Rational design, discovery, and synthesis of a novel series of potent growth hormone secretagogues

In the joint experimental and computational efforts reported here to obtain novel chemical entities as growth hormone secretagogues (GHSs), a small database of peptides and non-peptides known to have GHS activity was used to generate and assess a 3D pharmacophore for this activity. This pharmacophore was obtained using a systematic and efficient procedure, "DistComp", developed in our laboratory. The 3D pharmacophore identified was then used to search 3D databases to explore chemical structures that could be novel GHSs. A number of these were chosen for synthesis and assessment of their ability to release growth hormone (GH) from rat pituitary cells. Among the compounds tested, those with a benzothiazepin scaffold were discovered with micromolar activity. To facilitate lead optimization, a second program, a site-dependent fragment QSAR procedure was developed. This program calculates a library of chemical and physical properties of "fragments" or chemical components in a known pharmacophore and determines which, if any, of these properties are important for the observed activity. The combined use of the 3D pharmacophore and the results of the site-dependent fragment QSAR analysis led to the discovery and synthesis of a novel series of potent GHSs, a number of which had nanomolar in vitro activity.

Differentiation of delta, mu, and kappa opioid receptor agonists based on pharmacophore development and computed physicochemical properties

Compounds that bind with significant affinity to the opioid receptor types, delta, mu, and kappa, with different combinations of activation and inhibition at these three receptors could be promising behaviorally selective agents. Working on this hypothesis, the chemical moieties common to three different sets of opioid receptor agonists with significant affinity for each of the three receptor types delta, mu, or kappa were identified. Using a distance analysis approach, common geometric arrangements of these chemical moieties were found for selected delta, mu, or kappa opioid agonists. The chemical and geometric commonalities among agonists at each opioid receptor type were then compared with a non-specific opioid recognition pharmacophore recently developed. The comparison provided identification of the additional requirements for activation of delta, mu, and kappa opioid receptors. The distance analysis approach was able to clearly discriminate kappa-agonists, while global molecular properties for all compounds were calculated to identify additional requirements for activation of delta and mu receptors. Comparisons of the combined geometric and physicochemical properties calculated for each of the three sets of agonists allowed the determination of unique requirements for activation of each of the three opioid receptors. These results can be used to improve the activation selectivity of known opioid agonists and as a guide for the identification of novel selective opioid ligands with potential therapeutic usefulness.

Comparison of a new class of pyrrole containing benzodiazepine ligands to the pyrazoloquinolinones CGS 9896, 9895, and 8216

Four pyrazoloquninolinone compounds, variations of known high affinity ligands for the GABA A/Benzodiazepine receptors (BDZRs), were synthesized and their affinities for BDZRs in cerebellum and spinal cord measured and compared to the parent compounds, CGS 8216, CGS 9895, and CGS 9896. Using the techniques of computational chemistry, specific properties of both types of compounds were calculated and evaluated for the extent to which they fulfill the minimum postulated requirements for recognition of a cerebellum, "Type I", BDZR embodied in our current three dimensional pharmacophore. Additional properties were also calculated and examined as possible further determinants of recognition of the receptor subtype.

Quantum chemical studies of a model for peptide bond formation. 3. Role of magnesium cation in formation of amide and water from ammonia and glycine

The SN2 reaction between glycine and ammonia molecules with magnesium cation Mg2+ as a catalyst has been studied as a model reaction for Mg(2+)-catalyzed peptide bond formation using the ab initio Hartree-Fock molecular orbital method. As in previous studies of the uncatalyzed and amine-catalyzed reactions between glycine and ammonia, two reaction mechanisms have been examined, i.e., a two-step and a concerted reaction. The stationary points of each reaction including intermediate and transition states have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of each reaction. Substantial decreases in free energies of activation were found for both reaction mechanisms in the Mg(2+)-catalyzed amide bond formation compared with those in the uncatalyzed and amine-catalyzed amide bond formation. The catalytic effect of the Mg2+ cation is to stabilize both the transition states and intermediate, and it is attributed to the neutralization of the developing negative charge on the electrophile and formation of a conformationally flexible nonplanar five-membered chelate ring structure.

Influence of benzodiazepine binding site ligands on fear-conditioned contextual memory

Eight compounds that bind to the benzodiazepine binding site on the gamma-amino butyric acid(A) (GABA(A)) receptor were assessed for their influence on contextual memory, an aspect of memory affected in various cognitive disorders including Alzheimer's disease. Using a Pavlovian fear-conditioning paradigm, each ligand was evaluated in C57Bl/6 mice in regards to its direct affect on contextual memory and whether the ligand could attenuate scopolamine-induced contextual memory impairment. Of the eight ligands tested, one impaired contextual memory (agonist), six attenuated scopolamine-induced contextual memory impairment (inverse agonists), and one antagonized the ability of an inverse agonist to attenuate scopolamine-induced contextual memory impairment. Hence, further demonstrating the bi-directional influence benzodiazepine binding site ligands are able to exert on memory modulation. This study serves as an initial starting point in the development of pharmacological tools to be used in deciphering how GABA(A) receptors influence contextual memory.

Characterization of novel benzodiazepine ligands in Spodotera frugiperda (Sf-9) insect cells

The goals of the present work were to characterize the binding profile of nine benzodiazepine ligands in Spodotera frugiperda (Sf-9) insect cells expressing specific gamma aminobutyric acid (A) (GABA(A)) receptor subunit combinations and compare the affinities to those for the receptors in the rat cerebellum. Three recombinant baculovirus constructs, each harboring a different GABA(A) receptor subunit, were introduced into insect cells by simultaneous infection. Saturation and competition binding assays were carried out in membranes from Sf-9 cells infected with either alpha1beta2gamma2 or alpha6beta2gamma2 subunit combinations. The affinities of the ligands to the alpha1beta2gamma2 or alpha6beta2gamma2 receptors expressed in Sf-9 cells were similar to the affinities previously determined for the alpha1 or alpha6 subunit-containing GABA(A) receptors in the rat cerebellum, respectively, thus confirming the previously assigned receptor types in the cerebellum.

Molecular determinants of non-specific recognition of delta, mu, and kappa opioid receptors

Identification of the molecular determinants of recognition common to all three opioid receptors embedded in a single three-dimensional (3D) non-specific recognition pharmacophore has been carried out. The working hypothesis that underlies the computational study reported here is that ligands that bind with significant affinity to all three cloned opioid receptors, delta, mu, and kappa, but with different combinations of activation and inhibition properties at these receptors, could be promising behaviorally selective analgesics with diminished side effects. The study presented here represents the first step towards the rational design of such therapeutic agents. The common 3D pharmacophore developed for recognition of delta, mu, and kappa opioid receptors was based on the receptor affinities determined for 23 different opioid ligands that display no specificity for any of the receptor subtypes. The pharmacophore centers identified are a protonated amine, two hydrophobic groups, and the centroid of an aromatic group in a geometric arrangement common to all 23, non-specific, opioid ligands studied. Using this three-dimensional pharmacophore as a query for searching 3D structural databases, novel compounds potentially involved in non-specific recognition of delta, mu, and kappa opioid receptors were retrieved. These compounds can be valuable candidates for novel behaviorally selective analgesics with diminished or no side effects, and thus with potential therapeutic usefulness.

