Degree Of Conformational Flexibility Research Articles

Manipulating turn residues on de novo designed β-hairpin peptides for selectivity against drug-resistant bacteria

Synthetic β-hairpin antimicrobial peptides (AMPs) offer a useful source for the development of novel antimicrobial agents. β-hairpin peptides generally consist of two side strands bridged by a reverse turn. In literature, most studies focused on the modifications of the side strands to manipulate the stability and activity of β-hairpin peptides, and much less is known about the impact of the turn region. By designing a series of de novo β-hairpin peptides with identical side strands but varied turns, we demonstrated that mutations of only 2 to 4 amino acids at the turn region could impart a wide range of antimicrobial profiles among synthetic β-hairpin AMPs. BTT2–4 and BTT6 displayed selective potency against Gram-negative bacteria, with minimum inhibitory concentrations (MICs) of 4–8 µM. In contrast, BTT1 exhibited broad-spectrum activity, with MICs of 4–8 µM against both Gram-positive and Gram-negative strains. Additionally, BTT1 was potent against methicillin-resistant Staphylococcus aureus (MRSA) and colistin-resistant Enterobacterales. The antimicrobial potency of BTT1 persisted after 14 days of serial passage. Mechanistic studies revealed that interactions between lipopolysaccharide (LPS) and the peptides were critical to their membranolytic activity against the bacterial inner membrane. Aside from folding stability, we observed that a degree of conformational flexibility was required for disruptive membrane interactions. Statement of significanceBy examining the significance of the turn region of β-hairpin peptides, we present valuable knowledge to the design toolkit of novel antimicrobial peptides as alternative therapeutics to overcome antibiotic resistance. Our de novo designed synthetic peptides displayed selective activity against Gram-negative bacteria and potent activity against clinically relevant antibiotic-resistant strains (e.g. colistin-resistant Enterobacterales and methicillin-resistant Staphylococcus aureus). The bactericidal activity of our peptides was shown to be robust in the presence of proteolytic trypsin and saline, conditions that could suppress peptide activity. Our peptides were also determined to be non-cytotoxic against a human cell line.

Data-Driven Ensemble Docking to Map Molecular Interactions of Steroid Analogs with Hepatic Organic Anion Transporting Polypeptides.

Hepatic organic anion transporting polypeptides—OATP1B1, OATP1B3, and OATP2B1—are expressed at the basolateral membrane of hepatocytes, being responsible for the uptake of a wide range of natural substrates and structurally unrelated pharmaceuticals. Impaired function of hepatic OATPs has been linked to clinically relevant drug–drug interactions leading to altered pharmacokinetics of administered drugs. Therefore, understanding the commonalities and differences across the three transporters represents useful knowledge to guide the drug discovery process at an early stage. Unfortunately, such efforts remain challenging because of the lack of experimentally resolved protein structures for any member of the OATP family. In this study, we established a rigorous computational protocol to generate and validate structural models for hepatic OATPs. The multistep procedure is based on the systematic exploration of available protein structures with shared protein folding using normal-mode analysis, the calculation of multiple template backbones from elastic network models, the utilization of multiple template conformations to generate OATP structural models with various degrees of conformational flexibility, and the prioritization of models on the basis of enrichment docking. We employed the resulting OATP models of OATP1B1, OATP1B3, and OATP2B1 to elucidate binding modes of steroid analogs in the three transporters. Steroid conjugates have been recognized as endogenous substrates of these transporters. Thus, investigating this data set delivers insights into mechanisms of substrate recognition. In silico predictions were complemented with in vitro studies measuring the bioactivity of a compound set on OATP expressing cell lines. Important structural determinants conferring shared and distinct binding patterns of steroid analogs in the three transporters have been identified. Overall, this comparative study provides novel insights into hepatic OATP-ligand interactions and selectivity. Furthermore, the integrative computational workflow for structure-based modeling can be leveraged for other pharmaceutical targets of interest.

Curved Perylene Diimides Fused with Seven-Membered Rings.

Curved perylene diimides fused with seven-membered rings have been synthesized using a regioselective bay-functionalization method and Pd-catalyzed intramolecular C-H/C-Br coupling reaction. X-Ray analysis and temperature-dependent NMR spectroscopy revealed the curved molecular structure with a certain degree of conformational flexibility. The curved and expanded π-conjugation altered the electronic properties while retaining the intrinsic properties of the parent perylene diimide. Despite the absence of solubilizing N-substituents, the curved perylene diimides showed sufficient solubility for application in solution-processed organic photovoltaic devices. The devices showed superior performance with a power conversion efficiency of up to 2.76% due to suppressed charge recombination. Our detailed investigations suggest that the introduction of a curved structure enables the removal of the bulky N-substituents, which is an effective way to achieve a thin-film morphology suitable for photoelectric conversion.

