Redefining the structure-activity relationships of 2,6-methano-3-benzazocines. 5. Opioid receptor binding properties of N-((4'-phenyl)-phenethyl) analogues of 8-CAC

A series of aryl-containing N-monosubstituted analogues of the lead compound 8-[N-((4'-phenyl)-phenethyl)]-carboxamidocyclazocine were synthesized and evaluated to probe a putative hydrophobic binding pocket of opioid receptors. Very high binding affinity to the mu opioid receptor was achieved though the N-(2-(4'-methoxybiphenyl-4-yl)ethyl) analogue of 8-CAC. High binding affinity to mu and very high binding affinity to kappa opioid receptors was observed for the N-(3-bromophenethyl) analogue of 8-CAC. High binding affinity to all three opioid receptors were observed for the N-(2-naphthylethyl) analogue of 8-CAC.     

Redefining the structure–activity relationships of 2,6-methano-3-benzazocines. Part 9: Synthesis,characterization and molecular modeling of pyridinyl isosteres of N-BPE-8-CAC (1), a high affinity ligand for opioid receptors

Derivatives of the lead compound N-BPE-8-CAC (1) where each CH of the biphenyl group was individually replaced by N were prepared in hopes of identifying high affinity ligands with improved aqueous solubility. Compared to 1, binding affinities of the five possible pyridinyl derivatives for the μ opioid receptor were between threefold lower to fivefold higher with the K_i of the most potent compound being 0.064 nM. Docking of 8-CAC (2) into the unliganded binding site of the mouse μ opioid receptor (pdb: 4DKL) revealed that 8-CAC and β-FNA (from 4DKL) make nearly identical interactions with the receptor. However, for 1 and the new pyridinyl derivatives 4–8, binding is not tolerated in the 8-CAC binding mode due to the steric constraints of the large N-substituents. Either an alternative binding mode or rearrangement of the protein to accommodate these modifications may account for their high binding affinity.     

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.     

Multiple ligands in opioid research

The observation in 1979 that opioid receptors interact, led to the design of bivalent ligands in an attempt to improve selectivity and affinity towards the different subtypes( i.e. mu, delta, and kappa). Dimers of monovalent 'parent' opioid structures have been evaluated and include: (a) endogenous (e.g enkephalins) or exogenous (e.g dermorphin) peptide dimer analogues (b) mixed peptidic -non-peptidic bivalent ligands and (c) dual non-peptidic dimers. Chimeric structures, using an opioid pharmacophore in combination with a a non-opioid pharmacophore, have also been prepared. The common aim in all these studies is to improve the pharmacological profile of potential analgesics to minimize common opioid-induced side effects, such as physical dependence and tolerance. Here we present a brief overview efforts to develop bivalent opioid ligands for use in pain-related research.     

Syntheses of novel high affinity ligands for opioid receptors

A series of novel high affinity opioid receptor ligands have been made whereby the phenolic-OH group of nalbuphine, naltrexone methiodide, 6-desoxonaltrexone, hydromorphone and naltrindole was replaced by a carboxamido group and the furan ring was opened to the corresponding 4-OH derivatives. These furan ring ‘open’ derivatives display very high affinity for μ and κ receptors and much less affinity for δ. The observation that these target compounds have much higher receptor affinity than the corresponding ring ‘closed’ carboxamides significantly strengthens our underlying pharmacophore hypothesis concerning the bioactive conformation of the carboxamide group.     

Combined structure- and ligand-based pharmacophore modeling and molecular dynamics simulation studies to identify selective inhibitors of MMP-8

