Virtual Screening and Target Fishing for Natural Products Using 3D Pharmacophores

2013 ◽  
pp. 129-152
Keyword(s):  
Natural Products ◽  
Virtual Screening ◽  
Target Fishing

Virtual Screening for Novel Staphylococcus Aureus NorA Efflux Pump Inhibitors From Natural Products

2015 ◽  
Vol 11 (2) ◽  
pp. 135-155 ◽  
Author(s):  
Khac-Minh Thai ◽  
Trieu-Du Ngo ◽  
Thien-Vy Phan ◽  
Thanh-Dao Tran ◽  
Ngoc-Vinh Nguyen ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Natural Products ◽  
Virtual Screening ◽  
Efflux Pump ◽  
Efflux Pump Inhibitors

scholarly journals Natural products as inhibitors of COVID-19 main protease – A virtual screening by molecular docking

2020 ◽  
Author(s):  
Marzieh omrani ◽  
Mohammad Bayati ◽  
Parvaneh Mehrbod ◽  
Samad Nejad-Ebrahimi
Keyword(s):  
Natural Products ◽  
Virtual Screening ◽  
High Throughput ◽  
Herbal Medicines ◽  
Respiratory Illness ◽  
Fast Method ◽  
Main Protease ◽  
Glide Docking ◽  
Adme Properties ◽  
High Throughput Virtual Screening

Abstract Background: The novel coronavirus (2019-nCoV) causes a severe respiratory illness that was unknown in the human before. Its alarmingly quick transmission to many countries across the world resulted in a worldwide health emergency. It has caused a notable percentage of morbidity and mortality. Therefore, an imminent need for drugs to combat this disease has been increased. Global collaborative efforts from scientists are underway to find a therapy to treat infections and reduce death cases. Herbal medicines and purified natural products have been reported to have antiviral activity against Coronaviruses (CoVs).Methods: In this study, a High Throughput Virtual Screening (HTVS) protocol was used as a fast method on the discovery of novel drug candidates as the COVID-19 main protease inhibitors. Over 180,000 natural product-based compounds were obtained from the ZINC database and virtually screened against the COVID-19 main protease. In this study, the Glide docking program was applied for high throughput virtual screening. Extra precision (XP) and in a combination of Prime module, induced-fit docking (IFD) approach was also used. Additionally, the ADME properties of all compounds were analyzed, and the final selection was carried out based on the Lipinski rule of five. Results: The nineteen compounds were selected and introduced as new potential inhibitors. The compound ZINC08765174 (1-[3-(1H-indol-3-yl) propanoyl]-N-(4-phenylbutan-2-yl)piperidine-3-carboxamide) showed a strong binding affinity (-11.5 kcal/mol) to the crucial residues of COVID-19 main protease comparing to peramivir (-9.8 kcal/mol) as a positive control.Conclusions: The excellent ADME properties proposed the opportunity of this compound to be a promising candidate for the treatment of COVID-19.

Acetylcholinesterase Inhibitory Activity of Scopolin and Scopoletin Discovered by Virtual Screening of Natural Products†

2004 ◽  
Vol 47 (25) ◽  
pp. 6248-6254 ◽  
Author(s):  
Judith M. Rollinger ◽  
Ariane Hornick ◽  
Thierry Langer ◽  
Hermann Stuppner ◽  
Helmut Prast
Keyword(s):  
Natural Products ◽  
Virtual Screening ◽  
Inhibitory Activity ◽  
Acetylcholinesterase Inhibitory Activity

A primer on natural product-based virtual screening

2019 ◽  
Vol 4 (6) ◽  
Author(s):  
Eleni Koulouridi ◽  
Marilia Valli ◽  
Fidele Ntie-Kang ◽  
Vanderlan da Silva Bolzani
Keyword(s):  
Natural Products ◽  
Drug Discovery ◽  
Molecular Modeling ◽  
Virtual Screening ◽  
Natural Product ◽  
General Purpose ◽  
Target Type ◽  
Computational Techniques ◽  
Specific Subset ◽  
Virtual Libraries

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.

scholarly journals In Silico De Novo Curcuminoid Derivatives From the Compound Library of Natural Products Research Laboratories Inhibit COVID-19 3CLpro Activity

