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Abstract

Herbal medicinal plants play an important role as a source of therapeutic agents due to the presence of bioactive phytoconstituents such as alkaloids, flavonoids, tannins, glycosides, and phenolic compounds. Traditional methods for discovering the phytoconstituents in herbal plants are time-consuming and require more experimental work. In recent years, AI (artificial intelligence) has been improving drug discovery and rapidly growing in the herbal industry. AI, integrated with powerful tools, can significantly accelerate the drug discovery process from herbal plants. AI techniques such as deep learning, machine learning, molecular docking, QSAR modelling and virtual screening, etc. AI can analyse the phytoconstituents datasets and predict the biological activity from plant-derived compounds. AI is identifying the potential of a drug and predicting the drug-protein interaction. AI can also detect the nature, such as primary or secondary metabolites. The integration of artificial intelligence into the discovery of phytoconstituents marks a transformative phase in the development of herbal medicines. AI predict the drug toxicity and safety before clinical trials. AI has a vast scope in the modern era. So, using AI with powerful tools in drug discovery and development is essential for future perspectives to make drug discovery easy and faster. There are some kinds of limitations and challenges of artificial intelligence

Keywords

Artificial intelligence (AI), drug discovery, phytoconstituents, machine learning, molecular docking, QSAR modelling, and herbal medicines.

Introduction

Herbal medicinal plants have been used to treat various diseases since antiquity. Traditional systems like Ayush (Ayurveda, yoga, Unani, Siddha, homoeopathy) are based on plant-derived compounds for therapeutic purposes. The invention of bioactive compounds from herbal plants has been a very essential part in the development of various drugs for centuries. The herbal plants contain various bioactive chemical compounds, which are known as phytoconstituents. Which are responsible for pharmacological activities. Compounds like alkaloids, terpenoids, glycosides, flavonoids, tannins, and phenolic compounds. In recent years, various opportunities in pharmaceutical research and drug discovery have been opened due to the rapid advancement of artificial intelligence.

Numerous significant medications used today are derived from plants. For instance, morphine is obtained from Papaver somniferum, and quinine comes from various Cinchona species. Recently, artificial intelligence (AI) has emerged as a promising technology with the potential to revolutionise pharmaceutical research. AI is capable of analysing large volumes of chemical and biological data and can also forecast the biological activity of different compounds. The scientist can accelerate the identification of new plant-derived drugs by using or combining AI techniques in pharmaceutical phytochemical research work. AI techniques such as molecular docking, virtual screening, quantitative structure-activity relationship (QSAR) modelling, and network pharmacology are being increasingly utilised in the research of herbal drugs.

The integration of artificial intelligence into the discovery of phytoconstituents marks a transformative phase in the development of herbal medicines. By merging the age-old wisdom of medicinal plants with cutting-edge computational tools, scientists can enhance the precision, speed, and effectiveness of identifying new plant-derived therapeutic compounds. This review seeks to explore the contribution of artificial intelligence to phytoconstituent discovery and its potential influence on the future trajectory of herbal drug development.

PHYTOCONSTITUENTS AND THEIR ROLE IN DRUG DISCOVERY

Phytoconstituents are chemical compounds obtained from plants during their metabolic processes. These compounds are classified into primary and secondary metabolites. Secondary metabolites play a major role in pharmacological activities, and it includes alkaloid, flavonoids, terpenoids, phenolic compounds and glycosides. These phytochemicals have various therapeutic effects, such as antimicrobial, anticancer, anti-inflammatory, anti-viral, and antioxidant activities. Because of their diverse chemical structures and biological properties, they have become an important source in drug discovery.

Artificial intelligence is crucial to the development of phytoconstituent drugs. Because of this, phytochemistry research is increasingly being advanced through the application of contemporary computer techniques like artificial intelligence.

