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Cryo-EM reveals multiple mechanisms of ribosome inhibition by doxycycline

William S. Stuart, Michail N. Isupov, Mathew McLaren, Christopher H. Jenkins, Adam Monier, Bertram Daum, Isobel H. Norville, Vicki A.M. Gold, Nicholas J. Harmer

Posted on: 6 January 2026 , updated on: 7 January 2026

Preprint posted on 9 November 2025

Unconventional mechanisms of antibiotic action: Stacking and disorganizing

Selected by Leonie Brüne

Background

As a society, we are facing a crisis the extent of which can only be guessed at, but certainly cannot be predicted: antimicrobial resistance and the failure of our traditional antibiotics. That is why it is now more important than ever to efficiently search for new antibiotics with new mechanisms of action.

Coxiella burnetii (C. burnetii), a highly contagious zoonosis, is considered a major risk to public health, especially for humans who work closely with animals, such as butchers, farmers, and veterinarians, with inhalation being the predominant route of infection. Infection with C. burnetii leads to Q-fever, which in its acute stage is accompanied by fever, chills, and headache and is associated with secondary diseases such as hepatitis, chronic fatigue, and endocarditis [2]. In 1-5% of patients, infection can take a chronic course, which usually occurs 2 years after infection [1]. What makes the bacterium itself so dangerous is its dormant stage and its associated biphasic lifecycle, which allows the bacterium to survive for a long time in a “spore stage” [3].

Infection with Coxiella burnetii is treated with the antibiotic doxycycline, which has a low minimum inhibitory concentration (MIC) of 0.05 mg/L against Coxiella burnetii [4]. Doxycycline acts in the classic manner by targeting the bacterial ribosome, blocking the binding of tRNA to the A site by binding to the canonical tetracycline binding site within the ribosomal A site.

Using cryo-EM imaging, the group demonstrates two new mechanisms of action for doxycycline. While doxycycline blocks the exit tunnel of the large ribosomal subunit in Coxiella burnetii, doxycycline causes significant conformational changes within the peptide transfer centre, the catalytic core of the ribosome, in E. coli, blocking tRNA binding.

Key Findings

Hibernation factor HPFcold protects ribosomes via binding to the 16S anti-Shine Dalgarno Sequence

They identified the position of one of five hibernation factors, HPFcold, (described in the preprint: The evolutionary lifecycle of ribosome hibernation factors, DOI:

https://doi.org/10.1101/2025.11.04.686544) which comprises an N-terminal domain harbouring a sigma-54 fold and a cold sock domain fold (CSD) positioned at the C terminal. This CSD domain binds to the aSD sequence via hydrogen bonding and stacking interactions, limiting RNase binding to the ribosome. The ribosome therefore remains active and functional despite extended hibernation periods. This finding thus describes the first validation of a hibernation factor and its function. Although there are sequence similarities of HPFcold and other CSDs, the proteins clearly differ from one another, with similar structure but likely different functions.

Identification of a new large ribosomal protein called CLaSP

Electron density analyses revealed the existence of a previously unknown ribosomal protein, termed Coxiellaceae Large Subunit Peptide (CLcSP), part of the large ribosomal subunit. Although the exact function of CLaSP is still unknown, it is thought to play a role in the correct assembly of the ribosome, as CLaSP stabilizes the ribosome via anchoring of s23S and r5S.

Doxycycline molecules stack within the ribosomal exit tunnel of the 50S subunit, blocking peptide exit extensively

Analysis revealed a stack of three Doxycycline molecules blocking the peptide exit tunnel between bases U2606 and C2631, which sense ribosomal stalling and translational arrest. The stack is arranged around three magnesium ions, facilitated by the arrangement of the molecules in relation to each other.  Although blocking the exit tunnel is not a new mechanism of action per se, the extensive blocking facilitated due to molecule stacking is considered a new phenomenon, which can be traced back to the size of the tetracyclines. The authors therefore suggest, that this mechanism of action can only be performed by smaller tetracyclines, which means that the strong effect of Doxycycline and the low MIC can be attributed to the efficient binding of the large ribosomal subunit.

