Synthesis, Activity, and Molecular Modeling Studies of Novel Human Aldose Reductase Inhibitors Based on a Marine Natural Product

Natural Bioactive Compounds from Marine Invertebrates That Modulate Key Targets Implicated in the Onset of Type 2 Diabetes Mellitus (T2DM) and Its Complications

BACKGROUND

Type 2 diabetes mellitus (T2DM) is an ongoing, risky, and costly health problem that therefore always requires new treatment options. Moreover, although several drugs are available, only 36% of patients achieve glycaemic control, and patient adherence is a major obstacle. With monotherapy, T2DM and its comorbidities/complications often cannot be managed, and the concurrent administration of several hypoglycaemic drugs is required, which increases the risk of side effects. In fact, despite the efficacy of the drugs currently on the market, they generally come with serious side effects. Therefore, scientific research must always be active in the discovery of new therapeutic agents.

DISCUSSION

The present review highlights some of the recent discoveries regarding marine natural products that can modulate the various targets that have been identified as crucial in the establishment of T2DM disease and its complications, with a focus on the compounds isolated from marine invertebrates. The activities of these metabolites are illustrated and discussed.

OBJECTIVES

The paper aims to capture the relevant evidence of the great chemical diversity of marine natural products as a key tool that can advance understanding in the T2DM research field, as well as in antidiabetic drug discovery. The variety of chemical scaffolds highlighted by the natural hits provides not only a source of chemical probes for the study of specific targets involved in the onset of T2DM, but is also a helpful tool for the development of drugs that are capable of acting via novel mechanisms. Thus, it lays the foundation for the design of multiple ligands that can overcome the drawbacks of polypharmacology.

Fishing the Targets of Bioactive Compounds from Psidium guajava L. Leaves in the Context of Diabetes

Psidium guajava L. (guava) leaves have demonstrated their in vitro and in vivo effect against diabetes mellitus (DM). However, there is a lack of literature concerning the effect of the individual phenolic compounds present in the leaves in DM disease. The aim of the present work was to identify the individual compounds in Spanish guava leaves and their potential contribution to the observed anti-diabetic effect. Seventy-three phenolic compounds were identified from an 80% ethanol extract of guava leaves by high performance liquid chromatography coupled to electrospray ionization and quadrupole time-of-flight mass spectrometry. The potential anti-diabetic activity of each compound was evaluated with the DIA-DB web server that uses a docking and molecular shape similarity approach. The DIA-DB web server revealed that aldose reductase was the target protein with heterogeneous affinity for compounds naringenin, avicularin, guaijaverin, quercetin, ellagic acid, morin, catechin and guavinoside C. Naringenin exhibited the highest number of interactions with target proteins dipeptidyl peptidase-4, hydroxysteroid 11-beta dehydrogenase 1, aldose reductase and peroxisome proliferator-activated receptor. Compounds catechin, quercetin and naringenin displayed similarities with the known antidiabetic drug tolrestat. In conclusion, the computational workflow showed that guava leaves contain several compounds acting in the DM mechanism by interacting with specific DM protein targets.

Oxy-Polybrominated Diphenyl Ethers from the Indonesian Marine Sponge, Lamellodysidea herbacea: X-ray, SAR, and Computational Studies

Polybrominated diphenyl ether (PBDE) compounds, derived from marine organisms, originate from symbiosis between marine sponges and cyanobacteria or bacteria. PBDEs have broad biological spectra; therefore, we analyzed structure and activity relationships of PBDEs to determine their potential as anticancer or antibacterial lead structures, through reactions and computational studies. Six known PBDEs (1–6) were isolated from the sponge, Lamellodysdiea herbacea; ¹³C NMR data for compound 6 are reported for the first time and their assignments are confirmed by their theoretical ¹³C NMR chemical shifts (RMSE < 4.0 ppm). Methylation and acetylation of 1 (2, 3, 4, 5-tetrabromo-6-(3′, 5′-dibromo-2′-hydroxyphenoxy) phenol) at the phenol functional group gave seven molecules (7–13), of which 10, 12, and 13 were new. New crystal structures for 8 and 9 are also reported. Debromination carried out on 1 produced nine compounds (1, 2, 14, 16–18, 20, 23, and 26) of which 18 was new. Debromination product 16 showed a significant IC₅₀ 8.65 ± 1.11; 8.11 ± 1.43 µM against human embryonic kidney (HEK293T) cells. Compounds 1 and 16 exhibited antibacterial activity against Gram-positive Staphylococcus aureus and Gram-negative Klebsiella pneumoniae with MID 0.078 µg/disk. The number of four bromine atoms and two phenol functional groups are important for antibacterial activity (S. aureus and K. pneumoniae) and cytotoxicity (HEK293T). The result was supported by analysis of frontier molecular orbitals (FMOs). We also propose possible products of acetylation and debromination using analysis of FMOs and electrostatic charges and we confirm the experimental result.

Nucleophilic and redox properties of polybrominated diphenyl ether derived-quinone/hydroquinone metabolites are responsible for their neurotoxicity

Polybrominated diphenyl ethers (PBDEs) are a category of brominated flame retardants, which were widely used in industrial products since the 1970 s. Our previous studies indicated quinone-type metabolites of PBDEs (PBDE-Qs) cause neurotoxicity, however, their inherent toxicological mechanism remains unclear. Here, we first synthesized PBDE-Qs and corresponding reduced hydroquinone homologous (PBDE-HQs) with different pattern of bromine substitution. Their nucleophilic and redox properties were investigated. PBDE-Qs react with reduced glutathione (GSH) via Michael addition and bromine displacement reaction, whilst PBDE-HQs lack the ability of reacting with GSH. Of note, the displacement reaction only occurs with bromine on the quinone ring of PBDE-Qs but not phenyl ring. Next, electron paramagnetic resonance (EPR) analysis revealed the generation of SQ^•-, along with their downstream hydroxyl radical (HO^•) and methyl radical (^•CH₃) through a PBDE quinone/semiquinone/hydroquinone (Q/SQ^•-/HQ) futile cycle. In addition, a structure-dependent cytotoxicity pattern was found, the exposure of PBDE-Q/HQ with bromine substitution on the quinone ring resulted in higher level of apoptosis and autophagy in BV2 cells. In conclusion, this work clearly demonstrated that the nucleophilic and redox properties of PBDE-Qs/HQs are responsible for their neurotoxicity, and this finding provide better understanding of neurotoxicity of PBDEs.

