Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2

Influenza A virus M2 (A/M2) forms a homotetrameric proton selective channel in the viral membrane. It has been the drug target of antiviral drugs such as amantadine and rimantadine. However, most of the current virulent influenza A viruses carry drug-resistant mutations alongside the drug binding site, such as S31N, V27A, and L26F, etc., each of which might be dominant in a given flu season. Among these mutations, the V27A mutation was prevalent among transmissible viruses under drug selection pressure. Until now, V27A has not been successfully targeted by small molecule inhibitors, despite years of extensive medicinal chemistry research efforts and high throughput screening. Guided by molecular dynamics (MD) simulation of drug binding and the influence of drug binding on the dynamics of A/M2 from earlier experimental studies, we designed a series of potent spirane amine inhibitors targeting not only WT, but also both A/M2-27A and L26F mutants with IC(50)s similar to that seen for amantadine's inhibition of the WT channel. The potencies of these inhibitors were further demonstrated in experimental binding and plaque reduction assays. These results demonstrate the power of MD simulations to probe the mechanism of drug binding as well as the ability to guide design of inhibitors of targets that had previously appeared to be undruggable.     

Specific binding of adamantane drugs and direction of their polar amines in the pore of the influenza M2 transmembrane domain in lipid bilayers and dodecylphosphocholine micelles determined by NMR spectroscopy

The transmembrane domain of the influenza M2 protein (M2TM) forms a tetrameric proton channel important for the virus lifecycle. The proton-channel activity is inhibited by amine-containing adamantyl drugs amantadine and rimantadine, which have been shown to bind specifically to the pore of M2TM near Ser31. However, whether the polar amine points to the N- or C-terminus of the channel has not yet been determined. Elucidating the polar group direction will shed light on the mechanism by which drug binding inhibits this proton channel and will facilitate rational design of new inhibitors. In this study, we determine the polar amine direction using M2TM reconstituted in lipid bilayers as well as dodecylphosphocholine (DPC) micelles. (13)C-(2)H rotational-echo double-resonance NMR experiments of (13)C-labeled M2TM and methyl-deuterated rimantadine in lipid bilayers showed that the polar amine pointed to the C-terminus of the channel, with the methyl group close to Gly34. Solution NMR experiments of M2TM in DPC micelles indicate that drug binding causes significant chemical shift perturbations of the protein that are very similar to those seen for M2TM and M2(18-60) bound to lipid bilayers. Specific (2)H-labeling of the drugs permitted the assignment of drug-protein cross peaks, which indicate that amantadine and rimantadine bind to the pore in the same fashion as for bilayer-bound M2TM. These results strongly suggest that adamantyl inhibition of M2TM is achieved not only by direct physical occlusion of the channel, but also by perturbing the equilibrium constant of the proton-sensing residue His37. The reproduction of the pharmacologically relevant specific pore-binding site in DPC micelles, which was not observed with a different detergent, DHPC, underscores the significant influence of the detergent environment on the functional structure of this membrane protein.     

Heterodimers of Histidine and Amantadine as Inhibitors for Wild Type and Mutant M2 Channels of Influenza A

Inhibitors bearing the imidazole, adamantane and related structures were synthesized and tested against WT, S31N and S31N‐L26I mutant M2 channels. Although amantadine ( 1 ) only inhibited WT M2 channel, compound 6 containing the imidazole and adamantane groups showed good inhibitory activity to WT and mutant M2 channels. The stereochemistry and basic pK_a of α‐amine are important for the activity of inhibitors and our data showed that derivatives of natural histidine are more active for M2 channels than those of unnatural histidine. The significance of our present results is that we have established a prospective strategy of drug discovery of WT and mutant M2 channels against influenza A.     

