Posts Tagged ‘biochemistry’

To live and function the human body needs energy, the majority of which is produced by the electron transport chain.  The end products from these enzyme catalyzed reactions are oxidized by the oxygen that you breathe and converted into water.  At the center of this complicated process is an incredible  protein that selectively transports oxygen to tissues in need and releases it on demand.  Hemoglobin is a protein carried by red blood cells that has selective affinity for iron, a metal critical to proper function of the body.  The importance of this protein is exemplified by what happens when it is broken.  Sickle Cell Anemia, for example, is caused by a mutation in the gene that codes for the protein.   In this case, the change of a single amino acid (glutamic acid to valine) damages its functionality such that the average life expectancies of people with this disease are only 42 years in males and 48 in women (S).  During this time, those afflicted also experience a host of quality of life maligning health problems, like chronic pain, increased risk of infection and heart disease and vaso-occlusive crises that occur when the misshapen blood cells block blood vessels.

Considering the structure, hemoglobin is a large protein made of four polypeptide chains, sewn together into a tetramer.  There are 2 β chains and two α chains, each of which having a net-like porphyrin ring system.  In human red blood cells, an iron atom is placed in the center of the ring structure, creating a coordinated system called a heme group.  The iron atom is the star of the system and makes the binding of oxygen possible.  It is in the +2 state and has octahedral symmetry, allowing 6 ligands to bind.  The 4 nitrogen atoms of the ring bond equatorially holding the Fe+2 in place, while from the bottom, a histadine amino acid from the protein super structure locks the Fe+2 atom in place.  The open top position is reserved for O2 binding, but in its absence a molecule of water usually takes its place in normal circumstances.

3D images showing the positions of the porphyrin ring, iron and histidine in the heme group. Nitrogen atoms are in blue, iron in red and carbon in the usual grey-black. (3D images courtesy of http://www.3dchem.com By all means check out the structures for yourself using their tremendously useful java based web tool!)

This same system is common throughout other enzymes and respiratory systems.  In humans, Cytochrome C  of the electron transport chain has a similar structure, except that the 6th (top) ligand is a methionine group.  The protein in this case is designed to transport electrons rather than oxygen molecules.  Myoglobin, which is found in muscles and also used for O2 transport, is structurally different, but utilizes a single porphyrin ring system, rather than four.  Enzymes, such as catalase and peroxidase,  also contain Fe manipulating systems similar to the above.  In other kinds of organisms too, the porphyrin ring is utilized in a variety of situations and complexed to many different metals depending on the conditions and needs of the creature involved.  Photosynthetic plants, for example, utilize the same ring, but the metal is magnesium.  Further, some bacteria are also known to use copper as the porphyrin metal of choice.

To make full advantage of this heme system, the binding of O2 in red blood cells is facilitated by a buffer system.  The concentration of any of the components of it increase or decrease the binding affinity of O2 at the hemoglobin binding site.  Proton (H+), CO2, Cl-, and 2,3-Bisphosphoglycerate (BPG) concentrations all have a role in the binding and release of O2 from hemoglobin.  For example, in tissues where the pH (H+ concentration) is acidic and the partial pressure of CO2 is high, the binding affinity of O2 at the binding site will be lowered and will induce hemoglobin to release its contents.  In the lungs, however, the O2 concentration is high compared to that of CO2, facilitating O2 binding.  Normally, BPG is found in equal amounts to hemoglobin, but in situations where O2 is in short supply this balance is undone by the increased production of BPG.  With BPG, binding to one of the active sites reduces the O2 binding affinity by about 25 times, thus when BPG concentration is high it pushes for a release of O2 into tissues that need it.

The larger Fe staggers the planar porphyrin ring, where as the smaller version fits better, contributing to stability.

