Dr Zeinab Khalil
Dr

Zeinab Khalil

Email: 
Phone: 
+61 7 334 62980

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

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

  • 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.

Search Professor Zeinab Khalil’s works on UQ eSpace

115 works between 2010 and 2024
All (115) Journal Article (109) Book Chapter (1) Conference Publication (4) Other Outputs (1)

1 - 20 of 115 works

2024

Journal Article

Pullenvalenes E–H: Triterpenyl-Aminoglycosides from an Australian Soil-Derived Fungus, <i>Clonostachys</i> 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

Pullenvalenes E–H: Triterpenyl-Aminoglycosides from an Australian Soil-Derived Fungus, <i>Clonostachys</i> sp

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, 989. doi: 10.3390/antibiotics13100989

Goondapyrones A–J: Polyketide α and γ Pyrone Anthelmintics from an Australian Soil-Derived Streptomyces sp

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

Biosynthesis of novel non-proteinogenic amino acids β-hydroxyenduracididine and β-methylphenylalanine in Escherichia coli

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, 127793. doi: 10.1016/j.micres.2024.127793

Ancient and remote quartzite caves as a novel source of culturable microbes with biotechnological potential

2024

Journal Article

Australian Marine and Terrestrial Streptomyces-Derived Surugamides, and Synthetic Analogs, and Their Ability to Inhibit Dirofilaria immitis (Heartworm) Motility

Wu, Taizong, Hussein, Waleed M., Samarasekera, Kaumadi, Zhu, Yuxuan, Khalil, Zeinab G., Jin, Shengbin, Bruhn, David F., Moreno, Yovany, Salim, Angela A. and Capon, Robert J. (2024). Australian Marine and Terrestrial Streptomyces-Derived Surugamides, and Synthetic Analogs, and Their Ability to Inhibit Dirofilaria immitis (Heartworm) Motility. Marine Drugs, 22 (7) 312, 312. doi: 10.3390/md22070312

Australian Marine and Terrestrial Streptomyces-Derived Surugamides, and Synthetic Analogs, and Their Ability to Inhibit Dirofilaria immitis (Heartworm) Motility

2024

Journal Article

Cholesterol as an inbuilt immunoadjuvant for a lipopeptide vaccine against group A Streptococcus infection

Alharbi, Nedaa, Shalash, Ahmed O., Koirala, Prashamsa, Boer, Jennifer C., Hussein, Waleed M., Khalil, Zeinab G., Capon, Robert J., Plebanski, Magdalena, Toth, Istvan and Skwarczynski, Mariusz (2024). Cholesterol as an inbuilt immunoadjuvant for a lipopeptide vaccine against group A Streptococcus infection. Journal of Colloid and Interface Science, 663, 43-52. doi: 10.1016/j.jcis.2024.02.134

Cholesterol as an inbuilt immunoadjuvant for a lipopeptide vaccine against group A Streptococcus infection

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

Self-assembled monovalent lipidated mannose ligand as a standalone nanoadjuvant

2024

Journal Article

Miniaturized Cultivation Profiling (MATRIX)-Facilitated Discovery of Noonazines A–C and Noonaphilone A from an Australian Marine-Derived Fungus, Aspergillus noonimiae CMB-M0339

Kankanamge, Sarani, Bernhardt, Paul V., Khalil, Zeinab G. and Capon, Robert J. (2024). Miniaturized Cultivation Profiling (MATRIX)-Facilitated Discovery of Noonazines A–C and Noonaphilone A from an Australian Marine-Derived Fungus, Aspergillus noonimiae CMB-M0339. Marine Drugs, 22 (6) 243, 243. doi: 10.3390/md22060243

Miniaturized Cultivation Profiling (MATRIX)-Facilitated Discovery of Noonazines A–C and Noonaphilone A from an Australian Marine-Derived Fungus, Aspergillus noonimiae CMB-M0339

2024

Journal Article

Pullenvalenes A–D: Nitric oxide-mediated transcriptional activation (NOMETA) enables discovery of triterpene aminoglycosides from Australian Termite nest-derived fungi

Dewa, Amila Agampodi, Khalil, Zeinab G., Hussein, Waleed M., Jin, Shengbin, Wang, Yanan, Cruz-Morales, Pablo and Capon, Robert J. (2024). Pullenvalenes A–D: Nitric oxide-mediated transcriptional activation (NOMETA) enables discovery of triterpene aminoglycosides from Australian Termite nest-derived fungi. Journal of Natural Products, 87 (4), 935-947. doi: 10.1021/acs.jnatprod.3c01233

Pullenvalenes A–D: Nitric oxide-mediated transcriptional activation (NOMETA) enables discovery of triterpene aminoglycosides from Australian Termite nest-derived fungi

