Acyldepsipeptides (ADEPs) active against biofilm producers

Greetings

      Let me start with a question for you to think about. Whats the main problem associated with Clinical infections in terms of management. If you said "Antibiotic resistance" you are on the right track. Now a second question, what is the main problem in treating antibiotic resistant organisms? Think about it for a minute. Read further only if you have a come up with a well argued answer. The most probable response, that I usually get is mis-management of antibiotics. That is arguably true enough, but an equal contribution would be not having a new class of drugs. Think about it.



Fig 1: Kinetics of Antibiotic resistance.

       A little bit of explanation. One of the talks I attended, years ago made a statement. Antibiotic resistance is common in gram positive and gram negative organisms, but the antibiotics in the pipeline is being exhausted specially against the gram negative. Logically speaking we no more have a "magic silver bullet". I strongly refer that you listen to the interview with Julian (Link), who argues that antibiotics may indeed be a bacterial way of communication system. Having said that, what would be the most important key features of countering antibiotic resistance? I would say, there are 3 important basics- Rational use of drugs, Resistance detection in the laboratory and new classes of antibiotic in research pipeline. Refer to my earlier posts here and here.

     Is acquired antibiotic resistance a real problem? You would say, what sort of a dumb question is that. But give this a thought. A recent publication in nature, have shown convincingly that you needn't have the whole population converted to resistant type and bacterial community can take advantage of the ones that can deactivate the antibiotic for them. Bacteria can undergo dormancy or produce biofilm which doesn't require genetic changes, but confers antibiotic resistance. Resistance without acquiring resistance looks like an important problem.

    An understanding of this has motivated people to start looking inventing new classes of antibiotics. a lot of focus has been on phage therapy, meddling with quorum sensing system or drugs that can target dormant bacteria (for example new Anti-TB drugs, Link). In this post, am introducing one more approach- Biofilm disruption.

Fig 2: Biofilm formation.
Source



     Biofilms maybe casually defined as a large matrix embedding the bacterial population. The matrix (up to 90% of the total mass) is largely contributed by extracellular polymeric substances (EPS). The matrix has a slime like consistency that protects the bacterial community from (i) Environmental insults such as drying, Redox stress, (ii) Traps nutrients and keeps a tight integrity of cells which enables intimate cell-to-cell interactions and DNA exchange, (iii) Protects form immune system by avoiding antigen innate immune defenses (such as opsonization and phagocytosis) and Antibiotics. The intimate bacterial community can achieve division of labor, thus functioning at better efficiency. From clinical point of view, biofilms lead to chronic infections which are often difficult to treat especially if it is seen in prosthetic or catheters. The formation of Biofilm happens in 4 stages- Attachment to a surface, Micro-colony formation, biofilm maturation and dispersal (or persistence).

Fig 3: Anti-biofilm strategies

      There are a variety of Anti-Biofilm strategies that are under investigation. There are huge variety of compounds that are researched upon for attacking the biofilms, belonging to various classes of anti-biofilm (See Fig 3 to the right). perhaps the most publicized among them is the example of Staphylococcus epidermidids, producing a factor called Esp that can inhibit Staphylococcus aureus. Read my previous post here.

      A recent paper published in nature brought into my attention a compound called acyldepsipeptides (ADEPs) representing a novel class of drugs targetting ATP-dependent peptidase caseinolytic protease P (ClpP). ClpP has a central role in bacterial functioning by selective processing of protein by transcrip-tional regulation or remodelling of the proteome.

Fig 4: Caseinolytic protease P

            There have been previous papers suggesting that ADEP 4, a chemical derivative of ADEP1 (Factor A) can switch the ClpP controls and lead to activation which causes uncontrolled degradation of proteins. In the current paper, the authors noted that the non specific ClpP activation had lead to non specific degradation of almost 400 different proteins thereby self destructing the cells. How does that connect with the biofilm? This takes me back to the argument I posted above. Biofilm relies on active cells to coordinate with the persister cells. By atacking the dormant and persister cells the coordinated functioning is disrupted. The authors noted that mutants arose easily, thus elimating the chance of using this as a stand alone drug. But when combined with another antibiotic (in this case rifampin), they were able to show that the combination worked fantastic. In a sense you could argue that ADEP4 is not a Anti-biofilm but it does treat the chronic biofilm based resistance. Thats a breakthrough.

        If you throw a google search for "ADEP4 and ClpP", you will find multiple papers showing that it targets various different pathways such as attacking the FtsZ which is involved with cell division. Let me remind you, ClpP is a central protease, and when uncontrolled it can degrade almost everything. So, effecting anything is not surprise. The best edge is that it attacks dormant persisting cells.

Yurtsev EA, Chao HX, Datta MS, Artemova T, & Gore J (2013). Bacterial cheating drives the population dynamics of cooperative antibiotic resistance plasmids. Molecular systems biology, 9 PMID: 23917989

Kostakioti M, Hadjifrangiskou M, & Hultgren SJ (2013). Bacterial biofilms: development, dispersal, and therapeutic strategies in the dawn of the postantibiotic era. Cold Spring Harbor perspectives in medicine, 3 (4) PMID: 23545571

Gersch M, List A, Groll M, & Sieber SA (2012). Insights into structural network responsible for oligomerization and activity of bacterial virulence regulator caseinolytic protease P (ClpP) protein. The Journal of biological chemistry, 287 (12), 9484-94 PMID: 22291011

Conlon BP, Nakayasu ES, Fleck LE, Lafleur MD, Isabella VM, Coleman K, Leonard SN, Smith RD, Adkins JN, & Lewis K (2013). Activated ClpP kills persisters and eradicates a chronic biofilm infection. Nature PMID: 24226776

Sass P, Josten M, Famulla K, Schiffer G, Sahl HG, Hamoen L, & Brötz-Oesterhelt H (2011). Antibiotic acyldepsipeptides activate ClpP peptidase to degrade the cell division protein FtsZ. Proceedings of the National Academy of Sciences of the United States of America, 108 (42), 17474-9 PMID: 21969594