scholarly journals IN SILICO STUDIES OF N-(PHENYL SUBSTITUTED) 2-([PHENYL SUBSTITUTED) METHYLIDENE] AMINO)-N,4- DIPHENYL-6H-1,3-OXAZIN-6-AMINE DERIVATIVES AS POTENTIAL ANTIBACTERIAL AGENTS

2021 ◽  
Vol 12 (8) ◽  
pp. 41-45
Author(s):  
K.P. Beena
Keyword(s):  
Cell Wall ◽  
Binding Energy ◽  
Essential Role ◽  
Antibacterial Agents ◽  
Docking Study ◽  
Efficacy And Safety ◽  
Protein Target ◽  
In Silico Studies ◽  
Key Residues ◽  
Oxazine Derivatives

Resistance to bacteria is a growing threat to human health worldwide. The rate of discovery of new antibacterial is far outshined by the rate at which resistance is spreading. Therefore, there remains a pressing need for the development of new antibacterial drugs. Recent alarm estimates that deaths due to antimicrobial resistance may increase from 700,000 million lives annually by 2050. Glucosamine-6-phosphate (GlcN-6-P) synthase represents an interesting protein target because it plays an essential role in the protection of cell wall. The primary aim and objective of this study is to identify lead molecules as promising antibacterial agents by inhibiting Glucosamine-6-phosphate (GlcN-6-P) synthase enzyme. Autodock 4. 2, the effective tool for exploring the binding affinity of small molecule to enzyme target was used to study the interactions between the oxazine derivatives and the GlcN-6-P synthase binding site. The ligands were optimized for improving their efficacy and safety. Lead optimization was performed using Molinspiration server and the ligands were optimized for evaluating their oral bioavailability. With Glucosamine 6 phosphate synthase receptor, the binding energy was found to be best for 5 compounds SZ-3 (-5.27 kcal/mol), SZ-4 (-6.02 kcal/mol), SZ-5 (-5.35 kcal/mol), SZ-8 (-5.62kcal/mol), SZ-10 (-5.29 kcal/mol) when compared to the standard ligand, Ciprofloxacin (-5.09 kcal/mol) and were interacting well with the key residues TYR 304, GLU 438, LEU 484. Docking study strongly enhanced the activity of oxazine derivatives as new discovered hits.

De novo Design and in-silico Studies of Coumarin Derivatives as Inhibitors of Cyclin Dependent Kinase-2

2017 ◽  
Vol 4 (4) ◽  
pp. 46-56
Author(s):  
Ashok Sharma ◽  
Badvel Pallavi ◽  
Riddhidev Banerjee ◽  
Mariasoosai Ramya Chandar Charles ◽  
Mohane Selvaraj Coumar ◽  
...  
Keyword(s):  
Binding Energy ◽  
In Silico ◽  
De Novo ◽  
Docking Study ◽  
Binding Mode ◽  
Coumarin Derivatives ◽  
Standard Drug ◽  
Lipinski’S Rule ◽  
In Silico Studies ◽  
Binding Cavity

In the present study, around sixty-two novel coumarin derivatives were designed as CDK-2 inhibitors based on essential pharmacophoric requirements. All the designed compounds were subjected to docking study using AutoDock 4.2 against CDK-2 protein (PDB ID: 1HCK). Molinspiration and Osiris property explorer were used to predict Lipinski’s rule of five and toxicity profile. The Structure Activity Relationship study revealed that, the substitution at R1 and R4 of coumarin nucleus enhances the binding energy and inhibitory constant values from nanomolar to picomolar range. Among the designed analogues, compound 15, 28, 43 and 59 showed significant binding energy and inhibitory constant values as compared to the standard drug Olomoucine and Deschloroflavopiridol. Most of the designed analogues showed similar binding mode and orientation inside the active site of the protein as that of the standard drug, which strongly indicates that the designed molecules may emerge as potent inhibitors of CDK-2. Next, molecular dynamics study of the significantly active molecule 15 was studied for 10 ns, in order to determine the stability of the coumarin molecules inside the binding cavity of the protein. In-silico investigations suggest that the de novo designed coumarin derivatives were potentially in-silico bioactive and need to be synthesized and tested further.

