Precision-Guided (MALT-Targeting) Mucosal Vaccines

          That’s an extremely bold claim, so we invite any and all experts to approach it skeptically, and see if they can find any flaws in the path we have identified, or in any of the steps we’re using to explore and travel down that pathway. If you think you have spotted a flaw . . . or, if you think you might have figured out a better way to do something we’re doing . . . or, if you want to contact us, find out more, and possibly consider whether you might want to get involved at an early stage, while things are still wide open – feel free to contact us, via the last page of this website.

          Our approach starts with a crucial aspect of how immune systems function, in all vertebrate animals. Immune cells distinguish between “self” particles (which must be tolerated), versus “non‑self” invaders (which must be defended against) by using specialized “receptor proteins”, which have an exposed portion on the outer surface of the cell, and an internal portion, inside the cell.

          The details and mechanisms of how immune cells perform that task, and actually distinguish between “self” versus “invader”, (while also figuring out how to tolerate the “good” bacteria that help digest food) are extraordinarily complex; however, people don’t need to understand those details. Instead, the point that needs to be understood, for now, is simple: immune cells use “receptor proteins” on their surfaces, to distinguish between “non‑self” pathogens, versus “self” cells.

          So, that led to a first question: would it be possible to create new types of vaccine particles having “transport peptides” attached to their surfaces, which might be able to increase the speed and potency of how those modified vaccine particles are taken in and processed? Or, stated in alternate terms, would it be possible to “trick” and “fool” one or more types of immune cells into “believing” that vaccine particles – if those particles have “pathogen-signaling peptides” attached to their surfaces – are actually dangerous and important pathogens, which need to be responded to, and defended against, as rapidly as possible?

          That initial question led to two follow‑up questions:

          1. Which immune cells would be the best immune cells to “target”, if we began looking for ways to create vaccine particles that would be recognized rapidly by those “targeted” immune cells, and pulled into those cells, and processed in ways that will form antibodies?

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          2. What would be the best way to identify a set of “pathogen-signaling transport peptides” which could “trick and fool” a set of targeted immune cells into “believing” that vaccine particles carrying those “transport peptides” are dangerous and important pathogens?

          The best answers we’ve been able to come up with so far – and, this is where we challenge any experts to see if they can come up with any better answers (and, any experts are not just allowed, but encouraged, to use any AI system they know how to use, to help them analyze what we are doing) – can be summarized as listed below.

          Each header (in red, below) is a link; if you click on it, it will take you to a page with more information on that topic.

 

1. THE BEST TYPES OF IMMUNE CELLS TO TARGET ARE IN SURFACE-MOUNTED MUCOSAL LYMPH NODES CALLED “MALT PATCHES”

 

          We believe the best way to administer vaccines is by directly applying topical mucosal vaccines (i.e., with the vaccine particles suspended in a nasal spray, or embedded in lozenges or lollipops, rather than injections) to a set of specialized lymph nodes that are fully exposed, and directly accessible, on the outer surfaces of mucous membranes. Those types of lymph nodes are called “MALT patches”, and they include the tonsils and adenoids, in humans and other large animals.

          The immune cells in MALT patches offer two crucial advantages, over any other route we know of: (1) the particles in topical mucosal vaccines can contact those immune cells immediately, directly, and in large numbers, in ways that may lead to the fastest-acting vaccines ever created (which could be especially useful when an epidemic is gathering momentum); and, (2) if vaccine particles are pulled in via MALT patches, they can trigger and drive the formation of not just one, but two crucial types of antibodies. In addition to the Y-shaped internal (IgG) antibodies that injected vaccines can trigger (and which everyone has already heard about), if vaccines enter the body through a MALT patch, they can ALSO trigger the creation of an entirely different class of “secreted mucosal IgA antibody dimers”. Almost no one (other than physicians, and immunologists) has ever heard about those types of secreted antibody dimers, but they have the potential to provide huge benefits that have not been available before now, especially against “upper respiratory tract” infections (such as COVID, influenza, pneumonia, etc.), and sexually-transmitted diseases (such as herpes, AIDS, hepatitis, gonorrhea, etc.) Secreted mucosal IgA antibody dimers are described in more detail HERE.

 

2. THE BEST WAY TO IDENTIFY POTENT “MALT-TARGETING TRANSPORT PEPTIDES” IS BY USING A “SCREENING TEST” ON A “PHAGE LIBRARY”

 

          We believe the best way to identify peptide sequences which can be used as “MALT-targeting transport peptides” – which can potently trigger intake and processing – of vaccine particles having those transport sequences, on their outer surfaces – by immune cells in “MALT patches” (i.e., on the outer surfaces of surface-mounted lymph nodes – is by screening hundreds of millions of “candidate” or “contestant” phages, from a preparation called a “phage display library” (or simply a “phage library”).