Structural and mechanistic insight into DNA bending by antitumour calicheamicins

Among the class of enediyne antibiotics endowed with potent antitumour activities, the calicheamicin derivative known as ozogamicin is selectively targeted to several leukaemia cell types by means of tailor-made immunoconjugates. Binding of these drugs to the DNA minor groove in a sequence-specific fashion eventually causes double-stranded cleavage that results in cell death. Use of calicheamicin ε, an unreactive analogue of calicheamicin γ1I, has demonstrated that these structurally sophisticated molecules inflict bending on certain DNA oligonucleotides of defined sequence to the extent that they increase their circularization ratio upon ligation into multimers. By modelling and simulating several linear and circular DNA constructs containing high-affinity 5'-TCCT-3' and low-affinity 5'-TTGT-3' target sites in the presence and absence of calicheamicin ε, we have shed light into the structural distortions introduced by the drug upon binding to DNA. This new insight not only informs about the direction and magnitude of the DNA curvature but also provides a rationale for an improved understanding of the preferred structural and dynamic features associated with DNA target selection by calicheamicins.

Inhibitory Potential of Murraya Koenigii (L.) and Ficus Carica L. Extracts Against Aldose Reductase (ALR), Advanced Glycation End Products (AGEs) Formation and Sorbitol Accumulation

Introduction: Murraya koenigii (L.) and Ficus carica L. are traditionally used plants with significant medicinal and nutritional values. Aim and Objective: The present study was focused on the evaluation of hydro-alcoholic and aqueous extracts of M. koenigii (L.) leaves [MKHA (M. koenigii (L.) hydro-alcoholic extract) and MKAQ (M. koenigii (L.) aqueous extract)] and dried fruits of F. carica L. [FCHA (F. carica L. hydro-alcoholic extract) and FCAQ (F. carica L. aqueous extract)] in the attenuation of markers of microvascular complications associated with diabetes mellitus which can be further used to investigate the pharmacological activity of these plants in treatment of diabetes and its complications. Material and Method: The attenuating effect of the extracts was evaluated by calculating the ALR1 enzyme inhibition in a kidney of Wistar rat, anti-glycation activity in bovine serum albumin (BSA) and erythrocyte sorbitol accumulation inhibition in heparinized human blood. Results: A significant inhibitory effect (IC50 6.47μg/ml,7.26μg/ml,8.93 μg/ml and 9.66μg/ml) was observed with different concentrations of extracts (MKHA, MKAQ, FCHA and FCAQ) respectively, against ALR enzyme. After the 4th week of incubation, the inhibition of AGEs formation by MKHA, MKAQ, FCHA and FCAQ (500μg/ml) was found to be 82.58%, 78.58%, 74.39% and 69.56% respectively. MKHA, MKAQ, FCHA and FCAQ were found to exhibit significant inhibition against the accumulation of sorbitol in RBCs with IC50 188.88 μg/ml, 247.74μg/ml, 291.94μg/ml and 345.34μg/ml, respectively. Conclusion: The administration of different concentrations of MKHA, MKAQ, FCHA and FCAQ significantly attenuated ALR, AGEs and sorbitol accumulation; hence, it can provide a basis for identification and development of new inhibitors of these biomarkers.

40 Years of Research on Polybrominated Diphenyl Ethers (PBDEs)-A Historical Overview and Newest Data of a Promising Anticancer Drug

Polybrominated diphenyl ethers (PBDEs) are a group of molecules with an ambiguous background in literature. PBDEs were first isolated from marine sponges of Dysidea species in 1981 and have been under continuous research to the present day. This article summarizes the two research aspects, (i) the marine compound chemistry research dealing with naturally produced PBDEs and (ii) the environmental toxicology research dealing with synthetically-produced brominated flame-retardant PBDEs. The different bioactivity patterns are set in relation to the structural similarities and dissimilarities between both groups. In addition, this article gives a first structure-activity relationship analysis comparing both groups of PBDEs. Moreover, we provide novel data of a promising anticancer therapeutic PBDE (i.e., 4,5,6-tribromo-2-(2',4'-dibromophenoxy)phenol; termed P01F08). It has been known since 1995 that P01F08 exhibits anticancer activity, but the detailed mechanism remains poorly understood. Only recently, Mayer and colleagues identified a therapeutic window for P01F08, specifically targeting primary malignant cells in a low µM range. To elucidate the mechanistic pathway of cell death induction, we verified and compared its cytotoxicity and apoptosis induction capacity in Ramos and Jurkat lymphoma cells. Moreover, using Jurkat cells overexpressing antiapoptotic Bcl-2, we were able to show that P01F08 induces apoptosis mainly through the intrinsic mitochondrial pathway.

Virtual screening of epalrestat mimicking selective ALR2 inhibitors from natural product database: auto pharmacophore, ADMET prediction and molecular dynamics approach

Epalrestat is the only effective aldose reductase (ALR2) inhibitor available in the market for the treatment of diabetic neuropathy. Clinical effectiveness of epalrestat in diabetic neuropathy encouraged us to develop some more ALR2 inhibitors with a better therapeutic profile. Herein, we utilized the pharmacophoric features of epalrestat to search some novel ALR2 inhibitors from an InterBioScreen database of natural compounds. ADME and PAINS filters were applied to provide drug-likeness and to remove toxicophores from the screened hits. The pharmacophoric features of 4-hydroxy-2-nonenal (HNE), a well-known substrate of ALR1, were also explored to identify selective ALR2 inhibitors. The structure-based analysis was then adopted to find out the molecules showing interactions with ALR2 which are crucial for their therapeutic activity. These interaction patterns and binding modes were compared with that of epalrestat. Molecular dynamics (MD) analysis was also carried out to get more insight into the interactions of screened hits in the catalytic domain of ALR2. Additionally, the top hits were docked and simulated with aldehyde reductase (ALR1) to determine their selectivity for ALR2 over ALR1. Overall, five hits including STOCKIN-44771, STOCKIN-46041, STOCKIN-59369, STOCKIN-69620 and STOCKIN-88220 were found to possess a good therapeutic profile in terms of key interactions, binding energies and drug-likeness. Two hits, STOCKIN-46041 and STOCKIN-59369, were identified as the most selective ALR2 inhibitors when assessed their selectivity profile.Communicated by Ramaswamy H. Sarma.