Aside from outside effects promoting binding, there are effects coming essentially from the design of the system itself that have to be considered as well.  The question of why iron and not some other transition metal is of special relevance here.  Using iron as the central metal, in this case, yields benefits in terms of performance and binding specificity to oxygen.  Cobalt, for instance, is used in similar systems like those of vitamin B12’s corrin ring, but while both cobalt and iron contain d orbitals that could bind, only iron allows for the perfect balance between size and binding specificity in this system.  While unbound, the Fe+2 atom is just a little too large to fit into the normally planar porphyrin ring.  In this case, it is in a high spin state where the molecular orbitals are further away from the atom, giving it a larger size.  The high spin state is larger, because the Pauli exclusion principle prohibits the atom’s 3d electrons from getting too close to one another due to repulsions.  Thus, additional space is needed to house the electrons in orbitals further away.  However, when the Fe+2 binds to an oxygen molecule the electrons can be shuffled into orbitals that are closer to the atom.  Its orbital symmetry changes to a low spin symmetry and CLICK ! the Fe+2 shrinks just enough to fit snugly into the porphyrin ring system.

A silly, but useful comparison.

This part also contributes to a critically important finding: that the binding of O2 is cooperative, in that the binding of one O2 molecule will facilitate the binding of another until all four spaces are filled.  It has been experimentally determined that the binding energies (the Ka) are increasingly smaller for each molecule of O2 bound to hemoglobin.  This happens, in part, because of the protein’s structure.  When the O2 binds and the Fe+2 clicks into place, it pulls on the histadine residue below it, stretching the other protein superstructure bonds.  This pulls slightly on the other 3 Fe+2-histadine bonds.  Much like those dancing string toys, pulling on the string at the bottom causes the toy’s arms and legs to move in a concerted action, which is similar in a way to the physical reaction of the other binding sites.  The additional pulling on the other histadine residues facilitates binding of the other three, such that the binding energy is progressively reduced with each binding until all four slots are filled.

Other structural contributions also play a large role in binding specificity.  Above the plane of the porphyrin molecule lies another histadine residue that physically blocks the strongest and most effective bonding interactions from occurring.  Since the Fe+2 atom is locked into place, the best bonding interactions would come from ones that provide the most overlap of their molecular orbitals, which are those that are end-to-end.  However, with the histadine in the way, these are prevented from occurring.  This is a good thing, because strong covalent interactions in enzymatic reactions, like those seen in the binding of carbon monoxide (CO) for instance, are usually toxic and are difficult to break under normal conditions.  For head-to-head binding to CO, the interaction is estimated to approximately 1000 times as strong as those between O2, illustrating its toxic potential.  In this case, the CO-Fe binding is still strong, but not so much as to completely block removal.  People who have suffered CO inhalation are often given pure oxygen in an attempt to out pace CO binding and ensure that the person continues to have a supply of oxygen.  This hindered binding is also helpful in normal activity as well, since the binding symmetry to O2 is bent as well it further facilitates it’s release into tissues in need.

Yes, it’s about iron again, but it’s quite interesting stuff.

{sources available upon request}


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A little over 40 years ago it was discovered that bacteria utilize a class of metal chelators called siderophores to capture iron from their environments.  Iron is an important element for the growth and development of most kinds of bacteria.  It is used as a critical element in electron transport chains for energy production, the removal of dangerous reactive oxygen species and the functional element in the reactive sites of many important enzymes.  The finding was critically important to the field of medicine, as the iron scavenging activities of pathogenic bacteria are most often detrimental to the host.  Even though humans and other animals have developed sophisticated systems to sequester iron and make the body inhospitable to these bacteria, likewise they have developed a variety of means of out-competing their hosts for the valuable element.  Neisseria gonorrheae and N. meningitidis, for example, have evolved the ability to directly capture iron containing lactoferrin proteins from their human hosts, a testament to our continued co-evolution (1).  Still others have relied upon producing their own iron scavenging siderophores to fish out this valuable metal from fluid and protein sources.  Escherichia coli , for example, are known for producing enterobactin and have one of the most effective iron scavenging systems known, which at biological pH easily out competes endogenous defenses for iron.

Recently, it has been noted that these compounds are of critical importance to bacterial growth, especially in the ultra-low iron concentrations of bodily tissues.  Rather than tighten their belts in the toughest of times, some kinds of pathogenic bacteria turn on

'Like dissolves like': different kinds of Mycobactin are used in different mediums. The long aliphatic chain endows fat solubility to the molecule, allowing it to shuttle through the waxy mycobacterial membrane easily.

these scavenging systems to forcibly acquire the iron needed for growth.  Mycobacterium tuberculosis produces several siderophores, called mycobactins, that are medium specific in their activities.  The two differ by a water soluble or fat soluble group attached to the siderophore skeleton.  Water-soluble mycobactin T is released into aqueous mediums, whereas fat soluble mycobactin T is designed to take pirated iron across the waxy mycobacterial cell membrane (2).  When iron is in good supply, however, production of these is unnecessary and is down-regulated to conserve valuable energy and resources.  Below the level of production of these siderophores, however, lies a regulated system of control.

