About
Dirk Schnappinger is a researcher with extensive contributions to the study of bacterial gene regulation, particularly focusing on the tetracycline repressor system and its applications. His work includes detailed investigations into the molecular mechanisms of antibiotic action, uptake, and resistance, as well as the structural basis of gene regulation by tetracycline-inducible systems. Schnappinger has contributed to understanding protein-protein recognition and dimerization specificity in regulatory proteins, as well as the conformational changes induced by tetracycline binding. His research extends into the field of infectious diseases, with a significant focus on Mycobacterium tuberculosis, exploring the bacterial response to hypoxia, gene expression regulation within macrophages, and the pathogen's survival strategies against host immune defenses. Schnappinger has also been involved in developing genetic tools for controlling gene expression in mycobacteria, including the use of tetracycline repressors for gene silencing. His work has provided insights into the adaptation of both the pathogen and host during infection, contributing to the broader understanding of host-pathogen interactions and bacterial persistence mechanisms.
Research topics
- Biology
- Genetics
- Computational biology
- Medicine
- Evolutionary biology
- Chemistry
- Virology
- Bioinformatics
- Microbiology
- Pharmacology
- Cell biology
- Biochemistry
Selected publications
ACS Infectious Diseases · 2026-05-14
articleOpen accessremains a significant burden. Although effective treatment regimens exist, drug resistance has continued to emerge. This clinical resistance, combined with side effects and protracted treatment times from the current front-line therapies, means that there is a need to identify novel agents to combat this disease. Here, we report on a new chemical series, identified by whole-cell phenotypic growth inhibition screening, that demonstrates significant activity across multiple media. Mode of action studies indicate that this series targets the same biological pathway as ethambutol (EMB), a drug used in the current front-line treatment of tuberculosis. Screening selected analogues against clinical isolates, resistant to EMB, demonstrated differential sensitivity both across the molecules and against the different specific resistant mutations. The data obtained suggest that this series has potential to be developed into a viable alternative to EMB.
Nature Communications · 2026-03-21
articleOpen accessThe increasing prevalence of antimicrobial resistance is an important challenge that warrants new approaches to antibiotic development. Currently, all antibiotics inhibit biological processes. To explore whether activation of a biochemical pathway can elicit bactericidal effects we engineered variants of Mycobacterium tuberculosis ATP-phosphoribosyltransferase (ATP-PRT) that are resistant to allosteric inhibition by L-histidine, leading to supraphysiological activation of ATP-PRT and L-histidine overproduction. Upregulation of L-histidine biosynthesis significantly reduces the growth of M. tuberculosis in culture and causes a loss of fitness owing to nutrient and energy depletion. Moreover, the expression of allosteric variants in M. tuberculosis significantly reduced infections in human macrophages and in a mouse model of infection. Thus, metabolic activation represents a new mycobactericidal mechanism that could be applied to antimycobacterial drug discovery.
Metabolic control of drug resistance by a mycobacterial ion channel
bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-10
articleOpen accessABSTRACT Pyrazinamide (PZA) is a cornerstone of modern tuberculosis therapy, yet its context-dependent activity has obscured both its mode of action and resistance mechanisms. Using a host-mimicking culture system integrated with genome-wide CRISPRi profiling, metabolomics, and comparative genomics, we identify a previously unrecognized driver of PZA resistance in humans: loss of the ion channel Rv2571c. Rv2571c mediates α-ketoglutarate efflux, amplifying PZA-induced cytoplasmic acidification under host-relevant acidic conditions. Loss-of-function mutations confer resistance in vitro and in vivo and are under positive selection in clinical isolates, establishing this pathway as a resistance determinant in patients. Together, these findings define a novel, ion channel–mediated resistance mechanism, establish cytoplasmic acidification as the basis of PZA killing, and inform resistance detection and treatment-shortening drug development.