Distinct binding of cetirizine enantiomers to human serum albumin and the human histamine receptor H1

Cetirizine, a major metabolite of hydroxyzine, became a marketed second-generation H₁ antihistamine that is orally active and has a rapid onset of action, long duration of effects and a very good safety record at recommended doses. The approved drug is a racemic mixture of (S)-cetirizine and (R)-cetirizine, the latter being the levorotary enantiomer that also exists in the market as a third-generation, non-sedating and highly selective antihistamine. Both enantiomers bind tightly to the human histamine H₁ receptor (hH₁R) and behave as inverse agonists but the affinity and residence time of (R)-cetirizine are greater than those of (S)-cetirizine. In blood plasma, cetirizine exists in the zwitterionic form and more than 90% of the circulating drug is bound to human serum albumin (HSA), which acts as an inactive reservoir. Independent X-ray crystallographic work has solved the structure of the hH₁R:doxepin complex and has identified two drug-binding sites for cetirizine on equine serum albumin (ESA). Given this background, we decided to model a membrane-embedded hH₁R in complex with either (R)- or (S)-cetirizine and also the complexes of both ESA and HSA with these two enantiomeric drugs to analyze possible differences in binding modes between enantiomers and also among targets. The ensuing molecular dynamics simulations in explicit solvent and additional computational chemistry calculations provided structural and energetic information about all of these complexes that is normally beyond current experimental possibilities. Overall, we found very good agreement between our binding energy estimates and extant biochemical and pharmacological evidence. A much higher degree of solvent exposure in the cetirizine-binding site(s) of HSA and ESA relative to the more occluded orthosteric binding site in hH₁R is translated into larger positional fluctuations and considerably lower affinities for these two nonspecific targets. Whereas it is demonstrated that the two known pockets in ESA provide enough stability for cetirizine binding, only one such site does so in HSA due to a number of amino acid replacements. At the histamine-binding site in hH₁R, the distinct interactions established between the phenyl and chlorophenyl moieties of the two enantiomers with the amino acids lining up the pocket and between their free carboxylates and Lys179 in the second extracellular loop account for the improved pharmacological profile of (R)-cetirizine.

Substituted 2-thioxothiazolidin-4-one derivatives showed protective effects against diabetic cataract via inhibition of aldose reductase

In an effort to develop a new class of potent aldose reductase inhibitors against diabetic cataracts, a series of novel 2-thioxothiazolidine-4-one derivatives was synthesized in excellent yields via a facile synthetic route. These compounds were tested against aldehyde (ALR1) and aldose reductase (ALR2) enzymes, where they showed considerable inhibitory activity. Among the tested derivatives, compound 6e showed selective and excellent inhibition of ALR2 over ALR1. The experimental diabetes was induced by the intraperitoneal administration of streptozotocin in male Wistar rats. Compound 6e showed positive modulation of body weight, blood glucose, and blood insulin levels in diabetic rats. Compound 6e also showed ALR2 inhibition as evidenced by Western blot analysis in lens homogenates of Wistar rats having cataract. The docking study of 6e was also performed inside the active site of ALR2 to enumerate the key contacts for inhibitory activity.

Identification, cloning, expression and functional interrogation of the biosynthetic pathway of the polychlorinated triphenyls ambigol A–C from Fischerella ambigua 108b

The biosynthetic pathway to the ambigols A–C from Fischerella ambigua 108b has been identified, cloned, heterologously expressed and functionally studied, including in-depth analysis of the biaryl coupling biochemistry in vivo and in vitro.

Sponge-derived polybrominated diphenyl ethers and dibenzo-p-dioxins, irreversible inhibitors of the bacterial α-d-galactosidase

An integrated in vitro and in silico approach was applied to evaluate the potency of hydroxylated polybrominated diphenyl ethers (OH-PBDEs) and spongiadioxins (OH-PBDDs) isolated from Dysidea sponges on the activity of the recombinant α-d-galactosidase of the GH36 family. It was revealed for the first time that all compounds rapidly and apparently irreversibly inhibited the bacterial α-d-galactosidase. The structure-activity relationship study in the series of OH-PBDEs showed that the presence of an additional hydroxyl group in 5 significantly enhanced the potency (IC50 4.26 μM); the increase of bromination in compounds from 1 to 3 increased their potency (IC50 41.8, 36.0, and 16.0 μM, respectively); the presence of a methoxy group decreased the potency (4, IC50 60.5 μM). Spongiadioxins 6, 7, and 8 (IC50 16.6, 33.1, and 28.6 μM, respectively) exhibited inhibitory action comparable to that of monohydroxylated diphenyl ethers 1-3. Docking analysis revealed that all compounds bind in a pocket close to the catalytic amino acid residues. Molecular docking detected significant compound-enzyme interactions in the binding sites of α-d-galactosidase. Superimposition of the enzyme-substrate and the enzyme-inhibitor complexes showed that their binding sites overlap.

Rhizoma coptidis as a Potential Treatment Agent for Type 2 Diabetes Mellitus and the Underlying Mechanisms: A Review

Diabetes mellitus, especially type 2 diabetes mellitus (T2DM), has become a significant public health burden. Rhizoma coptidis (RC), known as Huang Lian, is widely used for treating diabetes in China. The bioactive compounds of RC, especially alkaloids, have the potential to suppress T2DM-induced lesions, including diabetic vascular dysfunction, diabetic heart disease, diabetic hyperlipidemia, diabetic nephropathy, diabetic encephalopathy, diabetic osteopathy, diabetic enteropathy, and diabetic retinopathy. This review summarizes the effects of RC and its bioactive compounds on T2DM and T2DM complications. Less research has been conducted on non-alkaloid fractions of RC, which may exert synergistic action with alkaloids. Moreover, we summarized the pharmacokinetic properties and structure-activity relationships of RC on T2DM with reference to extant literature and showed clearly that RC has potential therapeutic effect on T2DM.

CHARMM Force Field Parameterization of Peroxisome Proliferator-Activated Receptor γ Ligands

The peroxisome proliferator-activated receptor γ (PPARγ) ligands are important therapeutic drugs for the treatment of type 2 diabetes, obesity and cardiovascular diseases. In particular, partial agonists and non-agonists are interesting targets to reduce glucose levels, presenting few side effects in comparison to full agonists. In this work, we present a set of CHARMM-based parameters of a molecular mechanics force field for two PPARγ ligands, GQ16 and SR1664. GQ16 belongs to the thiazolidinedione class of drugs and it is a PPARγ partial agonist that has been shown to promote the “browning” of white adipose tissue. SR1664 is the precursor of the PPARγ non-agonist class of ligands that activates PPARγ in a non-classical manner. Here, we use quantum chemical calculations consistent with the CHARMM protocol to obtain bonded and non-bonded parameters, including partial atomic charges and effective torsion potentials for both molecules. The newly parameterized models were evaluated by examining the behavior of GQ16 and SR1664 free in water and bound to the ligand binding pocket of PPARγ using molecular dynamics simulations. The potential parameters derived here are readily transferable to a variety of pharmaceutical compounds and similar PPARγ ligands.