Double addition d'organometalliques sur des nitriles α-oxygenes R1 CN. Obtention d'amines primaires de type (R1RR')CNH2

Synthesis of the amines (R¹RR')CNH₂ (I) was carried out by the action of two organometallic compounds RM and R'M' on the α-oxygenated nitriles R¹ CN. Aliphatic and unhindered organolithium or α-ethylenic organomagnesium compounds must be used in the second addition. The nature of the two metallic atoms of the aminate (R¹RR')CN(MM'), precursor of the amine I, has an influence on the yield of this amine. If M = M' = Li an elimination reaction occurs and the amine I is obtained in low yields (2—34%). If M = Mg and M' = Li, the intermediate aminate is more stable, and the amine I is formed in good yields (48—75%). A mechanism explaining these results and the formation of by-products is proposed.     

Discovery of potential M2 channel inhibitors based on the amantadine scaffold via virtual screening and pharmacophore modeling

The M2 channel protein on the influenza A virus membrane has become the main target of the anti-flu drugs amantadine and rimantadine. The structure of the M2 channel proteins of the H3N2 (PDB code 2RLF) and 2009-H1N1 (Genbank accession number GQ385383) viruses may help researchers to solve the drug-resistant problem of these two adamantane-based drugs and develop more powerful new drugs against influenza A virus. In the present study, we searched for new M2 channel inhibitors through a combination of different computational methodologies, including virtual screening with docking and pharmacophore modeling. Virtual screening was performed to calculate the free energies of binding between receptor M2 channel proteins and 200 new designed ligands. After that, pharmacophore analysis was used to identify the important M2 protein-inhibitor interactions and common features of top binding compounds with M2 channel proteins. Finally, the two most potential compounds were determined as novel leads to inhibit M2 channel proteins in both H3N2 and 2009-H1N1 influenza A virus.     

A secondary gate as a mechanism for inhibition of the M2 proton channel by amantadine

The mechanism of inhibition of the influenza A virus M2 proton channel by the antiviral drug amantadine has been under intense investigation. The importance of a mechanistic understanding is heightened by the prevalence of amantadine-resistant mutations. To gain mechanistic insight at the molecular level, we carried out extensive molecular dynamics simulations of the tetrameric M2 proton channel in both apo and amantadine-bound forms in a lipid bilayer. The simulation of the apo form revealed that Val27 from the four M2 subunits can form a secondary gate near the channel entrance and break the water wire in the channel pore. This gate arises from physical occlusion and the elimination of hydrogen-bonding partners for water molecules. In the presence of amantadine, the secondary gate formed by Val27 and the drug molecule lying just below form an extended blockage, which breaks the water wire throughout the simulation. The location and orientation of amantadine inside of the channel pore as found in our simulation are supported by a host of experimental observations. Our study suggests a novel role for Val27 in the inhibition of the M2 proton channel by amantadine.     

Synthesis and human leukocyte elastase inhibitory activity of novel 2-spiro(2′,2′-diphenylcyclopropane) cephalosporin sulfones

A new series of 2-spiro(2,2-diphenylcyclopropane) cephalosporin sulfones was synthesizes as potent human leukocyte elastase inhibitors.SynPhar Laboratories Inc., #2 Taiho Alberta Centre, 4290-91A Street, Edmonton, Canada T6R 5V2. Published in Khimiya Geterotsiklicheskikh Soedinenii, No. 11, pp. 1517–1523, November, 1998.     

5-羟色胺(5-HT)和去甲肾上腺素(NE)重摄取抑制剂药效团模型的建立及比较分析

近年来的研究表明, 去甲肾上腺素(NE)能系统和5-羟色胺(5-HT)能系统可能共同参与了抑郁症的发病机制. 采用Catalyst软件的Hypogen方法, 利用22个不同结构类型的5-HT重摄取抑制剂和19个不同结构类型和活性的NE重摄取抑制剂分别建立了5-HT药效团模型和NE药效团模型, 它们的相关系数分别为0.935, 0.844, 这表明所得到的模型能较好地表征重摄取抑制剂化合物的特征; 此外, 我们还选择了四种不同活性的预测集分别对所建立的药效团模型进行检验, 结果表明所建立的药效团模型具有较好的预测能力. 对这两个药效团模型进行了比较分析, 其结果可以为设计高活性的双重5-HT和NE重摄取抑制剂提供依据.     

