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Natural Compound and Natural-Like Compound Database

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The MolPort natural product files are available for download via our FTP service

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What is MolPort's Database?

The MolPort database contains data and prices for over 7.9 million compounds.

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Natural Products

Natural products are chemical compounds found in nature originating in plants, animals, and microbial and marine sources. Such products are important in the cosmetics, food, and nutrition industries because of their many beneficial properties and positive commercial image. Many active pharmaceutical compounds are natural products or derivatives of natural compounds, and it is estimated that some 40% of the drugs marketed today are derived from chemical structures found in nature. Well known examples include the anticancer agent paclitaxel (sold as Taxol), originally extracted from the Pacific yew tree; the heart medicine digoxin, extracted from the foxglove plant; and aspirin, derived from a precursor found in the leaves of the willow tree, and used for its health benefits for thousands of years. Typically, such natural compounds have better bioavailability than synthetic compounds.

In recent years there has been a revival in interest in exploring and testing natural compounds in lead discovery, as they often present a wide range of novel and exploitable structural motifs. Examples include the study of marine natural products as potential antimicrobial agents, and plant extracts as antifungal agents. There are many free and paid-access databases of natural products. These databases extract information from the scientific literature and other sources and they usually contain detailed information about each compound. However, such databases typically lack information about commercial sources of samples of these natural products, and lead discovery scientists are often frustrated by the low success rate of sourcing samples for screening.

S. O'Hagan and D.B. Kell at the University of Manchester recently published an interesting comparison of MolPort and proprietary Natural Product database data, with the goal of creating available-to-purchase natural product diversity sets. In a follow up study authors selected a small library of Natural Products to cover chemical space inexpensively. Please contact us if you are considering purchasing this or a similar natural product set, as we can provide a unique offer to meet your needs.

Another very topical application of in silico techniques to the MolPort natural products database is described in a paper published by two Egyptian academic groups. In the search for potential therapeutics active against Covid-19, they searched the MolPort database for possible inhibitors of the main SARS-CoV-2 protease. They first screened and filtered the database using molecular docking techniques to locate 5000 potential leads. These were then processed by molecular dynamics (MD) simulations and molecular mechanics (MM) binding energy calculations. Combined MD/MM calculations revealed nine potent NLPs in the MolPort database with promising binding affinities and suitable drug-likeness characteristics. This shows the value of exploring MolPort's database of available, diverse natural and natural-like products as a source of potential therapeutic agents to address critical unmet medical needs.

  • The MolPort database of commercially available compounds aggregates the catalogues of reliable chemical suppliers, many of whom also offer natural products. We have collected information on over 10,000 unique natural and over 100,000 natural-like products from our suppliers and have made it available via downloadable files. Some of the natural compounds in our selection are not listed in other commercial natural product databases.
  • The MolPort natural product files are available for download via our FTP service. You will find them in the 'Natural Products' folder in SDfiles and SMILES formats. Both formats contain the compound structure, the MolPort ID, an identifier for the highest potential class of natural compound, class description, and a link to the dedicated molecule page on molport.com
  • You can request credentials for your free access to the MolPort FTP service by contacting our Customer Support or by clicking on the button below and submitting the form
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Natural Product Classification

Upon our request, suppliers classified their natural and natural-like products according to the following ranked classification rules:

Category Abbreviation Description
Naturally sourced NS Sample isolated from a natural source
Genuine natural GN Compound occurs in nature, but the specific product may have been produced synthetically
Natural compound derivatives ND Compound is a derivative of a GN
Natural-like NL Mimetics or analogs

Suppliers Offering Natural and Natural-like Compounds

The following suppliers have already provided their data for natural products classification:

# Supplier Name Number of Products
1. InterBioScreen Ltd. 66,798
2. AnalytiCon Discovery, GmbH 30,322
3. ChemDiv, Inc. 18,497
4. ChemFaces 5,149
5. BioBioPha 3,146
6. Life Chemicals Inc. 2,593
7. Cayman Europe 2,232
8. Otava, Ltd. 1,997
9. Specs 763
10. HTS Biochemie Innovationen 429
12. Alinda Chemical, Ltd. 200
13. BIONET/Key Organics Ltd. 183
14. EDASA Scientific 134
15. Ramidus AB 105

Questions & Answers

Q/A: Does MolPort have information about the source of natural products?

Some suppliers provide this information, whereas others do not, or at least not for free. Please contact us to discuss your request. Please note that the same compounds from the same supplier can sometimes be sourced from different species, depending on the batch.

Q/A: Does MolPort work with extracts or fractions (mix of compounds)?

No. However, some of our suppliers do.

2021 MolPort, v5.36, release date 26-11-2021 19:00 (+0200). All rights reserved.
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