Structural Determinants of the Selectivity of 3-Benzyluracil-1-acetic Acids toward Human Enzymes Aldose Reductase and AKR1B10

The human enzymes aldose reductase (AR) and AKR1B10 have been thoroughly explored in terms of their roles in diabetes, inflammatory disorders, and cancer. In this study we identified two new lead compounds, 2-(3-(4-chloro-3-nitrobenzyl)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetic acid (JF0048, 3) and 2-(2,4-dioxo-3-(2,3,4,5-tetrabromo-6-methoxybenzyl)-3,4-dihydropyrimidin-1(2H)-yl)acetic acid (JF0049, 4), which selectively target these enzymes. Although 3 and 4 share the 3-benzyluracil-1-acetic acid scaffold, they have different substituents in their aryl moieties. Inhibition studies along with thermodynamic and structural characterizations of both enzymes revealed that the chloronitrobenzyl moiety of compound 3 can open the AR specificity pocket but not that of the AKR1B10 cognate. In contrast, the larger atoms at the ortho and/or meta positions of compound 4 prevent the AR specificity pocket from opening due to steric hindrance and provide a tighter fit to the AKR1B10 inhibitor binding pocket, probably enhanced by the displacement of a disordered water molecule trapped in a hydrophobic subpocket, creating an enthalpic signature. Furthermore, this selectivity also occurs in the cell, which enables the development of a more efficient drug design strategy: compound 3 prevents sorbitol accumulation in human retinal ARPE-19 cells, whereas 4 stops proliferation in human lung cancer NCI-H460 cells.

The multi-targets integrated fingerprinting for screening anti-diabetic compounds from a Chinese medicine Jinqi Jiangtang Tablet

ETHNOPHARMACOLOGICAL RELEVANCE

Jinqi Jiangtang Tablet is a traditional Chinese anti-diabetic formula containing three ingredients: Coptis chinensis Franch. (dried rhizome of C. chinensis Franch., Coptis deltoidea C. Y. Cheng et Hsiao and Coptis teeta Wall.), Astragalus membranaceus (Fisch.) Bunge. (dried root of A. membranaceus (Fisch.) Bge. var. mongholicus (Bge. ) Hsiao and A. membranaceus (Fisch.) Bge. ) and Lonicera japonica Thunb. (dried alabastrum or with nascent flowers of L. japonica Thunb. ). Free radicals, α-glucosidase, α-amylase, aldose reductase and lipase are different targets related with diabetes. However, there are no chromatographic methods employed in screening the anti-diabetic compounds from natural products basing on these targets simultaneously. The present study was aimed at the establishment of a multi-targets integrated fingerprinting to clarify the possible mechanism of the action of Traditional Chinese Medicines which simultaneously contained multiple chemical characteristics and effects of constitutions.

MATERIALS AND METHODS

The multi-targets integrated fingerprinting was developed and validated to screen anti-diabetic compounds from natural products by using ultra-high-performance liquid chromatography/quadruple-time-of-flight mass spectrometry, fraction collector and microplate reader. Ultra performance liquid chromatography was employed to separate the components in Jinqi Jiangtang Tablet, which were identified by quadruple-time-of-flight mass spectrometry to acquire their structural information and collected by the fraction collector. Finally the active fractions were tested for scavenging 1, 1-diphenyl-2-picrylhydrazyl radical and inhibition of α-glucosidase, α-amylase, aldose reductase, and lipase activities in vitro by microplate reader.

RESULTS

Our tests revealed that the Jinqi Jiangtang Tablet showed inhibitory activity against α-glucosidase, α-amylase, aldose reductase and lipase with IC50 values of 0.80 ± 0.02 mg/mL, 1.28 ± 0.13 mg/mL, 0.80 ± 0.02 mg/mL, 1.90 ± 0.18 mg/mL respectively and the scavenging activity with IC50 value of 1.71 ± 0.178 mg/mL. The bioactive fractions were identified to be alkaloids, flavonoids and phenolic acids. The phenolic acids possessed antioxidant activities, namely the scavenging effect on 1, 1-diphenyl-2-picrylhydrazyl rull;). The alkaloids exhibited inhibitory activity against α-glucosidase, aldose reductase, α-amylase, and lipase. The flavonoids also showed mild inhibition on α-glucosidase, aldose reductase, α-amylase and lipase.

CONCLUSIONS

The results demonstrate that Jinqi Jiangtang Tablet can scavenge free radicals and inhibit α-glucosidase, aldose reductase, α-amylase and lipase, which may be the possible mechanism of action of Jinqi Jiangtang Tablet for the treatment of diabetes and associated complications. Compared with conventional chromatographic separation and activity assays, the multi-targets integrated fingerprinting, which simultaneously contains the chemical characteristics and multiple effects of constitutions could comprehensively and properly reveal the activity of Jinqi Jiangtang Tablet. The results also show that the multi-targets integrated fingerprinting is a novel and powerful tool for screening and identifying active ingredients from Traditional Chinese Medicines.

Complexity of naturally produced polybrominated diphenyl ethers revealed via mass spectrometry

Polybrominated diphenyl ethers (PBDEs) are persistent and bioaccumulative anthropogenic and natural chemicals that are broadly distributed in the marine environment. PBDEs are potentially toxic due to inhibition of various mammalian signaling pathways and enzymatic reactions. PBDE isoforms vary in toxicity in accordance with structural differences, primarily in the number and pattern of hydroxyl moieties afforded upon a conserved core structure. Over four decades of isolation and discovery-based efforts have established an impressive repertoire of natural PBDEs. Based on our recent reports describing the bacterial biosyntheses of PBDEs, we predicted the presence of additional classes of PBDEs to those previously identified from marine sources. Using mass spectrometry and NMR spectroscopy, we now establish the existence of new structural classes of PBDEs in marine sponges. Our findings expand the chemical space explored by naturally produced PBDEs, which may inform future environmental toxicology studies. Furthermore, we provide evidence for iodinated PBDEs and direct attention toward the contribution of promiscuous halogenating enzymes in further expanding the diversity of these polyhalogenated marine natural products.

