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

119 works between 2010 and 2025
All (119) Journal Article (113) Book Chapter (1) Conference Publication (4) Other Outputs (1)

81 - 100 of 119 works

2017

Journal Article

Amycolatopsins A-C: antimycobacterial glycosylated polyketide macrolides from the Australian soil Amycolatopsis sp. MST-108494

Khalil, Zeinab G., Salim, Angela A., Vuong, Daniel, Crombie, Andrew, Lacey, Ernest, Blumenthal, Antje and Capon, Robert J. (2017). Amycolatopsins A-C: antimycobacterial glycosylated polyketide macrolides from the Australian soil Amycolatopsis sp. MST-108494. The Journal of Antibiotics, 70 (12), 1097-1103. doi: 10.1038/ja.2017.119

Amycolatopsins A-C: antimycobacterial glycosylated polyketide macrolides from the Australian soil Amycolatopsis sp. MST-108494

2017

Journal Article

Cytochalasins from an Australian Marine Sediment-Derived Phomopsis sp. (CMB-M0042F): Acid-Mediated Intramolecular Cycloadditions Enhance Chemical Diversity

Shang, Zhuo, Raju, Ritesh, Salim, Angela A., Khalil, Zeinab G. and Capon, Robert J. (2017). Cytochalasins from an Australian Marine Sediment-Derived Phomopsis sp. (CMB-M0042F): Acid-Mediated Intramolecular Cycloadditions Enhance Chemical Diversity. Journal of Organic Chemistry, 82 (18), 9704-9709. doi: 10.1021/acs.joc.7b01793

Cytochalasins from an Australian Marine Sediment-Derived Phomopsis sp. (CMB-M0042F): Acid-Mediated Intramolecular Cycloadditions Enhance Chemical Diversity

2017

Conference Publication

2D C3 Marfey’s method for amino acid analysis and structure elucidation in peptidic natural products

Dewapriya, Pradeep, Prasad, Pritesh, Khalil, Zeinab G. and Capon, Robert J. (2017). 2D C3 Marfey’s method for amino acid analysis and structure elucidation in peptidic natural products. Queensland Annual Chemistry Symposium, Brisbane, Australia, 27 November 2017.

2D C3 Marfey’s method for amino acid analysis and structure elucidation in peptidic natural products

2016

Journal Article

Double adjuvanting strategy for peptide-based vaccines: trimethyl chitosan nanoparticles for lipopeptide delivery

Marasini, Nirmal, Giddam, Ashwini K., Khalil, Zeinab G., Hussein, Waleed M., Capon, Robert J., Batzloff, Michael R., Good, Michael F., Toth, Istvan and Skwarczynski, Mariusz (2016). Double adjuvanting strategy for peptide-based vaccines: trimethyl chitosan nanoparticles for lipopeptide delivery. Nanomedicine, 11 (24), 3223-3235. doi: 10.2217/nnm-2016-0291

Double adjuvanting strategy for peptide-based vaccines: trimethyl chitosan nanoparticles for lipopeptide delivery

2016

Journal Article

Lipid core peptide/poly(lactic-co-glycolic acid) as a highly potent intranasal vaccine delivery system against Group A streptococcus

Marasini, Nirmal, Khalil, Zeinab G., Giddam, Ashwini K., Abdul Ghaffar, Khairunnisa, Hussein, Waleed M., Capon, Robert J., Batzloff, Michael R., Good, Michael F., Skwarczynski, Mariusz and Toth, Istvan (2016). Lipid core peptide/poly(lactic-co-glycolic acid) as a highly potent intranasal vaccine delivery system against Group A streptococcus. International Journal of Pharmaceutics, 513 (1-2), 410-420. doi: 10.1016/j.ijpharm.2016.09.057

Lipid core peptide/poly(lactic-co-glycolic acid) as a highly potent intranasal vaccine delivery system against Group A streptococcus

2016

Journal Article

Roseopurpurins: chemical diversity enhanced by convergent biosynthesis and forward and reverse Michael additions

Shang, Zhuo, Khalil, Zeinab, Li, Li, Salim, Angela A., Quezada, Michelle, Kalansuriya, Pabasara and Capon, Robert J. (2016). Roseopurpurins: chemical diversity enhanced by convergent biosynthesis and forward and reverse Michael additions. Organic Letters, 18 (17), 4340-4343. doi: 10.1021/acs.orglett.6b02099

Roseopurpurins: chemical diversity enhanced by convergent biosynthesis and forward and reverse Michael additions

2016

Journal Article

Linear and branched polyacrylates as a delivery platform for peptide-based vaccines

