Design, synthesis, In-vitro, In-silico and DFT studies of novel functionalized isoxazoles as antibacterial and antioxidant agents.

A series of new isoxazolederivatives incorporating the sulfonate ester function has been synthesized from 2-benzylidenebenzofuran-3(2 H)-one, known as aurone. The synthesis of the target compounds was carried out following an efficient methodology that allows access to the desired products in a reproducible way and with good yield. The structures of the synthesized compounds were established using NMR (1H and 13C) spectroscopy and mass spectrometry. A theoretical study was performed to optimize the geometrical structures and to calculate the structural and electronic parameters of the synthesized compounds. The calculations were also carried out to understand the influence and the effect of substitutions on the chemical reactivity of the studied compounds. The synthesized isoxazoles were screened for their antioxidant and antibacterial activities. The findings demonstrate that the studied compounds exhibit good to moderate antibacterial activity against the tested bacteria (Staphylococcus aureus, Bacillus subtilis, and Escherichia coli). Moreover, a number of the tested isoxazole derivatives exhibit high effectiveness against DPPH free radicals. Besides that, molecular docking studies were carried out to predict binding affinity and identify the most likely binding interactions between the active molecules and the target microorganisms' proteins. A 100 ns molecular dynamics study was then conducted to examine the dynamic behavior and stability of the highly potent isoxazole 4e in complex with the target bacterial proteins. Finally, the ADMET analyses suggest that all the synthesized isoxazoles have good pharmacokinetic profiles and non-toxicity and non-carcinogenicity in biological systems.

Chromone-isoxazole hybrids molecules: synthesis, spectroscopic, MEDT, ELF, antibacterial, ADME-Tox, molecular docking and MD simulation investigations.

A mechanistic study was performed within the molecular electron density theory at the B3LYP/6-311G (d,p) computational level to explain the regioselectivity observed. An electron localization function analysis was also performed, and the results confirm the zwitterionic-type (zw-type) mechanism of the cycloaddition reactions between nitrile oxide and alkylated 4H-chromene-2-carboxylate derivatives and shed more light on the obtained regioselectivity experimentally. In silico studies on the pharmacokinetics, ADME and toxicity tests of the compounds were also performed, and it was projected that compounds 5a, 5b, 5c and 5d are pharmacokinetic and have favorable ADME profiles. Moreover, docking and molecular dynamics investigations were conducted to evaluate the interactions, orientation and conformation of the target compounds on the active sites of four distinct enzymes. The results of this investigation showed that two compounds, 5a and 5c, interacted effectively with the S. aureus active site while maintaining acceptable binding energy.Communicated by Ramaswamy H. Sarma.

Cyclohexane-1,3-dione Derivatives as Future Therapeutic Agents for NSCLC: QSAR Modeling, In Silico ADME-Tox Properties, and Structure-Based Drug Designing Approach.

The abnormal expression of the c-Met tyrosine kinase has been linked to the proliferation of several human cancer cell lines, including non-small-cell lung cancer (NSCLC). In this context, the identification of new c-Met inhibitors based on heterocyclic small molecules could pave the way for the development of a new cancer therapeutic pathway. Using multiple linear regression (MLR)-quantitative structure-activity relationship (QSAR) and artificial neural network (ANN)-QSAR modeling techniques, we look at the quantitative relationship between the biological inhibitory activity of 40 small molecules derived from cyclohexane-1,3-dione and their topological, physicochemical, and electronic properties against NSCLC cells. In this regard, screening methods based on QSAR modeling with density-functional theory (DFT) computations, in silico pharmacokinetic/pharmacodynamic (ADME-Tox) modeling, and molecular docking with molecular electrostatic potential (MEP) and molecular mechanics-generalized Born surface area (MM-GBSA) computations were used. Using physicochemical (stretch-bend, hydrogen bond acceptor, Connolly molecular area, polar surface area, total connectivity) and electronic (total energy, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels) molecular descriptors, compound 6d is identified as the optimal scaffold for drug design based on in silico screening tests. The computer-aided modeling developed in this study allowed us to design, optimize, and screen a new class of 36 small molecules based on cyclohexane-1,3-dione as potential c-Met inhibitors against NSCLC cell growth. The in silico rational drug design approach used in this study led to the identification of nine lead compounds for NSCLC therapy via c-Met protein targeting. Finally, the findings are validated using a 100 ns series of molecular dynamics simulations in an aqueous environment on c-Met free and complexed with samples of the proposed lead compounds and Foretinib drug.