Identification of a novel polyfluorinated compound as a lead to inhibit the human enzymes aldose reductase and AKR1B10: structure determination of both ternary complexes and implications for drug design

Aldo-keto reductases (AKRs) are mostly monomeric enzymes which fold into a highly conserved (α/β)8 barrel, while their substrate specificity and inhibitor selectivity are determined by interaction with residues located in three highly variable external loops. The closely related human enzymes aldose reductase (AR or AKR1B1) and AKR1B10 are of biomedical interest because of their involvement in secondary diabetic complications (AR) and in cancer, e.g. hepatocellular carcinoma and smoking-related lung cancer (AKR1B10). After characterization of the IC50 values of both AKRs with a series of polyhalogenated compounds, 2,2',3,3',5,5',6,6'-octafluoro-4,4'-biphenyldiol (JF0064) was identified as a lead inhibitor of both enzymes with a new scaffold (a 1,1'-biphenyl-4,4'-diol). An ultrahigh-resolution X-ray structure of the AR-NADP(+)-JF0064 complex has been determined at 0.85 Å resolution, allowing it to be observed that JF0064 interacts with the catalytic residue Tyr48 through a negatively charged hydroxyl group (i.e. the acidic phenol). The non-competitive inhibition pattern observed for JF0064 with both enzymes suggests that this acidic hydroxyl group is also present in the case of AKR1B10. Moreover, the combination of surface lysine methylation and the introduction of K125R and V301L mutations enabled the determination of the X-ray crystallographic structure of the corresponding AKR1B10-NADP(+)-JF0064 complex. Comparison of the two structures has unveiled some important hints for subsequent structure-based drug-design efforts.

Kinetics and molecular docking studies of an anti-diabetic complication inhibitor fucosterol from edible brown algae Eisenia bicyclis and Ecklonia stolonifera

In the present study, we investigated the anti-diabetic potential of fucosterol by evaluating the ability of this compound to inhibit rat lens aldose reductase (RLAR), human recombinant aldose reductase (HRAR), protein tyrosine phosphatase 1B (PTP1B), and α-glucosidase. Fucosterol displayed moderate inhibitory activity against RLAR, HRAR, and PTP1B. However, it showed weak or no activity against AGE formation and α-glucosidase. In addition, our kinetic study revealed that fucosterol showed a mixed type inhibition against RLAR and HRAR, while it noncompetitively inhibited PTP1B. Since fucosterol inhibited aldose reductase (AR), it holds great promise for use in the treatment of diabetic complications. Therefore, we predicted the 3D structure of AR in rat and human using the Autodock program to simulate binding between AR and fucosterol and evaluate the binding site-directed inhibition of AR by fucosterol. Results of the docking simulations of fucosterol demonstrated negative binding energies (-8.2 kcal/mol for RLAR and -8.5 kcal/mol for HRAR), which indicated a higher affinity and tighter binding capacity of fucosterol for the active site of the enzyme. In particular, the hydrophobic ring system and the aliphatic side chain of fucosterol were found to be tightly bound in a specificity pocket through apolar amino acid residues on AR, while the anion binding site on AR interacts with the 3-hydroxyl group and the double bond on the side chain of fucosterol. The results of the present study clearly demonstrated the potential of using fucosterol for the management and treatment of diabetes and diabetes-associated complications.

X-ray structure of the V301L aldo-keto reductase 1B10 complexed with NADP(+) and the potent aldose reductase inhibitor fidarestat: implications for inhibitor binding and selectivity

Only one crystal structure is currently available for tumor marker AKR1B10, complexed with NADP(+) and tolrestat, which is an aldose reductase inhibitor (ARI) of the carboxylic acid type. Here, the X-ray structure of the complex of the V301L substituted AKR1B10 holoenzyme with fidarestat, an ARI of the cyclic imide type, was obtained at 1.60Å resolution by replacement soaking of crystals containing tolrestat. Previously, fidarestat was found to be safe in phase III trials for diabetic neuropathy and, consistent with its low in vivo side effects, was highly selective for aldose reductase (AR or AKR1B1) versus aldehyde reductase (AKR1A1). Now, inhibition studies showed that fidarestat was indeed 1300-fold more selective for AR as compared to AKR1B10, while the change of Val to Leu (found in AR) caused a 20-fold decrease in the IC50 value with fidarestat. Structural analysis of the V301L AKR1B10-fidarestat complex displayed enzyme-inhibitor interactions similar to those of the AR-fidarestat complex. However, a close inspection of both the new crystal structure and a computer model of the wild-type AKR1B10 complex with fidarestat revealed subtle changes that could affect fidarestat binding. In the crystal structure, a significant motion of loop A was observed between AR and V301L AKR1B10, linked to a Phe-122/Phe-123 side chain displacement. This was due to the presence of the more voluminous Gln-303 side chain (Ser-302 in AR) and of a water molecule buried in a subpocket located at the base of flexible loop A. In the wild-type AKR1B10 model, a short contact was predicted between the Val-301 side chain and fidarestat, but would not be present in AR or in V301L AKR1B10. Overall, these changes could contribute to the difference in inhibitory potency of fidarestat between AR and AKR1B10.

Aldo-keto reductases in retinoid metabolism: search for substrate specificity and inhibitor selectivity

Biological activity of natural retinoids requires the oxidation of retinol to retinoic acid (RA) and its binding to specific nuclear receptors in target tissues. The first step of this pathway, the reversible oxidoreduction of retinol to retinaldehyde, is essential to control RA levels. The enzymes of retinol oxidation are NAD-dependent dehydrogenases of the cytosolic medium-chain (MDR) and the membrane-bound short-chain (SDR) dehydrogenases/reductases. Retinaldehyde reduction can be performed by SDR and aldo-keto reductases (AKR), while its oxidation to RA is carried out by aldehyde dehydrogenases (ALDH). In contrast to SDR, AKR and ALDH are cytosolic. A common property of these enzymes is that they only use free retinoid, but not retinoid bound to cellular retinol binding protein (CRBP). The relative contribution of each enzyme type in retinoid metabolism is discussed in terms of the different subcellular localization, topology of membrane-bound enzymes, kinetic constants, binding affinity of CRBP for retinol and retinaldehyde, and partition of retinoid pools between membranes and cytoplasm. The development of selective inhibitors for AKR enzymes 1B1 and 1B10, of clinical relevance in diabetes and cancer, granted the investigation of some structure-activity relationships. Kinetics with the 4-methyl derivatives of retinaldehyde isomers was performed to identify structural features for substrate specificity. Hydrophilic derivatives were better substrates than the more hydrophobic compounds. We also explored the inhibitory properties of some synthetic retinoids, known for binding to retinoic acid receptors (RAR) and retinoid X receptors (RXR). Consistent with its substrate specificity towards retinaldehyde, AKR1B10 was more effectively inhibited by synthetic retinoids than AKR1B1. A RARβ/γ agonist (UVI2008) inhibited AKR1B10 with the highest potency and selectivity, and docking simulations predicted that its carboxyl group binds to the anion-binding pocket.

