The protozoan parasite Trypanosoma cruzi, the etiological agent of Chagas’ disease, affects millions of individuals and continues to be an important global health concern. The poor efficacy and unfavorable side effects of current treatments necessitate novel therapeutics. Cruzain, the major cysteine protease of T. cruzi, is one potential novel target. Recent advances in a class of vinyl-sulfone inhibitors are encouraging; however, as most potential therapeutics fail in clinical trials and both disease progression and resistance call for combination therapy with several drugs, the identification of additional classes of inhibitory molecules is essential. Using an exhaustive virtual-screening and experimental-validation approach, we identify several additional small-molecule cruzain inhibitors. Further optimization of these chemical scaffolds could lead to the development of novel drugs useful in the treatment of Chagas’ disease.
cruzain; cruzipain; Chagas’ disease; Trypanosoma cruzi; computer-aided drug discovery; cysteine protease inhibitor
One common practice in drug discovery is to optimize known or suspected ligands in order to improve binding affinity. In performing these optimizations, it is useful to look at as many known inhibitors as possible for guidance. Medicinal chemists often seek to improve potency by altering certain chemical moieties of known/endogenous ligands while retaining those critical for binding. To our knowledge, no automated, ligand-based algorithm exists for systematically “swapping” the chemical moieties of known ligands in order to generate novel ligands with potentially improved potency. To address this need, we have created a novel algorithm called “LigMerge”. LigMerge identifies the maximum (largest) common substructure of two three-dimensional ligand models, superimposes these two substructures, and then systematically mixes and matches the distinct fragments attached to the common substructure at each common atom, thereby generating multiple compound models related to the known inhibitors that can be evaluated using computer docking prior to synthesis and experimental testing.
To demonstrate the utility of LigMerge, we identify compounds predicted to inhibit peroxisome proliferator-activated receptor gamma, HIV reverse transcriptase, and dihydrofolate reductase with affinities higher than those of known ligands. We are hopeful that LigMerge will be a helpful tool for the drug-design community.
One common practice in drug discovery is to optimize known or suspected ligands in order to improve binding affinity. In performing these optimizations, it is useful to look at as many known inhibitors as possible for guidance. Medicinal chemists often seek to improve potency by altering certain chemical moieties of known/endogenous ligands while retaining those critical for binding. To our knowledge, no automated, ligand-based algorithm exists for systematically ‘swapping’ the chemical moieties of known ligands to generate novel ligands with potentially improved potency. To address this need, we have created a novel algorithm called ‘LigMerge’. LigMerge identifies the maximum (largest) common substructure of two three-dimensional ligand models, superimposes these two substructures, and then systematically mixes and matches the distinct fragments attached to the common substructure at each common atom, thereby generating multiple compound models related to the known inhibitors that can be evaluated using computer docking prior to synthesis and experimental testing. To demonstrate the utility of LigMerge, we identify compounds predicted to inhibit peroxisome proliferator–activated receptor gamma, HIV reverse transcriptase, and dihydrofolate reductase with affinities higher than those of known ligands. We hope that LigMerge will be a helpful tool for the drug design community.
biophysical chemistry; drug design; structure-based drug design
On the basis of evidence that opioid compounds with a mixed μ agonist/δ antagonist profile may produce an antinociceptive effect with low propensity to induce side effects, bifunctional opioid peptides containing the μ agonist [Dmt1]DALDA (H-Dmt-D-Arg-Phe-Lys-NH2; Dmt = 2',6’-dimethyltyrosine) connected tail-to-tail via various α,ω-diaminoalkyl- or diaminocyclohexane linkers to the δ antagonists TICP[Ψ] (H-Tyr-TicΨ[CH2-NH]Cha-Phe-OH; Cha = cyclohexylalanine, Tic = 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid), H-Dmt-Tic-OH or H-Bcp-Tic-OH (Bcp = 4'-[N-((4'-phenyl)phenethyl)carboxamido]phenylalanine) were synthesized and pharmacologically characterized in vitro. Bifunctional [Dmt1]DALDA→NH-(CH2)n-NH←TICP[Ψ] compounds (n = 0–12) showed decreasing μ and δ receptor binding affinities with increasing linker length. As expected, several of the bifunctional peptides were μ agonist/δ antagonists with low nanomolar μ and δ receptor binding affinities. However, compounds with unexpected opioid activity profiles, including a μ partial agonist/δ partial agonist, μ antagonist/δ antagonists and μ agonist/δ agonists, were also identified. These results indicate that the binding affinities and intrinsic efficacies of these bifunctional compounds at both receptors depend on the length and type of the linker connecting the μ and δ components. An important recommendation emerging from this study is that the in vitro activity profiles of bifunctional compounds containing an agonist and an antagonist component connected via a linker need to be determined prior to their pharmacological evaluation in vivo.
