Since 1990, the National Cancer Institute (NCI) has screened more than 60,000 compounds against a panel of 60 human cancer cell lines. The 50-percent growth-inhibitory concentration (GI50) for any single cell line is simply an index of cytotoxicity or cytostasis, but the patterns of 60 such GI50 values encode unexpectedly rich, detailed information on mechanisms of drug action and drug resistance. Each compound's pattern is like a fingerprint, essentially unique among the many billions of distinguishable possibilities. These activity patterns are being used in conjunction with molecular structural features of the tested agents to explore the NCI's database of more than 460,000 compounds, and they are providing insight into potential target molecules and modulators of activity in the 60 cell lines. For example, the information is being used to search for candidate anticancer drugs that are not dependent on intact p53 suppressor gene function for their activity. It remains to be seen how effective this information-intensive strategy will be at generating new clinically active agents.

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Molecular hydrophobicity (lipophilicity), usually quantified as log P (the logarithm of 1-octanol/water partition coefficient), is an important molecular characteristic in drug discovery. ALOGP and CLOGP are two of the most widely used methods for the estimation of log P. This work describes an extensive reparametrization of the atomic log P values and a detailed comparison of the performance of ALOGP and CLOGP methods on the Pomona Medchem database. Only the “star list” compounds having precisely measured log P values were used in this analysis. While the overall results with both methods are similar, analysis shows that the CLOGP method is better for very small molecules in the range of 1−20 atoms. The two methods are almost comparable in the range of 21−45 atoms, while the ALOGP method has better accuracy for molecules with more than 45 atoms. Although the rms deviation and the correlation coefficient for CLOGP predictions were marginally better than those for corresponding ALOGP predictions, the latter showed a very stable performance for all classes of organic compounds analyzed. The ALOGP method can be used to compute estimates of most neutral organic compounds having C, H, O, N, S, Se, P, B, Si, and halogens. It also covers most zwitterionic compounds having amine and carboxylic acids and ammonium halide salts. The CLOGP method has improved considerably over the years to cover most neutral organic compounds, but it still has some undefined fragments. Finally, unlike CLOGP and other methods of predicting lipophilicity, the ALOGP method has multiple uses, such as the estimation of local hydrophobicity, the visualization of molecular hydrophobicity maps, and the evaluation of hydrophobic interactions in protein−ligand complexes.

Vanilloid receptor 1 (TRPV1), a membrane-associated cation channel, is activated by the pungent vanilloid from chili peppers, capsaicin, and the ultra potent vanilloid from Euphorbia resinifera, resiniferatoxin (RTX), as well as by physical stimuli (heat and protons) and proposed endogenous ligands (anandamide, Narachidonyldopamine, N-oleoyldopamine, and products of lipoxygenase). Only limited information is available in TRPV1 on the residues that contribute to vanilloid activation. Interestingly, rabbits have been suggested to be insensitive to capsaicin and have been shown to lack detectable [ 3 H]RTX binding in membranes prepared from their dorsal root ganglia. We have cloned rabbit TRPV1 (oTRPV1) and report that it exhibits high homology to rat and human TRPV1. Like its mammalian orthologs, oTRPV1 is selectively expressed in sensory neurons and is sensitive to protons and heat activation but is 100-fold less sensitive to vanilloid activation than either rat or human. Here we identify key residues (Met 547 and Thr 550 ) in transmembrane regions 3 and 4 (TM3/4) of rat and human TRPV1 that confer vanilloid sensitivity, [ 3 H]RTX binding and competitive antagonist binding to rabbit TRPV1. We also show that these residues differentially affect ligand recognition as well as the assays of functional response versus ligand binding. Furthermore, these residues account for the reported pharmacological differences of RTX, PPAHV (phorbol 12-phenyl-acetate 13-acetate 20-homovanillate) and capsazepine between human and rat TRPV1. Based on our data we propose a model of the TM3/4 region of TRPV1 bound to capsaicin or RTX that may aid in the development of potent TRPV1 antagonists with utility in the treatment of sensory disorders.The receptor for capsaicin (a small vanilloid molecule extracted from "hot" chili peppers), designated vanilloid receptor 1 (also known as VR1 and TRPV1 1 (1)) has been cloned and shown to be a nonselective cation channel with high permeability to calcium. TRPV1 belongs to a superfamily of ion channels known as transient receptor potential channels (TRPs) several of which appear to be sensors of temperature (2, 3). TRPV1 can be activated by exogenous agonists (capsaicin and RTX) and by physical stimuli such as heat (Ͼ42°C) and protons (pH 5). Possible endogenous ligands released during tissue injury have also been suggested, including anandamide (arachidonylethanolamine or AEA) and products of lipoxygenases such as 12-hydroperoxyeicosatetraenoic acid, N-arachidonyldopamine (NADA), and N-oleoyldopamine (OLDA) (4 -7). Ji et al. (8) reported that TRPV1 is detectable at increased levels after inflammatory injury in rodents and speculated that the increased level of TRPV1 protein combined with the confluence of stimuli present in inflammatory injury states leads to a reduced threshold of activation of nociceptors that express TRPV1, i.e. hyperalgesia. Indeed the converse is true that TRPV1-deficient mice display reduced thermal hypersensitivity following inflammatory tissue injury (9). Structure-func...