A structure-activity relationship study of catechol-O-methyltransferase inhibitors combining molecular docking and 3D QSAR methods

A panel of 92 catechol-O-methyltransferase (COMT) inhibitors was used to examine the molecular interactions affecting their biological activity. COMT inhibitors are used as therapeutic agents in the treatment of Parkinson's disease, but there are limitations in the currently marketed compounds due to adverse side effects. This study combined molecular docking methods with three-dimensional structure-activity relationships (3D QSAR) to analyse possible interactions between COMT and its inhibitors, and to incite the design of new inhibitors. Comparative molecular field analysis (CoMFA) and GRID/GOLPE models were made by using bioactive conformations from docking experiments, which yielded q2 values of 0.594 and 0.636, respectively. The docking results, the COMT X-ray structure, and the 3D QSAR models are in agreement with each other. The models suggest that an interaction between the inhibitor's catechol oxygens and the Mg2+ ion in the COMT active site is important. Both hydrogen bonding with Lys144, Asn170 and Glu199, and hydrophobic contacts with Trp38, Pro174 and Leu198 influence inhibitor binding. Docking suggests that a large R1 substituent of the catechol ring can form hydrophobic contacts with side chains of Val173, Leu198, Met201 and Val203 on the COMT surface. Our models propose that increasing steric volume of e.g. the diethylamine tail of entacapone is favourable for COMT inhibitory activity.     

Identification of potential CRAC channel inhibitors: Pharmacophore mapping, 3D-QSAR modelling,and molecular docking approach

Upregulation of store-operated Ca²⁺ influx via ORAI1, an integral component of the CRAC channel, is responsible for abnormal cytokine release in active rheumatoid arthritis, and therefore ORAI1 has been proposed as an attractive molecular target. In this study, we attempted to predict the mechanical insights of ORAI1 inhibitors through pharmacophore modelling, 3D-QSAR, molecular docking and free energy analysis. Various hypotheses of pharmacophores were generated and from that, a pharmacophore hypothesis with two hydrogen bond acceptors, one hydrogen bond donor and two aromatic rings (AADRR) resulted in a statistically significant 3D-QSAR model (r² = 0.84 and q² = 0.74). We believe that the obtained statistical model is a reliable QSAR model for the diverse dataset of inhibitors against the IL-2 production assay. The visualization of contours in active and inactive compounds generated from the 3D-QSAR models and molecular docking studies revealed major interaction with GLN108, HIS113 and ASP114, and interestingly, these residues are located near the Ca²⁺ selectivity filter region. Free energy binding analysis revealed that Coulomb energy, van der Waals energy and non-polar solvation terms are more favourable for ligand binding. Thus, the present study provides the physical and chemical requirements for the development of novel ORAI1 inhibitors with improved biological activity.     

Towards further understanding the structural insights of isoxazoles analogues against leishmaniasis using QSAR,molecular docking and molecular dynamics model

Leishmaniasis is one of the most well-known neglected infectious diseases, which is severe problem for public health. Heterocyclic derivatives are known to displays wide range of pharmacology activities including isoxazole ring that exhibit antileishmanial activity. Quantitative structure-activity relationship (QSAR) molecular docking and molecular dynamics are computational approaches to identify the relationships between structural properties and binding affinity of compounds. In the given paper series of 59, 4-aminomethyl 5-aryl-3-substituted isoxazoles were used to identify the structural insights and to find the binding affinity with protein. The designed model produced statistically significant results with of R² = 0.72, R²_adj = 0.65, and Q²_LMO = 0.72. Structure activity relationship (SAR) revealed that substitution of hydrophobic and steric groups may enhance the biological activity of compounds as antiprotozoal agents. Most potent compound formed hydrogen bonds with active amino acids Arg 87, Arg 104, Gly 112, His 117, Gly 118 and Asp 120. Molecular dynamics simulation (150 ns) on the docked complex of most active compound 3ba and 6 ab supported in the exploration of binding. Further MMPBSA investigations utilising MD trajectories verified compound 3bc higher binding affinity for nucleoside diphosphate kinases. The given strategies of computational studies could be an encouraging way for designing therapeutic targets against leishmaniasis.     