opioid peptide analogues; peptide synthesis; bifunctional μ/δ opioid compounds; opioid activity profiles; opioid peptide SAR; linkers in bifunctional opioid peptides
The development of highly selective small molecule inhibitors for individual caspases, a class of cysteine-dependent aspartate-specific proteases, has been challenging due to conservation of the active site. Previously we discovered an allosteric site at the dimer interface of caspases-3, -7 and -1 using disulfide trapping. Here we show this approach can generate selective tethered ligands and inhibitors for caspase-5 which is remarkable considering its high sequence similarity to caspase-1. Among the 62 hit out of a screen of ~15,000 thiol-containing fragments, a naphthyl-thiazole containing molecule was identified that selectively inhibited and labeled the allosteric cysteine in the p10 subunit of caspase-5, but caused very little inhibition or labeling of caspase-1. Interestingly, some of allosteric tethered compounds to caspase-5 did not inhibit its enzymatic activity, suggesting that thiol-labeling itself is not sufficient to drive inhibition. These studies validate an allosteric site on caspase-5 and provide a useful starting point to develop selective compounds to probe the role of caspase-5 separate from caspase-1 in the innate immune response.
caspase-5; disulfide trapping; allosteric inhibitor; inflammation
3,5-bis(2-fluorobenzylidine)-4-piperidone or EF24 is a potent anticancer derivative of curcumin. Using an amine derivative of EF24, we synthesized a hydrazinonicotinic acid conjugate, EFAH, for Tc-99m radiolabeling and SPECT imaging. The aqueous solubility of EFAH (3.5 mg/ml) was significantly more than that of EF24 (1.2 mg/ml); the octanol/water partition coefficient of EFAH was estimated at log P = 0.33. As an antiproliferative agent, EFAH was as effective as EF24 in suppressing the proliferation of H441, MiaPaCa-2 and Panc-1 cells. Daily intraperitoneal injection of EFAH (5 μg) for 3 weeks in mice carrying xenografts of Panc-1 pancreatic cancer showed a mean tumor volume reduction of 79%; the tumor weight decreased by 82% in the treated group. For imaging and biodistribution, EFAH was labeled with Tc-99m (98% RCY) and intravenously administered in rats. Approximately 23.7% and 14.3% of injected dose accumulated in liver and intestine, respectively, suggesting that EFAH is mostly eliminated by hepatobiliary route. The results indicate that HYNIC modification of EF24 for Tc-99m radiolabeling does not affect its anti-proliferative efficacy. For the first time, a visual biodisposition of EF24 in a live animal model has been demonstrated. Such knowledge could be of benefit in developing therapeutic curcuminoids, such as EF24.
Curcuminoid; Tc-99m; SPECT; Cancer; EF24; Imaging
The T box antiterminator RNA element is an important component of the T box riboswitch that controls the transcription of vital genes in many Gram-positive bacteria. A series of 1,4-disubstituted 1,2,3-triazoles was screened in a fluorescence-monitored thermal denaturation assay to identify ligands that altered the stability of antiterminator model RNA. Several ligands were identified that significantly increased or decreased the melting temperature (Tm) of the RNA. The results indicate that this series of triazole ligands can alter the stability of antiterminator model RNA in a structure-dependent manner.