Preprint Figure 4: Graphical representation of extensive blocking of the peptide exit tunnel via stacking of three Doxycycline molecules numbered by increased distance to the peptidyl transferase centre: DOX1, DOX2 and Dox 3.

Doxycycline binding induces structural rearrangements of E. Coli peptidyl transferase centre and early exit tunnel

Contrary to prevailing expectations, cryo-EM analysis indicates that the peptidyl transferase center (PTC) is less static than previously assumed. Doxycycline binding disrupts the essential A2450–C2063 interaction required for proper tRNA accommodation and renders residues 60–65 of the bL4 loop disordered, further compromising translational fidelity. In this doxycycline-bound, “zipped” ribosome state, the combined conformational changes are likely to inactivate the ribosome and abolish translation.

Why I highlight this work

Antibiotic resistance is becoming an ever-greater threat, which makes the development of new antibiotics all the more urgent. For this, however, it is crucial to understand in detail how antibiotics work and how these mechanisms can be leveraged therapeutically. What I find particularly striking in this paper is that even long-established antibiotics such as doxycycline can still reveal previously unrecognized mechanisms of action that may be pharmacologically important. At the same time, the study also exposes the weaknesses of some next-generation agents: doxycycline remains more potent than newer compounds like tigecycline or eravacycline.

Findings like these give hope that antibiotic design will become increasingly rational in the future, as we continue to learn which molecular properties are essential for successful therapy, including aspects as simple, yet impactful, as molecular size. I also think it is important to acknowledge that even long-held paradigms may turn out to be incomplete. This work clearly demonstrates that the peptidyl transferase centre is not as static as often assumed, but in fact capable of notable rearrangements.

And even if ribosomes or antibiotic mechanisms are not your primary interest, the paper is worth reading for its cryo-EM visualizations alone, the structural representations of the ribosome are genuinely impressive.

References:

[1] Sheila B Buijs, Chantal P Bleeker-Rovers, Sonja E van Roeden, Linda M Kampschreur, Andy I M Hoepelman, Peter C Wever, Jan Jelrik Oosterheert, Still New Chronic Q Fever Cases Diagnosed 8 Years After a Large Q Fever Outbreak, Clinical Infectious Diseases, Volume 73, Issue 8, 15 October 2021, Pages 1476–1483, https://doi.org/10.1093/cid/ciab476

[2] Million M, Raoult D. No Such Thing as Chronic Q Fever. Emerg Infect Dis. 2017 May;23(5):856-857. doi: 10.3201/eid2305.151159. PMID: 28418317; PMCID: PMC5403045.

[3] Eldin C, Mélenotte C, Mediannikov O, Ghigo E, Million M, Edouard S, Mege JL, Maurin M, Raoult D. From Q Fever to Coxiella burnetii Infection: a Paradigm Change. Clin Microbiol Rev. 2017 Jan;30(1):115-190. doi: 10.1128/CMR.00045-16. PMID: 27856520; PMCID: PMC5217791.

[4] Lever MS, Bewley KR, Dowsett B, Lloyd G. In vitro susceptibility of Coxiella burnetii to azithromycin, doxycycline, ciprofloxacin and a range of newer fluoroquinolones. Int J Antimicrob Agents. 2004 Aug;24(2):194-6. doi: 10.1016/j.ijantimicag.2004.05.001. PMID: 15288324.

Tags: antibiotics, coxiella burnetii, cryo-em

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Interview with the preprint authors

William S. Stuart and Nicholas J. Harmer shared

The backstory of the paper

I had the opportunity to speak with both Nicholas Harmer and William Stuart about their preprint.