 

TABLE: MAJOR CLASSES OF PHYTOCONSTITUENT AND THEIR PHARMACOLOGICAL ACTIVITIES

Class of phytoconstituent

Plant source

Example compound

Pharmacological activity

Alkaloid

Papaver somniferum

, Atropa belladonna

Morphine, quinine, reserpine

Analgesic, Antimalarial, anti-hypertensive

Flavonoids

Citrus plants, tea

Quercetin, Kaempferol

Antioxidant, Anti-inflammatory

Terpenoids

mint

Menthol, Artemisinin

Antimalarial, Antimicrobial

Glycosides

Digitalis purpurea

Digoxin

Cardiotonic is used in heart failure

Phenolic compounds

Grapes

Resveratrol

Antioxidant, Cardioprotective

 

ROLE OF ARTIFICIAL INTELLIGENCE IN DRUG DISCOVERY

In pharmaceutical research, artificial intelligence (AI) has become crucial for accelerating different stages of drug development since it is designed to carry out tasks that are typically completed by humans, such as learning from DATA, recognising patterns, and generating predictions. AI can be utilised in drug discovery for identification, biological activity prediction, drug design, and toxicity prediction. For example, machine learning algorithms examine chemical structure and biological data to forecast a drug's potential. Deep learning methods can be used to find molecules with high medicinal potential in huge chemical databases. Artificial intelligence significantly reduces the cost and time required in the drug discovery of phytoconstituents. AI can lessen the labour for humans by employing a variety of learning machines to identify the phytoconstituents of herbal drugs.

There are various AI tools used in herbal drug discovery, such as molecular docking software, QSAR modelling tools, natural language processing, ai based drug discovery platform (Deep Chem), machine learning platform.

 

TABLE: ARTIFICIAL INTELLIGENCE TECHNIQUES USED IN DRUG DISCOVERY

AI TECHNIQUE

APPLICATION IN PHYTOCONSTITUENTS DISCOVERY

Machine learning

Used for analysing phytochemical datasets and predict biological activity of plant-derived compounds

Deep learning

Help to identify the complex relationship between molecular structure and the pharmacological effect of phytoconstituent.

Visual screening

Enables rapid identification of plant-derived molecules with potential therapeutic activity

Molecular docking

Determines the interaction strength between phytoconstituents and proteins

Data mining

Used to extract useful information from large phytochemical databases to identify potential bioactive plant compounds.

 

AI TOOLS USED IN PHYTOCHEMICAL RESEARCH

  1. MOLECULAR DOCKING-

Molecular docking is used to predict the interaction between the ligand and target proteins or enzyme (receptor). Molecular docking helps to determine how well a compound binds to the active site of a protein and predict the binding stability and affinity of drug protein complex.

 

 

 

 

(Schematic illustration of docking a small molecule ligand (green) to a protein target (black), producing a stable complex)

 

Common software-

Auto dock

Swiss dock

Deep dock

Alpha fold 3

Example –

Curcumin from Curcuma longa can be docked with the COX-2 enzyme to study anti-inflammatory activity.

  1. QSAR MODELLING –

The QSAR (quantitative structure-activity relationship) model is used to predict the biological activity based on chemical structure. QSAR reduces the need for extensive laboratory experiments.

 

 

QSAR modelling tools-

PADEL-Descriptor

KNIME

QSAR toolbox

Auto QSAR

 

 

  1. MACHINE LEARNING-

Machine learning is an algorithm that is commonly used in drug discovery, chemical structure prediction, and analysis of biological activity and datasets. Machine learning is also used in the classification of plant metabolites.

 

Example of machine learning tools-

Weka

Scikit-learn

TensorFlow

PyTorch

 

Role of AI technology in different phases of drug discovery

Fig-Role of AI technology in different phases of drug discovery

 

  1. Virtual screening-

Virtual screening is a computational technique used to identify the potential of a drug molecule by screening large libraries of chemical compounds using computer-based methods. Virtual screening is used to analysis plant derived compounds and predict their biological activity before lab experiments.

Example of virtual screening-

Screening phytochemicals against the COVID-19 main protease.

 

 

 

 

AI WORKFLOW IN HERBAL DRUG DISCOVERY

 

 

 

 

 

 

Process-

 

 

Herbal plant collection

 

 

Identification of phytoconstituent

 

 

Ai screening

 

 

Molecular docking

 

 

Optimisation of lead compound

 

 

Experimental validation

 

APPLICATIONS OF AI IN HERBAL DRUG DEVELOPMENT

  • Identification of phytoconstituent (bioactive compound)
  • Prediction of pharmacological activity
  • Prediction of toxicity
  • Analysis of plant database
  • Prediction of drug-target interaction
  • Analysis of herbal drug formulation
  • study the therapeutic effect
  • Identify the metabolites
  • Analyse the medicinal data
  • Virtual screening
  • Molecular docking
  • Data mining and protein engineering
  • To know active phytoconstituents using various AI tools, etc.

