Goodbye MRSA ~ Hello Malacidins!

It's very early on but scientists have identified a "natural" antibiotic to treat several bacterial diseases that have become resistant to most existing antibiotics, including MRSA.

I'm sure corslight and the other really smart people here have more understanding of this...

it may never make it past clinicals but

https://www.nature.com/articles/s41564-018-0110-1

Abstract said:
Despite the wide availability of antibiotics, infectious diseases remain a leading cause of death worldwide. In the absence of new therapies, mortality rates due to untreatable infections are predicted to rise more than tenfold by 2050. Natural products (NPs) made by cultured bacteria have been a major source of clinically useful antibiotics. In spite of decades of productivity, the use of bacteria in the search for new antibiotics was largely abandoned due to high rediscovery rates. As only a fraction of bacterial diversity is regularly cultivated in the laboratory and just a fraction of the chemistries encoded by cultured bacteria are detected in fermentation experiments, most bacterial NPs remain hidden in the global microbiome. In an effort to access these hidden NPs, we have developed a culture-independent NP discovery platform that involves sequencing, bioinformatic analysis and heterologous expression of biosynthetic gene clusters captured on DNA extracted from environmental samples. Here, we describe the application of this platform to the discovery of the malacidins, a distinctive class of antibiotics that are commonly encoded in soil microbiomes but have never been reported in culture-based NP discovery efforts. The malacidins are active against multidrug-resistant pathogens, sterilize methicillin-resistant Staphylococcus aureus skin infections in an animal wound model and did not select for resistance under our laboratory conditions
 
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Mike95060

Work In Progress
Why do you think it wont make it past clinicals? I have a feeling when the numbers of people dying from common infections spiked we will rush anything we can into use.
 
Rat test Process said:
Methicillin-resistant Staphylococcus aureus strain MW2 was grown in Mueller Hinton broth at 37°C with shaking overnight. The culture was centrifuged, supernatant aspirated and the bacteria were gently washed once in sterile saline. The optical density was determined at 600 nm. The bacterial suspension was diluted to provide a challenge inoculum of approximately 500 CFU per wound in a volume of 0.05 ml in sterile 0.9% NaCl. The inoculum count was verified by viable counts on Mannitol Salt Agar plates spread with proper dilutions of the inoculum and incubated at 37 °C for 24–48 h.

For the wound infection model, 8-week-old male (~200 g) Sprague Dawley rats were given two wounds each. Two rats were used at each time point (day 1 and day 3) for each treatment group for a total of 4 rats (8 wounds) per drug. This sample size was statistically calculated on the basis of previous in-house wound burden studies comparing vehicle-treated groups with antibiotic controls. Rats were randomly selected into the treatment groups.

To generate wounds, the rats were anaesthetized by intraperitoneal injection of 100 mg kg−1 ketamine + 10 mg kg−1 xylazine and the dorsal side of the rats was shaved with electrical clippers and then depilated with Nair. The exposed skin was wiped with betadine. Two symmetrical wounds were made on the dorsum of each rat using a 0.8-cm-diameter disposable biopsy punch. Sterile polyurethane rings serving as wound chambers were placed over the fresh wounds and attached by surgical adhesive.

After the wound creation, rats from each group were infected with 0.05 ml of the bacterial suspension for a final infection dose of 500 CFU per wound. Wounds were covered with Tegaderm visible adhesive dressing, and the rats were rehydrated with physiological saline administered via intraperitoneal injection. The analgesic buprenorphine (0.05 mg kg−1) was administered to minimize pain during surgical recovery.

At 30 min post infection, rats were given single daily topical treatments of vehicle (25 mM CaCl2 in sterile water), or 0.5 mg malacidin A or daptomycin suspended in 25 mM CaCl2, and the wounds were covered in fresh Tegaderm dressing.

At 1 day and 3 days post infection, the rats were humanely euthanized and wounds were excised and assessed for bacterial burdens by plating on MSA. Rats were observed twice daily for morbidity and possible signs of acute toxicity. Abnormal clinical signs were recorded if observed. Rats were housed in the Public Health Research Institute’s Animal Biosafety Level-2 Research Animal Facility (ICPH RAF), a centre of the New Jersey Medical School, Rutgers University (NJMS-Rutgers).

The animal facility follows the Public Health Service and National Institute of Health Policy of Humane Care and Use of Laboratory Animals. All experimental protocols were approved by the Rutgers Institutional Animal Care and Use Committee (IACUC).

4 rats, 8 wounds

very early
 

CoorsLight

Well-known member
Why do you think it wont make it past clinicals? I have a feeling when the numbers of people dying from common infections spiked we will rush anything we can into use.

