in silico molecular docking
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2022 ◽  
Vol 146 ◽  
pp. 112611
Lenh Vo Van ◽  
Em Canh Pham ◽  
Cuong Viet Nguyen ◽  
Ngoc Thoi Nguyen Duong ◽  
Tuong Vi Le Thi ◽  

BMC Chemistry ◽  
2022 ◽  
Vol 16 (1) ◽  
Mona Fekadu ◽  
Digafie Zeleke ◽  
Bayan Abdi ◽  
Anuradha Guttula ◽  
Rajalakshmanan Eswaramoorthy ◽  

Abstract Background Quinolines have demonstrated various biological activities such as antimalarial, antibacterial and anticancer. Hence, compounds with such scaffold have been used as lead in drug development. This project is, therefore, aimed to synthesis and evaluates some biological activities of quinoline analogs. Methods 2-Chloro-7-fluoroquinoline-3-carbaldehydes were synthesized by the application of Vilsmeier–Haack reaction. The chlorine in the fluoroquinoline-3-carbaldehyde was replaced with various nucleophiles. The aldehyde functional group was also converted to carboxylic acid and imine groups using oxidizing agent and various amines, respectively. The structures of the compounds synthesized were characterized by spectroscopic methods. Disc diffusion and DPPH assays were used to evaluate the antibacterial and antioxidant activities, respectively. The in silico molecular docking analysis of the synthesized compounds were done using AutoDock Vina against E. coli DNA Gyrase B and human topoisomerase IIα. The drug likeness properties were assessed using SwissADME and PreADMET. Results Nine novel quinoline derivatives were synthesized in good yields. The in vitro antibacterial activity of the synthesized compounds was beyond 9.3 mm inhibition zone (IZ). Compounds 4, 5, 6, 7, 8, 10, 15, and 16 exhibited activity against E. coli, P. aeruginosa, S. aureus and S. pyogenes with IZ ranging from 7.3 ± 0.67 to 15.3 ± 0.33 mm at 200 μg/mL. Compound 9 displayed IZ against three of the bacterial strains except S. aureus. The IC50 for the radical scavenging activity of the synthesized compounds were from 5.31 to 16.71 μg/mL. The binding affinities of the synthesized compounds were from − 6.1 to − 7.2 kcal/mol against E. coli DNA gyrase B and − 6.8 to − 7.4 kcal/mol against human topoisomerase IIα. All of the synthesized compounds obeyed Lipinski’s rule of five without violation. Conclusion Compounds 4, 5, 6, 7, 8, 10, 15, and 16 displayed activity against Gram positive and Gram negative bacterial strains indicating that these compounds might be used as broad spectrum bactericidal activity. Compound 8 (13.6 ± 0.22 mm) showed better IZ against P. aeruginosa compared with ciprofloxacin (10.0 ± 0.45 mm) demonstrating the potential of this compound as antibacterial agent against this strain. Compounds 5, 6, 7, 8, 9 and 10 showed comparable binding affinities in their in silico molecular docking analysis against E. coli DNA gyrase B. All of the synthesized compounds also obeyed Lipinski’s rule of five without violation which suggests these compounds as antibacterial agents for further study. Compounds 7 and 8 were proved to be a very potent radical scavenger with IC50 values of 5.31 and 5.41 μg/mL, respectively. Compound 5, 6, 8, 10 and 16 had comparable binding affinity against human topoisomerase IIα suggesting these compounds as a possible candidate for anticancer drugs.

Molecules ◽  
2022 ◽  
Vol 27 (2) ◽  
pp. 492
Anamul Hasan ◽  
Partha Biswas ◽  
Tohmina Afroze Bondhon ◽  
Khoshnur Jannat ◽  
Tridib K. Paul ◽  

The focus of this roadmap is to evaluate the possible efficacy of Artemisia herba-alba Asso. (Asteraceae) for the treatment of COVID-19 and some of its symptoms and several comorbidities using a combination of in silico (molecular docking) studies, reported ethnic uses, and pharmacological activity studies of this plant. In this exploratory study, we show that various phytochemicals from Artemisia herba-alba can be useful against COVID-19 (in silico studies) and for its associated comorbidities. COVID-19 is a new disease, so reports of any therapeutic treatments against it (traditional or conventional) are scanty. On the other hand, we demonstrate, using Artemisia herba-alba as an example, that through a proper search and identification of medicinal plant(s) and their phytochemicals identification using secondary data (published reports) on the plant’s ethnic uses, phytochemical constituents, and pharmacological activities against COVID-19 comorbidities and symptoms coupled with the use of primary data obtained from in silico (molecular docking and molecular dynamics) studies on the binding of the selected plant’s phytochemicals (such as: rutin, 4,5-di-O-caffeoylquinic acid, and schaftoside) with various vital components of SARS-CoV-2, it may be possible to rapidly identify plants that are suitable for further research regarding therapeutic use against COVID-19 and its associated symptoms and comorbidities.

2022 ◽  
Vol 2 (1) ◽  
pp. 19
I Made Harimbawa Putra ◽  
I Putu Ari Anggara Catur Pratama ◽  
Komang Dian Aditya Putra ◽  
G. A. Desya Pradnyaswari ◽  
Ni Putu Linda Laksmiani

HER-2 overexpression is present in approximately 20% of breast cancer. This research aims to study the interactions of α-humulene to HER-2 protein by using in silico molecular docking. The experiment was carried out by HER-2 protein preparation (PDB ID 3PP0), docking validation, α-humulene optimization, and α-humulene docking. The results showed that α-humulene had binding energy of -7.50 kcal/mol, Van der Waals binding energy of -7.48 kcal/mol, and electrostatic energy of -0.02 kcal/mol. α-Humulene is potential as anti-breast cancer towards HER-2 in silico.