Generally siderophore production is controlled by gram negative bacteria’s “Fur” and gram positive’s “DtxR” systems, which have  transcription elements that are bound by iron.  Thus, when intracellular iron concentrations fall below a threshold (approximately 10^-6 M for many pathogenic bacteria) the iron lynchpin holding back the transcription element is gone, activating the siderophore production system.  In 1999, researchers at the University of Queensland showed that Mycobacteria require the production of siderophores for growth in human tissues and macrophages (2).  They used genetic engineering techniques to remove the instructions for the enzyme MbtB, which is a critical component of mycobactin synthesis.  MtbB effects the final step in mycobactin synthesis, the coupling of a salicylic acid group to the siderophore’s finished structure.  After creating an MtbB knockout strain, its ability to produce siderophores was tested by an assay that measured the absorbance of the growth medium.  They used a colored dye compound that has a known affinity for iron in solution.  If a bacteria were to produce something that has a higher affinity for iron than the dye, this would be measured as a drop in absorbance, as the siderophore would compete with the dye for the iron.  They found that after comparing these bacteria against wild type strains that they were unable to produce siderophores and the deficient strains experienced retarded growth both in plate medium and in live macrophages (in vivo vs. in vitro tests).

The understanding of how important these chemicals are for bacterial growth has led to renewed attempts to develop antibiotics against them.  In the late 80 and early 90’s the ‘trojan horse’ tactic of using siderophore-antibiotic conjugates and piggybacking them into a cell began to bear fruit with successes being discovered in a wide variety human diseases (3)(4)(5).  One group of scientists developed conjugates using the carbacephem antibiotic, loracarbef.  They found that the mixed catecholate-hydroximate siderophore they used gave the conjugate compound 2,000 times more potency than the parent drug alone (6).  Though resistances to this tactic still developed, these are thought to leave the bacteria at a disadvantage, because the mutations hinder the siderophore uptake system rather than attack the antibiotics themselves.  This limits access to a vital nutrient and leaves the mutants more susceptible to iron starvation and hindered growth.

Though the trojan horse tactic has yielded positive results, there are opportunities for even greater exploitation.  Techniques involving small molecules that attack that actual production of siderophores could provide another avenue to beneficial therapy for these diseases.  These drugs, much like statins that block the enzyme HMG-coA, would block a critical piece of the siderophore production pathway.  In the particular case of mycobactins, the final step in biosynthesis is the attachment of a salicylate group to the mycobactin skeleton.  Researchers at Cornell published results in 2005 showing that inhibitors of the enzymes that accomplish this task are potent inhibitors of M. tuberculosis and Yersinia pestis (7).  They synthesized a compound, SAL-AMS, that closely resembled a reaction intermediate and measured its effect upon the growth of bacterial cultures in mediums of low iron concentration.  They found that it successfully inhibited the enzyme and drastically reduced bacterial growth in the cultures.  It was shown to have an IC50(*) of 2.2 ± 0.3 μM for M. tuberculosis and about 51.2 ± 4.7 μM for Y. pestis in an iron limited medium.  Though in mediums with high concentration of iron the chemical was ineffective against Y. pestis, but it was found that the chemical might have unknown inhibitory properties against M. tuberculosis, as:

“Salicyl-AMS (tested at up to 8 X IC 50) was not active against Y. pestis in iron-supplemented medium, in which siderophore production is not required for growth.  Under these conditions, salicyl-AMS (tested at up to 180 x IC50) did inhibit M. tuberculosis growth, albeit with an 18-fold increase in IC50 (39.9 ± 7.6 μM).  This suggests that, in addition to blocking siderophore biosynthesis, salicyl-AMS may also inhibit M. tuberculosis growth by other mechanisms.”

