Biomolecular and Molecular Docking: A Modern Tool in Drug Discovery and Virtual Screening of Natural Products

Author(s):  
Khemchand R. Surana ◽  
Eknath D. Ahire ◽  
Vijayraj N. Sonawane ◽  
Swati G. Talele
2020 ◽  
Vol 840 ◽  
pp. 221-229
Author(s):  
Elsafira Ariavianti ◽  
Filia Stephanie ◽  
Usman Sumo Friend Tambunan

Dengue is one of the crucial diseases in human-caused by dengue virus (DENV) infection. However, the development of DENV antiviral is often facing a problem because no effective drug to treat infection caused by all DENV serotypes. The inhibition of host protein involved in DENV life cycle can be a potential approach in dengue drug discovery, and also avoiding antiviral resistance. Endoplasmic Reticulum (ER) α-glucosidase II is one of the target host protein in DENV endoplasmic reticulum that plays an important role in the maturation process of DENV envelope glycoprotein. Natural products have been known as an essential source of a lead compound for drug discovery due to their therapeutic potency. In this research, pharmacophore-based virtual screening and molecular docking simulations were performed to find ligand that has potential to inhibit α-glucosidase II activity. About 67,609 natural products from InterBioScreen (IBS) database were used in the simulation as ligands with α-glucosidase II as the protein target. After subjected to Lipinski’s Rule of Five, druglikeness, nasty functions, and toxicity screening using DataWarrior software, 17,462 ligands were obtained. The pharmacophore features for molecular docking simulation was obtained from Protein-Ligand Interaction Fingerprint (PLIF) analysis using eight α-glucosidase II protein with different ligands. Based on virtual screening, rigid, and flexible docking simulations using Molecular Operating Environment (MOE) software, 32 ligands have lower Gibbs free binding energy (ΔGbinding) compared to the standards. Two best ligands, namely STOCK1N-85545 and STOCK1N-86400 which belong alkaloid derivatives, showed the exceptional ligand interaction and had the lowest ΔGbinding of-11.204 and-10.276 kcal/mol, respectively. The ligands were identified to have a binding interaction with amino acid Asp564 and Asp640 in α-glucosidase II catalytic site. STOCK1N-85545 and STOCK1N-86400 were also identified to have a good pharmacological properties after subjected to ADME-tox test using Toxtree, SwissADME, admetSAR, and pkCSM software.


2020 ◽  
Author(s):  
Mohammad Seyedhamzeh ◽  
Bahareh Farasati Far ◽  
Mehdi Shafiee Ardestani ◽  
Shahrzad Javanshir ◽  
Fatemeh Aliabadi ◽  
...  

Studies of coronavirus disease 2019 (COVID-19) as a current global health problem shown the initial plasma levels of most pro-inflammatory cytokines increased during the infection, which leads to patient countless complications. Previous studies also demonstrated that the metronidazole (MTZ) administration reduced related cytokines and improved treatment in patients. However, the effect of this drug on cytokines has not been determined. In the present study, the interaction of MTZ with cytokines was investigated using molecular docking as one of the principal methods in drug discovery and design. According to the obtained results, the IL12-metronidazole complex is more stable than other cytokines, and an increase in the surface and volume leads to prevent to bind to receptors. Moreover, ligand-based virtual screening of several libraries showed metronidazole phosphate, metronidazole benzoate, 1-[1-(2-Hydroxyethyl)-5- nitroimidazol-2-yl]-N-methylmethanimine oxide, acyclovir, and tetrahydrobiopterin (THB or BH4) like MTZ by changing the surface and volume prevents binding IL-12 to the receptor. Finally, the inhibition of the active sites of IL-12 occurred by modifying the position of the methyl and hydroxyl functional groups in MTZ. <br>


2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Eleni Koulouridi ◽  
Marilia Valli ◽  
Fidele Ntie-Kang ◽  
Vanderlan da Silva Bolzani

Abstract Databases play an important role in various computational techniques, including virtual screening (VS) and molecular modeling in general. These collections of molecules can contain a large amount of information, making them suitable for several drug discovery applications. For example, vendor, bioactivity data or target type can be found when searching a database. The introduction of these data resources and their characteristics is used for the design of an experiment. The description of the construction of a database can also be a good advisor for the creation of a new one. There are free available databases and commercial virtual libraries of molecules. Furthermore, a computational chemist can find databases for a general purpose or a specific subset such as natural products (NPs). In this chapter, NP database resources are presented, along with some guidelines when preparing an NP database for drug discovery purposes.


