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)

61 - 80 of 119 works

2020

Book Chapter

Microbioreactor techniques for the production and spectroscopic characterization of microbial peptides

Khalil, Zeinab G., Salim, Angela A. and Capon, Robert J. (2020). Microbioreactor techniques for the production and spectroscopic characterization of microbial peptides. Peptide synthesis: methods and protocols. (pp. 303-322) edited by Waleed M. Hussein, Mariusz Skwarczynski and Istvan Toth. New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-0227-0_21

Microbioreactor techniques for the production and spectroscopic characterization of microbial peptides

2019

Journal Article

Trivirensols: selectively bacteriostatic sesquiterpene trimers from the Australian termite nest-derived fungus Trichoderma virens CMB-TN16

Jiao, Wei-Hua, Salim, Angela A., Khalil, Zeinab G., Dewapriya, Pradeep, Lin, Hou-Wen, Butler, Mark S. and Capon, Robert J. (2019). Trivirensols: selectively bacteriostatic sesquiterpene trimers from the Australian termite nest-derived fungus Trichoderma virens CMB-TN16. Journal of Natural Products, 82 (11), 3165-3175. doi: 10.1021/acs.jnatprod.9b00760

Trivirensols: selectively bacteriostatic sesquiterpene trimers from the Australian termite nest-derived fungus Trichoderma virens CMB-TN16

2019

Journal Article

Talarophenol sulfate and talarophilones from the Australian mud dauber wasp-associated fungus, Talaromyces sp. CMB-W045

Kalansuriya, Pabasara, Khalil, Zeinab G., Salim, Angela A. and Capon, Robert J. (2019). Talarophenol sulfate and talarophilones from the Australian mud dauber wasp-associated fungus, Talaromyces sp. CMB-W045. Tetrahedron Letters, 60 (43) 151157, 151157. doi: 10.1016/j.tetlet.2019.151157

Talarophenol sulfate and talarophilones from the Australian mud dauber wasp-associated fungus, Talaromyces sp. CMB-W045

2019

Journal Article

Chrysosporazines A–E: P-glycoprotein inhibitory piperazines from an Australian marine fish gastrointestinal tract-derived fungus, Chrysosporium sp. CMB-F214

Elbanna, Ahmed H., Khalil, Zeinab G., Bernhardt, Paul V. and Capon, Robert J. (2019). Chrysosporazines A–E: P-glycoprotein inhibitory piperazines from an Australian marine fish gastrointestinal tract-derived fungus, Chrysosporium sp. CMB-F214. Organic Letters, 21 (19) acs.orglett.9b03094, 8097-8100. doi: 10.1021/acs.orglett.9b03094

Chrysosporazines A–E: P-glycoprotein inhibitory piperazines from an Australian marine fish gastrointestinal tract-derived fungus, Chrysosporium sp. CMB-F214

2019

Journal Article

Scopularides revisited: molecular networking guided exploration of lipodepsipeptides in Australian marine fish gastrointestinal tract-derived fungi

Elbanna, Ahmed H., Khalil, Zeinab G., Bernhardt, Paul V. and Capon, Robert J. (2019). Scopularides revisited: molecular networking guided exploration of lipodepsipeptides in Australian marine fish gastrointestinal tract-derived fungi. Marine Drugs, 17 (8) 475, 475. doi: 10.3390/md17080475

Scopularides revisited: molecular networking guided exploration of lipodepsipeptides in Australian marine fish gastrointestinal tract-derived fungi

2019

Journal Article

Cholic acid-based delivery system for vaccine candidates against Group A Streptococcus

Azuar, Armira, Zhao, Lili, Hei, Tsui Ting, Nevagi, Reshma J., Bartlett, Stacey, Hussein, Waleed M., Khalil, Zeinab G., Capon, Robert J., Toth, Istvan and Skwarczynski, Mariusz (2019). Cholic acid-based delivery system for vaccine candidates against Group A Streptococcus. ACS Medicinal Chemistry Letters, 10 (9) acsmedchemlett.9b00239, 1253-1259. doi: 10.1021/acsmedchemlett.9b00239

Cholic acid-based delivery system for vaccine candidates against Group A Streptococcus

2019

Journal Article

Self-assembly of trimethyl chitosan and poly(anionic amino acid)-peptide antigen conjugate to produce a potent self-adjuvanting nanovaccine delivery system

Nevagi, Reshma J., Dai, Wei, Khalil, Zeinab G., Hussein, Waleed M., Capon, Robert J., Skwarczynski, Mariusz and Toth, Istvan (2019). Self-assembly of trimethyl chitosan and poly(anionic amino acid)-peptide antigen conjugate to produce a potent self-adjuvanting nanovaccine delivery system. Bioorganic and Medicinal Chemistry, 27 (14), 3082-3088. doi: 10.1016/j.bmc.2019.05.033