High-resolution crystal structures reveal a mixture of conformers of the Gly61-Asp62 peptide bond in an oxidized flavodoxin from Bacillus cereus.

Flavodoxins (Flds) are small proteins that shuttle electrons in a range of reactions in microorganisms. Flds contain a redox‐active cofactor, a flavin mononucleotide (FMN), and it is well established that when Flds are reduced by one electron, a peptide bond close to the FMN isoalloxazine ring flips to form a new hydrogen bond with the FMN N5H, stabilizing the one‐electron reduced state. Here, we present high‐resolution crystal structures of Flavodoxin 1 from Bacillus cereus in both the oxidized (ox) and one‐electron reduced (semiquinone, sq) state. We observe a mixture of conformers in the oxidized state; a 50:50 distribution between the established oxidized conformation where the peptide bond is pointing away from the flavin, and a conformation where the peptide bond is pointing toward the flavin, approximating the conformation in the semiquinone state. We use single‐crystal spectroscopy to demonstrate that the mixture of conformers is not caused by radiation damage to the crystal. This is the first time that such a mixture of conformers is reported in a wild‐type Fld. We therefore carried out a survey of published Fld structures, which show that several proteins have a pronounced conformational flexibility of this peptide bond. The degree of flexibility seems to be modulated by the presence, or absence, of stabilizing interactions between the peptide bond carbonyl and its surrounding amino acids. We hypothesize that the degree of conformational flexibility will affect the Fld ox/sq redox potential.

The Structure of TAX1BP1 UBZ1 + 2 Provides Insight into Target Specificity and Adaptability

TAX1BP1 is a novel ubiquitin-binding adaptor protein involved in the negative regulation of the NF-kappaB transcription factor, which is a key player in inflammatory responses, immunity and tumorigenesis. TAX1BP1 recruits A20 to the ubiquitinated signaling proteins TRAF6 and RIP1, leading to their A20-mediated deubiquitination and the disruption of IL-1-induced and TNF-induced NF-kappaB signaling, respectively. The two zinc fingers localized at its C-terminus function as novel ubiquitin-binding domains (UBZ, ubiquitin-binding zinc finger). Here we present for the first time both the solution and crystal structures of two classical UBZ domains in tandem within the human TAX1BP1. The relative orientation of the two domains is slightly different in the X-ray structure with respect to the NMR structure, indicating some degree of conformational flexibility, which is rationalized by NMR relaxation data. The observed degree of flexibility and stability between the two UBZ domains might have consequences on the recognition mechanism of interacting partners.

Towards Fast and Accurate Calculation of Protein pKa Values Exploiting Various Degrees of Conformational Flexibility

Virtually every biological process is pH dependent. Many fundamental biological phenomena including protein folding, enzyme catalysis, protein-protein interactions and pathological conditions are profoundly influenced by the pH of their environment. Accurate prediction of the pKa values of residues that can adopt variable protonation states would be a significant step towards probing the effects of pH on proteins. Despite the progress in pKa prediction algorithms, developing a method that can incorporate extensive protein conformational flexibility while retaining a relatively small computational resource footprint remains a significant challenge. We developed a fast and accurate method to predict pKas of residues that commonly exhibit variable protonation states in proteins. The algorithm utilizes Metropolis Monte Carlo strategy to incorporate conformational flexibility through extensive amino-acid side-chain sampling and is based on Rosetta score function with an explicit term to account for protonation probabilities of individual amino-acids. We tested the technique by predicting pKas for an assembled dataset comprising 306 residues from 44 proteins resulting in a root-mean-square deviation (RMSD) of 0.81 from experimental values. We analyzed the effects of employing increasing levels of conformational flexibility by (1) sampling the side-chains of neighboring residues and (2) using a generated ensemble of 50 diverse backbone conformers resulting in 77% and 79% predictions < 1 pH unit from experimental values respectively. Using additional degrees of freedom allowed capture of vital hydrogen-bonding and charge-charge interactions, but resulted in structural rearrangements negating pKa shifts in some cases. The method yielded good results when used to predict large pKa shifts in point mutants from Staphylococcal nuclease. Finally, we employed our method to dynamically alter the ionization states of residues during protein-protein docking simulations to seek improvements in accuracy of prediction of complexes.