antiterminator; Tm; riboswitch; tRNA; ligand screening
The aspartate biosynthetic pathway provides essential metabolites for many important biological functions, including the production of four essential amino acids. Since this critical pathway is only present in plants and microbes any disruptions will be fatal to these organisms. An early pathway enzyme, L-aspartate-β-semialdehyde dehydrogenase (ASADH), produces a key intermediate at the first branch point of this pathway. Developing potent and selective inhibitors against several orthologs in the ASADH family can serve as lead compounds for antibiotic development. Kinetic studies of two small molecule fragment libraries have identified inhibitors that show good selectivity against ASADHs from two different bacterial species, Streptococcus pneumoniae and Vibrio cholerae, despite the presence of an identical constellation of active site amino acids in this homologous enzyme family. Structural characterization of enzyme-inhibitor complexes have elucidated different modes of binding between these structurally related enzymes. This information provides the basis for a structure guided approach to the development of more potent and more selective inhibitors.
enzyme inhibition; enzyme inactivation; structural studies; X-ray crystallography; ASA dehydrogenase
The Keap1-Nrf2 interaction plays important roles in regulation of Nrf2 activity and induction of chemopreventive enzymes. To better understand the interaction and to determine the minimal Nrf2 sequence required for Keap1 binding, we synthesized a series of Nrf2 peptides containing ETGE motif and determined their binding affinities to the Kelch domain of Keap1 in solution using a surface plasmon resonance (SPR)-based competition assay. The equilibrium dissociation constant for the interaction between 16mer Nrf2 peptide and Keap1 Kelch domain in solution (KDsolution) was found to be 23.9 nM, which is 10× lower than the surface binding constant (KDsurface) of 252 nM obtained for the direct binding of Keap1 Kelch domain to the immobilized 16mer Nrf2 peptide on a SPR sensor chip surface. The binding affinity of Nrf2 peptides to Keap1 Kelch domain was not lost until after deletion of 8 residues from the N-terminus of the 16mer Nrf2 peptide. The 9mer Nrf2 peptide has a moderate binding affinity with a KDsolution of 352 nM and the affinity was increased 15× upon removal of the positive charge at the peptide N-terminus by acetylation. These results suggest that the minimal Nrf2 peptide sequence required for Keap1 binding is the 9mer sequence of LDEETGEFL.
Keap1; Nrf2; protein-protein interaction; surface plasmon resonance; solution binding assay
Here we describe the design and synthesis of two series of 4-pyrrylamino quinazolines as new analogues of the EGFR inhibitor Gefitinib. In vitro antitumor activity of these novel compounds against pancreatic (Miapaca2) and prostate (DU145) cancer cell lines was evaluated. Compared with the parental Gefitinib, all the 18 derivatives show a greatly increased cytotoxicity to cancer cells. In vitro kinase inhibitory activity on EGFR was also investigated. Among them, compounds GI-6, GII-4, GII-6, GII-8, and GII-9 are more potential RTK inhibitors. Based on these results, we propose simple structure-activity relationship to provide information for designing and developing more potent antitumor agents.
4-pyrrylamino quinazoline; Gefitinib; antitumor activity; cancer cells; receptor tyrosine kinase
Phosphorylation of L-serine-containing enkephalin analogs has been explored as an alternative to glycosylation in an effort to increase blood-brain barrier (BBB) permeability and CNS bioavailability of peptide pharmacophores. Two enkephalin-based peptides were modified for these studies, a set related to DTLES, a mixed μ/δ-agonist, and one related to DAMGO, a highly selective μ-agonist. Each unglycosylated peptide was compared to its phosphate, its mono-benzylphosphate ester, and its β-D-glucoside. Binding was characterized in membrane preparations from CHO cells expressing human μ, δ and κ-opiate receptors (MOR, DOR and KOR). Antinociception was measured in mice using the 55°C tail flick assay. In order to estimate bioavailability, the antinociceptive effect of each opioid agonist was evaluated after intracerebroventricular (i.c.v.) or intravenous administration (i.v.) of the peptides. Circular dichroism (CD) methods and high field nuclear magnetic resonance (NMR) were used in the presence and absence of sodium dodecylsulfate (SDS) to understand how the presence of a membrane might influence the peptide conformations.
