Cytochrome P450 (P450) 3A4 is the most abundant human P450 enzyme and has broad selectivity for substrates. The enzyme can show marked catalytic regioselectivity and unusual patterns of homotropic and heterotropic cooperativity, for which several models have been proposed. Spectral titration studies indicated one binding site for the drug indinavir (M(r) 614), a known substrate and inhibitor. Several C-terminal aminated peptides, including the model morphiceptin (YPFP-NH(2)), bind with spectral changes indicative of Fe-NH(2) bonding. The binding of the YPFP-NH(2) N-terminal amine and the influence of C-terminal modification on binding argue that the entire molecule (M(r) 521) fits within P450 3A4. YPFP-NH(2) was not oxidized by P450 3A4 but blocked binding of the substrates testosterone and midazolam, with K(i) values similar to the spectral binding constant (K(s)) for YPFP-NH(2). YPFP-NH(2) inhibited the oxidations of several typical P450 substrates with K(i) values 10-fold greater than the K(s) for binding YPFP-NH(2) and its K(i) for inhibiting substrate binding. The n values for cooperativity of these oxidations were not altered by YPFP-NH(2). YPFP-NH(2) inhibited the oxidations of midazolam at two different positions (1'- and 4-) with 20-fold different K(i) values. The differences in the K(i) values for blocking the binding to ferric P450 3A4 and the oxidation of several substrates may be attributed to weaker binding of YPFP-NH(2) to ferrous P450 3A4 than to the ferric form. The ferrous protein can be considered a distinct form of the enzyme in binding and catalysis because many substrates (but not YPFP-NH(2)) facilitate reduction of the ferric to ferrous enzyme. Our results with these peptides are considered in the context of several proposed models. A P450 3A4 model based on these peptide studies contains at least two and probably three distinct ligand sites, with testosterone and alpha-naphthoflavone occupying distinct sites. Midazolam appears to be able to bind to P450 3A4 in two modes, one corresponding to the testosterone binding mode and one postulated to reflect binding in a third site, distinct from both testosterone and alpha-naphthoflavone. The work with indinavir and YPFP-NH(2) also argues that room should be present in P450 3A4 to bind more than one smaller ligand in the "testosterone" site, although no direct evidence for such binding exists. Although this work with peptides provides evidence for the existence of multiple ligand binding sites, the results cannot be used to indicate their juxtaposition, which may vary through the catalytic cycle.

Drug toxicity is frequently caused by electrophilic reactive metabolites that covalently bind to proteins. Epoxides comprise a large class of three-membered cyclic ethers. These molecules are electrophilic and typically highly reactive due to ring tension and polarized carbon–oxygen bonds. Epoxides are metabolites often formed by cytochromes P450 acting on aromatic or double bonds. The specific location on a molecule that undergoes epoxidation is its site of epoxidation (SOE). Identifying a molecule’s SOE can aid in interpreting adverse events related to reactive metabolites and direct modification to prevent epoxidation for safer drugs. This study utilized a database of 702 epoxidation reactions to build a model that accurately predicted sites of epoxidation. The foundation for this model was an algorithm originally designed to model sites of cytochromes P450 metabolism (called XenoSite) that was recently applied to model the intrinsic reactivity of diverse molecules with glutathione. This modeling algorithm systematically and quantitatively summarizes the knowledge from hundreds of epoxidation reactions with a deep convolution network. This network makes predictions at both an atom and molecule level. The final epoxidation model constructed with this approach identified SOEs with 94.9% area under the curve (AUC) performance and separated epoxidized and non-epoxidized molecules with 79.3% AUC. Moreover, within epoxidized molecules, the model separated aromatic or double bond SOEs from all other aromatic or double bonds with AUCs of 92.5% and 95.1%, respectively. Finally, the model separated SOEs from sites of sp2 hydroxylation with 83.2% AUC. Our model is the first of its kind and may be useful for the development of safer drugs. The epoxidation model is available at http://swami.wustl.edu/xenosite.

