Current Clinical Treatments of AIDS

Piquing artificial intelligence towards drug discovery: Tools, techniques, and applications

The purpose of this study was to discuss how artificial intelligence (AI) methods have affected the field of drug development. It looks at how AI models and data resources are reshaping the drug development process by offering more affordable and expedient options to conventional approaches. The paper opens with an overview of well-known information sources for drug development. The discussion then moves on to molecular representation techniques that make it possible to convert data into representations that computers can understand. The paper also gives a general overview of the algorithms used in the creation of drug discovery models based on AI. In particular, the paper looks at how AI algorithms might be used to forecast drug toxicity, drug bioactivity, and drug physicochemical properties. De novo drug design, binding affinity prediction, and other AI-based models for drug-target interaction were covered in deeper detail. Modern applications of AI in nanomedicine design and pharmacological synergism/antagonism prediction were also covered. The potential advantages of AI in drug development are highlighted as the evaluation comes to a close. It underlines how AI may greatly speed up and improve the efficiency of drug discovery, resulting in the creation of new and better medicines. To fully realize the promise of AI in drug discovery, the review acknowledges the difficulties that come with its uses in this field and advocates for more study and development.

Artificial intelligence for drug discovery: Resources, methods, and applications

Conventional wet laboratory testing, validations, and synthetic procedures are costly and time-consuming for drug discovery. Advancements in artificial intelligence (AI) techniques have revolutionized their applications to drug discovery. Combined with accessible data resources, AI techniques are changing the landscape of drug discovery. In the past decades, a series of AI-based models have been developed for various steps of drug discovery. These models have been used as complements of conventional experiments and have accelerated the drug discovery process. In this review, we first introduced the widely used data resources in drug discovery, such as ChEMBL and DrugBank, followed by the molecular representation schemes that convert data into computer-readable formats. Meanwhile, we summarized the algorithms used to develop AI-based models for drug discovery. Subsequently, we discussed the applications of AI techniques in pharmaceutical analysis including predicting drug toxicity, drug bioactivity, and drug physicochemical property. Furthermore, we introduced the AI-based models for de novo drug design, drug-target structure prediction, drug-target interaction, and binding affinity prediction. Moreover, we also highlighted the advanced applications of AI in drug synergism/antagonism prediction and nanomedicine design. Finally, we discussed the challenges and future perspectives on the applications of AI to drug discovery.

TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations

Drug combinations have demonstrated great potential in cancer treatments. They alleviate drug resistance and improve therapeutic efficacy. The fast-growing number of anti-cancer drugs has caused the experimental investigation of all drug combinations to become costly and time-consuming. Computational techniques can improve the efficiency of drug combination screening. Despite recent advances in applying machine learning to synergistic drug combination prediction, several challenges remain. First, the performance of existing methods is suboptimal. There is still much space for improvement. Second, biological knowledge has not been fully incorporated into the model. Finally, many models are lack interpretability, limiting their clinical applications. To address these challenges, we have developed a knowledge-enabled and self-attention transformer boosted deep learning model, TranSynergy, which improves the performance and interpretability of synergistic drug combination prediction. TranSynergy is designed so that the cellular effect of drug actions can be explicitly modeled through cell-line gene dependency, gene-gene interaction, and genome-wide drug-target interaction. A novel Shapley Additive Gene Set Enrichment Analysis (SA-GSEA) method has been developed to deconvolute genes that contribute to the synergistic drug combination and improve model interpretability. Extensive benchmark studies demonstrate that TranSynergy outperforms the state-of-the-art method, suggesting the potential of mechanism-driven machine learning. Novel pathways that are associated with the synergistic combinations are revealed and supported by experimental evidences. They may provide new insights into identifying biomarkers for precision medicine and discovering new anti-cancer therapies. Several new synergistic drug combinations have been predicted with high confidence for ovarian cancer which has few treatment options. The code is available at https://github.com/qiaoliuhub/drug_combination.

HIV protease inhibitors block oral epithelial cell DNA synthesis

OBJECTIVES

Anti-retroviral therapy regimens that include HIV protease inhibitors (PIs) are associated with diverse adverse effects including increased prevalence of oral warts, oral sensorial deficits and gastrointestinal toxicities suggesting that PIs may perturb epithelial cell biology. To test the hypothesis that PIs could affect specific biological processes of oral epithelium, the effects of these agents were evaluated in several oral epithelial cell-lines.

DESIGN

Primary and immortalized oral keratinocytes and squamous carcinoma cells of oropharyngeal origin were cultured in the presence of pharmacologically relevant concentrations of PIs. Their affects on cell viability, cytotoxicity and DNA synthesis were assessed by enzymatic assays and incorporation of 5-bromo-2'-deoxyuridine (BrdU) into DNA.

RESULTS

Viability of primary and immortalized oral keratinocytes as well as squamous carcinoma cells of oropharyngeal origin was significantly reduced by select PIs at concentrations found in plasma. Of the seven PIs evaluated, nelfinavir was the most potent with a mean 50% inhibitory concentration [IC(50)] of 4.1 microM. Lopinavir and saquinavir also reduced epithelial cell viability (IC(50) of 10-20 microM). Atazanavir and ritonovir caused minor reductions in viability, while amprenavir and indinavir were not significant inhibitors. The reduced cell viability, as shown by BrdU incorporation assays, was due to inhibition of DNA synthesis rather than cell death due to cytotoxicity.

CONCLUSION

Select PIs retard oral epithelial cell proliferation in a drug and dose-dependent manner by blocking DNA synthesis. This could account for some of their adverse effects on oral health.