d-boroAla was previously characterized as an inhibitor of bacterial alanine racemase and d-Ala-d-Ala ligase enzymes [Duncan, K., et al Biochemistry 1989, 28:3541–9]. In the present study, d-boroAla was identified and characterized as an antibacterial agent. d-boroAla has activity against both Gram-positive and Gram-negative organisms, with MICs down to 8 µg/mL. A structure-function study on the alkyl side chain (NH2-CHR-B(OR’)2) revealed that d-boroAla is the most effective agent in a series including boroGly, d-boroHomoAla, and d-boroVal. l-boroAla was much less active, and N-acetylation completely abolished activity. An LC-MS/MS assay was used to demonstrate that d-boroAla exerts its antibacterial activity by inhibition of d-Ala-d-Ala ligase (DDL). d-boroAla is bactericidal at 1× MIC against Staphylococcus aureus and Bacillus subtilis – which each encode one copy of DDL, and at 4× MIC against Escherichia coli and Salmonella enterica serovar Typhimurium – which each encode two copies of DDL. d-boroAla demonstrated a frequency of resistance of 8×10−8 at 4× MIC in S. aureus. These results demonstrate that d-boroAla has promising antibacterial activity, and could serve as the lead agent in a new class of DDL targeted antibacterial agents. This study also demonstrates d-boroAla as a possible probe for DDL function.
antibacterial; cell wall; alanine branch; broad spectrum; d-Ala-d-Ala ligase
A detailed understanding of factors influencing the binding specificity
of a ligand to a set of desirable targets and undesirable decoys is a key step
in the design of potent and selective therapeutics. We have developed a general
method for optimizing binding specificity in ligand–receptor complexes
based on the theory of electrostatic charge optimization. This methodology can
be used to tune the binding of a ligand to a panel of potential targets and
decoys, along the continuum from narrow binding to only one partner to broad
binding to the entire panel. Using HIV-1 protease as a model system, we probe
specificity in three distinct ways. First, we probe interactions that could make
the promiscuous protease inhibitor pepstatin more selective toward HIV-1
protease. Next, we study clinically approved HIV-1 protease inhibitors and probe
ways to broaden the binding profiles toward both wild-type HIV-1 protease and
drug-resistant mutants. Finally, we study a conformational ensemble of wild-type
HIV-1 protease to “design in” broad specificity to known drugs
before resistance mutations arise. The results from this conformational ensemble
were similar to those from the drug-resistant ensemble, suggesting the use of a
conformational wild-type ensemble as a tool to develop escape-mutant resistant
binding affinity; continuum electrostatics; charge optimization
The anticancer prodrug 1,2-bis(methylsulfonyl)-1-(2-chloroethyl)-2-[[1-(4-nitrophenyl)ethoxy]carbonyl]hydrazine (KS119) selectively releases a short-lived cytotoxin following enzymatic reduction in hypoxic environments found in solid tumors. KS119, in addition to two enantiomers, has two stable atropisomers (conformers differing in structure owing to hindered bond rotation) that interconvert at 37 °C in aqueous solution by first order kinetics with t1/2 values of ~50 and ~64 hours. The atropisomers differ in physical properties such as partition coefficients that allow their chromatographic separation on non-chiral columns. A striking difference in the rate of metabolism of the two atropisomers occurs in intact EMT6 murine mammary carcinoma cells under oxygen deficient conditions. A structurally related molecule, 1,2-bis(methylsulfonyl)-1-(2-chloroethyl)-2-[[1-(3-hydroxy-4-nitrophenyl)ethoxy]carbonyl]hydrazine (KS119WOH), was also found to exist in similar stable atropisomers. The ratio of the atropisomers of KS119 and structurally related agents has the potential to impact the bioavailability, activation and therapeutic activity. Thus, thermally stable atropisomers/conformers in small molecules can result in chemically and enantiomerically pure compounds having differences in biological activities.
