Natural products · Bioinformatics · AI & machine learning

Dr. Abdul Bari Shah

Natural product chemist working across bioinformatics and AI & machine learning to discover and understand bioactive molecules.

KBTU
Associate ProfessorKazakh-British Technical University, Almaty
KazNU
Associate ProfessorAl-Farabi Kazakh National University, Almaty
BP
Brain Pool ScientistNational Research Foundation of Korea

01 · About

From natural molecules to predictive models

I am an Associate Professor at the Kazakh-British Technical University (KBTU) and at Al-Farabi Kazakh National University (KazNU) in Almaty, and a Brain Pool Scientist supported by the National Research Foundation of Korea.

Before Kazakhstan, I was a Research Professor at the College of Pharmacy, Korea University, and a postdoctoral researcher at the Natural Products Research Institute, Seoul National University. I earned my PhD in Applied Life Science (Organic and Natural Product Chemistry) at Gyeongsang National University.

Natural product chemistry

Isolating and characterising bioactive molecules from plants, fungi, bacteria, and the human microbiota with NMR and LC-MS.

Bioinformatics

Molecular networking, network pharmacology, and docking and simulation to link compounds to targets and pathways.

AI & machine learning

Data-driven models that predict bioactivity, annotate spectra, and optimise chemical and extraction processes.

02 · Research focus

Computation first, then the bench

Natural products are chemically rich but slow to study. I use machine learning and bioinformatics to decide what to isolate, predict what a molecule will do, and design the process that produces it, so lab time goes to the most promising candidates.

01Natural product structure 02Molecular fingerprint 03Neural network 04Prediction: bioactivity, yield, process conditions
Discover

Prioritise extracts

ML ranking of extracts and fractions from LC-MS and molecular networking data.

Identify

Annotate spectra

AI-assisted MS/MS annotation and dereplication of known compounds.

Predict

Model activity

QSAR and deep learning for enzyme inhibition and multi-target activity.

Explain

Map mechanisms

Network pharmacology, docking, and simulation to interpret predictions.

Produce

Design processes

Data-driven optimisation of extraction and purification.

03 · Expertise

Chemistry, data, and models

MS/MS annotation
AI · ML

AI & machine learning

  • Bioactivity and enzyme-inhibition prediction (QSAR)
  • AI-assisted MS/MS spectra annotation
  • Virtual screening of natural product libraries
  • Machine learning in chemical engineering and process design
Pythonscikit-learnRDKitQSARRSM
Compound–target–pathway network
BIOINF

Bioinformatics & systems pharmacology

  • Network pharmacology and target–pathway mapping
  • Molecular docking, scoring, and simulation
  • Molecular networking and dereplication (GNPS, AntiMarin)
  • Integrative metabolomics and system pharmacology
GNPSCytoscapeDocking & scoringMassHunterMestReNova
¹H NMR · 800 MHz · CD₃OD
NP · CHEM

Natural product chemistry

Isolation of bioactive compounds from bacteria, fungi, and plants, including endophytes cultivated at small and large scale, with structure elucidation by 1D/2D NMR and LC-MS.

NMR 400–800 MHzLC-QTOF-MS/MSMPLC · prep-HPLCSephadex · ODS · MCI-gel
Enzyme inhibition · dose–response
BIO · ACT

Bioactivity & human microbiome

Enzyme kinetics and cell-based studies on PTP1B, DPP-IV, α-glucosidase, neuraminidase, cholinesterases, tyrosinase, β-secretase and more, plus antibiotics and peptides from the human microbiome and probiotics.

Enzyme kineticsBiofilm inhibitionLDL oxidationCell assays

04 · Process design

AI & machine learning in chemical engineering

Turning a promising natural product into a usable ingredient or drug depends on how well it can be extracted, purified, and scaled. I apply machine learning to these chemical engineering problems, building on my work optimising extraction with response surface methodology.

Bayesian optimisation of extraction yieldLow High
Extraction time (min) →
Temperature (°C) →
Hover the map to read the model

Illustrative model. Amber points are optimisation steps, each chosen by the model from earlier results.

Surrogate process models

Models trained on experimental and simulation data that predict yield, purity, and energy use far faster than full process simulations.

Optimisation of process conditions

Response surface methodology and Bayesian optimisation to find the best solvent, temperature, time, and ultrasound settings with fewer experiments.