2024

Journal Article

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. (2024). Tepuazines A–E: Phenazine Glycosides from a Venezuelan Quartz-Rich (Tepui) Cave Soil-Derived Streptomyces virginiae CMB-CA091. Journal of Natural Products, 87 (4), 1084-1091. doi: 10.1021/acs.jnatprod.4c00042

Tepuazines A–E: Phenazine Glycosides from a Venezuelan Quartz-Rich (Tepui) Cave Soil-Derived <i>Streptomyces virginiae</i> CMB-CA091

2024

Journal Article

Polymeric nanoparticles as oral and intranasal peptide vaccine delivery systems: the role of shape and conjugation

Koirala, Prashamsa, Shalash, Ahmed O., Chen, Sung-Po R., Faruck, Mohammad O., Wang, Jingwen, Hussein, Waleed M., Khalil, Zeinab G., Capon, Robert J., Monteiro, Michael J., Toth, Istvan and Skwarczynski, Mariusz (2024). Polymeric nanoparticles as oral and intranasal peptide vaccine delivery systems: the role of shape and conjugation. Vaccines, 12 (2) 198, 1-14. doi: 10.3390/vaccines12020198

Polymeric nanoparticles as oral and intranasal peptide vaccine delivery systems: the role of shape and conjugation

2024

Journal Article

Jugiones A–D: Antibacterial xanthone–Anthraquinone heterodimers from Australian soil-derived Penicillium shearii CMB-STF067

Sritharan, Thulasi, Salim, Angela A., Khalil, Zeinab G. and Capon, Robert J. (2024). Jugiones A–D: Antibacterial xanthone–Anthraquinone heterodimers from Australian soil-derived Penicillium shearii CMB-STF067. Antibiotics, 13 (1) 97, 1-12. doi: 10.3390/antibiotics13010097

Jugiones A–D: Antibacterial xanthone–Anthraquinone heterodimers from Australian soil-derived Penicillium shearii CMB-STF067

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

Synthesis of the Corrected Structure Assigned to Clonorosin B, an Alkaloid Obtained from the Soil-derived Fungus Clonostachys rosea YRS-06

2023

Journal Article

Talarolides Revisited: Cyclic Heptapeptides from an Australian Marine Tunicate-Associated Fungus, Talaromyces sp. CMB-TU011

Salim, Angela A., Hussein, Waleed M., Dewapriya, Pradeep, Hoang, Huy N., Zhou, Yahao, Samarasekera, Kaumadi, Khalil, Zeinab G., Fairlie, David P. and Capon, Robert J. (2023). Talarolides Revisited: Cyclic Heptapeptides from an Australian Marine Tunicate-Associated Fungus, Talaromyces sp. CMB-TU011. Marine Drugs, 21 (9) 487, 1-17. doi: 10.3390/md21090487

Talarolides Revisited: Cyclic Heptapeptides from an Australian Marine Tunicate-Associated Fungus, Talaromyces sp. CMB-TU011

2023

Journal Article

Editorial: Advances in biotechnological applications of extreme microorganisms

Núñez-Montero, Kattia, Barrientos, Leticia, Khalil, Zeinab G. and Lo Giudice, Angelina (2023). Editorial: Advances in biotechnological applications of extreme microorganisms. Frontiers in Microbiology, 14 1276435, 1-2. doi: 10.3389/fmicb.2023.1276435

Editorial: Advances in biotechnological applications of extreme microorganisms

2023

Journal Article

Activity relationship of poly(ethylenimine)-based liposomes as group A Streptococcus vaccine delivery systems

Jin, Shengbin, Zhang, Jiahui, Nahar, Ummey J., Huang, Wenbin, Alharbi, Nedaa A., Shalash, Ahmed O., Koirala, Prashamsa, Yang, Jieru, Kiong, Jolynn J. E., Khalil, Zeinab G., Capon, Robert J., Stephenson, Rachel J., Skwarczynski, Mariusz, Toth, Istvan and Hussein, Waleed M. (2023). Activity relationship of poly(ethylenimine)-based liposomes as group A Streptococcus vaccine delivery systems. ACS Infectious Diseases, 9 (8), 1570-1581. doi: 10.1021/acsinfecdis.3c00159

Activity relationship of poly(ethylenimine)-based liposomes as group A Streptococcus vaccine delivery systems

2023

Journal Article

Total syntheses of favolasins A, E, G and K, polyketides isolated from cultures of the Basidiomycetes fungi Favolaschia sp . BCC 18686 and Favolaschia calocera BCC 36684

Sheng, Bingbing, Lan, Ping, Kiong, Jolynn, Khalil, Zeinab G., Capon, Robert J. and Banwell, Martin G. (2023). Total syntheses of favolasins A, E, G and K, polyketides isolated from cultures of the Basidiomycetes fungi Favolaschia sp . BCC 18686 and Favolaschia calocera BCC 36684. Chinese Journal of Chemistry, 41 (12), 1450-1464. doi: 10.1002/cjoc.202200822

