scholarly journals Natural products as anti-COVID-19 agents: An in silico study

Coronaviruses ◽  
2020 ◽  
Vol 01 ◽  
Author(s):  
Chandan Sarkar ◽  
Sarmin Jamaddar ◽  
Milon Mondal ◽  
Abul Bashar Ripon Khalipha ◽  
Muhammad Torequl Islam ◽  
...  
Keyword(s):  
In Silico ◽  
Rna Virus ◽  
Antiviral Agents ◽  
Antiviral Agent ◽  
Docking Study ◽  
Asiatic Acid ◽  
Molecular Docking Study ◽  
Viral Protease ◽  
In Silico Study ◽  
To Come

Background: The coronavirus disease 2019 (COVID-19) is a life threatening viral infection caused by a positivestrand RNA virus belonging to Coronaviridae family called severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2). This virus has infected millions of peoples, and caused hundreds of thousands of deaths around the world. Unfortunately, to date, there is no specific cure for SARS-CoV-2 infection, although researchers are working tirelessly to come up with a drug against this virus. Recently, the main viral protease has been discovered, and is regarded as an appropriate target for antiviral agents in the search for treatment of SARS-CoV-2 infection, due to its role in polyproteins processing during coronavirus replication. Methodology: This investigation (an in silico study) explores the effectiveness of 16 natural compounds from a literature survey against the protease of SARS-CoV-2 in an attempt to identify a promising antiviral agent through a molecular docking study. Results: Among the 16 compounds studied, apigenin, alpha-hederin, and asiatic acid exhibited significant docking performance and interacted with several amino acid residues of the main protease of SARS-CoV-2. Conclusion: In summary, apigenin, alpha-hederin, and asiatic acid protease inhibitors may be effective potential antiviral agents against the main viral protease (Mpro) to combat SARS-CoV-2.

Evaluation of the Binding Affinity of Anti-Viral Drugs against Main Protease of SARS-CoV-2 through a Molecular Docking Study

2020 ◽  
Vol 20 ◽  
Author(s):  
Milon Mondal ◽  
Chandan Sarkar ◽  
Sarmin Jamaddar ◽  
Abul Bashar Ripon Khalipha ◽  
Muhammad Torequl Islam ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Protease Inhibitors ◽  
Binding Affinity ◽  
Rna Virus ◽  
Antiviral Treatment ◽  
Antiviral Agents ◽  
Docking Study ◽  
Multiple Organ ◽  
Molecular Docking Study ◽  
Viral Protease

Background: Coronavirus disease 2019 (COVID-19) is a life intimidating viral infection caused by a positive sense RNA virus belonging to the Coronaviridae family, named severe acute respiratory distress syndrome coronavirus 2 (SARA-CoV-2). Since its outbreak in December 2019, the pandemic has spread to more than 200 countries, infected more than 26 million, and claimed the lives of more than 800,000 people. As a disease, COVID-19 can lead to severe and occasionally fatal respiratory problems in humans. Infection with this virus is associated with fever, cough, dyspnea, and muscle aches, and it may progress to pneumonia, multiple organ failure, and death. To date, there is no specific antiviral treatment against this virus. However, the main viral protease has been recently discovered and it is regarded as an appropriate target for antiviral agents in the search for treatment of COVID-19, due to its pivotal role in polyproteins processing during viral replication. Aim: Consequently, this study intends to evaluate the effectiveness of FDA-approved anti-viral drugs against SARA-CoV-2 through a molecular docking study. Methods: AutoDock Vina in PyRx platform was used for docking analysis against the main viral protease (Mpro) (PDB ID 6LU7), and Computed Atlas of Surface Topography of proteins (CASTp 3.0) was applied for detecting and characterizing cavities, pockets, and channels of this protein structure. Results: Results revealed that among the conventional antiviral drugs, the protease inhibitors, lopinavir, amprenavir, indinavir, maraviroc, saquinavir, and daclatasvir showed high binding affinity and interacted with amino acid residues of the binding site. Conclusion: In conclusion, protease inhibitors may be effective potential antiviral agents against Mpro to combat SARSCoV-2.

scholarly journals In silico Study of the Interactions between Schiff Base Polyphenols and HPV 16 E6/E6AP/p53 complex