Furthermore, researchers at the university of Minnesota developed similar nucleoside inhibitors of MbtA, one of which ” rivals the first-line antitubercular isoniazid” in activity against the bacteria (8).  This tactic follows the same reasoning as SAL-AMP above, as the nucleoside inhibitors attack the same pathway to inhibit siderophore end production.  The research was centered around making logical functional modifications to known structures of inhibitors and choosing the most effective ones for further testing.

Comparison of the pathway intermediate, the Cornell inhibitor and one of the Minnesota nucleoside inhibitors.

These findings are coming just in the nick of time it seems, as certain drug resistant strains of M. tuberculosis have become big news recently.  Extensively drug resistant tuberculosis is a kind of tuberculosis that is resistant to at least two of the top line drugs used to normally treat it (typically isoniazid and/or rifampicin) and a member of the quinolone antibiotics (ciprofloxacin).  Tuberculosis is generally a challenge to treat in the first place, with treatments typically taking up to a year or more to complete.  The loss of the first line drugs and reliance upon second line increases the risk of side effects and patient noncompliance to the already long course of therapy.    This can further complicate the issue, as it could lead to the obsolescence of the few active  drugs used to treat the disease, because resistances to one drug are usually useful against the whole family of drugs.

β-lactamases typically attack the carbonyl in the β-lactam structure, destroying the ring. Nafcillin has a large group that hinders these enzymes from getting too close.

An example of this can be seen in bacteria that produce β-lactamases, as these strains are often cross-resistant to all unprotected β-lactam antibiotics.  Some  penicillins have been designed with bulky groups attached to the skeleton in an attempt to hinder these enzymes.  Nafcillin, with its large 2-ethoxy-1-naphthoyl group, is very effective at blocking these enzymes for the most part.  However, even this tactic has its limits as methicillin resistant Staphylococcus aureus (MRSA) and oxacillin resistant Staphylococcus aureus (ORSA), both have developed resistances against these drugs such that, “From 1999 through 2005, the estimated number of S. aureus–related hospitalizations increased 62%, from 294,570 to 477,927 (9),” and “MRSA accounts for an estimated 12% of all nosocomial bacteremias, 28% of surgical wound infections, and 21% of nosocomial skin infections.  Infections secondary to MRSA result in excess costs of approximately $4,000 per patient per hospitalization compared with patients infected with methicillin-susceptible S aureus (MSSA)”(10)(11).

Since the discovery of penicillin, Alexander Fleming hypothesized that bacteria would develop resistances to the antibiotics used to treat them.  Now, more than ever, the development of new antibiotics must be pursued.  Human defenses have always provoked a counter-response from our pathogens, the most successful tactic selected out.  Much like the pathogens that infect us, we must ‘evolve’ a newer understanding of bacterial biology, which will offer us a foothold to better, more effective treatments.


(1) Genetics and Molecular Biology of Siderophore-Mediated Iron Transport in Bacteria


(2) The salicylate-derived mycobactin siderophores of Mycobacterium tuberculosis are essential for growth in macrophages

James J. De Voss, Kerry Rutter, Benjamin G. Schroeder, Hua Su, YaQi Zhu, and Clifton E. Barry III

(3) Design, Synthesis, and Study of a Mycobactin−Artemisinin Conjugate That Has Selective and Potent Activity against Tuberculosis and Malaria

Marvin J. Miller, Andrew J. Walz, Helen Zhu, Chunrui Wu,Garrett Moraski, Ute MÖllmann, Esther M. Tristani, Alvin L. Crumbliss, Michael T. Ferdig, Lisa Checkley, Rachel L. Edwards, and Helena I. Boshoff

(4) Species Selectivity of New Siderophore-Drug Conjugates That Use Specific Iron Uptake for Entry into Bacteria


(5) Siderophore-Based Iron Acquisition and Pathogen Control

Miethke M, Marahiel MA.

