Unified QSAR and network-based computational chemistry approach to antimicrobials, part 1: multispecies activity models for antifungals

There are many pathogen microbial species with very different antimicrobial drugs susceptibility. In this work, we selected pairs of antifungal drugs with similar/dissimilar species predicted-activity profile and represented it as a large network, which may be used to identify drugs with similar mechanism of action. Computational chemistry prediction of the biological activity based on quantitative structure-activity relationships (QSAR) susbtantially increases the potentialities of this kind of networks, avoiding time and resource-consuming experiments. Unfortunately, most QSAR models are unspecific or predict activity against only one species. To solve this problem we developed a multispecies QSAR classification model, in which the outputs were the inputs of the aforementioned network. Overall model classification accuracy was 87.0% (161/185 compounds) in training, 83.4% (50/61) in validation, and 83.7% for 288 additional antifungal compounds used to extend model validation for network construction. The network predicted has 59 nodes (compounds), 648 edges (pairs of compounds with similar activity), low coverage density d = 37.8%, and distribution more close to normal than to exponential. These results are more characteristic of a not-overestimated random network, clustering different drug mechanisms of actions, than of a less useful power law network with few mechanisms (network hubs).     

Tomocomd-Cardd, a novel approach for computer-aided ‘ rational’ drug design: I. Theoretical and experimental assessment of a promising method for computational screening and in silico design of new anthelmintic compounds

Summary In this work, the TOMOCOMD-CARDD approach has been applied to estimate the anthelmintic activity. Total and local (both atom and atom-type) quadratic indices and linear discriminant analysis were used to obtain a quantitative model that discriminates between anthelmintic and non-anthelmintic drug-like compounds. The obtained model correctly classified 90.37% of compounds in the training set. External validation processes to assess the robustness and predictive power of the obtained model were carried out. The QSAR model correctly classified 88.18% of compounds in this external prediction set. A second model was performed to outline some conclusions about the possible modes of action of anthelmintic drugs. This model permits the correct classification of 94.52% of compounds in the training set, and 80.00% of good global classification in the external prediction set. After that, the developed model was used in virtual in silicoscreening and several compounds from the Merck Index, Negwers handbook and Goodman and Gilman were identified by models as anthelmintic. Finally, the experimental assay of one organic chemical (G-1) by an in vivo test coincides fairly well (100) with model predictions. These results suggest that the proposed method will be a good tool for studying the biological properties of drug candidates during the early state of the drug-development process.     

Arylpyrazole as selective anti-enterococci; synthesis and biological evaluation of novel derivatives for their antimicrobial efficacy

Exploring the structure–activity relationships (SAR) of a new set of phenylpyrazoles unveiled a potential anti-enterococcus lead compound 12 . The benzofuran moiety linked to the phenylpyrazole 12 was 32 times better than vancomycin against Enterococcus faecalis ATCC 51299. Besides, compound 12 is expected to have an excellent oral bioavailability according to the in silico studies. Of SAR analysis, we found that the benzofuran side chain was essential for the activity. Changing the benzofuran with either benzothiophene, phenyl, pyridinyl, tolyl, or naphthyl reduces/nullifies the pharmacological action. Besides the anti-enterococcal activity, derivatives 4 and 6 can be used to develop new broad-spectrum antibiotics as they exhibited activity against the wild-type highly virulent Escherichia coli isolate. Moreover, compound 13 was proved to show antifungal activity (MIC = 4 μg/ml) against the Candida albicans SS5314 (wild type). Finally, the in silico analysis showed that those compounds have good profiles regarding the absorption, distribution, metabolism, and excretion studies, drug-likeness and pharmacokinetics properties.     

Enhancement of Different Biomedical Activities of Newly Synthesized Quinazoline Derivatives

A series of newly synthesized compounds of quinazolinone by various substituents was screened for its pharmacological activities. These included their action as antibacterial agents against pathogenic bacteria (Staphylococcus aureus, Streptococcus pneumoniae, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa) and as antifungal agents against Aspergillus niger and pathogenic yeast (Candida albicans). The presently investigated compounds were synthesized in higher yields, and the structure features were elucidated on the basis of IR, ¹H‐NMR, and mass and elemental analysis data. These compounds were also evaluated as antioxidant agent. The results revealed that six compounds ( 2a , 11b , 11a , 2b , 13a , and 3c ) exhibited higher antimicrobial activity against the tested pathogenic strains. In addition, it was found that compound 6a exhibited a radical scavenging activity higher than other studied compounds.     

