New Antibiotics, Biofilm Inhibitors, Vitamin Deficiency

I was not expecting my recent reading of an article on femtosecond reaction kinetics to produce another discussion of quorum sensing, biofilms and vitamins. The idea behind the article was to identify new targets for drug design based on the ephemeral transition states that occur as enzymes bind substrates, stabilize transition states and yield product molecules. Drugs that mimic the transition states make good enzyme inhibitors. One of the target enzymes for the control of disease is an enzyme, MTAN, involved in the synthesis of quorum sensing molecules that orchestrate the construction of common biofilms. The idea is to inhibit MTAN and also avoid selection for antibiotic resistance. Unfortunately, targeting quorum sensing molecules also may produce vitamin deficiencies, since many of these molecules, in this case vitamin K, are also quorum sensing molecules.

Drugs have too many Side Effects
Specificity in the binding of molecules to the thousands of proteins that are coded by the ca. 20,000 human genes depends on a very tight fit between the molecular "key" and the binding site "lock" of the protein. Just as in physical world, a small key/drug molecule with limited surface detail is not as safe/specific as a larger key with many surface features, and a larger lock/enzyme active site that is harder to pick/has fewer interactions with random enzymes. Unfortunately, most drugs are small molecules with limited surface features that make them like molecular skeleton keys that produce many side effects by interacting with unintended proteins/enzymes.

Transition States are more Specific
A recent focus on drug research is to exploit molecular computation and modeling to design molecules that will bind to the part of an enzyme that actually participates in binding substrates and catalyzing chemical reactions. These designed molecules can interact with an expanded region of the enzyme and bind more strongly than the normal substrate. The designed molecules can be very effective inhibitors that will not react as nonspecifically as inhibitors identified by trial an error, e.g. statins.

Biofilm Inhibitors are Targets for Antibiotic Development
The enzymes involved in the synthetic pathways of biofilm quorum sensing signals have been identified and powerful inhibitors of some of these enzymes have now been designed and synthesized. These inhibitors are very effective in inhibiting biofilm formation by some common bacterial pathogens (and essential gut flora.)

Biofilm Inhibitors will also Block Vitamin Production in Gut Biofilms
The new biofilm inhibitor antibiotics may have enhanced specificity, but they target enzymes that also provide essential functions in biofilms that are needed for healthy gut and immune system function. Many of the vitamins that are produced by gut flora are also quorum sensing signal molecules in healthy gut biofilms. Thus, blocking MTAN to block biofilm formation of a pathogen, will also block gut synthesis of vitamin K, which is made in gut bacteria using the MTAN pathway. These inhibitors would be expected to be particularly damaging to the specialized gut flora of breastfed babies, since these gut bacteria are known producers of vitamin K.

Osteoporosis

Bone density is based on the balance between bone production and demineralization. Inflammatory cell signaling is required for release of calcium. Muscle building exercise favors increased bone density.

Newborns do not have fully formed bones in their limbs. The reason that milk has so much calcium, is that babies mineralize their cartilage bone scaffolds after they are born. Cartilage is made by chondrocytes (sisters of blood vessel endothelial cells and fat adipocytes, with the same stem cell parents) and the chondrocytes will continue to burrow through existing cartilage and make new cartilage, if mineralization does not take place. The cells that synthesize bone are called osteoblasts. They adhere to a framework of cartilage and begin to secrete collagen I, the major protein of bone and osteocalcin, the calcium binding protein that initiates the deposition of hydroxyapatite [Ca5(PO4)3(OH)]. As the bone forms, the osteoblasts become trapped in lacunae within the bone and stop secreting osteocalcin and begin to secrete hormones in response to the mechanical stress on the bone.

Bone is degraded by osteoclasts that colonize the completed bone after migrating from bone marrow. The total bone mass and density is determined by the dynamic balance between the deposition of bone by osteoblasts and disassembly of bone by osteoclasts. Approximately 10% of bone is being remodeled at any time and the porus trabecular bone in the pelvis, hips, wrist and spine is most actively remodeled. If there is an imbalance that leads to a bone deficit, it usually shows in weak trabecular bone.

Problems with low bone density, i.e. osteoporosis, can result from decreased estrogen (menopause), inadequate vitamin D/sunlight/dietary calcium, or medication, e.g. heparin or warfarin.

The ability of heparin to cause osteoporosis with prolonged use caught my attention. Heparin is anti-inflammatory and inflammation reduces heparin production. Thus, the inflammation caused by high blood glucose levels in diabetics results in loss of heparin production in kidneys and loss of protein from the urine. If heparin causes loss of bone mass, then it might be decreasing inflammation that is needed for bone accumulation.

Osteoclasts are activated by the RANK (receptor activator of nuclear factor κB) system. As the name states, RANK is a receptor that activates the inflammatory transcription factor NFkB. The cytokine that binds to RANK is the corresponding ligand, RANK-L, which is related in structure (and function) to TNF. RANK-L is secreted by osteoblasts, binds to RANK on osteoclasts, activates NFkB and stimulates bone demineralization. A protein called osteoprotegerin, is a soluble receptor of RANK-L that binds the bone and immobilizes the RANK-L and keeps it from activating osteoclasts.

Heparin could interact with many of these components. For example, the binding of RANK and RANK-L is mediated by heparan sulfate proteoglycans. The heparin deficiency that usually accompanies inflammation, and in this case excitation of osteoclasts, could be decreased by administration of heparin. Thus, demineralization would result in osteoporosis.

Warfarin-based osteoporosis could be based on upsetting vitamin K metabolism in osteoblasts. Vitamin K recycling is inhibited by warfarin and vitamin K is needed for a special modification of glutamic acids in particular proteins, such as osteocalcin. The action of osteocalcin in binding calcium is based on three glutamic acids that have been carboxylated using vitamin K. This is shown in the figure as three green calcium atoms bound to red dicarboxylic glutamic acids. You can also notice that the osteocalcin also has a substantial heparin binding domain (blue) at the top. Thus warfarin could cause osteoporosis by disrupting mineralization.

When I was trying to figure out the warfarin/osteoporosis relationship, I tried to find protein structures in the NCBI data base, which had warfarin bound. All I found was warfarin bound to human serum albumin, the protein that carries warfarin and many alkaloids through the blood. I was always suspicious of the use of heparin and warfarin somewhat interchangeably in many different settings in which the mode of action was assumed to be anticoaggulation of blood. I was not surprised when I found that the aromatic rings of warfarin (oxygens in red) were bound to arginines (blue) in a ligand-binding pit on the serum albumin.

A practical note on osteoporosis is that this disease is an exception to many of the degenerative and autoimmune diseases that are based on an inflammatory diet. Osteoporosis is more similar to the problem of gut injury by aspirin. Aspirin blocks COX-2 the enzyme that produces inflammatory and anti-inflammatory prostaglandins from omega-6 and omega-3 fatty acids, resp. Taking aspirin can block inflammation, but the integrity of the lining of the stomach and intestines requires inflammatory prostaglandins, so aspirin can also lead to a bleeding gut. Osteoclasts require NFkB signaling and other aspects of bone production may also require an inflammatory environment. This may explain why corticosteroids also lead to osteoporosis.

Deposition of bone is stimulated by weight bearing exercise that is consistent with the anti-inflammatory lifestyle.