Process design & scale-up

Data-driven design of extraction, chromatographic purification, and membrane separation, from laboratory scale to pilot plant.

Sustainable & green processing

Predictive screening of greener solvents and lower-energy routes for valorising Central Asian medicinal plants.

05 · Career

Experience & education

Positions

Sept 2026 – presentAssociate ProfessorKazakh-British Technical University (KBTU), Almaty
2025 – presentAssociate ProfessorFaculty of Chemistry and Chemical Technology, Al-Farabi Kazakh National University
PresentBrain Pool ScientistNational Research Foundation of Korea
2025 – 2026Research Scientist (Joint Research Projects)The Research Center for Medicinal Plants, Al-Farabi Kazakh National University
2024 – 2025Research ProfessorCollege of Pharmacy, Korea University, Sejong
2023 – 2024Postdoctoral Research AssociateNatural Products Research Institute, Seoul National University
2017 – 2018Research AssistantDepartment of Chemistry, University of Malakand, Pakistan

Oral presentations

2026
Advanced system pharmacology and molecular docking approaches revealing the multi-target antioxidant mechanisms of Psoralea corylifoliaHTM2026, Bangkok, Thailand
2024
Targeting bacterial neuraminidase: harnessing the potency of ugonins for inhibitory action and biofilm disruptionInt. Conference on Medicinal Plants and Natural Drug Research, Almaty

Education

2020 – 2023PhD, Applied Life ScienceOrganic & Natural Product Chemistry, Gyeongsang National University · GPA 4.32 / 4.5
2018 – 2020MSc, Applied Life ScienceOrganic & Natural Product Chemistry, Gyeongsang National University · GPA 4.38 / 4.5
2012 – 2016BS (Hons), ChemistryBiochemistry, University of Malakand · GPA 3.69 / 4.0

Awards & projects

2021, 22
Young Pioneer Research AwardTwice, for excellent research performance
MSc – PhD
BK21+ and BK21 Four scholarshipsBrain Korea 21 programme
2025
Scientific Consultant, AP19577056Cichorium intybus cultivation, metabolites, antidiabetic and hepatoprotective effects
2024 – 25
Contributing Researcher, NRF KoreaProjects RS-2019-NR040070 and RS-2021-NR058871