Restoration of DNA‐binding and growth‐suppressive activity of mutant forms of p53 via a PCAF‐mediated acetylation pathway

Tumor-derived mutant forms of p53 compromise its DNA binding, transcriptional, and growth regulatory activity in a manner that is dependent upon the cell-type and the type of mutation. Given the high frequency of p53 mutations in human tumors, reactivation of the p53 pathway has been widely proposed as beneficial for cancer therapy. In support of this possibility p53 mutants possess a certain degree of conformational flexibility that allows for re-induction of function by a number of structurally different artificial compounds or by short peptides. This raises the question of whether physiological pathways for p53 mutant reactivation also exist and can be exploited therapeutically. The activity of wild-type p53 is modulated by various acetyl-transferases and deacetylases, but whether acetylation influences signaling by p53 mutant is still unknown. Here, we show that the PCAF acetyl-transferase is down-regulated in tumors harboring p53 mutants, where its re-expression leads to p53 acetylation and to cell death. Furthermore, acetylation restores the DNA-binding ability of p53 mutants in vitro and expression of PCAF, or treatment with deacetylase inhibitors, promotes their binding to p53-regulated promoters and transcriptional activity in vivo. These data suggest that PCAF-mediated acetylation rescues activity of at least a set of p53 mutations. Therefore, we propose that dis-regulation of PCAF activity is a pre-requisite for p53 mutant loss of function and for the oncogenic potential acquired by neoplastic cells expressing these proteins. Our findings offer a new rationale for therapeutic targeting of PCAF activity in tumors harboring oncogenic versions of p53.

Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity

BackgroundComputational comparison of two protein structures is the starting point of many methods that build on existing knowledge, such as structure modeling (including modeling of protein complexes and conformational changes), molecular replacement, or annotation by structural similarity. In a commonly used strategy, significant effort is invested in matching two sets of atoms. In a complementary approach, a global descriptor is assigned to the overall structure, thus losing track of the substructures within.ResultsUsing a small set of geometric features, we define a reduced representation of protein structure, together with an optimizing function for matching two representations, to provide a pre-filtering stage in a database search. We show that, in a straightforward implementation, the representation performs well in terms of resolution in the space of protein structures, and its ability to make new predictions.ConclusionsPerhaps unexpectedly, a substantial discriminating power already exists at the level of main features of protein structure, such as directions of secondary structural elements, possibly constrained by their sequential order. This can be used toward efficient comparison of protein (sub)structures, allowing for various degrees of conformational flexibility within the compared pair, which in turn can be used for modeling by homology of protein structure and dynamics.

Structural and Functional Characterization of a Mutant of Pseudocerastes persicus Natriuretic Peptide

We hereby report on a mutational analysis of a novel natriuretic peptide (PNP), recently isolated by us from the Iranian snake venom. The PNP variant (mutPNP) with four substitutions (G16T, K18S, R21S, G23R) and a disulfide bonded ring shortened by 3 residues. mutPNP peptide was expressed in pET32 and purified by affinity separation on nickel resin followed by RP-HPLC chromatography. The conformation of mutPNP was characterized in solution by 1H nuclear magnetic resonance spectroscopy, where it was found that the 14-residue disulfide bonded ring, like the 17-residue ring in PNP, retains a high degree of conformational flexibility. The conformation of mutPNP bound to NPR-C receptor was predicted by homology protein structure modeling. When injected intravenously into rats, mutPNP, in contrast to PNP had no physiological effect on blood pressure or on diuresis. The loss of physiological activity is explained in terms of the modeled bound conformation and the ensemble of solution conformations obtained using the NMR constraints.

Structure and Conformation of Tetra-meso-, Octa-β-, and Dodecasubstituted 22,24-Dihydroporphyrins (Porphyrin Dications)