Determinants of recognition of ligands binding to benzodiazepine receptor/GABA(A) receptors initiating sedation

Complementary behavioral and computational studies of 21 structurally diverse, gamma-amino butyric acid (GABA)(A) benzodiazepine receptor ligands that influence spontaneous locomotor activity have been performed in this work. This behavioral endpoint is a well-accepted indicator of sedation particularly for GABA(A)/benzodiazepine receptor ligands. The goal of the work presented here is the identification and assessment of the minimum requirements for ligand recognition of GABA(A)/benzodiazepine receptors leading to activity at the sedation endpoint embedded in a common 3D pharmacophore for recognition. Using the experimental results, together with a systematic computational procedure developed in our laboratory, a five-component 3D pharmacophore for recognition of the GABA(A) receptor subtypes associated with the sedative behavioral response has been developed consisting of: two proton-accepting moieties, a hydrophobic region, a ring with polar moieties and an aromatic ring in a common geometric arrangement in all ligands having an effect at the sedation endpoint. To provide further evidence that the 3D pharmacophore developed embodied common requirements for receptor recognition, a pharmacophore analysis was performed for agonists, inverse agonists and antagonists separately. Each of the resulting pharmacophores contained the same five moieties at comparable distances to those found for the pharmacophore generated using all of them together. This result confirms that this pharmacophore constitutes a recognition pharmacophore representing required features in the overlapping portion of their binding sites. The reliability of this 3D pharmacophore was then assessed in several ways. First, it was determined that ligands that had no effect at the sedation endpoint did not comply with the pharmacophore requirements. Second, four benzodiazepine receptor ligands known to have an effect at the sedation endpoint, but not used in the pharmacophore development were found to satisfy the requirements of this pharmacophore. Third, the geometric and chemical requirements embedded in this pharmacophore were used to search 3D databases resulting in the identification of benzodiazepine receptor ligands known to affect sedation, but not included in the pharmacophore development. Finally, a 3D-quantitative structure analysis procedure (QSAR) model was developed based upon the ligands in the training set superimposed at their sedation pharmacophore points. The 3D-QSAR model shows good predictivity for binding of these ligands to receptor subtypes containing alpha1 but not alpha5 subunits. The pharmacophore developed for the sedation endpoint thus provides a predictive binding model for diverse ligand binding to alpha1 containing receptor subtypes.

Characterization of benzodiazepine receptors in the cerebellum

1. The goals of the work reported here were to further characterize benzodiazepine/GABA(A) (BDZR) receptor heterogeneity in the cerebellum and to measure the affinities and selectivities of structurally diverse benzodiazepines at each site identified. 2. Five chemical families were included in these studies. These were 1,4-benzodiazepines (flunitrazepam), imidazobenzodiazepines (RO15-1788 and RO15-4513 and RO16-6028), beta-carbolines (Abecarnil) and pyrazoloquinolines (CGS 8216, CGS 9895 and CGS 9896). 3. Saturation and competition binding assays were combined with powerful data analysis software developed in our laboratory. Among the capabilities of this software is the identification of multiple binding sites for a cold ligand using a non-selective labeled ligand that binds with equal, but high, affinity to all the binding sites 4. Saturation binding assays using either [3H]-RO15-1788 or [3H]-RO15-4513 revealed only one apparent binding site, with a higher affinity for RO15-4513 than for RO15-1788. However, using [3H]-RO15-4513 for the competition binding studies in the cerebellum, together with our data analysis software, led to the identification of two distinct binding sites with equal densities for the diverse benzodiazepines studied. 5. In rat cerebellum one of the sites identified corresponds to GABA(A) receptors exhibiting alpha1 subunit pharmacology and the other to GABA(A) receptors exhibiting alpha6 subunit pharmacology. In general, the diverse families of BDZR ligands studied had much lower affinities for the alpha6 containing receptors.

Unraveling the identity of benzodiazepine binding sites in rat hipppocampus and olfactory bulb

The goals of the work reported here were (i) to identify distinct GABA(A)/benzodiazepine receptors in the rat hippocampus and olfactory bulb using receptor binding assays, and (ii) to determine the affinities and selectivities of benzodiazepine receptor ligands from structurally diverse chemical families at each site identified. These studies were aided by the use of software AFFINITY ANALYSIS SYSTEM, developed in our laboratory for analysis of receptor binding data that allows the determination of receptor heterogeneity using non-selective radioligands. Saturation binding assays using [3H]RO15-4513 (ethyl 8-azido-6-dihydro-5-methyl-6-oxo-4H-imidazo[1, 5-a]-[1,4]benzodiazepine-3-carboxylate) revealed two binding sites in each of these two tissues. The higher affinity site corresponds to alpha(5) subunit-containing GABA(A) receptor and the lower affinity site to a combination of alpha(1), alpha(2), and alpha(3) subunit-containing receptors. These results should be useful in the challenging task of identifying the various functional GABA(A) receptors in the central nervous system, and in providing a link between receptor affinities and in vivo activities of the GABA(A)/benzodiazepine receptor ligands studied.

Development of a 3D pharmacophore for nonspecific ligand recognition of alpha1, alpha2, alpha3, alpha5, and alpha6 containing GABA(A)/benzodiazepine receptors

Transfected cells containing GABA(A) benzodiazepine receptors (BDZRs) have been utilized to systematically determine the affinity of ligands at alpha1, alpha2, alpha3, alpha5 and alpha6 subtypes in combination with beta2 and gamma2. All but a few of the ligands thus far studied have relatively high affinities for each of these alpha subtype receptors. Thus, these ligands must contain common stereochemical properties favorable for recognition by each of the subtype combinations. In the present work, such a common three-dimensional (3D) pharmacophore for recognition of alpha1, alpha2, alpha3, alpha5 and alpha6 containing GABA(A)/BDZRs types of receptors has been developed and assessed, using as a database receptor affinities measured in transfected cells for 27 diverse compounds. The 3D-recognition pharmacophore developed consists of three proton accepting groups, a hydrophobic group, and the centroid of an aromatic ring found in a common geometric arrangement in the 19 nonselective ligands used. Three tests were made to assess this pharmacophore: (i) Four low affinity compounds were used as negative controls, (ii) Four high affinity compounds, excluded from the pharmacophore development, were used as compounds for pharmacophore validation, (iii) The 3D pharmacophore was used to search 3D databases. The results of each of these types of assessments provided robust validation of the 3D pharmacophore. This 3D pharmacophore can now be used to discover novel nonselective ligands that could be activation selective at different behavioral end points. Additionally, it may serve as a guide in the design of more selective ligands, by determining if candidate ligands proposed for synthesis conform to this pharmacophore and selecting those that do not for further experimental assessment.

Benzodiazepine-induced hyperphagia: development and assessment of a 3D pharmacophore by computational methods

Benzodiazepine receptor (BDZR) ligands are structurally diverse compounds that bind to specific binding sites on GABA(A) receptors and allosterically modulate the effect of GABA on chloride ion flux. The binding of BDZR ligands to this receptor system results in activity at multiple behavioral endpoints, including anxiolytic, sedative, anticonvulsant, and hyperphagic effects. In the work presented here, a computational procedure developed in our laboratory has been used to obtain a 3D pharmacophore for ligand recognition of the GABA(A)/BDZRs initiating the hyperphagic response. To accomplish this goal, 17 structurally diverse compounds, previously assessed in our laboratory for activity at the hyperphagic endpoint, were used. The result is a four-component 3D pharmacophore. It consists of two proton acceptor atoms, the centroid of an aromatic ring and the centroid of a hydrophobic moiety in a common geometric arrangement in all compounds with activity at this endpoint. This 3D pharmacophore was then assessed and successfully validated using three different tests. First, two BDZR ligands, which were included as negative controls in the set of seventeen compounds used for the pharmacophore development, did not fit the pharmacophore. Second, some benzodiazepine ligands known to have activity at the hyperphagia endpoint, but not included in the pharmacophore development, were used as positive controls and were found to fit the pharmacophore. Finally, using the 3D pharmacophore developed in the present work to search 3D databases, over 50 classical benzodiazepines were found. Among them, were benzodiazepine ligands known to have an effect at the hyperphagic endpoint. In addition, the novel compounds also found in this search are promising therapeutic agents that could beneficially affect feeding behavior.