(6) Iron Transport-Mediated Antibacterial Activity of and Development of Resistance to Hydroxamate and Catechol Siderophore-   Carbacephalosporin Conjugates


(7) Small-molecule inhibition of siderophore biosynthesis in Mycobacterium tuberculosis and Yersinia pestis

Julian A Ferreras, Jae-Sang Ryu, Federico Di Lello, Derek S Tan & Luis E N Quadri

(8) Antitubercular Nucleosides That Inhibit Siderophore Biosynthesis: SAR of the Glycosyl Domain

Ravindranadh V. Somu, Daniel J. Wilson, Eric M. Bennett, Helena I. Boshoff, Laura Celia, Brian J. Beck, Clifton E. Barry, III, and Courtney C. Aldrich

(9) Hospitalizations and Deaths Caused by Methicillin-Resistant Staphylococcus aureus, United States, 1999–2005

Eili Klein, David L. Smith, and Ramanan Laxminarayan

(10) Baquero F. Gram-positive resistance: Challenge for the development of new antibiotics. J Antimicrob Chemother. 1997;39(suppl A):1–6.

(11) Kopp BJ, Nix DE, Armstrong EP. Clinical and economic analysis of methicillin-susceptible and -resistant Staphylococcus aureus infections. Ann Pharmacother. 2004;38:1377–1382.

(*) The IC 50 is the half maximum inhibitory concentration of antibiotics, a typical measure of effectiveness of the drug.

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First and foremost, cancer is a disease of broken genes. For as long as medicine has existed, cancer has defied our attempts to cure it. It is estimated that one in 3 people will experience cancer in their life time(1). More so, “greater than 60 years ago there were no treatments for children with leukemia that could cause remission of the disease, but today this is possible in about 96% of cases!”(2) Though we have made leaps in our understanding and treatment of cancer, the golden fleece: freedom from this oldest plague of man has long eluded us. Perhaps some day we will achieve this ultimate prize, but it seems for the time being we must be satisfied with our current progress. Here’s a few reasons why the Tigers still stalk us in the halls when Sally Kimball is away:

1. Biological Immortality and unlimited growth:

To keep cells fit and in good working order, ordinary cells are limited by how many times they can divide. This is known as the Hayflick limit. A cell’s DNA has a non-coding region at the end of the strand called the telomere, which can be likened to a docking station for the DNA replication machinery. Every time the strands are copied this machinery takes a small piece of the telomere leaving behind a smaller and smaller piece. Once the telomere runs out, the cell enters senescence, stops cell division and dies. Somatic cells have about 50 divisions in them before this happens.

In cancer cells, an enzyme called telomerase actively replaces these lost pieces of telomeres, allowing them to divide beyond the Hayflick limit and evade the natural cell death program. Normally, this limitation keeps a cell line’s genetic package healthy and mutations from accumulating. However, for cancer cells this is not a problem, as the mutations sometimes serve to provide a survival advantage over normal cells. The tumor suppressing genes Rb1 and TP53, for example, are known to have roles in controlling cell growth, but once they are damaged or turned off they allow a cell to break free of the systemic growth of normal cells.

Retinoblastoma protein (Rb), the protein produced by the Rb gene, does its work by prohibiting a cell with damaged DNA from replicating. When this situation occurs, it binds and blocks the transcriptional machinery in cells, keeping it from copying the genome and consequently, proceeding into the next stage of cell division. Many cancer cells have mutations to this gene. In fact, the protein produced by this gene was discovered in a kind of eye cancer called retinoblastoma. This should not be misconstrued as only affecting the eyes, however, as it is a significant regulatory protein in almost every cell in the body.

P-53’s main job is to protect the genome from mutation. It acts as a watchdog right before cell division, making sure that the DNA has been faithfully reproduced. If there is DNA damage, then P-53 can stop the cell cycle and activate DNA repair proteins that can hopefully fix the damage. If the damage is too extensive to repair, then it can also signal apoptosis, the cell’s death program. Without this protein functioning properly, the risk of developing cancer is increased greatly. More so, “greater than 50% of all human cancers contain a deletion or mutation of the TP53 gene” (3).

Mutations of these genes generally allow a cell unrestrained, unlimited growth and are a cause of the massive growth of cells, known as a tumor. In this situation, cancerous cells have an advantage over normal cells, in that they have easier access to nutrient resources from the surrounding tissues.  They will grow in size until they are limited only by the availability of resources. An interesting observation is that the inner portion of many tumors is lower in oxygen (hypoxic), than the outer portions. This is a direct result of Fick’s law of diffusion, which describes the flow of nutrients and oxygen from blood vessels into tissues. It shows that as a tumor grows increasingly larger, it becomes harder to provide cells further away from blood vessels nutrition. This is a natural limitation on cell growth and body structure, but tumor cells have a way to bend this rule, which is described in the next section.