We discussed how the idea for the study came about and the fundamental question that shaped it: ‘Why is Coxiella so sensitive to doxycycline?’ Thanks to the ability to use cryo-EM, Nicholas and William decided to take a structural biology approach to determine binding sites of doxycycline within the Coxiella ribosome that were previously unknown. During their analysis, the two scientists encountered many unexpected results that were only possible thanks to rapid improvements and progress in the field of electron microscopy.

The biggest surprise was probably the stack of three doxycycline rings in the exit tunnel, which provides a good explanation not only for why doxycycline works so well at such low concentrations, but also why other antibiotics are not as effective.

Science thrives on interdisciplinary exchange of both technical skills and knowledge. After reading the preprint, one question remained unanswered: is stacking within the exit tunnel specific to Coxiella ribosome? In order to place this question in a broader context, the authors refer to another preprint, ‘Structures redefine the mechanism of action for tetracyclines’ (DOI: https://doi.org/10.1101/2025.09.25.678686). This preprint was able to show that doxycycline also extensively blocks the NPET at multiple locations in the ribosome of E. coli, which is a complementary result to the preprint discussed here and fills in gaps in knowledge nicely.

Question 1: Several of the structural states you captured may represent transient or low-occupancy conformations. Do you have data (e.g., toeprinting, ribosome profiling, or chemical probing) that support the presence and stability of these doxycycline-bound states inside the cell?

For the Coxiella burnetii structures, approximately 55% of our particles showed HPFcold binding, whilst around 42% show the doxycycline triple stack binding. Although the approach that we used means that we cannot be sure that particles are binding either HPFcold or the doxycycline triple stack, the proportions make it likely. Our C. burnetii sample likely contained a mixture of growing cells and spore-like cells. We interpret this as the spore-like cells most likely providing the HPFcold bound, dormant ribosomes. HPFcold appears to compete directly with 30S doxycycline binding. 50S binding will likely not compete with the hibernation factor directly. Unfortunately, C. burnetii grows very slowly and is challenging to prepare ribosomes from, so the quantities that we recovered were not sufficient for some of these confirmatory methods. We are currently thinking about other routes to detecting this 50S behaviour of doxycycline through assay, rather than through cost and time intensive further cryo-EM data collection.

In contrast, it would be a good thought to consider some complementary methods to estimate the proportion of ribosomes that show the rearranged peptidyl transfer centre in E. coli. We hope to shortly obtain a strain that is more susceptible to doxycycline and which we anticipate will show more pronounced binding to this site, which should offer an excellent sample for such studies.

Question 2: Based on your structural analysis, are there specific interactions or binding pockets that could explain known resistance mutations to tetracyclines? And do your findings suggest potential sites for the design of next-generation doxycycline derivatives with improved efficacy?

Due to the highly conserved nature of these drug binding sites (A-site decoding or peptidyl transferase centre), tetracycline resistance most commonly arises from the production of additional proteins that stop the drug from performing its effect on the ribosome. These can be efflux pumps, enzymes that break the tetracycline structure, or proteins that protect the A-site and remove tetracyclines from this site. The latest generation of tetracyclines have been designed to specifically prevent efflux and A-site protection. The novel effects of doxycycline that we have seen would not prevent it being effluxed (the most common route in E. coli) or the structure being broken. They would overcome the A-site protecting proteins.

We are very hopeful that our findings could be used to generate a new generation of doxycycline derivatives. Indeed, another excellent recent pre-print (Structures redefine the mechanism of action for tetracyclines; DOI: https://doi.org/10.1101/2025.09.25.678686) demonstrated that, at high concentrations, similar stacks of doxycycline molecules form in the exit tunnel of the E. coli and Cutibacterium acnes ribosomes. Although this required concentrations well above the active concentration of these antibiotics, the results show that tetracyclines binding in the ribosome exit tunnel is likely possible across all bacteria. If we can understand better what makes a bacterium bind doxycycline well in the exit tunnel, this will help us design new antibiotics that will hopefully have the very high potency that doxycycline has for C. burnetii. This is the topic of my next grant application so I hope that the research council will see things the same way!