scholarly journals New Benzoxazole Derivatives as Antiprotozoal Agents: In Silico Studies, Synthesis, and Biological Evaluation

2021 ◽  
Vol 2021 ◽  
pp. 1-11
Author(s):  
Mohamed A. Abdelgawad ◽  
Mohammad M. Al-Sanea ◽  
Mohamed A. Zaki ◽  
Enas I. A. Mohamed ◽  
Shabana I. Khan ◽  
...  
Keyword(s):  
Antimicrobial Agents ◽  
Antimalarial Activity ◽  
Biological Activities ◽  
Docking Study ◽  
Antimicrobial Activities ◽  
Biological Evaluation ◽  
Molecular Docking Study ◽  
Chromatographic Separations ◽  
Major Mechanism ◽  
In Silico Studies

Background. Benzoxazole derivatives have different biological activities. In pursuit of designing novel chemical entities with antiprotozoal and antimicrobial activities, benzoxazolyl aniline was utilized as a privileged scaffold of a series of (3-benzoxazole-2-yl) phenylamine derivatives, 3-benzoxazoloyl acetamide, and butyramide derivatives. Methods. These novel analogs were synthesized in straightforward simple chemistry without any quantitative chromatographic separations in reasonable yields. The biological evaluation of all target compounds as potential antimalarial, antileishmanial, antitrypanosomal, and antimicrobial agents was performed by various well-established cell-based methods. Results. Compounds 6d and 5a showed promising biological screening data. The amidation of 3-benzoxazolyl aniline 1 with the chloroacetyl functional group resulted in a good antimalarial activity and showed moderate inhibitory activities against leishmanial and trypanosomal spp. Moreover, chloroacetyl functionalization of benzoxazolyl aniline serves as a good early goal for constructing and synthesizing new antimicrobial and antiprotozoal agents. The molecular docking study rationalizes the relative inhibitory activity of compound 5a as an antimalarial agent with the deregulation of PfPNP activity which has emerged as a major mechanism of these targets.

IN VITRO AND IN SILICO ALPHA-AMYLASE INHIBITION POTENTIAL (ANTI-DIABETIC ACTIVITY) OF PSEUDERANTHEMUM BICOLOR (SIMS) RADIK

2020 ◽  
pp. 157-161
Author(s):  
RAMESH BS ◽  
LOKESH RAVI
Keyword(s):  
Binding Energy ◽  
Hydrogen Bonds ◽  
Ethyl Acetate ◽  
Bioactive Compounds ◽  
Methyl Ether ◽  
Docking Study ◽  
Alpha Amylase ◽  
Ligand Docking ◽  
Standard Drug ◽  
Reference Drug

Objective: Aim of this study is to evaluate theanti-diabetic activity of Pseuderanthemum bicolor commonly called limang-sugat by inhibiting alpha-amylase protein. Methods: Leaves of P. bicolor were extracted with methanol, chloroform, and ethyl acetate. The extracts were subjected for alpha-amylase inhibition assay and gas chromatography–mass spectrometry (GC–MS) analysis. Phytochemical compounds identified by GC-MS were subjected for protein-ligand docking study against alpha-amylase protein. Acarbose was used as a positive standard drug. Results: The major bioactive compounds obtained from methanol, chloroform, and ethyl acetate extracts were 1,6;2,3-Dianhydro-4-Deoxy-Beta-D-Ribo-Hexopyranose, Pseduosarsasapogenin-5,20-Dien, methyl ether/Hexatriacontane, Di-N-decylsulfone/Octadecanal, and squalene, respectively. A total of 19 secondary metabolites were subjected for protein–ligand docking study against the alpha-amylase protein. The reference drug acarbose demonstrated binding energy of −7.8 Kcal/mol and formed 20 hydrogen bonds with the enzyme. Acarbose signified high polar interaction with the amylase enzyme. Among the 19 test ligands, “2,2-Dibromocholestanone” from ethyl acetate extract exemplified the highest binding energy of −9.3 Kcal/mol. The next highest remarkable inhibition was showed by “Pseduosarsasapogenin-5,20-Dien Methyl Ether” present in the methanol extract, with a binding energy of -9.3 Kcal/mol with the formation of 2 hydrogen bonds. Conclusion: From the result, it could be concluded that the P. bicolor leaves contain various bioactive compounds which are considered as a good anti-diabetic drug.

