The article “Clathriamide, an hexapeptide isolated from the marine sponge Clathria (Clathria) nicoleae” results of part of Vitor F. Freire PhD project on the investigation of marine sponge metabolites. The sample of Clathria (Clathria) nicoleae was provided to us by the Rio de Janeiro research team at Jardim Botânico, Fernando C. Moraes, Wladimir C. Paradas, Leonardo T. Salgado, Renato C. Pereira, Rodrigo L. Moura and Gilberto M. Amado-Filho. This team participated directly in the expedition to the Amazon river mouth that resulted in the discovery of a very extense coral reef. The discovery of this coral reef was a major breakthrough, reported in the article “An extensive reef system at the Amazon River mouth“. During the expedition several species of marine sponges were collected. One of which was Clathria (Clathria) nicoleae, investigated by Vitor.

The beautiful sponge picture was provided by the late Professor Gilberto M. Amado-Filho, who very sadly passed away in a motorcycle accident in 2019.

Clathriamide was isolated and identified from the sponge aqueous extract, using a procedure developed in our laboratory. The absolute configuration of the amino acids was established by hydrolysis of the peptide followed by derivatization with the recently developed reagent 5-fluoro-2,4-dinitrophenyl-Nα-L-tryptophanamide and UPLC-MS analysis. The 5-fluoro-2,4-dinitrophenyl-Nα-L-tryptophanamide reagent was developed by Mariam N. Salib and Professor Tadeusz Molinski, at the University of California, San Diego. See their article, here.

Why the use of Professor Molinski’s reagent was absolutely necessary to establish the complete absolute stereochemistry of clathriamide?

Because the regular Marfey-derivatized isoleucine standards did not resolved by UPLC-MS analyses. The use of Molinski’s reagent and of a UPLC C8 reversed phase column were essential to resolve the two isoleucine standards we used to complete the absolute configuration assignment of clathriamide. The authors thank to Professor Molinski for the generous gift of his reagent.

Clathriamide article was submitted to the Brazilian Journal of Pharmacognosy, in recognition to the outstanding editorial work by Professor Cid Aimbiré M. dos Santos (Departamento de Farmácia, Universidade Federal do Paraná) to the Brazilian Journal of Pharmacognosy. As the editor-in-chief of the journal, Professor Cid devoted large efforts to increase its quality and visibility, which increased the IF of this journal to almost 2.0.

The article is open-access, and can be downloaded here.

This post had to be written a while ago.

Professor Koji Nakanishi’s death meant very much to the natural products chemistry community. Needless to say, his achievements are beyond words. Two of the perhaps less-known facts of Professor Nakanishi’s career are worth of mention.

The first is his 1962 book on infrared spectroscopy, with a foreword by Professor Carl Djerassi. I was lucky in finding this book in an Ann Arbor (Michigan) old books bookstore. It is perhaps one of the best books on infrared interpretation ever written.

The book opens with an impressive statement:

“The infrared spectrum (IR) is said to be one of the most characteristic properties of a compound”.

Who would ever think in IR nowawadys representing a specific feature of an organic compound? Professor Nakanishi’s thought has to be placed in a historical context, and represents a truth until today. The fact is that IR data is very often considered of minor importance, and frequently recorded with not much care, even if state-of-art Fourier transform-based instruments are currently available. But the fact is that IR data remains a unique feature for each organic compound. Even if very similar compounds can be hardly differentiated by analysis of IR data, IR spectra of very similar, but not identical, organic compounds are distinct. The structure of sebastianine B, for example, needed a good quality IR spectrum to be completely elucidated in 2001.

The book has extensive and very well organized tables of IR functional groups. A plethora of examples are discussed in detail for relevant IR absoprtions. Very useful for teaching purposes, the book includes a set of 85 problems with answers and all the spectra included are of excellent quality.

The second story is that Professor Nakanishi visited Brazil in 1996. And I was also lucky in meeting and talking to him in person. He came to participate in a meeting to discuss a very challenging endeavour – the proposal to setup the PROBEM program in the Amazon forest, a program to explore the forest chemistry for biodiscovery.

I don’t know the details on how the meeting in Brasilia, Brazil’s capital, was organized. I went as an invited observer. Among many scholars, Professor Nakanishi and Professor Jerry Meinwald were invited as advisors. Since I knew in advance that he was coming, I took with me my copy of Professor Nakanishi’s autobiography, “A Wandering Natural Products Chemist”. He was extremely kind to sign it for me, for which I was very grateful. I remain inspired by him and his achievements. Rest in peace, Professor.