The bar is low for new antibiotics, but there are a number of potential issues for getting this to patients. Here's a few unknowns that probably represent the top risks, but really there can be pitfalls anywhere:

Process: it's synthesized by natural instead of chemical means, so purification and stability becomes an issue. Also, biosynthesis may produce toxins that may be hard to separate from the desired chemical. Sometimes natural products like this are prohibitively expensive to isolate and store for reasons like this. And looking at this compound, I'd think it impossible to synthesize by traditional chemical means; it's too complex a molecule. And I can already see that it contains a reactive site that would oxidize super fast.

Toxicity: dunno if these compounds are tolerated in humans. Tolerability is not typically a barrier to approval by health agencies when bacterial infection is a life and death situation. But if there are significant undesired effects, it reduces the chance of a company trying to develop it and it reduces the chances of doctors using it.

Metabolism/pharmacokintetics: the malacidin they used in the rat may not be stable in humans due to differences in the detoxification machinery between the species. Sometimes these differences can be life and death (e.g. dogs can die from chocolate--this is due to metabolic differences).

Anyway, this paper is not so much a paper on malacidins, it's about the "discovery platform" these researchers have created. Basically it allows them to "see" genes that are related to each other in a biosynthetic pathway that creates an anti-bacterial chemical. They can do this using a big data approach instead of using bacterial culture to detect active chemicals. The malacidin is just one discovery they've made from this platform. It's exciting to have a discovery tool like this available to humankind when we can see an antibiotic-free future on the horizon.
 
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Mike95060

Work In Progress
The bar is low for new antibiotics, but there are a number of potential issues for getting this to patients. Here's a few unknowns that probably represent the top risks, but really there can be pitfalls anywhere:

Process: it's synthesized by natural instead of chemical means, so purification and stability becomes an issue. Also, biosynthesis may produce toxins that may be hard to separate from the desired chemical. Sometimes natural products like this are prohibitively expensive to isolate and store for reasons like this. And looking at this compound, I'd think it impossible to synthesize by traditional chemical means; it's too complex a molecule. And I can already see that it contains a reactive site that would oxidize super fast.

Toxicity: dunno if these compounds are tolerated in humans. Tolerability is not typically a barrier to approval by health agencies when bacterial infection is a life and death situation. But if there are significant undesired effects, it reduces the chance of a company trying to develop it and it reduces the chances of doctors using it.

Metabolism/pharmacokintetics: the malacidin they used in the rat may not be stable in humans due to differences in the detoxification machinery between the species. Sometimes these differences can be life and death (e.g. digs can die from chocolate--this is due to metabolic differences).

Anyway, this paper is not so much a paper on malacidins, it's about the "discovery platform" these researchers have created. Basically it allows them to "see" genes that are related to each other in a biosynthetic pathway that creates an anti-bacterial chemical. They can do this using a big data approach instead of using bacterial culture to detect active chemicals. The malacidin is just one discovery they've made from this platform. It's exciting to have a discovery tool like this available to humankind when we can see an antibiotic-free future on the horizon.


Thank you. So if we can "see" these helpful genes what the chance we can CRISPR the fuck out of them and dump them into a system that is more tolerable to humans and more easily manufacturer-able?
 

CoorsLight

Well-known member
Thank you. So if we can "see" these helpful genes what the chance we can CRISPR the fuck out of them and dump them into a system that is more tolerable to humans and more easily manufacturer-able?

There is a chance, but it really depends on what the real-world hurdles end up being. The current state of the art in biosynthesis is still pretty rudimentary. Biosynthesis is like an orchestra with specialized enzymatic pathways serving as the instruments. In a living organism, the instruments are being used at just the right time and cooperation with others. Currently, we are OK at playing one instrument at a time (and CRISPR can definitely help us to increase the number of instruments in the orchestra), but we are crap at playing a song with multiple instruments. I don't see how CRISPR can really help put an orchestra together given our current capabilities.

Typically, only a few select reactions are currently done by enzymatic means, and the rest of the work is done by traditional organic chemistry. Mixing the two approaches together can allow access to a high degree of molecular complexity, but currently I know of nothing that remotely approaches the complexity of the malacidin that can be done on large scale.
 

Snaggy

Well-known member
So far, it's a topical antibiotic. For one reason or another, even if approved, it might never be used to treat serious systemic infections.
 

CoorsLight

Well-known member
Macrocycle compounds like this are typically formulated for IV administration. There is nothing about this study or the compound itself to indicate that this would be limited to transdermal. This study was limited to doing a topical administration due to the way they introduced the local infections and due to limitations in controlling and maintaining blood levels when administered IV.
 
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