Peptide and protein biological activities depend on their three dimensionals structures in the free state and when interacting with their receptors/acceptors. The backbone conformations such as α‐helix, β‐sheet, β‐turn, and so forth provide critical templates for the three‐dimensional structure, but the overall shape and intrinsic stereoelectronic properties of the peptide or protein important for molecular recognition, signal transduction, enzymatic specificity, immunomodulation, and other biological effects depend on arrangement of the side chain groups in three‐dimensional chi space (their χ1, χ2, etc. torsional angles) In this paper we explore approaches to the de novo design of polypeptides and peptidomimetics with biased or specific conformational/topographical properties in chi space. We consider computational and experimental methods that can be used to examine the effects of specific structural modifications in constraining side chain groups of amino acid residues and their similarities in chi space to the natural amino acids to evaluate what sort of mimetics are likely to minic normal amino acids. We then examine some of the asymmetric synthetic methods that are being developed to obtain the amino acid mimetics. Finally, we consider selected examples in the literature where these specialized amino acids have been incorporated in biologically active peptides and the specific insights they have provided regarding the topographical requirements for bioactive peptide potency, selectivity, and other biochemical and pharmacological properties. Constraints in chi space show great promise as useful tools in peptide, protein, and peptidomimetic de novo design of structures and pharmacophores with specific stereostructural, biochemical and biological properties. © 1997 John Wiley & Sons, Inc. Biopoly 43: 219–266, 1997

SUMMARY Activating mutations in Gαq proteins, which form the a subunit of certain heterotrimeric G proteins, drive uveal melanoma oncogenesis by triggering multiple downstream signaling pathways, including PLC/PKC, Rho/Rac, and YAP. Here we show that the small GTPase ARF6 acts as a proximal node of oncogenic Gαq signaling to induce all of these downstream pathways as well as β-catenin signaling. ARF6 activates these diverse pathways through a common mechanism—the trafficking of GNAQ and β-catenin from the plasma membrane to cytoplasmic vesicles and the nucleus, respectively. Blocking ARF6 with a small molecule reduces uveal melanoma cell proliferation and tumorigenesis in a mouse model, confirming the functional relevance of this pathway and suggesting a therapeutic strategy for Gα-mediated diseases.

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A series of side-chain constrained tyrosine derivatives, 2′,6′-dimethyl-β-methyltyrosines (TMT), has been designed and incorporated into position 1 of the highly selective δ opioid agonists DPDPE (Tyr-D-Pen 2 -Gly-Phe-D-Pen 5 -OH) and deltorphin I (DELT I, Tyr-D-Ala-Phe-Asp-Val-Val-Gly-NH 2 ). Molecular mechanics calculations on isolated TMT residues and nuclear magnetic resonance (NMR) studies of the TMT 1 -containing peptides in DMSO showed that each of the four stereoisomers of TMT favors one particular rotamer of the side-chain χ 1 torsional angle. Therefore, substitution of four TMT isomers for Tyr 1 allows us to perform a systematic conformational scan through three staggered rotamers of the aromatic side chain, gauche (-), trans, and gauche (+), and to explore specific binding requirements of the receptor in relation to the side chain conformation. The potency and selectivity of four isomers of [TMT 1 ]DPDPE and four isomers of [TMT 1 ]DELT I were evaluated by radioreceptor binding assays in the rat brain using µ-and δ-selective radiolabeled ligands and by bioassays with guinea pig ileum (GPI, µ receptor) and mouse vas deferens (MVD, δ receptor). In the DPDPE series only one isomer, [(2S,3R)-TMT 1 ]-DPDPE showed high potency and selectivity for the δ opioid receptors. The favorable side-chain rotamers found for this analogue, i.e., the trans rotamer of TMT 1 and the gauche (-) rotamer of Phe 4 , were proposed as the most probable δ receptor-binding conformations of DPDPE analogues. Two [TMT 1 ]DELT I isomers possessed considerable δ receptor potencies. The (2S,3R)-TMT 1 isomer appeared to be a superpotent, but moderately δ-selective agonist, while the (2S,3S)-TMT 1 isomer showed the highest selectivity for the δ receptors in this series. Surprisingly, [(2R,3R)-TMT 1 ]DELT I also was moderately potent at the δ receptor. These results suggest that the δ receptor requirements for the linear DELT I analogues may be satisfied with two different modes of binding of the (2S,3S)-and (2S,3R)-TMT 1 isomers. This study provides important guidance for the design of peptide and non-peptide ligands selective for the δ opioid receptor. conformation of the 14-membered disulfide ring of DPDPE.

Mutations in HIV-1 drug targets lead to resistance and consequent therapeutic failure of antiretroviral drugs. Phenotypic resistance assays are time-consuming and costly, and genotypic rules-based interpretations may fail to predict the effects of multiple mutations. We have developed a computational procedure that rapidly evaluates changes in the binding energy of inhibitors to mutant HIV-1 PR variants. Models of WT complexes were produced from crystal structures. Mutant complexes were built by amino acid substitutions in the WT complexes with subsequent energy minimization of the ligand and PR binding site residues. Accuracy of the models was confirmed by comparison with available crystal structures and by prediction of known resistance-related mutations. PR variants from clinical isolates were modeled in complex with six FDA-approved PIs, and changes in the binding energy (⌬E bind ) of mutant versus WT complexes were correlated with the ratios of phenotypic 50% inhibitory concentration (IC 50 ) values. The calculated ⌬E bind of five PIs showed significant correlations (R 2 ‫ס‬ 0.7-0.8) with IC 50 ratios from the Virco Antivirogram assay, and the ⌬E bind of six PIs showed good correlation (R 2 ‫ס‬ 0.76-0.85) with IC 50 ratios from the Virologic PhenoSense assay. ⌬E bind cutoffs corresponding to a four-fold increase in IC 50 were used to define the structure-based phenotype as susceptible, resistant, or equivocal. Blind predictions for 78 PR variants gave overall agreement of 92% (kappa ‫ס‬ 0.756) and 86% (kappa ‫ס‬ 0.666) with PhenoSense and Antivirogram phenotypes, respectively. The structural phenotyping predicted drug resistance of clinical HIV-1 PR variants with an accuracy approaching that of frequently used cell-based phenotypic assays.Keywords: HIV protease inhibitors; drug resistance; molecular modeling; binding energy; structure-based phenotyping Antiretroviral drugs targeting the RT and PR enzymes of HIV-1 may result in dramatic suppression of viral replication in infected individuals (Palella Jr. et al. 1998;Carpenter et al. 2000). However, when viral replication is incompletely suppressed, drug-resistant variants emerge through the accumulation of mutations in the HIV-1 RT or PR genes, leading to therapeutic failure . Genotypic testing for resistance is a relatively rapid and inexpensive method to identify PR and RT amino acid substitutions leading to drug resistance (Baxter et al. 2000;Schinazi et al. 2000;Shafer 2002). Genotyping is recommended for use in clinical practice . However, rules-based interpretation systems are retrospective in nature and must be frequently updated to accommodate new mutational patterns and new antiretrovirals. As a result, genotypic predictions for complex mutational patterns and for new antiretrovirals may be inaccurate (Baxter et al. 2000). Cell-based viral phenotyping assays (Hertogs et Reprint requests to: Mark D. Shenderovich, Cengent Therapeutics Inc., 10929 Technology Place, San Diego, CA 92127, USA; e-mail: marksh@cengent.com; fax: (858) 451-3828.Abbre...