06 · Publications

Selected highlights

# equal contribution · * corresponding

First, equal & corresponding author

  1. Stilbenoids from Vitis amurensis bind to the GATA-3 DNA-binding domain and inhibit the transcription by GATA-3Yu, H.#; Shah, A. B.#; Moon, H.; Kang, M.; Lee, H.; Kim, H.; Lee, K. S.; Byun, Y.; Jung, Y. W.; Lee, K. Y.; Jeo, Y. H.
    Journal of Natural Products 2026 IF 3.7 · Q1doi ↗
  2. Natural products modulating interleukin-mediated pathways for anti-allergic and immunomodulatory effectsShah, A. B.; Kim, Y. J.; Lee, K. S.; Han, S. H.; Byun, Y.; Lee, K. Y.
    Natural Product Reports 2026 IF 12.5 · Q1doi ↗
  3. Dual inhibition of PTP1B and DPP-IV by metabolites from Artocarpus elasticus leaves enhances insulin signaling and sensitivityShah, A. B.; Khan, M. T.; Ullah, S.; Baiseitova, A.; Idrees, M.; Kong, I.-K.; Park, K. H.
    Journal of Pharmaceutical Innovation 2026, 21(6), 563 IF 2.6 · Q2doi ↗
  4. Exploring the bioactive landscape: peptides and non-peptides from the human microbiotaShah, A. B.; Cho, H. J.; Shim, S. H.
    npj Biofilms and Microbiomes 2025, 11:76 IF 11.4 · Q1doi ↗
  5. α-Glucosidase inhibition-guided network pharmacology and molecular docking reveal the antidiabetic potential of Cichorium intybus as a functional foodShah, A. B.; Baiseitova, A.; Amzeyeva, U.; Shang, X.; Jenis, J.
    International Journal of Molecular Sciences 2025, 26(19), 9497 IF 5.6 · Q1doi ↗
  6. Integrative metabolomics and system pharmacology reveal the antioxidant blueprint of Psoralea corylifoliaShah, A. B.; Lee, K. Y.
    Scientific Reports 2025, 15, 28632 IF 4.9 · Q1doi ↗
  7. Isolation, characterization, antidiabetic and antityrosinase potentials of compounds isolated from Anabasis articulataJan, M.#; Shah, A. B.#; Al-Joufi, F. A.; Zahoor, M.; Esa, M.; Rashid, H. U.; Gulfam, N.; Shahzad, M. S.; Haseena
    Applied Food Research 2025, 100949 IF 5.4 · Q1doi ↗
  8. Human microbiota peptides: important roles in human healthShah, A. B.; Shim, S. H.
    Natural Product Reports 2024 IF 12.5 · Q1doi ↗
  9. Probiotic significance of Lactobacillus strains: a comprehensive review on health impacts, research gaps, and future prospectsShah, A. B.*; Baiseitova, A.; Zahoor, M.; Ahmad, I.; Ikram, M.; Bakhsh, A.; Shah, M. A.; Ali, I.; Idress, M.; Ullah, R.; Nasr, F. A.; Al-Zharani, M.
    Gut Microbes 2024, 16(1), 2431643 IF 15.3 · Q1doi ↗
  10. Therapeutic potential of ugonins: bioactive flavonoids from Helminthostachys zeylanica with multifaceted biological activitiesShah, A. B.; Baiseitova, A.; Kim, Y. J.; Lee, K. Y.
    Planta Medica 2026, 92(02), 112–122 IF 2.1 · Q2doi ↗
  11. Investigation of responsible phenolic metabolites for PTP1B inhibition from Artocarpus elasticusShah, A. B.; Baiseitova, A.; Lee, G.; Kim, J. H.; Park, K. H.
    ACS Omega 2024, 9(8), 9053–9062 IF 5.2 · Q1doi ↗
  12. Antioxidant potentials of furanodihydrobenzoxanthones from Artocarpus elasticus and their protection against oxLDL induced injury in SH-SY5Y cellsBaiseitova, A.#; Shah, A. B.#; Idress, M.; Kong, L. K.; Park, K. H.
    Biomedicine & Pharmacotherapy 2023, 165, 115278 IF 7.5 · Q1doi ↗
  13. Inhibition of bacterial neuraminidase and biofilm formation by ugonins isolated from Helminthostachys zeylanica (L.) HookShah, A. B.; Baiseitova, A.; Kim, J. H.; Lee, Y. H.; Park, K. H.
    Frontiers in Pharmacology 2022, 13 IF 5.4 · Q1doi ↗
  14. Effectiveness of cyclohexyl functionality in ugonins from Helminthostachys zeylanica to PTP1B and α-glucosidase inhibitionsShah, A. B.; Yoon, S.; Kim, J. H.; Zhumanova, K.; Ban, Y. J.; Lee, K. W.; Park, K. H.
    International Journal of Biological Macromolecules 2020, 165, 1822–1831 IF 8.7 · Q1doi ↗