______________________________

I would like to thank the authors once again for taking the time to engage in scientific exchange and for the very stimulating discussion. I am happy to take this mindset with me into my own work: it is always worth taking a second look and critically questioning your findings, especially in the context of the broadly presented literature, because sometimes the pieces of the puzzle fit together in unexpected ways.

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List by Martin Estermann

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

CellBio 2022 – An ASCB/EMBO Meeting

This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.

 



List by Nadja Hümpfer et al.

Fibroblasts

The advances in fibroblast biology preList explores the recent discoveries and preprints of the fibroblast world. Get ready to immerse yourself with this list created for fibroblasts aficionados and lovers, and beyond. Here, my goal is to include preprints of fibroblast biology, heterogeneity, fate, extracellular matrix, behavior, topography, single-cell atlases, spatial transcriptomics, and their matrix!

 



List by Osvaldo Contreras

EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)

A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.

 



List by Alex Eve

FENS 2020

A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020

 



List by Ana Dorrego-Rivas

Planar Cell Polarity – PCP

This preList contains preprints about the latest findings on Planar Cell Polarity (PCP) in various model organisms at the molecular, cellular and tissue levels.

 



List by Ana Dorrego-Rivas

BioMalPar XVI: Biology and Pathology of the Malaria Parasite

[under construction] Preprints presented at the (fully virtual) EMBL BioMalPar XVI, 17-18 May 2020 #emblmalaria

 



List by Dey Lab, Samantha Seah

1

Cell Polarity

Recent research from the field of cell polarity is summarized in this list of preprints. It comprises of studies focusing on various forms of cell polarity ranging from epithelial polarity, planar cell polarity to front-to-rear polarity.

 



List by Yamini Ravichandran

TAGC 2020

Preprints recently presented at the virtual Allied Genetics Conference, April 22-26, 2020. #TAGC20

 



List by Maiko Kitaoka et al.

3D Gastruloids

A curated list of preprints related to Gastruloids (in vitro models of early development obtained by 3D aggregation of embryonic cells). Updated until July 2021.

 



List by Paul Gerald L. Sanchez and Stefano Vianello

ECFG15 – Fungal biology

Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome

 



List by Hiral Shah

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

EMBL Seeing is Believing – Imaging the Molecular Processes of Life

Preprints discussed at the 2019 edition of Seeing is Believing, at EMBL Heidelberg from the 9th-12th October 2019

 



List by Dey Lab

Autophagy

Preprints on autophagy and lysosomal degradation and its role in neurodegeneration and disease. Includes molecular mechanisms, upstream signalling and regulation as well as studies on pharmaceutical interventions to upregulate the process.

 



List by Sandra Malmgren Hill

Lung Disease and Regeneration

This preprint list compiles highlights from the field of lung biology.

 



List by Rob Hynds

Cellular metabolism

A curated list of preprints related to cellular metabolism at Biorxiv by Pablo Ranea Robles from the Prelights community. Special interest on lipid metabolism, peroxisomes and mitochondria.

 



List by Pablo Ranea Robles

BSCB/BSDB Annual Meeting 2019

Preprints presented at the BSCB/BSDB Annual Meeting 2019

 



List by Dey Lab

Biophysical Society Annual Meeting 2019

Few of the preprints that were discussed in the recent BPS annual meeting at Baltimore, USA

 



List by Joseph Jose Thottacherry

ASCB/EMBO Annual Meeting 2018

This list relates to preprints that were discussed at the recent ASCB conference.

 



List by Dey Lab, Amanda Haage

Also in the molecular biology category:

October in preprints – DevBio & Stem cell biology

Each month, preLighters with expertise across developmental and stem cell biology nominate a few recent developmental and stem cell biology (and related) preprints they’re excited about and explain in a single paragraph why. Short, snappy picks from working scientists — a quick way to spot fresh ideas, bold methods and papers worth reading in full. These preprints can all be found in the October preprint list published on the Node.

