Nonsteroidal anti-inflammatory drugs (NSAIDs) are one of the most widely consumed pharmaceuticals, yet both the mechanisms involved in their therapeutic actions and side-effects, notably gastrointestinal (GI) ulceration/bleeding, have not been clearly defined. In this study, we have used a number of biochemical, structural, computational and biological systems including; Fourier Transform InfraRed (FTIR). Nuclear Magnetic Resonance (NMR) and Surface Plasmon Resonance (SPR) spectroscopy, and cell culture using a specific fluorescent membrane probe, to demonstrate that NSAIDs have a strong affinity to form ionic and hydrophobic associations with zwitterionic phospholipids, and specifically phosphatidylcholine (PC), that are reversible and non-covalent in nature. We propose that the pH-dependent partition of these potent anti-inflammatory drugs into the phospholipid bilayer, and possibly extracellular mono/multilayers present on the luminal interface of the mucus gel layer, may result in profound changes in the hydrophobicity, fluidity, permeability, biomechanical properties and stability of these membranes and barriers. These changes may not only provide an explanation of how NSAIDs induce surface injury to the GI mucosa as a component in the pathogenic mechanism leading to peptic ulceration and bleeding, but potentially an explanation for a number of (COX-independent) biological actions of this family of pharmaceuticals. This insight also has proven useful in the design and development of a novel class of PC-associated NSAIDs that have reduced GI toxicity while maintaining their essential therapeutic efficacy to inhibit pain and inflammation.

Aptamer-related technologies represent a revolutionary advancement in the capacity to rapidly develop new classes of targeting ligands. Structurally distinct RNA and DNA oligonucleotides, aptamers mimic small, protein-binding molecules and exhibit high binding affinity and selectivity. Although their molecular weight is relatively small—approximately one-tenth that of monoclonal antibodies—their complex tertiary folded structures create sufficient recognition surface area for tight interaction with target molecules. Additionally, unlike antibodies, aptamers can be readily chemically synthesized and modified. In addition, aptamers’ long storage period and low immunogenicity are favorable properties for clinical utility. Due to their flexibility of chemical modification, aptamers are conjugated to other chemical entities including chemotherapeutic agents, siRNA, nanoparticles, and solid phase surfaces for therapeutic and diagnostic applications. However, as relatively small sized oligonucleotides, aptamers present several challenges for successful clinical translation. Their short plasma half-lives due to nuclease degradation and rapid renal excretion necessitate further structural modification of aptamers for clinical application. Since the US Food and Drug Administration (FDA) approval of the first aptamer drug, Macugen® (pegaptanib), which treats wet-age-related macular degeneration, several aptamer therapeutics for oncology have followed and shown promise in pre-clinical models as well as clinical trials. This review discusses the advantages and challenges of aptamers and introduces therapeutic aptamers under investigation and in clinical trials for cancer treatments.

The solution structure of domain III from the New York West Nile virus strain 385-99 (WN-rED3) has been determined by NMR methods. The West Nile domain III structure is a ␤-barrel structure formed from seven antiparallel ␤-strands in two ␤-sheets. One anti-parallel ␤-sheet consists of ␤-strands ␤1 In 2002, the mosquito-borne West Nile virus (WNV) 1 (family Flaviviridae, genus Flavivirus) was responsible for the largest outbreak of arthropod-borne encephalitis recorded in the Western hemisphere. In that year, 4156 human infections and 284 deaths were reported in the United States (1). In 2003, the WNV epidemic continued with large numbers of human and animal disease across North America, and it was detected for the first time in Mexico and Central America (e.g. Refs. 2-4). The objective of this study was to solve the solution structure for the putative envelope (E) protein, the receptor-binding domain of WNV with the long term goal of using these findings for the development of structure-based vaccines or antiviral agents. Currently, there are no approved vaccines for WNV or therapeutic treatments for West Nile encephalitis.The flaviviruses are small, enveloped, positive-sense RNA viruses that are transmitted primarily by either mosquitoes or ticks. The translation of the single open reading frame within the viral genome, followed by co-and posttranslational cleavage, results in ten viral proteins, three structural proteins (core, membrane, and E) and seven non-structural proteins. The non-structural proteins are involved in viral replication and pathogenesis, whereas the three structural proteins are assembled into the mature virus particle.The E protein is the major surface protein of the flavivirus virions. The E protein is also the primary immunogen and plays a central role in virus attachment and entry to cells via membrane fusion. The x-ray crystallographic structures of the E protein ectodomains of both the tick-borne central European encephalitis virus (5) and the mosquito-borne dengue-2 virus (6) have been solved. Both proteins contain three distinct structural domains (domains I, II, and III) that correspond to previously characterized antigenic domains (7). Domain III (D3) of the E protein was initially proposed as the likely receptorbinding domain of the flaviviruses because of its structural characteristics. These include an IgC-like fold and a four-amino-acid loop that contains an RGD integrin-binding motif in several of the mosquito-borne flaviviruses (5). More recent studies have shown that D3 is directly associated with binding of dengue-2 virus (DEN2V) (8), WNV, and the tick-borne Langat virus 2 to cells. Domain 3 of WNV (WN-rED3) has also been shown to contain epitopes recognized by virus-neutralizing monoclonal antibodies (9). X-ray crystallography (5, 6) and cryo-electron microscopy studies (6, 10, 11) of the mosquitoborne WNV, DEN2V, and yellow fever virus have found that the E protein is arranged in dimeric form on the virus surface. Located at the 5-and 3-fold axes of symmetry, D3 projects...

2D NMR has been used to examine the structure and dynamics of a 12-mer DNA duplex, d(T(1)A(2)G(3)T(4)C(5)A(6)A(7)G(8)G(9)G(10)C(11)A(12))-d(T(13)G(14)C( 15)C(16)C(17)T(18)T(19)G(20)A(21)C(22)T(23)A(24)), containing a 10R adduct at dA(7) that corresponds to trans addition of the N(6)-amino group of dA(7) to (-)-(7S,8R,9R,10S)-7,8-dihydroxy-9, 10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene [(-)-(S,R,R,S)-BP DE-2]. This DNA duplex contains the base sequence for the major dA mutational hot spot in the HPRT gene when Chinese hamster V79 cells are given low doses of the highly carcinogenic (+)-(R,S,S,R)-BP DE-2 enantiomer. NOE data indicate that the hydrocarbon is intercalated on the 5'-side of the modified base as has been seen previously for other oligonucleotides containing BP DE-2 (10R)-dA adducts. 2D chemical exchange-only experiments indicate dynamic behavior near the intercalation site especially at the 10R adducted dA, such that this base interconverts between the normal anti conformation and a less populated syn conformation. Ab initio molecular orbital chemical shift calculations of nucleotide and dinucleotide fragments in the syn and anti conformations support these conclusions. Although this DNA duplex containing a 10R dA adduct exhibits conformational flexibility as described, it is nevertheless more conformationally stable than the corresponding 10S adducted duplex corresponding to trans opening of the carcinogenic isomer (+)-(R,S,S, R)-BP DE-2, which was too dynamic to permit NMR structure determination. UV and imino proton NMR spectral observations indicated pronounced differences between these two diastereomeric 12-mer duplexes, consistent with conformational disorder at the adduct site and/or an equilibrium with a nonintercalated orientation of the hydrocarbon in the duplex containing the 10S adduct. The existence of conformational flexibility around adducts may be related to the occurrence of multiple mutagenic outcomes resulting from a single DE adduct.