2020 ◽  
Vol 15 (9) ◽  
pp. 1934578X2095326
Author(s):  
Jai-Sing Yang ◽  
Jo-Hua Chiang ◽  
Shih‑Chang Tsai ◽  
Yuan-Man Hsu ◽  
Da-Tian Bau ◽  
...  
Keyword(s):  
Natural Products ◽  
Virtual Screening ◽  
Binding Affinity ◽  
High Throughput ◽  
In Silico ◽  
De Novo ◽  
Compound Library ◽  
Therapeutic Success ◽  
High Throughput Virtual Screening

The coronavirus disease 2019 (COVID‐19) outbreak caused by the 2019 novel coronavirus (2019-nCOV) is becoming increasingly serious. In March 2019, the Food and Drug Administration (FDA) designated remdesivir for compassionate use to treat COVID-19. Thus, the development of novel antiviral agents, antibodies, and vaccines against COVID-19 is an urgent research subject. Many laboratories and research organizations are actively investing in the development of new compounds for COVID-19. Through in silico high-throughput virtual screening, we have recently identified compounds from the compound library of Natural Products Research Laboratories (NPRL) that can bind to COVID-19 3Lpro polyprotein and block COVID-19 3Lpro activity through in silico high-throughput virtual screening. Curcuminoid derivatives (including NPRL334, NPRL339, NPRL342, NPRL346, NPRL407, NPRL415, NPRL420, NPRL472, and NPRL473) display strong binding affinity to COVID-19 3Lpro polyprotein. The binding site of curcuminoid derivatives to COVID-19 3Lpro polyprotein is the same as that of the FDA-approved human immunodeficiency virus protease inhibitor (lopinavir) to COVID-19 3Lpro polyprotein. The binding affinity of curcuminoid derivatives to COVID-19 3Lpro is stronger than that of lopinavir and curcumin. Among curcuminoid derivatives, NPRL-334 revealed the strongest binding affinity to COVID-19 3Lpro polyprotein and is speculated to have an anti-COVID-19 effect. In vitro and in vivo ongoing experiments are currently underway to confirm the present findings. This study sheds light on the drug design for COVID-19 3Lpro polyprotein. Basing on lead compound development, we provide new insights on inhibiting COVID-19 attachment to cells, reducing COVID-19 infection rate and drug side effects, and increasing therapeutic success rate.

scholarly journals Cover Picture: Inhibitors of HIV-1 Integrase-Human LEDGF/p75 Interaction Identified from Natural Products via Virtual Screening (Chin. J. Chem. 12/2012)

2012 ◽  
Vol 30 (12) ◽  
pp. 2729-2729
Author(s):  
Guoping Hu ◽  
Xi Li ◽  
Yaozong Li ◽  
Xianqiang Sun ◽  
Guixia Liu ◽  
...  
Keyword(s):  
Natural Products ◽  
Virtual Screening ◽  
Hiv 1

Identification of new p300 histone acetyltransferase inhibitors from natural products by a customized virtual screening method

RSC Advances ◽  
2016 ◽  
Vol 6 (66) ◽  
pp. 61137-61140 ◽  
Author(s):  
Guo-Bo Li ◽  
Lu-Yi Huang ◽  
Hui Li ◽  
Sen Ji ◽  
Lin-Li Li ◽  
...  
Keyword(s):  
Natural Products ◽  
Virtual Screening ◽  
Histone Acetyltransferase ◽  
Screening Method ◽  
Natural Compounds

The natural compounds NP-2, NP-3, NP-9, and NP-15 were found to be potent p300 HAT inhibitors by a customized structure-based virtual screening method.

Network pharmacology-based virtual screening of natural products from Clerodendrum species for identification of novel anti-cancer therapeutics

2017 ◽  
Vol 13 (2) ◽  
pp. 406-416 ◽  
Author(s):  
Barbi Gogoi ◽  
Dhrubajyoti Gogoi ◽  
Yumnam Silla ◽  
Bibhuti Bhushan Kakoti ◽  
Brijmohan Singh Bhau
Keyword(s):  
Natural Products ◽  
Virtual Screening ◽  
Cancer Therapeutics ◽  
Network Pharmacology ◽  
Anticancer Compounds ◽  
Pharmacological Approach ◽  
Anti Cancer

In the present work, latest network pharmacological approach has been used for the screening of natural anticancer compounds from Clerodendrum species.

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