3D modeling, ligand binding and activation studies of the cloned mouse delta, mu; and kappa opioid receptors

Refined 3D models of the transmembrane domains of the cloned delta, mu and kappa opioid receptors belonging to the superfamily of G-protein coupled receptors (GPCRs) were constructed from a multiple sequence alignment using the alpha carbon template of rhodopsin recently reported. Other key steps in the procedure were relaxation of the 3D helix bundle by unconstrained energy optimization and assessment of the stability of the structure by performing unconstrained molecular dynamics simulations of the energy optimized structure. The results were stable ligand-free models of the TM domains of the three opioid receptors. The ligand-free delta receptor was then used to develop a systematic and reliable procedure to identify and assess putative binding sites that would be suitable for similar investigation of the other two receptors and GPCRs in general. To this end, a non-selective, 'universal' antagonist, naltrexone, and agonist, etorphine, were used as probes. These ligands were first docked in all sites of the model delta opioid receptor which were sterically accessible and to which the protonated amine of the ligands could be anchored to a complementary proton-accepting residue. Using these criteria, nine ligand-receptor complexes with different binding pockets were identified and refined by energy minimization. The properties of all these possible ligand-substrate complexes were then examined for consistency with known experimental results of mutations in both opioid and other GPCRs. Using this procedure, the lowest energy agonist-receptor and antagonist-receptor complexes consistent with these experimental results were identified. These complexes were then used to probe the mechanism of receptor activation by identifying differences in receptor conformation between the agonist and the antagonist complex during unconstrained dynamics simulation. The results lent support to a possible activation mechanism of the mouse delta opioid receptor similar to that recently proposed for several other GPCRs. They also allowed the selection of candidate sites for future mutagenesis experiments.

Homology modeling and substrate binding study of human CYP2C18 and CYP2C19 enzymes

It is well established that the variable binding-site architecture and composition of the P450 metabolizing heme proteins are major modulators of substrate and product specificity. Even the three closely related human liver isozymes, CYP2C9, CYP2C18, and CYP2C19, do not share all substrates and do not always lead to the same preferred hydroxylation products. The lack of knowledge of their three-dimensional (3D) structures has hindered efforts to understand the differences in their specificities. Building on previous work for the CYP2C9 enzyme, 3D models of CYP2C18 and 2C19 have been constructed and validated by computational methods developed and tested in our laboratory. They were used to characterize explicit enzyme-substrate complexes using the isoform-specific substrates progesterone and (S)-mephenytoin for 2C19 and 2-[2,3-dichloro-4-(3-hydroxypropyloxy)benzoyl]thiophene for 2C18. The results allowed both common and unique binding-site residues to be identified in each model. The calculated preferred hydroxylation site was obtained for each substrate and was found to be consistent with experimental observation. Comparisons were made among the 2C9, 2C18, and 2C19 model binding sites to investigate the subtle differences among them. These models can be used as structure-based guides for mutagenesis studies and screening of potential pharmaceuticals or toxins.

Homology modeling and substrate binding study of human CYP2C9 enzyme

The CYP2C subfamily of human liver P450 isozymes is of major importance in drug metabolism. The most abundant 2C isozyme, CYP2C9, regioselectively hydroxylates a wide variety of substrates. A major obstacle to understanding this specificity in human CYP2C9 is the absence of a 3D structure. A 3D model of CYP2C9 was built, assessed, and used to characterize explicit enzyme-substrate complexes using methods previously developed in our laboratory. The 3D model was assessed by determining its stability to unconstrained molecular dynamics and by comparison of specific properties with those of known protein structures. The CYP2C9 model was then used to characterize explicit enzyme complexes with three structurally and chemically diverse substrates: (S)-naproxen, phenytoin, and progesterone. Each substrate was found to bind to the enzyme with a favorable interaction energy and to remain in the binding site during unconstrained molecular dynamics. Moreover, the mode of binding of each substrate led to calculated preferred hydroxylation sites consistent with experiment. Binding-site residues identified for the models included Arg 105 and Arg97 as key cationic residues, as well as Asn 202, Asp 293, Pro 101, Leu 102, Gly 296, and Phe 476. Site-specific mutations are proposed for further integrated computational and experimental study.

Molecular dynamics simulations of P450 BM3--examination of substrate-induced conformational change

Cytochrome P450 BM3, of bacterial origin, is one of only five isozymes of the ubiquitous family of over 400 metabolizing heme proteins with a known crystal structure and only one of two with both substrate-free and substrate-bound forms determined. P450 BM3 is of particular interest since it has a similar function and similar substrates as mammalian P450s particularly of the 4A subfamily. Thus, the extent to which the substrate-free form of P450 BM3 undergoes a conformational change upon binding of a typical fatty acid substrate, palmitoleic acid, has been the subject of recent active experimental effort. Surprisingly, direct examination of the substrate-free (pdb2hpd.ent and pdb2bmh.ent) and substrate-bound (pdb1fag.ent) forms do not provide a clear answer to this question. The main reason for this ambiguity is that the two substrate-free monomers reported in the crystal structures themselves have significantly different conformations from each other, one with a more open substrate-access channel than the other. Since there is no way to tell to which substrate-free form the substrate binds, the effect of substrate binding cannot be deduced directly from comparisons of the experimental substrate-bound and substrate-free forms. The computational studies reported here have been designed to more robustly establish the effect of substrate binding on this isozyme. Specifically, molecular dynamics simulations were performed for each of the two substrate-free forms found in the asymmetric unit of the X-ray structure and for the two corresponding substrate-bound forms, constructed by docking palmitloeic acid into each of them. Comparisons of the results showed that palmitoleic acid binding had little effect on the conformation of the more closed substrate-free form of P450 BM3. By contrast, in the more open substrate-free form, this same substrate induced a closing of the entrance to the substrate-binding channel. The MD averaged structure of these two complexes obtained from docking of pamitoleic acid into the two asymmetric units of the substrate-free form were also compared to that obtained starting with the X-ray structure of the substrate-bound form. These results taken together led to the conclusion that, if indeed the substrate induces conformational changes in P450 BM3, the mouth of the substrate-access channel first closes down in response to the presence of the substrate, followed by rotation of the F-G domain to further optimize the P450 BM3-substrate interaction that would occur at a later stage.

Homology modeling and substrate binding study of human CYP4A11 enzyme

Although both bacterial CYP102 (P450BM3) and mammalian CYP4A isozymes share a common function as fatty acid hydroxylases, distinctly different preferred sites of oxidation are observed with the CYP102 performing the usual non-terminal hydroxylation or epoxidation and the CYP4A enzymes performing the unusual and enigmatic terminal hydroxylation. The origin of this unique product specificity in human CYP4A11 has been explored in this work, focusing on possible differences in the binding site architecture of the two isozymes as the cause. To this end, 3D model structures of the human CYP4A11 enzyme were built and compared to the X-ray structure of CYP102. The substrate-binding channel identified in CYP4A11 was found to have a much more sterically restricted active site than that in CYP102 that could cause limited access of long-chain fatty acid to the ferryl oxygen leading to the preferred omega-hydroxylation. Results of docking of a common substrate, lauric acid, into the binding site of both CYP4A11 and CYP102 and molecular dynamics simulations provided additional support for this hypothesis. Specifically, in the CYP4A11-lauric acid simulations, the omega hydrogens were closest to the ferryl oxygen most of the time. By contrast, in the CYP102-lauric acid complex, the substrate could penetrate further into the active site providing access of the non-terminal (omega-1, omega-2) positions to the ferryl oxygen. These results, taken together, have elucidated the origin of the unusual product specificity of CYP4A11 and illustrated the central role of binding site architecture in subtle modulation of function.

Construction of a 3D model of cytochrome P450 2B4

A three-dimensional structural model of rabbit phenobarbital-inducible cytochrome P450 2B4 (LM2) was constructed by homology modeling techniques previously developed for building and evaluating a 3D model of the cytochrome P450choP isozyme. Four templates with known crystal structures including cytochrome P450cam, terp, BM-3 and eryF were used in multiple sequence alignments and construction of the cytochrome P450 2B4 coordinates. The model was evaluated for its overall quality using available protein analysis programs and found to be satisfactory. The model structure was stable at room temperature during a 140 ps unconstrained full protein molecular dynamics simulation. A putative substrate access channel and binding site were identified. Two different substrates, benzphetamine and androstenedione, that are metabolized by cytochrome P450 2B4 with pronounced product specificity were docked into the putative binding site. Two orientations were found for each substrate that could lead to the observed preferred products. Using a geometric fit method three regions on the surface of the model cytochrome P450 structure were identified as possible sites for interaction with cytochrome b5, a redox partner of P450 2B4. Residues that may interact with the substrates and with cytochrome b5 have been identified and mutagenesis studies are currently in progress.

