Comparative modeling of proteins in the design of novel renin inhibitors

Renin, the first enzyme in the renin-angiotensin system, is critically important for the maintenance of blood pressure, and, therefore, as a target for antihypertensive therapy. The three-dimensional structure of renin would be an invaluable aid in understanding the functional properties of renin as well as in the design of novel, potent inhibitors. Three-dimensional models of renin have been developed by a number of different groups based on comparative homology modeling from the other known aspartic proteinase structures. These models have been used widely in the drug design process to suggest targets for synthesis and to rationalize the structure-activity relationships of compounds. This review describes the different published renin models and compares them to the extent possible. Applications of these model renin and renin-inhibitor complex structures to biological function and inhibitor design are summarized.     

Differences in Binding Sites of Two Melatonin Receptors Help to Explain Their Selectivity to Some Melatonin Analogs: A Molecular Modeling Study

Abstract

Numerous diseases have been linked to the malfunction of G-protein coupled receptors (GP-CRs). Their adequate treatment requires rational design of new high-affinity and high-selectivity drugs targeting these receptors. In this work, we report three-dimensional models of the human MT₁ and MT₂ melatonin receptors, members of the GPCR family. The models are based on the X-ray structure of bovine rhodopsin. The computational approach employs an original procedure for optimization of receptor-ligand structures. It includes rotation of one of the transmembrane α-helices around its axis with simultaneous assessment of quality of the resulting complexes according to a number of criteria we have developed for this purpose. The optimal geometry of the receptor-ligand binding is selected based on the analysis of complementarity of hydrophobic/hydrophilic properties between the ligand and its protein environment in the binding site. The elaborated “optimized” models are employed to explore the details of protein-ligand interactions for melatonin and a number of its analogs with known affinity to MT₁ and MT₂ receptors. The models permit rationalization of experimental data, including those that were not used in model building. The perspectives opened by the constructed models and by the optimization procedure in the design of new drugs are discussed.     

A Theoretical Study of Formation of DNA Noncanonical Structures Under Negative Superhelical Stress

Abstract

The development of statistical mechanical models of the formation of noncanonical structures in circular DNA and the finding of the energy parameters for these models made it possible to predict the appearance of such structures in a DNA with any given sequence. It does not seem feasible, however, to perform such calculations for DNA sequences of considerable length by allowing for all the possible states. We propose a special algorithm for calculating the thermodynamic characteristics of various conformational rearrangements in DNA that occur under negative supercoilings, allowing for several possible states of each base pair in the chain. Calculations have been performed for a number of natural DNAs. According to these calculations, the most likely noncanonical structures in DNA under normal conditions are cruciform structures and the Z form. The results of the calculations are compared with the experimental data reported in the literature. State diagrams have been computed for a number of inserts in circular DNA that can adopt both the cruciform conformation and the left-handed helical Z form.     

Understanding the dual mechanism of bioactive peptides targeting the enzymes involved in Renin Angiotensin System (RAS): An in-silico approach

Abstract

Understanding the dual inhibition mechanism of food derivative peptides targeting the enzymes (Renin and Angiotensin Converting enzyme) in the Renin Angiotensin System. Two peptides RALP and WYT were reported to possess antihypertensive activity targeting both renin and ACE, and we have used molecular docking and molecular dynamics simulation, in order to understand the underlying mechanism. The selected peptides (RALP and WYT) from the series of peptides reported were docked to renin and ACE and two binding modes were selected based on the binding energy, interaction pattern and clusters of docking simulation. The enzyme-peptide complexes for renin and ACE (Renin/RALP_1,2; ACE/RALP_1,2; Renin/WYT_1,2 and ACE/WYT_1,2) were subjected to molecular dynamics simulation. Our results identified that the peptides inhibiting renin, tends to move out of the binding pockets (S1’ S2’) which is critical for potent binding and occupies the less important pockets (S4 and S3). This could possibly be the reason for its low potency. Whereas, the same peptides targeting ACE, tends to be intact in the pocket because of the metal ion coordination and there is an ample room to improve on its efficacy. Our results further pave way for the biochemist, medicinal chemist to design dual peptides targeting the RAS effectively.