Surface arrays of single-stranded DNA are at the center of some of the most active areas in biological research. These include conventional applications in genome sequencing and disease diagnostics, as well as more novel emerging examples, such as combinatorial drug and reaction discovery. 1 Most methods of oligonucleotide immobilization rely on traditional nucleophilicelectrophilic reactions to achieve coupling of the oligonucleotide to the surface. 2 Unfortunately, this strategy is susceptible to side reactions, for instance, with amino groups on the nucleotides or the small molecule contaminants inherent to oligonucleotide synthesis. 3 Additionally, popular reactive electrophiles, such as N-hydroxysuccinimide esters, are prone to hydrolysis before and during the coupling reaction, which both reduce coupling yields and can make the yields irreproducible. 4 Accurate and reproducible detection of target oligonucleotides depends on the accuracy and reproducibility with which the surface can be functionalized. In this paper, we report a chemoselective approach to the formation of oligonucleotide probe surfaces using copper(I) tris(benzyltriazolylmethyl)amine (TBTA)-catalyzed triazole formation between a controlled density of azide groups on densely packed selfassembled monolayers (SAMs) and acetylene groups on the oligonucleotide probe to be immobilized. We have found this strategy to be highly predictable, very fast, and resistant to side reactions, unaffected even by the presence of excess nucleophilic or electrophilic impurities.Recently, we have demonstrated that Sharpless "click" chemistry can be used to covalently attach acetylene-bearing molecules to azide-terminated SAMs. 5,6 The surface reaction is quantitative and regioselective, exclusively yielding a single product at a single orientation. The chemistry is orthogonal to most typical organic transformations and thus is chemoselective. 7 Recent studies have demonstrated that the chemistry is well suited for the coupling of biomolecules to surfaces. 8 Although application of this chemistry to the attachment of oligonucleotides may appear straightforward, the majority of past work used free Cu(I), typically generated and maintained in aqueous solution by an excess of reducing agent. Unfortunately, in the presence of dioxygen, Cu(I) rapidly damages DNA via the generation of reactive oxygen species. 9 In order for a surface array of oligonucleotides to be useful as a sensor, the structure of the oligonucleotides must be preserved. Recently, the Sharpless group has introduced a triazolylamine copper ligand, tris-(benzyltriazolylmethyl)amine, that can accelerate the cycloaddition reaction. 10 At the same time, this ligand was found to significantly deter the redox chemistry of Cu(I) with oxygen, which is essential for preventing damage to the oligonucleotides. Encouraged by the highly desirable features of the Cu(I)TBTA-catalyzed azide-alkyne cycloaddition, we studied its applicability to the attachment of oligonucleotide probes onto well-defined SAMs.Oligode...

We recently reported a novel system shown schematically in Figure 1A in which intact lipid vesicles were assembled on a fluidsupported bilayer using oligonucleotide tethers. 1 Functionalized oligonucleotides were covalently attached to the surface of preformed lipid vesicles by incorporating a small fraction of lipids with reactive headgroups during vesicle assembly. Vesicles displaying oligonucleotides were then tethered to a fluid-supported bilayer displaying oligonucleotides of complementary sequence. These tethered vesicles retain their integrity and diffuse parallel to the plane of the supporting bilayer. Encoded arrays of tethered vesicles were created by displaying orthogonal sequences of oligonucleotides on a patterned bilayer surface. 2,3 A major drawback of this method is the requirement for the inclusion of a reactive lipid during the vesicle assembly process. This may be incompatible with vesicles containing proteins (proteoliposomes), the ultimate target of the tethering strategy, due to side reactions with the protein or special features of the proteoliposome assembly. Furthermore, it is desirable to control as much as possible the number of oligonucleotides displayed on the surface and to avoid side reactions such as hydrolysis of the reactive headgroup that leaves unwanted and uncontrolled levels of impurities on the vesicle surface. We now report the synthesis of an amphiphilic oligonucleotide species ( Figure 1B) which is soluble in buffer but inserts cleanly into preformed vesicles and proteoliposomes of varying composition under mild conditions for sequence-specific tethering onto a fluidsupported bilayer ( Figure 1C). This method should be more generally useful not only for synthetic vesicles and proteoliposomes but also for native vesicles and cells.To achieve this goal, we utilized a simple method for functionalization and subsequent modification of oligonucleotides on the 5′-end prior to cleavage from the DNA synthesis column. 