scholarly journals An organometallic structure-activity relationship study reveals the essential role of a Re(CO)3moiety in the activity against gram-positive pathogens including MRSA

2015 ◽  
Vol 6 (1) ◽  
pp. 214-224 ◽  
Author(s):  
Malay Patra ◽  
Michaela Wenzel ◽  
Pascal Prochnow ◽  
Vanessa Pierroz ◽  
Gilles Gasser ◽  
...  
Keyword(s):  
Essential Role ◽  
Antibacterial Agents ◽  
Structure Activity Relationship ◽  
Activity Relationship ◽  
Gram Positive ◽  
Structural Class ◽  
Structure Activity ◽  
Systematic Structure ◽  
Relationship Study

A systematic structure activity relationship reveals the contribution of individual organometallic moieties to the potency of a new structural class of hetero-trimetallic antibacterial agents.

scholarly journals Molecular insight into isoform specific inhibition of PI3K-α and PKC-η with dietary agents through an ensemble pharmacophore and docking studies

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Baki Vijaya Bhaskar ◽  
Aluru Rammohan ◽  
Tirumalasetty Munichandra Babu ◽  
Gui Yu Zheng ◽  
Weibin Chen ◽  
...  
Keyword(s):  
Binding Energy ◽  
Anticancer Agents ◽  
Drug Targets ◽  
Binding Pocket ◽  
Pharmacophore Modeling ◽  
Boswellic Acid ◽  
Lead Compounds ◽  
Donor And Acceptor ◽  
In Silico Studies ◽  
Dietary Agents

AbstractDietary compounds play an important role in the prevention and treatment of many cancers, although their specific molecular mechanism is not yet known. In the present study, thirty dietary agents were analyzed on nine drug targets through in silico studies. However, nine dietary scaffolds, such as silibinin, flavopiridol, oleandrin, ursolic acid, α-boswellic acid, β-boswellic acid, triterpenoid, guggulsterone, and oleanolic acid potentially bound to the cavity of PI3K-α, PKC-η, H-Ras, and Ras with the highest binding energy. Particularly, the compounds silibinin and flavopiridol have been shown to have broad spectrum anticancer activity. Interestingly, flavopiridol was embedded in the pockets of PI3K-α and PKC-η as bound crystal inhibitors in two different conformations and showed significant interactions with ATP binding pocket residues. However, complex-based pharmacophore modeling achieved two vital pharmacophoric features namely, two H-bond acceptors for PI3K-α, while three are hydrophobic, one cat-donor and one H-bond donor and acceptor for PKC-η, respectively. The database screening with the ChemBridge core library explored potential hits on a valid pharmacophore query. Therefore, to optimize perspective lead compounds from the hits, which were subjected to various constraints such as docking, MM/GBVI, Lipinski rule of five, ADMET and toxicity properties. Henceforth, the top ligands were sorted out and examined for vital interactions with key residues, arguably the top three promising lead compounds for PI3K-α, while seven for PKC-η, exhibiting binding energy from − 11.5 to − 8.5 kcal mol−1. Therefore, these scaffolds could be helpful in the development of novel class of effective anticancer agents.

scholarly journals Ethers and esters derived from apocynin avoid the interaction between p47phox and p22phox subunits of NADPH oxidase: evaluation in vitro and in silico

