Overview
Background
I completed my PhD in 2013 and I am currently a Senior Research Fellow and the Managing Director of the Soils of Science (S4S) Program at the University of Queensland. I am recognised as an emerging leader in antibiotic biodiscovery research. I have multidisciplinary research skills and expertise spanning the fields of organic chemistry and microbiology. I have made a significant contribution to the field of microbial biodiscovery employing high-throughput, high efficiency, natural product discovery to explore the chemical and biological properties of natural products produced by Australian marine and terrestrial microbes. I have identified and evaluated >40 new drugs targeting infectious diseases that attracted >$3M in research funding. I have led multi-year projects with industry, targeting animal health (ELANCO) and crop (NEXGEN Plants) and microbial chemical diversity (Microbial Screening Technologies; BioAustralis). I am a co-inventor on a UQ pending patent application documenting a new soil microbiome-inspired crop protection agent. This invention has attracted industry investment (NEXGEN Plants), to establish its potential, ahead of licensing and commercialisation. Therefore, I have co-led a project with industrial partner NEXGEN Plants, to investigate a new natural product that activates innate plant immunity defences against significant pathogens (patent pending). Since 2015, I have established the antibiotic biodiscovery capability at IMB targeting multidrug resistant (MDR) human pathogens and developed new approaches that have had significant knowledge impact in the antibiotic development and host defence research areas directed to combat MDR pathogens. This has resulted in the establishment of the Biodiscovery@UQ facility, a university-wide networking initiative designed to support excellence in biodiscovery research across UQ. I have secured funding from UQ to develop a new antitubercular drug lead (CIA), an ARC Linkage grant (LP19, CIB) to develop new anthelmintics and a grant from the University de La Frontera (collaborator), Chile to discover new antibiotics from Antarctic microbes, Marine CRC fund (CIA) to map the chemical diversity in Australian marine microbes and ARC LIEF grant. I co-led THE FIRST citizen science initiative, S4S, including developing the APP, website and running regional public workshops, with the aim of increasing public awareness about the role of soil microbes in antibiotic discovery. This initiative has attracted ~$1M in institutional and philanthropic support.
Availability
- Dr Zeinab Khalil is:
- Available for supervision
- Media expert
Qualifications
- Bachelor (Honours) of Pharmaceutical Sciences, Helwan University
- Masters (Research) of Microbiology, Helwan University
- Doctor of Philosophy, The University of Queensland
Research interests
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Cultivation Profiling (MATRIX)
An innovative high throughput miniaturized 24-well plate technology for the analytical cultivation of fungi and bacteria (MATRIX), supportive of multiple culture media and additive conditions, under broth static, broth shaken and solid phase. The MATRIX greatly accelerates, lowers the cost and increases the productivity of our microbial biodiscovery research.
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Chemical Profiling (UPLC-QTOF and GNPS)
An in situ MATRIX extraction to support rapid UPLC-DAD and UPLC-QTOF (MS/MS) profiling of crude extracts (and chromatographic fractions and pure metabolites), and data visualisation using global natural products social networking (GNPS) protocols. This greatly enhances our capacity to (i) assess chemical diversity in crude extracts/fractions, (ii) detect new from known, rare from common, and related from unrelated natural products, and (iii) detect transcriptional activation of silent biosynthetic gene clusters.
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Nitric oxide mediated transcriptional activation (NOMETA)
The use of nitric oxide as a transcriptional activator of silent biosynthetic gene clusters (BGCs) that code for bacterial and fungal defensive chemistry, including new classes of antibiotic and antiparasitic. This process allows for the addition of either (a) very low (sub nM) levels of Gram –ve bacteria lipopolysaccharide to fungal cultures to induce nitric oxide release, or (b) the direct addition of very low levels of an NO donor such as sodium nitric prusside to bacterial or fungal cultures, to induce the activation of silent BGCs encoded with microbial genomes.