European Journal of Medicinal Chemistry · 2026-04-08
articleScience Advances · 2026-04-01
articleOpen access(Mtb) is a major barrier to effective tuberculosis (TB) treatment and is largely due to its complex, impermeable cell envelope. We identified a periplasmic protein complex comprising FecB and Rv3035 that is essential for maintaining envelope integrity and mediating intrinsic multidrug resistance in Mtb. FecB interacts with Rv3035, forming a stable heterodimer that associates with the cell envelope biosynthesis protein AftB. We report the structures of Rv3035 alone and in complex with FecB and identify critical residues for complex formation and function. Coessentiality and genetic interaction analyses support a functional link between FecB, Rv3035, and AftB, an arabinofuranosyltransferase that synthesizes arabinogalactan and lipoarabinomannan. Loss of FecB or Rv3035 disrupted AftB-mediated arabinan synthesis, suggesting that these proteins support AftB's enzymatic activity. FecB is required for Mtb virulence in mice, underscoring its physiological relevance. These findings highlight FecB, Rv3035, and AftB as promising therapeutic targets.
Integrating chemical, genetic, and feasibility assessments for anti-tubercular target validation
EMBO Molecular Medicine · 2026-04-07
articleOpen access1st authorCorrespondingDespite the approval of two first-in-class anti-tuberculars over the past two decades, the global burden of tuberculosis (TB) remains unacceptably high, in part due to the emergence and spread of drug-resistant strains of Mycobacterium tuberculosis (Mtb). This review summarizes advances and ongoing challenges in anti-TB drug discovery, focusing on identifying and validating novel targets. Highlighted is a framework developed by the TB Drug Accelerator (TBDA) consortium for target validation in Mtb. Two computational platforms, DAIKON and PARSNIP, allow the systematic evaluation of targets across multiple dimensions, including chemical validation, genetic essentiality, vulnerability, and the feasibility to identify drug-like molecules for a target of interest. Case studies of Pks13 and NadE illustrate how these parameters guide target prioritization and risk assessment. By integrating these metrics, the framework enables dynamic, transparent target ranking, supporting development of both pan-TB and treatment-shortening regimens. This paradigm is adaptable to other bacterial pathogens and is designed to improve evidence-based decision-making in antibacterial drug discovery.
bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-30
articleOpen accessremains a significant disease burden. Although effective treatment regimens exist, drug resistance continues to emerge. This clinical resistance, combined with side effects and protracted treatment times from the current front-line therapies, means there is a need to identify novel agents to combat this disease. Here we report on a new chemical series, identified by whole-cell phenotypic growth inhibition screening that demonstrates significant activity across multiple media. Mode of action studies indicate that this series targets the same biological pathway as Ethambutol (EMB), a drug used in the current frontline treatment of tuberculosis. Screening selected analogues against clinical isolates, resistant to EMB, demonstrated differential sensitivity both across the molecules and against the different specific resistant mutations. The data obtained suggests that this series has potential to be developed into a viable, alternative to EMB.
mBio · 2026-04-20
articleOpen accessABSTRACT Mycobacterium tuberculosis (Mtb) remains a leading cause of infectious disease mortality worldwide, largely due to its ability to survive within host macrophages. Despite advances in understanding the environmental pressures Mtb encounters in vivo , the genetic requirements for adaptation and survival within the intracellular niche remain incompletely defined. Here, we employed a genome-wide CRISPR interference (CRISPRi) screen in an ex vivo model exploiting single-cell suspensions from Mtb-infected mouse lung homogenates to identify genes critical for intracellular survival at different time points in the infection continuum. Using a library comprising ~20,000 sgRNAs covering >96% of Mtb open reading frames, we identified genes required for growth within the changing immune microenvironment. Mutant depletion patterns varied across immune environments sampled at 2, 4, and 6 weeks post-infection, which revealed a weighted dependency on cell wall biosynthesis genes early and the reliance on cholesterol catabolism and iron acquisition across all time points. Functional validation of three genes— embB , fadE29 , and mbtI —confirmed their temporal significance in vivo . This screen provides increased resolution of the differential metabolic vulnerabilities in Mtb in the evolving immune environments during infection, stressing the temporal nature of conditional essentiality in vivo . IMPORTANCE Mycobacterium tuberculosis (Mtb) remains a leading cause of infectious disease mortality worldwide, largely due to its ability to survive within host macrophages. Despite advances in understanding the environmental pressures Mtb encounters in vivo , the genetic requirements for adaptation and survival within the intracellular niche remain incompletely defined. Here, we employed a genome-wide CRISPR interference (CRISPRi) screen in an ex vivo model exploiting single-cell suspensions from Mtb-infected mouse lung homogenates to identify genes critical for intracellular survival at different time points in the infection continuum. This novel approach enabled us to identify how different bacterial metabolic pathways were of greater importance to the bacterium at different time points post-infection. The results provide insights into how the evolving immune response to infection shapes the metabolic and replicative status of the bacterium. This information has significance in the design of therapeutic strategies toward cure.