2013 ◽  
Vol 33 (4) ◽  
Author(s):  
Martha Edith Macías-Pérez ◽  
Federico Martínez-Ramos ◽  
Itzia Irene Padilla-Martínez ◽  
José Correa-Basurto ◽  
Lowell Kispert ◽  
...  
Keyword(s):  
Nadph Oxidase ◽  
In Silico ◽  
Transmembrane Protein ◽  
Vascular Diseases ◽  
Docking Study ◽  
Free Radical Scavengers ◽  
Phenyl Ester ◽  
Paramagnetic Resonance ◽  
In Silico Studies

NOX (NADPH oxidase) plays an important role during several pathologies because it produces the superoxide anion (O2•−), which reacts with NO (nitric oxide), diminishing its vasodilator effect. Although different isoforms of NOX are expressed in ECs (endothelial cells) of blood vessels, the NOX2 isoform has been considered the principal therapeutic target for vascular diseases because it can be up-regulated by inhibiting the interaction between its p47phox (cytosolic protein) and p22phox (transmembrane protein) subunits. In this research, two ethers, 4-(4-acetyl-2-methoxy-phenoxy)-acetic acid (1) and 4-(4-acetyl-2-methoxy-phenoxy)-butyric acid (2) and two esters, pentanedioic acid mono-(4-acetyl-2-methoxy-phenyl) ester (3) and heptanedioic acid mono-(4-acetyl-2-methoxy-phenyl) ester (4), which are apocynin derivatives were designed, synthesized and evaluated as NOX inhibitors by quantifying O2•− production using EPR (electron paramagnetic resonance) measurements. In addition, the antioxidant activity of apocynin and its derivatives were determined. A docking study was used to identify the interactions between the NOX2′s p47phox subunit and apocynin or its derivatives. The results showed that all of the compounds exhibit inhibitory activity on NOX, being 4 the best derivative. However, neither apocynin nor its derivatives were free radical scavengers. On the other hand, the in silico studies demonstrated that the apocynin and its derivatives were recognized by the polybasic SH3A and SH3B domains, which are regions of p47phox that interact with p22phox. Therefore this experimental and theoretical study suggests that compound 4 could prevent the formation of the complex between p47phox and p22phox without needing to be activated by MPO (myeloperoxidase), this being an advantage over apocynin.

scholarly journals Fluconazole and Lipopeptide Surfactin Interplay During Candida albicans Plasma Membrane and Cell Wall Remodeling Increases Fungal Immune System Exposure

Pharmaceutics ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 314 ◽  
Author(s):  
Jakub Suchodolski ◽  
Daria Derkacz ◽  
Jakub Muraszko ◽  
Jarosław J. Panek ◽  
Aneta Jezierska ◽  
...  
Keyword(s):  
Cell Wall ◽  
Candida Albicans ◽  
Plasma Membrane ◽  
Immune System ◽  
Antifungal Drugs ◽  
Stable Complex ◽  
Host Immune System ◽  
Chitin Synthesis ◽  
Fungal Cell ◽  
In Silico Studies

Recognizing the β-glucan component of the Candida albicans cell wall is a necessary step involved in host immune system recognition. Compounds that result in exposed β-glucan recognizable to the immune system could be valuable antifungal drugs. Antifungal development is especially important because fungi are becoming increasingly drug resistant. This study demonstrates that lipopeptide, surfactin, unmasks β-glucan when the C. albicans cells lack ergosterol. This observation also holds when ergosterol is depleted by fluconazole. Surfactin does not enhance the effects of local chitin accumulation in the presence of fluconazole. Expression of the CHS3 gene, encoding a gene product resulting in 80% of cellular chitin, is downregulated. C. albicans exposure to fluconazole changes the composition and structure of the fungal plasma membrane. At the same time, the fungal cell wall is altered and remodeled in a way that makes the fungi susceptible to surfactin. In silico studies show that surfactin can form a complex with β-glucan. Surfactin forms a less stable complex with chitin, which in combination with lowering chitin synthesis, could be a second anti-fungal mechanism of action of this lipopeptide.

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