Thermodynamics of ligand binding to the cloned delta-opioid receptor

The goal of this study was to determine the relative contribution of entropy and enthalpy to the free energies of binding to recombinant mouse delta-opioid receptors for the peptide agonist, DPDPE ([D-Pen2,D-Pen5]enkephalin), the peptide antagonist, TIPP(psi) (Tyr-Tic(psi)[CH2NH]Phe-Phe-OH), the nonpeptide agonist, SNC80 ((+)-4-[(alphaR)-alpha-((2S,5R)-4-allyl-2,5-dimethyl-1-piperazinyl )-3-methoxybenzyl]-N,N-diethylbenzamide), and the nonpeptide antagonist, naltrindole. Competitive binding studies were carried out using [3H]naltrindole at 0 degrees C, 12 degrees C, 25 degrees C and 37 degrees C, the affinities calculated and van't Hoff plots constructed for each ligand. The temperature dependence of binding and van't Hoff plots indicated that the entropy contribution is the major component of the free energy, for all four ligands, independent of its activity or chemical nature.

Refinement of 3D models of horseradish peroxidase isoenzyme C: predictions of 2D NMR assignments and substrate binding sites

In this study, two alternative three-dimensional (3D) models of horseradish peroxidase (HRP-C)-differing mainly in the structure of a long untemplated insertion-were refined, systematically assessed, and used to make predictions that can both guide and be tested by future experimental studies. A key first step in the model-building process was a procedure for multiple sequence alignment based on structurally conserved regions and key conserved residues, including those side chains providing ligands to the two Ca2+ binding sites. The model refinements reported here include (1) optimization of side-chain conformations; (3) addition of structural waters using a template-independent procedure; (2) structural refinement of the untemplated 34 amino acid insertion located between the F and G helices, using both energy criteria and NMR data; (4) unconstrained energy optimization of the refined models. Using these procedures, two refined structures of HRP-C were obtained, differing mainly in the conformation of this long insertion. The presence of residues in this insertion that could potentially interact with bound substrates suggests a functional role that may be related to the general ability of class III peroxidases to form stable 1:1 complexes with a variety of substrates. The structural validity of the models was systematically assessed by a variety of criteria. Most notably, the ProsaII z scores and Profiles 3D scores of the two HRP-C models indicated that they are significantly better than would be obtained by simple amino acid replacement, using any of the known structures as a template. These two 3D HRP-C models, were then used to predict candidate residues for the assignment of NOESY cross-peaks previously noted in 2D-NMR studies. Specifically, the residues known as Ile X, Phe A, Phe B, aliphatic residue Q, and Ile T. Candidate substrate binding sites were also identified and compared with experimentally based predictions. This work is timely because new X-ray structures are anticipated that will facilitate the validation of these procedures.

Evidence for mu1-opioid receptor involvement in fentanyl-mediated respiratory depression

Several fentanyl analogs (Bagley et al., 1989, J. Med. Chem. 32, 663) were compared to fentanyl and morphine for their effects on respiratory depression as determined by arterial blood gas (pH, pCO2 and pO2) measurements. Fentanyl (0.1 mg/kg), morphine (10 mg/kg), #16 (1-phenethyl-4-[N-(pyridin-2-yl)-N-(methoxymethylcarbonyl)amino] piperidine, 1 mg/kg), #17 (1-phenethyl-4-[N-(pyridin-2-yl) -N-(2-furoyl)amino]piperidine, 0.5 mg/kg) and #29 (1-phenethyl-4-[N- (pyrimidin-2-yl)-N-(methoxy-methylcarbonyl) amino]piperidine, 10 mg/kg) produced significant respiratory depression in rats. Pretreatment with the mu1-opioid receptor selective antagonist, naloxonazine (10 mg/kg), blocked the respiratory effect of fentanyl and its analogs, but not that of morphine. The results suggest that the mu1-opioid receptor plays an important role in the respiratory effects of fentanyl and its analogs. Hence, the mechanism of fentanyl-induced respiratory depression appears to be distinct from that produced by morphine. The most likely explanation for this difference is the possible contribution of muscle rigidity and catalepsy to the observed changes in blood gas parameters caused by the fentanyl analogs, while the respiratory depression of morphine, measured by these same parameters, appears to be independent of its effect on muscle rigidity.

Construction and evaluation of a three-dimensional structure of cytochrome P450choP enzyme (CYP105C1)

The purpose of this work was to develop and carefully evaluate improved strategies for constructing reliable 3-D models of P450 isozymes. To this end, a unique combination of steps for building and evaluating a model structure was used to build a homology model of the P450choP isozyme, based on knowledge of the X-ray structures of P450cam, P450terp, P450BM-3 and P450eryF. Specifically, the reliability of this model was examined by systematic comparisons of its conformational, energetic, environmental and packing properties and those of the four reference proteins with corresponding properties from the database of proteins with known structures. The results showed that the examined properties of this model structure are well within the criteria established for reliable structures and are of nearly as good quality as those of the reference proteins. In addition, the result from a 120 ps unconstrained MD simulation of the model with structural waters provided evidence that the model is stable at room temperature. This 3-D model can now be reliably used for explicit characterization of substrate and inhibitor complexes. Most importantly, although it is envisioned that building models for mammalian P450s will be even more challenging, the steps described here should be very useful in future construction of 3-D models of mammalian P450 isozymes.

Investigation of the proton-assisted pathway to formation of the catalytically active, ferryl species of P450s by molecular dynamics studies of P450eryF

The recently determined crystal structure of cytochrome P450eryF (6-deoxyerythronolide B hydroxylase; CYP107A1) in its ferric heme substrate-bound form has been used to address one of the most fundamental unresolved aspects of the mechanism of oxidation common to this ubiquitous family of metabolizing heme proteins, the pathway from the twice reduced dioxygen species to the putative catalytically active ferryl oxygen species. Both of these species are too transient to have been characterized experimentally, and the transformation from one to the other has been only partially characterized. The observed requirement of two protons and the formation of water in this transformation suggests a proton-assisted dioxygen bond cleavage as a plausible pathway. However, this pathway is difficult to establish by experiment alone, and the source of the protons in the largely hydrophobic binding pocket of the P450s remains unclear. In this work we have performed molecular dynamics simulations of the twice reduced dioxygen substrate-bound form of this isozyme in order to (i) determine the plausibility of the proposed pathway to compound I formation, a proton-assisted cleavage of the dioxygen bond, and (ii) investigate the possible source of these protons. The analysis of the molecular dynamics trajectories of this species does indeed provide further evidence for this pathway and points to a source of protons. Specifically, two dynamically stable hydrogen bonds to the distal oxygen atom of the dioxygen ligand, one by the substrate and the other by a bound water, are found, consistent with the proposed proton-assisted cleavage of the bond and formation of water. In addition, an extensive dynamically stable hydrogen bond network is formed that connects the distal oxygen to Glu 360, a well-conserved residue in a channel accessible to solvent that could be the ultimate source of protons. The simulations were done for both a protonated and unprotonated Glu and led to a proposed mechanism of proton transfer by it to the distal oxygen atom. In order to validate the procedures used for the simulation of this transient twice-reduced species, we have used these same procedures to perform molecular dynamics simulations of two other forms of P450eryF, the ferric and ferryl substrate-bound species, and compared the results with experiment. The results for the ferric substrate-bound species were assessed by comparisons to the experimentally determined X-ray structure and fluctuations, and good agreement was found. The simulations performed for the ferryl substrate-bound species led to the correct prediction of the observed regio- and stereospecific hydroxylation of its natural substrate, 6-deoxyerythronolide B (6-DEB) at the 6S position. The results of these two additional studies lend credibility to the important mechanistic inferences from the simulations of the transient twice reduced dioxygen species: further evidence for a proton-assisted pathway from it to the catalytically active ferryl species and a possible source of the protons.