Crystal packing modifies ligand binding affinity: the case of aldose reductase

The relationship between the structures of protein-ligand complexes existing in the crystal and in solution, essential in the case of fragment-based screening by X-ray crystallography (FBS-X), has been often an object of controversy. To address this question, simultaneous co-crystallization and soaking of two inhibitors with different ratios, Fidarestat (FID; K(d) = 6.5 nM) and IDD594 (594; K(d) = 61 nM), which bind to h-aldose reductase (AR), have been performed. The subatomic resolution of the crystal structures allows the differentiation of both inhibitors, even when the structures are almost superposed. We have determined the occupation ratio in solution by mass spectrometry (MS) Occ(FID)/Occ(594) = 2.7 and by X-ray crystallography Occ(FID)/Occ(594) = 0.6. The occupancies in the crystal and in solution differ 4.6 times, implying that ligand binding potency is influenced by crystal contacts. A structural analysis shows that the Loop A (residues 122-130), which is exposed to the solvent, is flexible in solution, and is involved in packing contacts within the crystal. Furthermore, inhibitor 594 contacts the base of Loop A, stabilizing it, while inhibitor FID does not. This is shown by the difference in B-factors of the Loop A between the AR-594 and AR-FID complexes. A stable loop diminishes the entropic energy barrier to binding, favoring 594 versus FID. Therefore, the effect of the crystal environment should be taken into consideration in the X-ray diffraction analysis of ligand binding to proteins. This conclusion highlights the need for additional methodologies in the case of FBS-X to validate this powerful screening technique, which is widely used.

Kinetics and molecular docking studies of kaempferol and its prenylated derivatives as aldose reductase inhibitors

Aldose reductase inhibitors (ARIs) suppressing the hyperglycemia-induced polyol pathway have been provided as potential therapeutic candidates in the treatment and prevention of diabetic complications. Based upon structure-activity relationships of desmethylanhydroicaritin (1) and sophoflavescenol (2) as promising ARIs, 3,4'-dihydroxy flavonols with a prenyl or lavandulyl group at the C-8 position and a hydroxyl or methoxy group at the C-5 position are important for aldose reductase (AR) inhibition. In order to prove the above results, a combination of computational prediction and enzyme kinetics has begun to emerge as an effective screening technique for the potential. In the present study, we predicted the 3D structure of AR in rat and human using a docking algorithm to simulate binding between AR and prenylated flavonoids (1 and 2) and kaempferol (3) and scrutinized the reversible inhibition of AR by these ARIs. Docking simulation results of 1-3 demonstrated negative binding energies (Autodock 4.0=-9.11 to -7.64 kcal/mol; Fred 2.0=-79.54 to -51.84 kcal/mol) and an additional hydrogen bond through Phe122 and Trp219, in addition to the previously proposed interaction of AR and phenolics through Trp20, Tyr48, His110, and Trp111 residues, indicating that the presence of 8-prenyl and 5-methyl groups might potentiate tighter binding to the active site of the enzyme and more effective AR inhibitors. Moreover, types of AR inhibition were different depending on the presence or absence of the 8-prenyl group, in that 1 and 2 are mixed inhibitors with respective Ki values of 0.69 μM and 0.94 μM, while 3 showed noncompetitive inhibition with a Ki value of 4.65 μM. The present study suggests that an effective strategy for screening potential ARIs could be established by predicting 3D structural conformation of prenylated flavonoids and the orientation within the enzyme as well as by simultaneously determining the mode of enzyme inhibition.

Inhibitory activities of prenylated flavonoids from Sophora flavescens against aldose reductase and generation of advanced glycation endproducts

Important targets for the prevention and treatment of diabetic complications include aldose reductase (AR) inhibitors (ARIs) and inhibitors of advanced glycation endproduct (AGE) formation. Here we evaluate the inhibitory activities of prenylated flavonoids isolated from Sophora flavescens, a traditional herbal medicine, on rat lens AR (RLAR), human recombinant AR (HRAR) and AGE formation. Among the tested compounds, two prenylated chalcones — desmethylanhydroicaritin (1) and 8-lavandulylkaempferol (2) — along with five prenylated flavanones — kurarinol (8), kurarinone (9), (2S)-2′-methoxykurarinone (10), (2S)-3β,7,4′-trihydroxy-5-methoxy-8-(γ,γ-dimethylally)-flavanone (11), and kushenol E (13) were potent inhibitors of RLAR, with IC50 values of 0.95, 3.80, 2.13, 2.99, 3.77, 3.63 and 7.74 μM, respectively, compared with quercetin (IC50 7.73 μM). In the HRAR assay, most of the prenylated flavonoids tested showed marked inhibitory activity compared with quercetin (IC50 2.54 μM). In particular, all tested prenylated flavonols, such as desmethylanhydroicaritin (1, IC50 0.45 μM), 8-lavandulylkaempferol (2, IC50 0.79 μM) and kushenol C (3, IC50 0.85 μM), as well as a prenylated chalcone, kuraridin (5, IC50 0.27 μM), and a prenylated flavanone, (2S)-7,4′-dihydroxy-5-methoxy-8-(γ,γ-dimethylally)-flavanone (12, IC50 0.37 μM), showed significant inhibitory activities compared with the potent AR inhibitor epalrestat (IC50 0.28 μM). Interestingly, prenylated flavonoids 1 (IC50 104.3 μgmL−1), 2 (IC50 132.1 μgmL−1), 3 (IC50 84.6 μgmL−1) and 11 (IC50 261.0 μgmL−1), which harbour a 3-hydroxyl group, also possessed good inhibitory activity toward AGE formation compared with the positive control aminoguanidine (IC50 115.7 μgmL−1). Thus, S. flavescens and its prenylated flavonoids inhibit the processes that underlie diabetic complications and related diseases and may therefore have therapeutic benefit.

Anti-diabetic potential of alkaloid rich fraction from Capparis decidua on diabetic mice

ETHNO PHARMACOLOGICAL RELEVANCE

Capparis decidua (CD) is a xerophytic shrub, found widely in the western parts of India, Pakistan and some of the Asian countries. The dried fruits are used as an ingredient in anti-diabetic compositions.

AIM OF THE STUDY

The present study was carried out to test the effect of alkaloid rich (AR) fraction from this plant in the management of diabetes.

