Brazilian database of natural products receives international recognition

Journal of Natural Products highlights database that includes information on the potential of these secondary metabolites for use in medicinal chemistry, ecological chemistry, and metabolomics.

By José Tadeu Arantes

Agência FAPESP – Two important international organizations recently attested to the quality of the NuBBE Database, which is a landmark database of the isolated natural products from Brazil’s biodiversity and includes information on the potential of these secondary metabolites for use in medicinal chemistry, ecological chemistry, and metabolomics.  

The first recognition of this resource was from the publication of the article “Development of a Natural Products Database from the Biodiversity of Brazil” in the Journal of Natural Products, which penned a piece on the NuBBE Database. Coedited by the American Society of Pharmacognosy and the American Chemical Society, this periodical is considered one of the best in the world in the area of natural products chemistry. 

The second recognition was ZINC’s request to establish a cross-link to the NuBBE Database, which would effectively connect the two databases. ZINC is a service of the Shoicet Laboratory of the University of California San Francisco's Department of Pharmaceutical Chemistry and is a reference in the field of medicinal chemistry because it provides information on the more than 21 million pharmaceutical compounds that are available in the market.

Strengthened by the international acclaim, the NuBBE Database was created through cooperation between the Centers of Biotesting, Biosynthesis, and Ecophysiology (NuBBE) at the Universidade Estadual Paulista (Unesp) Araraquara campus and the Laboratory of Medicinal and Computational Chemistry (LQMC), the São Carlos Physics Institute, and Universidade de São Paulo (USP).

The database makes data available on 640 compounds of natural origins that have been studied by NuBBE over its 15 years of existence. The coordinators – professors Vanderlan Bolzani of Unesp and Adriano Defini Andricopulo of USP São Carlos – expect the database to continue to grow until it encompasses all of the compounds with potential medicinal uses that are isolated in Brazilian biomes. To this end, the coordinators are seeking state and federal institutional support.

The inspiration for the creation of this database came after its participation in a 2005 scientific congress in China, commented Bolzani, full professor at the Unesp’s Chemistry Institute at the Araraquara campus and idealizer of the NuBBE Database. “I was fascinated by the database on natural products utilized by Chinese medicine,” affirmed Bolzani, who is also a member of the BIOTA-FAPESP coordination team.

The idea took shape in a conversation with Andricopulo, coordinator of LQMC, who has broad experience in the development of robust databases, such as PK/DB, which is the first database on pharmacokinetics in Latin America and was created in the Medicinal and Computational Chemistry Laboratory. The result was a successful partnership between the two institutions.

Doctoral students Marilia Valli (NuBBE) and Ricardo Nascimento dos Santos (LQMC), both of whom are FAPESP fellows, and scientific initiation student, Cíntia Hiromi Nakajima (company fellow) are firmly engaged in the systemization of the data, which were previously dispersed into 170 scientific articles produced by NuBBE. Leandro Figueira, who holds a master’s in computer science, installed this information in the computing environment to create an open virtual database that can be expanded and updated. 

Nature as a laboratory

The database is hosted on the site nubbe.iq.unesp.br/nubbeDB.html. At the moment, the portal is in its testing stages, and access may be difficult because of the adjustments that are being made to the system. The intention of the coordinators, however, is for the portal to be up and running in the first half of 2013, at which point the portal should allow full access to associated research groups. Soon after some security mechanisms are developed, the general public will be able access the database.

Once given access, users can select any of the 640 compounds described – from Acremonium sp. to Xylopia aethiopica – and obtain detailed information, such as the compound’s origin, classification, three-dimensional molecular structure, solubility, hydrogen bonds, and violations of the Lipinski rules (which establishes the potential of a molecule to be orally active). “These are fundamental parameters when investigating a molecule for the production of a prototype intended for pharmaceutical means,” explained Bolzani.

“Nature is the most sophisticated laboratory that exists. We need to study its compounds, to investigate its medicinal potential, and to discover how this chemical wealth is affected by biotic and abiotic factors, ecosystems, associations, location or time of collection, isolation processes, and identification. Understanding the universe is advancing the knowledge on species from tropical or equatorial environments such as ours such that we can ultimately reproduce it through biotechnology or synthesize these compounds in laboratories.”

As an example of a class of substances that interest NuBBE, the researcher cited an alkaloid that, after slight modifications, functioned as an acetylcholinesterase inhibitor. The inhibition of acetylcholinesterase (an enzyme responsible for breaking down the molecule of the acetylcholine neurotransmitter) is one of the most promising strategies for the treatment of Alzheimer’s disease, which affects almost 40 million people worldwide.

Due to its extremely wealthy biodiversity, which accounts for approximately 20% of the planet’s species, Brazil presents enormous potential for the production of knowledge and high-value-added products, including natural medicine or derivatives, food supplements, cosmetics, and materials to control plagues and agricultural parasites.

An initiative such as the NuBBE database offers consistent scientific fundamentals to take advantage of natural products from our biomes, i.e., to transform this potential into reality.