Pharmacotranscriptomic profiles, which capture drug-induced changes in gene expression, offer vast potential for computational drug discovery and are widely used in modern medicine. However, current computational approaches neglected the associations within gene‒gene functional networks and unrevealed the systematic relationship between drug efficacy and the reversal effect. Here, we developed a new genome-scale functional module (GSFM) transformation framework to quantitatively evaluate drug efficacy for in silico drug discovery. GSFM employs four biologically interpretable quantifiers: GSFM_Up, GSFM_Down, GSFM_ssGSEA, and GSFM_TF to comprehensively evaluate the multi-dimension activities of each functional module (FM) at gene-level, pathway-level, and transcriptional regulatory network-level. Through a data transformation strategy, GSFM effectively converts noisy and potentially unreliable gene expression data into a more dependable FM active matrix, significantly outperforming other methods in terms of both robustness and accuracy. Besides, we found a positive correlation between RS_GSFM and drug efficacy, suggesting that RS_GSFM could serve as representative measure of drug efficacy. Furthermore, we identified WYE-354, perhexiline, and NTNCB as candidate therapeutic agents for the treatment of breast-invasive carcinoma, lung adenocarcinoma, and castration-resistant prostate cancer, respectively. The results from in vitro and in vivo experiments have validated that all identified compounds exhibit potent anti-tumor effects, providing proof-of-concept for our computational approach.

Objective To explore the effects of Jingling Oral Liquid(mainly composed of Polygoni Multiflori Radix,Polygonati Rhizoma,Platycladi Semen,Nelumbinis Semen,Ligustri Lucidi Fructus,Poria,and Lilii Bulbus)as an adjunctive therapy on cognitive,motor,and social abilities in children with global developmental delay(GDD).Methods A total of 120 children with GDD who visited the Department of Neurological Rehabilitation at Hebei Children's Hospital from July 2021 to November 2023 were selected as the study subjects.The children were randomly divided into a control group and a trial group using a random number table,with 60 children in each group.The control group received conventional comprehensive rehabilitation training,while the trial group received Jingling Oral Liquid as an adjunctive therapy in addition to the control group's treatment.The treatment course lasted 12 weeks.Before and after treatment,the changes in Gesell Developmental Scale(GDS)scores,Peabody Developmental Motor Scales(PDMS)scores,motor function scores,and language ability scores in both groups were observed to evaluate the cognitive,motor,and social abilities of the children.Results(1)After treatment,the scores of all dimensions of the GDS,including adaption,developmental quotient of fine motor,language developmental quotient,and personal-social developmental quotient,were significantly increased in both groups compared to those before treatment(P＜0.01),and the improvement of GDS scores in the trial group was significantly superior to that in the control group(P＜0.01).(2)After treatment,the scores of all dimensions of the PDMS,including fine developmental quotient score,standardized score of visual-motor integration,and standardized score of grasping,were significantly increased in both groups compared to those before treatment(P＜0.01),and the improvement of PDMS scores in the trial group was significantly superior to that in the control group(P＜0.01).(3)After treatment,the scores of motor function indicators of fine motor quotient(FMQ),gross motor quotient(GMQ),and total motor quotient(TMQ)were significantly increased in both groups compared to those before treatment(P＜0.01),and the improvement of motor function scores in the trial group was significantly superior to that in the control group(P＜0.01).(4)After treatment,the language ability scores were significantly increased in both groups compared to those before treatment(P＜0.01),and the improvement of language ability scores in the trial group was significantly superior to that in the control group(P＜0.01).Conclusion The combination of Jingling Oral Liquid with conventional comprehensive rehabilitation training can effectively improve the cognitive,motor,and social abilities of children with GDD.