KS119; prodrug; atropisomers; conformers; hypoxia; targeting; cytotoxicity; chemotherapy
Candida albicans and Candida glabrata cause fungal bloodstream infections that are associated with significant mortality. As part of an effort to develop potent and selective antifolates that target dihydrofolate reductase (DHFR) from Candida species, we report three ternary crystal structures of Candida albicans DHFR (CaDHFR) bound to novel propargyl-linked analogs. Consistent with earlier modeling results, these structures show that hydrophobic pockets in the binding site may be exploited to increase ligand potency. The crystal structures also confirm that loop residues Thr 58- Phe 66, which flank the active site and influence ligand potency and selectivity, adopt multiple conformations. To aid the development of a dual Candida spp. inhibitor, three new crystal structures of C. glabrata DHFR (CgDHFR) bound to similar ligands as those bound in the ternary structures of CaDHFR are also reported here. Loop residues 58-66 in CgDHFR and human DHFR are 1 Å and 3 Å closer to the folate binding site, respectively, than loop residues in CaDHFR, suggesting that a properly size ligand could be a potent and selective dual inhibitor of CaDHFR and CgDHFR.
Candida albicans; Candida glabrata; X-ray crystallography; structure-based drug design; DHFR; antifolate
Smooth muscle cell (SMC) proliferation has been accepted as a common event in the pathophysiology of vascular diseases, including atherogenesis and intimal hyperplasia. Delivery of the nitric oxide synthase (NOS) substrate L-arginine, pharmacological nitric oxide (NO) donors, NO gas or over-expression of NOS proteins can inhibit SMC proliferation and reduce the injury responses within the blood vessel wall. Though commercial development of NO-donors that attempt to provide exogenous delivery of NO has accelerated over the last few years. None of the currently available products can provide controlled, sustained, time tunable release of NO. Nitrosamine-based NO donors, prepared in our laboratory, present a unique and innovative alternative for possible treatments for long-term NO deficiency related diseases including atherosclerosis, asthma, erectile dysfunction, cancer and neurodegenerative diseases. A family of secondary amines prepared via nucleophilic aromatic displacement reactions could be readily N-nitrosated to produce NO donors. NO release takes place in three distinct phases. During the initial phase, the release rate is extremely fast. In the second phase, the release is slower and the rate remains essentially the same during the final stage. These compounds inhibited up to 35% human aortic smooth muscle cell (HASMC) proliferation in a concentration-dependent manner.
nitric oxide; nitric oxide donors; nitric oxide synthase; human aortic smooth muscle cells; atherosclerosis; N-nitrosamines; proliferation
Eph receptor tyrosine kinases and ephrin ligands control many physiological and pathological processes, and molecules interfering with their interaction are useful probes to elucidate their complex biological functions. Moreover, targeting Eph receptors might enable new strategies to inhibit cancer progression and pathological angiogenesis as well as promote nerve regeneration. Because our previous work suggested the importance of the salicylic acid group in antagonistic small molecules targeting Eph receptors, we screened a series of salicylic acid derivatives to identify novel Eph receptor antagonists. This identified a disalicylic acid-furanyl derivative that inhibits ephrin-A5 binding to EphA4 with an IC50 of 3 μM in ELISA assays. This compound, which appears to bind to the ephrin-binding pocket of EphA4, also targets several other Eph receptors. Furthermore, it inhibits EphA2 and EphA4 tyrosine phosphorylation in cells stimulated with ephrin while not affecting phosphorylation of EphB2, which is not a target receptor. In endothelial cells, the disalicylic acid-furanyl derivative inhibits EphA2 phosphorylation in response to TNFα and capillary-like tube formation on Matrigel, two effects that depend on EphA2 interaction with endogenous ephrin-A1. These findings suggest that salicylic acid derivatives could be used as starting points to design new small molecule antagonists of Eph receptors.
small molecule; antagonist; dymethylpyrrole derivative; protein tyrosine kinase; angiogenesis; nerve regeneration
New drugs are needed to treat Human African Trypanosomiasis because the currently approved treatments are toxic or limited in efficacy. One strategy for developing new drugs involves discovering novel genes whose products can be targeted for modulation by small molecule chemotherapeutic agents. The Trypanosoma brucei genome contains many genes with the potential to become such targets. Kinases represent one group of genes that regulate many important cell functions and can be modulated by small molecules, thus represent a promising group of enzymes to screen for potential therapeutic targets. RNAi screens could help identify the most promising kinase targets, but the lack of suitable assays represents a barrier for optimizing the use of this technology in T. brucei. Here we describe an RNAi screen of a small RNAi library targeting 30 members of the T. brucei kinome utilizing a luciferase-based assay. This screen both validated the luciferase-based assay as a suitable method for conducting RNAi screens in T. brucei, and also identified 2 kinases (CRK12 and ERK8) that are essential for normal proliferation by the parasite.