3D-QSAR, molecular docking, DFT and ADMET studies on quinazoline derivatives to explore novel DHFR inhibitors.

Resistance to folate antagonists is caused by mutations in the dihydrofolate reductase (DHFR) genes. These mutations affect the amino acids at positions 51, 59, 108 and 164 of DHFR, which appear to play a major role in malaria treatment failure. Therefore, the design of new drugs able to overcome the problem of antifolate drug resistance should receive urgent attention. In this study, a three-dimensional quantitative structure-activity relationship (3 D-QSAR) and molecular docking studies have been performed on antimalarial quinazoline derivatives. The CoMFA (Q2 = 0.63, R2 = 0.83 and Rpred2 = 0.70) and the CoMSIA (Q2 = 0.584, R2 = 0.816, and Rpred2= 0.73) models show a good prediction of antimalarial activity. The reliability and robustness of the proposed models have been tested using several validation methods, which showed that the steric, electrostatic, hydrophobic and H-bond acceptor fields of the CoMSIA model play a key role in the prediction of antimalarial activity. Molecular docking studies reveal important interactions between two isomeric compounds (meta and para) and the DHFR receptor in its wild and mutant forms. The obtained outcomes of molecular docking studies have been validated using a new method based on visual inspection. The DFT study of the two isomeric compounds confirms clearly the trends of 3 D-QSAR and molecular docking for the design of new compounds. Moreover, the consistency between theoretical, 3 D-QSAR and molecular docking analysis provides guidance for the design of new drug candidates, which have been tested using ADMET properties and drug likeness analysis.Communicated by Ramaswamy H. Sarma.

A computer-aided drug design approach to explore novel type II inhibitors of c-Met receptor tyrosine kinase for cancer therapy: QSAR, molecular docking, ADMET and molecular dynamics simulations.

Small molecules such as 4-phenoxypyridine derivatives have remarkable inhibitory activity against c-Met enzymatic activity and proliferation of cancer cell lines. Since there is a relationship between structure and biological activity of these molecules, these little compounds may have great potential for clinical pharmaceutical use against various types of cancer caused by c-Met activity. The purpose of this study was to remodel the structures of 4-phenoxypyridine derivatives to achieve strong inhibitory activity against c-Met and provide favorable pharmacokinetic properties for drug design and discovery. Therefore, this paper describes the structure-activity relationship and the rationalization of appropriate pharmacophore sites to improve the biological activity of the investigated molecules, based on bioinformatics techniques represented by a computer-aided drug design approach. Accordingly, robust and reliable 3D-QSAR models were developed based on CoMFA and CoMSIA techniques. As a result, 46 lead molecules were designed and their biological and pharmacokinetic activities were predicted in silico. Screening filters by 3D-QSAR, Molecular Docking, drug-like and ADME-Tox identified the computer-designed compounds P54 and P55 as the best candidates to achieve high inhibition of c-Met enzymatic activity compared to the synthesized template compound T14. Finally, through molecular dynamics simulations, the structural properties and dynamics of c-Met free and complex (PDB code: 3LQ8) in the presence of 4-phenoxypyridine-derived compounds in an aqueous environment are discussed. Overall, the rectosynthesis of the designed drug inhibitors (P54 and P55) and their in vitro and in vivo bioactivity evaluation may be attractive for design and discovery of novel drug effective to inhibit c-Met enzymatic activity.Communicated by Ramaswamy H. Sarma.

Synthesis, Characterization, DFT Mechanistic Study, Antimicrobial Activity, Molecular Modeling, and ADMET Properties of Novel Pyrazole-isoxazoline Hybrids.