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Microbial Biodiscovery and metabolite expression profiling
Many past studies into microbial secondary metabolism gene activation (autoregulators) have relied heavily on (i) the observation of morphological differentiation (which may or may not be linked to activation of new secondary metabolism), (ii) the up-regulation of a known metabolite/antibiotic(s) (which does not address the activation of silent “new” genes), or (iii) the appearance of pigmentation or antibiotic activity (which cannot differentiate new from old chemistry). A high throughput modern approach to the detection of gene activation events needs to rapidly and directly assess metabolite profiles. This project will develop and implement innovative methodologies and protocols for the HPLC-DAD-ELSD-HRMS analysis of >1M microbial metabolites – characterized by retention time, UV-vis spectrum and MW plus elemental composition. These analyses will be facilitated by the use of semi-automated and automated systems, including data archival and profiling software, to annotate, compare and evaluate similarities and differences in metabolite expression. This innovation implements a high throughput approach to detecting gene activation events by directly observing and providing a qualitative and quantitative assessment of microbial secondary metabolite production. This approach can be used to (i) detect, (ii) guide the isolation of, and (iii) evaluate the impact of, new gene activators, and their activated gene products.
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Gene activators
Whereas most microbial biodiscovery seeks to isolate new bioactive secondary metabolites produced under standard fermentation conditions, this project is innovative in that it seeks to challenge the microbial genome and activate otherwise silent secondary metabolite gene clusters. While this project will undoubtedly discover new microbial secondary metabolites, the main objective of the project is to discover and evaluate microbial metabolites that activate secondary metabolism – gene activators. This innovation addresses the unmet need to discover gene activators and assess their value in both basic science - as molecular probes to better understand microbial genomics and systems biology - as well as applied science – as molecular reagents to switch on “silent” microbial secondary metabolite gene clusters.
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Antibiotic and Cytotoxicity Profiling
Quantitative antibiotic screening against multiple Gram +ve and –ve bacteria, and fungi, including multidrug resistant clinical isolates such as methicillin resistant Staphylococcus aureus and Mycobacterium tuberculosis, as well as cytotoxicity screening against multiple mammalian (human) cancerous and non-cancerous cell lines, including multidrug resistant cancer cells over-expressing ABC transporter efflux pumps. This screening allows us to rapidly assemble a bioactivity profile on all prospective extracts.
Research impacts
In 2019, > 1.2 M people worldwide died from multidrug resistant (MDR) bacterial infections due to the lack of effective antibiotics, and we are in desperate need of chemical inspiration, to replenish the antibiotic pipeline. Our Antimicrobial Research and Development program has contributed significant NEW KNOWLEDGE through applying medicinal chemistry to the discovery of translational solutions to antimicrobial resistance (>100 new antibiotics) as well as novel basic research tools to help better understand the interactions between antibiotics and resistant bacteria. Specifically, our program has applied novel transcriptomics approaches to identify and activate silent genes within the microbial genome that informed the development of effective antibiotics.
Works
Search Professor Zeinab Khalil’s works on UQ eSpace
2026
Journal Article
