Design of anti-fungal agents by 3D-QSAR

An increase in the number of invasive fungal infections especially in immunocompromised patients is increasing the mortality rate worldwide. Due to the emergence of drug-resistant fungi, the currently available antifungal drugs have become ineffective. Because no alternative treatment is available, some existing drugs are still used. Therefore, there is a need to design and develop novel and effective anti-fungal drugs. Molecular docking and 3-dimensional quantitative structure-activity relationship (3D-QSAR) methods have been useful approaches for the design of novel molecules. A set of 30 molecules reported in the literature containing azoles and non-azoles have been used in this study to derive 3D-QSAR.CoMFA and CoMSIA models for the most active compound and least active compounds have been developed. The structural requirements were obtained by analysing the contour maps. The partial least square analysis for CoMFA and CoMSIA showed a significant cross-validated correlation coefficient of 0.625 and 0.67 and a non-cross validated correlation coefficient of 0.991 and 0.99, respectively. The model was validated by observing the predicted correlation for test molecules with the value of 0.699 and 0.659, respectively

In-Depth Molecular Characterization of Mycobacterium tuberculosis from New Delhi – Predominance of Drug Resistant Isolates of the ‘Modern’ (TbD1−) Type

BACKGROUND: India has the highest estimated burden of tuberculosis in the world, accounting for 21% of all tuberculosis cases world-wide. However, due to lack of systematic analysis using multiple markers the available information on the genomic diversity of Mycobacterium tuberculosis in India is limited. METHODOLOGY/PRINCIPAL FINDINGS: Thus, 65 M. tuberculosis isolates from New Delhi, India were analyzed by spoligotyping, MIRU-VNTR, large deletion PCR typing and single nucleotide polymorphism analysis (SNP). The Central Asian (CAS) 1 _DELHI sub-lineage was the most prevalent sub-lineage comprising 46.2% (n = 30) of all isolates, with shared-type (ST) 26 being the most dominant genotype comprising 24.6% (n = 16) of all isolates. Other sub-lineages observed were: East-African Indian (EAI)-5 (9.2%, n = 6), EAI6_BGD1 (6.2%, n = 4), EAI3_IND, CAS and T1 with 6.2% each (n = 4 each), Beijing (4.6%, n = 3), CAS2 (3.1%, n = 2), and X1 and X2 with 1 isolate each. Genotyping results from five isolates (7.7%) did not match any existing spoligopatterns, and one isolate, ST124, belonged to an undefined lineage. Twenty-six percent of the isolates belonged to the TbD1+ PGG1 genogroup. SNP analysis of the pncA gene revealed a CAS-lineage specific silent mutation, S65S, which was observed for all CAS-lineage isolates (except two ST26 isolates) and in 1 orphan. Mutations in the pncA gene, conferring resistance to pyrazinamide, were observed in 15.4% of all isolates. Collectively, mutations in the rpoB gene, the katG gene and in both rpoB and katG genes, conferring resistance to rifampicin and isoniazid, respectively, were more frequent in CAS1_DELHI isolates compared to non-CAS_DELHI isolates (OR: 3.1, CI95% [1.11, 8.70], P = 0.045). The increased frequency of drug-resistance could not be linked to the patients' history of previous anti-tuberculosis treatment (OR: 1.156, CI95% [0.40, 3.36], P = 0.79). Fifty-six percent of all new tuberculosis patients had mutations in either the katG gene or the rpoB gene, or in both katG and rpoB genes. CONCLUSION: CAS1_DELHI isolates circulating in New Delhi, India have a high frequency of mutations in the rpoB and katG genes. A silent mutation (S65S) in the pncA gene can be used as a putative genetic marker for CAS-lineage isolates

Conformational studies of antiradiation agents by NMR: cysteamine and its derivatives

The conformations of cysteamine, thiazolidine, and thia-zolidine-4-carboxylic acid were determined in aqueous solutions using NMR spectroscopy. At physiological pH, the population ratio of gauche- and trans- conformers was 3:1. The gauche-rotamer is probably responsible for the antiradiation activity and acts through metal chelation involving sulfur and nitrogen atoms. The puckering of the thiazolidine ring was calculated using NMR coupling constants. The observed results were compared with those obtained in the solid state using X-ray diffraction