CHALLENGES AND LIMITATIONS

  • Limited phytochemical data- there are many medicinal plant phytoconstituent are not well documented in databases.
  • Data quality issue – inconsistent or incomplete data can reduce the accuracy of the prediction
  • Computational requirements- advanced AI tools require powerful software
  • Need for experimental validation- after AI prediction, it will still require experimental validation
  • Difficult to analyse- the plant contains many phytoconstituents, which make it difficult to identify and predict
  • Difficulty with software handling – required trained person to handle the software and predict the data.

FUTURE PERSPECTIVES

  • AI drug discovery- advanced AI helps to faster and more effective identification
  • Safety and toxicity- AI predict the toxicity and safety before clinical testing.
  • Analysis of phytoconstituent- AI helps to analyse the phytoconstituent in the herbal medicinal plant
  • Detect the metabolite- AI Fastly detect the nature of the metabolite
  • Predict the pharmacological activity- AI can predict the pharmacological action, depending on the chemical nature of the herbal drug medicine
  • Research- AI bring automation in the research field
  • Time- AI reduces the time of drug discovery research
  • Acceptance- AI is rapidly growing in the modern era
  • Therapeutic effect- AI can identify the therapeutic effect of a drug based on its biological activity
  • Prediction- AI can predict the adverse effect using various AI tools

CONCLUSION

Artificial intelligence is the new era in drug development and drug discovery of phytoconstituents from plant-derived sources. AI helps to analyse the phytochemicals by using various tools. Such as molecular docking, QSAR modelling, virtual screening, and machine learning. Artificial intelligence predicts the toxicity and safety before clinical testing. All these AI tools are very helpful in the drug discovery of phytoconstituents. Artificial intelligence is one of the most valuable tools in modern pharmaceutical research, such as drug discovery and drug development. The integration of artificial intelligence with phytochemical research provides new opportunities for identifying novel plant-derived therapeutic agents. Some challenges and limitations of artificial intelligence, such as limited phytochemical data, difficulty with software handling, etc, but AI has great potential to accelerate herbal drug discovery and development. Therefore, the combination of artificial intelligence and herbal drug research play important role in the pharmaceutical industry for prospects.