Unlocking microbial dark matter: A biotechnology framework for replenishing the antibiotic pipeline
Hamed, Ahmed A. and Khalil, Zeinab G. (2026). Unlocking microbial dark matter: A biotechnology framework for replenishing the antibiotic pipeline. Biotechnology Advances, 94 109054, 109054-109054. doi: 10.1016/j.biotechadv.2026.109054
2026
Journal Article
A non-conjugated peptide-adjuvant system of synthetic peptide-vaccine elicited potent antibody response and opsonic protection against clinical GAS strains
Fan, Jingyi, Khalil, Zeinab G., Hussein, Waleed M., Toth, Istvan, Skwarczynski, Mariusz and Stephenson, Rachel J. (2026). A non-conjugated peptide-adjuvant system of synthetic peptide-vaccine elicited potent antibody response and opsonic protection against clinical GAS strains. Bioorganic Chemistry, 176 109861, 1-11. doi: 10.1016/j.bioorg.2026.109861
2026
Journal Article
Correction to “Tepuazines A–E: Phenazine Glycosides from a Venezuelan Quartz-Rich (Tepui) Cave Soil-Derived <i>Streptomyces virginiae</i> CMB-CA091”
Kankanamge, Sarani, Khalil, Zeinab G. and Capon, Robert J. (2026). Correction to “Tepuazines A–E: Phenazine Glycosides from a Venezuelan Quartz-Rich (Tepui) Cave Soil-Derived Streptomyces virginiae CMB-CA091”. Journal of Natural Products, 89 (7), 2221-2221. doi: 10.1021/acs.jnatprod.6c00728
2026
Journal Article
Mitochondrial fission mediates an evolutionarily conserved antibacterial defense response
Kapetanovic, Ronan, Afroz, Syeda Farhana, Curson, James E. B., Kirmes, Ina, Ramnath, Divya, Nothjunge, Stephan, Liu, Jinting, Atkinson, Jordan D., Ahier, Arnaud, Raven, Karoline D., Bosch, Marta, Keller, Bernhard, Lawrence, Grace M. E. P., Gupta, Kaustav Das, Shakespear, Melanie R., Ferguson, Charles, Stocks, Claudia J., Bokil, Nilesh J., Matthias, Gabriele, Nguyen, Tam T. K., Khalil, Zeinab G., Reid, Robert C., Hansford, Karl A., Hansbro, Philip M., Cooper, Matthew A., Schembri, Mark A., Blumenthal, Antje, Schroder, Kate, Fairlie, David P. ... Sweet, Matthew J. (2026). Mitochondrial fission mediates an evolutionarily conserved antibacterial defense response. Science Immunology, 11 (118) eaed2623, 1-17. doi: 10.1126/sciimmunol.aed2623
2026
Journal Article
Development of a novel polyleucine-based immunopotentiator for subunit vaccines against Group A Streptococcus
Lu, Lantian, Cruz, Jazmina L. Gonzalez, Giri, Rabina, Zhang, Yuexiao, Bashiri, Sahra, Cadena, Leslie C. Domínguez, Li, Shuhang, Khalil, Zeinab G., Hussein, Waleed M., Wang, Jingwen, Kiong, Jolynn, Lu, Xuehan, Zhang, Jiahui, Lu, Miao, Huang, Wenbin, Kong, Wei Yang, Nahar, Ummey Jannatun, Koirala, Prashamsa, Guo, Zhong, Walden, Patricia, Blumenthal, Antje, Begun, Jakob, Alexandrov, Kirill, Toth, Istvan, Stephenson, Rachel J. and Skwarczynski, Mariusz (2026). Development of a novel polyleucine-based immunopotentiator for subunit vaccines against Group A Streptococcus. Small, 22 (22) e11459, 1-20. doi: 10.1002/smll.202511459
2026
Journal Article
Goondoxazoles A–C: anthelmintic spiroketal polyketide alkaloids and other benzoxazoles from Australian pasture soil-derived Streptomyces spp.
Jin, Shengbin, Bruhn, David F., Burkman, Erica J., Childs, Cynthia T., Han, Jianying, Khalil, Zeinab G., Moreno, Yovany, Salim, Angela A., Samarasekera, Kaumadi, Tangerina, Marcelo M. P. and Capon, Robert J. (2026). Goondoxazoles A–C: anthelmintic spiroketal polyketide alkaloids and other benzoxazoles from Australian pasture soil-derived Streptomyces spp.. Antibiotics, 15 (3) 302, 302-3. doi: 10.3390/antibiotics15030302
2026
Journal Article
Investigation of physical mixtures versus disulfide crosslinking self-adjuvanting peptide-based subunit vaccines against Group A Streptococcus
Fan, Jingyi, Wang, Jingwen, Lu, Lantian, Nahar, Ummey Jannatun, Kong, Wei Yang, Zhang, Jiahui, Stephenson, Rachel J., Cruz, Jazmina Gonzalez, Skwarczynski, Mariusz, Toth, Istvan, Khalil, Zeinab G. and Hussein, Waleed M. (2026). Investigation of physical mixtures versus disulfide crosslinking self-adjuvanting peptide-based subunit vaccines against Group A Streptococcus. International Journal of Pharmaceutics, 689 126513, 126513. doi: 10.1016/j.ijpharm.2025.126513