Matrix metalloproteinase-8 (MMP-8) is the key mediator in initiating type I collagen degradation and is associated with rheumatoid arthritis. In the present study, a pharmacophore hypothesis was developed based on selective non zinc binding inhibitors of MMP-8. The pharmacophore hypothesis was refined manually and validated by observing structures and the interactions of MMP-8 inhibitors. The refined pharmacophore model was able to discriminate the non-zinc binding inhibitors of MMP-8 with respect to other inhibitors. Hence this study proposes a combined structure- and ligand-based pharmacophore model that is suitable for retrieving the novel inhibitors of MMP-8. The pharmacophore hypothesis AADRH was used as query for retrieving potential compounds from the Zinc database and hits were selected based on the catalytic selective amino acid residues of Arg 222, and Tyr 227. We identified six compounds as potent inhibitors and their selectivity profile were checked against different subtypes of MMPs using the cross-docking method. Molecular dynamics results indicated that ZINC 00673680 forms a stable interaction with the key amino acid residues and avoids the zinc atom with a distance of 5.49?Å. Our computational study might be useful for further development of selective MMP-8 inhibitors.     

The LMC delta opioid recognition pharmacophore: comparison of SNC80 and oxymorphindole

A recognition pharmacophore for the delta opioid receptor was developed de novo. Through the use of the pharmacophore and a novel four-point recognition model, major differences were observed between oxymorphindole and SNC80. This work suggests that these two classes of delta selective opioids do not bind to the delta opioid receptor in the same orientation.     

Opioid and melanocortin receptors: do they have overlapping pharmacophores?

We have identified compound 1 as a novel ligand for opioid and melanocortin (MC) receptors, which is derived from the overlapping of a well known structure for the delta opioid receptor, 2,6-dimethyltyrosine (Dmt)-1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic), and a small molecule for the MC receptor, Tic-DPhe(p-Cl)-piperidin-4-yl-N-phenyl-propionamide. Ligand 1 showed that there is an overlapping pharmacophore between opioid and MC receptors through the Tic residue. The ligand displayed high biological activities at the delta opioid receptor (Ki = 0.38 nM in binding assay, EC(50) = 0.48 nM in GTP-gamma-S binding assay, IC(50) = 74 nM in MVD) as an agonist instead of an antagonist and showed selective binding affinity (IC(50) = 2.3 muM) at the MC-3 receptor rather than at the MC-5 receptor. A study of the structure-activity relationships demonstrated that the residues in positions 2, 3, and the C-terminus act as a pharmacophore for the MC receptors, and the residues in positions 1 and 2 act as a pharmacophore for the opioid receptors. Thus, this structural construct can be used to prepare chimeric structures with adjacent or overlapping pharmacophores for opioid and MC receptors.     

Conformation-activity relationships of opioid peptides with selective activities at opioid receptors

The discovery of endogenous opioid peptides 25 years ago opened up a new chapter in efforts to understand the origins and control of pain, its relationships to other biological functions, including inflammatory and other immune responses, and the relationships of opioid peptides and their receptors to a variety of undesirable or toxic side effects often associated with the nonpeptide opiates such as morphine including addiction, constipation, a variety of neural toxicities, tolerance, and respiratory depression. For these investigations the need for potent and highly receptor selective agonists and antagonists has been crucial since they in principle allow one to distinguish unequivocally the roles of the different opioid receptors (mu, delta, and kappa) in the various biological and pathological roles of the opioid peptides and their receptors. Conformational and topographical constraint of the linear natural endogenous opioid peptides has played a major role in developing peptide ligands with high selectivity for mu, delta, and kappa receptors, and in understanding the conformational, topographical, and stereoelectronic structural requirements of the opioid peptides for their interactions with opioid receptors. In turn, this had led to insights into the three-dimensional pharmacophore for opioid receptors. In this article we review and discuss some of the developments that have led to potent, selective, and stable peptide and peptidomimetic ligands that are highly potent and selective, and that have delta agonist, mu antagonist, and kappa agonist biological activities (other authors in this issue will discuss the development of other types of activities and selectivities). These have led to ligands that provide unique insight into opioid pharmacophores and the critical roles opioid ligands and receptor scan play in pain, addiction, and other human maladies.     