          Phages (originally called bacteriophages) and phage libraries are described HERE. It took decades to develop good “phage display libraries,” but now, anyone can buy one for less than $1000. The most widely-used versions use “filamentous” phages which are comparable to a flexible arm, with five long finger-like “tentacles” extending out from one end, which hunt for and grab hold of a bacterial cell, which a phage will try to infect, and hijack, to make more phages. All of the billions of different phage particles in a library are identical, EXCEPT FOR a randomly-generated sequence of 12 amino acids, which have been attached to the outer tips of all five of the long finger-like proteins, in a manner analogous to gluing rhinestones onto all five fingernails, on a hand . . . except for a crucial fact: a small number of truly valuable gems have been sprinkled in, among the billions of rhinestones.

          “Screening tests” are a specialized category of tests, which scientists create and use, to try to identify those few phage particles that happen to be carrying “important and useful peptide sequences” (i.e., the valuable gems, hidden in huge piles of unhelpful rhinestones), among the billions of different phages in a phage library. A scientist who wants to find new peptide sequences which can perform “the XYZ trick” will try to think up some new way to use an affinity column, a batch of cells, some type of tissue culture, or a live animal (usually a fruit fly, mouse, or rat), to identify and somehow isolate (and then analyze) those few phages which happen to be carrying foreign peptide inserts that can perform the type of interaction the scientist is looking for. More information on screening tests is available HERE.

          As the science progresses (with AlphaFold and AI being two major components), scientists can (and will) use computer models to try to predict which peptide sequences are likely to work well at various tasks. However, one of the hurdles that computer models cannot deal with adequately is the question of whether the best-performing peptides, in some computer model, are likely to bind to or react with non-targeted proteins and/or cell types, either before they accomplish the desired task, or in ways that create unwanted side effects. Therefore, it can be more effective (and enlightening) to simply give millions of phages a fair chance to compete against each other, to see which ones will do best, in actually performing a desired task. So, that is how “screening tests” are designed and run.

          And, pitting millions of “candidate/contestant” phages against each other, in a fair contest to see which ones actually work best, is even better, in this setting, since the goal is to identify phages which can trigger and drive – all the way to completion – not just one or two specific cell responses, but an entire sequence of 5 different steps, which must be performed by two very different types of immune cells, as described in the next section. No computer model can do something like that, as well (or as reliably) as simply giving the phages a chance to show what they can do.

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3. THE SCREENING TEST WE CREATED CAN IDENTIFY PEPTIDE SEQUENCES THAT WILL DRIVE AN ENTIRE SERIES OF FIVE RESPONSES, BY TWO DIFFERENT TYPES OF IMMUNE CELLS, ALL THE WAY TO TRANSFORMING AN “IMMATURE” DENDRITIC CELL INTO A “MOBILE ANTIGEN-PRESENTING CELL”. THAT IS A PERFECT PLATEAU TO AIM FOR, AND REACH, IN A SCREENING TEST.

 

          To understand the statement above, readers need to know that surface-exposed “MALT patch” lymph nodes contain two crucial types of immune cells, which “internal” lymph nodes do not have. The “sampling” cells on the outer surfaces of MALT patches are called “M cells” (from “membrane” or “microvilli”). If their surface receptors detect what appears to be a “pathogen pattern” on a particle which contacts them, they will grab that potential/apparent/likely pathogen, and pull it in, inside a membrane bubble called a “phagosome”. However, rather than processing that phagosome, an M cell will actively hustle and push it through the cell (that process is called “trans-cytosis”), and press it against the “basal” membrane on the underside of the cell. When those two membranes merge, that merger will eject the particle out of the cell, in naked/exposed form again, into a “docking site” that holds a dendritic cell.

          Dendritic cells are the “genius-caliber” cells which control how an immune system will respond to “non-self” particles. They are too complex for a summary in this first page of this website, so they are described in more detail HERE. The main point that needs to be recognized, to understand the header above, is that when a dendritic cell – waiting, in the docking site of an M cell, for a particle to be delivered to it by that M cell – receives such a particle, it must make a yes-or-no, all-or-nothing “commitment” to one of two mutually-exclusive options:

          OPTION 1: if a particle appears to be a pathogen that is both dangerous and important, the dendritic cell will initiate and trigger an antibody-forming response, which will require that cell to undergo a major change, and then leave the docking site, to go off in search of the B and T cells which can perform the next steps in that response;

          – or –

          OPTION 2: if a particle appears to be common, run-of-the-mill, and not really dangerous, the dendritic cell will pull it in, digest it, and release its “building block” molecules, while staying in the docking site, to await the next particle delivery.

          Therefore, the goal of the screening test which we have developed – which will involve 10 to 20 million phage particles, “infused” (using droplets from a micro-pipette, rather than needles) into the nostrils of each mouse or rat used in the tests – is to identify those few phages which happen to be carrying foreign inserts which appear to be so dangerous, and so important, that they will potently and rapidly trigger, and then drive, all the way to completion, every step in a series of five different cellular responses. The first three steps must be performed by M cells; as summarized above, they require: (i) intake; then, (ii) “trans-cytosis”; and then, (iii) ejection into a docking site, by an M cell. The final two steps require: (iv) analysis, by a dendritic cell;  and, (v) an irreversible, irrevocable commitment, by that M cell, to transform itself in a way that will launch an antibody-forming response.

