At Divergence, our approach to finding safe and effective products for the control of infectious agents in agriculture and medicine is to use genome data up-front as the first screen in discovery. This strategy directs research away from molecules that could have host organism toxicity, focusing instead on targets that are pharmacologically distinct and vital for the life cycle of the infecting organism. This approach provides Divergence and its collaborators with an enormous advantage because it decreases the risk of late-stage project failure due to product safety or environmental issues and can potentially decrease the time and cost of regulatory studies. Our first application of this innovative strategy has been the study of parasitic nematodes, roundworms that are major pathogens of plants, animals, and humans.
  Recent years have seen an exponential growth in available DNA sequence data from numerous species, radically changing the information available about the genes of many life-forms. In fact, the Divergence method of comparative genomics was not possible as recently as the mid-1990’s since the necessary data did not yet exist. Publicly available DNA sequence, measured in its building blocks of individual nucleotide bases has grown from less than 50 million units in 1990 to over 20 billion by 2002. The genome sequences of human and mouse (3 billion base pairs each), fly (120 million), the nematode C. elegans (100 million), bread yeast (6 million), the plants Arabidopsis (100 million) and rice (420 million), as well as hundreds of microbes (1-4 million each) have been completely sequenced or are in draft form. Washington University’s Genome Sequencing Center in St. Louis is one of the world’s leading genome centers, playing key roles in the sequencing of the C. elegans, human, and mouse genomes. The center has also generated much of the genome data available from parasitic nematodes, 250,000 expressed sequence tags from 30 nematode species including parasites of plants, animals, and humans, under the direction of Divergence founder James McCarter, M.D., Ph.D. By using this public data, Divergence avoids infrastructure costs and focuses its resources on rapidly turning sequence discoveries into patent-protected targets, leads, and products. Divergence in house expertise includes a cross-species gene discovery team that can rapidly clone gene orthologs from parasites of interest.

  Divergence's bioinformatics team, led by Vice President of Discovery Research Jeremy Williams, Ph.D. and SAB Chair Sean Eddy, Ph.D., has taken a comparative genomics approach to prioritizing nematode target genes. Historically, nematicides have been general toxins, dangerous to vertebrates as well as nematodes. The origin of this cross-toxicity is often a highly conserved molecular target, such as the enzyme acetylcholinesterase. Comparative and functional genomics reveal that mammals, including humans, share many genes with nematodes and that the more conserved a gene, the more likely it is to play an essential role. By using the genomes of mammals, plants, and beneficial microbes in the company's proprietary Automated Specificity Filter, Divergence has identified the subset of nematode genes present in many parasites with sequence signatures absent in vertebrate and other non-target genomes. In C. elegans for instance, the company prioritized 1,200 of the 20,000 genes in the genome for functional genomics studies. Divergence maintains a database recording these relationships and regularly re-runs revised and updated versions of its algorithms as new sequences become available. Divergence's skilled team in bioinformatics and its hardware and software infrastructure has also enabled the company to apply its approach to other areas of infectious disease and pest control including the analysis of protozoan and insect genomes. Targets for endecticides able to control both endoparasitic and ectoparasitic species have been identified and prioritized within the target collection.
  In addition to knowing that a target gene has the potential to provide specificity to the pathogen, Divergence believes it is also critical to determine whether or not the target is essential for the organism’s lifecycle. Many target genes in fact have only minor effects on a species’ fitness when deleted, making them poor targets for inhibitory drugs or pesticides. To individually test the role of each target gene, Divergence uses RNA interference (RNAi). RNAi is a revolutionary technique that was named the “Breakthrough of the Year” for 2002 by Science magazine. Divergence can now disclose that the company has been using the RNAi technique, co-developed by our SAB member Craig Mello, Ph.D. since 1999, making us one of the earliest industry adopters. In 2001, the Company completed its own large scale RNAi “knock-out” screen of 1,200 selected target genes in C. elegans, generating most of this information over 18 months prior to its public availability. RNAi works by introducing into the organism double-stranded RNA (dsRNA) bearing sequence similarity to the gene of interest triggering an endogenous biochemical pathway that results in mRNA degradation and transient gene knockout. The Divergence RNAi screen of 1,200 targets yielded approximately 100 targets that when knocked-out have strong deleterious effects on the worms’ lifecycle (lethality, sterility, etc.). Divergence has continued to improve the sophistication of its C. elegans RNAi pipeline generating extensive information missing from public databases and has also applied the technique to other nematode species.
  Targets that pass Divergence’s filters for specificity and essential function above form the basis of the Company’s proprietary target gene collection, one of the Company’s key intellectual property assets. Our 100 initial targets, and others that have been added based on new informatic or experimental validation, have been curated, prioritizing them for projects that can rapidly lead to the identification of nematicidal compounds. Curation has allowed Divergence to focus on fewer than one dozen of these targets. Over 30 patents have been filed on specific gene sequences as well as nematicidal chemistries and transgenes resulting from discoveries using these targets. The identities of additional targets are maintained as a trade secret. Divergence has developed expertise in two target categories in particular: enzymes and surface accessible targets. Projects in these areas are led by Senior Director of Discovery Research Michelle Hresko, Ph.D. Multiple chemistries have progressed into successful greenhouse testing led by Senior Director of Plant Protection Research Barry Shortt, Ph.D.
  Status of Selected Divergence Projects:
Divergence science focuses on rapid movement of projects from target gene concept to product candidates, a downstream focus that has been highly successful. Divergence combines its innovative approaches to target selection and validation with state-of-the-art in house and collaborative programs in chemical lead identification through molecular expression, biochemistry, chemical synthesis and SAR (structure-activity-relationship) model development, in vitro and in vivo physiological screens, rapid in planta testing systems for parasite control, and toxicity screening, allowing the progression of lead molecules from test tube to field. Cost and time-effective systems have also been developed for in planta testing of transgenic parasite resistance traits. Divergence maintains over a dozen nematode species in its laboratories and greenhouses including the major crop parasites root knot, cyst, lesion, and sting nematode.

 


Divergence has discovered:

  • Chemicals Based on Multiple Specific Enzyme Targets
  • Multiple Families of Lead Chemistry
    • Effective In Laboratory Nematode Assays against Animal, Human, and Plant Parasites
    • Effective in Greenhouse Assays in Soil with Plant Parasitic Nematodes
    • Effective in Greenhouse Assays by Foliar and Seed Treatment, thus Indicating Systemic Activity.

Divergence's Most Studied Lead Chemical:

  • Controls a Wide Spectrum of Nematode Species
  • Shows an Excellent Safety Profile in Mammals and Other Non-Target Organisms
  • Is Derived From a Natural Plant Product and Has Been Successfully Manufactured

Additional Chemical Synthesis In Progress for Multiple Families of Lead Chemistry
 


Development of Plants with Nematode Resistance in Progress Based on the Characterization of:

  • Novel Nematicidal Metabolites Based on Enzyme Targets
  • Novel Nematicidal Peptides Based on Surface Accessible Targets
  • Novel Nematicidal Nucleic Acids

Vaccine Antigens Based on Surface Accessible Targets

 

 

© 2000-2006 Divergence Inc. All rights reserved. Divergence ® is a registered trademark of Divergence, Inc.