药效假说在配体从头设计中的适用性探讨

在基于靶蛋白结构的多肽分子设计中,药效假说是从头设计方法的基本前提。虽然该假说是否成立已有不少议论,但尚未见到系统分析的报道。通过对８个蛋白质复物界面做了氨基酸模拟图谱,并从模拟图谱的结构偏差与能量分量的关系,对药效假说的适用条件进行了讨论。同时也给出一个ＨＩＶ－１蛋白酶及抑制剂复合物的功能图谱。从所得结果来看,药效假说在以氨基酸为药效基团时,尽管不少情况下仍然有效,但不是谱遍成立的。     

药效假说在配体从头设计中的适用性探讨

在基于靶蛋白结构的多肽分子设计中,药效假说是从头设计方法的基本前提。虽然该假说是否成立已有不少议论,但尚未见到系统分析的报道。通过对８ 个蛋白质复合物界面做了氨基酸模拟图谱,并从模拟图谱的结构偏差与能量分量的关系,对药效假说的适用条件进行了讨论。同时也给出一个ＨＩＶ－ １ 蛋白酶及抑制剂复合物的功能图谱。从所得结果来看,药效假说在以氨基酸为药效基团时,尽管不少情况下仍然有效,但不是普遍成立的。     

X-ray studies on ligands

Advances in x-ray crystallographic data collection, structure solution, and refinement/validation have reduced the time required and expanded the range of samples amenable to x-ray crystallographic studies. Consequently, we can now collect complete atomic resolution data sets on physically smaller crystals and solve larger problems by direct methods beyond what could have been accomplished even five years ago. Applying these improved methods to the study of opioid ligands has enhanced our knowledge of the opioid pharmacophore. Despite considerable progress, it is still difficult to define the pharmacophoric parameters required for highly selective and potent opioid peptides. In part this is due to the conformational flexibility remaining even in conformationally constrained peptides.     

Design and synthesis of quinolinopropellane derivatives with selective δ opioid receptor agonism

Indolopropellane 2 was reported to show almost no binding affinity to the δ opioid receptor (DOR) in spite of the fact that 2 has both the propellane fundamental skeleton (message part) with binding ability to the opioid receptors and a possible DOR address structure (indole moiety). We developed the working hypothesis that almost no binding affinity of 2 to the DOR would be derived from its possibly stable bent conformer. To enable the propellane skeleton to adopt an extended conformation which would reasonably interact with the DOR, quinolinopropellanes 3a–d were designed which had an additional pharmacophore, quinoline nitrogen. The calculated binding free energies of ligand–DOR complexes strongly supported our working hypothesis. The synthesized quinolinopropellane 3a was a selective DOR full agonist, confirming our working hypothesis and the results of in silico investigation.     

Structural insights of JAK2 inhibitors: pharmacophore modeling and ligand-based 3D-QSAR studies of pyrido-indole derivatives

Abstract

In this study we have performed pharmacophore modeling and built a 3D QSAR model for pyrido-indole derivatives as Janus Kinase 2 inhibitors. An efficient pharmacophore has been identified from a data set of 51 molecules and the identified pharmacophore hypothesis consisted of one hydrogen bond acceptor, two hydrogen bond donors and three aromatic rings, i.e. ADDRRR. A powerful 3D-QSAR model has also been constructed by employing Partial Least Square regression analysis with a regression coefficient of 0.97 (R²) and Q² of 0.95, and Pearson-R of 0.98.     

Crystallographic study of inhibitors of tRNA-guanine transglycosylase suggests a new structure-based pharmacophore for virtual screening

The enzyme tRNA-guanine transglycosylase (TGT) is involved in the pathogenicity of Shigellae. As the crystal structure of this protein is known, it is a putative target for the structure-based design of inhibitors. Here we report a crystallographic study of several new ligands exhibiting a 2,6-diamino-3H-quinazolin-4-one scaffold, which has been shown recently to be a promising template for TGT-inhibitors. Crystal structure analysis of these complexes has revealed an unexpected movement of the side-chain of Asp102. A detailed analysis of the water network disrupted by this rotation has lead to the derivation of a new composite pharmacophore. A virtual screening has been performed based on this pharmacophore hypothesis and several new inhibitors of micromolar binding affinity with new skeletons have been discovered.     