Synthesis,Characterization, and Molecular Docking Study of Some Novel Imidazole Derivatives as Potential Antifungal Agents

The azole pharmacophore is still regarded as a viable lead structure for the synthesis of more effective antifungal agents. In this study, two novel series of imidazole derivatives containing dithiocarbamate (5a–5g) and (benz)azolethiol (6a–6n) side chains that are structurally related to the famous antifungal azole pharmacophore were synthesized, and the structures of them were characterized by spectral (IR, ¹H NMR, ¹³C NMR, and MS spectra) analyses. The synthesized compounds were screened in vitro antifungal activity against pathogenic strains fungi. Theoretical ADME (absorption, distribution, metabolism, and excretion) predictions were calculated for final compounds. A molecular docking study of the most active compound with target “lanosterol 14α‐demethylase” (CYP51) was performed to unravel the mode of antifungal action. Compound 5e , which features imidazole and 4‐methoxybenzyl piperazine scaffolds, showed the most promising antifungal activity with an MIC₅₀ value of 0.78 μg/mL against C. krusei. Effect of the compound 5e against ergosterol biosynthesis was observed by LC–MS–MS method, which is based on quantification of ergosterol level in C. krusei.     

3D QSAR and molecular docking studies of benzimidazole derivatives as hepatitis C virus NS5B polymerase inhibitors

The urgent need for novel HCV antiviral agents has provided an impetus for understanding the structural requisites of NS5B polymerase inhibitors at the molecular level. Toward this objective, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of 67 HCV NS5B polymerase inhibitors were performed using two methods. First, ligand-based 3D QSAR studies were performed based on the lowest energy conformations employing the atom fit alignment method. Second, receptor-based 3D QSAR models were derived from the predicted binding conformations obtained by docking all NS5B inhibitors at the allosteric binding site of NS5B (PDB ID: 2dxs). Results generated from the ligand-based model were found superior (r2cv values of 0.630 for CoMFA and 0.668 for CoMSIA) to those obtained by the receptor-based model (r2cv values of 0.536 and 0.561 for CoMFA and CoMSIA, respectively). The predictive ability of the models was validated using a structurally diversified test set of 22 compounds that had not been included in a preliminary training set of 45 compounds. The predictive r2 values for the ligand-based CoMFA and CoMSIA models were 0.734 and 0.800, respectively, while the corresponding predictive r2 values for the receptor-based CoMFA and CoMSIA models were 0.538 and 0.639, respectively. The greater potency of the tryptophan derivatives over that of the tyrosine derivatives was interpreted based on CoMFA steric and electrostatic contour maps. The CoMSIA results revealed that for a NS5B inhibitor to have appreciable inhibitory activity it requires hydrogen bond donor and acceptor groups at the 5-position of the indole ring and an R substituent at the chiral carbon, respectively. Interpretation of the CoMFA and CoMSIA contour maps in context of the topology of the allosteric binding site of NS5B provided insight into NS5B-inhibitor interactions. Taken together, the present 3D QSAR models were found to accurately predict the HCV NS5B polymerase inhibitory activity of structurally diverse test set compounds and to yield reliable clues for further optimization of the benzimidazole derivatives in the data set.     

Novel Substituted Imidazo[2,1‐b][1,3,4]Thiadiazole Derivatives: Synthesis,Characterization, Molecular Docking Study,and Investigation of Their In Vitro Antifungal Activities