Trypanosoma brucei; HTS; RNAi; ATP-bioluminescence; target
From the molecular mechanism of antagonist unbinding in the β1 and β2 adrenoceptors investigated by steered molecular dynamics, we attempt to provide further possibilities of ligand subtype and subspecies selectivity. We have simulated unbinding of β1-selective Esmolol and β2-selective ICI-118551 from both receptors to the extracellular environment and found distinct molecular features of unbinding. By calculating work profiles, we show different preference in antagonist unbinding pathways between the receptors, in particular, perpendicular to the membrane pathway is favourable in the β1 adrenoceptor, whereas the lateral pathway involving helices 5, 6 and 7 is preferable in the β2 adrenoceptor. The estimated free energy change of unbinding based on the preferable pathway correlates with the experimental ligand selectivity. We then show that the non-conserved K347 (6.58) appears to facilitate in guiding Esmolol to the extracellular surface via hydrogen bonds in the β1 adrenoceptor. In contrast, hydrophobic and aromatic interactions dominate in driving ICI-118551 through the easiest pathway in the β2 adrenoceptor. We show how our study can stimulate design of selective antagonists and discuss other possible molecular reasons of ligand selectivity, involving sequential binding of agonists and glycosylation of the receptor extracellular surface.
adrenergic receptors; drug design; G protein-coupled receptors; molecular dynamics; selectivity
Matrix metalloproteinases (MMPs) are zinc-containing enzymes capable of degrading all components of the extracellular matrix. Due to their role in human disease, MMPs have been the subject of extensive study. A bioinorganic approach was recently used to identify novel inhibitors based on a maltol zinc-binding group, but accompanying molecular-docking studies failed to explain why one of these inhibitors, AM-6, had ~2500-fold selectivity for MMP-3 over MMP-2.
A number of studies have suggested that the MMP active site is highly flexible, leading some to speculate that differences in active-site flexibility may explain inhibitor selectivity. In order to extend the bioinorganic approach in a way that accounts for MMP-2 and MMP-3 dynamics, we here investigate the predicted binding modes and energies of AM-6 docked into multiple structures extracted from MMP MD simulations. Our findings suggest that accounting for protein dynamics is essential for the accurate prediction of binding affinity and selectivity. Additionally, AM-6 and other similar inhibitors likely select for and stabilize only a subpopulation of all MMP conformations sampled by the apo protein. Consequently, when attempting to predict ligand affinity and selectivity using an ensemble of protein structures, it may be wise to disregard protein conformations that cannot accommodate the ligand.
matrix metalloproteinases; inhibitors; computer-aided drug design; docking; protein flexibility
It has been estimated that nearly one third of functional proteins contain a metal ion. These constitute a wide variety of possible drug targets including metalloproteinases, dehydrogenases, oxidoreductases, hydrolases, deacetylases or many others in which the metal ion is either of catalytic or structural nature. Despite the predominant role of a metal ion in so many classes of drug targets, current high-throughput screening techniques do not usually produce viable hits against these proteins, likely due to the lack of proper metal binding pharmacophores in the current screening libraries. Herein we describe a novel fragment based drug discovery approach using a metal targeting fragment library that is based on a variety of distinct classes of metal-binding groups designed to reliably anchor the fragments at the target's metal ions. We show that the approach can effectively identify novel, potent and selective agents that can be readily developed into metalloprotein-targeted therapeutics.