Combinatorial library of five-membered iminocyclitol and the inhibitory activities against glyco-enzymes.

BACKGROUND: Oligosaccharide processing enzymes are important classes of catalysts involved in synthesizing specific oligosaccharide structures on proteins and sphingolipids. Development of specific inhibitors of such enzymes is of current interest as these inhibitors may be used to control cellular functions. Five-membered iminocyclitols have been shown to be potent inhibitors of such enzymes. Since a rational design and synthesis of inhibitors is often extremely difficult due to the limited information regarding the structure of the active site, we carried out a combinatorial library approach. RESULTS: To create diversity, we decided to use an aldehyde group of a protected iminocyclitol for reductive amination and the Strecker reaction. After transformation of the nitrile group introduced by the Strecker reaction into an amine and amide and complete deprotection, a small library of five-membered iminocyclitols consisting of 27 compounds was synthesized. A series of compounds obtained by reductive amination was first screened as potential inhibitors of glycosidases and glycosyltransferases. Among them, compounds carrying a C(10)-alkyl group showed marked enhancement of inhibitory activity against alpha-mannosidase at 10 microM concentration when compared with its parent compound and deoxymannojirimycin. Furthermore, compounds having the phenylethyl group showed an extremely strong inhibitory effect against alpha-galactosaminidase at a K(i) value of 29.4 nM. Compounds with an aminomethyl and amide group at the C-1' position of these two molecules showed a decrease in inhibitory activities. CONCLUSIONS: A combinatorial approach based on five-membered iminocyclitols with a galacto-configuration was exploited. The potential usefulness of the library as a source of inhibitors of glycoenzymes is clearly shown in this study.     

Theoretical analysis of peptidyl alpha-ketoheterocyclic inhibitors of human neutrophil elastase: Insight into the mechanism of inhibition and the application of QM/MM calculations in structure-based drug design

It has been suggested from QSAR data (P. D. Edwards, D. J. Wolanin, D.A. Andisik and M. W. Davis, J. Med. Chem., 1995, 38, 76) that the inhibition of elastase by peptidyl alpha-ketoheterocyclic inhibitors can occur in two ways, the less potent inhibitors forming a non-bonded Michaelis complex and the more potent set a covalently bonded enzyme-substrate intermediate. We report QM/MM studies of both binding and reactivity that confirm these findings, showing that the activity of the least potent set of inhibitors correlates with the calculated binding energy, and that of the more potent set correlates with the stability of the intermediate. These calculations show that QM/MM methods can be successfully employed to understand complicated structure-activity relationships and might be employed in the design and assessment of new inhibitors.     

Structure-based design of potent non-peptide MDM2 inhibitors

A successful structure-based design of a class of non-peptide small-molecule MDM2 inhibitors targeting the p53-MDM2 protein-protein interaction is reported. The most potent compound 1d binds to MDM2 protein with a Ki value of 86 nM and is 18 times more potent than a natural p53 peptide (residues 16-27). Compound 1d is potent in inhibition of cell growth in LNCaP prostate cancer cells with wild-type p53 and shows only a weak activity in PC-3 prostate cancer cells with a deleted p53. Importantly, 1d has a minimal toxicity to normal prostate epithelial cells. Our studies provide a convincing example that structure-based strategy can be employed to design highly potent, non-peptide, cell-permeable, small-molecule inhibitors to target protein-protein interaction, which remains a very challenging area in chemical biology and drug design.     

