Unraveling the Molecular Mechanism of Clindamycin Binding in Cutibacterium acnes and Resistance Development: Insights From Cryo-EM

A recent study utilizing cryogenic electron microscopy (cryo-EM) has provided new insights into the mechanisms behind clindamycin resistance in Cutibacterium acnes. The study, published in the Journal of Investigative Dermatology, examined clindamycin’s binding to the C acnes ribosome at a resolution of 2.53 Å, offering a detailed structural map of how the antibiotic interacts with the ribosome and revealing the molecular basis of resistance.¹

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Clindamycin, a key antibiotic for treating acne,² works by inhibiting bacterial protein synthesis. However, rising resistance to clindamycin³ presents a significant challenge in dermatology, highlighting the need for a deeper understanding of the mechanisms behind this resistance and innovative ways to circumvent it.

Principal investigator and senior author of the study, Christopher G. Bunick, MD, PhD, editor in chief of Dermatology Times, said, “Antibiotic stewardship is such an important topic across medicine, and one way to advance our understanding of antibiotics and their use is to determine the correlation between molecular structure and function in disease-relevant bacterial species and how that impacts clinical outcomes, such as disease improvement or antimicrobial resistance.”

Understanding Clindamycin’s Mechanism of Action

Clindamycin, a lincosamide antibiotic, inhibits bacterial protein synthesis by binding to the 50S ribosomal subunit, blocking the transfer of aminoacyl groups between transfer RNAs (tRNAs) and halting peptide bond formation. This action is effective across most bacteria, including gram-positive and anaerobic bacterium C acnes.²

Previously, x-ray crystallography and cryo-EM studies have detailed how clindamycin binds to the 23S ribosomal RNA (rRNA) within the ribosome’s peptidyl transferase center (PTC), blocking protein synthesis.⁴ Recent cryo-EM studies at 2.53 Å resolution further elaborate on clindamycin’s binding specifically to the dermatology-relevant C acnes ribosome,⁵ providing clinical and translational insights into the molecular mechanisms of resistance. According to the study’s lead author, Ivan Lomakin, PhD, “Having an atomic resolution structure of a drug bound to not a model, but its actual clinical target, is crucial for development of narrow-spectrum, species-specific antibiotics, which will have less side effects and reduced drug resistance.”

In addition to its antibacterial properties, clindamycin has demonstrated anti-inflammatory effects, which may contribute to its efficacy in acne treatment. Recent reviews, including those coauthored by Bunick and James Del Rosso, DO, have highlighted this aspect of clindamycin’s mechanism of action.^6-7 Bunick is also a director on the board of the American Acne and Rosacea Society, where Del Rosso serves as president.

“The best overall study data with any topical acne formulation that we have to date incorporates clindamycin along with adapalene and benzoyl peroxide, including versus the dual combinations that do not include all 3 agents,” Del Rosso said. “This was a very important observation which further convinced me that clindamycin has earned some of its own bragging rights in bringing something extra to the table for acne.”

Clindamycin Binding to the C acnes Ribosome

In the recent study, authored by Lomakin et al, researchers utilized cryo-EM to examine the interaction between clindamycin and the 50S ribosomal subunit of C acnes. The researchers mapped the detailed structure of clindamycin bound to the ribosome, providing a clear view of how the antibiotic inhibits protein synthesis.

Clindamycin binds tightly to the 23S rRNA within the PTC of the ribosome, forming direct and water-mediated hydrogen bonds with several nucleotides. The galactose sugar moiety of clindamycin interacts with nucleotides A2241, A2242, G2244, and G2687 within the rRNA, stabilizing the antibiotic-ribosome complex. In particular, hydrogen bonds between the oxygen atoms of the galactose moiety and the nitrogen atoms of A2241(2058) (E coli 23S rRNA numbering is provided in parentheses) are crucial for maintaining this binding, which poised clindamycin to sterically interfere with the transfer of aminoacyl groups between tRNAs, effectively preventing protein synthesis and bacterial proliferation.¹

This molecular model of clindamycin binding in C acnes mirrors previous findings in other bacterial species, providing a consistent understanding of how lincosamide antibiotics function.⁶ The study also noted that the galactose ring of clindamycin is positioned near the nascent peptide exit tunnel, a site crucial for protein synthesis. This positioning further reiterates the ability of clindamycin to inhibit bacterial growth.⁸