REFERENCES

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  2. Saldívar-González FI, Aldas-Bandera A, Gómez-García A, Medina-Franco JL. Natural product drug discovery in the artificial intelligence era. Chem Sci. 2022;13(6):1526-1546.
  3. Vamathevan J, Clark D, Czodrowski P, et al. Applications of machine learning in drug discovery and development. Nature Reviews Drug Discovery. 2019;18(6):463–477.
  4. Paul D, Sanap G, Shenoy S, Kalyane D, Kalia K, Tekade RK. Artificial intelligence in drug discovery and development. Drug Discov Today. 2021;26(1):80-93.
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  8. Ekins S. The next era: Deep learning in pharmaceutical research. Pharmaceutical Research. 2016;33:2594–2603
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  10. Jing Y, Bian Y, Hu Z, Wang L, Xie X. Deep learning for drug design: an artificial intelligence paradigm for drug discovery. Acta Pharmaceutica Sinica B. 2018;8(6):911–922.
  11. Zhavoronkov A, Ivanenkov YA, Aliper A, et al. Deep learning enables rapid identification of potent DDR1 kinase inhibitors. Nature Biotechnology. 2019;37:1038–1040.
  12. Ekins S, Puhl AC, Zorn KM, et al. Exploiting machine learning for end-to-end drug discovery and development. Nature Materials. 2019;18:435–441.
  13. Stokes JM, Yang K, Swanson K, et al. A deep learning approach to antibiotic discovery. Cell. 2020;180(4):688–702.
  14. Mullowney MW, et al. Artificial intelligence for natural product drug discovery. Nat Rev Drug Discov. 2023;22:1-21.
  15. Walters WP, Murcko MA. Assessing the impact of generative AI on medicinal chemistry. Nature Biotechnology. 2020;38:143–145.
  16. Sliwoski G, Kothiwale S, Meiler J, Lowe EW. Computational methods in drug discovery. Pharmacological Reviews. 2014;66:334–395.
  17. Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery. Nature Reviews Drug Discovery. 2004;3:935–949.
  18. Trott O, Olson AJ. AutoDock Vina: Improving the speed and accuracy of docking. Journal of Computational Chemistry. 2010;31(2):455–461.
  19. Ferreira LG, dos Santos RN, Oliva G, Andricopulo AD. Molecular docking and structure-based drug design strategies. Molecules. 2015;20:13384–13421.
  20. 20.https://www.researchgate.net/figure/Role-of-AI-technology-in-different-phases-of-drug-discovery_fig8_352692045
  21. https://pmc.ncbi.nlm.nih.gov/articles/PMC9716588/
  22. https://www.researchgate.net/figure/Schematic-illustration-of-the-anti-COVID-19-discover-procedure-of-virtual-screening_fig1_345101777
  23. Morris GM, Huey R, Olson AJ. Using AutoDock for ligand–receptor docking. Current Protocols in Bioinformatics. 2008;24:8.14.1–8.14.40.
  24. Pagadala NS, Syed K, Tuszynski J. Software for molecular docking: A review. Biophysical Reviews. 2017;9:91–102.
  25. Lionta E, Spyrou G, Vassilatis DK, Cournia Z. Structure-based virtual screening for drug discovery. Current Topics in Medicinal Chemistry. 2014;14:1923–1938.
  26. Sliwoski G, Kothiwale S, Meiler J, Lowe EW. Computational methods in drug discovery. Pharmacological Reviews. 2014;66:334–395.
  27. Yuriev E, Holien J, Ramsland PA. Improvements, trends, and new ideas in molecular docking. Journal of Molecular Recognition. 2015;28:581–604.
  28. Gorgulla C, Boeszoermenyi A, Wang ZF. An open-source drug discovery platform using molecular docking. Nature Protocols. 2020;15:4059–4085
  29. Sousa SF, Ribeiro AJM, Coimbra JT, Neves RP, Martins SA. Protein–ligand docking: Current status and future challenges. Proteins. 2013;81:15–26
  30. Schneider G, Walters WP, Plowright AT, Sieroka N, Listgarten J, Goodnow RA, et al. Rethinking drug design in the artificial intelligence era. Nat Rev Drug Discov. 2020;19(5):353-364.
  31. Walters WP, Murcko MA. Assessing the impact of generative AI on medicinal chemistry. Nat Biotechnol. 2020;38(2):143-145.
  32. Chen Y, Butkiewicz M, Fenner J, et al. Prediction of drug-target interactions using machine learning. J Chem Inf Model. 2019;59(4):1391-1400.