A 3D model of the delta opioid receptor and ligand-receptor complexes

A model for the 3D structure of the transmembrane domain of the delta opioid receptor was predicted from the sequence divergence analysis of 42 sequences of G-protein coupled peptide hormone receptors belonging to the opioid, somatostatin and angiotensin receptor families. No template was used in the prediction steps, which include multiple sequence alignment, calculation of a variability profile of the aligned sequences, use of the variability profile to identify the boundaries of transmembrane regions, prediction of their secondary structure, optimization of the packing shape in a helix bundle, prediction of side chain conformations and structural refinement. The general shape of the model is similar to that of the low resolution rhodopsin structure in that the TM3 and TM7 helices are most buried in the bundle and the TM1 and TM4 helices are most exposed to the lipid phase. An initial assessment of this model was made by determining to what extent a binding site identified using four structurally disparate high affinity delta opioid ligands was consistent with known mutational studies. With the assumption that the protonated amine nitrogen, a feature common to all delta opioid ligands, interacts with the highly conserved Asp127 in TM3, a pocket was found that satisfied the criteria of complementarity to the requirements for receptor recognition for these four diverse ligands, two delta selective antagonists (the fused ring naltrindole and the peptide Tyr-Tic-Phe-Phe-NH2) and the two agonists lofentanil and BW373U86 deduced from previous studies of the ligands alone. These ligands could be accommodated in a similar region of the receptor. The receptor binding site identified in the optimized complexes contained many residues in positions known to affect ligand binding in G-protein coupled receptors. These results also allowed identification of key residues as candidates for point mutations for further assessment and refinement of this model as well as preliminary indications of the requirements for recognition of this receptor.

Characterization of the bioactive form of linear peptide antagonists at the omega-opioid receptor

The stereochemical requirements for omega-opioid receptor binding of a series of linear peptide antagonists with a novel conformationally restricted Phe analogue (Tic) as a second residue were examined by using a variety of computational chemistry methods. The omega-opioid receptor analogues with significant affinity, Tyr-Tic-NH2(TI-NH2), Tyr-Tic-Phe-OH(TIP), Tyr-Tic-Phe-NH2(TIP-NH2), Tyr-Tic-Phe-Phe-OH(TIPP), Tyr-Tic-Phe-Phe-NH2)(TIPP-NH2), and the low affinity omega-opioid peptides Tyr-Pro-Phe-Pro-NH2(morphiceptin) and Tyr-Phe-Phe-Phe-NH2 (TPPP-NH2), were included in this study. The conformational profiles of these peptides were obtained by consecutive cycles of high and low temperature molecular dynamic stimulations, coupled to molecular mechanical energy minimization carried out until no new conformational minima were obtained. Comparing the results for TPPP-NH2 and TIPP-NH2, the presence of the conformationally restricted Tic residue did not greatly reduce the number of unique low energy conformations, but did allow low energy conformers involving cis bonds between the first two residues. The conformational libraries of these peptides were examined for their ability to satisfy the three key ligand components for receptor recognition already identified by previous studies of high affinity cyclic (Tyr1-D-Pen2-Gly3-Phe4-D-Pen5) enkephalin (DPDPE) type agonists: a protonated amine group, an aromatic ring, and a lipophilic moiety in a specific geometric arrangement. Two types of conformations common to the five high omega-opioid affinity L-Tic analogues were found that satisfied these requirements, one with a cis and the other with a trans peptide bond between the Tyr1 and Tic2 residues. Moreover, both the Tic2 and Phe3 residues could mimic the hydrophobic interactions with the receptor of the Phe4 moiety in the cyclic DPDPE type agonists, consistent with the appreciable affinity of both di- and tripeptides. The low omega-opioid receptor affinity of morphiceptin can be understood as the result of conformational preferences that prevent the fulfillment of this pharmacophore for recognition.

The hyperphagic effect of 3 alpha-hydroxylated pregnane steroids in male rats

Like benzodiazepines receptor (BDZR) ligands, 3 alpha-hydroxylated, 5 alpha, or 5 beta pregnane steroids are sedative, anticonvulsant, and anxiolytic. BDZR ligands also modulate the feeding response. Therefore, in this study we have investigated the effects of four 3 alpha-hydroxylated pregnane steroids-Pregnanolone (3 alpha-hydroxy-5 beta-pregnan-20-one), allopregnanolone (3 alpha-hydroxy-5 alpha-pregnan-20-one), alphaxalone (3 alpha-hydroxy-5 alpha-pregnan-11,20-dione), and 5 beta-pregnanediol (5 beta-pregnan-3 alpha,20 alpha-diol) on food intake. In non-food deprived male rats, all four steroids increased the consumption of a palatable diet. For pregnanolone (1-10 mg/kg), hyperphagia was found at lower doses than its anxiolytic effect (5-10 mg/kg) as determined using the elevated plus maze test. The presumed steroid antagonists, isopregnanolone (3 beta-hydroxy-5 alpha-pregnan-20-one) (10 mg/kg) and pregnenolone sulfate (2 mg/kg), and the BDZ antagonist, Ro15-1788 (20 mg/kg), did not reverse the hyperphagic effect of pregnanolone. Picrotoxin, a GABAA receptor antagonist, dose dependently and at a subconvulsive dose (1.5 mg/kg), reversed the hyperphagic effect of pregnanolone and alphaxalone, but had no effect on allopregnanolone- and 5 beta-pregnanediol-induced hyperphagia. These results indicate that the hyperphagic effects of pregnanolone and alphaxalone are mediated by the GABAA receptor but not by direct interaction with BDZ receptors. However, allopregnanolone- and 5 beta-pregnanediol-induced hyperphagia may be mediated by other receptor systems. Because some 3 alpha-hydroxylated pregnane steroids are endogenous progesterone metabolites, they may play an important role in appetite control.

Putative benzodiazepine partial agonists demonstrate receptor heterogeneity

This study explored whether the behavioral heterogeneity of benzodiazepine receptor (BDZR) ligands is a consequence of multiple receptor subtypes or partial agonism. Putative partial agonists Ro16-6028, Ro23-1590, Ro23-0364, and abecarnil were compared with U78875, a mixed agonist-antagonist, and CGS8216, an inverse agonist, in five BDZR-mediated functions: hyperphagia, anxiolysis, sedation, hypothermia, and anticonvulsant activity. Only abecarnil was an agonist in all end points. Each of the other drugs exhibited qualitatively different responses at these end points. Specifically, Ro23-0364 produced no effect on body temperature, but was an agonist at other tests. Ro23-1590 had no effect on anxiolysis and hypothermia, but was an agonist at other tests. In contrast to other putative partial agonists, Ro16-6028 was found to be an antagonist in sedation and U78875 was an antagonist in hypothermia, but both were agonists at other end points. These qualitative differences in activity in the five behavioral end points studied cannot be explained by partial agonism at a single receptor and indicate that these ligands differentially activate multiple BDZR subtypes.

Computer modeling of 3D structures of cytochrome P450s

The understanding of structure-function relationship of enzymes requires detailed information of their three-dimensional structure. Protein structure determination by X-ray and NMR methods, the two most frequently used experimental procedures, are often difficult and time-consuming. Thus computer modeling of protein structures has become an increasingly active and attractive option for obtaining predictive models of three-dimensional protein structures. Specifically, for the ubiquitous metabolizing heme proteins, the cytochrome P450s, the X-ray structures of four isozymes of bacterial origin, P450cam, P450terp, P450BM-3 and P450eryF have now been determined. However, attempts to obtain the structure of mammalian forms by experimental means have thus far not been successful. Thus, there have been numerous attempts to construct models of mammalian P450s using homology modeling methods in which the known structures have been used to various extents and in various strategies to build models of P450 isozymes. In this paper, we review these efforts and then describe a strategy for structure building and assessment of 3D models of P450s recently developed in our laboratory that corrects many of the weaknesses in the previous procedures. The results are 3D models that for the first time are stable to unconstrained molecular dynamics simulations. The use of this method is demonstrated by the construction and validation of a 3D model for rabbit liver microsomal P450 isozyme 2B4, responsible for the oxidative metabolism of diverse xenobiotics including widely used inhalation anesthetics. Using this 2B4 model, the substrate access channel, substrate binding site and plausible surface regions for binding with P450 redox partners were identified.