A comparative crystallographic analysis of the conformation of porphyrin diacids with various substituent types reveals considerable differences in the degree of nonplanarity and distortion modes. Diacids of 5,10,15,20-tetraarylporphyrins generally exhibit typical saddledistorted macrocycles with displacements of the Cb positions in the range of 0.7-1.0 Å. Adding peripheral substituents, i.e., using dodecasubstituted porphyrins for the diacid formation yields similar distortion types albeit with larger out-of-plane displacements. As a result of the combined effect of both peripheral (interaction between the Cb and Cm substituents) and core (interaction between the four inner hydrogen atoms) steric strain the maximum Cb displacements reach 1.3-1.5 Å. Quite a different situation is observed for the diacids of 2,3,7,8,12,13,17,18-octaalkylporphyrins. Here, macrocycles with pair-wise displacement of neighboring pyrrole rings and significant NH pyramidalization and those with classic saddle distortion are found. Generally, octa- β-substituted porphyrin diacids show smaller degrees of nonplanarity; Cb displacements ranged from 0.06 to 0.72 Å. On the basis of the overall degree of conformational distortion (⊿24 = average deviation of the 24 macrocycles atoms from the mean plane), the three different types of porphyrin macrocycles studied differ considerably in their degree of conformational flexibility. For several porphyrin crystal structures with different counterions and/or solvate molecules were obtained. Taking into account results from the literature 2,3,7,8,12,13,17,18-octaethyl-22,24-dihydro-5,10,15.,20-tetraphenylporphyrin (13) shows the smallest degree of flexibility (⊿24 = 0.61-0.63 Å; four different X-ray structures), while 22,24-dihydro-5,10,15,20-tetraphenylporphyrin (1) is more flexible (Z⊿24 = 0.42-0.52 Å; four structures). The largest flexibility is observed for 2,3,7,8,12,13,18-octaethyl- 22,24-dihydroporphyrin (7) (⊿24 = 0.02-0.33 Å; four structures).

The mechanics of minor groove width variation in DNA, and its implications for the accommodation of ligands

In duplex DNA, groove width and depth are salient structural features that may influence the binding of drugs and proteins. These features are affected by movement of the bases, which for example may enforce groove compression or expansion through a rolling action of the adjacent base-pairs. Moreover, the sugar-phosphate backbone can also undergo limited movement, independently of the bases, which will affect the groove shape. We have examined how the movement of the sugar-phosphate backbone may affect the minor groove width for a fixed base geometry. In agreement with earlier studies, the sugar-phosphate backbone is found to have a certain degree of conformational flexibility in A and B-like helices, and we note a comparable freedom even in the highly curved TATA element of the TATA-binding protein/DNA complex. Phosphate mobility is highly anisotropic in all cases with favoured directions that can significantly change the groove width, independent of any changes in base geometry. We describe how the movement of the sugar-phosphate backbone may affect the accommodation of drugs and proteins in the minor groove, and we present a co-ordinate scheme which emphasises the groove adjustments associated with ligand binding. The observations have implications for the related problem of how cognate molecules are accommodated in the major groove.

Structure-Property Relationships in Organic Nonlinear Optical Materials

ABSTRACTTuning the degree of bond-length alternation in organic nonlinear optical materials is a powerful paradigm for the design of organic materials with large molecular hyperpolarizabilities (β). Several research groups have employed this paradigm in the design and synthesis of NLO materials incorporating donor-acceptor polyenes. Increased bond-length alternation in polyenes leads to decreased barriers to rotation about C=C bonds and, hence, increased conformational flexibility. Since the degree of bond-length alternation is solvent dependent, so is the degree of conformational flexibility. In an effort to probe the influence of conformational flexibility on NLO response, we synthesized a series of simple donor-acceptor polyenes that are either conformationally flexible (la, 2a, 3a) or rigid (1b, 2b, 3b). For each pair of molecules ZINDO sum-over-states calculations predict a larger value of βμ, for the conformationally flexible isomer, but EFISH measurements (CHCl3) display mixed results. Various explanations for this behavior will be considered.

MO ab initio study of the structural and electronic properties of the 5-lipoxygenase inhibitor zileuton

The conformational space of zileuton was investigated by MO ab initio calculations at the HF/6–31G ∗∗ level. The computed energies of the three most stable conformers were found to lie in a small range (< 4.0 kcal/mol), indicating a certain degree of conformational flexibility. The preferred protonation site in vacuo and in water (simulated within the Onsager reaction field model) was characterised; the cation resulting from carbonyl oxygen protonation was predicted to be the most stable, both in vacuo and in water. The UV spectrum of zileuton was also recorded in different solvents and the experimental results were implemented by the outcome of a CI-Singles theoretical study of the excited state properties of the model compound benzothiophene, which is the chromophoric moiety of zileuton.

Role of the omega-loop in the activity, substrate specificity, and structure of class A beta-lactamase.