Books & chapters

  1. From mortar to machine: evolution of metabolite isolation techniques in natural products researchShah, A. B.; Baiseitova, A.
    Springer Nature monograph Proposal accepted
  2. Bridging traditional and modern medicine with phytopharmaceuticals: from heritage to innovationShah, A. B.; Baiseitova, A.; Zahoor, M. (Eds.)
    Bentham Science, edited book, 2026 In process
  3. Endophytes as a source of antioxidant and antiaging agentsShah, A. B.; Baiseitova, A.
    Invited chapter, Apple Academic Press / Taylor & Francis In press
  4. Biodiversity of the national parks and nurseries in the alpine zonesBibi, Y.; Bibi, A.; Rahman, M. U.; Ahmad, N.; Shah, S. N.; Shah, A. B.; Ozdemir, F. A.; Gemechu, T. M.
    In: Conservation, Climate, and Sustainable Use in Alpine Ecosystems, 2026, pp. 137–164 Published
  5. Genistein’s role in menopause and hormonal balanceShah, A. B.; Baiseitova, A.
    Book chapter With editor
  6. Pharmaceutical chemistry: drug design and structural modificationShah, A. B.; Baiseitova, A.
    Book chapter With editor
Co-authored publications
  1. Phytochemical evaluation, nutritional and pharmacological values of Trigonella foenum-graecum: a comprehensive review
    Frontiers in Chemistry 2026, 14, 1849521 IF 5.3 · Q1 Correspondingdoi ↗
  2. Solvent-dependent bioactive composition and antifungal potential of neem (Azadirachta indica) seed extracts against mycotoxigenic Aspergillus species
    Chemistry & Biodiversity 2026 IF 2.5 · Q2 Correspondingdoi ↗
  3. Identification of anti-inflammatory constituents of Lindera glauca using cell extraction coupled with LC-QTOF MS/MS
    Natural Product Research 2025 IF 1.6 · Q2doi ↗
  4. Phytochemical characterization, mycotoxigenic fungi inhibition and aflatoxins detoxification using Ocimum basilicum whole seed extracts
    Notulae Botanicae Horti Agrobotanici Cluj-Napoca 2026, 54 IF 1.3 · Q2 Correspondingdoi ↗
  5. Natural products targeting Alzheimer’s disease via NF-κB pathway: a review
    CNS & Neurological Disorders – Drug Targets 2025 IF 3.0 · Q2 Correspondingdoi ↗
  6. Comparative phytochemical, colloidal, and antioxidant profiling of Artemisia albida, A. leucodes, and A. scopaeformis for cosmeceutical and nutraceutical applications
    Molecules 2025 IF 4.6 · Q1doi ↗
  7. Response surface methodology optimization of ultrasonic-assisted extraction of chicory (Cichorium intybus L.), UPLC-ESI-QTOF-MS analysis, antioxidant and hepatoprotective activity
    eFood 2025, 6, e70081 IF 5.7 · Q1doi ↗
  8. Characterization and pharmacological insights into silver nanoparticles derived from Juncus articulatus L.
    Applied Organometallic Chemistry 2025, 39, e70284 IF 3.7 · Q1doi ↗
  9. Protective effect of Helicteres isora on hepatorenal toxicity and management of diabetes in animal models
    Open Chemistry 2025 IF 1.9 · Q3doi ↗
  10. Synthesis and exploration of the anti-inflammatory and antioxidant potential of silver nanoparticles of propolis and GC–MS profiling
    Applied Organometallic Chemistry 2025, 39, e70182 IF 3.7 · Q1doi ↗
  11. Fungicidal effect of Azadirachta indica extracts against Rhizopus stolonifer and Monilinia fructicola in postharvest peaches
    Discover Plants 2025, 2, 1–14doi ↗
  12. Synthesis, in vitro and in-silico evaluation of amide derivatives as prospective antimicrobial and antileishmanial agents
    Future Medicinal Chemistry 2025, 17, 789–802 IF 3.4 · Q2doi ↗
  13. Symptomatic evidence of begomovirus disease in vegetable crops from selected districts of Khyber Pakhtunkhwa, Pakistan
    Applied Ecology and Environmental Research 2025, 23(3) IF 0.6 · Q4doi ↗
  14. Lipoxygenase inhibitory activity of phytoconstituents isolated from the rhizomes of Boesenbergia albosanguinea
    Bulletin of the Chemical Society of Ethiopia 2025, 39 IF 2.3 · Q3doi ↗
  15. Allergy inhibition using naturally occurring compounds targeting thymic stromal lymphopoietin pathways: a comprehensive review
    Biomolecules & Therapeutics 2025, 33, 249–267 IF 3.2 · Q2doi ↗
  16. Application of Azadirachta indica (neem) crude extracts against postharvest decay of fruits caused by Penicillium expansum, Colletotrichum gloeosporioides and Botrytis cinerea
    Notulae Botanicae Horti Agrobotanici Cluj-Napoca 2025, 53 IF 1.3 · Q3doi ↗
  17. Inorganic-polymer composite electrolytes: basics, fabrications, challenges and future perspectives
    Reviews in Inorganic Chemistry 2024 IF 3.1 · Q2doi ↗
  18. Antioxidant, antibacterial, enzyme inhibition and fluorescence characteristics of unsymmetrical thiourea derivatives
    Heliyon 2024, 10, e31563 IF 4.0 · Q1 Correspondingdoi ↗
  19. Phytochemical profiling and anticancer potential of Gardenia latifolia extracts against arsenic trioxide induced liver fibrosis in rat model
    Frontiers in Pharmacology 2024, 15 IF 4.8 · Q1doi ↗
  20. Estimation of genetic polymorphism in quince (Cydonia oblonga Mill.) genotypes using morphological traits and DNA barcoding
    PLOS ONE 2024, 19(11), e0310048 IF 2.6 · Q2doi ↗