Communicated by Ramaswamy H. Sarma     

A new design strategy with stochastic optimization on the preparation of magnetite cross-linked tyrosinase aggregates (MCLTA)

In this study, a new design strategy with a systematic optimization process is proposed for the preparation of magnetite cross-linked tyrosinase aggregates (MCLTA) by using the concentration of magnetite nanoparticle, glutaraldehyde and tyrosinase enzyme as design variables. A comprehensive study on multiple non-linear neuro-regression analysis has been performed as a compelling alternative to the insufficient approaches on modeling-design-optimization of MCLTA. For this aim, the experimental process has been modeled with 13 candidate functional structures by using a hybrid method to test the accuracy of their predictions. R²_training, R²_testing values, and boundedness of the functions have been checked to reveal the realistic ones. Then four different design approaches in terms of three distinct scenarios have been used to optimize the process. The results show that, all models define the process well, depending on R²_training. However, only five and nine models are appropriate based on R²_testing for the first use activity and residual activity, respectively. On the other hand, depending on to be a realistic value, model TON best describes the "first use activity," while the best one is FONT for residual activity. It is also concluded that the scenario types and selection of constraints for design variables affect the optimization results.     

Models of Monoamine Oxidase A and B Active Sites Obtained by using 3D QSAR with CoMFA Analysis

Abstract

The monoamine oxidase catalyses the oxidative deamination of neuroactive amines. This enzyme exists in two forms A and B, which differ by substrates preference and inhibitors specificity. Investigation of the structures of these enzymes and design new selective inhibitors are of greatly interesting since MAO A inhibitors are used in therapeutic practice as antidepressants and MAO B inhibitors – in the treatment Parkinson's diseases. The three dimension structures of monoamine oxidases are still unknown. Therefore, one of the most perspective approach to define significant features of structure active site is method based on analysis of structure-activity relationship (3D QSAR) with comparison of molecular fields analysis (CoMFA) allowing to get the spatial distribution of important properties affecting the activity.

In present study we investigate the structures of active sites MAO A and B using 16 pyrazinocarbazole derivatives in variant conformation. Majority of pyrazinocarbazole derivatives have a rigit conformation, but three of those is sufficiently flexible. The latters can be in two conformation types: long molecules (substitution accommodate along axis of main structure) and short molecules (substitution accommodate at acute angle about of main structure). Several 3D QSAR and CoMFA models of MAO A and B active sites were design for data sets containing various types of flexible molecules conformation. All obtained models are statistical reliable and have sufficient predictive power for tested compound tetrindole. The best MAO A model that include two flexible molecules in long conformations was obtained, and the longest one of those in short conformation. In contrast, for MAO B model containing all flexible molecules in the short conformations is more preferred.

On the basis of obtained data the schematic models of MAO A and B active sites structures are proposed. According to these models MAO A active site have the narrow long cavity that accommodate long molecules, while MAO B active site is broader and shorter.     

Benchmarking of ONIOM method for the study of NH<Subscript>3</Subscript> dissociation at open ends of BNNTs

The reliability of ONIOM approach have been examined in calculations of adsorption energies, transition structures, change of HOMO-LUMO energy gaps and equilibrium geometries of the interaction between NH₃ and N-enriched (A) or B-enriched (B) open ended boron nitride nanotubes. To these ends, four models of the A or B, with different inner and outer layers have been studied. In addition, various low-levels including, AM1, PM3, MNDO and UFF have been examined, applying B3LYP/6-31 G* in all high-levels. It was shown, that in the case of A, (choosing two atom layers of the tube open-end as inner layer) the results of ONIOM approach are in best agreement with those of the pure density functional theory (DFT) calculations, while their results significantly differ from those of DFT in the case of B in same conditions. All above and population analysis demonstrate that the ONIOM may be a reliable scheme in the study of weak interactions while it is a controversial approach and should be applied cautiously in the case of strong interactions. We also probed the effect of tube length and diameter on the consistency between ONIOM and DFT results, showing that this consistency is independent of the mentioned parameters.     

A DNA polymorphism,consistent with gene duplication,correlates with high renin levels in the mouse submaxillary gland

The renin regulatory locus (Rnr) is a genetic element governing mouse submaxillary gland (SMG) renin levels. A 45,000 dalton polypeptide detectable after in vitro translation of mouse SMG mRNA has been identified by genetic and physical criteria as SMG renin. A cDNA recombinant clone specific for SMG renin has been isolated and used to demonstrate that the previously described genetic regulation of SMG renin levels is manifest at the level of renin mRNA concentration. The renin cDNA clone has also been used in Southern blot analyses to study the organization of homologous DNA sequences in strains carrying different alleles at the Rnr locus. Restriction digest patterns of high renin strains (Rnr^s) are characteristically distinct from patterns observed for low renin strains (Rnr^b) and are suggestive of a structural gene duplication at the chromosome 1 locus in high renin strains. However, gene dosage cannot account for the increased levels in high renin strains, since SMG renin levels in Rnr^s and those in Rnr^b may differ up to 100-fold.     

