- Home
- A-Z Publications
- Current Computer - Aided Drug Design
- Previous Issues
- Volume 14, Issue 1, 2018
Current Computer - Aided Drug Design - Volume 14, Issue 1, 2018
Volume 14, Issue 1, 2018
-
-
Quantitative Structure-Activity Relationships of Aquatic Narcosis: A Review
Authors: Chandana Adhikari and Bijay k. MishraBackground: Prior estimation of toxicity of each and every, existing and yet to be synthesized chemicals is a must to elude their adverse effect on the environment. Experimental determination of such parameters is time consuming, cost effective and above all, it demands the sacrifice of many vertebrates. At this end, the REACH regulations advocate for the use of non-testing predictive methods such as read-across, weight-of-evidence and QSAR (quantitative structure–activity relationship) techniques. Among these methods, QSAR is found to be the best as it is based on molecular structure only. The descriptors used in deriving the model in QSAR vary according to the nature of the narcotics as well as the species used for. The success of a model in predicting the toxicity of a narcotic purely depends on the type of descriptors selected that explains the structural features closely related to the property under study. In this review, we have focused on the different types of descriptors and QSAR models used to explain the narcosis phenomenon. Methods: Literature was scanned for acute toxicity of chemicals on species like tadpoles, protozoa, planktonic crustaceans, and small fishes like million fish, rainbow fish etc. from different sources. The toxicity and toxicants were classified considering their polarity and specific interactions of the compounds. Due to complex nature of the substrate, the mechanism of action of toxicant is uncertain. However, the overall results obtained from the biological study have been subjected to QSAR studies to obtain various models, which can provide some ideas on the mode of toxicological action. Different types of molecular descriptors derived both experimentally and theoretically have been used in the QSAR studies. Results: Mostly biochemicals have a specific signature on oil/water partition (Ko/w, P), which is the crux in biological activity. Accordingly, the toxicological activities have good correlations with log P. Addition of some more structural descriptors improves the structure-toxicity relationship. Among these, electronic descriptors like EHOMO, ELUMO and ΔE derived from molecular orbitals have been used in the QSAR. ELUMO describing the energy of excited species of the molecule is found to be the most suitable one. Other molecular descriptors used in the QSAR include constitutional, topological and Abraham's solute descriptors. The models derived from the QSAR studies were found to be highly significant to predict the toxicology as well as to throw light on the mechanism. Conclusion: The best descriptor for aquatic narcosis is the KO/W or P. Addition of an electronic parameter (ELUMO) improves the QSAR to some extent. However, substitution of ELUMO by other class of molecular descriptors has also some statistical significance. To have a global QSAR model, in addition to P, some more appropriate descriptors are to be derived either experimentally or theoretically, latter being the more cost effective and easy in derivation.
-
-
-
Binding Site and Potency Prediction of Teixobactin and other Lipid II Ligands by Statistical Base Scoring of Conformational Space Maps
Authors: Claudiu N. Lungu and Mircea V. DiudeaBackground: Lipid II, a peptidoglycan, is a precursor in bacterial cell synthesis. It has both hydrophilic and lipophilic properties. The molecule translocates a bacterial membrane to deliver and incorporate “building blocks” from disaccharide-pentapeptide into the peptidoglican wall. Lipid II is a valid antibiotic target. A receptor binding pocket may be occupied by a ligand in various plausible conformations, among which only few ones are energetically related to a biological activity in the physiological efficiency domain. This paper reports the mapping of the conformational space of Lipid II in its interaction with Teixobactin and other Lipid II ligands. Methods: In order to study computationally the complex between Lipid II and ligands, a docking study was first carried on. Docking site was retrieved form literature. After docking, 5 ligand conformations and further 5 complexes (denoted 00 to 04) for each molecule were taken into account. For each structure, conformational studies were performed. Statistical analysis, conformational analysis and molecular dynamics based clustering were used to predict the potency of these compounds. A score for potency prediction was developed. Results: Appling lipid II classification according to Lipid II conformational energy, a conformation of Teixobactin proved to be energetically favorable, followed by Oritravicin, Dalbavycin, Telvanicin, Teicoplamin and Vancomycin, respectively. Scoring of molecules according to cluster band and PCA produced the same result. Molecules classified according to standard deviations showed Dalbavycin as the most favorable conformation, followed by Teicoplamin, Telvanicin, Teixobactin, Oritravicin and Vancomycin, respectively. Total score showing best energetic efficiency of complex formation shows Teixobactin to have the best conformation (a score of 15 points) followed by Dalbavycin (14 points), Oritravicin (12v points), Telvanicin (10 points), Teicoplamin (9 points), Vancomycin (3 points). Conclusion: Statistical analysis of conformations can be used to predict the efficiency of ligand - target interaction and consecutively to find insight regarding ligand potency and postulate about favorable conformation of ligand and binding site. In this study it was shown that Teixobactin is more efficient in binding with Lipid II compared to Vancomycin, results confirmed by experimental data reported in literature.