2025
Journal Article
Rational development of a novel emulgel adjuvant for single‐shot effective vaccination: a multivariate analysis approach
Shalash, Ahmed O., Hussein, Waleed M., Nahar, Ummey J., Wang, Jingwen, Lu, Lantian, Azuar, Armira, Kiong, Jolynn J. E., Koirala, Prashamsa, Khalil, Zeinab G. and Toth, Istvan (2025). Rational development of a novel emulgel adjuvant for single‐shot effective vaccination: a multivariate analysis approach. Advanced Materials, 37 (33) 2506496, 1-17. doi: 10.1002/adma.202506496
2025
Journal Article
Evaluation of peptide-based vaccines against Group A Streptococcus in Staphylococcus aureus-infected mice
Shalash, Ahmed O., Sun, Haolan, Cui, Yiru, Wang, Jingwen, Arnts, Barb, Bauer, Jannah, Hussein, Waleed M., Khalil, Zeinab G., Skwarczynski, Mariusz and Toth, Istvan (2025). Evaluation of peptide-based vaccines against Group A Streptococcus in Staphylococcus aureus-infected mice. Vaccines, 13 (6) 632, 1-29. doi: 10.3390/vaccines13060632
2025
Journal Article
Studies concerned with the structure and synthesis of the anti-viral tropolone glycoside liriosmaside A
Chen, Qi, Zhan, Yaping, Gardiner, Michael G., Khalil, Zeinab G., Dewa, Amila A., Sritharan, Thulasi, Capon, Robert J., Lan, Ping, Tan, Shen and Banwell, Martin G. (2025). Studies concerned with the structure and synthesis of the anti-viral tropolone glycoside liriosmaside A. ChemistryOpen, 14 (8) e202500011. doi: 10.1002/open.202500011
2025
Journal Article
Influence of component structural arrangement on cholesterol-antigen conjugate immunogenicity and antisera bactericidal activity against group A Streptococcus
Skwarczynski, Mariusz, Alharbi, Nedaa, Nahar, Ummey J., Shalash, Ahmed O., Azuar, Armira, Koirala, Prashamsa, Khisty, Shefali J., Wang, Jingwen, Marasini, Nirmal, Hussein, Waleed M., Khalil, Zeinab G. and Toth, Istvan (2025). Influence of component structural arrangement on cholesterol-antigen conjugate immunogenicity and antisera bactericidal activity against group A Streptococcus. Bioorganic Chemistry, 157 108248, 108248. doi: 10.1016/j.bioorg.2025.108248
2025
Journal Article
MATRIX: a platform for cultivation profiling and bioactive discovery in natural product research
Khalil, Zeinab G., Sritharan, Thulasi, Salim, Angela A. and Capon, Robert J. (2025). MATRIX: a platform for cultivation profiling and bioactive discovery in natural product research. Frontiers in Natural Products, 3 1532543, 1-13. doi: 10.3389/fntpr.2024.1532543
2025
Journal Article
A synthetic cyclic peptide for promoting antigen presentation and immune activation
Zhang, Jiahui, Madge, Harrison Y. R., Mahmoud, Asmaa, Lu, Lantian, Wang, Wanyi, Huang, Wenbin, Koirala, Prashamsa, Gonzalez Cruz, Jazmina L., Kong, Wei Yang, Bashiri, Sahra, Shalash, Ahmed O., Hussein, Waleed M., Khalil, Zeinab G., Wells, James W., Toth, Istvan and Stephenson, Rachel J. (2025). A synthetic cyclic peptide for promoting antigen presentation and immune activation. NPJ Vaccines, 10 (1) 9, 9-1. doi: 10.1038/s41541-024-01050-4
2025
Book Chapter
Advancements in microbioreactor technology: high-throughput cultivation and peptide profiling in microbial research
Khalil, Zeinab G. (2025). Advancements in microbioreactor technology: high-throughput cultivation and peptide profiling in microbial research. Peptide synthesis: methods and protocols. (pp. 123-141) edited by Waleed M. Hussein and Mariusz Skwarczynski. New York, NY, U.S.A.: Humana Press. doi: 10.1007/978-1-0716-4562-8_11
2024
Journal Article
Pullenvalenes E–H: triterpenyl-aminoglycosides from an Australian soil-derived fungus, Clonostachys sp
