Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop

Abstract

We report the major conclusions of the online open-access workshop “Computational Applications in Secondary Metabolite Discovery (CAiSMD)” that took place from 08 to 10 March 2021. Invited speakers from academia and industry and about 200 registered participants from five continents (Africa, Asia, Europe, South America, and North America) took part in the workshop. The workshop highlighted the potential applications of computational methodologies in the search for secondary metabolites (SMs) or natural products (NPs) as potential drugs and drug leads. During 3 days, the participants of this online workshop received an overview of modern computer-based approaches for exploring NP discovery in the “omics” age. The invited experts gave keynote lectures, trained participants in hands-on sessions, and held round table discussions. This was followed by oral presentations with much interaction between the speakers and the audience. Selected applicants (early-career scientists) were offered the opportunity to give oral presentations (15 min) and present posters in the form of flash presentations (5 min) upon submission of an abstract. The final program available on the workshop website (https://caismd.indiayouth.info/) comprised of 4 keynote lectures (KLs), 12 oral presentations (OPs), 2 round table discussions (RTDs), and 5 hands-on sessions (HSs). This meeting report also references internet resources for computational biology in the area of secondary metabolites that are of use outside of the workshop areas and will constitute a long-term valuable source for the community. The workshop concluded with an online survey form to be completed by speakers and participants for the goal of improving any subsequent editions.

Microbial metabolites: cause or consequence in gastrointestinal disease?

“…Although different in their sequences, PKS modules share similarities that can easily be recognized using bioinformatic mining of bacterial genomes ( 23 , 24 , 79 – 81 ). BGCs encoding polyketide-type molecules are identified within the human microbiome in bacterial phyla including Actinobacteria, Proteobacteria, Bacteroidetes, and Firmicutes.…”

“…Generally, computational approaches (e.g., anti-SMASH) are used to identify BGCs or family of BGCs, followed by the heterologous expression of the identified gene in a genetically tractable and easy-to-culture organism (e.g., E. coli ), and extraction and chemical characterization of the produced metabolite using analytical approaches (HPLC, MS, NMR, etc.) ( 28 , 80 , 81 ). In the context of the human microbiota where a vast number of bacteria has been sequenced, genome mining has been applied to microbiome sequences to identify new functional molecules ( 156 ).…”

Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds

“…Professor Johan Gasteiger, the first speaker in the Colloquium, stated three of the fundamental questions in chemistry: (1) what structure do I need for a certain property?, (2) how do I make this structure?, and (3) how do I synthesize this and characterize this compound? Answers to the first question involve structure-property or structure-activity relationships, to the second question involve synthesis design, and to the third question involve reaction prediction and structure elucidation.…”

“…In the setting of a growing number of applications and developments of computational approaches to drug discovery and related fields, of an increasing frequency of virtual meetings [1,2], and of efforts to enhance the education of students [3,4], the first Chemoinformatics and Artificial Intelligence (AI) Colloquium organized by a Latin American country was held in Mexico City, June 15-17, 2022. The virtual meeting featured talks by 15 international experts.…”