4 The terminal dimethoxytrityl (DMT) group was removed and reacted with an iodination reagent, (PhO) 3 PCH 3 I, to render the 5′-end electrophilic. Treatment with a lipid-thiolate 5 followed by deprotection, cleavage, and reverse-phase HPLC purification yielded the desired product ( Figure 1B) (see Supporting Information for details). A complementary set of 24-mer oligonucleotides (sequences A and A′) were synthesized and modified in this way ((C 18 ) 2 -A, (C 18 ) 2 -A′). 7 Egg yolk phosphatidylcholine (PC) vesicles containing Texas Red 1,2-dihexadecanoyl-phosphatidylethanolamine (Texas Red DHPE) (1 mol %) for visualization and unlabeled PC vesicles containing 2 mol % 1,2-dipalmitoyl phosphatidylserine (DPPS) were prepared by extrusion through 100 nm polycarbonate membranes at approximate lipid concentrations of 10 mg/mL. (C 18 ) 2 -A and (C 18 ) 2 -A′ were dissolved in a 50/50 (v/v) mixture of buffer and acetonitrile to 10 µM and added to these preformed Texas Red DHPE and unlabeled PC/DPPS vesicles, respectively, and incubated at 4°C for 4 h. 8 The (C 18 ) 2 -DN...

Most small-molecule drug candidates fail before entering the market, frequently because of unexpected toxicity. Often, toxicity is detected only late in drug development, because many types of toxicities, especially idiosyncratic adverse drug reactions (IADRs), are particularly hard to predict and detect. Moreover, drug-induced liver injury (DILI) is the most frequent reason drugs are withdrawn from the market and causes 50% of acute liver failure cases in the United States. A common mechanism often underlies many types of drug toxicities, including both DILI and IADRs. Drugs are bioactivated by drug-metabolizing enzymes into reactive metabolites, which then conjugate to sites in proteins or DNA to form adducts. DNA adducts are often mutagenic and may alter the reading and copying of genes and their regulatory elements, causing gene dysregulation and even triggering cancer. Similarly, protein adducts can disrupt their normal biological functions and induce harmful immune responses. Unfortunately, reactive metabolites are not reliably detected by experiments, and it is also expensive to test drug candidates for potential to form DNA or protein adducts during the early stages of drug development. In contrast, computational methods have the potential to quickly screen for covalent binding potential, thereby flagging problematic molecules and reducing the total number of necessary experiments. Here, we train a deep convolution neural network—the XenoSite reactivity model—using literature data to accurately predict both sites and probability of reactivity for molecules with glutathione, cyanide, protein, and DNA. On the site level, cross-validated predictions had area under the curve (AUC) performances of 89.8% for DNA and 94.4% for protein. Furthermore, the model separated molecules electrophilically reactive with DNA and protein from nonreactive molecules with cross-validated AUC performances of 78.7% and 79.8%, respectively. On both the site- and molecule-level, the model’s performances significantly outperformed reactivity indices derived from quantum simulations that are reported in the literature. Moreover, we developed and applied a selectivity score to assess preferential reactions with the macromolecules as opposed to the common screening traps. For the entire data set of 2803 molecules, this approach yielded totals of 257 (9.2%) and 227 (8.1%) molecules predicted to be reactive only with DNA and protein, respectively, and hence those that would be missed by standard reactivity screening experiments. Site of reactivity data is an underutilized resource that can be used to not only predict if molecules are reactive, but also show where they might be modified to reduce toxicity while retaining efficacy. The XenoSite reactivity model is available at .