2. Decreased dependence on natural growth factors:

Cancer cells are like ‘rebels without a cause’, the James Deans of human cells. Normally, the signals for growth are usually sent by the endocrine/paracrine system. Platelet derived growth factor, epidermal growth factor and insulin-like growth factor are just a few regulatory chemicals that trigger cell division and cell proliferation. The collective mass of these signals make up a system that tells cells when and under what circumstances to begin division. To have a body and the organizational benefits that it brings, individual cells must perform the tasks they’ve been assigned in the developmental process. Cancer cells, however, produce their own growth factors, often self signal and/or develop a means to receive more signaling. Since they require no outside signals for growth, they are not limited by this systematic control. They effectively work outside the system to effect their own self centered proliferation, at the expense of the body supporting them.

One example of this is an activity called angiogenesis, the production of new capillaries and blood vessels from main branches. Normally, fetal tissue relies on the function of vascular endothelial growth factor (VEGF) to produce new capillaries in its rapidly growing tissues. More capillaries means that a greater volume of nutrients and oxygen can diffuse to important tissues. In adults this process is usually indicative of cancerous activity, with wound healing and the female reproductive cycle being the major exceptions. Tumors produce VEGF to get around the limitations posed by Fick’s law of diffusion. Tumor growth is limited to the short distance nutrients and oxygen can diffuse through tissues. Without the production of new blood vessels the mass of tumor cells would slowly starve.

VEGF has been found in almost every kind of human tumor and is at peak concentration around newly formed blood vessels and the hypoxic, inner regions of the tumors. Research has shown that by blocking VEGF by binding it to monoclonal antibodies, one can suppress tumor growth in mice(4). Other efforts are currently targeting VEGF receptors that are specific to kinds of tumors. Inhibition of a VEGF receptor called FLK1 has been similarly shown to reduce growth of tumors of certain cancer cell lines such as fibrosarcoma cell line HT-1080(5).

Another method cancer cells use to circumvent normal regulation involves the over expression of epidermal growth factor receptors (6). Normally, epidermal growth factor signals limited cell proliferation and its receptor is usually expressed in epithelial cells. However, cancer cells over-express it allowing for greater than normal signaling and as a result, increased proliferation. This over-expression is usually indicative of a poor prognosis, a situation occurring in many advanced stage cancers. In certain types of breast cancer, which comprise a little more than 20% of the total number of cases, the EGF receptor uses a protein called ‘HER’ to pass on the growth signal inside the cell. The bio-engineering giant Genentech recently made headlines for passing its drug herceptin through clinical trials. This is a monoclonal antibody that specifically targets HER proteins. Since cancer cells that over express EGF receptors have a greater preponderance of this protein, they will be targeted for destruction by the immune system specifically over ordinary cells.

Recent drug advances have allowed for the selective targeting of these receptors, effectively blocking this excessive, cancerous signaling. Specifically, several new tactics have been devised to target these receptors and block their activation. Recent successes with monoclonal antibodies, selective toxins and small molecules that block receptor signaling activity have made it into general therapy. Monoclonal antibodies are specifically targeted to these receptors to bind and block them from being activated. Toxins can take a variety of roles to block receptor activity, whether as allosteric inhibitors or by covalently binding to the receptor’s active site. Essentially, the end result is the same with these two kinds of weapons. With small molecule drugs, the tactic is usually to inhibit signal transduction from the receptor. The drug erlotnib is an example of this, in which it blocks a critical signaling component so signals can’t be sent from the receptor. Erlotnib is from a class of drugs called tyrosine kinase inhibitors, that have found great usefulness as selective inhibitors of these kind of over-expressed tumor receptors.

3. Loss of anchorage in tissues and cell adhesion:

Normally, cells will undergo apoptosis once they become separated from their host tissue. It’s tricky to grow normal cells outside of their home tissues, because they communicate with neighboring cells and require paracrine interaction for normal function. However, cancerous cells don’t require these regulatory signals and can be grown in solution or on agar medium. Normal cells are usually held in place by a matrix of proteins and structural elements, as well as being linked directly to neighboring cells by physical junctions. These structural components often give important regulatory information to a cell. The point where this breaks down is the beginning of what is called metastasis, the ability of a cancer cell to travel to other tissues, invade them and start a tumor there.