Total syntheses of favolasins A, E, G and K, polyketides isolated from cultures of the Basidiomycetes fungi Favolaschia sp . BCC 18686 and Favolaschia calocera BCC 36684

2023

Journal Article

The development of surface-modified liposomes as an intranasal delivery system for group A Streptococcus vaccines

Yang, Jieru, Boer, Jennifer C., Khongkow, Mattaka, Phunpee, Sarunya, Khalil, Zeinab G., Bashiri, Sahra, Deceneux, Cyril, Goodchild, Georgia, Hussein, Waleed M., Capon, Robert J., Ruktanonchai, Uracha, Plebanski, Magdalena, Toth, Istvan and Skwarczynski, Mariusz (2023). The development of surface-modified liposomes as an intranasal delivery system for group A Streptococcus vaccines. Vaccines, 11 (2) 305. doi: 10.3390/vaccines11020305

The development of surface-modified liposomes as an intranasal delivery system for group A Streptococcus vaccines

2023

Journal Article

Noonindoles G–L: Indole diterpene glycosides from the Australian marine-derived fungus Aspergillus noonimiae CMB-M0339

Kankanamge, Sarani, Khalil, Zeinab G., Sritharan, Thulasi and Capon, Robert J. (2023). Noonindoles G–L: Indole diterpene glycosides from the Australian marine-derived fungus Aspergillus noonimiae CMB-M0339. Journal of Natural Products, 86 (3), 508-516. doi: 10.1021/acs.jnatprod.2c01024

Noonindoles G–L: Indole diterpene glycosides from the Australian marine-derived fungus Aspergillus noonimiae CMB-M0339

2023

Journal Article

Polymeric nanoparticles as a self‐adjuvanting peptide vaccine delivery system: the role of shape

Koirala, Prashamsa, Chen, Sung‐Po R., Boer, Jennifer C., Khalil, Zeinab G., Deceneux, Cyril, Goodchild, Georgia, Lu, Lantian, Faruck, Mohammad Omer, Shalash, Ahmed O., Bashiri, Sahra, Capon, Robert J., Hussein, Waleed M., Monteiro, Michael J., Plebanski, Magdalena, Toth, Istvan and Skwarczynski, Mariusz (2023). Polymeric nanoparticles as a self‐adjuvanting peptide vaccine delivery system: the role of shape. Advanced Functional Materials, 33 (12) 2209304, 2209304. doi: 10.1002/adfm.202209304

Polymeric nanoparticles as a self‐adjuvanting peptide vaccine delivery system: the role of shape

Current funding

  • 2025 - 2028
    Novel antibacterials from nature targeting the bacterial cell envelope
    NHMRC IDEAS Grants
    Open grant
  • 2024 - 2029
    Soils for Science
    Research Donation Generic
    Open grant
  • 2024 - 2027
    Towards the sustainable discovery and development of new antibiotics
    ARC Future Fellowships
    Open grant
  • 2023 - 2025
    Mapping chemical diversity in Australian marine microbes and microalgae
    Marine Bioproducts Cooperative Research Centre
    Open grant
  • 2021 - 2025
    New antiparasitics to protect Australian livestock
    ARC Linkage Projects
    Open grant

Past funding

  • 2023 - 2024
    Enhancing Australian biodiscovery molecule generation, storage and access (ARC LIEF administered by Griffith University)
    Griffith University
    Open grant
  • 2016
    Wollamide B, a new anti-tubercular agent
    UQ Early Career Researcher
    Open grant

Availability

Dr Zeinab Khalil is:
Available for supervision

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Available projects

  • Mapping chemical diversity in Australian marine microbes

    This project seeks to develop advanced and optimised methods in UPLC-QTOF-MS/MS molecular networking, to rapidly, cost effectively, reproducibly and quantitatively map the small molecule and peptide chemical diversity of taxonomically and geographically diverse Australian marine microbes and microalgae, including fresh and processed biomass, biorefinery fractions and outputs, and formulated marine bioproducts – to advance the discovery and development of valuable new marine bioproducts.

  • Soils for Science

    Soils for Science (S4S) seeks to build a partnership between UQ researchers and the public, to fast-track the discovery of new antibiotics. S4S will engage pastoralists, farmers, homeowners, schools and others, to assemble a collection of 100,000 Australian soil samples, from which we will recover a living library of >2,000,000 microbes (bacteria and fungi) rich in new antibiotics, including against important crop pathogens.

    This project seeks to discover the next generation of new antibiotics against multi-drug resistant pathogens.

Supervision history

Current supervision

Completed supervision

Enquiries

Contact Dr Zeinab Khalil directly for media enquiries about:

  • Antibiotics biodiscovery

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