In this study, a new series of substituted imidazo[2,1‐b][1,3,4]thiadiazole derivatives were synthesized. To this end, first 2‐amino‐1,3,4‐thiadiazole derivatives (compounds 2a and 2b ), the starting materials, were synthesized with high yields (82% and 79%, respectively). Then imidazo[2,1‐b][1,3,4]thiadiazole derivatives ( 4 – 16 ), the target compounds, were synthesized from reactions of 2‐amino‐1,3,4‐thiadiazole derivatives ( 2a and 2b ) with 2‐bromoacetophenone derivatives ( 3a – 3i ) (in yields of 52% to 71%). All of the synthesized compounds were characterized by ¹H NMR, ¹³C NMR, Fourier transform infrared, elemental analysis, mass spectroscopy, and X‐ray diffraction analysis (compounds 4 – 12 , 14 , and 15 ) techniques. In vitro antifungal activity tests were performed for all of the synthesized compounds. Inhibition zones, percentage of inhibition, minimum fungicidal activity, minimum inhibitory concentration, and lethal dose values of the target compounds were determined against some plant pathogens. According to the results of the biological activity tests, all of the synthesized compounds showed moderate to high levels of antifungal activity. Theoretical calculations were performed to support the experimental results. The geometric parameters of selected compounds ( 5 , 6 , and 8 ) were optimized using the density functional theory B3LYP/6‐31G(d) method in the Gaussian 09W package program, and the frontier molecular orbitals (highest occupied molecular orbital–lowest unoccupied molecular orbital) were calculated theoretically. Finally, molecular docking studies were performed for antifungal activity studies of the selected compounds and to determine whether or not these compounds could be inhibitor agents for the 2RKV protein structure.     

Heteroleptic transition metal complexes of Schiff‐base‐derived ligands exert their antifungal activity by disrupting membrane integrity

Development of new treatment strategies and chemotherapeutic agents is urgently needed to combat the growing multidrug resistant species of Candida. In this direction, a new series of Cu (II), Co (II), Ni (II) and Zn (II) heteroleptic complexes were synthesized, characterized and evaluated for antifungal activity. Based on spectral characterization and physical measurements, an octahedral geometry was assigned to [Co(L1)(L2)ClH₂O] ( C2 ), [Ni(L1)(L2)ClH₂O] ( C3 ), [Zn(L1)(L2)ClH₂O] ( C4 ) complexes, while a distorted octahedral geometry was assigned to [Cu(L1)(L2)ClH₂O] ( C1 ) complex. All the synthesized compounds were tested for antifungal activity against 11 Candida albicans isolates, including fluconazole (FLC)‐resistant isolates, by determining minimum inhibitory concentrations (MIC) and minimum fungicidal concentrations (MFC), following CLSI guidelines. The mechanism of their antifungal activity was assessed by studying their effect on the plasma membrane using flow cytometry and quantifying the ergosterol contents. All the test compounds showed varying levels of antifungal activity. Both the ligands showed moderate antifungal activity with a median MIC value of 100 μg/mL with no fungicidal activity. Compound C3 was the most potent compound with median MIC and MFC values of 0.10 and 1.60 μg/mL, respectively. Flow cytometry analysis revealed that these compounds at MFC values disrupt the cell membrane, resulting in propidium iodide entering the cells. These compounds also reduced a considerable amount of ergosterol content after treating the cells with MIC and sub‐MIC values. This study indicates that these compounds have high antifungal activity against C. albicans, and have the potential to be developed as novel antifungal drugs.     

Antifungal evaluation of cholic acid and its derivatives on Candida albicans by microcalorimetry and chemometrics

In the last few years, several fungus infections caused by multidrug-resistant pathogenic agents have got tremendous emergence and prevalence. Screening for novel antifungal agents is in great demand, but traditional microbiological techniques are far from sufficient to meet that requirement. In this study, a non-invasive and non-destructive microcalorimetric method was performed to investigate the antifungal activities of cholic acid (CA) and its derivatives, glycocholic acid (GCA) and taurocholic acid (TCA) on the multiplying and non-multiplying metabolism of Candida albicans. Then, the heat-flow power-time curves of C. albicans growth affected by different concentrations of CA, GCA and TCA were studied by similarity analysis (SA), the quantitative thermokinetic parameters from these curves were analyzed by multivariate analysis of variance (MANOVA) and principal component analysis (PCA). By comparing the values of two main parameters, P₂ (the heat-flow output power of the highest peak) and Q₂ (the heat output of the second exponential growth phase) of C. albicans, it could be found that CA had the strongest antifungal activity among the three steroid compounds, which might be used as a potential antifungal agent in the future. This study provided a useful method and idea of microcalorimetry with chemometrics to efficiently evaluate the antifungal activities of bile acid derivatives, giving some references for screening out new antifungal agents.However, it has to be stressed that all these experiments are carried out in vitro and they still require clinical validation.