2021 ◽  
pp. 3973-3980
Author(s):  
Jeremiah I. Ogah ◽  
Olatunji M. Kolawole ◽  
Steven O. Oguntoye ◽  
Muhammed Mustapha Suleiman
Keyword(s):  
Molecular Docking ◽  
Anticancer Agents ◽  
In Silico ◽  
In Silico Analysis ◽  
Docking Study ◽  
Hydrogen Atoms ◽  
Molecular Docking Study ◽  
Hpv 16 ◽  
In Silico Study

The rise in the incidence of cervical cancer globally has accentuate attention to the potential role of polyphenols as anticancer agents. Different studies have demonstrated the role of some polyphenols in altering Human Papillomavirus (HPV) carcinogenesis. Thus, this study was aimed at establishing the potentials of Schiff-based polyphenols from imesatin and satin as anticancer agents through in silico analysis. The polyphenols were synthesized and characterized using elemental analyses, spectroscopic analyses, UV-visible, Infrared, and Nuclear Magnetic Resonance (1H NMR and 13C, NMR). Molecular docking study of the polyphenols was carried out using Auto Dock Vina. The oncogenic E6 protein structure of HPV 16 was obtained from the protein bank (ID: 4XR8). The E6 proteins were prepared using AutoDock tools. Water molecules were removed from the protein molecules while hydrogen atoms were added. Also, the structures of Curcumin and Isomericitrin were obtained from PubChem. Results showed that three different Schiff based polyphenols were obtained from the synthesis; 3-(2’,4’-dimethoxy benzylidene hydrazono) indoline-2-one (DMBH), 3-(2’-hydroxy-4’-methoxy benzylidene hydrazono) indoline-2-one (HMBD), and 3-((4-4’-((2’’, 4’’-dimethoxy benzylidene amino) benzyl)phenyl)imino) indoline-2-one (DMBP). Higher ability of the docked polyphenols to bind to the E6/E6AP/p53 complex when compared to Curcumin was revealed. Also, results showed that the binding energy of Curcumin and Isomericitrin were -7.1kcal/mol and -8.4kcal/mol respectively while that of the polyphenols ranged from -7.4kcal/mol to -7.9kcal/mol. The molecular docking results of the polyphenols used in this study further confirm their potentials as strong anti-cancer agents.

scholarly journals Design and In Silico Study of the Novel Small Molecular MDM2 Inhibitors

2020 ◽  
Vol 11 (1) ◽  
pp. 8052-8064
Keyword(s):  
Protein Interaction ◽  
In Silico ◽  
P53 Protein ◽  
Docking Study ◽  
Rational Approach ◽  
The Novel ◽  
Molecular Docking Study ◽  
Protein Protein Interaction ◽  
In Silico Study ◽  
Cancer Agent

Protein-protein Interaction (PPIs) plays a central role in many diseased conditions. Therefore to target and to modulate PPIs is an efficient approach for the disease treatment. Cancer is also arising because of Protein-protein interaction. In cancer, the tumor suppressor p53 protein got inhibited by the MDM2 protein. p53 protein regulates the cell cycle and apoptosis. Interaction between the p53-MDM2 proteins is responsible for the inhibition of the p53 function. By this interaction, MDM2 degrades and inhibits the p53 protein. Hence, to target and inhibit the p53-MDM2 interaction for the treatment of cancer is the rational approach. By targeting this interaction with the drugs, we can selectively kill the cancer cells over the normal cells. Recently, p53-MDM2 interaction inhibitor drugs have been reported by many researchers and pharmaceutical companies. And several drugs entered into the clinical trials. In this study, a novel 1,2,4-triazole based molecules were designed as MDM2 inhibitors and performed their in-silico study. We designed the novel compound 01 and Lead 1a. In this work, In silico study of the Lead 1a and reference compounds (Nutlin 3a, RG7112) was carried out. The molecular docking study of the Novel 1,2,4-triazole based lead 1a and reference compounds was carried out. The docking score of the Lead 1a found to be better than Nutlin 3a and close to RG7112. The various possible conformations and binding affinity values were also determined by the docking study. These results indicate the Lead 1a as a potential MDM2 inhibitor and anti-cancer agent.