In silico study of remdesivir with and without ionic liquids having different cations using DFT calculations and molecular docking

The new coronavirus is trying best to kill the humanity with its highly infectious nature and its first infection was reported in 2019; later this infection was named as COVID-19. Health-care systems are still the using repurposing drugs to cure the patients from this infection. Remdesivir is found to have good potential to cure the patients from this infection and is being extensively used during the 1^st and 2^nd wave of COVID-19. Therefore, in the present work, authors have studied the interaction of remdesivir with different ionic liquids with change in cations using density functional theory calculation in gaseous and water. Based on the DFT calculations, it was found that remdesivir interacts effectively with different ionic liquids based on the energy; further, the change in free energy for Remdesivir-[Bet-ester][Lev] (1) was found to be ?3223.5758 and ?3223.6533 hartree per particle in gaseous and water respectively and most stable; further, 2 and 3 have the comparable free energies. Further, the potential of remdesivir with and without ionic liquids against the main protease of SARS-CoV-2 was investigated using molecular docking. Results revealed that Remdesivir-[Chol][Lev] (2) and Remdesivir-[Chol-ether][Lev] (3) have shown promising results with binding energy of ?129.64 ?kcal/mol and ?125.44 ?kcal/mol respectively while Remdesivir [Bet-ester][Lev] (1) have a binding energy of -123.86 kcal/mol. It is important to mention that changing the cations in ionic liquid play an important role in the docking. It is also observed that the ionic liquid having sodium as cation, then the binding energy against Mpro of CoV is poor and even less than the remdesivir alone.     

In silico drug design and molecular docking of novel amidophosphonates and sulfamidophosphonates as inhibitors of urokinase-type plasminogen activator

Cancer is one of the most serious health problems worldwide, affecting individuals from different sexes, ages, and races. However, the most frequent cancer types in the world are lung, prostate, stomach, colorectal, and esophagus in men; and breast, lung, stomach, colorectal and cervical in women. Currently, the search for new active substances used in oral targeted therapies are legitimate and opens up the possibility of an "ambulatory shift" in cancer treatment. In order to design anti-tumor drug candidates endowed with oral bioavailability, we studied trough an in silico approach the oral bioavailability of newly synthesized biomolecules; α-sulfamidophosphonates and α-amidophosphonates as well as their mechanism of action on the new target urokinase-type plasminogen activator (uPA). The studied compounds have been found to meet the five criteria of. Lipinski's rule. The Osiris, Molinspiration and SWISS/ADME calculations related to the compounds (1d, 2a) have shown that these compounds could be good candidates for interacting with the different targets, they have convincing characteristics in relation to the standard drug used. It can be concluded that these compounds are biologically important and possessing molecular properties desirable for being a drug candidate for oral use.The molecular docking results of the studied compounds revealed a good ligand-target interactions, the compounds (1d, 2a) presented a possibility of interacting as an inhibitor of the anticancer target: urokinase-type plasminogen activator (uPA).     

Cytotoxicity activity,in silico molecular docking,protein- and DNA-binding study of a new Ni(II) Schiff base complex

Abstract

One new nickel(II) complex, [Ni(L)] (1), was synthesized from the Schiff base ligand derived from pyrrole-2-carboxaldehyde and 1,3-diaminopropane. Complex 1 was characterized by elemental analysis, IR, UV-Vis and ESI mass spectroscopy, cyclic voltammetry, and single-crystal X-ray structure analysis. Crystallographic results show that two Ni(II) monomeric moieties are present with similar structural features but with slightly different bond lengths and bond angles. The geometry around the Ni(II) center is distorted square planar. DNA-binding properties of complex 1 were well explored by employing UV-Vis and fluorescence spectral methods, cyclic voltammetry, and by viscosity measurements. Similarly the protein-binding study was studied by multispectroscopic techniques using both BSA and HSA. The cytotoxicity study of the compound has also been evaluated. Notably, the in vitro cytotoxicity of complex 1 on two cancer cell lines (AGS and A549) demonstrates that complex 1 has very good anticancer activity. MTT assay, cell-cycle analysis, and annexin-V assay have been performed to know the extent of effect of complex 1 as anticancer agent. Further, in silico molecular docking study revealed that the nickel(II) complex fits into the minor groove of duplex DNA by hydrophobic interaction with functional groups of B-DNA.     