2018 ◽  
Vol 8 (5) ◽  
pp. 504-509 ◽  
Author(s):  
Surabhi Surabhi ◽  
BK Singh

Discovery and development of a new drug is generally known as a very complex process which takes a lot of time and resources. So now a day’s computer aided drug design approaches are used very widely to increase the efficiency of the drug discovery and development course. Various approaches of CADD are evaluated as promising techniques according to their need, in between all these structure-based drug design and ligand-based drug design approaches are known as very efficient and powerful techniques in drug discovery and development. These both methods can be applied with molecular docking to virtual screening for lead identification and optimization. In the recent times computational tools are widely used in pharmaceutical industries and research areas to improve effectiveness and efficacy of drug discovery and development pipeline. In this article we give an overview of computational approaches, which is inventive process of finding novel leads and aid in the process of drug discovery and development research. Keywords: computer aided drug discovery, structure-based drug design, ligand-based drug design, virtual screening and molecular docking


Author(s):  
Ahmad Abu Turab Naqvi ◽  
Md. Imtaiyaz Hassan

Molecular docking is the prediction of conformational complementarity between ligand and receptor molecule. The process of docking integrates two schematic approaches namely sampling of ligand conformations and ranking of selected conformations based on scoring functions. The authors have discussed established methodologies for molecular docking and well-known tools implementing these methods. A brief account of different classes of scoring functions such as force field based, empirical, knowledge based, and descriptor based scoring functions is given along with the exemplary implementations of these scoring functions. By replacing test and trial based ligand screening with structure based virtual screening, molecular docking has helped in shortening the duration of novel drug discovery up to some extent. However, the developments made in the field of drug discovery are assisted by the advances in the techniques of molecular docking, but there is strong need of enrichment in the techniques, especially in scoring functions, to tackle the inbound problems of de novo drug discovery.


2022 ◽  
Vol 44 (1) ◽  
pp. 383-408
Author(s):  
Renata Priscila Barros de Menezes ◽  
Jéssika de Oliveira Viana ◽  
Eugene Muratov ◽  
Luciana Scotti ◽  
Marcus Tullius Scotti

Schistosomiasis is a chronic parasitic disease caused by trematodes of the genus Schistosoma; it is commonly caused by Schistosoma mansoni, which is transmitted by Bioamphalaria snails. Studies show that more than 200 million people are infected and that more than 90% of them live in Africa. Treatment with praziquantel has the best cost–benefit result on the market. However, hypersensitivity, allergy, and drug resistance are frequently presented after administration. From this perspective, ligand-based and structure-based virtual screening (VS) techniques were combined to select potentially active alkaloids against S. mansoni from an internal dataset (SistematX). A set of molecules with known activity against S. mansoni was selected from the ChEMBL database to create two different models with accuracy greater than 84%, enabling ligand-based VS of the alkaloid bank. Subsequently, structure-based VS was performed through molecular docking using four targets of the parasite. Finally, five consensus hits (i.e., five alkaloids with schistosomicidal potential), were selected. In addition, in silico evaluations of the metabolism, toxicity, and drug-like profile of these five selected alkaloids were carried out. Two of them, namely, 11,12-methylethylenedioxypropoxy and methyl-3-oxo-12-methoxy-n(1)-decarbomethoxy-14,15-didehydrochanofruticosinate, had plausible toxicity, metabolomics, and toxicity profiles. These two alkaloids could serve as starting points for the development of new schistosomicidal compounds based on natural products.