Chandrudu, Saranya, Bartlett, Stacey, Khalil, Zeinab G., Jia, Zhongfan, Hussein, Waleed M., Capon, Robert J., Batzloff, Michael R., Good, Michael F., Monteiro, Michael J., Skwarczynski, Mariusz and Toth, Istvan (2016). Linear and branched polyacrylates as a delivery platform for peptide-based vaccines. Therapeutic Delivery, 7 (9), 601-609. doi: 10.4155/tde-2016-0037

Linear and branched polyacrylates as a delivery platform for peptide-based vaccines

2016

Journal Article

Fungal biotransformation of tetracycline antibiotics

Shang, Zhuo, Salim, Angela A., Khalil, Zeinab, Bernhardt, Paul V. and Capon, Robert J. (2016). Fungal biotransformation of tetracycline antibiotics. Journal of Organic Chemistry, 81 (15), 6186-6194. doi: 10.1021/acs.joc.6b01272

Fungal biotransformation of tetracycline antibiotics

2016

Journal Article

C3 and 2D C3 Marfey’s methods for amino acid analysis in natural products

Vijayasarathy, Soumini, Prasad, Pritesh, Fremlin, Leith J., Ratnayake, Ranjala, Salim, Angela A., Khalil, Zeinab and Capon, Robert J. (2016). C3 and 2D C3 Marfey’s methods for amino acid analysis in natural products. Journal of Natural Products, 79 (2), 421-427. doi: 10.1021/acs.jnatprod.5b01125

C3 and 2D C3 Marfey’s methods for amino acid analysis in natural products

2015

Journal Article

Viridicatumtoxins: Expanding on a Rare Tetracycline Antibiotic Scaffold

Shang, Zhuo, Salim, Angela A., Khalil, Zeinab, Quezada, Michelle, Bernhardt, Paul V. and Capon, Robert J. (2015). Viridicatumtoxins: Expanding on a Rare Tetracycline Antibiotic Scaffold. Journal of Organic Chemistry, 80 (24), 12501-12508. doi: 10.1021/acs.joc.5b02367

Viridicatumtoxins: Expanding on a Rare Tetracycline Antibiotic Scaffold

2015

Journal Article

New PKS-NRPS tetramic acids and pyridinone from an Australian marine-derived fungus, Chaunopycnis sp.

Shang, Zhuo, Li, Li, Esposito, Breno P., Salim, Angela A., Khalil, Zeinab G., Quezada, Michelle, Bernhardt, Paul V. and Capon, Robert J. (2015). New PKS-NRPS tetramic acids and pyridinone from an Australian marine-derived fungus, Chaunopycnis sp.. Organic and Biomolecular Chemistry, 13 (28), 7795-7802. doi: 10.1039/c5ob01058f

New PKS-NRPS tetramic acids and pyridinone from an Australian marine-derived fungus, Chaunopycnis sp.

2015

Journal Article

Aranciamycins I and J, Antimycobacterial Anthracyclines from an Australian marine-derived Streptomyces sp.

Khalil, Zeinab G., Raju, Ritesh, Piggott, Andrew M., Salim, Angela A., Blumenthal, Antje and Capon, Robert J. (2015). Aranciamycins I and J, Antimycobacterial Anthracyclines from an Australian marine-derived Streptomyces sp.. Journal of Natural Products, 78 (4), 949-952. doi: 10.1021/acs.jnatprod.5b00095

Aranciamycins I and J, Antimycobacterial Anthracyclines from an Australian marine-derived Streptomyces sp.

2015

Journal Article

Atropselective syntheses of (-) and (+) rugulotrosin A utilizing point-to-axial chirality transfer

Qin, Tian, Skraba-Joiner, Sarah L., Khalil, Zeinab G., Johnson, Richard P., Capon, Robert J. and Porco, John A. Jr (2015). Atropselective syntheses of (-) and (+) rugulotrosin A utilizing point-to-axial chirality transfer. Nature Chemistry, 7 (3), 234-240. doi: 10.1038/nchem.2173

Atropselective syntheses of (-) and (+) rugulotrosin A utilizing point-to-axial chirality transfer

2015

Journal Article

Levofloxacin and indolicidin for combination antimicrobial therapy

Ghaffar, Khairunnisa Abdul, Hussein, Waleed M., Khalil, Zeinab G., Capon, Robert J., Skwarczynski, Mariusz and Toth, Istvan (2015). Levofloxacin and indolicidin for combination antimicrobial therapy. Current Drug Delivery, 12 (1), 108-114. doi: 10.2174/1567201811666140910094050