Communications Biology · 2026-04-18
articleOpen accessThe human pathogen Mycobacterium tuberculosis (Mtb) thrives in lipid-rich microenvironments. A strong body of evidence demonstrated that, during infection, Mtb utilizes long-chain fatty acids (LCFA) as a preferred carbon source. However, LCFA also have antimicrobial properties. Mtb must therefore employ mechanisms to utilize LCFA while mitigating their toxicity. Using transposon sequencing (TnSeq), we defined the Mtb LCFA resistome as comprising 38 genes. Surprisingly, LCFA resistance requires diverse metabolic pathways, indicating pleiotropic effects of LCFA on Mtb physiology. We investigated the function of the TnSeq top-hit, the universal stress protein TB15.3, and demonstrate that it participates in a "metabolic brake" mechanism restricting LCFA uptake and catabolism to prevent membrane hyperpolarization. TB15.3 absence caused Mtb to lose viability during chronic infection in mice and in an in vitro caseum model. Our work highlights Mtb LCFA resistance mechanisms as an important host adaptation and a promising target space for drug development.
Journal of Medicinal Chemistry · 2026-04-22
articleWe recently reported C48, a potent and orally effective inhibitor targeting biotin biosynthesis in Mycobacterium tuberculosis (Mtb). Notably, C48 exhibited a favorable pharmacokinetic profile and suppressed Mtb growth in a mouse model that recapitulates human biotin physiology, demonstrating that biotin is a validated target for antibacterial agents. This paper details the previously undisclosed lead optimization studies, which employed rational drug design by the strategic introduction of fluorine, reduction of rotatable bonds, and incorporation of nitrogen atom to enhance π–π stacking. A series of novel BioA inhibitors were designed, synthesized, and evaluated with respect to their biochemical properties, in vitro ADME, and pharmacokinetic profiles. Key analogues were tested against isogenic Mtb strains (BioA underexpressed or overexpressed) to confirm on-target engagement. C48 emerged as the most potent candidate with minimum inhibitory concentrations (MICs) ranging from 0.012 to 0.093 μM against a panel of drug-sensitive and drug-resistant Mtb strains.
Recent grants
NIH · $1.4M · 2010
Decoding the roles of critical genes of unknown function in M. tuberculosis
NIH · $21.4M · 2013–2019
NIH · $3.0M · 2016
NIH · $562k · 2012
Targeting Biotin Metabolism in Mycobacterium Tuberculosis
NIH · $3.9M · 2019–2023
Frequent coauthors
- 116 shared
Sabine Ehrt
Cornell University
- 47 shared
Kyu Y. Rhee
Weill Cornell Medicine
- 46 shared
Curtis A. Engelhart
Cornell University
- 36 shared
Véronique Dartois
Hackensack Meridian Health
- 28 shared
Helena I. Boshoff
National Institutes of Health
- 28 shared
Thomas R. Ioerger
- 26 shared
Carolina Trujillo
Hospital Nacional Cayetano Heredia
- 25 shared
Matthew Zimmerman
Center for Discovery
Labs
- Resume-aware match score
- Save to shortlist
- AI-drafted outreach
See your match with Dirk Schnappinger
PhdFit ranks faculty by your research interests, methods, and publications — grounded in their actual work, not templates.
- Free to start
- No credit card
- 30-second signup