Ray Ranken

Bio: Ray Ranken is an academic researcher from Isis Pharmaceuticals. The author has contributed to research in topics: Electrophilic fluorination & Pyrimidine. The author has an hindex of 8, co-authored 12 publications receiving 360 citations.

SAR by MS: Discovery of a New Class of RNA-Binding Small Molecules for the Hepatitis C Virus: Internal Ribosome Entry Site IIA Subdomain

Abstract: A new class of small molecules that bind the HCV RNA IRES IIA subdomain with sub-micromolar affinity is reported. The benzimidazole ‘hit' 1 with a KD ∼100 μM to a 29-mer RNA model of Domain IIA was...

Structure-Based Design, Synthesis, and A-Site rRNA Cocrystal Complexes of Functionally Novel Aminoglycoside Antibiotics: C2'' Ether Analogues of Paromomycin

Abstract: A series of 2‘ ‘-O-substituted ether analogues of paromomycin were prepared based on new site-selective functionalizations. X-ray cocrystal complexes of several such analogues revealed a new mode of binding in the A-site rRNA, whereby rings I and II adopted the familiar orientation and position previously observed with paromomycin, but rings III and IV were oriented differently. With few exceptions, all of the new analogues showed potent inhibitory activity equal or better than paromomycin against a sensitive strain of S. aureus. Single digit μM MIC values were obtained against E. coli, with some of the ether appendages containing polar or basic end groups. Two analogues showed excellent survival rate in a mouse septicemia protection assay. Preliminary histopathological analysis of the kidney showed no overt signs of toxicity, while controls with neomycin and kanamycin were toxic at lower doses.

Synthesis and biological activity of 5-fluorotubercidin.

Abstract: The electrophilic fluorination of 4‐chloropyrrolo[2,3‐d]pyrimidine (1) was studied culminating a 59% conversion of compound 1 to 4‐chloro‐5‐fluoropyrrolo[2,3‐d]pyrimidine (2) using Selectfluor. This transformation proceeded via the 4‐chloro‐5,6‐dihydro‐5‐fluoro‐6‐hydroxypyrrolo[2,3‐d]pyrimidine (3) in a 9:1 trans:cis ratio. The trans isomer of compound 3 was studied by 1H NMR and 19F NMR, and the 5‐H tautomer (4) was observed as another intermediate. A modified Vorbruggen procedure of compound 2 and tetra‐O‐acetylribose gave 4‐chloro‐5‐fluoro‐7‐(2,3,5,‐tri‐O‐benzoyl‐β‐d‐ribofuranosyl)pyrrolo[2,3‐d]pyrimidine (6) in a 65% yield. Treatment of compound 6 with ammonia (l) in dioxane gave 5‐fluorotubercidin (7). No antibacterial activity was observed. An MTT assay (Promega) against Huh‐7 liver cells, normal mouse spleen cells stimulated with Con A (a T‐cell mitogen), and normal mouse spleen stimulated with LPS (a B‐cell mitogen) showed no significant toxicity. Increased activity of 7 over tubercidin was observ...