A series of new heterocycle hybrids incorporating pyrazole and isoxazoline rings was successfully synthesized, characterized, and evaluated for their antimicrobial responses. The synthesized compounds were obtained utilizing N-alkylation and 1,3-dipolar cycloaddition reactions, as well as their structures were established through spectroscopic methods and confirmed by mass spectrometry. To get more light on the regioselective synthesis of new hybrid compounds, mechanistic studies were performed using DFT calculations with B3LYP/6-31G(d,p) basis set. Additionally, the results of the preliminary screening indicate that some of the examined hybrids showed potent antimicrobial activity, compared to standard drugs. The results confirm that the antimicrobial activity is strongly dependent on the nature of the substituents linked pyrazole and isoxazoline rings. Furthermore, molecular docking studies were conducted to highlight the interaction modes between the investigated hybrid compounds and the Escherichia coli and Candida albicans receptors. Notably, the results demonstrate that the investigated compounds have strong protein binding affinities. The stability of the formed complexes by the binding between the hybrid compound 6c, and the target proteins was also confirmed using a 100 ns molecular dynamics simulation. Finally, the prediction of ADMET properties suggests that almost all hybrid compounds possess good pharmacokinetic profiles and no signs of observed toxicity, except for compounds 6e, 6f, and 6g.

Crystallographic study, biological assessment and POM/Docking studies of pyrazoles-sulfonamide hybrids (PSH): Identification of a combined Antibacterial/Antiviral pharmacophore sites leading to in-silico screening the anti-Covid-19 activity.

The discovery and development of new potent antimicrobial and antioxidant agents is an essential lever to protect living beings against pathogenic microorganisms and free radicals. In this regard, new functionalized pyrazoles have been synthesized using a simple and accessible approach. The synthesized aminobenzoylpyrazoles 3a-h and pyrazole-sulfonamides 4a-g were obtained in good yields and were evaluated in vitro for their antimicrobial and antioxidant activities. The structures of the synthesized compounds were determined using IR, NMR, and mass spectrometry. The structure of the compound 4b was further confirmed by single crystal X-ray diffraction. The results of the in vitro screening show that the synthesized pyrazoles 3 and 4 exhibit a promising antimicrobial and antioxidant activities. Among the tested compounds, pyrazoles 3a, 3f, 4e, 4f, and 4g have exhibited remarkable antimicrobial activity against some microorganisms. In addition, compounds 3a, 3c, 3e, 4a, 4d, 4f, and 4g have shown a significant antioxidant activity in comparison with the standard butylhydroxytoluene (BHT). Hence, compounds 3a, 4f, and 4g represent interesting dual acting antimicrobial and antioxidant agents. In fact, pyrazole derivatives bearing sulfonamide moiety (4a-g) have displayed an important antimicrobial activity compared to pyrazoles 3a-h, this finding could be attributed to the synergistic effect of the pyrazole and sulfonamide pharmacophores. Furthermore, Molecular docking results revealed a good interaction of the synthesized compounds with the target proteins and provided important information about their interaction modes with the target enzyme. The results of the POM bioinformatics investigations (Petra, Osiris, Molinspiration) show that the studied heterocycles present a very good non toxicity profile, an excellent bioavailability, and pharmacokinetics. Finally, an antiviral pharmacophore (O δ-, O δ-) was evaluated in the POM investigations and deserves all our attention to be tested against Covid-19 and its Omicron and Delta mutants.

Combined Pharmacophore Modeling, 3D-QSAR, Molecular Docking and Molecular Dynamics Study on Indolyl-aryl-sulfone Derivatives as New HIV1 Inhibitors.

The present study deals with the in silico of 45 indolyl-aryl-sulfones known as anti-HIV1. The data were collected from recent previously reported inhibitors and divided into a sub-set of 33 compounds as the training set and the remaining 12 compounds were kept in the test set. The selected pharmacophore-ADRRR-yielded a statistically significant 3D-QSAR model containing high confidence scores (R2 = 0.930, Q2 = 0.848, and RMSE = 0.460). The predictive power of the established pharmacophore model was validated with an external test (r2 = 0.848). A systematic virtual screening workflow shows an enrichment factor and has revealed a high predictive power. Then the model was used to screen the filtered PubChem database mapping all chemical features of model pharmacophore. The recognized hits were further assessed by in silico ADMET studies. Molecular dynamics also used to explore the stability of obtained complexes. Finally, these selected compounds are probably to become a good lead molecule for the development of effective anti-HIV-1 drugs.