Levofloxacin and indolicidin for combination antimicrobial therapy

2015

Journal Article

Self-assembling lipopeptides with a potent activity against Gram-positive bacteria, including multidrug resistant strains

Azmi, Fazren, Elliott, Alysha G., Khalil, Zeinab G., Hussein, Waleed M., Kavanagh, Angela, Huang, Johnny X., Quezada, Michelle, Blaskovich, Mark A. T., Capon, Robert J., Cooper, Matthew A., Skwarczynski, Mariusz and Toth, Istvan (2015). Self-assembling lipopeptides with a potent activity against Gram-positive bacteria, including multidrug resistant strains. Nanomedicine, 10 (22), 3359-3371. doi: 10.2217/nnm.15.137

Self-assembling lipopeptides with a potent activity against Gram-positive bacteria, including multidrug resistant strains

2015

Conference Publication

Viridicatumtoxins: Exploring structural diversity and antibiotic properties

Shang, Z., Salim, A. A., Khalil, Z. G., Quezada, M., Bernhardt, P. V. and Capon, R. J. (2015). Viridicatumtoxins: Exploring structural diversity and antibiotic properties. Annual Meeting of the American-Society-of-Pharmacognosy, Copper Mountain, CO, United States, 25-29 July 2015. Stuttgart, Germany: Georg Thieme. doi: 10.1055/s-0035-1556338

Viridicatumtoxins: Exploring structural diversity and antibiotic properties

2014

Journal Article

Isolation and synthesis of N-acyladenine and adenosine alkaloids from a southern Australian marine sponge, Phoriospongia sp.

Farrugia, Michelle, Trotter, Nicholas, Vijayasarathy, Soumini, Salim, Angele A., Khalil, Zeinab G., Lacey, Ernest and Capon, Robert J. (2014). Isolation and synthesis of N-acyladenine and adenosine alkaloids from a southern Australian marine sponge, Phoriospongia sp.. Tetrahedron Letters, 55 (43), 5902-5904. doi: 10.1016/j.tetlet.2014.08.116

Isolation and synthesis of N-acyladenine and adenosine alkaloids from a southern Australian marine sponge, Phoriospongia sp.

2014

Journal Article

Wollamides: antimycobacterial cyclic hexapeptides from an Australian soil Streptomyces

Khalil, Zeinab G., Salim, Angela A., Lacey, Ernest, Blumenthal, Antje and Capon, Robert J. (2014). Wollamides: antimycobacterial cyclic hexapeptides from an Australian soil Streptomyces. Organic Letters, 16 (19), 5120-5123. doi: 10.1021/ol502472c

Wollamides: antimycobacterial cyclic hexapeptides from an Australian soil Streptomyces

2014

Journal Article

Shornephine A: structure, chemical stability, and P-Glycoprotein inhibitory properties of a rare Diketomorpholine from an Australian marine-derived Aspergillus sp.

Khalil, Zeinab G., Huang, Xiao-cong, Raju, Ritesh, Piggott, Andrew M. and Capon, Robert J. (2014). Shornephine A: structure, chemical stability, and P-Glycoprotein inhibitory properties of a rare Diketomorpholine from an Australian marine-derived Aspergillus sp.. Journal of Organic Chemistry, 79 (18), 8700-8705. doi: 10.1021/jo501501z

Shornephine A: structure, chemical stability, and P-Glycoprotein inhibitory properties of a rare Diketomorpholine from an Australian marine-derived Aspergillus sp.

2014

Journal Article

ChemInform Abstract: Callyspongisines A—D: Bromopyrrole Alkaloids from an Australian Marine Sponge, Callyspongia sp.

Plisson, Fabien, Prasad, Pritesh, Xiao, Xue, Piggott, Andrew M., Huang, Xiao‐cong, Khalil, Zeinab and Capon, Robert J. (2014). ChemInform Abstract: Callyspongisines A—D: Bromopyrrole Alkaloids from an Australian Marine Sponge, Callyspongia sp.. ChemInform, 45 (27). doi: 10.1002/chin.201427211

ChemInform Abstract: Callyspongisines A—D: Bromopyrrole Alkaloids from an Australian Marine Sponge, Callyspongia sp.

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

Past funding

  • 2023 - 2025
    Enhancing Australian biodiscovery molecule generation, storage and access (ARC LIEF administered by Griffith University)
    Griffith University
    Open grant
  • 2021 - 2025
    New antiparasitics to protect Australian livestock
    ARC Linkage Projects
    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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