Recent Developments in Fragment-Based Drug Discovery

Abstract: The field of fragment-based drug discovery (FBDD) has developed significantly over the past 10 years and is now recognized as a tangible alternative to more traditional methods of hit identification, such as high throughput screening (HTS). The number of commercial and academic groups actively engaged in fragment-based research has increased, and as a consequence, there has been continued development and refinement of techniques and methods. From its inception, the fragment-based approach had two central tenets that were critical to its success and that have set it apart from HTS and other hit identification techniques. The first is the concept that chemical space can be more efficiently probed by screening collections of small fragments rather than libraries of larger molecules. The number of potential fragments with up to 12 heavy atoms (not including threeand four-membered ring structures) has been estimated at 10, whereas the number of potential druglike molecules with up to 30 heavy atoms is estimated at more than 10. Therefore, a much greater proportion of “fragment-like” chemical space can feasibly be screened in FBDD compared to “druglike” chemical space covered in a HTS where molecular size is much larger. The second idea is that, because by definition fragment molecules are small in size (typically less than 250 Da), they should typically bind with lower affinity to their target protein (micromolar to millimolar range) compared with druglike molecules that can form many more interactions (nanomolar to micromolar range) but that the binding efficiency per atom is at least as high as for larger hit molecules. Implicitly, the screening techniques employed in FBDD must be correspondingly much more sensitive than a HTS bioassay. Generally, sensitive biophysical techniques are employed to detect these weak binding events and to characterize the fragment interactions with the target active site. Nuclear magnetic resonance (NMR) and protein X-ray crystallography have been used extensively in fragment-based research because these techniques are highly sensitive in detecting low affinity fragment binding and also give information about the fragmentprotein interactions being formed. There have been a number of recently published general review articles that have discussed the various aspects of the FBDD field. In addition, there are now two books on the subject. In this journal in 2004, Erlanson et al. summarized the major developments in FBDD since the original publication by Fesik and co-workers of the “SAR by NMR” approach in the late 1990s. Particular note was given to the biophysical methods employed to screen for fragment binding and the merits and drawbacks of each of these techniques, along with the approaches that can be used to optimize fragments into lead molecules. Herein, the trends and developments over the past 4 years will be outlined and some selected examples that are illustrative of the approaches being utilized by those active in the field examined. Additionally, this review will look in some detail at representative protein-ligand complexes observed between fragment-sized molecules and their protein targets from the Protein Data Bank (PDB). Finally, some conclusions will be drawn from these data and the future of FBDD discussed.

Pneumococcal Capsules and Their Types: Past, Present, and Future.

Abstract: Streptococcus pneumoniae (the pneumococcus) is an important human pathogen. Its virulence is largely due to its polysaccharide capsule, which shields it from the host immune system, and because of this, the capsule has been extensively studied. Studies of the capsule led to the identification of DNA as the genetic material, identification of many different capsular serotypes, and identification of the serotype-specific nature of protection by adaptive immunity. Recent studies have led to the determination of capsular polysaccharide structures for many serotypes using advanced analytical technologies, complete elucidation of genetic basis for the capsular types, and the development of highly effective pneumococcal conjugate vaccines. Conjugate vaccine use has altered the serotype distribution by either serotype replacement or switching, and this has increased the need to serotype pneumococci. Due to great advances in molecular technologies and our understanding of the pneumococcal genome, molecular approaches have become powerful tools to predict pneumococcal serotypes. In addition, more-precise and -efficient serotyping methods that directly detect polysaccharide structures are emerging. These improvements in our capabilities will greatly enhance future investigations of pneumococcal epidemiology and diseases and the biology of colonization and innate immunity to pneumococcal capsules.

Principles for targeting RNA with drug-like small molecules

Abstract: RNA molecules are essential for cellular information transfer and gene regulation, and RNAs have been implicated in many human diseases. Messenger and non-coding RNAs contain highly structured elements, and evidence suggests that many of these structures are important for function. Targeting these RNAs with small molecules offers opportunities to therapeutically modulate numerous cellular processes, including those linked to 'undruggable' protein targets. Despite this promise, there is currently only a single class of human-designed small molecules that target RNA used clinically - the linezolid antibiotics. However, a growing number of small-molecule RNA ligands are being identified, leading to burgeoning interest in the field. Here, we discuss principles for discovering small-molecule drugs that target RNA and argue that the overarching challenge is to identify appropriate target structures - namely, in disease-causing RNAs that have high information content and, consequently, appropriate ligand-binding pockets. If focus is placed on such druggable binding sites in RNA, extensive knowledge of the typical physicochemical properties of drug-like small molecules could then enable small-molecule drug discovery for RNA targets to become (only) roughly as difficult as for protein targets.