Reference

  1. Jing Y, Bian Y, Hu Z, Wang L, Xie XQ. Deep learning for drug design: an artificial intelligence paradigm for drug discovery. Acta Pharm Sin B. 2021;11(3): 803-821.
  2. Saldívar-González FI, Aldas-Bandera A, Gómez-García A, Medina-Franco JL. Natural product drug discovery in the artificial intelligence era. Chem Sci. 2022;13(6):1526-1546.
  3. Vamathevan J, Clark D, Czodrowski P, et al. Applications of machine learning in drug discovery and development. Nature Reviews Drug Discovery. 2019;18(6):463–477.
  4. Paul D, Sanap G, Shenoy S, Kalyane D, Kalia K, Tekade RK. Artificial intelligence in drug discovery and development. Drug Discov Today. 2021;26(1):80-93.
  5. Schneider P, Walters WP, Plowright AT, et al. Rethinking drug design in the artificial intelligence era. Nature Reviews Drug Discovery. 2020;19:353–364.
  6. Chen H, Engkvist O, Wang Y, Olivecrona M, Blaschke T. The rise of deep learning in drug discovery. Drug Discovery Today. 2018;23(6):1241–1250.
  7. Rodrigues T, Reker D, Schneider P, Schneider G. Counting on natural products for drug design. Nature Chemistry. 2016;8:531–541.
  8. Ekins S. The next era: Deep learning in pharmaceutical research. Pharmaceutical Research. 2016;33:2594–2603
  9. Atanasov AG, Waltenberger B, Pferschy-Wenzig EM, et al. Discovery and resupply of pharmacologically active plant-derived natural products. Biotechnology Advances. 2015;33:1582–1614.
  10. Jing Y, Bian Y, Hu Z, Wang L, Xie X. Deep learning for drug design: an artificial intelligence paradigm for drug discovery. Acta Pharmaceutica Sinica B. 2018;8(6):911–922.
  11. Zhavoronkov A, Ivanenkov YA, Aliper A, et al. Deep learning enables rapid identification of potent DDR1 kinase inhibitors. Nature Biotechnology. 2019;37:1038–1040.
  12. Ekins S, Puhl AC, Zorn KM, et al. Exploiting machine learning for end-to-end drug discovery and development. Nature Materials. 2019;18:435–441.
  13. Stokes JM, Yang K, Swanson K, et al. A deep learning approach to antibiotic discovery. Cell. 2020;180(4):688–702.
  14. Mullowney MW, et al. Artificial intelligence for natural product drug discovery. Nat Rev Drug Discov. 2023;22:1-21.
  15. Walters WP, Murcko MA. Assessing the impact of generative AI on medicinal chemistry. Nature Biotechnology. 2020;38:143–145.
  16. Sliwoski G, Kothiwale S, Meiler J, Lowe EW. Computational methods in drug discovery. Pharmacological Reviews. 2014;66:334–395.
  17. Kitchen DB, Decornez H, Furr JR, Bajorath J. Docking and scoring in virtual screening for drug discovery. Nature Reviews Drug Discovery. 2004;3:935–949.
  18. Trott O, Olson AJ. AutoDock Vina: Improving the speed and accuracy of docking. Journal of Computational Chemistry. 2010;31(2):455–461.
  19. Ferreira LG, dos Santos RN, Oliva G, Andricopulo AD. Molecular docking and structure-based drug design strategies. Molecules. 2015;20:13384–13421.
  20. 20.https://www.researchgate.net/figure/Role-of-AI-technology-in-different-phases-of-drug-discovery_fig8_352692045
  21. https://pmc.ncbi.nlm.nih.gov/articles/PMC9716588/
  22. https://www.researchgate.net/figure/Schematic-illustration-of-the-anti-COVID-19-discover-procedure-of-virtual-screening_fig1_345101777
  23. Morris GM, Huey R, Olson AJ. Using AutoDock for ligand–receptor docking. Current Protocols in Bioinformatics. 2008;24:8.14.1–8.14.40.
  24. Pagadala NS, Syed K, Tuszynski J. Software for molecular docking: A review. Biophysical Reviews. 2017;9:91–102.
  25. Lionta E, Spyrou G, Vassilatis DK, Cournia Z. Structure-based virtual screening for drug discovery. Current Topics in Medicinal Chemistry. 2014;14:1923–1938.
  26. Sliwoski G, Kothiwale S, Meiler J, Lowe EW. Computational methods in drug discovery. Pharmacological Reviews. 2014;66:334–395.
  27. Yuriev E, Holien J, Ramsland PA. Improvements, trends, and new ideas in molecular docking. Journal of Molecular Recognition. 2015;28:581–604.
  28. Gorgulla C, Boeszoermenyi A, Wang ZF. An open-source drug discovery platform using molecular docking. Nature Protocols. 2020;15:4059–4085
  29. Sousa SF, Ribeiro AJM, Coimbra JT, Neves RP, Martins SA. Protein–ligand docking: Current status and future challenges. Proteins. 2013;81:15–26
  30. Schneider G, Walters WP, Plowright AT, Sieroka N, Listgarten J, Goodnow RA, et al. Rethinking drug design in the artificial intelligence era. Nat Rev Drug Discov. 2020;19(5):353-364.
  31. Walters WP, Murcko MA. Assessing the impact of generative AI on medicinal chemistry. Nat Biotechnol. 2020;38(2):143-145.
  32. Chen Y, Butkiewicz M, Fenner J, et al. Prediction of drug-target interactions using machine learning. J Chem Inf Model. 2019;59(4):1391-1400.

Photo
Anuj Algude
Corresponding author

Pravara rural college of pharmacy,pravaranagar,loni,maharastra,india-413736

Photo
Yogiraj Mohite
Co-author

Pravara rural college of pharmacy,pravaranagar,loni,maharastra,india-413736

Photo
Nikhil Bhoite
Co-author

Pravara rural college of pharmacy,pravaranagar,loni,maharastra,india-413736

Anuj Algude, Yogiraj Mohite, Bhoite Nikhil, Artificial Intelligence-Assisted Discovery of Phytoconstituent: A New Era in Herbal Drug Development, Int. J. of Pharm. Sci., 2026, Vol 4, Issue 3, 2016-2023. https://doi.org/10.5281/zenodo.19088889

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