 



List by Deevitha Balasubramanian et al.

October in preprints – Cell biology edition

Different preLighters, with expertise across cell biology, have worked together to create this preprint reading list for researchers with an interest in cell biology. This month, most picks fall under (1) Cell organelles and organisation, followed by (2) Mechanosignaling and mechanotransduction, (3) Cell cycle and division and (4) Cell migration

 



List by Matthew Davies et al.

September in preprints – Cell biology edition

A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading list. This month, categories include: (1) Cell organelles and organisation, (2) Cell signalling and mechanosensing, (3) Cell metabolism, (4) Cell cycle and division, (5) Cell migration

 



List by Sristilekha Nath et al.

June in preprints – the CellBio edition

A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: (1) Cell organelles and organisation (2) Cell signaling and mechanosensation (3) Genetics/gene expression (4) Biochemistry (5) Cytoskeleton

 



List by Barbora Knotkova et al.

May in preprints – the CellBio edition

A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) Biochemistry/metabolism 2) Cancer cell Biology 3) Cell adhesion, migration and cytoskeleton 4) Cell organelles and organisation 5) Cell signalling and 6) Genetics

 



List by Barbora Knotkova et al.

Keystone Symposium – Metabolic and Nutritional Control of Development and Cell Fate

This preList contains preprints discussed during the Metabolic and Nutritional Control of Development and Cell Fate Keystone Symposia. This conference was organized by Lydia Finley and Ralph J. DeBerardinis and held in the Wylie Center and Tupper Manor at Endicott College, Beverly, MA, United States from May 7th to 9th 2025. This meeting marked the first in-person gathering of leading researchers exploring how metabolism influences development, including processes like cell fate, tissue patterning, and organ function, through nutrient availability and metabolic regulation. By integrating modern metabolic tools with genetic and epidemiological insights across model organisms, this event highlighted key mechanisms and identified open questions to advance the emerging field of developmental metabolism.

 



List by Virginia Savy, Martin Estermann

April in preprints – the CellBio edition

A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry/metabolism 2) cell cycle and division 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) (epi)genetics

 



List by Vibha SINGH et al.

Biologists @ 100 conference preList

This preList aims to capture all preprints being discussed at the Biologists @100 conference in Liverpool, UK, either as part of the poster sessions or the (flash/short/full-length) talks.

 



List by Reinier Prosee, Jonathan Townson

February in preprints – the CellBio edition

A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry and cell metabolism 2) cell organelles and organisation 3) cell signalling, migration and mechanosensing

 



List by Barbora Knotkova et al.

Community-driven preList – Immunology

In this community-driven preList, a group of preLighters, with expertise in different areas of immunology have worked together to create this preprint reading list.

 



List by Felipe Del Valle Batalla et al.

January in preprints – the CellBio edition

A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry/metabolism 2) cell migration 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) genetics/gene expression

 



List by Barbora Knotkova et al.

2024 Hypothalamus GRC

This 2024 Hypothalamus GRC (Gordon Research Conference) preList offers an overview of cutting-edge research focused on the hypothalamus, a critical brain region involved in regulating homeostasis, behavior, and neuroendocrine functions. The studies included cover a range of topics, including neural circuits, molecular mechanisms, and the role of the hypothalamus in health and disease. This collection highlights some of the latest advances in understanding hypothalamic function, with potential implications for treating disorders such as obesity, stress, and metabolic diseases.

 



List by Nathalie Krauth

BSCB-Biochemical Society 2024 Cell Migration meeting

This preList features preprints that were discussed and presented during the BSCB-Biochemical Society 2024 Cell Migration meeting in Birmingham, UK in April 2024. Kindly put together by Sara Morais da Silva, Reviews Editor at Journal of Cell Science.