The structure of class A beta-lactamases contains an omega-loop associated with the active site, which carries a key catalytic residue, Glu166. A 16-residue omega-loop deletion mutant of beta-lactamase from Staphylococcus aureus PC1, encompassing residues 163-178, was produced in order to examine the functional and structural role of the loop. The crystal structure was determined and refined at 2.3 A, and the kinetics of the mutant enzyme was characterized with a variety of beta-lactam antibiotics. In general, the wild-type beta-lactamase hydrolyzes penicillin compounds better than cephalosporins. In contrast, the deletion of the omega-loop led to a variant enzyme that acts only on cephalosporins, including third generation compounds. Kinetic measurements and electrospray mass spectrometry revealed that the first and third generation cephalosporins form stable acyl-enzyme complexes, except for the chromogenic cephalosporin, nitrocefin, which after acylating the enzyme undergoes hydrolysis at a 1000-fold slower rate than that with wild-type beta-lactamase. Hydrolysis of the acyl-enzyme adducts is prevented because the deletion of the omega-loop eliminates the deacylation apparatus comprising Glu166 and its associated nucleophilic water site. The crystal structure reveals that while the overall fold of the mutant enzyme is similar to that of the native beta-lactamase, local adjustments in the vicinity of the missing loop occurred. The altered beta-lactam specificity is attributed to these structural changes. In the native structure, the omega-loop restricts the conformation of a beta-strand at the edge of the active site depression. Removal of the loop provides the beta-strand with a new degree of conformational flexibility, such that it is displaced inward toward the active site space. Modeled Michaelis complexes with benzylpenicillin and cephaloridine show that the perturbed conformation of the beta-strand is inconsistent with penicillin binding because of steric clashes between the beta-lactam side chain substituent and the beta-strand. In contrast, no clashes occur upon cephalosporin binding. Recognition of third generation cephalosporins is possible because the bulky side chain substituents of the beta-lactam ring typical of these compounds can be accommodated in the space freed by the deletion of the omega-loop.

Time-resolved energy transfer measurements of donor-acceptor distance distributions and intramolecular flexibility of a CCHH zinc finger peptide.

Time-resolved frequency-domain fluorescence energy transfer measurements have been used to investigate the solution structure of a single-domain CCHH-type zinc finger peptide. These measurements reveal not only the range of accessible distances for a given donor-acceptor pair within the molecule but also the degree of conformational flexibility that occurs in solution. Two donor-acceptor (D-A)-pair zinc finger peptides have been synthesized. A single tryptophan residue located at the midpoint of the sequence was the energy donor for two different acceptors. One acceptor, attached at the amino terminus was a 5-(dimethylamino)-1-naphthalenesulfonyl (DNS) group; the second acceptor was a 7-amino-4-methyl-coumarin-3-acetyl (AMCA) group, attached to the epsilon-amino function of a carboxy-terminal lysine residue. Distance distributions and the mutual site-to-site diffusion coefficients were determined for these two D-A-labeled peptides under zinc-bound, metal-free, and denatured conditions. The D-A distance distributions determined for these two peptides under metal-free and zinc-bound conditions indicated a shorter distance and a unique conformation (narrow distribution) when metal was bound and a longer distance with greater conformational flexibility when metal ion was absent. No site-to-site diffusion was detected for the zinc-bound peptide, whereas an appreciable amount of diffusion was measured for both metal-free and denatured peptide. Anisotropy measurements on the peptides indicated increased flexibility of all regions of the peptide chain in the absence of zinc and a more compact, less flexible structure when zinc was bound. It was concluded from these results that the metal-bound conformation represents a unique, well-defined structure. Comparison of distance distributions measured for metal-free and denatured peptide indicated that there is some residual structure present in the metal-free peptide.

Static and dynamic molecular mechanics modelling and X‐ray scattering calculations for a cyclic siloxane macromolecule

AbstractA liquid crystalline system consisting of cyclic penta(methylsiloxane) cores with biphenylyl 4‐propoxybenzoate mesogens is studied with respect to its molecular conformation and the intermolecular ordering of pendant groups by employing molecular mechaincs calculations, while a molecular dynamics simulation indicates the degree of conformational flexibility. The calculated X‐ray scattering patterns for these structures provide insight into the origin of the experimentally observed results. A good agreement is found between the calculated and experimental reflections data, supporting the ‘cylinder’ global topology as the basis for forming a ‘columnar’ structure. Further, a comparison of the calculated and experimental meriodional sections shows a strong similarity of both the meridional intensities and d‐spacings.