  21. Selective induction of furanocoumarins in Angelica acutiloba roots by ethylene and their monoamine oxidase inhibition
    Industrial Crops and Products 2024, 213, 118418 IF 6.2 · Q1doi ↗
  22. Bioaccumulation of lead in different organs of Ctenopharyngodon idella (grass fish) and Tor putitora (mahseer) fish
    Brazilian Journal of Biology 2024, 84 IF 1.6doi ↗
  23. 1-Aminocyclopropane-1-carboxylic acid enhances phytoestrogen accumulation in soy plants by accelerating the isoflavone biosynthetic pathway
    Journal of Agricultural and Food Chemistry 2023, 71 IF 6.2 · Q1doi ↗
  24. Bacterial neuraminidase inhibition of xanthones bearing geranyl and prenyl groups from Cratoxylum cochinchinense
    Frontiers in Chemistry 2023, 11 IF 4.2 · Q2doi ↗
  25. Enzymatic evaluation of chromenone derivatives from Flemingia philippinensis as viral neuraminidase (H3N2) inhibitors
    Journal of Molecular Structure 2023, 1293 IF 4.7 · Q2doi ↗
  26. Cold-acclimation effect on cadmium absorption and biosynthesis of polyphenolics, free proline and photosynthetic pigments in Spirogyra aequinoctialis
    Open Chemistry 2023, 21 IF 1.9 · Q3doi ↗
  27. The DNA threat probing of some chromophores using UV/VIS spectroscopy
    World Journal of Biology and Biotechnology 2023, 8(2) IF 4.2doi ↗
  28. Heavy metal transportation from polluted water into humans through fodder plants and farmed animals
    Zeitschrift für Physikalische Chemie 2023 IF 3.2 · Q3doi ↗
  29. Changes in secondary metabolites in soybean (Glycine max L.) roots by salicylic acid treatment and their anti-LDL oxidation effects
    Frontiers in Plant Science 2022, 13 IF 4.8 · Q1doi ↗
  30. Soybean phytochemicals responsible for bacterial neuraminidase inhibition and their characterization by UPLC-ESI-TOF/MS
    Food & Function 2022, 13(13) IF 5.4 · Q1doi ↗
  31. New dihydrobenzoxanthone derivatives with bacterial neuraminidase inhibitory activity isolated from Artocarpus elasticus
    Bioorganic Chemistry 2022, 127 IF 4.7 · Q1doi ↗
  32. Bacterial oxidoreductive enzymes as molecular weapons for the degradation and metabolism of toxic azo dyes in wastewater: a review
    Zeitschrift für Physikalische Chemie 2022 IF 3.2 · Q3doi ↗
  33. The chemically modified leaves of Pteris vittata as efficient adsorbent for zinc (II) removal from aqueous solution
    Water 2022, 14(24), 4039 IF 3.0 · Q3doi ↗
  34. Biodegradation of azo dye methyl red by Pseudomonas aeruginosa: optimization of process conditions
    Int. J. Environ. Res. Public Health 2022, 19(16) IF 4.6doi ↗
  35. Biological mineralization of methyl orange by Pseudomonas aeruginosa
    Water 2022, 14(10), 1551 IF 3.0 · Q3doi ↗
  36. O-Alkylated quercetins with selective acetylcholinesterase and β-secretase inhibitions from Melicope glabra leaves
    Journal of Functional Foods 2021, 84 IF 4.0 · Q2doi ↗
  37. Inhibitory mechanism of O-methylated quercetins, highly potent β-secretase inhibitors isolated from Caragana balchaschensis
    Journal of Ethnopharmacology 2021, 272 IF 5.4 · Q1doi ↗
  38. A significant change in free amino acids of soybean (Glycine max L. Merr) through ethylene application
    Molecules 2021, 26(4) IF 4.6 · Q2doi ↗
  39. Biodegradation of Brown 706 dye by bacterial strain Pseudomonas aeruginosa
    Water 2021, 13(21) IF 3.0 · Q3doi ↗
  40. Genetic diversity in local and exotic Avena sativa L. (oat) germplasm using multivariate analysis
    Agronomy 2021, 11(9) IF 3.4 · Q1doi ↗
  41. HPLC characterization of phytochemicals and antioxidant potential of Alnus nitida (Spach) Endl.
    Horticulturae 2021, 7(8) IF 3.2 · Q3doi ↗
  42. Thiourea derivatives, simple in structure but efficient enzyme inhibitors and mercury sensors
    Molecules 2021, 26(15) IF 3.0 · Q1doi ↗
  43. Tyrosinase inhibition and kinetic details of puerol A having but-2-enolide structure from Amorpha fruticosa
    Molecules 2020, 25(10) IF 4.6 · Q2doi ↗
  44. Isolation of quercetin from Rubus fruticosus, concentration through NF/RO membranes, and recovery through carbon nanocomposite: a pilot plant study
    BioMed Research International 2020 IF 2.3 · Q3doi ↗
  45. Biological evaluation of antimicrobial activity of Calotropis procera against a range of bacteria
    Journal of Pharmacognosy and Phytochemistry 2020, 9
  46. Biological and phytochemical evaluation of Cotoneaster microphyllus, Ficus auriculata and Calotropis procera
    Latin American Journal of Pharmacy 2019 IF 0.2
  47. Therapeutic applications of coconut water mitigate diabetes mellitus in Oryctolagus cuniculus (rabbit)
    Biomedical Journal of Scientific & Technical Research 2019, 16(4)doi ↗
  48. HPLC-UV analysis of antioxidants in Citrus sinensis stem and root extracts
    Journal of the Chemical Society of Pakistan 2018, 40(3) IF 0.5 · Q4
  49. Screening of potential drug–drug interactions in the neurology ward of a tertiary care hospital, Peshawar
    Pharmacologyonline 2018
  50. Determination of antioxidants, antibacterial activities, total phenolic, polyphenol and pigment contents in Nasturtium officinale
    Pharmacologyonline 2017