-
-
-
Hybrid Docking-QSAR Studies of 1, 4-dihydropyridine-3, 5-Dicarboxamides as Potential Antitubercular Agents
Authors: Yasaman Rasouli and Asghar DavoodBackground: Tuberculosis is one of the main medical problems and some people are suffering still from this infectious disease. 1, 4-dihydropyridines are multi-target ligands that recently are recognized as anti-tubercular agents. Methods: In the current research, computational studies were conducted of some synthesized 1, 4- dihydropyridine-3, 5-dicarboxamides in non-hydrolyzed and hydrolyzed forms to find the drugreceptor interactions profile. Results: Among equations obtained for non-hydrolyzed compounds, the model with better statistical parameters such as R2= 0.9462, q2 of LOO= 0.8318 and q2 of LMO= 0.7987 was considered as the best one and EEig08d, LAI, Mor23m, GATS3e, Mor28m descriptors were identified as the most significant factors that affect the biological activity of non-hydrolyzed compounds. Conclusion: In the hydrolyzed compounds, the model which has R2= 0.9731, q2 of LOO= 0.91154462 and q2 of LMO= 0.742 was considered as the best one and Mor27e and BEHv2 were also revealed as the most important descriptors in hydrolyzed compounds.
-
-
-
A Comparative Study on Selective PPAR Modulators through Quantitative Structure-activity Relationship, Pharmacophore and Docking Analyses
Authors: Ashis Nandy, Kunal Roy and Achintya SahaBackground: Metabolic syndrome is a matrix of different metabolic disorders which are the leading cause of death in human beings. Peroxysome proliferated activated receptor (PPAR) is a nuclear receptor involved in metabolism of fats and glucose. Objective: In order to explore structural requirements for selective PPAR modulators to control lipid and carbohydrate metabolism, the multi-cheminformatics studies have been performed. Methods: In silico modeling studies have been performed on a diverse set of PPAR modulators through quantitative structure-activity relationship (QSAR), pharmacophore mapping and docking studies. Results: It is observed that the presence of an amide fragment (–CONHRPh) has a detrimental effect while an aliphatic ether linkage has a beneficial effect on PPARα modulation. On the other hand, the presence of an amide fragment has a positive effect on PPARδ modulation, but the aliphatic ether linkage and substituted aromatic ring in the molecular scaffold are very much essential for imparting potent and selective PPARγ modulation. Negative ionizable features (i.e. polar fragments) must be present in PPARδ and α modulators, but a hydrophobic feature is the prime requirement for PPARγ modulation. Conclusion: Here, the essential structural features have been explored for selective modulation of each subtype of PPAR in order to design new modulators with improved activity/selectivity.
-
-
-
Molecular Docking Studies Applied to a Dataset of Cruzain Inhibitors
Background: Chagas' disease is one of the main causes of heart failure in developing countries. The disadvantages of current therapy include the undesirable side-effects, resistance, and therapeutic adhesion. The development of new efficient and safe drugs is, therefore, an issue of extreme importance. Objectives: In order to gain a better understanding of how the compounds interact with the target, computational methods are essential. Methods: In this theoretical study, we report a docking protocol applied to a dataset of 173 cruzain inhibitors with IC50 values of less than 10 μM, belonging 16 different chemical classes. A preliminary analysis was performed, where the best protein structure for the study was identified. Results: The enzyme was validated by redocking and a fingerprint graph for the ligand-enzyme interactions was generated, allowing the identification of the main amino acid residues related to the activity. Additionally, a larger cluster was generated, allowing the visualization of the orientation of the compounds and providing binding information for the different classes of compounds as well as their interaction in the cruzain active site. Amino acid residues other than those known as the catalytic triad (Gly23, Cys25, and Gly65) were identified, for example, Gln19 and Asp158. Conclusion: This provides a better insight into the mode of interaction of various cruzain inhibitors, which show IC50 values in the nanomolar range but which do not interact with the triad. These findings can help researchers to find new cruzain inhibitors for use in the fight against the Chagas disease.