Syntheses and opioid receptor binding properties of carboxamido-substituted opioids

A series of 15 novel opioid derivatives were made where the prototypic phenolic-OH group of traditional opioids was replaced by a carboxamido (CONH₂) group. For 2,6-methano-3-benzazocines and morphinans similar or, in a few instances, enhanced affinity for μ, δ and κ opioid receptors was observed when the OH → CONH₂ switch was applied. For 4,5α-epoxymorphinans, binding affinities for the corresponding carboxamide derivatives were much lower than the OH partner consistent with our pharmacophore hypothesis concerning carboxamide bioactive conformation. The active metabolite of tramadol and its carboxamide counterpart had comparable affinities for the three receptors.     

Pharmacophore models generation by catalyst and phase consensus-based virtual screening protocol against PI3Kα inhibitors

Phosphoinositide 3-kinases (PI3Ks) family has emerged as promising targets for novel therapeutic agents against neoplastic diseases. Pharmacophore and 3D-quantitative structure–activity relationship modelling were applied to study the structure–activity relationship of PI3K inhibitors. The best HypoGen pharmacophore hypothesis Hypo1 with a correlation coefficient of 0.961 consists of one hydrogen-bond acceptor, one hydrogen-bond donor and two hydrophobic features, whereas the best phase hypothesis AADRRR.378 with favourable statistics (q² = 0.7368, r² = 0.9863) has two hydrogen-bond acceptors, one hydrogen-bond donor and three ring aromatic features. Multiple methods, such as Fischer validation, molecular docking and mapping of test set molecules, were carried out to validate these pharmacophore models. Furthermore, a comparative molecular similarity indices analysis candidate hypothesis model was generated as a supplement of pharmacophore hypothesis. Detailed protein–ligand binding information obtained by Glide was utilised in compound optimisation and virtual screening. A molecular database of 133 known inhibitors and 6179 decoys was built for a screening test to quantitatively analyse various hypotheses and scoring parameters. Finally, we designed a workflow integrating HypoGen pharmacophore searching, phase pharmacophore searching and molecular docking for screening the database. With an improved criterion of enrichment factor (EF = 17.43) and ROC curve (AUC = 0.946), this workflow would provide us an original method for novel PI3K inhibitors.     

Design and synthesis of trivalent ligands targeting opioid,cholecystokinin, and melanocortin receptors for the treatment of pain

It has been known that co-administration of morphine with either cholecystokinin (CCK) receptor or melanocortin (MC) receptor antagonists enhance morphine’s analgesic efficacy by reducing serious side effects such as tolerance and addiction.1, 2, 3, 4 Considering these synergistic effects, we have designed trivalent ligands in which all three different pharmacophores for opioid, CCK, and MC receptors are combined in such a way as to conserve their own topographical pharmacophore structures. These ligands, excluding the cyclic compound, were synthesized by solid phase synthesis using Rink-amide resin under microwave assistance in very high yields. These trivalent ligands bind to their respective receptors well demonstrating that the topographical pharmacophore structures for the three receptors were retained for receptor binding. Ligand 10 was a lead compound to show the best biological activities at all three receptors.     

Insights into subtype selectivity of opioid agonists by ligand-based and structure-based methods

To probe the selective mechanism of agonists binding to three opioid receptor subtypes, ligand-based and receptor-based methods were implemented together and subtype characteristics of opioid agonists were clearly described. Three pharmacophore models of opioid agonists were generated by the Catalyst/HypoGen program. The best pharmacophore models for μ, δ and κ agonists contained four, five and five features, respectively. Meanwhile, the three-dimensional structures of three receptor subtypes were modeled on the basis of the crystal structure of β2-adrenergic receptor, and molecular docking was conducted further. According to these pharmacophore models and docking results, the similarities and differences among agonists of three subtypes were identified. μ or δ agonists, for example, could form one hydrogen bond separately with Tyr129 and Tyr150 at TMIII, whereas κ ones formed a π-π interaction in that place. These findings may be crucial for the development of novel selective analgesic drugs.