A behaviorally selective class of thiophene-containing benzodiazepine receptor ligands

In a continued effort to probe the role of the aromatic rings in classical 1,4-benzodiazepine (BDZ) ligand pharmacology, a series of new thiophene-containing benzodiazepine receptor (BDZR) ligands were synthesized. As a first step in determining the binding profile and selectivity to BDZR functional subtypes, the affinities in two central nervous system (CNS) regions, cerebellum, in which a single 'Type I' BDZR could be labeled; and spinal cord, in which we have previously demonstrated some receptor heterogeneity, were determined. These compounds were also assessed for their compliance with a recently developed three dimensional pharmacophore for recognition and activation of the 'Type I' BDZR, using the techniques of computational chemistry. The computations showed all ligands synthesized fulfilled the minimum requirements for recognition, further validating the current pharmacophore. Using the criteria for activation, the new ligands were all predicted to be agonists at the cerebellar 'Type I' BDZR. Since the compounds showed reasonable affinity, the behavioral profile of one of them at five in vivo endpoints was determined. This compound demonstrated more behavioral selectivity than the typical 1,4-BDZ ligand. While they fulfilled the requirements for agonist activity at the 'Type I' BDZR, these ligands showed significantly greater delocalization in the electron density distribution in the lowest unoccupied molecular orbital (LUMO), so that either aromatic ring could serve as an electron accepting site, not just the one comparable to the more classical BDZR agonist, flunitrazepam. It is possible that the ability of the second ring in the tested compound (5a) to also function as an electron acceptor can affect the recognition and activation of other receptor types leading to the more discriminate behavioral profile of this thiophene analog compared to flunitrazepam.

Binding of 1,4-benzodiazepines to a novel [3H]Ro15-4513 binding site in the rat spinal cord

An alpidem-insensitive benzodiazepine binding site in the rat spinal cord has recently been identified in our laboratory. We report here the binding of 23 1,4-benzodiazepines to this site using [3H]Ro15-4513 (ethyl-8-azido-6-dihydro-5-methyl-4H-imidazo[1,2- a][1,4]benzodiazepine-3-carboxylate) in the presence of 65 microM alpidem (6-chloro-2-(4-chlorophenyl)-N,N- dipropylimidazo[1,2-a]pyridine-3-acetamide). This binding site displays a wide affinity for 1,4-benzodiazepines, most of which show much higher affinity for benzodiazepine receptors in various brain regions and transfected cell systems. The highest affinity ligands are: brotizolam (1-bromo-4-(2-chlorophenyl)-9-methyl-6H-thieno[3,2- f][1,2,4]triazolo[4,3-a][1,4]diazepine) (4.3 nM), Ro15-4513 (5.0 nM), Ro42-8773 (7-chloro-3-[3-(cyclopropylmethoxy)-1-propynyl]-4,5-dihydro- 5-methyl-6H-imidazo[1,5-a][1,4]benzodiazepine-6-one) (5.7 nM), Ro16-6028 (t-butyl (s)-8-bromo-11,12,13,13a-tetrahydro-9-oxo-9H- imidazo[1,5-a][1,4]benzodiazepine-1-carboxylate) (5.9 nM) and triazolam (8-chloro-6-(2-chlorophenyl)-1-methyl-4H- [1,2,4]triazolo[4,3-a][1,4]benzodiazepine) (7.9 nM). The structural feature common to these compounds is an imidazo- or triazolo-ring on the 1- and 2-position of the benzodiazepine. However, the presence of this feature does not guarantee high affinity binding as Ro15-1788 (8-fluoro-5,6-dihydro-5-methyl-6-oxo-4H-imidazo[1,5- a][1,4]benzodiazepine-3-carboxylic acid ethyl ester) (100 nM) and Ro23-0364 (6-[2-chlorophenyl]-4H- imidazo[1,5-a][1,4]benzodiazepine-3-carboxamide) (360 nM) display much lower affinity for this site. Studies are currently underway to investigate the functional significance of this unusual benzodiazepine binding site.

Food palatability and hunger modulated effects of CGS 9896 and CGS 8216 on food intake

The effect of food palatability and duration of food deprivation on the modulation of food intake by two benzodiazepine receptor (BDZR) ligands, CGS 9896 and CGS 8216, were investigated. Three diets differing in palatability (high, medium, or standard) and three different periods of food deprivation (0, 16, or 24 h) were used in all combinations to compare the effect of these variations on the observed modulation of food consumption by both BDZR ligands. Increasing diet palatability and/or food deprivation increased the baseline food consumption and reduced the sensitivity of the test to the detection of the hyperphagic effect of CGS 9896 but increased the sensitivity to detect the anorexic effect of CGS 8216. Only for the intermediate conditions of food deprivation (16 h) and for a standard or medium palatable diet were both significant hyperphagic effect of CGS 9896 and anorexic effect of CGS 8216 detected. Neither increased palatability nor hunger enhanced the modulation of feeding, indicating that neither "taste preference" nor "hunger" is the key factor in the mechanism of BDZR ligand-induced feeding response.

Resolving receptor heterogeneity using Fourier-derived affinity spectrum analysis and LIGAND: benzodiazepine receptors in the rat spinal cord

In the present study, we combined a powerful and novel receptor binding data analysis technique. Fourier-derived affinity spectrum analysis (FASA), with the nonlinear regression analysis program LIGAND to resolve benzodiazepine receptor heterogeneity in rat spinal cord. With FASA, we identified three distinct [3H]Ro15-1788 binding populations: two high-affinity sites (0.4 and 5 nM) for the radioligand and a lower-affinity site (150 nM) that is insensitive to the imidazopyridine alpidem. With the affinities for the radioligand determined with FASA, the Ki values of 13 competing ligands were calculated with LIGAND. All of the ligands studied displayed the highest affinity for site 1 (the highest-affinity [3H]Ro15-1788 binding site), with the exception of AHR 11797. Site 2 had high affinity for Ro15-1788, lower affinity for flunitrazepam and beta-CCM and very low, but measurable, affinity for zolpidem. The alpidem-insensitive binding site, studied in isolation by performing competitive binding assays in the presence of 65 microM alpidem, showed relatively low affinity for all of the ligands studied, and its physiological relevance is not yet known.

Interaction of an amphiphilic peptide with a phospholipid bilayer surface by molecular dynamics simulation study

Corticotropin-releasing factor (CRF) is the principal neuroregulator of adrenocorticotropic hormone (ACTH) secretion. Previous experiments have demonstrated that CRF binds avidly to the surface of single egg phosphatidylcholine vesicles and its amphiphilic secondary structure might play an important role in the function. In this study, the interaction of the residues 13-41 in human CRF with the surface of a DOPC bilayer was investigated by molecular dynamics (MD) simulation in order to understand the role of the membrane surface in the formation of the amphiphilic alpha helix as well as to determine the effects of the peptide on the lipid bilayer. The model used included 60 DOPC molecules, 1 helical peptide (CRF13-41) on the bilayer surface, and explicit waters of solvation in the lipid polar head group regions, together with constant-volume periodic boundary conditions in three dimensions. The MD simulation was carried out for 510 ps. In addition, CRF13-41, initially in a helical form, was simulated in vacuo as a control. The results indicate that while it was completely unstable in vacuo, the peptide helical form was generally maintained on the bilayer surface, but with distortions near the terminal ends. The peptide was confined to the bilayer headgroup/water region, similar to that reported from neutron diffraction measurement of tripeptides bound to the phosphatidylcholine bilayer surface (Ref 1). The amphiphilicity of the peptide matched that of the bilayer headgroup environment, with the hydrophilic side oriented toward water and the hydrophobic side making contact with the bilayer hydrocarbon core. These results support the hypothesis that the amphiphilic environment of a membrane surface is important in the induction of peptide amphiphilic alpha-helical secondary structure. Two major effects of the peptide on the lipids were found: the first CH2 segment in the lipid chains was significantly disordered and the lipid headgroup distribution was broadened towards the water region.