Cluster‐based molecular docking study for in silico identification of novel 6‐fluoroquinolones as potential inhibitors against Mycobacterium tuberculosis

A classical protein sequence alignment and homology modeling strategy were used for building three Mycobacterium tuberculosis‐DNA gyrase protein models using the available topoII‐DNA‐6FQ crystal structure complexes originating from different organisms. The recently determined M. tuberculosis‐DNA gyrase apoprotein structures and topoII‐DNA‐6FQ complexes were used for defining the 6‐fluoroquinolones (6‐FQs) binding pockets. The quality of the generated models was initially validated by docking of the cocrystallized ligands into their binding site, and subsequently by quantitative evaluation of their discriminatory performances (identification of active/inactive 6‐FQs) for a set of 145 6‐FQs with known biological activity values. The M. tuberculosis‐DNA gyrase model with the highest estimated discriminatory power was selected and used afterwards in an additional molecular docking experiment on a mixed combinatorial set of 427 drug‐like 6‐FQ analogs for which the biological activity values were predicted using a prebuilt counter‐propagation artificial neural network model. A novel three‐level Boolean‐based [T/F (true/false)] clustering algorithm was used to assess the generated binding poses: Level 1 (geometry properties assessment), Level 2 (score‐based clustering and selection of the (T)‐signed highly scored Level 1 poses), and Level 3 (activity‐based clustering and selection of the most “active” (T)‐signed Level 2 hits). The frequency analysis of occurrence of the fragments attached at R₁ and R₇ position of the (T)‐signed 6‐FQs selected in Level 3 revealed several novel attractive fragments and confirmed some previous findings. We believe that this methodology could be successfully used in establishing novel possible structure‐activity relationship recommendations in the 6‐FQs optimization, which could be of great importance in the current antimycobacterial hit‐to‐lead processes. © 2012 Wiley Periodicals, Inc.     

Novel indan-1,3-dione derivatives: Design,green synthesis,effect against tomato damping-off disease caused by Fusarium oxysporum and in silico molecular docking study

An effective method for synthesizing series of twenty-two new compounds 1, 2a,b, 3, 4a,b, 5a-e, 7, 8, 9, 10, 12, 13a-d, 15a,b was performed starting from reaction of 1,2,3-indenetrione thiourea, and ethyl cyanoacetate under microwave irradiation and / or 2-(1,3-dioxo-1H-inden-2(3H)-ylidene) hydrazine carbothioamide with acetic anhydride. Chemical structure of the obtained products has been established by spectroscopic techniques including FTIR, ¹H NMR, ¹³C NMR, DEPT-135, and mass spectroscopy. The designed new compounds have been successfully examined in-vitro for their antifungal activities. The relation between the structure of the synthesized compounds and their activity against tomato damping-off disease caused by Fusarium oxysporum fungi was studied and favourable results were obtained. The antifungal studies indicated that compounds 1, 7, 4a and 5a-d exerted the highest antifungal activities, while 3 and 4b recorded the lowest effect. The obtained results confirmed the possibility of the application of ethyl 6′-amino-1,3-dioxo-2′-thioxo-1,2′,3,3′-tetrahydro-1′H-spiro[indene-2,4′-pyrimidine]-5′-carboxylate 1 as a new effective regulator of the vegetative growth of tomatoes. The molecular docking analysis was performed within succinate dehydrogenase (SDH) as a target enzyme in order to rationalize the promising findings obtained for the active compounds 1, 2a,b, 5a-d, 7, 8, 9, 10, 12, and 13a.     