 

We are pleased to have new researchers in the QOSBIO research group at the Universidade de São Paulo, São Carlos.

Dr. Camila M. Crnkovic joined the group earlier this year. Dr. Camila was awarded with a PhD degree at the University of Illinois, Chicago School of Pharmacy, under the supervision of Professor Jimmy Orjala. Dr. Camila recently presented a seminar entitled “Metabolomics for the Discovery of Natural Products from Cyanobacteria”, based on her PhD thesis, which was truly interesting, showing innovative approaches for the discovery of new cyanobacterial metabolites. Dr. Camila joined the group as a post-doctoral fellow with the very prestigious FAPESP post-doctoral scholarship. Congratulations!

Leandro da S. Oliveira also is a new group member. Leandro graduated in Chemistry at the Universidade Federal de São Carlos. His honors project was developed at QOSBIO, when he decided to apply for the MSc program at the Chemistry Institute of São Carlos, Universidade de São Paulo. He was awarded with a MSc scholarship since did very well in the selection exam at the Chemistry Institute of São Carlos. Congratulations, Leandro!

Other group members are the undergraduate students Giovanna Lima, Lucas Rodrigues, Laura Paulino, Carolina Lucia and Fernando Bermude. Giovanna, Lucas, Laura and Carolina are undergraduate students at the Chemistry Institute of São Carlos, while Fernando is a student of the Physics and Biomolecular Science course at the Physics Institute of São Carlos. We are still waiting for the photos of Carolina and Fernando, though. Lucas has been awarded with a FAPESP undergraduate researcher scholarship – very nice, congratulations Lucas!

Welcome to the QOSBIO group!

The recent investigation of new bromopyrrole alkaloids by a former MSc. student, Renata Torres, resulted in the discovery of 4-debromooroidin (1), 4-debromougibohlin (2), 5-debromougibohlin (3) and 5-bromopalau’amine (4) from the MeOH extract of the sponge Dictyonella sp. These new alkaloids were isolated along with the known hymenidin (5) and (+)-monobromoisophakellin (6). Curiously, the bromination pattern of compounds 1–4 is rather unusual for the marine sponge brominated pyrrole alkaloids. Usually, bromination at C-3 is more frequently observed for these compounds. The alkaloids were tested as proteasome inhibitors by the group of Dr. Daniela Trivella, researcher at the LNBio Laboratory at CNPEM. Results showed that 5-bromopalau’amine (4) was the most active alkaloid, in agreement with previous results observed for these metabolites when tested as proteasome inhibitors. Samples of the sponge were made available by a group of researchers of the Rio de Janeiro Botanical Garden and Federal University of Rio de Janeiro, who collected the animal during an expedition at the mouth of the Amazon river. Spectroscopic data collection and analyses were performed collaboratively with Prof. Antonio G. Ferreira at the Federal University of São Carlos and with Dr. David E. Williams and Prof. Raymond J. Andersen at the University of British Columbia. This investigation was published in the Journal of Natural Products, and corresponds to the MSc dissertation project of Renata Torres.

Among the articles published in 2018 by our group, a new review titled Natural Products from Marine Invertebrates and Microorganisms in Brazil between 2004 and 2017: Still the Challenges, More Rewards covers the research by Brazilian investigators on marine natural products from 2004 until 2017. It is an update of our previous review on the same subject, published in 2004 in the Journal of Natural Products. The fine work performed by the PhD student Laura P. Ióca and by Dr. Karen J. Nicácio comprehensively discuss the research on isolation, structure analysis, biological activities and biosynthesis. Total syntheses of marine natural products performed by Brazilian synthetic chemists is discussed as well, including research by Luiz Carlos Dias (UNICAMP), Ronaldo A. Pilli (UNICAMP), Carlos Roque Duarte Correia (UNICAMP), Fernando A. S. Coelho (UNICAMP), Luiz Cláudio de Almeida Barbosa (UFMG), the later Luiz Fernando da Silva Júnior (USP) and Ângelo da Cunha Pinto (UFRJ). The review clearly shows the growing interest on marine natural products in Brazil during the last 13 years, in particular by the chemistry of marine microbes (bacteria and fungi). The review is one of the articles of the prestigious Journal of the Brazilian Chemical Society special issue dedicated to the IUPAC 2017 meeting, held in São Paulo, Brazil. We thank the JBCS editors for the very kind invitation to submit a manuscript to this JBCS special issue. Read the complete open access article here.