Unsymmetrical aromatic disulfides as SARS-CoV-2 Mpro inhibitors: Molecular docking, molecular dynamics, and ADME scoring investigations.

COVID-19 pandemic caused by very severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) agent is an ongoing major global health concern. The disease has caused more than 452 million affected cases and more than 6 million death worldwide. Hence, there is an urgency to search for possible medications and drug treatments. There are no approved drugs available to treat COVID-19 yet, although several vaccine candidates are already available and some of them are listed for emergency use by the world health organization (WHO). Identifying a potential drug candidate may make a significant contribution to control the expansion of COVID-19. The in vitro biological activity of asymmetric disulfides against coronavirus through the inhibition of SARS-CoV-2 main protease (Mpro) protein was reported. Due to the lack of convincing evidence those asymmetric disulfides have favorable pharmacological properties for the clinical treatment of Coronavirus, in silico evaluation should be performed to assess the potential of these compounds to inhibit the SARS-CoV-2 Mpro. In this context, we report herein the molecular docking for a series of 40 unsymmetrical aromatic disulfides as SARS-CoV-2 Mpro inhibitor. The optimal binding features of disulfides within the binding pocket of SARS-CoV-2 endoribonuclease protein (Protein Data Bank [PDB]: 6LU7) was described. Studied compounds were ranked for potential effectiveness, and those have shown high molecular docking scores were proposed as novel drug candidates against SARS-CoV-2. Moreover, the outcomes of drug similarity and ADME (Absorption, Distribution, Metabolism, and Excretion) analyses have may have the effectiveness of acting as medicines, and would be of interest as promising starting point for designing compounds against SARS-CoV-2. Finally, the stability of these three compounds in the complex with Mpro was validated through molecular dynamics (MD) simulation, in which they displayed stable trajectory and molecular properties with a consistent interaction profile.

In silico investigation of phytoconstituents from Cameroonian medicinal plants towards COVID-19 treatment.

In silico studies performed on the metabolites of four Cameroonian medicinal plants with a view to propose potential molecules to fight against COVID-19 were carried out. At first, molecular docking was performed for a set of 84 selected phytochemicals with SARS-CoV-2 main protease (PDB ID: 6lu7) protein. It was further followed by assessing the pharmacokinetics and pharmacological abilities of 15 compounds, which showed low binding energy values. As the screening criteria for their ADMET properties were performed, only two compounds have shown suitable pharmacological properties for human administration which were shortlisted. Furthermore, the stability of binding of these compounds was assessed by performing molecular dynamics (MD) simulations. Based on further analysis through molecular dynamics simulations and reactivity studies, it was concluded that only the Pycnanthuquinone C (17) and the Pycnanthuquinone A (18) extracted from the Pycnanthus angolensis could be considered as candidate inhibitors for targeted protein. Indeed, we expect that these compounds could show excellent in vitro and in vivo activity against SARS-CoV-2. Supplementary information: The online version contains supplementary material available at 10.1007/s11224-022-01939-7.

3D-QSAR, ADME-Tox, and molecular docking of semisynthetic triterpene derivatives as antibacterial and insecticide agents.