Molecular modeling studies of human immunodeficiency virus type 1 protease inhibitors using three‐dimensional quantitative structure‐activity relationship,virtual screening,and docking simulations

In this paper, two 3‐dimensional quantitative structure‐activity relationship models for 60 human immunodeficiency virus (HIV)‐1 protease inhibitors were established using random sampling analysis on molecular surface and translocation comparative molecular field vector analysis (Topomer CoMFA). The non–cross‐validation (r²), cross‐validation (q²), correlation coefficient of external validation (Q²_ext), and F of 2 models were 0.94, 0.80, 0.79, and 198.84 and 0.94, 0.72, 0.75, and 208.53, respectively. The results indicated that 2 models were reasonable and had good prediction ability. Topomer Search was used to search R groups in the ZINC database, 20 new compounds were designed, and the Topomer CoMFA model was used to predicate the biological activity. The results showed that 18 new compounds were more active than the template molecule. So the Topomer Search is effective in screening and can guide the design of new HIV/AIDS drugs. The mechanism of action was studied by molecular docking, and it showed that the protease inhibitors and Ile50, Asp25, and Arg8 sites of HIV‐1 protease have interactions. These results have provided an insight for the design of new potent inhibitors of HIV‐1 protease.     

A comparative QSAR analysis and molecular docking studies of phenyl piperidine derivatives as potent dual NK1R antagonists/serotonin transporter (SERT) inhibitors

Depression is a critical mood disorder that affects millions of patients. Available therapeutic antidepressant agents are associated with several undesirable side effects. Recently, it has been shown that Neurokinin 1 receptor (NK₁R) antagonists can potentiate the antidepressant effects of serotonin-selective reuptake inhibitors (SSRIs). In this study, a series of phenyl piperidine derivatives as potent dual NK₁R antagonists/serotonin transporter (SERT) inhibitors were applied to quantitative structure–activity relationship (QSAR) analysis. A collection of chemometrics methods such as multiple linear regression (MLR), factor analysis–based multiple linear regression (FA-MLR), principal component regression (PCR), and partial least squared combined with genetic algorithm for variable selection (GA-PLS) were applied to make relations between structural characteristics and NK₁R antagonism/SERT inhibitory of these compounds. The best multiple linear regression equation was obtained from GA-PLS and MLR for NK₁R and SERT, respectively. Based on the resulted model, an in silico-screening study was also conducted and new potent lead compounds based on new structural patterns were designed for both targets. Molecular docking studies of these compounds on both targets were also conducted and encouraging results were acquired. There was a good correlation between QSAR and docking results. The results obtained from validated docking studies indicate that the important amino acids inside the active site of the cavity that are responsible for essential interactions are Glu33, Asp395 and Arg26 for SERT and Ala30, Lys7, Asp31, Phe5 and Tyr82 for NK₁R receptors.     

Synthesis,molecular modeling of N-acyl benzoazetinones and their docking simulation on fungal modeled target

A series of stable N-acyl benzoazetinones have been synthesized in moderate to good yields (58–85%) from easily available substrates such as 2-(N-acyl) amino benzoic acids through intramolecular amidation under mild conditions. These geometry-optimized benzoazetinones were docked in the model target of P450, class CYP53A15, a benzoate 4-monooxygenase abundantly found in the genome of ascomycetes and Basidiomycetes classes of pathogenic fungi. Low per residue root-mean-square deviation (RMSD) of modeled structure of the enzyme indicated similar topology as template (4D6Z.pdb). Observed score judges site-specific docking, and the interaction of quantum mechanically optimized benzoazetinone derivatives with the target enzyme. These results suggest that 3i is the best antifungal agent. The specific hydrophobic substituent in the benzoazetinones contributed to the stability of ligand–target complex. Overall, the study provided insight into the specificity of the site-specific interactions, thereby, facilitating the possibility of development of broad-spectrum antifungal agents against opportunistic and infectious fungi.     

Conformational study of fosinopril sodium in solution using NMR and molecular modeling

Two conformers of fosinopril sodium in methanol were unambiguously established using 2D NMR methods and variable‐temperature NMR experiments. Differences in their conformational structure were shown to be related to the rotational energy barrier about the amide bond and hydrophobic interaction. The relationship between the 3D structure and activity is discussed. It is suggested that the trans‐conformer may be more biologically active owing to its stacking structure and strong hydrophobic interaction and the cis‐conformer could be more easily hydrolyzed because of its extended structure. Copyright © 2003 John Wiley & Sons, Ltd.     

