Potential Antibiotics to Treat Multidrug Resistant Gram Negative Bacterial Infections

Jerome Parness MD PhD

This PAAD is dedicated to the memory of Rabbi Dr. Moses D. Tendler, former Chairman of the Department of Biology at Yeshiva University, a towering intellect and bioethicist, my teacher and mentor, who toiled in the field of soil bacteria and their products, searching for new antibiotics and anti-cancer natural products.

It is no news to any physician that our antibiotic armamentarium against multi-drug resistant Gram-negative bacterial infections is seriously dwindling, dramatically decreasing the survival probabilities of those seriously ill in our intensive care units.^1,2 This is largely due to over treatment with antibiotics on the part of physicians, but more significantly, due to the creation of more “me-too” antibiotics, all designed and primed to inhibit bacterial cell wall synthesis. It is much easier and cheaper for the pharmaceutical industry to design drugs based on the target they already know, than to develop completely new targets and the drugs to target them in the struggle to treat in-hospital infections with ever more resilient and virulent Gram negative bacteria.

The development of and selection for bacterial drug resistance occurs through a number of mechanisms: antibiotic overuse in the general population, drug resistance selection in pockets of high acuity medical facilities (ICUs in particular, and the development of “me-too” antibiotic derivatives making small genetic changes sufficient for the development of resistance, all of which have pockets of development within our natural environment. Drug run-off from industrial poultry, pig and beef farms, where the animals are routinely treated with antibiotics, contribute to the development of antibiotic resistant bacteria in nature. The problem of antibiotics and other drugs making it into the environment has gotten so bad as to have reached the coral and coral reef animals in the Red Sea and the South China Sea. These are the seas that have been examined, and one must assume that they are representative of much of the world’s coral reefs.^3,4 The evolutionary pressure on the bacterial communities in nature to develop antibiotic resistance is now world-wide. As noted by Wellington et al., “Antibiotic resistance develops through complex interactions, with resistance arising by de-novo mutation under clinical antibiotic selection or frequently by acquisition of mobile genes that have evolved over time in bacteria in the environment. The reservoir of resistance genes in the environment is due to a mix of naturally occurring resistance and those present in animal and human waste and the selective effects of pollutants, which can co-select for mobile genetic elements carrying multiple resistant genes. Less attention has been given to how anthropogenic activity might be causing evolution of antibiotic resistance in the environment. Although the economics of the pharmaceutical industry continue to restrict investment in novel biomedical responses, action must be taken to avoid the conjunction of factors that promote evolution and spread of antibiotic resistance.⁵ What I am here to tell you is that all is not lost. Though we are not yet there in terms of clinically available compounds, we are on our way.

How does the medical-scientific community approach this problem? How does the research community go about identifying new targets in multi-drug resistant bacteria (MDRB)? The simple answer is by going back to basics - the basic understanding that Nature is much longer lived than human civilization and that the bacteria and molds and fungi in Nature have had a far longer, evolutionary time frame to develop molecular mechanisms to protect themselves from other single cell attackers and their potentially dangerous molecules. Scientists have gone back to the earth, to the soil, to search for new molecules that will attack multi-drug (cell wall synthesis-targeted) resistant bacteria. The good thing is that one need not know a priori the target of such a compound; one simply needs to assay the MDRB killing. Today, simply combining bacterial co-cultures of isolated soil bacteria and MDRB, one can determine whether such a soil bacterium kills MDRB. Using the power of mass spectrometry, one can identify the mass and structure of all compounds produced by the soil bacteria, identify which structures are unique and test them specifically for their ability to kill MDRB. One such molecule, Streptothiricin, was isolated from soil Actinomyces in the 1940s and found to be extremely active against a variety of pathogens, including Mycobacterium tuberculosis, Brucella, and Salmonella infections. Unfortunately, it was thought to be nephrotoxic, and interest in this potential antibiotic was dropped. It was recently resurrected and the compound was actually found to be a mixture of two compounds renamed S-F and S-D (see Fig. below), with the former being the potentially nephrotoxic one and the latter found not to be so at therapeutic MDR bacterial killing concentrations in laboratory animals in preclinical testing. It’s target has been identified not as part of the machinery involved in cell wall synthesis, but as the 30S subunit of the 70S ribosome, paralyzing protein synthesis.⁶ A mechanism of antibiotic resistance against S-D is found in bacteria via acetylation of the beta-amino group in lysine of the antibiotic. The prevalence of such resistance is not yet known.

Streptothricin F is a bactericidal antibiotic effective against highly drug-resistant gram-negative bacteria that interacts with the 30S subunit of the 70S ribosome

doi: https://doi.org/10.1371/journal.pbio.3002091.g001

Fig.1 Structure of S-F and S-D.

Streptothricins share streptolidine and carbamoylated gulosamine sugar moieties. They are distinguished by differing numbers of β-lysines attached end-to-end through amide bonds to the ε-amino groups. Nourseothricin is the natural product mixture of several streptothricins, predominantly S-F (1 β-lysine) and S-D (3 β-lysines). Acetylation of the β-amino group blocks activity and is the major known mechanism of antimicrobial resistance to streptothricins. S-D, streptothricin D; S-F, streptothricin-F.