Microwave-assisted synthesis and biological evaluation of new thiazolylhydrazone derivatives as tyrosinase inhibitors and antioxidants

In this work, we have synthesized a series of 2-thiazolylhydrazone derivatives ( 1–27 ) and investigated their biological activities as tyrosinase inhibitors and antioxidants. Some compounds showed potent tyrosinase inhibitory activities and 4-(2-(2-(1-(4-Aminophenyl)ethylidene)-hydrazinyl)thiazol-4-yl) phenol ( 26 ) showed more potent inhibitory effect than the standard tyrosinase inhibitor kojic acid (IC₅₀: 9.8 μM vs. 23.6 μM). Compounds 2 , 14 , and 26 exhibited high antioxidant activities in 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azinobis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) assays. The structure–activity relationship (SAR) indicated that the substitutions of bromine, hydroxyl group, and amino groups cause great effect to the inhibition effect against tyrosinase. The mechanism and kinetic studies demonstrated that the inhibitory effect of compound 26 on the tyrosinase by acting as the reversible and uncompetitive inhibitor. Docking studies suggests that compound 26 interacts strongly with mushroom tyrosinase via hydrogen bonding.     

Synthesis of (E)- and (Z)-fluoro-olefin analogues of potent dipeptidyl peptidase IV inhibitors

(E)- and (Z)-fluoro-olefin analogues of potent dipeptidyl peptidase IV inhibitors were synthesized. A Wadsworth-Horner-Emmons reaction, followed by amide formation and reduction of the amide were used for the construction of the α-fluoro-α,β-unsaturated amine functionality.     

Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D

Background: The identification of potent small molecule ligands to receptors and enzymes is one of the major goals of chemical and biological research. Two powerful new tools that can be used in these efforts are combinatorial chemistry and structure-based design. Here we address how to join these methods in a design protocol that produces libraries of compounds that are directed against specific macromolecular targets. The aspartyl class of proteases, which is involved in numerous biological processes, was chosen to demonstrate this effective procedure.Results: Using cathepsin D, a prototypical aspartyl protease, a number of low nanomolar inhibitors were rapidly identified. Although cathepsin D is implicated in a number of therapeutically relevant processes, potent nonpeptide inhibitors have not been reported previously. The libraries, synthesized on solid support, displayed nonpeptide functionality about the (hydroxyethyl)amine isostere. The (hydroxyethyl)amine isostere, which targets the aspartyl protease class, is a stable mimetic of the tetrahedral intermediate of amide hydrolysis. Structure-based design, using the crystal structure of cathepsin D complexed with the peptide-based natural product pepstatin, was used to select the building blocks for the library synthesis. The library yielded a ‘hit rate’ of 6–7% at 1 μM inhibitor concentrations, with the most potent compound having a K_i value of 73 nM. More potent, nonpeptide inhibitors (K_i = 9–15 nM) of cathepsin D were rapidly identified by synthesizing and screening a small second generation library.Conclusions: The success of these studies clearly demonstrates the power of coupling the complementary methods of combinatorial chemistry and structure-based design. We anticipate that the general approaches described here will be successful for other members of the aspartyl protease class and for many other enzyme classes.     

Hydrogen-atom transfer in open-shell organometallic chemistry: the reactivity of Rh(II)(cod) and Ir(II)(cod) radicals