Molecular dynamics simulation of anesthetic-phospholipid bilayer interactions

To probe the hypothesis of a lipid-mediated mechanism of general anesthetic action on a molecular level, and to help elucidate the nature of the interactions of bioactive compounds with membranes, the effects of trichloroethylene (TCE), an inhalational general anesthetic, on a dioleoylphosphatidylcholine (DOPC) lipid bilayer have been investigated by molecular dynamics (MD) simulations at 37 degrees C and 1 atm and the results compared with 31P and 2H NMR experimental studies (Ref 1). The model used included a single TCE molecule embedded in a lipid bilayer consisting of 24 DOPC molecules and an 8 A layer of explicit water of solvation in each polar head group region of the bilayer, together with constant-pressure periodic boundary conditions in three dimensions. A comparison of the bilayer properties calculated in the presence and absence of the anesthetic led to the detection of three major perturbations of the bilayer caused by the anesthetic at 1 atm: i) an increase in the ratio of the effective areas of hydrocarbon tails and the head group per lipid, predicting the tendency of lipids near the anesthetic site of action to form a hexagonal phase (HII); ii) a slight increase in the frequency of chain dihedral angles found in the gauche conformation; and iii) a significant increase in the lateral mean-square displacement of lipid molecules, an indication of increased lipid lateral diffusion and membrane fluidity. The pressure antagonism of these effects was also studied by MD simulations at pressures of 200 and 400 atm. The study of the pressure reversibility of these effects at 200 and 400 atm indicated that they were partially prevented at 200 atm and essentially blocked at 400 atm, suggesting their probable relevance to the pressure reversal effect seen with general anesthesia. These results may thus provide insights into the interaction between general anesthetics and similar small organic molecules with membranes.

Theoretical study of model compound I complexes of horseradish peroxidase and catalase

Theoretical studies of the electronic structure and spectra of models for the ferric resting state and Compound I intermediates of horseradish peroxidase (HRP-I) and catalase (CAT-I) have been performed using the INDO-RHF/CI method. The goals of these studies were twofold: i) to determine whether the axial ligand of HRP is best described as imidazole or imidazolate, and ii) to address the long-standing question of whether HRP-I and CAT-I are a1u and a2u tau cation radicals. Only the imidazolate HRP-I model led to a calculated electronic spectra consistent with the experimentally observed significant reduction in the intensity of the Soret band compared with the ferric resting state. These results provide compelling evidence for significant proton transfer to the conserved Asp residue by the proximal histidine. The origin of the observed reduction of the Soret band intensity in HRP-I and CAT-I spectra has been examined and found to be caused by the mixing of charge transfer transitions into the predominantly porphyrin tau-tau transitions. For both HRP-I and CAT-I, the a1u porphyrin tau cation state is the lowest energy, and it is further stabilized by both the anionic form of the ligand and the porphyrin ring substituents of protoporphyrin-IX. The calculated values of quadrupole-splitting observed in the Mossbauer resonance of HRP-I and CAT-I are similar for the a1u and a2u tau cation radicals. Electronic spectrum of the a1u tau cation radical of HRP-I are more similar to the observed spectra, whereas the spectra of both a1u tau and a2u tau cation radicals of CAT-I resemble the observed spectra. These results also indicate the limitations of using any one observable property to try to distinguish between these states. Taken together, comparison of calculated and observed properties indicate that there is no compelling reason to invoke the higher energy a2u tau cation radical as the favored state in HRP-I and CAT-I. Both ground-state properties and electronic spectra are consistent with the a1u tau cation radical.

A role for Thr 252 in cytochrome P450cam oxygen activation

Molecular dynamics simulations of the ferrous dioxygen bound form of wild type cytochrome P450cam were performed and the results analyzed to reveal the time-dependent interactions of T252 with surrounding residues as well as with bound oxygen. The results indicate a time-dependent bimodal interaction of T252 with both G248 and the terminal oxygen of the bound dioxygen. The hydrogen bonding interaction of T252 with these two moieties is "anticorrelated" in the sense that the breaking of the T252-G248 hydrogen bond is concurrent with formation of the T252-dioxygen interaction. These simulations support the probability of a role of T252 in stabilization of the initial dioxygen bound complex and promotion of subsequent formation of compound I previously indicated by several experimental studies.

Homology models of two isozymes of manganese peroxidase: prediction of a Mn(II) binding site

The three-dimensional structures of two isozymes of manganese peroxidase (MnP) have been predicted from homology modeling using lignin peroxidase as a template. Although highly homologous, MnP differs from LiP by the requirement of Mn(II) as an intermediate in its oxidation of substrates. The Mn(II) site is absent in LiP and unique to the MnP family of peroxidases. The model structures were used to identify the unique Mn(II) binding sites, to determine to what extent they were conserved in the two isozymes, and to provide insight into why this site is absent in LiP. For each isozyme of MnP, three candidate Mn(II) binding sites were identified. Energy optimizations of the three possible Mn(II) enzyme complexes allowed the selection of the most favorable Mn(II) binding site as one with the most anionic oxygen moieties best configured to act as ligands for the Mn(II). At the preferred site, the Mn(II) is coordinated to the carboxyl oxygens of Glu-35, Glu-39, and Asp-179, and a propionate group of the heme. The predicted Mn(II) binding site is conserved in both isozymes. Comparison between the residues at this site in MnP and the corresponding residues in LiP shows that two of the three anionic residues in MnP are replaced by neutral residues in LiP, explaining why LiP does not bind Mn(II).

Molecular determinants of recognition and activation at the cerebellar benzodiazepine receptor site

Semiempirical quantum mechanical and molecular mechanics calculations were carried out to identify and characterize the steric and electronic properties that modulate ligand recognition and activation of the cerebellar GABAA/benzodiazepine (BDZ) receptor. For this hypothesis development, thirteen compounds belonging to structurally diverse chemical families were selected for study. Among the compounds selected were nine that bind and four that do not bind with appreciable affinity to this receptor and some that are known agonists, antagonists and inverse agonists, as measured by their modulation of GABA (gamma-aminobutyric acid) enhanced chloride ion flux in cerebellum. The stereoelectronic requirements for recognition deduced from commonalities among the ligands are the presence of at least two of three hydrogen bonding centers, and a lipophilic aromatic ring, in a specific spatial relationship. The results suggest that the selectivity for the cerebellar or Type I subtype, demonstrated by some of these ligands, could be failure to meet the requirements for binding at other receptors because of the absence of one of the proton accepting centers or the larger surface area and volume of these ligands. The requirement for activation, deduced from comparisons of agonist, antagonist, and inverse agonist properties is the presence of an electron accepting aromatic ring in a specific geometric arrangement with respect to the components of recognition. The validity of the '3D-Pharmacophore' developed was probed by using it for predictions of the behavior of 11 additional compounds not used for its development.

Evidence for central benzodiazepine receptor heterogeneity from behavior tests

To explore behavioral selectivity as a consequence of multiple receptor subtypes, four benzodiazepine receptor ligands, flunitrazepam, CGS 9896, zolpidem, and AHR 11797, were tested at five in vivo endpoints: anticonvulsant action, anxiolysis/anxiogenesis as determined in the plus-maze test, locomotor activity, changes in food consumption, and hypothermia. All compounds produced hypothermia. In the plus-maze test, flunitrazepam, CGS 9896, and a low dose of zolpidem (0.05 mg/kg) increased the time spent in the open arms, although AHR 11797 and higher doses of zolpidem decreased time spent in the open arms. Flunitrazepam and zolpidem greatly reduced, CGS 9896 slightly reduced, and AHR 11797 did not affect locomotor activity. Flunitrazepam and CGS 9896 increased food consumption, but AHR 11797 and zolpidem had no effect. Only flunitrazepam fully protected the animals from pentylenetetrazol-induced seizures. The qualitative differences in the effects of these compounds observed are difficult to explain by activation of a single benzodiazepine receptor subtype. As Ro15-1788 antagonized all the observed effects, these compounds act through multiple central benzodiazepine receptors.