Tumor cells express a set of metal containing enzymes called matrix metalloproteinases (MMPs). These are responsible for the matrix degradation seen in metastatic cancers. They chop away at the extracellular matrix holding them in place, eventually freeing the cells to do damage elsewhere. The expression of these proteins is considered indicative of progression to metastasis, because ordinary adult cells do not express them. High levels of matrilysin (MMP-7), for example, is a known indicator of prostate cancer. Additionally, MMPs are known for attacking cell to cell adhesion proteins like E-cadherins, β-catenin and α-catenin. MMP-3, also known as stromelysin, is known for cutting apart E-cadherin cell junctions. The loss of their function is a known cause of tumorigenicity and cancer cell invasiveness.

Once a tumor cell escapes it has two routes it can metastasize through: blood or lymphatic. The tumors often have patterns of invasion that are indicative of their tissue origin. For example, tumors of the head and neck are often spread through regional lymph nodes (7). Tumor cells manufacture special tools they use to attach to new host tissues called invadopodia. These are similar in a way to bacterial pilli in that they contain various proteases and adhesive proteins that aid in attachment to the new cells and help the cell cross barriers.

The invadopodia bind to membrane components such as laminin, fibronectin, type IV collagen, and proteoglycans. Normally, these interact with receptor regulatory proteins called integrins that send regulatory signals to the cell. Cancer cells often change the binding preferences of their integrin receptor subunits to match those of degraded extracellular matrix proteins. The new types are thought to match the pieces damaged by MMP degradation and are often associated with invasive, metastatic cells (8). Binding to these pieces functions as a discovery signal that the cell has found a place that is susceptible to invasion. The fact that cancer cell integrin expression has changed in a distinct way, might also reveal a way to specifically target these cancerous cells. This could lead to therapeutic advances targeting the most aggressive, late stage types of cancers.

4. Loss of sensitivity to apoptotic stimuli:

Apoptosis is a form of cell death that is essential for tissue remodeling during embryogenesis and maintaining the number of cells in adult life. It functions to cull damaged, nonviable and potentially dangerous cells by acting as a failsafe that kills a cell when it has acquired too many mutations or unusual activities. It functions through cellular signaling pathways to block cell mitochondrial function, which eventually leads to the degradation of critical cell components and then ultimately, death.

The apoptotic program can be divided into three phases: initiation phase, decision/effector phase and the degradation/execution phase. The initiation phase typically is a response phase to outside stimuli, like death receptor ligands, or to inside stimuli like DNA damage. The decision/effector phase works to clarify the signal and open the door for action. Changes that occur in mitochondrial membrane permeability signal the end: the release of an key respiratory protein called cytochrome C into the cytoplasm. The degradation/ execution phase sees the activation of proteases and nucleases, which degrade proteins and nucleic acids, respectively. The key target is the mitochondrion, as well as other important cell machinery. As this is the main power source for the cell, this is typically fatal for it.

Apoptosis acts through signal transduction pathways controlled by receptors of the Fas cluster (CD95), tumor necrosis factor receptor 1 (TNRF1) and death receptors 3, 4 and 5 (DR 3, 4, 5). Each of these kind of receptors contains a special amino acid sequence called the “death domain” that functions as a specific binding site for special death signaling proteins. These proteins pass the baton on to other proteins in the chain, much like a relay. Eventually they activate the main downstream effectors, the actual ‘doers’ of the hard work, the caspases. Caspases are a family of cysteine proteases that are responsible for much of the cellular degradation mentioned earlier.

The point of no return in this deadly relay is the release of cytochrome C, which is controlled by a set of proteins in the mitochondrial membrane that regulate its release. The first of these was identified in a cancer called B-cell lymphoma and was aptly named the B-cell lymphoma-2 (Bcl-2) protein. This particular protein is a negative regulator of apoptotic signals. This group of regulatory proteins contains both positive (Bax, Bak, Bik, Bid) and negative regulators (Bcl-2, Bcl-x) of these signals. Positive regulators encourage apoptosis, whereas negative regulators discourage it. The key factor determining cytochrome C release is the relative ratio of positive and negative signals.