Minor-Groove Binding Models for Acetylaminofluorene Modified DNA

Abstract

Minimized potential energy calculations have been employed to locate and evaluate energetically a number of different models for DNA modified at carbon-8 of guanine by acetylaminofluorene (AAF). Three different duplex nonamer sequences were investigated. In addition to syn guanine models which have some denaturation and a Z-DNA model, we have found two new types of structures in which guanine remains syn and the AAF is placed in the minor groove of a B-DNA helix. One type features Hoogsteen base pairing between the modified guanine and protonated cytosine, with a sharply bent helix. The other (here termed the “wedge” model because the aromatic amine is wedged into the minor groove) maintains a single hydrogen bond between O6 of the modified guanine and N3 of protonated cytosine, with much less deformation of the helix, and close Van der Waals contacts between the AAF and the walls of the minor groove. Both types of structures (as well as the related forms produced by deprotonation of cytosine) are energetically important in all three sequences examined. The wedge-type model, which is most favored except in alternating G-C sequences, has been previously observed in a combined NMR and computational characterization of an aminofluorene (AF) modified guanine opposite adenine in a DNA duplex undecamer (D. Norman, P. Abuaf, B.E. Hingerty, D. Live, D. Grunberger, S. Broyde and D.J. Patel, Biochemistry 28, 7462 (1989)).     

Structure-based design of a new series of N-(piperidin-3-yl)pyrimidine-5-carboxamides as renin inhibitors

The action of the aspartyl protease renin is the rate-limiting initial step of the renin-angiotensin-aldosterone system. Therefore, renin is a particularly promising target for blood pressure as well as onset and progression of cardiovascular and renal diseases. New pyrimidine derivatives 5–14 were designed in an attempt to enhance the renin inhibitory activity of compound 3 identified by our previous fragment-based drug design approach. Introduction of a basic amine essential for interaction with the two aspartic acids in the catalytic site and optimization of the S1/S3 binding elements including an induced-fit structural change of Leu114 (‘Leu-in’ to ‘Leu-out’) by a rational structure-based drug design approach led to the discovery of N-(piperidin-3-yl)pyrimidine-5-carboxamide 14, a 65,000-fold more potent renin inhibitor than compound 3. Surprisingly, this remarkable enhancement in the inhibitory activity of compound 14 has been achieved by the overall addition of only seven heavy atoms to compound 3. Compound 14 demonstrated excellent selectivity over other aspartyl proteases and moderate oral bioavailability in rats.     

Therapeutic potential of hesperidin and its aglycone hesperetin: Cell cycle regulation and apoptosis induction in cancer models

BackgroundThe ability of cancer cells to divide without restriction and to escape programmed cell death is a feature of the proliferative state. Citrus flavanones are flavonoids with potential multiple anticancer actions, from antioxidant and chemopreventive, to anti-inflammatory, anti-angiogenic, cytostatic and cytotoxic in different cancer models.PurposeThis review aims to summarize the current knowledge on the antiproliferative actions of the citrus flavanones hesperidin (HSD) and hesperetin (HST), with emphasis on cell cycle arrest and apoptosis.MethodsCochrane Library, Scopus, Pubmed and Web of Science collection databases were queried for publications reporting antiproliferative effects of HSD and HST in cancer models.ResultsHSD and HST have been proven to delay cell proliferation in several cancer models. Depending on the compound, dose and cell line studied, different effects have been reported. Cell cycle arrest associated with cytostatic effects has been reported in cells with increased levels of p53 and also cyclin-dependent kinase inhibitors, as well as decreased levels of specific cyclins and cyclin-dependent kinases. Moreover, apoptotic effects have been found to be associated with altered ratios of pro-/antiapoptotic proteins, caspase activation, c-Jun N-terminal kinase (JNK) pathway activation and caspase-independent pathways.ConclusionAvailable scientific literature data indicate complex effects, dependent on cell lines and exposure conditions, suggesting that HSD and HST doses need to be optimized according to the cellular and organismal context. The establishment of the main antiproliferative mechanisms is of utmost importance for a possible therapeutic benefit of citrus flavanones in the context of cancer.     