 



List by Reinier Prosee

‘In preprints’ from Development 2022-2023

A list of the preprints featured in Development's 'In preprints' articles between 2022-2023

 



List by Alex Eve, Katherine Brown

CSHL 87th Symposium: Stem Cells

Preprints mentioned by speakers at the #CSHLsymp23

 



List by Alex Eve

9th International Symposium on the Biology of Vertebrate Sex Determination

This preList contains preprints discussed during the 9th International Symposium on the Biology of Vertebrate Sex Determination. This conference was held in Kona, Hawaii from April 17th to 21st 2023.

 



List by Martin Estermann

Alumni picks – preLights 5th Birthday

This preList contains preprints that were picked and highlighted by preLights Alumni - an initiative that was set up to mark preLights 5th birthday. More entries will follow throughout February and March 2023.

 



List by Sergio Menchero et al.

CellBio 2022 – An ASCB/EMBO Meeting

This preLists features preprints that were discussed and presented during the CellBio 2022 meeting in Washington, DC in December 2022.

 



List by Nadja Hümpfer et al.

EMBL Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture (2021)

A list of preprints mentioned at the #EESmorphoG virtual meeting in 2021.

 



List by Alex Eve

FENS 2020

A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020

 



List by Ana Dorrego-Rivas

ECFG15 – Fungal biology

Preprints presented at 15th European Conference on Fungal Genetics 17-20 February 2020 Rome

 



List by Hiral Shah

ASCB EMBO Annual Meeting 2019

A collection of preprints presented at the 2019 ASCB EMBO Meeting in Washington, DC (December 7-11)

 



List by Madhuja Samaddar et al.

Lung Disease and Regeneration

This preprint list compiles highlights from the field of lung biology.

 



List by Rob Hynds

MitoList

This list of preprints is focused on work expanding our knowledge on mitochondria in any organism, tissue or cell type, from the normal biology to the pathology.

 



List by Sandra Franco Iborra

Also in the pharmacology and toxicology category:

April in preprints – the CellBio edition

A group of preLighters, with expertise in different areas of cell biology, have worked together to create this preprint reading lists for researchers with an interest in cell biology. This month, categories include: 1) biochemistry/metabolism 2) cell cycle and division 3) cell organelles and organisation 4) cell signalling and mechanosensing 5) (epi)genetics

 



List by Vibha SINGH et al.

FENS 2020

A collection of preprints presented during the virtual meeting of the Federation of European Neuroscience Societies (FENS) in 2020

 



List by Ana Dorrego-Rivas

COVID-19 / SARS-CoV-2 preprints

List of important preprints dealing with the ongoing coronavirus outbreak. See http://covidpreprints.com for additional resources and timeline, and https://connect.biorxiv.org/relate/content/181 for full list of bioRxiv and medRxiv preprints on this topic

 



List by Dey Lab, Zhang-He Goh

1

Drug use in special populations

Any drugs that are being used in special populations: Patients with liver and kidney failure, in paediatrics, in geriatrics, and in pregnant or lactating patients. Includes the discovery of factors that could potentially affect drug use in these special populations.

 



List by Zhang-He Goh

Toxicology of toxicants, existing therapeutics, and investigational drugs

Preprints that describe the toxicology of environmental pollutants and existing and upcoming drugs. Includes both toxicokinetics and toxicodynamics, as well as technological improvements that will help in the characterisation of this field.

 



List by Zhang-He Goh

Antimicrobials: Discovery, clinical use, and development of resistance

Preprints that describe the discovery of new antimicrobials and any improvements made regarding their clinical use. Includes preprints that detail the factors affecting antimicrobial selection and the development of antimicrobial resistance.

 



List by Zhang-He Goh

Anticancer agents: Discovery and clinical use

Preprints that describe the discovery of anticancer agents and their clinical use. Includes both small molecules and macromolecules like biologics.

 



List by Zhang-He Goh

Advances in Drug Delivery

Advances in formulation technology or targeted delivery methods that describe or develop the distribution of small molecules or large macromolecules to specific parts of the body.

 



List by Zhang-He Goh