Antibiotics ◽  
2022 ◽  
Vol 11 (1) ◽  
pp. 79
Kamal A. Qureshi ◽  
Mahrukh Imtiaz ◽  
Adil Parvez ◽  
Pankaj K. Rai ◽  
Mariusz Jaremko ◽  

Thymoquinone (2-methyl-5-propan-2-ylcyclohexa-2,5-diene-1,4-dione; TQ), a principal bioactive phytoconstituent of Nigella sativa essential oil, has been reported to have high antimicrobial potential. Thus, the current study evaluated TQ’s antimicrobial potential against a range of selected human pathogens using in vitro assays, including time-kill kinetics and anti-biofilm activity. In silico molecular docking of TQ against several antimicrobial target proteins and a detailed intermolecular interaction analysis was performed, including binding energies and docking feasibility. Of the tested bacteria and fungi, S. epidermidis ATCC 12228 and Candida albicans ATCC 10231 were the most susceptible to TQ, with 50.3 ± 0.3 mm and 21.1 ± 0.1 mm zones of inhibition, respectively. Minimum inhibitory concentration (MIC) values of TQ are in the range of 12.5–50 µg/mL, while minimum biocidal concentration (MBC) values are in the range of 25–100 µg/mL against the tested organisms. Time-kill kinetics of TQ revealed that the killing time for the tested bacteria is in the range of 1–6 h with the MBC of TQ. Anti-biofilm activity results demonstrate that the minimum biofilm inhibitory concentration (MBIC) values of TQ are in the range of 25–50 µg/mL, while the minimum biofilm eradication concentration (MBEC) values are in the range of 25–100 µg/mL, for the tested bacteria. In silico molecular docking studies revealed four preferred antibacterial and antifungal target proteins for TQ: D-alanyl-D-alanine synthetase (Ddl) from Thermus thermophilus, transcriptional regulator qacR from Staphylococcus aureus, N-myristoyltransferase from Candida albicans, and NADPH-dependent D-xylose reductase from Candida tenuis. In contrast, the nitroreductase family protein from Bacillus cereus and spore coat polysaccharide biosynthesis protein from Bacillus subtilis and UDP-N-acetylglucosamine pyrophosphorylase from Aspergillus fumigatus are the least preferred antibacterial and antifungal target proteins for TQ, respectively. Molecular dynamics (MD) simulations revealed that TQ could bind to all four target proteins, with Ddl and NADPH-dependent D-xylose reductase being the most efficient. Our findings corroborate TQ’s high antimicrobial potential, suggesting it may be a promising drug candidate for multi-drug resistant (MDR) pathogens, notably Gram-positive bacteria and Candida albicans.

2021 ◽  
Vol 1 (1) ◽  
pp. 15
I Gede Bayu Krisnayana ◽  
Putu Dewi Febyani ◽  
Ida Ayu Yadnyaningtias Permata Sari ◽  
Ni Putu Linda Laksmiani

The accumulation of UV exposure resulted in the loss of skin elasticity, and the appearance of wrinkles on the skin is commonly known as photoaging. Matrix metalloproteinase-1 (MMP-1) is an enzyme that degrades type I and III fibrillar collagen. This study aims to determine the mechanism of MMP-1 inhibition by lutein, a carotenoid compound with high antioxidant activity, using in silico molecular docking. This study was conducted by optimization of lutein structure using HyperChem 8, preparation of MMP-1 (PDB ID: 966C) using Chimera 1.10.1, validation of the method, and docking lutein against MMP-1 using Autodock 4.2. The results showed lutein had binding energy of -12.28 kcal/mol, lower than RS2 native ligand (-10.83 kcal/mol). The hydrogen bond formed between lutein and MMP-1 through HIS228 residue. To conclude, lutein may be developed as an anti-photoaging agent by inhibiting the MMP-1.

2021 ◽  
Vol 20 (2) ◽  
pp. 177-183
Sajan Das ◽  
Muhammad Shah Mohtasim Khan ◽  
Md Shawkatul Islam Bakhtiar ◽  
Mohammad Shahriar

In this present world COVID-19 pandemic is one of the biggest concern. An appealing medication focus among Covids is the fundamental protease; SARS-CoV-2 protease Mpro (6Y2F) due to its fundamental role in handling the polyproteins that are interpreted from the viral RNA. The present study showed the interaction of favipiravir, ganciclovir, raltegravir and remdesivir against 6Y2F, using molecular docking were analyzed. Among those ligands’ interaction with protein structure, 6Y2F on raltegravir (-7.4 kcal/mol) and remdesivir (-6.9 kcal/mol), respectively displayed maximum binding affinity. The interactions of four ligands were contrasted with each other in that ganciclovir and raltegravir form highest number of hydrogen bond with 6Y2F. The interacting amino acids residues (Gly143, Ser144, Cys145) were studied and all selected ligands were predicted to be non-carcinogens and non-AMES toxic. Dhaka Univ. J. Pharm. Sci. 20(2): 177-183, 2021 (December)

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