A second example of a new class of antibiotics targeted at a bacterial target protein is the Darobactins, isolated from the genus of Photorhabdus symbionts of soil nematodes.⁷ Darobactin is a protein antibiotic that targets a gram negative bacterial cell wall protein, BamA, whose function is to help other proteins responsible for bacterial cell wall functioning to insert themselves into the membrane, i.e., a bacterial cell wall chaperone. In the absence of functional BamA, these proteins cannot insert, thereby depriving the bacterium of vital life-sustaining processes, and they die. Darobactin is ribosomal synthesized, but induction of antibiotic protein production under laboratory conditions is difficult.

https://pubs.acs.org/doi/10.1021/acsinfecdis.4c00412?fig=fig2&ref=pdf

Recently, scientists have successfully engineered a darobactin biosynthetic pathway in E. coli to produce a variety of ‘non-natural’ darobactin derivatives that are capable of being produced in commercial amounts in laboratory bioreactors and have shown activity against MDRB in laboratory screening.^8,9

While the Streptothricins and Darobactins have a long way to go to find their way to clinical usage, they point the way out of our present trap of MDRB infections.

Send your thoughts and comments to Myron who will post in a Friday reader response.

References

1. Viasus D, Gudiol C, Carratalà J. Treatment of multidrug-resistant Gram-negative bloodstream infections in critically ill patients: an update. Curr Opin Crit Care. 2024 Oct 1;30(5):448-455. doi: 10.1097/MCC.0000000000001190. Epub 2024 Jul 8. PMID: 39150047.

2. Karampatakis T, Tsergouli K, Roilides E. (2023) Infection control measures against multidrug-resistant Gram-negative bacteria in children and neonates.

Future Microbiol. Jul;18:751-765. doi: 10.2217/fmb-2023-0072. Epub 2023 Aug 16.

PMID: 37584552

3. Zhang R, Yu K, Li A, Wang Y, Pan C, Huang X. Antibiotics in coral reef fishes from the South China Sea: Occurrence, distribution, bioaccumulation, and dietary exposure risk to human. Sci Total Environ. 2020 Feb 20;704:135288. doi: 10.1016/j.scitotenv.2019.135288. Epub 2019 Nov 23. PMID: 31796281.Available at https://www.sciencedirect.com/science/article/abs/pii/S0048969719352805,

4. Traces of ten common pharmaceutical products detected in Red Sea corals. Available at https://oceansconnectes.org/en/des-traces-de-dix-produits-pharmaceutiques-courants-detectees-dans-les-coraux-de-la-mer-rouge/

5. Wellington EM, Boxall AB, Cross P, Feil EJ, Gaze WH, Hawkey PM, Johnson-Rollings AS, Jones DL, Lee NM, Otten W, Thomas CM, Williams AP. (2013) The role of the natural environment in the emergence of antibiotic resistance in gram-negative bacteria. Lancet Infect Dis. Feb;13(2):155-65. doi: 10.1016/S1473-3099(12)70317-1. PMID: 23347633

6. Morgan CE, Kang YS, Green AB, Smith KP, Dowgiallo MG, Miller BC, Chiaraviglio L, Truelson KA, Zulauf KE, Rodriguez S, Kang AD, Manetsch R, Yu EW, Kirby JE. Streptothricin F is a bactericidal antibiotic effective against highly drug-resistant gram-negative bacteria that interacts with the 30S subunit of the 70S ribosome. PLoS Biol. 2023 May 16;21(5):e3002091. doi: 10.1371/journal.pbio.3002091. PMID: 37192172. Available at https://doi.org/10.1371/journal.pbio.3002091

7. Imai Y, Meyer KJ, Iinishi A, Favre-Godal Q, Green R, Manuse S, Caboni M, Mori M, Niles S, Ghiglieri M, Honrao C, Ma X, Guo JJ, Makriyannis A, Linares-Otoya L, Böhringer N, Wuisan ZG, Kaur H, Wu R, Mateus A, Typas A, Savitski MM, Espinoza JL, O'Rourke A, Nelson KE, Hiller S, Noinaj N, Schäberle TF, D'Onofrio A, Lewis K. A new antibiotic selectively kills Gram-negative pathogens. Nature. 2019 Dec;576(7787):459-464. doi: 10.1038/s41586-019-1791-1. Epub 2019 Nov 20. Erratum in: Nature. 2020 Apr;580(7802): E3. doi: 10.1038/s41586-020-2063-9. PMID: 31747680. Available at https://www.nature.com/articles/s41586-019-1791-1)

8. Groß S, Panter F, Pogorevc D, Seyfert CE, Deckarm S, Bader CD, Herrmann J, Müller R. Improved broad-spectrum antibiotics against Gram-negative pathogens via darobactin biosynthetic pathway engineering. Chem Sci. 2021 Aug 12;12(35):11882-11893. doi: 10.1039/d1sc02725e. PMID: 34659729.

9. Dutta A, Sharma P, Dass D, Yarlagadda V. Exploring the Darobactin Class of Antibiotics: A Comprehensive Review from Discovery to Recent Advancements. ACS Infect Dis. 2024 Aug 9;10(8):2584-2599. doi: 10.1021/acsinfecdis.4c00412. Epub 2024 Jul 19. PMID: 39028949.