MIBiG 3.0 : a community-driven effort to annotate experimentally validated biosynthetic gene clusters

With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/

Docking studies on bacterial encymes MurD and PBP2a

Zunehmende mikrobielle Resistenz gegen Antibiotika ist ein weltweites Ge- sundheitsproblem. Antibiotika mit neuartigen Wirkungsmechanismen sind dringend gesucht, da sich Bakterien schnell an Substanzen anpassen und Kreuzresistenzen häufig sind. In der vorliegenden Arbeit wurde versucht dieser Entwicklung mittels computergestützter Methoden entgegenzusteuern. Untersucht wurden die Proteine PBP2a und MurD, die beide eine Schlüssel- position in der bakteriellen Zellwandsynthese einnehmen. Genutzt wurden die Programme LiSiCA, ein ”Similarity-Search” Programm, sowie AutoDock Vina, ein ”Molecular Docking” Programm. Die am besten bewerteten Mole- küle wurden erworben und biologisch validiert. Dabei wurde über die ”Sim- ilarity Search” Methode ein Molekül mit niedrig mikromolarer inhibitorischer Aktivität gegenüber PBP2a gefunden. Die Bestimmung der minimalen Hemm- konzentration (MIC) von 16 μg/mL an S. aureus und MRSA bestätigte diesen Treffer. Dieses Molekül könnte sich in der drohenden ”post-antibiotischen Ära” noch als nützlich erweisen.Increasing microbial resistance against antibiotics is a major worldwide health problem. Antimicrobial agents with novel mechanisms of action are urgently needed. In the present work, we addressed this problem by using compu- tational methods to investigate bacterial cell-wall related proteins PBP2a and MurD, in particular through recently developed similarity search pro- gram LiSiCA and docking program AutoDock Vina. The best-performing compounds were purchased and biologically tested. The similarity search ap- proach yielded a compound with low micromolar inhibitory activity against PBP2a. The compound was further confirmed through examination of min- imal inhibitory concentrations (MIC) at 16 μg/mL. This might be an inter- esting molecule to further prolong the threatening ”post-antibiotic” era

A biaryl-linked tripeptide from Planomonospora reveals a widespread class of minimal RiPP gene clusters

Microbial natural products impress by their bioactivity, structural diversity, and ingenious biosynthesis. While screening the less exploited actinobacterial genus Planomonospora, two cyclopeptides were discovered, featuring an unusual Tyr-His biaryl bridging across a tripeptide scaffold, with the sequences N-acetyl-Tyr-Tyr-His and N-acetyl-Tyr-Phe-His. Planomonospora genomes pointed toward a ribosomal synthesis of the cyclopeptide from a pentapeptide precursor encoded by 18-bp bytA, to our knowledge the smallest coding gene ever reported. Closely linked to bytA is bytO, encoding a cytochrome P450 monooxygenase likely responsible for biaryl installment. In Streptomyces, the bytAO segment was sufficient to direct production of the crosslinked N-acetylated Tyr-Tyr-His tripeptide. Bioinformatic analysis of related cytochrome P450 monooxygenases indicated that they constitute a widespread family of enzymes, and the corresponding genes are closely linked to 5-amino acid coding sequences in approximately 200 (actino)bacterial genomes, all with potential for biaryl linkage between amino acids 1 and 3. We propose the named biarylitides this family of RiPPs

Effective approaches to discover new microbial metabolites in a large strain library

Natural products have provided many molecules to treat and prevent illnesses in humans, animals and plants. While only a small fraction of the existing microbial diversity has been explored for bioactive metabolites, tens of thousands of molecules have been reported in the literature over the past 80 years. Thus, the main challenge in microbial metabolite screening is to avoid the re-discovery of known metabolites in a cost-effective manner. In this perspective, we report and discuss different approaches used in our laboratory over the past few years, ranging from bioactivity-based screening to looking for metabolic rarity in different datasets to deeply investigating a single Streptomyces strain. Our results show that it is possible to find novel chemistry through a limited screening effort, provided that appropriate selection criteria are in place

Discovery of mycobacterium tuberculosis InhA inhibitors by binding sites comparison and ligands prediction

Drug discovery is usually focused on a single protein target; in this process, existing compounds that bind to related proteins are often ignored. We describe ProBiS plugin, extension of our earlier ProBiSi-ligands approach, which for a given protein structure allows prediction of its binding:sites and, for each binding site, the ligands from similar binding sites in the Protein Data Bank. We developed a new database of precalculated binding site comparisons of about 290000 proteins to allow fast prediction of binding sites in existing proteins. The plugin enables advanced viewing of predicted binding sites, ligands' poses, and their interactions in three-dimensional graphics. Using the InhA query protein, an enoyl reductase enzyme in the Mycobacterium tuberculosis fatty acid biosynthesis pathway, we predicted its possible ligands and assessed their inhibitory activity experimentally. This resulted in three previously unrecognized inhibitors with novel scaffolds, demonstrating the plugin's utility in the early drug discovery process

Discovery of Mycobacterium tuberculosis InhA Inhibitors by Binding Sites Comparison and Ligands Prediction

Drug discovery is usually focused on a single protein target; in this process, existing compounds that bind to related proteins are often ignored. We describe ProBiS plugin, extension of our earlier ProBiS-ligands approach, which for a given protein structure allows prediction of its binding sites and, for each binding site, the ligands from similar binding sites in the Protein Data Bank. We developed a new database of precalculated binding site comparisons of about 290000 proteins to allow fast prediction of binding sites in existing proteins. The plugin enables advanced viewing of predicted binding sites, ligands’ poses, and their interactions in three-dimensional graphics. Using the InhA query protein, an enoyl reductase enzyme in the Mycobacterium tuberculosis fatty acid biosynthesis pathway, we predicted its possible ligands and assessed their inhibitory activity experimentally. This resulted in three previously unrecognized inhibitors with novel scaffolds, demonstrating the plugin’s utility in the early drug discovery process