Patent 7,553,674 : Methods of identifying compounds useful for modulating intraflagellar transport . Granted June 30, 2009. full text from USPTO.

Inventors:  George B. Witman, Gregory J. Pazour, Joel L. Rosenbaum (Yale faculty), Douglas G.Cole.

Background

It’s the goal of any cell biologist to discover and describe a totally new molecular mechanism or cellular process.  Just such a discovery was made during the mid-90s, in the laboratory of Joel Rosenbaum at Yale.

Cross-section of two Chlamydamonas cilia. Click for Wikipedia entry.

Rosenbaum and colleagues were looking at the green algae Chlamydamonas–specifically at the long, slender cilia that project outward from its cell body.  Cilia, called flagella in cells that have only one of these structures, are present in many eukaryotic cells and can function both as a type of cellular paddle (as in the case of a swimming sperm cell) or as an antenna, positioned to sense the surrounding environment.

What the Yale researchers saw when they looked carefully inside the cilia, at high magnifications, were tiny granules that were moving along the cilia.  What became clear in subsequent experiments is that these particles move back and forth along the cilium, like miniature cargo elevators, to transport proteins and lipids.  These cargo include sensory molecules, as well as the building blocks needed to extend the growing structure.

Rosenbaum and colleagues termed this mechanism intraflagellar transport (IFT). Most importantly, though it was discovered in the model green algae cells, IFT is a mechanism that has been exquisitely conserved during evolution.  Microscopic parasites and human beings, confronted alike with the necessity of building and maintaining cilia and flagella in many different types of cells, all use the same basic transport molecules, with only minor variations.

As with any molecules so central to diverse cellular functions, when something goes wrong, like an inherited mutation in the gene coding for an IFT protein, severe diseases can develop.  In humans, difficulty building and maintaining cilia and flagella contribute to diseases of organs that depend on these structures, like the kidneys, the eyes and the heart during early development

Patent implications

The new patent claims the use, for “diagnostic, screening, and therapeutic” purposes, of 14 key proteins that are present in humans and other organisms with flagella.  These proteins are assembled together within the cell to make a multi-molecular machine for transporting cargo in the flagellum.  The exact workings of these protein complexes are still poorly understood.

The patent claims any pharmaceutical agent to diagnose or treat a problem with these complexes, or at least those drugs designed to interact with the 14 patented proteins, for uses including to “modulate flagellar function”.  Although much of the biomedical research into IFT has been directed at curing human genetic disorders, this patent would also appear to cover the design of any antibiotics targeting the IFT proteins in human parasites, such as Leishmania or Trypanosoma brucei,  which rely on their flagella for survival.

The diagnostic claim appears to broaden the scope of the patent in a significant way.  Severe diseases resulting from cilia defects, such as Bardet-Biedl syndrome, may not be cured by drugs that target IFT proteins, because there are many other molecules involved.  However, a diagnostic test, using IFT proteins to evaluate the “size”, “beating” or “cell motility” of a sample, as is imagined by the authors of the patent, may not be as far-fetched.

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Read this recent New York Times article on ciliary diseases, flagellum research and IFT.

US Patent Application 20080260706 : Transient Transfection with RNA. Received October 23, 2008. Full text from Patent Office

Inventors: Peter M. Rabinovich, Sherman M. Weissman, Marina E. Komarovskaya, Erkut Bahceci

Background

Biologists frequently transfect foreign DNA into cells; if the DNA encodes a functional gene, the normal machinery within the cell will transcribe the DNA into RNA, which will be translated to protein.  Expressing either foreign proteins or altered versions of native proteins within cells is extremely useful for determining protein function, or for altering cell behavior.  “Gene therapy” involves introducing foreign genes within cells in the human body to ameliorate disease.

Though it is possible to introduce the proteins themselves into a cell, the techniques for doing so are very cumbersome relative to nucleic acid introduction.  Additionally, the location of expression is very important–different cells may introduce modifications into proteins as they are expressed, so the same protein may have different properties depending on the cell that produces it.  A foreign protein may not have the same properties as one that is produced locally.