Wang, Yanan, Kiong, Jolynn, Dewa, Amila Agampodi, Salim, Angela A., Khalil, Zeinab G. and Capon, Robert J. (2024). Pullenvalenes E–H: triterpenyl-aminoglycosides from an Australian soil-derived fungus, Clonostachys sp. Journal of Natural Products, 87 (11), 2649-2656. doi: 10.1021/acs.jnatprod.4c01068
2024
Journal Article
Goondapyrones A–J: Polyketide α and γ pyrone anthelmintics from an Australian soil-derived Streptomyces sp
Jin, Shengbin, Bruhn, David F., Childs, Cynthia T., Burkman, Erica, Moreno, Yovany, Salim, Angela A., Khalil, Zeinab G. and Capon, Robert J. (2024). Goondapyrones A–J: Polyketide α and γ pyrone anthelmintics from an Australian soil-derived Streptomyces sp. Antibiotics, 13 (10) 989, 1-13. doi: 10.3390/antibiotics13100989
2024
Journal Article
Biosynthesis of novel non-proteinogenic amino acids β-hydroxyenduracididine and β-methylphenylalanine in Escherichia coli
Gillane, Rosemary, Daygon, Dara, Khalil, Zeinab G. and Marcellin, Esteban (2024). Biosynthesis of novel non-proteinogenic amino acids β-hydroxyenduracididine and β-methylphenylalanine in Escherichia coli. Frontiers in Bioengineering and Biotechnology, 12 1468974, 1-11. doi: 10.3389/fbioe.2024.1468974
2024
Journal Article
Self-assembled monovalent lipidated mannose ligand as a standalone nanoadjuvant
Nahar, Ummey J., Wang, Jingwen, Shalash, Ahmed O., Lu, Lantian, Islam, Md. T., Alharbi, Nedaa, Koirala, Prashamsa, Khalil, Zeinab G., Capon, Robert J., Hussein, Waleed M., Toth, Istvan and Skwarczynski, Mariusz (2024). Self-assembled monovalent lipidated mannose ligand as a standalone nanoadjuvant. Vaccine, 42 (23) 126060, 126060. doi: 10.1016/j.vaccine.2024.06.027
2024
Journal Article
Ancient and remote quartzite caves as a novel source of culturable microbes with biotechnological potential
Ghezzi, Daniele, Salvi, Luca, Costantini, Paolo E., Firrincieli, Andrea, Iorio, Marianna, Lopo, Ettore, Sosio, Margherita, Elbanna, Ahmed H., Khalil, Zeinab G., Capon, Robert J., De Waele, Jo, Vergara, Freddy, Sauro, Francesco and Cappelletti, Martina (2024). Ancient and remote quartzite caves as a novel source of culturable microbes with biotechnological potential. Microbiological Research, 286 127793, 1-16. doi: 10.1016/j.micres.2024.127793
2024
Journal Article
Synthesis of the corrected structure assigned to Clonorosin B, an alkaloid obtained from the soil-derived fungus Clonostachys rosea YRS-06
Han, Yong-Ying, Yang, Weiguang, Lan, Ping, Khalil, Zeinab G., Capon, Robert J. and Banwell, Martin G. (2024). Synthesis of the corrected structure assigned to Clonorosin B, an alkaloid obtained from the soil-derived fungus Clonostachys rosea YRS-06. Journal of Natural Products, 87 (9), 2310-2316. doi: 10.1021/acs.jnatprod.4c00777
Funding
Current funding
Past funding
Supervision
Availability
- Dr Zeinab Khalil is:
- Available for supervision
Looking for a supervisor? Read our advice on how to choose a supervisor.
Available projects
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New antibiotics targeting Gram-negative cell wall formation
Gram-negative “superbugs” are among the most urgent threats to global health, and few new drug classes have reached the clinic in decades. Supported by an NHMRC Ideas Grant, this project will look for microbial natural products that disrupt how Gram-negative bacteria build their cell walls. Students will cultivate Australian microbes, guide chemical isolation with bioassays, determine structures (NMR and MS), and study mechanism of action with collaborators.
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Unlocking silent microbial genes for drug discovery
Most of the gene clusters microbes use to make natural products stay “silent” under standard lab conditions. Building on our NOMETA approach (nitric oxide–mediated transcriptional activation) and microbioreactor platforms, this project will develop new ways to switch these genes on. It will combine metabolomics, molecular networking and genome mining to rank and characterise new chemistry with antibiotic, anticancer or anti-inflammatory potential.