A series of new metalloradical rhodium and iridium complexes [M(II)(cod)(N-ligand)](2+) in the uncommon oxidation state +II were synthesized by one-electron oxidation of their [M(I)(cod)(N-ligand)](+) precursors (M=Rh, Ir; cod=(Z,Z)-1,5-cyclooctadiene; and N-ligand is a podal bis(pyridyl)amine ligand: N,N-bis(2-pyridylmethyl)amine (dpa), N-(2-pyridylmethyl)-N-(6-methyl-2-pyridylmethyl)amine (pla), or N-benzyl-N,N-bis(6-methyl-2-pyridylmethyl)amine (Bn-dla). EPR spectroscopy, X-ray diffraction, and DFT calculations reveal that each of these [M(II)(cod)(N-ligand)](2+) species adopts a square-pyramidal geometry with the two cod double bonds and the two pyridine fragments in the basal plane and the N(amine) donor at the apical position. The unpaired electron of these species mainly resides at the metal center, but the apical N(amine) donor also carries a considerable fraction of the total spin density (15-18 %). Density functional calculations proved a valuable tool for the analysis and simulation of the experimental EPR spectra. Whereas the M(II)(olefin) complexes are quite stable as solids, in solution they spontaneously transform into a 1:1 mixture of M(III)(allyl) species and protonated M(I)(olefin) complexes (in the forms [M(I)(olefin)(protonated N-ligand)](2+) for M=Rh and [M(III)(H)(olefin)(N-ligand)](2+) for M=Ir). Similar reactions were observed for the related propene complex [M(II)(propene)(Me(2)tpa)](2+) (Me(2)tpa=N,N,N-tris(6-methyl-2-pyridylmethyl)amine). The decomposition rate of the [M(II)(cod)(N-ligand)](2+) species decreases with increasing N-ligand bulk in the following order: dpa>pla>Bn-dla. Decomposition of the most hindered [M(II)(cod)(Bn-dla)](2+) complexes proceeds by a second-order process. The kinetic rate expression v=k(obs)[M(II)](2) in acetone with k(obs)=k'[H(+)][S], where [S] is the concentration of additional coordinating reagents (MeCN), is in agreement with ligand-assisted dissociation of one of the pyridine donors. Solvent coordination results in formation of more open, reactive species. Protonation of the noncoordinating pyridyl group increases the concentration of this species, and thus [H(+)] appears in the kinetic rate expression. The kinetic data are in agreement with bimolecular hydrogen-atom transfer from M(II)(cod) to another M(II) species (DeltaH( not equal)=11.5+/-2 kcal mol(-1), DeltaS( not equal)=-27+/-10 cal K(-1) mol(-1), and DeltaG( not equal)(298 K)=19.5+/-5 kcal mol(-1)).     

Cyclic amidine sugars as transition-state analogue inhibitors of glycosidases: potent competitive inhibitors of mannosidases

A series of monocyclic glycoamidines bearing different exocyclic amine, alcohol, or alkyl functionalities and bicyclic amidines derived from D-glucose and D-mannose were synthesized and tested as inhibitors of various glycosidases. All the prepared compounds demonstrated good to excellent inhibition toward glycosidases. In particular, the biscationic D-mannoamidine 9b bearing an exocyclic ethylamine moiety proved to be a selective competitive inhibitor of alpha- and beta-mannosidases (K(i) = 6 nM) making it the most potent inhibitor of these glycosidases reported to date. A favorable B(2,5) boat conformation might explain the selectivity of mannosidase inhibition compared to other glycosidases.     

Analysis of frankincense from various Boswellia species with inhibitory activity on human drug metabolising cytochrome P450 enzymes using liquid chromatography mass spectrometry after automated on-line extraction

In our search for herbal remedies with inhibitory activity on cytochrome P450 (CYP) enzymes, we identified extracts of the gum-resin of Boswellia carteri, Boswellia frereana, Boswellia sacra and Boswellia serrata as equally potent, non-selective inhibitors of the major drug metabolising CYP enzymes 1A2/2C8/2C9/2C19/2D6 and 3A4. LC/LC/ESI-MS fingerprint analyses of the boswellic acids 11-keto-beta-boswellic acid, alpha-boswellic acid, beta-boswellic acid and their 3-O-acylated derivatives were used for the authentication of the commercially obtained frankincense samples. Although the boswellic acids could be identified as moderate to potent inhibitors of the applied CYP enzymes, they are not the major CYP inhibitory principle of frankincense.     