The patent

The patent application prepared by Rabinovich, et al., aims to protect an improvement on the expression of foreign proteins: the transfection of the gene-coding RNA itself.  The authors claim that transfecting RNA is more efficient than transfecting DNA and also has a number of other advantages, including allowing more precise regulation of the quantities of protein produced, something that would be particularly important in a gene-therapy context.  The introduction of RNA is also inherently transient, avoiding the long-term exposure to exogenous genes that results from other forms of gene therapy, such as those employing viral vectors.  Short-term gene therapy would be particularly useful for a protein-based treatment regimen, rather than the permanent genetic change intended by viral gene-therapy.

Specifically, the patent application specifies the transfection of RNA “that encodes a therapeutic, prophylactic or diagnostic polypeptide or nucleic acid molecule”.    This process includes the in vitro transcription into RNA of DNA including a gene and other sequence elements necessary for efficient transcription and translation.

Implications

If granted, the patent would appear to protect the use of one of the two information-containing biological polymers, RNA, for medical puposes involving transient transfection.  Moreover, it claims invention of the process for production of RNA molecules for those medical purposes.

Viral gene therapy systems have been patented, including this patent held by Mount Sinai School of Medicine.

Update, October 7, 2009: The description of ribosome structure, including the work protected by these patents, was awarded the 2009 Nobel Prize in Chemistry, announced today.  A new post discusses the implications.

Patent 7,504,486 : Determination and uses of the atomic structures of the large ribosomal subunit and ribosomal subunits and their ligand complexes. Granted March 17, 2009. full text from USPTO.

This is the most recent from a set of similar Yale patents, most importantly: Patent 6,638,908: Crystals of the large ribosomal subunit. Granted October 28, 2003. full text from USPTO.

Inventors:  Thomas A. Steitz (Yale faculty), Peter B. Moore (Yale faculty), et al.

Background

Ribosomes translate messenger RNA into protein.  To accomplish this most basic biological task, at the very center of the “central dogma” of biology, requires a large molecular machine composed of both protein and RNA pieces.  The genes coding for these components are among the most evolutionarily conserved (i.e. sharing similar sequences), indicating the ribosome’s essential and highly optimized function.  Because of the absolute biological requirement of synthesizing proteins, the ribosome is an attractive target for antibiotics.  Designing drugs that inhibit the ribosomes of human pathogens efficiently and specifically is a major goal of ribosome biology.

Our modern understanding of molecular mechanism in the cell comes from x-ray crystallography.  This technique relies on x-rays, directed through highly-pure crystals of the molecule to be examined.  Based on the structure of the molecular components of the crystal, the x-rays are diffracted into a complex pattern.  This pattern may be deconvolved–computationally reconstructed–into a three-dimensional model of the molecule-of-interest, at atomic-scale resolution.

Acquiring these fascinating 3D molecular models is complicated by a number of factors, particularly the difficulty of procuring a sufficiently large, pure sample of the subject molecule.  This protein, nucleic acid, etc. must then self-assemble into a highly ordered crystal–a requirement for high-resolution crystallography.  RNA, a major component of the ribosome, is notoriously tricky to crystallize and diffract, and the crystallization of the large ribosomal subunit in 2000 (by Steitz and colleagues at Yale) represented a huge breakthrough in our understanding of not only the ribosome, but of the structure of RNA molecules generally–that is, how they interact physically with themselves and other molecules.

Patent implications

A key patent on the work of Steitz, et al., 6,638,908, claims the crystallization of the large ribosomal subunit, from any organism, with attached ligands (drugs), to a resolution of 5 angstroms.  Other patents (7,504,486, 6,952,650, 6,947,845, 6,947,844, 6,939,848, 6,631,329) deal with other details of crystallization and methods for identifying “modulators of ribosome function” and protein synthesis, such as antibiotic drugs.

These patents have been licensed by Yale to Rib-X pharmaceuticals, co-founded by Dr. Steitz and Dr. Moore and based in greater New Haven.

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