Prediction of the substrate for nonribosomal peptide synthetase (NRPS) adenylation domains by virtual screening

Abstract

Nonribosomal peptide synthetases (NRPSs) synthesize a diverse array of bioactive small peptides, many of which are used in medicine. There is considerable interest in predicting NRPS substrate specificity in order to facilitate investigation of the many "cryptic" NRPS genes that have not been linked to any known product. However, the current sequence similarity-based methods are unable to produce reliable predictions when there is a lack of prior specificity data, which is a particular problem for fungal NRPSs. We conducted virtual screening on the specificity-determining domain of NRPSs, the adenylation domain, and found that virtual screening using experimentally determined structures results in good enrichment of the cognate substrate. Our results indicate that the conformation of the adenylation domain and in particular the conformation of a key conserved aromatic residue is important in determining the success of the virtual screening. When homology models of NRPS adenylation domains of known specificity, rather than experimentally determined structures, were built and used for virtual screening, good enrichment of the cognate substrate was also achieved in many cases. However, the accuracy of the models was key to the reliability of the predictions and there was a large variation in the results when different models of the same domain were used. This virtual screening approach is promising and is able to produce enrichment of the cognate substrates in many cases, but improvements in building and assessing homology models are required before the approach can be reliably applied to these models.

Structure of the adenylation domain Thr1 involved in the biosynthesis of 4‐chlorothreonine in Streptomyces sp. OH‐5093—protein flexibility and molecular bases of substrate specificity

“…The sequence alignment of a number of adenylation domains of known substrate specificity, homology modeling and docking simulations led to the identification of the conserved residues lining the active site in domains activating specific amino acid . Structure‐based in silico virtual screening methods have also been developed .…”

The Adenylate-Forming Enzymes AfeA and TmpB Are Involved in Aspergillus nidulans Self-Communication during Asexual Development

“…The α-carboxylate of phenylalanine is stabilized by an electrostatic interaction with the invariant 517 K from the C-terminal domain. A conserved aromatic residue (F, W, or H), proposed to play a key role in the positioning of α-amino and α-carboxylate groups (Lee et al, 2015 ) corresponds to 239 W in PheA. These critical residues are conserved ( 238 D, 309 G, 315 I, 242 W, and 495 K) in TmpB and have a very similar orientation in the TmpB model (Figure S10B ).…”

Illustrating and homology modeling the proteins of the Zika virus

“…Others have also described homology models that may be an excellent alternative when crystal structures are unavailable for human GPCRs 93 , 94 , and have led to the first identification of inhibitors of the Mycobacterium tuberculosis Topoisomerase I after virtual screening 95 , 96 prior to the crystal structure becoming available 97 . Certainly there are still considerable challenges using homology models such as prediction of the correct binding pose 98 but there are plenty of success stories 98 – 100 . While databases of homology models exist like MODBASE 101 and SWISS-MODEL 50 , 51 , 71 – 73 neither of these have any ZIKV protein homology models at the time of writing.…”