Self-assembly of trimethyl chitosan and poly(anionic amino acid)-peptide antigen conjugate to produce a potent self-adjuvanting nanovaccine delivery system

2019

Journal Article

Structure-activity relationship of group A streptococcus lipopeptide vaccine candidates in trimethyl chitosan-based self-adjuvanting delivery system

Nevagi, Reshma J., Dai, Wei, Khalil, Zeinab G., Hussein, Waleed M., Capon, Robert J., Skwarczynski, Mariusz and Toth, Istvan (2019). Structure-activity relationship of group A streptococcus lipopeptide vaccine candidates in trimethyl chitosan-based self-adjuvanting delivery system. European Journal of Medicinal Chemistry, 179, 100-108. doi: 10.1016/j.ejmech.2019.06.047

Structure-activity relationship of group A streptococcus lipopeptide vaccine candidates in trimethyl chitosan-based self-adjuvanting delivery system

2019

Journal Article

Solvolysis artifacts: leucettazoles as cryptic macrocyclic alkaloid dimers from a Southern Australian marine sponge, Leucetta sp.

Prasad, Pritesh, Salim, Angela A., Khushi, Shamsunnahar, Khalil, Zeinab G., Quezada, Michelle and Capon, Robert J. (2019). Solvolysis artifacts: leucettazoles as cryptic macrocyclic alkaloid dimers from a Southern Australian marine sponge, Leucetta sp.. Marine Drugs, 17 (2) md17020106, 106. doi: 10.3390/md17020106

Solvolysis artifacts: leucettazoles as cryptic macrocyclic alkaloid dimers from a Southern Australian marine sponge, Leucetta sp.

2019

Journal Article

Bromocatechol conjugates from a Chinese marine red alga, Symphyocladia latiuscula

Xu, Xiuli, Yang, Haijin, Khalil, Zeinab G., Yin, Liyuan, Xiao, Xue, Salim, Angela A., Song, Fuhang and Capon, Robert J. (2019). Bromocatechol conjugates from a Chinese marine red alga, Symphyocladia latiuscula. Phytochemistry, 158, 20-25. doi: 10.1016/j.phytochem.2018.10.026

Bromocatechol conjugates from a Chinese marine red alga, Symphyocladia latiuscula

2019

Journal Article

Structure-activity relationships of wollamide cyclic hexapeptides with activity against drug-resistant and intracellular

Khalil, Zeinab G., Hill, Timothy A., De Leon Rodriguez, Luis M., Lohman, Rink-Jan, Hoang, Huy N., Reiling, Norbert, Hillemann, Doris, Brimble, Margaret A., Fairlie, David, Blumenthal, Antje and Capon, Robert J. (2019). Structure-activity relationships of wollamide cyclic hexapeptides with activity against drug-resistant and intracellular. Antimicrobial Agents and Chemotherapy, 63 (3) e01773-18. doi: 10.1128/AAC.01773-18

Structure-activity relationships of wollamide cyclic hexapeptides with activity against drug-resistant and intracellular

2019

Conference Publication

Development of polymer-based nanoparticulate intranasal lipopeptide vaccine constructs against group A streptococcus

Nevagi, Reshma Jayprakash, Dai, Wei, Khalil, Zeinab, Hussein, Waleed, Capon, Robert, Skwarczynski, Mariusz and Toth, Istvan (2019). Development of polymer-based nanoparticulate intranasal lipopeptide vaccine constructs against group A streptococcus. National Meeting of the American Chemical Society (ACS), Orlando, FL, United States, 31 March - 4 April, 2019. Washington, DC, United States: American Chemical Society.

Development of polymer-based nanoparticulate intranasal lipopeptide vaccine constructs against group A streptococcus

2018

Journal Article

Divirensols: Sesquiterpene Dimers from the Australian Termite Nest-Derived Fungus Trichoderma virens CMB-TN16

Jiao, Wei-Hua, Dewapriya, Pradeep, Mohamed, Osama, Khalil, Zeinab G., Salim, Angela A., Lin, Hou-Wen and Capon, Robert J. (2018). Divirensols: Sesquiterpene Dimers from the Australian Termite Nest-Derived Fungus Trichoderma virens CMB-TN16. Journal of Natural Products, 82 (1) acs.jnatprod.8b00746, 87-95. doi: 10.1021/acs.jnatprod.8b00746

Divirensols: Sesquiterpene Dimers from the Australian Termite Nest-Derived Fungus Trichoderma virens CMB-TN16

2018

Journal Article

Talaropeptides A-D: Structure and Biosynthesis of Extensively N-methylated Linear Peptides From an Australian Marine Tunicate-Derived Talaromyces sp