2020 ◽  
Author(s):  
Mohammad Seyedhamzeh ◽  
Bahareh Farasati Far ◽  
Mehdi Shafiee Ardestani ◽  
Shahrzad Javanshir ◽  
Fatemeh Aliabadi ◽  
...  

Studies of coronavirus disease 2019 (COVID-19) as a current global health problem shown the initial plasma levels of most pro-inflammatory cytokines increased during the infection, which leads to patient countless complications. Previous studies also demonstrated that the metronidazole (MTZ) administration reduced related cytokines and improved treatment in patients. However, the effect of this drug on cytokines has not been determined. In the present study, the interaction of MTZ with cytokines was investigated using molecular docking as one of the principal methods in drug discovery and design. According to the obtained results, the IL12-metronidazole complex is more stable than other cytokines, and an increase in the surface and volume leads to prevent to bind to receptors. Moreover, ligand-based virtual screening of several libraries showed metronidazole phosphate, metronidazole benzoate, 1-[1-(2-Hydroxyethyl)-5- nitroimidazol-2-yl]-N-methylmethanimine oxide, acyclovir, and tetrahydrobiopterin (THB or BH4) like MTZ by changing the surface and volume prevents binding IL-12 to the receptor. Finally, the inhibition of the active sites of IL-12 occurred by modifying the position of the methyl and hydroxyl functional groups in MTZ. <br>


2019 ◽  
Vol 20 (4) ◽  
pp. 293-301 ◽  
Author(s):  
Baoyu Yang ◽  
Jing Mao ◽  
Bing Gao ◽  
Xiuli Lu

Background:Computer-assisted drug virtual screening models the process of drug screening through computer simulation technology, by docking small molecules in some of the databases to a certain protein target. There are many kinds of small molecules databases available for drug screening, including natural product databases.Methods:Plants have been used as a source of medication for millennia. About 80% of drugs were either natural products or related analogues by 1990, and many natural products are biologically active and have favorable absorption, distribution, metabolization, excretion, and toxicology.Results:In this paper, we review the natural product databases’ contributions to drug discovery based on virtual screening, focusing particularly on the introductions of plant natural products, microorganism natural product, Traditional Chinese medicine databases, as well as natural product toxicity prediction databases.Conclusion:We highlight the applications of these databases in many fields of virtual screening, and attempt to forecast the importance of the natural product database in next-generation drug discovery.


Marine Drugs ◽  
2021 ◽  
Vol 20 (1) ◽  
pp. 29
Author(s):  
Lianxiang Luo ◽  
Ai Zhong ◽  
Qu Wang ◽  
Tongyu Zheng

Background: In the past decade, several antibodies directed against the PD-1/PD-L1 interaction have been approved. However, therapeutic antibodies also exhibit some shortcomings. Using small molecules to regulate the PD-1/PD-L1 pathway may be another way to mobilize the immune system to fight cancer. Method: 52,765 marine natural products were screened against PD-L1(PDBID: 6R3K). To identify natural compounds, a structure-based pharmacophore model was generated, following by virtual screening and molecular docking. Then, the absorption, distribution, metabolism, and excretion (ADME) test was carried out to select the most suitable compounds. Finally, molecular dynamics simulation was also performed to validate the binding property of the top compound. Results: Initially, 13 small marine molecules were screened based on the pharmacophore model. Then, two compounds were selected for further evaluation based on the molecular docking scores. After ADME and toxicity studies, molecule 51320 was selected for further verification. By molecular dynamics analysis, molecule 51320 maintains a stable conformation with the target protein, so it has the chance to become an inhibitor of PD-L1. Conclusions: Through structure-based pharmacophore modeling, virtual screening, molecular docking, ADMET approaches, and molecular dynamics (MD) simulation, the marine natural compound 51320 can be used as a small molecule inhibitor of PD-L1.


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