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Microbial solutions for sustainable crop protection
Fungal pathogens such as Fusarium in sugarcane and blackleg in canola cause major losses for Australian agriculture. With industry and agricultural partners, this project will screen our microbial library for new antifungals and plant-immunity elicitors. Students will move promising leads from discovery to greenhouse testing and help create safer, biologically derived alternatives to synthetic agrochemicals.
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Gut microbiome-inspired functional foods
In collaboration with industry partners, this project will explore gut-associated microbes and the molecules they produce as the basis for next-generation functional foods. It combines microbial cultivation, metabolite profiling and bioactivity testing to find candidates that support gut health.
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Mining Australia’s soil microbiome for new medicines
More than 1,000 soil samples from BLOOM program have produced one of Australia’s most diverse microbial collections. This project will use high-throughput cultivation, genomics and chemical profiling to find new antibiotics and other bioactive molecules in that collection.
Supervision history
Current supervision
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Doctor Philosophy
Uncovering Novel Bioactive Compounds from Soil Microbiomes through Genomic and Bioinformatic Approaches
Principal Advisor
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Doctor Philosophy
Towards the sustainable discovery and development of new antibiotics
Principal Advisor
Other advisors: Professor Esteban Marcellin
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Doctor Philosophy
Developing natural insecticides from plant and microbial metabolites
Associate Advisor
Other advisors: Dr Kayvan Etebari, Dr Run Zhang, Professor Yasmina Sultanbawa, Dr Maral Seididamyeh
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Doctor Philosophy
Peptide-based antimicrobials: Identification and Engineering of Novel Antibiotics and Investigationof Their Modes of Action
Associate Advisor
Other advisors: Associate Professor Peter Moyle
Completed supervision
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2025
Doctor Philosophy
New antiparasitics to protect Australian livestock
Associate Advisor
Other advisors: Professor Rob Capon
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2025
Master Philosophy
Exploring Australian marine microbes for novel natural products
Associate Advisor
Other advisors: Professor Rob Capon
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2024
Doctor Philosophy
Production of the Mannopeptimycin Antibiotic and Other Unknown Biosynthetic Gene Clusters from Streptomyces hygroscopicus
Associate Advisor
Other advisors: Professor Esteban Marcellin
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2023
Doctor Philosophy
Applying Advanced Molecular Networking Techniques to Explore Chemical Diversity of Australian Microbes
Associate Advisor
Other advisors: Professor Rob Capon
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2023
Doctor Philosophy
Microbial biodiscovery from Australian marine-derived and Venezuelan quartz-rich cave-derived microorganisms.
Associate Advisor
Other advisors: Professor Rob Capon
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2022
Doctor Philosophy
Microbial Biodiversity: Expanding acess to microbial chemical diversity using new techniques
Associate Advisor
Other advisors: Professor Rob Capon
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2021
Doctor Philosophy
Microbial Biodiversity: Exploring Australian Microbial Natural Products
Associate Advisor
Other advisors: Professor Rob Capon
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2019
Doctor Philosophy
Exploring the Natural Products of Australian Sheep Coprophilous Fungi
Associate Advisor
Other advisors: Professor Rob Capon
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2019
Doctor Philosophy
Fungal Biodiscovery: Strategies to Explore Fungal Secondary Metabolite Potential
Associate Advisor
Other advisors: Professor Rob Capon
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2019
Doctor Philosophy
Adventures in Australian Microbial Biodiscovery
Associate Advisor
Other advisors: Professor Rob Capon
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2016
Doctor Philosophy
Microbial Chemical Diversity: Strategies to Stimulate Microbial Secondary Metabolite Potential
Associate Advisor
Other advisors: Professor Rob Capon
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2016
Doctor Philosophy
Biodiscovery of Plant Growth-Promoting Rhizobacteria (PGPR) and their role in plant-microbe interactions
Associate Advisor
Other advisors: Professor Rob Capon, Dr Lilia Carvalhais
Media
Enquiries
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- Antibiotics biodiscovery
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