Dewapriya, Pradeep, Khalil, Zeinab G., Prasad, Pritesh, Salim, Angela A., Cruz-Morales, Pablo, Marcellin, Esteban and Capon, Robert J. (2018). Talaropeptides A-D: Structure and Biosynthesis of Extensively N-methylated Linear Peptides From an Australian Marine Tunicate-Derived Talaromyces sp. Frontiers in Chemistry, 6 394, 394. doi: 10.3389/fchem.2018.00394

Talaropeptides A-D: Structure and Biosynthesis of Extensively N-methylated Linear Peptides From an Australian Marine Tunicate-Derived Talaromyces sp

2018

Journal Article

Inter-Kingdom beach warfare: Microbial chemical communication activates natural chemical defences

Khalil, Zeinab G., Cruz-Morales, Pablo, Licona-Cassani, Cuauhtemoc, Marcellin, Esteban and Capon, Robert J. (2018). Inter-Kingdom beach warfare: Microbial chemical communication activates natural chemical defences. The ISME journal, 13 (1), 147-158. doi: 10.1038/s41396-018-0265-z

Inter-Kingdom beach warfare: Microbial chemical communication activates natural chemical defences

2018

Journal Article

Trichodermides A-E: New peptaibols isolated from the Australian termite nest-derived fungus trichoderma virens CMB-TN16

Jiao, Wei-Hua, Khalil, Zeinab, Dewapriya, Pradeep, Salim, Angela A, Lin, Hou-Wen and Capon, Robert J (2018). Trichodermides A-E: New peptaibols isolated from the Australian termite nest-derived fungus trichoderma virens CMB-TN16. Journal of Natural Products, 81 (4), 976-984. doi: 10.1021/acs.jnatprod.7b01072

Trichodermides A-E: New peptaibols isolated from the Australian termite nest-derived fungus trichoderma virens CMB-TN16

2018

Journal Article

Prolinimines: N-Amino-l-Pro-methyl Ester (Hydrazine) Schiff Bases from a Fish Gastrointestinal Tract-Derived Fungus, Trichoderma sp. CMB-F563

Mohamed, Osama G, Khalil, Zeinab G and Capon, Robert J (2018). Prolinimines: N-Amino-l-Pro-methyl Ester (Hydrazine) Schiff Bases from a Fish Gastrointestinal Tract-Derived Fungus, Trichoderma sp. CMB-F563. Organic letters, 20 (2), 377-380. doi: 10.1021/acs.orglett.7b03666

Prolinimines: N-Amino-l-Pro-methyl Ester (Hydrazine) Schiff Bases from a Fish Gastrointestinal Tract-Derived Fungus, Trichoderma sp. CMB-F563

2018

Conference Publication

Talaropeptides A–D: Structure and biosynthesis of extensively N-methylated linear peptides from an Australian marine tunicate-derived Talaromyces sp.

Dewapriya, Pradeep, Khalil, Zeinab G., Prasad, Pritesh, Salim, Angela A., Morales, Pablo C., Marcellin, Esteban and Capon, Robert J. (2018). Talaropeptides A–D: Structure and biosynthesis of extensively N-methylated linear peptides from an Australian marine tunicate-derived Talaromyces sp.. American Society of Pharmacognosy Annual Meeting ASP 2018, Lexington, KY United States, 21-25 July 2018.

Talaropeptides A–D: Structure and biosynthesis of extensively N-methylated linear peptides from an Australian marine tunicate-derived Talaromyces sp.

2018

Journal Article

Polyglutamic acid-trimethyl chitosan-based intranasal peptide nano-vaccine induces potent immune responses against group A streptococcus

Nevagi, Reshma J., Khalil, Zeinab G., Hussein, Waleed M., Powell, Jessica, Batzloff, Michael R., Capon, Robert J., Good, Michael F., Skwarczynski, Mariusz and Toth, Istvan (2018). Polyglutamic acid-trimethyl chitosan-based intranasal peptide nano-vaccine induces potent immune responses against group A streptococcus. Acta Biomaterialia, 80, 278-287. doi: 10.1016/j.actbio.2018.09.037

Polyglutamic acid-trimethyl chitosan-based intranasal peptide nano-vaccine induces potent immune responses against group A streptococcus

2017

Journal Article

Chemical Diversity from a Chinese Marine Red Alga, Symphyocladia latiuscula

Xu, Xiuli, Yang, Haijin, Khalil, Zeinab G, Yin, Liyuan, Xiao, Xue, Neupane, Pratik, Bernhardt, Paul V, Salim, Angela A, Song, Fuhang and Capon, Robert J (2017). Chemical Diversity from a Chinese Marine Red Alga, Symphyocladia latiuscula. Marine drugs, 15 (12) 374, 1-10. doi: 10.3390/md15120374

Chemical Diversity from a Chinese Marine Red Alga, Symphyocladia latiuscula

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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