Molecular dynamics simulations of phospholipid bilayers

Molecular dynamics (MD) simulations at 37 degrees C have been performed on three phospholipid bilayer systems composed of the lipids DLPE, DOPE, and DOPC. The model used included 24 explicit lipid molecules and explicit waters of solvation in the polar head group regions, together with constant-pressure periodic boundary conditions in three dimensions. Using this model, a MD simulation samples part of an infinite planar lipid bilayer. The lipid dynamics and packing behavior were characterized. Furthermore, using the results of the simulations, a number of diverse properties including bilayer structural parameters, hydrocarbon chain order parameters, dihedral conformations, electron density profile, hydration per lipid, and water distribution along the bilayer normal were calculated. Many of these properties are available for the three lipid systems chosen, making them well suited for evaluating the model and protocols used in these simulations by direct comparisons with experimental data. The calculated MD behavior, chain disorder, and lipid packing parameter, i.e. the ratio of the effective areas of hydrocarbon tails and head group per lipid (a(t)/ah), correctly predict the aggregation preferences of the three lipids observed experimentally at 37 degrees C, namely: a gel bilayer for DLPE, a hexagonal tube for DOPE, and a liquid crystalline bilayer for DOPC. In addition, the model and conditions used in the MD simulations led to good agreement of the calculated properties of the bilayers with available experimental results, demonstrating the reliability of the simulations. The effects of the cis unsaturation in the hydrocarbon chains of DOPE and DOPC, compared to the fully saturated one in DLPE, as well as the effects of the different polar head groups of PC and PE with the same unsaturated chains on the lipid packing and bilayer structure have been investigated. The results of these studies indicate the ability of MD methods to provide molecular-level insights into the structure and dynamics of lipid assemblies.

Molecular mechanism of delta-selectivity of indole analogs of nonpeptide opioids

A combined experimental and computational approach was used to understand the mechanism of delta-receptor selectivity of a series of nonpeptide opioids. Six pairs of fused ring opioids/indole derivatives were studied. Receptor-binding assays using [3H][D-Ala2-MePhe4-Gly-ol]-enkephalin (mu), [3H][D-Pen2-D-Pen5]-enkephalin (delta), and [3H]U-69593 (kappa) were performed in guinea pig whole-brain membranes. Agonist activity was determined in norbinaltorphimine- or beta-funaltrexamine-treated guinea pig ileum (mu and kappa) and beta-funaltrexamine-treated mouse vas deferens (delta). Steric and electronic properties were calculated for each compound. Although the parent compounds were selective for the mu-receptor, the indole analogs displayed selectivity for the delta-site because of a decrease in mu-affinity accompanied by an increase in delta-affinity. The indole analogs displayed little or no activity at the delta-receptor. The role of the indole in enhanced delta-recognition is likely interaction with a lipophilic site in the receptor. The diminished mu-affinity of the indole analogs is a result of the loss of the carbonyl oxygen as the proton-accepting center, which we have previously determined to be important for recognition of the mu-receptor.

Zinc selectively inhibits flux through benzodiazepine-insensitive gamma-aminobutyric acid chloride channels in cortical and cerebellar microsacs

The effects of Zn2+ on the activity of gamma-aminobutyric acid (GABA)A receptor-Cl- ionophore complexes found in adult rat cortex and cerebellum were tested by measuring 36Cl- influx into microsacs. In both preparations, the concentration-response curves were biphasic, with 25% of the cerebellar and 20% of the cortical Cl- flux being blocked by less than 10 microM Zn2+ and 45% of the cerebellar and 50% of the cortical flux being blocked by concentrations of Zn2+ exceeding 10 microM. Zn2+ (100 microM) did not affect basal Cl- flux but inhibited that stimulated by 100 microM GABA in a noncompetitive manner. The ability of 1 microM flunitrazepam to enhance Cl- flux was unaffected by 100 microM Zn2+. These results demonstrate that, in adult rat cerebellum and cortex, there are three populations of GABAA receptors, two that are sensitive to Zn2+ and insensitive to benzodiazepines (BDZ) and the remainder that are the reverse, i.e., insensitive to Zn2+ but fully sensitive to BDZ enhancement. This result is consistent with the idea that Zn2+ blocks only those GABAA receptor-Cl- ionophore complexes that lack a gamma subunit, which is required for modulation by BDZ. The results obtained in this study also show that the proportion of Zn(2+)-sensitive GABA receptors is substantial, suggesting that they play an important role in the functioning of the adult central nervous system.

The reaction of atomic oxygen with methanethiol. A theoretical study of the structures and the potential energy surface

Ab initio calculations at the Hartree-Fock, MP2 and MP4 levels were performed to find structures of the equilibrium and transition states and the reaction energies and energies of activation of several competing reaction pathways of O (3P)+CH3SH. A 6-31G* basis set was used in all calculations. The mechanism of hydrogen atom abstraction from the S-H group methanethiol was found to be very competitive with the oxygen atom addition to the sulfur atom.

Characterization of the bioactive form and molecular determinants of recognition of cyclic enkephalin peptides at the delta-opioid receptor

An extensive and systematic search strategy to determine the conformational profile of 12 cyclic disulfide-bridged opioid peptides with varying affinities at the delta receptor has been carried out to identify the structure that is recognized by the delta receptor for each analogue. The methods and procedures used here for the conformational search have already been validated for [D-Pen2,D-Pen5] enkephalin (DPDPE), one member of this family. Use of these methods led to a low-energy solution conformation of DPDPE in excellent agreement with all the geometric properties deduced from its solution nmr spectra. Each of the analogue was subjected to the same procedure, involving a combination of molecular dynamics simulations at high and low temperature. The study was repeated in two environmental conditions, an apolar environment, simulated by using a distance-dependent dielectric constant, and a polar environment by embedding the peptides in a high constant dielectric (epsilon = 80). An automated comparison of the different conformers based on their backbone rms and average distance between the key aromatic moieties was followed by graphic analysis using maximum structural overlap. The cross-comparison of the conformations for each analogue revealed a unique conformer that may be recognized by the delta receptor for each high-affinity analogue that permitted maintaining the critical elements required for recognition in a simple spatial orientation, while maximizing similarity in other regions.

Strategies for indirect computer-aided drug design

This review is intended to describe some of the methods and procedures used for computer-aided drug design when the structure of the macromolecular target is unknown, as is the case for CNS active drugs. Strategies and methods used in computer-aided design of drugs in such instances must be "indirect," i.e., focusing on the characterization of the ligands themselves. This situation is different from one in which the three-dimensional structure of the macromolecular target for a drug is known, for example, for drugs that are enzyme inhibitors, allowing "direct" characterization of ligand-receptor interactions. Two qualitatively different "indirect" approaches are described here. One, called 2D-QSAR, is briefly reviewed. It is based on delineating regression relationships between a specified biological end point and properties of the compounds eliciting it. The other, based on pharmacophore development, constitutes the main part of this review. Several levels of pharmacophore development are described, which differ in the extent to which they encompass fundamental molecular properties that are determinants of receptor recognition and activation. The strengths and limitations of each procedure are discussed and illustrated by examples. Two methods for obtaining model receptor structures are then briefly described. Both rely on the prior success of the indirect methods in obtaining ligand properties that modulate receptor recognition and activation. These emerging capabilities have the potential to bridge the gap between indirect and direct methods of drug design, since, if successful, the design process can continue in a direct mode using explicit characterization of drug-receptor interactions. Strategies for hypothesis validation and use of hypothesis for drug design and discovery are also briefly reviewed. The final sections of this review describe specific computational tools such as molecular mechanics and quantum mechanical methods used to characterize and identify relevant molecular properties and indicate some areas for future development of computational chemistry methods that could increase its effectiveness in the design of novel drugs.

Comparison of behavioral and central BDZ binding profile in three rat lines

The performance of three widely used rat lines (Sprague-Dawley, Wistar, and Long Evans hooded) were evaluated in behavioral test systems that are sensitive to benzodiazepines. The in vivo effects of flunitrazepam and the brain [3H]Ro 15-1788 binding were determined and compared in these rat lines. The behavioral end points evaluated in this study were anxiolysis, measured using the automated elevated plus-maze; sedation by modification of locomotor activity; hyperphagia following food deprivation; protection for pentylenetetrazol-induced convulsions; and hypothermia. There were comparable results in the hypnotic, hypothermic, anticonvulsant, and feeding tests in these lines following flunitrazepam administration. However, the behavior of the Long Evans hooded rat was most amenable to the detection of drug-induced changes in the anxiety test. There was no difference in the maximum number of binding sites (Bmax) or the affinity (Ki) of the Ro 15-1788 or flunitrazepam binding in either the cerebellum or whole brain (minus cerebellum) in the three rat lines as determined by the competitive binding against [3H]Ro 15-1788. Thus, while these rat lines exhibited similar behavioral profiles in most tests the modest differences in the baseline responses and the ability to detect anxiolysis at lower doses of flunitrazepam observed with Long Evans hooded rats makes them particularly suited for these types of studies.