Identification and in silico molecular modelling study of newly isolated Bacillus subtilis SI-18 strain against S9 protein of Rhizoctonia solani

The numerous bioactive components from Bacillus subtilis are commonly used as antimicrobial agents for reducing plant diseases caused by fungal pathovars. In this study, we isolated and identified B. subtilis SI-18 strain from twenty isolates of rhizosphere soil through morphological and molecular approaches, and explored its inhibitory activities against Rhizoctonia solani. According to morphological features and 16S rRNA and gyrB gene sequence analysis, B. subtilis SI-18 strain was identified. Additionally, the culture filtrate of B. subtilis SI-18 resulted in the suppression of R. solani mycelium growth and material leakage from the cells. Then, we have performed homology modelling and molecular docking study of S9 protein from R. solani where three potential compounds (D1, D2, and D3) were identified among 134 antimicrobial compounds derived from B. subtilis group based on higher binding energy and interaction at the active grove of the target protein. The D1 compound creates alkyl bond at Val48 whereas D2 also binds with Val48 by creating hydrogen bond. On the other hand, two hydrogen bonds were observed at Val48 and Ile52 by D3, which might be responsible for possible blocking of the target S9 protein of R. solani. To validate the docking study and understand the change in drug-ligand conformation, molecular dynamics simulation was assessed where rigid conformation was found for D1, D2 and D3 complexes. Moreover, ADMET study confirms that no toxicity and carcinogenicity were found for screened compounds. Based on our studies, we demonstrated that compounds D1, D2, and D3 derived from B. subtilis can be a potential inhibitor of S9 protein of R. solani that might be a possible strategy for fungal disease prevention.     

Synthesis,characterization, antimicrobial activity, 3D-QSAR,DFT, and molecular docking of some ciprofloxacin derivatives and their copper(II) complexes

Six new derivatives of ciprofloxacin compounds and their copper(II) complexes were synthesized, characterized by spectroscopic methods (ultraviolet–visible [UV–vis], Fourier transform infrared [FTIR], nuclear magnetic resonance [NMR], mass spectrometry [MS], and electron paramagnetic resonance [EPR]), and tested for antibacterial activities against gram-negative and gram-positive bacteria. The data showed that ciprofloxacin derivatives act as bidentate ligands and the metal ions coordinate through the pyridone carbonyl and the carboxylate oxygen atoms. Tetragonally distorted octahedral ligand fields were assumed for all complexes based on their spectral studies. Copper(II) complexes of the synthesized ciprofloxacin derivatives revealed higher antibacterial activities against gram-positive and gram-negative bacterial species than the parent ciprofloxacin antibiotic. Furthermore, three-dimensional quantitative structure–activity relationship (3D-QSAR) models were evaluated by studying 30 antibiotic compounds of the quinolone class. Density function theory (DFT) calculations were applied to evaluate the optimized geometrical structures using the B3LYP method and 6-311G(d,p) basis set. The 3D-QSAR study revealed that there are eight optimum parameters that give the best predictive modulation with good reliability (R² = 0.996, F = 12.004, sigma = 0.426). In silico molecular docking was also performed on the derivatives, and the results revealed the presence of two types of interactions between the Escherichia coli and the derivatives, H-bonding and Van der Waals interactions, and an effective inhibition at the docked site.     