07 · Editorial

Editorial & review roles

Editorial Board Member

Journals
Journal of Translational MedicineAssoc. EditorPLOS ONEAssoc. EditorFrontiers in MicrobiologyAssoc. EditorFrontiers in Natural ProductsAssoc. EditorBMC BioinformaticsScientific ReportsDiscover Pharmaceutical ScienceDiscover ChemistryCurrent Bioactive Compounds

Guest Editor

Special issue · Pharmaceuticals
Advancements in the Study of Biological Activities of Plant Extracts and Components

Topic Editor

Frontiers in Natural Products
Fungal Natural Products: Biosynthesis, Bioactivity, and Biotechnological Applications

Review Editor

Sections
Frontiers in Molecular BiosciencesMetabolomics Frontiers in MicrobiologyMicrobial Physiology Frontiers in Natural ProductsIsolation & Purification

Peer Reviewer

Selected journals
Int. J. Biological MacromoleculesScientific ReportsBioorganic ChemistryFood ChemistryBiomedicine & PharmacotherapyACS OmegaRSC AdvancesApplied Biological ChemistryHeliyonInt. J. Molecular SciencesMetabolitesMicroorganismsMoleculesNutrientsSportsWater

08 · Contact

Collaborations, students & invited talks

Collaboration

Natural product drug discovery

Isolation, structure elucidation, and bioactivity of compounds from plants, fungi, and microbes.

Collaboration

Bioinformatics & network pharmacology

Molecular networking, docking, and systems-level analysis of multi-target mechanisms.

Collaboration

AI & ML in chemical engineering

Machine learning for process design, modelling, and optimisation of extraction and chemical processes.

Collaboration

AI-driven compound discovery

Predictive models for bioactivity, spectra annotation, and virtual screening.

Students

MSc & PhD supervision

Students at KBTU and KazNU interested in natural products, bioinformatics, or AI in chemistry are welcome to write.

Talks

Invited talks & lectures

Seminars, conference talks, and workshops on natural products, system pharmacology, and AI in chemistry.

Email

abs.uom28@gmail.com
a.shah@kbtu.kz
abdul.shah@kaznu.edu.kz

Almaty, Kazakhstan