Many effective medications have their roots in naturally occurring organisms, including plants, fungus, and bacteria, yet it is still challenging to screen natural items for therapeutic potential.
According to a study published November 30 in Proceedings of the National Academy of Sciences, a novel strategy using molecular biology, analytical chemistry, and bioinformatics to integrate data from various screening platforms addresses some of the most difficult problems in finding new natural drugs.
Determining a novel bioactive compound’s mode of action and biological target has proven to be a significant problem. Finding the molecule or molecules that are responsible for biological action in a complicated mixture of natural ingredients is another major difficulty.
This research finding these two concerns together in a fully integrated manner, according to corresponding author John MacMillan, a professor of chemistry and biochemistry drugs at UC Santa Cruz. “These two big notions have been at the center of our collaborative program.”
Along with MacMillan, the collaboration includes Roger Linington from Simon Fraser University in British Columbia; Michael White from the University of Texas Southwestern Medical Center; and Scott Lokey, professor of chemistry and biochemistry and director of the Chemical Screening Center at UC Santa Cruz.
The researchers developed a special and effective framework for natural product biological characterization by merging the outcomes of two very diverse screening platforms with next-generation metabolomics analysis of their natural product libraries. They were able to identify a known compound (trichostatin A) and confirm its mode of action using this method to screen a small collection of randomly chosen microbial natural product fractions. They were also able to link a known compound (surugamide) with novel biological activity (cyclin-dependent kinase inhibition) and discover new compounds (parkamycins A and B) with complex biological activity.
Finding a known molecule that behaves as predicted indicates that it is working drugs, and later, MacMillan added, “we were able to associate a known compound with a new mechanism of action.” “Finally, we identified a novel chemical molecule that differs from other chemicals in its distinctive biological signature.” “We want to look at that discovery more since it’s intriguing.”
The researchers combined data from two natural product screening systems their labs had created using a bioinformatic technique called Similarity Network Fusion (SNF), which was created for merging complex information. By combining pattern-matching algorithms with gene expression patterns elicited in cells by known and unknown substances, one platform (Functional Signature Ontology, or FUSION) created by MacMillan’s team employs “guilt by association” to suggest mechanisms of action.
“If we observe outcomes resembling those of a recognized drug, this raises the possibility of a related mechanism of action.” “We have successfully applied this approach to comprehend the biological function of several distinct tiny compounds,” added MacMillan.
The second platform, a cytological profiling (CP) tool created by Lokey’s team, analyzes high-content images of cells exposed to the samples being screened and then uses a panel of fluorescent probes to highlight important cytological traits. Each sample produces a total of 251 distinctive cytological characteristics from automated fluorescence microscopy photographs.
The scientists screened sophisticated natural product libraries created by MacMillan and Linington’s labs using the CP and FUSION technologies. These libraries were from marine bacteria that the two labs isolated.
The researchers cultivate the bacterial strains in the lab, make a crude extract of every compound each strain produces, and then use chromatography to separate each extract into a series of fractions, each of which contains two to twenty compounds, in order to look for bioactive natural products.
When studying tiny molecules on a large scale (“metabolomics”), mass spectrometry techniques are frequently used and can be used to determine the chemical components of each fraction. Compound Activity Mapping, a method created by Linington and colleagues, combines biological screening data with mass spectrometry-based metabolomics to determine which chemicals in a mixture are responsible for a specific biological signature.
With the help of mass spectrometry and a modified version of their compound activity mapping platform, the researchers created a sample processing workflow for the new study that incorporates the combined outcomes of their screening technologies obtained through similarity network fusion.
“Can we use all of that to identify the molecules that are responsible for a specific signature and develop more accurate predictions of the mechanism of action?” “We were able to do it with our strategy to a fairly significant degree,” added MacMillan.
Anam Shaikh, Rachel Vaden, Jeon Lee, Shuguang Wei, Michael White, Suzie Hight, Elizabeth McMillan, Anam Shaikh, Kenji Kurita, Jake Haecki, and Fausto Carnevale-Neto at the University of Texas Southwestern Medical Center; Walter Bray, Aswad Khadilkar, Scott La, and Akshar Lohith at the University of California, Santa Cruz; and Trevor Clark, Kenji Kurita, and Jake Haecki The National Institutes of Health provided funding for this research.