Investigation of DNA/BSA binding of three Ru(II) complexes by various spectroscopic methods,molecular docking and their antimicrobial activity

An intercalative ligand, ppip (ppip = {2-(4-(piperidin-1-yl)phenyl)-1H-imidazo[4,5-f][1,10]phenanthroline}), and its mononuclear Ru(II) polypyridyl complexes, [Ru(phen)₂(ppip)]²⁺ (1) (phen=1,10-phenanthrolene), [Ru(bpy)₂(ppip)]²⁺ (2) (bpy=2,2′-bipyridine) and [Ru(dmb)₂(ppip)]²⁺ (3) (dmb=4,4′-dimethyl-2,2′-bipyridine), have been synthesized and characterized by elemental analysis and spectroscopic techniques such as UV–vis, IR, ¹H, as well as ¹³C NMR and ESI-MS. The interaction of these complexes with DNA/BSA (bovine serum albumin) was investigated using absorption, emission spectroscopy, viscosity measurements and molecular docking studies. The docking study infers that the binding strength (K_b) of these complexes was in agreement with results from absorption and emission techniques. These studies reveal that these three Ru(II) polypyridyl complexes bind to DNA/BSA. The binding ability of these complexes in the presence of different ions and solvents were also reported. All complexes were effectively cleaving pBR322 DNA in different forms and follows order which is similar to absorption and emission studies. These complexes were effective exhibiting the antimicrobial activity against different microbes Bacillus subtilis, Escherichia coli and Staphylococcus aureus.     

Exploring the structural requirements in multiple chemical scaffolds for the selective inhibition of Plasmodium falciparum calcium-dependent protein kinase-1 (PfCDPK-1) by 3D-pharmacophore modelling,and docking studies

Current research on antimalarial protein kinases has provided an opportunity to design kinase-based antimalarial drugs. We have developed a common feature-based pharmacophore model from a set of multiple chemical scaffolds including derivatives of 3,6-imidazopyridazines, pyrazolo[2,3-d]pyrimidines and imidazo[1,5-a]pyrazines, in order to incorporate the maximum structural diversity information in the model for the Plasmodium falciparum calcium-dependent protein kinase-1 (PfCDPK-1) target. The best pharmacophore model (Hypo-1) with the essential features of two hydrogen bond donors (HBD), one hydrophobic aromatic (HYAr) and one ring aromatic (RA) showed the classification accuracies of 86.27%, 78.43% and 100.00% in labelling the training and test set (test set-1 and test set-2) compounds into more active and less active classes. In order to identify the crucial interaction between multiple scaffold ligands and the target protein, we first developed the homology model using a template structure of P. bergheii (PbCDPK1; PDB ID: 3Q5I), and thereafter performed the docking studies. The residues such as Lys85, Phe147, Tyr148, Leu198, Val211, and Asp212 were found to be the most important interacting residues for possessing PfCDPK-1 inhibitory activity.     

DNA Binding,amelioration of oxidative stress,and molecular docking study of Zn(II) metal complex of a new Schiff base ligand

Abstract

A new Schiff base ligand, H₂L, and its Zn(II) complex were prepared and characterized by different analytical and spectroscopic techniques. The elemental analysis results suggest the stoichiometry of the complex to be 1:1. The molar conductance study shows the non-electrolytic nature of the complex. Infrared spectra reveal that the metal ion is coordinated in tetradentate fashion which was further confirmed by NMR study. The synthesized complex was found to interact with CT-DNA quite efficiently. The DNA binding study of the complex was explored by UV–vis and viscosity measurement. Fluorescence titration studies and the experimental results suggest that the complex might bind to DNA via an intercalative mode. The in silico target prediction and molecular docking experiments confirm that, apart from high interaction potentiality with nucleotides, the complex has possible implications in carcinogenesis, too.     

Comparison of 3D quantitative structure-activity relationship methods: Analysis of the in vitro antimalarial activity of 154 artemisinin analogues by hypothetical active-site lattice and comparative molecular field analysis

Two three-dimensional quantitative structure-activity relationship (3D-QSAR) methods, comparative molecular field analysis (CoMFA) and hypothetical active site lattice (HASL), were compared with respect to the analysis of a training set of 154 artemisinin analogues. Five models were created, including a complete HASL and two trimmed versions, as well as two CoMFA models (leave-one-out standard CoMFA and the guided-region selection protocol). Similar r2 and q2 values were obtained by each method, although some striking differences existed between CoMFA contour maps and the HASL output. Each of the four predictive models exhibited a similar ability to predict the activity of a test set of 23 artemisinin analogues, although some differences were noted as to which compounds were described well by either model.