Molecular Mechanisms Behind Clindamycin Resistance

The study also uncovered the molecular mechanisms that enable C acnes to resist clindamycin. Key mutations in the 23S rRNA were identified as central to this resistance. One notable mutation is a substitution of adenine (A) to guanine (G) at position A2241(2058), which weakens the interaction between clindamycin and the ribosome. This mutation disrupts the hydrogen bonding between the galactose ring of clindamycin and the 23S rRNA, resulting in a less stable antibiotic-ribosome complex. As a result, the antibiotic’s binding affinity is significantly reduced, allowing the bacteria to survive in the presence of clindamycin.¹

Additionally, mutations at position A2242(2059), such as A to G substitutions, further destabilize the clindamycin-ribosome interaction, contributing to resistance. These mutations prevent the formation of a key hydrogen bond between the N6 of A2241 and the O6 of clindamycin, thus compromising the antibiotic’s efficacy. The study’s cryo-EM data reveal that these changes directly contribute to the macrolide, lincosamide, and streptogramin B resistance phenotype observed in some C acnes strains.

Mutations at other nucleotide positions, such as C2793(2611)U, further exacerbate resistance. These mutations replace canonical base pairs with wobble base pairs, which likely affect the hydrogen bonds between the rRNA and the galactose sugar of clindamycin, diminishing its binding strength.¹

Treatment and Resistance Management

The findings of this study have significant implications for the treatment of acne and other C acnes-related conditions. The structural characterization of specific mutations responsible for clindamycin resistance provides important insights into treatment failure, and a molecular blueprint for innovating newer inhibitors with reduced risk of resistance.

The study authors suggest that monitoring resistance patterns in clinical isolates is now more critical than ever. Strains harboring mutations such as A2241G or A2242G exhibit reduced efficacy to clindamycin, making it essential for dermatology clinicians to consider alternative treatment strategies. This could involve using antibiotics that target different regions of the ribosome or exploring other classes of antibiotics with distinct mechanisms of action.¹

Moreover, the study’s structural data could guide the design of novel antibiotics or modifications to existing drugs that can circumvent these resistance mechanisms. The findings highlight the importance of continued research into antibiotic resistance and the need for clinicians to stay informed about evolving resistance patterns to make informed treatment decisions, according to study authors.

References

1. Lomakin IB, Devarkar SC, Grada A, Bunick CG. Mechanistic basis for the translation inhibition of Cutibacterium acnes by clindamycin. J Invest Dermatol. 2024;144(11):2553-2561.e3. doi:10.1016/j.jid.2024.07.013
2. Murphy PB, Bistas KG, Patel P, Le JK. Clindamycin. In: StatPearls [Internet]. StatPearls Publishing; January 2025. Accessed February 14, 2025. https://www.ncbi.nlm.nih.gov/books/NBK519574/
3. White BP, Siegrist EA. Increasing clindamycin resistance in group A streptococcus. Lancet Infect Dis. 2021;21(9):1208-1209. doi:10.1016/S1473-3099(21)00456-4
4. Krawczyk SJ, Leśniczak-Staszak M, Gowin E, Szaflarski W. Mechanistic insights into clinically relevant ribosome-targeting antibiotics. Biomolecules. 2024;14(10):1263. doi:10.3390/biom14101263
5. Fréchin L, Holvec S, von Loeffelholz O, Hazemann I, Klaholz BP. High-resolution cryo-EM performance comparison of two latest-generation cryo electron microscopes on the human ribosome. J Struct Biol. 2023;215(1):107905. doi:10.1016/j.jsb.2022.107905
6. Del Rosso JQ, Armillei MK, Lomakin IB, Grada A, Bunick CG. Clindamycin: a comprehensive status report with emphasis on use in dermatology. J Clin Aesthet Dermatol. 2024;17(8):29-40.
7. Armillei MK, Lomakin IB, Del Rosso JQ, Grada A, Bunick CG. Scientific rationale and clinical basis for clindamycin use in the treatment of dermatologic disease. Antibiotics (Basel). 2024 Mar 17;13(3):270. doi:10.3390/antibiotics13030270
8. van Dun SCJ, Verheul M, Pijls BGCW, et al. Effectiveness of clindamycin-based exposure strategies in experimental mature staphylococcal biofilms. Microbiol Spectr. Published online January 30, 2025. doi:10.1128/spectrum.01947-24