Comparative 2D and 3D-QSAR of antifungal griseofulvin analogues

194-201A series of griseofulvin analogues has been examined to determine the structural requirements of antifungal activity by three-dimensional quantitative structure-activity relationship studies using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA ) methods. Evaluation of 22 compounds (training set) has established the CoMFA and CoMSIA models, which have been validated by evaluation of a set of four compounds (test set). The lowest energy conformer of the most active molecule obtained from systematic search has been used as the template structure for the alignment. In this study, the superimposition of molecules was carried out by atom-based fit (rms), multi fit and field fit. Along with steric and electronic fields, ClogP has been taken as additional descriptor to account for lipophilicity. Further, a QSAR analysis has been carried out using Tools for Structure-Activity Relationship software. For this study, various chemical descriptors such as electronic, steric, lipophilic, topological have been calculated and multiple regression carried out. The QSAR models from these three methods exhibit considerable correlative and predictive properties. The models obtained from the present study may be useful for the development of new griseofulvin analogues as potential antifungals

Conformational structure of propranolol: A β-adrenergic blocking drug studied by NMR and PCILO methods

The conformational structure of propranolol, a β-adrenergic blocking drug, has been investigated by pcilo calculations and 270-MHz proton nuclear magnetic resonance in D2O solution. The molecules coexist in at least two conformational states in solution with a low energy barrier. Both preferred conformations have extended structures which allow a three-point drug-receptor binding involving the aromatic moiety, the β-hydroxyl group, and -NH+2 groups of propranolol. The previously postulated "rigid" bicyclic structure does not exist to an appreciable extent in D2O solution

Azole compounds designed by molecular modelling show antifungal activity as predicted

372-381Rational approaches involving drug discovery technologies such as computational and combinatorial chemistry and high throughput screening have been useful tools to design and discover new drugs more efficiently. The interplay among structure-activity relationships, computer modelling, chemical synthesis and pharmacological testing can lead to better products for a particular therapeutic purpose. The work presented in this paper reports an example of successful application of computer-aided drug design method to find new azole antifungal agents. The designed compounds have been synthesized in the laboratory and tested for anti fungal activity against Candida albicans ATCC 24433 in vitro. Two compounds exhibit good activity in vitro, which can be optimized for better activity

Design of anti-fungal agents by 3D-QSAR

744-754An increase in the number of invasive fungal infections especially in immunocompromised patients is increasing the mortality rate worldwide. Due to the emergence of drug-resistant fungi, the currently available antifungal drugs have become ineffective. Because no alternative treatment is available, some existing drugs are still used. Therefore, there is a need to design and develop novel and effective anti-fungal drugs. Molecular docking and 3-dimensional quantitative structure-activity relationship (3D-QSAR) methods have been useful approaches for the design of novel molecules. A set of 30 molecules reported in the literature containing azoles and non-azoles have been used in this study to derive 3DQSAR. CoMFA and CoMSIA models for the most active compound and least active compounds have been developed. The structural requirements were obtained by analysing the contour maps. The partial least square analysis for CoMFA and CoMSIA showed a significant cross-validated correlation coefficient of 0.625 and 0.67 and a non-cross validated correlation coefficient of 0.991 and 0.99, respectively. The model was validated by observing the predicted correlation for test molecules with the value of 0.699 and 0.659, respectively

PHARMACOPHORE MODELING AND ATOM-BASED 3D-QSAR STUDIES OF ANTIFUNGAL BENZOFURANS

A novel series of benzofuran analogs was reported as nonpeptidic Myristoyl-CoA: protein N -myristoyltransferase (Nmt) inhibitors. To find out the common structural requirement of these benzofurans inhibitors, a ligand based pharmacophore and atom-based 3D-QSAR model was generated. A five-point pharmacophore model was developed with two hydrogen bond acceptors (AA), one positive ionic atom (P) and two aromatic ring residues (RR). This is denoted as AAPRR. A statistically significant 3D-QSAR model for training set of 24 compounds was obtained using this pharmacophore hypothesis with correlation coefficient (r2 = 0.916) and high Fisher ratio (F =113.9). Also, the predictive power of generated model for test set of 5 compounds was found to be significant which was confirmed by the high value of cross validated correlation coefficient (q2 = 0.804) and Pearson-R (0.917). The results of ligand based pharmacophore hypothesis and atom based 3D-QSAR model explore the detailed structural perceptivities and also highlights the important binding features of benzofurans with Nmt.Â