Protein-protein interactions control signaling, specific adhesion and many other biological functions. The three dimensional structures of the interfaces and bound ligand can be approached with Tr-NOESY NMR, which can be applied to much larger proteins than conventional NMR and requires less concentrated protein. However, it is not clear how accurately the structures of protein-bound peptides can be determined by Tr-NOESY. We studied the structure of a biotin-mimetic peptide (FSHPQNT) bound to streptavidin, since the x-ray structure of the complex is available to 1.74Å resolution and we found that conditions could be adjusted so that the off-rates were fast enough for Tr-NOESY NMR. The off-rate was determined with 19F NMR, using a para-fluoro-phenylalanine analog of the peptide. A new criterion for a lower limit on kinetic off-rate was found, which allowed accurate structure determination at a slower off-rate. Non-specific binding of the peptide to streptavidin was not significant, since biotin blocked the peptide Tr-NOESY. Protein mediation for the long range peptide Tr-NOESY cross-peaks was corrected by a Tr-NOESY/ROESY averaging procedure. The protein-bound structure of the peptide was determined by Tr-NOESY constrained and simulated annealing. The structure deduced from the NMR was close to the x-ray structure.
Peptide-protein interactions; Transferred NOESY; Tr-NOESY accuracy; Ligand off-rates; Fluorine NMR; comparison of x-ray and NMR structures
Several novel norcamphor (bicycloheptane) based compounds were designed and synthesized as noncompetitive NMDA receptor antagonists at the Phencyclidine (PCP) binding sites. The heterocyclic ring was also varied to examine piperidine, pyrrolidine and morpholine groups. We examined pharmacological activities of these compounds in vitro (binding studies) and in vivo (MES test). Pharmacological evaluations revealed one of the compounds, 5a, to be a good lead, exhibiting moderate binding at NMDA receptors (IC50 = 7.86 μM; Ki = 5.28 μM), MES neuroprotection activity at 100 mg/kg and acceptable toxicity profile.
NMDA receptor antagonist; Phencyclidine (PCP) Binding Site; Anticonvulsant Activity; MES test; Bicycloheptane derivatives
Conformational selection is a primary mechanism in biomolecular recognition. The conformational ensemble may determine the ability of a drug to compete with a native ligand for a receptor target. Traditional docking procedures which use one or few protein structures are limited and may not be able to represent a complex competition among closely related protein receptors in agonist and antagonist ensembles. Here, we test a protocol aimed at selecting a drug candidate based on its ability to synergistically bind to distinct conformational states. We demonstrate, for the case of estrogen receptor α (ERα) and estrogen receptor β (ERβ), that the functional outcome of ligand binding can be inferred from its ability to simultaneously bind both ERα and ERβ in agonist and antagonist conformations as calculated docking scores. Combining a conformational selection method with an experimental reporter gene system in yeast, we propose that several phytoestrogens can be novel estrogen receptor β selective agonists. Our work proposes a computational protocol to select estrogen receptor subtype selective agonists. Compared with other models, present method gives the best prediction in ligands’ function.
conformational ensemble; conformational selection; docking; phytoestrogen; SERMs; two-state theory
Compstatin family peptides are potent inhibitors of the complement system and promising drug candidates against diseases involving under-regulated complement activation. Compstatin is a 13-residue cyclized peptide that inhibits cleavage of complement protein C3, preventing downstream complement activation. We present three new compstatin variants, characterized by tryptophan replacement at positions 1 and/or 13. Peptide design was based on physicochemical reasoning and was inspired by earlier work which identified tryptophan substitutions at positions 1 and 13 in peptides with predicted C3c binding abilities (Bellows, M. L.; Fung, H. K.; Taylor, M. S.; Floudas, C. A.; López de Victoria, A.; Morikis, D. (2010) Biophys J 98: 2337–2346). The new variants preserve distinct polar and nonpolar surfaces of compstatin, but have altered local interaction capabilities with C3. All three peptides exhibited potent C3 binding by surface plasmon resonance (SPR) and potent complement inhibition by ELISAs. We also present ELISA data and detailed SPR kinetic data of three peptides from previous computational design.
Structure-Based Drug Design; Peptide Design; Compstatin Family; Complement System; Complement System Inhibitors