In the present work, 27 triterpene derivatives have been subjected to 3D-QSAR, ADME-Tox, and molecular docking for their insecticidal activity. The selected derivatives are previously semi-synthesized based on compounds obtained from Euphorbia resinifera and Euphorbia officinarum latex. The in silico studies were used to predict and to evaluate the antibacterial and insecticidal properties of the 3D structure of triterpene derivatives. The 3D-QSAR models are developed using CoMFA and CoMSIA techniques, and they have showed excellent statistical results (R 2 = 0.99; Q 2 = 0.672; R 2 pred = 0.91 for CoMFA and R 2 = 0.97; Q2 = 0.61; R 2 pred = 0.94 for CoMSIA). The results indicate that the built models are able to describe the relationship between the structure of triterpene derivatives and the pLD50 bioactivity. Based on contour maps obtained from CoMFA and CoMSIA models, 38 new molecules are designed and their pLD50 activities are predicted. The drug-like and ADME-Tox properties of the molecule designed are examined and led to the selection of four molecules (55, 56, 59, 64) as promising antibacterial and insecticidal agents. Compounds 55, 56, 59, and 64 are able to inhibit the MurE (PDB code: 1E8C) and EcR (PDB code: 1R20) proteins involved in the process of antibacterial and insecticidal activities. This hypothesis is confirmed by the implementation of a molecular docking test. This test predicted the most important referential interactions that occur between the structure of triterpene derivatives and the targeted receptors. Among the four docked molecules, three molecules (55, 56, and 59) showed greater stability than the reference molecule 16 inside the MurE and EcR receptors pocket. Therefore, the structure of the three new triterpene derivatives can be adopted as reference for the synthesis of antibacterial drugs and also in the development of insecticides.

Cameroonian medicinal plants as potential candidates of SARS-CoV-2 inhibitors.

Coronavirus disease 2019 (COVID-19) is an ongoing pandemic instigated by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) which changed the daily train of the world's population and cause several dead. Despite the significant efforts made in developing vaccines and therapeutic drugs, there is currently no available effective treatment against this new coronavirus infection, hence the need to continue research which is aimed at limiting the progression of this virus. The present study which has as objective to carry out in silico studies on the metabolites of some Cameroonian medicinal plants of the Asteraceae family with a view to propose potential molecules to fight against COVID-19. The selected plants are commonly used to treat respiratory infectious diseases, and for this reason they may contain some constituents which could exhibit an antiviral activity against SARS-CoV-2. In this work, a set of 74 naturally occurring compounds are computed with SARS-CoV-2 main protease protein (PDB ID: 6lu7) and spike protein (PDB ID: 6m0j) for their affinity and stability using binding energy analysis and molecular docking. Chrysoeriol-7-O-ß-D-glucuronopyranoside (compound 16) has showed promising results including excellent Absorption, Distribution, Metabolism and Excretion (ADME) parameters as well as insignificant toxicity. Finally, the stability of this compound is complex with the two proteins validated through molecular dynamics (MD) simulation, they displayed stable trajectory and molecular properties with consistent interaction profile in molecular dynamics simulations. These findings call for further in vitro and in vivo challenges of phytoconstituents against the COVID-19 as a potential agent to fight the spread of this dramatic pandemic.Communicated by Ramaswamy H. Sarma.

QSAR study of unsymmetrical aromatic disulfides as potent avian SARS-CoV main protease inhibitors using quantum chemical descriptors and statistical methods.

In silico research was executed on forty unsymmetrical aromatic disulfide derivatives as inhibitors of the SARS Coronavirus (SARS-CoV-1). Density functional theory (DFT) calculation with B3LYP functional employing 6-311 â€‹+ â€‹G(d,p) basis set was used to calculate quantum chemical descriptors. Topological, physicochemical and thermodynamic parameters were calculated using ChemOffice software. The dataset was divided randomly into training and test sets consisting of 32 and 8 compounds, respectively. In attempt to explore the structural requirements for bioactives molecules with significant anti-SARS-CoV activity, we have built valid and robust statistics models using QSAR approach. Hundred linear pentavariate and quadrivariate models were established by changing training set compounds and further applied in test set to calculate predicted IC50 values of compounds. Both built models were individually validated internally as well as externally along with Y-Randomization according to the OECD principles for the validation of QSAR model and the model acceptance criteria of Golbraikh and Tropsha's. Model 34 is chosen with higher values of R2, R2 test and Q2cv (R2 â€‹= â€‹0.838, R2 test â€‹= â€‹0.735, Q2 cv â€‹= â€‹0.757). It is very important to notice that anti-SARS-CoV main protease of these compounds appear to be mainly governed by five descriptors, i.e. highest occupied molecular orbital energy (EHOMO), energy of molecular orbital below HOMO energy (EHOMO-1), Balaban index (BI), bond length between the two sulfur atoms (S1S2) and bond length between sulfur atom and benzene ring (S2Bnz). Here the possible action mechanism of these compounds was analyzed and discussed, in particular, important structural requirements for great SARS-CoV main protease inhibitor will be by substituting disulfides with smaller size electron withdrawing groups. Based on the best proposed QSAR model, some new compounds with higher SARS-CoV inhibitors activities have been designed. Further, in silico prediction studies on ADMET pharmacokinetics properties were conducted.

