Artificial intelligence in the discovery and modification of biological elements in medicinal plants

Figures (2) Tables (2)

Figure 1.
AI prediction of biological elements in medicinal plants.
Figure 2.
Enzyme modification and rational design of natural product pathways in medicinal plants.

Types	Active ingredients	Enzymes	Plant source	Medicinal activity	Ref.
Terpenoid	QS-21	CCL1, PKSIII, KR, ACT2/3, UGT73CZ2	Quillaja Saponaria	Vaccine adjuvant	[3,10]
	Limonoid	OSC, CYP71CD1, MOI2, L21AT, SDR, L1AT, AKR, LFS	Citrus sinensis, Melia azedarach	Biopesticide	[12,20,21]
	Astragaloside	AmOSC3, AmCYP88D25, AmCYP88D7, AmCYP71D756	Astragalus membranaceus	Anticancer	[13]
Alkaloid	Paclitaxel	TOT1, T9αOH, TS, T5αOH, T13αOH, T10βOH, TAT, T7βOH, T2αOH, TBT, DBAT, T1βOH	Taxus chinensis	Anticancer	[2,22]
	Amaryllidaceae alkaloid	CYP96T1, CYP96T6, CYP96T5, NtSDR2, NtODD2, NtOMT1, NtNMT1, NtAKR1	Narcissus tazetta	Treating Alzheimer's disease	[14]
	Colchicine	GsOMT1, GsNMT, GsCYP75A109, GsOMT2, GsOMT3, GsCYP75A110, GsOMT4, GsCYP71FB1	Gloriosa superba	Antigout	[15]
	Strychnine	SnvGO, SnvNS1, SnvNO, SnvWS, SnvAT, AAE13, Snv10H, SnvOMT, Snv11H	Strychnos nux-vomica	Biopesticide	[16]
Flavonoid	Homoisoflavonoid	ChOMT	Medicago truncatula	Anti-neuroinflammatory	[17]
	Liquiritin apioside	GuApiGT	Glycyrrhiza uralensis	Cough suppressing	[18]
	Polymethoxyflavone	CreOMT3, CreOMT4, CreOMT5	Mandarin	Anticancer	[19]

Table 1.

Recent progress in dissecting natural product pathways in medicinal plants.

Data type	Models	Architecture	Data sources	Ref.
Protein sequence	ESM-2/3	BERT	UniRef50, UniRef90, PDB	[8,29]
Protein sequence	AlphaFold2/3	Transformer (attention mechanism)	PDB, BFD, UniRef90, MGnify, RFam, RNAcentral, JASPAR	[7,37]
Protein sequence and structure	ProtT5	Transformer	PDB, AFDB	[39]
DNA/RNA	Enformer	Transformer	Gencode	[40]
DNA/RNA	RNABERT	BERT	Rfam, BRAliBase2.1	[41]
Whole-genome	Evo	StripedHyena	GTDB, IMG/VR, IMG/PR, NCBI RefSeq, MGnify, MGRAST, UHGG, JGI IMG	[9]

Table 2.

Biological pre-trained models.