Synthesis, antineoplastic activity and in silico studies of (S)-N-(1-hydroxy-3-methylbutan-2-yl)-3-(p-tolyl)-1,2,4-oxadiazole-5-carboxamide

2021 ◽  
Vol 25 (7) ◽  
pp. 167-176
Author(s):  
Cláudia Laís Araújo Almeida Santos ◽  
Jonh Anderson Macêdo Santos ◽  
Rodrigo Ribeiro Alves Caiana ◽  
Silvia Maria Souza ◽  
Jucleiton José Rufino Freitas ◽  
...  
Keyword(s):  
In Silico ◽  
Low Cost ◽  
Docking Study ◽  
New Drugs ◽  
Molecular Docking Study ◽  
Traditional Medicines ◽  
In Silico Studies ◽  
In Silico Study ◽  
Pharmacokinetic Properties ◽  
Low Toxicity

The development of chemotherapy agents without side effects is a major challenge, since traditional medicines usually have undesirable properties such as high toxicity, resistance and low bioavailability. In this sense, computational methods play a crucial role in the discovery and optimization of new drugs, as they combine speed and efficiency with low cost. The 1,2,4-oxadiazoles are one of the main classes of heterocyclics due to their numerous biological applications. In this work, we report the synthesis, antineoplastic evaluation and in silico study of a new 1,2,4-oxadiazole. The (S)-N-(1-hydroxy-3-methylbutan-2-yl)-3-(p-toluyl)-1,2,4-oxadiazole-5-carboxamide was obtained after two reaction steps in excellent yield. Although it has shown low activity in relation to the MCF-7, HCT116 and HL60 tumor cell lines, the molecular docking study indicates that this compound acts in the colchicine site and can inhibit tubulin polymerization. From the calculation of pharmacokinetic properties by the SwissADME and Osiris Property Explorer programs, it is possible to infer that the compound meets the Lipinski rules presenting good oral bioavailability and low toxicity.

scholarly journals In-silico molecular docking study of some n-substituted thiazoles derivatives as FabH inhibitors

2020 ◽  
Vol 8 (2) ◽  
pp. 043-055
Author(s):  
Shivkant Sharma ◽  
Manish Devgun ◽  
Karan Wadhwa ◽  
Sahil Banwala
Keyword(s):  
Hydrogen Bonding ◽  
In Silico ◽  
Antimicrobial Agents ◽  
Docking Study ◽  
Thiazole Derivatives ◽  
Molecular Docking Study ◽  
Molegro Virtual Docker ◽  
In Silico Study ◽  
In Silico Molecular Docking ◽  
Therapeutic Activities

Heterocyclic compounds with thiazole moiety are one of the most promising compounds in the medicinal chemistry possessing numerous therapeutic activities. The present was designed to study the high throughput in silico screening of 10 designed 2-phenyl-amino thiazole derivatives as a potent FABH inhibitor in Molegro virtual docker software (Version 6.0) using 3iL9 as PDB. The docking results showed mol dock score of -90.94 with four hydrogen bonding for the standard drugs griseofulvin, while on the other hand, N-substituted thiazole derivatives S2, S5, S6, S7, S8, and S9 exhibited excellent mol dock score, ranged from -102.612 to -144.236, hydrogen bonding (4-10), and docking score ranged from -104.873 to -143.593. Similarly, another in silico study was done using online PASS software and the compounds S1, S2, S5, S6, S7, S8, and S9 have Pa ranged between 0.310 to 0.411 and showed good antibacterial activity whereas, compounds having Pa ranged between 0.216 to 0.334 demonstrated potent antifungal activity when compared to standard drugs. Thus, the present study affirmed the significant antimicrobial potential of some designed N-substituted thiazole derivatives based on their mol dock values and other parameters when studies in silico and the obtained results will provide data support and offer perspectives in future researches to develop potent antimicrobial agents from these N-substituted thiazole derivatives.

scholarly journals Mekanisme Katekin Sebagai Obat Antidislipidemia (Uji In Silico)

2018 ◽  
Vol 46 (3) ◽  
pp. 147-154 ◽  
Author(s):  
Rosa Adelina
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Cholesterol Metabolism ◽  
Ldl Receptor ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Hmg Coa Reductase ◽  
Action Mechanisms ◽  
In Silico Study ◽  
Coa Reductase

