AI-assisted structural consensus-proteome prediction of human monkeypox viruses isolated within a year after the 2022 multi-country outbreak

Abstract

The 2022 outbreak of the monkeypox virus already involves, by April 2023, 110 countries with 86,956 confirmed cases and 119 deaths. Understanding an emerging disease on a molecular level is essential to study infection processes and eventually guide drug discovery at an early stage. To support this, we provide the so far most comprehensive structural proteome of the monkeypox virus, which includes 210 structural models, each computed with three state-of-the-art structure prediction methods. Instead of building on a single-genome sequence, we generated our models from a consensus of 3,713 high-quality genome sequences sampled from patients within 1 year of the outbreak. Therefore, we present an average structural proteome of the currently isolated viruses, including mutational analyses with a special focus on drug-binding sites. Continuing dynamic mutation monitoring within the structural proteome presented here is essential to timely predict possible physiological changes in the evolving virus.

Keywords: AlphaFold2; BioNeMo; ESMFold; MPX; brincidofovir; consensus genome; epidemic; homology modeling; monkeypox; structural genomics; structure prediction; tecovirimat; viral genome; viral proteome.

Fig 1

Length distribution (A) and average conservation (B) of putative ORFs in the consensus genome sequence. ORF lengths (in amino acids) are displayed in (A) for ORFs matching to the NCBI reference proteome, the nr database (excluding ORFs matching to the reference proteome), and not matching any proteins in these databases. The average conservation (in %) across the ORFs (including stop codons) is displayed in (B), along with the conservation of 182 nucleotide bases not included in any of the theoretical ORFs. Notably, the number of ORFs (N) in (A) is lower than in (B) because (A) includes only distinct ORFs and (B) treats all identified ORFs (also duplicated regions) as single elements.

Fig 2

Genomic map of the putative structural consensus proteome. The consensus genome sequence, colored by conservation, is shown (at y = 0) along with the identified ORFs in the respective frame (shown on the y-axis), which matched to the nr database (black, green, and blue horizontal bars). ORFs that were identified in the forward strand (frames 1 to 3) are depicted above the genome sequence, whereas ORFs identified in the reverse strand (frames −1 to −3) are depicted below. Blue- and green-colored bars represent ORFs which additionally match the NCBI reference proteome. Green-colored ORFs do not match to proteins deposited in the PDB, thus ESMFold and AlphaFold2 models were built. The latter are depicted in the figure, colored by their pLDDT with the PyMOL color range “rainbow_rev,” given a minimum of 0 (red) and a maximum of 100 (dark blue). Blue-colored ORFs do match with proteins in the PDB, and therefore, additionally to AlphaFold2 and ESMFold models, homology models (depicted in gray) were generated.

Fig 3

Mutation events in drug targets phospholipase F13 and DNA polymerase. (A) Homology model of ORF ID_6924, representing tecovirimat-targeted phospholipase F13 (left) and experimentally determined 3D structure of brincidofovir-targeted DNA polymerase [PDB 8HG1 (39), chains B and C are not shown], referring to ORF ID_8713 (right). Cα-atoms of mutated positions detected before the 2022 MPX outbreak are shown as spheres, colored with the PyMOL “rainbow” palette (minimum = 0, maximum = 100) by the mutations’ frequency (labeled in %) in all genome samples where the respective protein sequence was identified. Residues previously predicted to interact with tecovirimat (37) (left) and brincidofovir (38) (right) are shown as black lines, and the respective binding site cavity is colored by the electrostatics of its surroundings (blue-white-red spectrum ranging from −1 to +1). (B) Structural representation as in (A), showing mutated positions detected within 1 year after the 2022 MPX outbreak. (C) A cumulative number of genomes detected per day from April 2022 to April 2023, which contain mutations at respective positions (positions labeled on the right of each line) in ID_6924 (left) and ID_8713 (right). The graphs are aligned with the number of genomes containing a mutation at the position of the consensus mutation (top: dark gray) as well as the total number of genomes sampled during the time period (top: light gray). More details on mutation numbers are available in the Supplementary Information (see Data S4 at https://doi.org/10.6084/m9.figshare.22730459.v5).