MATERIALS AND METHODS

Streptozotocin-induced diabetic mice were treated with the AR fraction for 28 days. On completion of the treatment, a range of parameters were tested including oral glucose tolerance test (OGTT), blood lipid profile, expression patterns of various glucose homeostatic enzyme genes and their activities.

RESULTS

Treatment of diabetic mice with AR fraction for 28 days significantly inhibited the acute elevation of blood glucose level during OGTT and also reduced total cholesterol (TC) and triglyceride (TG) content (p<0.05). Activity of glucose-6-phosphatase (G6Pase) was attenuated by 44%, also liver and muscle glycogen content showed significant improvement (p<0.05). The expression of different target genes like G6Pase, phosphoenolpyruvate carboxykinase (PEPCK), aldose reductase and tumor necrosis factor-alpha (TNF-alpha) showed significant reduction whereas glucose transporter-4 (Glut-4), peroxisome proliferator activated receptor-gamma (PPAR-gamma) and glucokinase (GK) improved remarkably.

CONCLUSIONS

AR fraction showed promising results in terms of anti-diabetic activities establishing its candidacy for further purification and characterization of the individual alkaloids, in order to understand their mechanism of action.

Inhibitors of aldose reductase and formation of advanced glycation end-products in moutan cortex (Paeonia suffruticosa)

The methanol extract of Moutan cortex (Paeonia suffruticosa) afforded two new compounds, 8-O-benzoylpaeonidanin (1) and 5-hydroxy-3S-hydroxymethyl-6-methyl-2,3-dihydrobenzofuran (2), in addition to 4-O-butylpaeoniflorin (3) as an artifact of the separation, seven monoterpene glycosides (4-10), two monoterpenes (11, 12), four acetophenones (13-16), and two triterpenes (17, 18). The structures of the compounds were determined by spectroscopic methods, and the compounds were evaluated for inhibitory effects against rat lens aldose reductase (RLAR) and advanced glycation end-product (AGEs) formation. Compounds 17 and 18 showed the most potent inhibitory activity against RLAR, with IC(50) values of 11.4 and 28.8 microM, respectively. Compounds 3 and 6 also inhibited RLAR with IC(50) values of 36.2 and 44.6 microM, respectively. The positive control, 3,3-tetramethyleneglutamic acid, had an IC(50) value of 31.8 microM. Compounds 3 and 6 inhibited AGE formation with IC(50) values of 10.8 and 11.3 microM, respectively. Compound 2 had an IC(50) value of 177.0 microM, whereas the positive control, aminoguanidine, had an IC(50) value of 1026.8 microM.

Docking and molecular dynamics studies toward the binding of new natural phenolic marine inhibitors and aldose reductase

Phenolic marine natural product is a kind of new potential aldose reductase inhibitors (ARIs). In order to investigate the binding mode and inhibition mechanism, molecular docking and dynamics studies were performed to explore the interactions of six phenolic inhibitors with human aldose reductase (hALR2). Considering physiological environment, all the neutral and other two ionized states of each phenolic inhibitor were adopted in the simulation. The calculations indicate that all the inhibitors are able to form stable hydrogen bonds with the hALR2 active pocket which is mainly constructed by residues TYR48, HIS110 and TRP111, and they impose the inhibition effect by occupying the active space. In all inhibitors, only La and its two ionized derivatives La_ion1 and La_ion2, in which neither of the ortho-hydrogens of 3-hydroxyl is substituted by Br, bind with hALR2 active residues using the terminal 3-hydroxyl. While, all the other inhibitors, at least one of whose ortho-sites of 3- and 6-hydroxyls are substituted by Br substituent which take much electron-withdrawing effect and steric hindrance, bind with hALR2 through the lactone group. This means that the Br substituent can effectively regulate the binding modes of phenolic inhibitors. Although the lactone bound inhibitors have relatively high RMSD values, our dynamics study shows that both binding modes are of high stability. For each inhibitor molecule, the ionization does not change its original binding mode, but it does gradually increase the binding free energy, which reveals that besides hydrogen bonds, the electrostatic effect is also important to the inhibitor-hALR2 interaction.

CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol

Parametrization of the additive all-atom CHARMM force field for acyclic polyalcohols, acyclic carbohydrates and inositol is conducted. Initial parameters were transferred from the alkanes and hexopyranose carbohydrates, with subsequent development and optimization of parameters unique to the molecules considered in this study. Using the model compounds acetone and acetaldehyde, nonbonded parameters for carbonyls were optimized targeting quantum mechanical interaction data for solute-water pairs and pure solvent thermodynamic data. Bond and angle parameters were adjusted by comparing optimized geometries to small molecule crystal survey data and by performing vibrational analyses on acetone, acetaldehyde and glycerol. C-C-C-C, C-C-C-O, C-C-OH and O-C-C-O torsional parameters for polyol chains were fit to quantum mechanical dihedral potential energy scans comprising over 1500 RIMP2/cc-pVTZ//MP2/6-31G(d) conformations using an automated Monte Carlo simulated annealing procedure. Comparison of computed condensed-phase data, including crystal lattice parameters and densities, NMR proton-proton couplings, densities and diffusion coefficients of aqueous solutions, to experimental data validated the optimized parameters. Parameter development for these compounds proved particularly challenging because of the flexibility of the acyclic sugars and polyalcohols as well as the intramolecular hydrogen bonding between vicinal hydroxyls for all of the compounds. The newly optimized additive CHARMM force field parameters are anticipated to be of utility for atomic level of detail simulations of acyclic polyalcohols, acyclic carbohydrates and inositol in solution.

RAGE (Receptor for Advanced Glycation Endproducts), RAGE ligands, and their role in cancer and inflammation

The Receptor for Advanced Glycation Endproducts [RAGE] is an evolutionarily recent member of the immunoglobulin super-family, encoded in the Class III region of the major histocompatability complex. RAGE is highly expressed only in the lung at readily measurable levels but increases quickly at sites of inflammation, largely on inflammatory and epithelial cells. It is found either as a membrane-bound or soluble protein that is markedly upregulated by stress in epithelial cells, thereby regulating their metabolism and enhancing their central barrier functionality. Activation and upregulation of RAGE by its ligands leads to enhanced survival. Perpetual signaling through RAGE-induced survival pathways in the setting of limited nutrients or oxygenation results in enhanced autophagy, diminished apoptosis, and (with ATP depletion) necrosis. This results in chronic inflammation and in many instances is the setting in which epithelial malignancies arise. RAGE and its isoforms sit in a pivotal role, regulating metabolism, inflammation, and epithelial survival in the setting of stress. Understanding the molecular structure and function of it and its ligands in the setting of inflammation is critically important in understanding the role of this receptor in tumor biology.