          In other words, the “winning” phages in the screening test we have developed will be those phages will happen to be carrying foreign peptide sequences that we have nicknamed, “HYPER-pathogen peptides”. Those pathogen-signaling peptides must make any phages – or, any vaccine particles – carrying those signaling peptides, appear to be so infective, and so dangerous, that they will be able to trigger and drive – within only about 90 minutes – M cells to pull them in, hustle them through, and hand them off, directly to dendritic cells, and then – still within the 90 minute limit – they must also provoke “immature” dendritic cells to fully commit to analyzing them carefully, and to then commit, irrevocably, to the type of transformation (aka maturation or activation) that will launch an antibody-forming process.

          Because that is exactly what – in an ideal world, with ideal vaccines – vaccine particles should be designed to do, and should be able to do.

          We also believe that the transformation of an “immature dendritic cell” into a “mobile antigen-presenting cell” is the perfect target, step, and plateau to aim for, in our screening test. When that transformation occurs, everything changes. It is entirely reasonable to state that . . . when an “immature” dendritic cell, commits to transforming into an antigen-presenting cell, well . . . THAT is the moment when an antibody-forming response begins, within an animal’s immune system.

          Therefore, if each vaccine particle is carrying only a small and limited number of “MALT-targeting transport peptides” (such as somewhere from about 10 to about 30 copies per particle, prominently displayed on the outer surfaces of each vaccine particle), while carrying multiple hundreds of copies of an “antigen” sequence (derived from a surface protein on the type of disease-causing microbe which that vaccine is designed to protect against), then a very large majority of antibodies that will be formed, will bind to the antigen sequence, rather than the transport sequence. And, that means that any antibodies that are created, in response to the ANTIGEN sequence on the VACCINES . . . will ALSO be able to bind directly to the pathogenic microbe itself (since it will have the same “antigen” sequences, on its surfaces), if that pathogen ever tries to invade and infect a vaccine-inoculated animal . . . or human).

 

4. THE BEST WAY TO IDENTIFY “IMMATURE” DENDRITIC CELLS THAT HAVE TRANSFORMED – INTO “MOBILE ANTIGEN-PRESENTING CELLS” – USES A CRUCIAL “TRANSLOCATION” WHICH MOVES CCR7 RECEPTORS FROM INSIDE THE CELLS, TO THE OUTER SURFACES OF THOSE CELLS

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          To understand the behavior of dendritic cells, one must understand the crucial role of a very unusual protein, called the CCR7 protein. One of the things that makes it so unusual is that it has two cysteine residues, directly next to each other (which led to the “CC” portion of the name). Cysteine residues have a highly reactive “side group” (called a sulfhydryl group, -S-H) which can react with a second sulfhydryl group, on a different cysteine residue, to form a strong and durable bond, called a disulfide bond. Those bonds – usually between two different cysteine residues that are located well apart from each other – play crucial roles in creating and then maintaining the three-dimensional shapes (also called conformations) of proteins. The shapes of proteins are crucial to their ability to perform their roles; therefore, cysteine residues (and the disulfide bonds) they form, are crucial, in protein shapes, structures, and interactions.

          When an “immature” dendritic cell is first formed, multiple copies of the CCR7 protein are hidden inside the cell, where they cannot be contacted by any molecules outside the cell. That allows that cell to remain in a docking site beneath an M cell for as long as it takes, until it detects that some particle which has been delivered to it – by the M cell which owns and controls that docking site – is important enough to merit an antibody-forming response.

          And, when that happens, that dendritic cell will “translocate” its CCR7 proteins from inside the cell, to the outer surfaces of the cell.

          And, when that happens, those CCR7 proteins become “surface receptors”, which can be contacted, and activated, by a chemo-attractant signaling molecule called CCL19 (which also has two cysteine residues, directly next to each other).

          An “activated” (aka “transformed” or “maturing”) dendritic cell will always travel in the direction of the largest number of signals it is getting, from CCL19 signaling molecules which are contacting and triggering the CCR7 proteins, which are distributed around the entire outer surface of the cell. That mechanism enables “activated” dendritic cells to travel toward, and eventually find and enter, “germinal centers” inside lymph nodes. T cells located in those germinal centers slowly and constantly release CCL19 molecules; and, since they are the source of that chemo-attractant, the highest concentrations of those signaling molecules will eventually lead “activated” dendritic cells to a source of the chemo-attractant, in a process called “climbing the gradient”.

 

          That completes an overview of the main facts and factors that have guided our work. A summary of the screening test we created – which uses those factors – is provided on the next page.

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          The two “PDF” buttons below will enable anyone to download, at no charge: (i) a complete copy of this website, in pdf format; and, (ii) the entire Background section, and list of cited references, from one of several pending (but not-yet-published) patent applications that describe and claim MALT-targeting vaccines, and the methods used to create them.

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