Cancer cells evade apoptosis by overexpression of Bcl-2. The Bcl-2 gene is usually moved to a different, more active location in the chromosome (typically the IgH promoter, a highly active portion). With more of this protein floating around, the pro-apoptotic signals are drowned out and sensitivity to them is significantly reduced. Lastly, cancer cells suppress apoptotic receptors by mutations that affect binding and proper function of the pathway. Slight mutations to the receptors or relay proteins can drastically affect the ability of the apoptotic signal to reach the critical stage.

5. Genetic instability:

Genetic instability is considered a major causative problem in cancers and one that we have few effective weapons against. Our battle strategy is reactive and revolves around destroying the cells that display these characteristics when they become a noticeable problem, which is often the time with the least efficacy in treatment. A truly proactive strategy will require advances in technology and bioengineering that will enable us to manipulate our genetic code, to edit out or silence problematic parts and correct mutations when they occur. The promise of gene therapy holds the hopes of many to pick up and wear that mantle, but these experiments are a ways off from useable therapies. Today though, like any good general, we make do with the tools we have on hand.

Cancer cells are often distinguished from normal cells by the loss or gain of a specific chromosome, or even the accumulation of an entire extra set of chromosomes. Extra chromosomes can provide cancer cells with extra copies of growth promoting genes. They can utilize these extra copies to amplify ordinary levels of signaling, causing the increased growth response and proliferation seen in tumors. Mutation is common in human tumors where changes at the sequence level can affect growth controlling genes, DNA repair or decreased fidelity during replication. Furthermore, it has long been known that misreplicated DNA can provide a causative explanation for some inherited cancer prone syndromes.

Translocations of genetic material from different chromosomes can lead to the abnormal gene expression seen in cancer. Chromosomal rearrangements, for example, are known to cause cancers like chronic myelogenous leukemia (CML) and Burkitt’s lymphoma. CML is caused by an abnormal chromosome, called the Philadelphia chromosome (named after two scientists from Philly). In CML, two unrelated genes from chromosomes 9 and 22 switch places and parts of the genes are spliced together. This causes a new protein called “BCR/abl” to be produced that remains constantly active, driving cell division by activating cell cycle control proteins continuously and inhibiting DNA repair responses.

Fortunately, since CML is caused by a single protein, it represents a good target for drug based therapeutics. New tyrosine kinase inhibitors, like imatinib, are used to block BCR/abl’s activity and has become the standard treatment for the disease over previous less specific antimetabolite chemotherapies and bone marrow transplants. This drug represents a different level of complexity in the treatment of the disease. An intimate molecular understanding of the disease, lead to the search for drugs that could effectively inhibit the protein’s activity. Drug designers searched protein libraries, through thousands of possible candidates to find the best ones, eventually coming up with imatinib.

Imatinib is representative of a new kind of drug design, where a drug is designed from known specifications of the biological machinery. Specific understanding of the processes involved will ideally improve drug activity and binding specificity and hopefully open the door to more effective therapies. Even though it can not cure this disease, it makes management of the disease possible and improves the lives of patients over that of previous chemotherapy based treatments.

6. The Loss of Cell Cycle Control: Until next time…

Some sources:

(1)http://en.wikipedia.org/wiki/Cancer (In epidemiology section.)

(2) Gale encyclopedia of cancer, pg. 11 intro, Helen A. Pass, M.D., F.A.C.S.

(3) http://en.wikipedia.org/wiki/P53

(4) ask me later, lost it…

(5)B. Millauer, M. P. Longhi, K. H. Plate, L. K. Shawver, W. Risau, A. Ullrich, and L. M. Strawn, Cancer Res., 56, 1615-1620 (1996).

(6) 60. N. Ferrara, and W. J. Henzel, Biochem. Biophys. Res. Commun., 161,851-858 (1989).

(7) Burger’s Medicinal chemistry and Drug Discovery 6th ed., vol. 5 Chemotherapeutic agents. Wiley 2003. Pg12

(8) Burger’s Medicinal chemistry and Drug Discovery 6th ed., vol. 5 Chemotherpeutic agents. Wiley 2003. Pg13

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