Characterization of metabolites of a NK1 receptor antagonist, CJ-11,972, in human liver microsomes and recombinant human CYP isoforms by liquid chromatography/tandem mass spectrometry

The in vitro metabolism of CJ-11,972, (2-benzhydryl-1-aza-bicyclo[2.2.2]oct-3-yl)-(5-tert-butyl-2-methoxybenzyl)amine, an NK1 receptor antagonist, was studied in human liver microsomes and recombinant human CYP isoforms. Liquid chromatography/mass spectrometry (LC/MS) and tandem mass spectrometry (LC/MS/MS) coupled to radioactive detection were used to detect and identify the metabolites. CJ-11,972 was extensively metabolized in human liver microsomes and recombinant human CYP 3A4/3A5 isoforms. A total of fourteen metabolites were identified by a combination of various MS techniques. The major metabolic pathways were due to oxidation of the tert-butyl moiety to form an alcohol (M6) and/or O-demethylation of the anisole moiety. The alcohol metabolite M6 was further oxidized to the corresponding aldehyde (M7) and carboxylic acid (M4). Two unusual metabolites (M13, M17), formed by C-demethylation of the tert-butyl group, were identified as 2-{3-[(2-benzhydryl-1-aza-bicyclo[2.2.2]oct-3-ylamino)methyl]-4-methoxyphenyl}propan-2-ol and (2-benzhydryl-1-aza-bicyclo[2.2.2]oct-3-yl)-(5-isopropenyl-2-methoxybenzyl)amine. A plausible mechanism for C-demethylation may involve oxidation of M6 to form an aldehyde metabolite (M7), followed by cytochrome P450-mediated deformylation leaving an unstable carbon-centered radical, which would quickly form either the alcohol metabolite M13 and the olefin metabolite M17.     

Drug Design,Synthesis and Biological Evaluation of Heterocyclic Molecules as Anti-Inflammatory Agents

Non-steroidal anti-inflammatory drugs (NSAIDs) are generally utilized for numerous inflammatory ailments. The long-term utilization of NSAIDs prompts adverse reactions such as gastrointestinal ulceration, renal dysfunction and hepatotoxicity; however, selective COX-2 inhibitors prevent these adverse events. Various scientific approaches have been employed to identify safer COX-2 inhibitors, as in any case, a large portion of particular COX-2 inhibitors have been retracted from the market because of severe cardiovascular events. This study aimed to develop and synthesize a novel series of indomethacin analogues with potential anti-inflammatory properties and fewer side effects, wherein carboxylic acid moiety was substituted using DCC/DMAP coupling. This study incorporates the docking of various indomethacin analogues to detect the binding interactions with COX-2 protein (PDB ID: 3NT1). MD simulation was performed to measure the stability and flexibility of ligand–protein interactions at the atomic level, for which the top-scoring ligand–protein complex was selected. These compounds were evaluated in vitro for COX enzymes inhibition. Likewise, selected compounds were screened in vivo for anti-inflammatory potential using the carrageenan-induced rat paw oedema method and their ulcerogenic potential. The acute toxicity of compounds was also predicted using in silico tools. Most of the compounds exhibited the potent inhibition of both COX enzymes; however, 3e and 3c showed the most potent COX-2 inhibition having IC50 0.34 µM and 1.39 µM, respectively. These compounds also demonstrated potent anti-inflammatory potential without ulcerogenic liability. The biological evaluation revealed that the compound substituted with 4-nitrophenyl was most active.     

Quinazoline Antifolate Thymidylate Synthase Inhibitors: Replacement of Glutamic Acid by Aminophosphonic Acids

The synthesis of six analogues of the potent thymidylate synthase (TS) inhibitor N -[4-[ N -[(3,4-dihydro-2-methyl-4-oxo-6-quinazolinoyl)-methyl]- N -prop-2-ynylamino]benzoyl]- L -glutamic acid 2 is described in which the glutamic acid residue has been replaced by DL -aminophosphonic acids. New antifolates were tested as inhibitors of TS isolated from mouse L1210 leukemic cells as well as inhibitors of growth mouse leukemic L5178Y cells. In general these modifications result in compounds that are considerably less potent than 2 as TS inhibitors with K i 's 0.17-1.10 w M. Very poor solubility in water limited their proper assay of growth cells inhibition.