-
-
-
Pharmacophore Modelling and 4D-QSAR Study of Ruthenium(II) Arene Complexes as Anticancer Agents (Inhibitors) by Electron Conformational- Genetic Algorithm Method
Authors: Sevtap C. Yavuz, Nazmiye Sabanci and Emin SaripinarObjective: The EC-GA method was employed in this study as a 4D-QSAR method, for the identification of the pharmacophore (Pha) of ruthenium(II) arene complex derivatives and quantitative prediction of activity. Methods: The arrangement of the computed geometric and electronic parameters for atoms and bonds of each compound occurring in a matrix is known as the electron-conformational matrix of congruity (ECMC). It contains the data from HF/3-21G level calculations. Compounds were represented by a group of conformers for each compound rather than a single conformation, known as fourth dimension to generate the model. ECMCs were compared within a certain range of tolerance values by using the EMRE program and the responsible pharmacophore group for ruthenium(II) arene complex derivatives was found. For selecting the sub-parameter which had the most effect on activity in the series and the calculation of theoretical activity values, the non-linear least square method and genetic algorithm which are included in the EMRE program were used. In addition, compounds were classified as the training and test set and the accuracy of the models was tested by cross-validation statistically. Results: The model for training and test sets attained by the optimum 10 parameters gave highly satisfactory results with R2 training= 0.817, q 2=0.718 and SEtraining=0.066, q2 ext1 = 0.867, q2 ext2 = 0.849, q2 ext3 =0.895, ccctr = 0.895, ccctest = 0.930 and cccall = 0.905. Conclusion: Since there is no 4D-QSAR research on metal based organic complexes in the literature, this study is original and gives a powerful tool to the design of novel and selective ruthenium(II) arene complexes.
-
-
-
Design, Synthesis, and Biological Evaluation of Vanillin Hydroxamic Acid Derivatives as Novel Peptide Deformylase Inhibitors
Authors: Jian Gao, Shengzhi Qiu, Li Liang, Zhixiang Hao, Qianqian Zhou, Fanfan Wang, Jie Mou and Qisi LinBackground: Infectious disease is increasingly hampering human health, which challenge the discovery of new antibacterial target. Peptide deformylase (PDF), a metalloenzyme responsible for catalyzing the removal of the N-formyl group from nascent proteins, was considered as an important target in antibacterial drug discovery. Objective: Reported here are the design, synthesis and biological evaluation of vanillin hydroxamic acid derivatives. Methods and Results: Analysis of the structure-activity relationships lead to the discovery of compound 8, which exhibits promising antibacterial activity against Escherichia coli, Staphylococcus aureus, Aspergillus oryzae, and Aspergillus foetidus with the MIC value of 0.32 μg/ml, 0.32 μg/ml, 0.16 μg/ml and 0.16 μg/ml, respectively. Furthermore, molecular docking study was applied to elucidate binding interaction between compound 8 and PDF, which indicate that compound 8 not only shares the same binding pocket with actinonin, but also has a similar binding pattern. In silico pharmacokinetic and toxicity prediction studies also suggested that compound 8 has a relatively high drug score of 0.80, and has no risk of toxicity. Conclusion: Compound 8 might represent a promising scaffold for the further development of novel antibacterial drugs.
-
Volumes & issues
-
Volume 21 (2025)
-
Volume 20 (2024)
-
Volume 19 (2023)
-
Volume 18 (2022)
-
Volume 17 (2021)
-
Volume 16 (2020)
-
Volume 15 (2019)
-
Volume 14 (2018)
-
Volume 13 (2017)
-
Volume 12 (2016)
-
Volume 11 (2015)
-
Volume 10 (2014)
-
Volume 9 (2013)
-
Volume 8 (2012)
-
Volume 7 (2011)
-
Volume 6 (2010)
-
Volume 5 (2009)
-
Volume 4 (2008)
-
Volume 3 (2007)
-
Volume 2 (2006)
-
Volume 1 (2005)
Most Read This Month
![Loading](/images/jp/spinner.gif)