Phenolic marine natural products as aldose reductase inhibitors

Four different types of marine natural compounds isolated from tunicates were found to inhibit human aldose reductase. They all are characterized by a heterocyclic system, and at least two phenolic groups are present in the structure. Two of the compounds tested showed an inhibitory potency 5/6-fold higher than that of the known AR inhibitor sorbinil. One notable structural feature of these active compounds is the lack of either the carboxylic acid or the spiro-hydantoin commonly present in the principal classes of currently used inhibitors.

Bioassay-guided isolation of aldose reductase inhibitors from Artemisia dracunculus

An ethanolic extract of Artemisia dracunculus L. having antidiabetic activity was examined as a possible aldose reductase (ALR2) inhibitor, a key enzyme involved in diabetic complications. At 3.75 microg/mL, the total extract inhibited ALR2 activity by 40%, while quercitrin, a known ALR2 inhibitor, inhibited its activity by 54%. Bioactivity guided fractionation and isolation of the compounds that inhibit ALR2 activity was carried out with the total ethanolic extract yielding four bioactive compounds with ALR2 inhibitory activity ranging from 58% to 77% at 3.75 microg/mL. Using LC/MS, (1)H NMR, (13)C NMR and 2D NMR spectroscopic analyses, the four compounds were identified as 4,5-di-O-caffeoylquinic acid, davidigenin, 6-demethoxycapillarisin and 2',4'-dihydroxy-4-methoxydihydrochalcone. This is the first report on their isolation from A. dracunculus and the ALR2 inhibitory activity of 4,5-di-O-caffeoylquinic acid, 6-demethoxycapillarisin and 2',4'-dihydroxy-4-methoxydihydrochalcone. These results suggest a use of the extract of A. dracunculus for ameliorating diabetic complications.

Lactandrate: a D-homo-aza-androsterone alkylator in the treatment of breast cancer

The sensitivity of breast neoplasms to hormonal control provides the basis of novel investigational treatments with steroidal alkylators. An androsterone D-lactam steroidal ester, the 3beta-hydroxy-13alpha-amino-13,17-seco- 5alpha-androstan-17-oic-13,17-lactam, p-bis(2-chloroethyl)amino phenyl acetate (lactandrate) was synthesized and tested for antitumor activity against six human breast cancer cell lines in vitro and against two murine and one xenograft mammary tumors in vivo. A docking study on the binding interactions of lactandrate with the ligand-binding domain (LBD) of estrogen receptor-alpha (ERalpha) was inquired. In vitro testing of lactandrate cytostatic and cytotoxic activity was performed on T47D, MCF7, MDA-MB-231, BT-549, Hs578T, MDA-MB-435 breast adenocarcinoma human cell lines. In vivo testing was performed on two murine mammary tumors, the MXT tumor and CD8F1 adenocarcinoma, as well as on human mammary carcinoma MX-1 xenograft. Molecular modeling techniques were adopted to predict a possible location and interaction mode of the molecule into LBD. Lactandrate induced significantly high antitumor effect against all tested in vitro and in vivo models. The cell lines with positive ER expression found to be significantly more sensitive to lactandrate. Moreover, lactandrate found to be positioned inside the binding cavity with its steroidal moiety, whilst the alkylating moiety protrudes out of receptor's pocket. Lactandrate produced important anticancer activity on breast cancer in vitro and in vivo. Some correlation between ER and lactandrate effect was demonstrated. Docking studies provide the basis for the structure-based design of improved steroidal alkylating esters for the treatment of estrogen-related cancers.

Molecular determinants of topoisomerase I poisoning by lamellarins: comparison with camptothecin and structure-activity relationships

A series of lamellarin derivatives have been studied as topoisomerase I (Top1) inhibitors. Molecular models of the ternary complexes formed between the DNA-Top1 ensemble and lamellarin D (LMD) or camptothecin (CPT) fully intercalated into the duplex DNA have been built and studied by means of nanosecond molecular dynamics simulations in aqueous solution. Our results show that the 20-OH and 8-OH of LMD can participate in hydrogen-bonding interactions with the side chains of Glu356 and Asn722, respectively, the latter being consistent with the finding that CEM/C2 cells, which are resistant to CPT, are cross-resistant to LMD. Our models also account for the observation that LMD stabilizes Top1 cleavage at CG sites in addition to the TG sites observed for CPT and rationalize the structure-activity relationships within the series. The deleterious effect of replacing the 20-OH in LMD with a hydrogen was confirmed using a set of thermodynamic integration free energy simulations.

The Molecular Basis of Resilience to the Effect of the Lys103Asn Mutation in Non-Nucleoside HIV-1 Reverse Transcriptase Inhibitors Studied by Targeted Molecular Dynamics Simulations

A series of targeted molecular dynamics simulations have been carried out in an attempt to assess the effect that the common Lys103Asn mutation in HIV-1 reverse transcriptase (RT) has on the binding of three representative non-nucleoside RT inhibitors (NNRTI), nevirapine, efavirenz, and etravirine. We have shown previously that, in the absence of an incoming inhibitor, creation of the NNRTI binding pocket is hampered due to the existence of a hydrogen bond between the side chains of Asn103 and Tyr188 for which no equivalent exists in the wild-type enzyme. As an extension of this work, we now apply the same methodology to drive the enzyme's conformation from the unbound state to the drug-bound state in the presence of the NNRTI. The location of each drug outside the binding pocket was determined by an automated docking program, and steering into the binding pocket followed a route that is likely to represent the actual entrance pathway. The additional hurdle to inhibitor entry imposed by the extra Asn103-Tyr188 hydrogen bond is seen to affect each NNRTI differently, with the ability to disrupt this interaction increasing in the order etravirine >> efavirenz > or = nevirapine, in good accord with the experimental findings. This coherent picture strongly suggests that attempts to overcome resistance through structure-based drug design may be considerably more successful if dynamic structural aspects of the type studied here are considered, particularly in cases where binding energy-based structure-activity relationship methods are unable to provide the required information.

Marine natural products

This review covers the literature published in 2003 for marine natural products, with 619 citations (413 for the period January to December 2003) referring to compounds isolated from marine microorganisms and phytoplankton, green algae, brown algae, red algae, sponges, coelenterates, bryozoans, molluscs, tunicates and echinoderms. The emphasis is on new compounds (656 for 2003), together with their relevant biological activities, source organisms and country or origin. Biosynthetic studies or syntheses that lead to the revision of structures or stereochemistries have been included (78), including any first total syntheses of a marine natural product.