HIV-1 reverse transcriptase. Further, presence of electrostatic, hydrophobic and steric field descriptors significantly affects the ability of benzoxazinone derivatives to inhibit HIV-1 reverse transcriptase. The selected descriptors could serve as a primer for the design of novel and potent antagonists of HIV-1 reverse transcriptase.

Efficient sonochemical synthesis of thiazolidinones from piperonilamine

An efficient multicomponent reaction of arenealdehydes, mercaptoacetic acid and piperonilamine under ultrasound irradiation to afford 2-aryl-3-(piperonylmethyl)-1,3-thiazolidin-4-ones is reported. Applying this methodology, eleven heterocycles were synthesized and isolated in good yields after short reaction times.

4-(Pyrimidin-2-yl)-1-thia-4-aza-spiro-[4.5]decan-3-one

The title compound, C(12)H(15)N(3)OS, features an envelope conformation for the 1,3-thia-zolidin-4-one ring with the S atom as the flap atom. The pyrimidine ring is almost orthogonal to the 1,3-thia-zolidin-4-one ring as indicated by the N-C-C-N torsion angle of -111.96 (18)°. Supra-molecular dimers are formed in the crystal structure through the agency of C-H⋯O contacts occurring between centrosymmetrically related mol-ecules. These are linked into supra-molecular tapes along [100] via C-H⋯S contacts.