Crystal structure of ethyl 2-amino-4-(4-chloro-phen-yl)-4H-1-benzothieno[3,2-b]pyran-3-carboxyl-ate.

The title compound, C20H16ClNO3S, is built up from three fused rings, one five- and two six-membered rings, linked to a 3-eth-oxy-carbonyl group and to a 4-chloro-phenyl ring. The hydropyran ring has a flattened envelope conformation, with the C atom substituted by the 4-chloro-phenyl ring as the flap (displaced by 0.077 (2) Šfrom the plane through the other atoms). The fused three-ring system is quasi-planar (r.m.s. deviation = 0.057 Å), with the largest deviation from the mean plane being 0.106 (1) Šfor the C atom substituted by the 4-chloro-phenyl ring. The 4-chloro-phenyl ring is approximately perpendicular to the mean plane of the fused ring system, as indicated by the dihedral angle of 77.32 (6)° between their mean planes. There is an intra-molecular N-H⋯O hydrogen bond forming an S(6) ring motif. In the crystal, mol-ecules are linked by pairs of N-H⋯O hydrogen bonds, forming inversion dimers with an R 2 (2)(12) ring motif. There are also short inter-molecular Cl⋯O inter-actions present [3.1226 (12) Å] between neighbouring mol-ecules.

Crystal structure of ethyl 2-amino-4-(4-meth-oxy-phen-yl)-4H-1-benzothieno[3,2-b]pyran-3-carboxyl-ate.

The mol-ecule of the title compound, C21H19NO4S, features a fused ring system whereby a five-membered ring is flanked by two six-membered rings. This is linked to an ethyl 3-carboxyl-ate group and to a meth-oxy-benzene group. The fused-ring system is quasi-planar, with the greatest deviation from the mean plane being 0.131 (1) Šfor the methine C atom. The plane through the meth-oxy-benzene ring is nearly perpendicular to that through the fused-ring system, as indicated by the dihedral angle of 85.72 (6)°. An intra-molecular N-H⋯O hydrogen bond is noted. In the crystal, mol-ecules are linked by N-H⋯O hydrogen bonds, forming layers that stack along the a axis.

Crystal structure of 2-amino-3-cyano-4-(4-meth-oxy-phen-yl)-4H-1-benzo-thieno[3,2-b]pyran.

The three fused five- and six-membered rings in the title compound, C19H14N2O2S, are virtually coplanar, with the maximum deviation from the mean plane being 0.060 (1) Å. This benzothieno[3,2-b]pyran ring system is nearly perpendic-ular to the plane of the 4-meth-oxy-phenyl ring, forming a dihedral angle of 83.65 (5)°. In the crystal, mol-ecules are linked by pairs of N-H⋯N hydrogen bonds into inversion dimers. The dimeric units are further connected by an N-H⋯O hydrogen bond into a tape running along the b axis. The tapes are linked together by C-H⋯N and π-π inter-actions [centroid-centroid distance = 3.7743 (8) Å], forming a three-dimensional network.

Ethyl 2-amino-4-(3-nitro-phen-yl)-4H-1-benzothieno[3,2-b]pyran-3-carboxyl-ate.

The mol-ecule of the title compound, C20H16N2O5S, is built up by one fused five-membered and two fused six-membered rings linked to eth-oxy-carbonyl and 3-nitro-phenyl groups. The benzothieno-pyran ring system is nearly planar (r.m.s deviation = 0.0392 Å) and forms a dihedral angle of 86.90 (6)° with the aromatic ring of the nitro-benzene group. In the crystal, mol-ecules are linked by N-H⋯O hydrogen bonds and by π-π inter-actions between the phenyl ring and the six-membered heterocyle [inter-centroid distance = 3.5819 (8) Å], forming a three-dimensional network.