Indonesia has a large biodiversity that can be used as a medicinal plant, one of that is Gambir. The high content of catechin in gambir has the potential to be an antidyslipidemic drug. The mechanism of catechin as antidyslipidemic drug can be traced using a molecular docking study which is one of the studies of the in silico study model used to filter compounds based on their mechanism of action against target proteins. In this study, the molecular docking of catechin was done using Molecular on Environment Software (MOE) to identify the affinity and interaction with HMG-CoA reductase and LDL enzymes that contribute to fat/cholesterol metabolism. The results of molecular docking showed that catechin interaction against HMG-CoA reductase and LDL receptor enzymes had Gibbs value of -6,5758 kcal/mol and -16,1709 kcal/mol, respectively. Potential catechin action mechanisms as antidyslipidemic use two pathways, inhibition of HMG-CoA reductase enzyme and increased LDL receptor.   Abstrak  Indonesia memiliki kekayaan hayati yang besar dan dapat dimanfaatkan sebagai tanaman obat, salah satunya gambir. Kandungan senyawa katekin yang tinggi dalam gambir berpotensi sebagai antidislipidemia. Mekanisme katekin sebagai antidislipidemia dapat ditelusuri menggunakan studi docking molekuler yang merupakan salah satu studi model studi in silico yang digunakan untuk menapis senyawa berdasarkan mekanisme kerjanya terhadap protein target. Pada penelitian ini senyawa katekin dilakukan docking secara molekuler dengan menggunakan Software Moleculer on Environtment (MOE) dengan tujuan untuk mengetahui daya afinitas dan interaksinya terhadap enzim HMG-CoA reduktase dan reseptor LDL yang berperan terhadap metabolisme kolesterol. Hasil docking molekuler menunjukkan bahwa interaksi katekin terhadap enzim HMG-CoA reduktase dan reseptor LDL memiliki nilai Gibbs  masing-masing sebesar -6,5758 kacl/mol dan -16,1709 kcal/mol. Potensi mekanisme aksi katekin sebagai antidislipidemia menggunakan dua jalur yaitu penghambatan enzim HMG-CoA reduktase dan peningkatan reseptor LDL.  

EVALUATION OF IN-SILICO ANTICANCER POTENTIAL OF PYRETHROIDS: A COMPARATIVE MOLECULAR DOCKING STUDY

2015 ◽  
Author(s):  
Manik Ghosh ◽  
Kamal Kant ◽  
Anoop Kumar ◽  
Padma Behera ◽  
Naresh Rangra ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Docking Study ◽  
Molecular Docking Study

Synthesis, SAR, In-Silico appraisal and Anti-Microbial Study of substituted 2-aminobenzothiazoles derivatives

2019 ◽  
Vol 15 ◽  
Author(s):  
Devidas G. Anuse ◽  
Suraj N. Mali ◽  
Bapu R. Thorat ◽  
Ramesh S. Yamgar ◽  
Hemchandra K. Chaudhari
Keyword(s):  
Antimicrobial Activity ◽  
In Silico ◽  
Docking Study ◽  
Moderate Activity ◽  
Molecular Docking Study ◽  
Mass Spectral ◽  
Gram Positive Bacteria ◽  
Ft Ir ◽  
In Silico Molecular Docking

Background: Antimicrobial resistance is major global health problem, which is being rapidly deteriorating the quality of human health. Series of substituted N-(benzo[d]thiazol-2-yl)-2-(4-(6-fluorobenzo[d]isoxazol-3-yl)piperidin-1-yl)acetamide (3a-j) were synthesized from substituted N-(benzo[d]thiazol-2-yl)-2-chloroacetamide/bromopropanamide (2a-j) and 6-fluoro-3-(piperidin-4-yl)benzo[d]isoxazole (2) and further evaluated for their docking properties and antimicrobial activity. Methods: All synthesized compounds were characterized by FT-IR, NMR and Mass spectral analysis. All compounds were allowed to dock against different antimicrobial targets having PDB ID: 1D7U and against common antifungal target having PDB ID: 1EA1. Results: The compounds 3d and 3h were showed good activity against Methicillin-resistant Staphylococcus aureus (MRSA, resistance Gram-positive bacteria). All synthesized compounds showed good to moderate activity against selected bacterial and fungal microbial strains. If we compared the actual in-vitro antimicrobial activity and in-silico molecular docking study, we found that molecules 3i and 3h were more potent than the others. Conclusion: Our current study would definitely pave the new way towards designing and synthesis of more potent 2-aminobenzothiazoles derivatives.

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