Kinetic roles and conformational properties of the non-native two-disulphide intermediates in the refolding of bovine pancreatic trypsin inhibitor

The most productive folding pathway of reduced bovine pancreatic trypsin inhibitor (BPTI) proceeds through the disulphide intermediates (30–51), (30–51, 5–14), and (30–51, 5–38); these are important kinetic intermediates in folding, even though the latter pair contain non-native disulphide bonds. Analogues of these intermediates have been prepared by protein engineering methods and their conformational properties examined by circular dichroism and 1H-nuclear magnetic resonance. The (30–51), (30–51, 5–14) and (30–51, 5–38) analogues exhibit comparable degrees of stable structure, which cannot include those portions of the polypeptide chain involving Cys5, Cys14 and Cys38. These properties are consistent with the roles of (30–51, 5–14) and (30–51, 5–38) in the folding pathway of BPTI, which demand that they exhibit a considerable degree of conformational flexibility in part of the molecule.

Comparative conformational analysis of % MathType!MTEF!2!1!+-% feaafeart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaae4waKaaGi% aabseakiaab2cajaaOcaqGqbGcdaqgaaqaaKaaGkaabwgacaqGUbGc% daahaaWcbeqaaiaabkdaaaGccaGGSaqcaaIaaeiraiaab2cajaaOca% qGqbGaaeyzaaWcbaaakiaawYa7aKaaGkaab6gakmaaCaaaleqabaGa% aeynaaaakiaac2faaaa!475D!\[{\text{[D - P}}{\text{n}}^{\text{5}} ]\] enkephalin (DPDPE): A molecular mechanics study

A theoretical conformational analysis (molecular mechanics study) of the δ opioid receptor-selective enkephalin analog % MathType!MTEF!2!1!+-% feaafeart1ev1aaatCvAUfeBSjuyZL2yd9gzLbvyNv2CaerbuLwBLn% hiov2DGi1BTfMBaeXatLxBI9gBaerbd9wDYLwzYbItLDharqqtubsr% 4rNCHbGeaGqiVu0Je9sqqrpepC0xbbL8F4rqqrFfpeea0xe9Lq-Jc9% vqaqpepm0xbba9pwe9Q8fs0-yqaqpepae9pg0FirpepeKkFr0xfr-x% fr-xb9adbaqaaeGaciGaaiaabeqaamaabaabaaGcbaGaaeisaiaab2% cacaqGubGaaeyEaiaabkhacaqGTaqcaaIaaeiraiaab2cajaaOcaqG% qbGcdaqgaaqaaKaaGkaabwgacaqGUbGaaeylaiaabEeacaqGSbGaae% yEaiaab2cacaqGqbGaaeiAaiaabwgacaqGTaqcaaIaaeiraiaab2ca% jaaOcaqGqbGaaeyzaaWcbaaakiaawYa7aKaaGkaab6gacaqGTaGaae% 4taiaabIeaaaa!51A0!\[{\text{H - Tyr - D - P}}{\text{n - OH}}\] (DPDPE) was performed, based on the use of the SYBYL software. The study led to the identification of several conformers that were significantly lower in energy than previously reported candidate conformers of DPDPE which, for comparative purposes, were also minimized by using the standard SYBYL force field. The results revealed a considerable degree of conformational flexibility of the DPDPE molecule, and suggested that incorporation of further conformational constraints into this enkephalin analog will be necessary in order to elucidate its receptor-bound conformation.

Synthesis and biological activity of 1,2,4-oxadiazole derivatives: highly potent and efficacious agonists for cortical muscarinic receptors

The synthesis and biochemical evaluation of novel 1,2,4-oxadiazole-based muscarinic agonists which can readily penetrate into the CNS is reported. Efficacy and binding of these compounds are markedly influenced by the structure and physicochemical properties of the cationic head group. In a series of azabicyclic ligands efficacy and affinity are influenced by the size of the surface area presented to the receptor, at the active site, and the degree of conformational flexibility. The exo-1-azanorbornane 16a represents the optimum arrangement, and this compound is one of the most efficacious and potent muscarinic agonists known. In a series of isoquinuclidine based muscarinic agonists efficacy and affinity are influenced by the geometry between the cationic head.group and hydrogen bond acceptor pharmacophore and steric bulk in the vicinity of the base. The anti configuration represented by 22a is optimal for muscarinic activity. Ligands with pKa below 6.5 show poor binding to the muscarinic receptor as exemplified by the diazabicyclic derivative 42.