Peperomia pellucida (L.) Kunth as an angiotensin-converting enzyme inhibitor in two-kidney,one-clip Goldblatt hypertensive rats

BackgroudPeperomia pellucida (L.) Kunth has been used widely to treat headache, kidney disease, fever, and hypertension. Previous in vitro studies discovered that the flavonoid-rich extract of this plant has potential hypotensive effects, specifically angiotensin-converting enzyme (ACE)-inhibitory activity. However, there is insufficient scientific evidence to validate the result in vivo.PurposeThis study investigated the dose dependencies of the effects of the ethyl acetate fraction of the ethanolic extract of this plant on blood pressure and biomarkers associated with the renin–angiotensin–aldosterone systems (RAAS), such as angiotensin II (AII) and the plasma renin concentration (PRC).Study designIn total, 30 two-kidney, one-clip (2K1C) hypertensive model rats were divided into five groups (n = 6 each): model group, captopril 25 mg/kg BW group, and three different ethyl acetate groups (25, 50, and 100 mg/kg BW). Another six rats comprised the sham group.MethodsRenal hypertensive rats (RHRs) were generated using stainless steel modification clips. Drugs were administered via oral gavage for 2 consecutive weeks. Blood pressure was measured weekly prior to treatment. Blood samples were collected before treatment and after the last dose to measure AII and PRC. The left kidney was isolated for histopathological examination.ResultsBlood pressure, AII levels, and PRC were elevated after 6 weeks in RHRs. Treatment with captopril and the ethyl acetate fraction of P. pellucida (L.) Kunth decreased blood pressure, AII levels, and PRC. The ethyl acetate fraction at a dose of 50 mg/kg BW had similar ACE-inhibitory effects as captopril. Histopathological examination disclosed coagulative necrosis in clipped kidneys. Impairment was alleviated in a dose-dependent manner by P. pellucida (L.) Kunth, similarly as observed in the captopril group.ConclusionP. pellucida (L.) Kunth targets the renin–angiotensin–aldosterone system, which might explain its antihypertensive effects.     

Oxygen-oxygen distances in protein-bound crystallographic water suggest the presence of protonated clusters

BackgroundThe availability of high-resolution X-ray structures has shown that proteins contain numerous water molecules, but their role is still not fully understood. Protonated and deprotonated water species are often involved in biochemical reactions. However protons are exceedingly difficult to detect directly because they are electron-poor species.MethodsThe oxygen‑oxygen distance of the crystallographic water molecules was analyzed in a large high-resolution data set. Moreover, a detailed analysis was carried out on the protein-bound water in the available structures of carbonic anhydrase II and cytochrome c oxidase, chosen as protein models in which protonated and deprotonated water species play a significant role.ResultsThe analysis shows an excess of water-water distances below the expected value for hydrogen bond. In the cavities and on the surface of the considered model proteins, clusters of water molecules are found, whose structure suggests the presence of chemical species deriving from self-ionization of water.ConclusionsThe presence of a small maximum below the hydrogen bond threshold in the oxygen‑oxygen distance distribution of crystallographic water molecules, along with the location of many of these water clusters, suggest the presence of Zundel-like structures in, or near, the proteins. Particularly significant is the presence of such structures in protein regions which have been identified as proton antennae or channels.General significanceThis work shows the possibilities, still unexplored, offered by this type of analysis in detecting in structures obtained by X-ray diffraction the presence of aqueous protons or hydroxide ions, which are chemical species as important as elusive.     

Prion-based nanomaterials and their emerging applications

ABSTRACT

Protein misfolding and aggregation into highly ordered fibrillar structures have been traditionally associated with pathological processes. Nevertheless, nature has taken advantage of the particular properties of amyloids for functional purposes, like in the protection of organisms against environmental changing conditions. Over the last decades, these fibrillar structures have inspired the design of new nanomaterials with intriguing applications in biomedicine and nanotechnology such as tissue engineering, drug delivery, adhesive materials, biodegradable nanocomposites, nanowires or biosensors. Prion and prion-like proteins, which are considered a subclass of amyloids, are becoming ideal candidates for the design of new and tunable nanomaterials. In this review, we discuss the particular properties of this kind of proteins, and the current advances on the design of new materials based on prion sequences.     

An Update on the Louisiana and Texas Rigs-to-Reefs Programs in the Gulf of Mexico

Abstract

The Louisiana and Texas Rigs-to-Reefs programs enjoy widespread public, industry, and government support and have become models for similar programs around the world. Louisiana’s Rigs-to-Reefs program is the largest in the world, and since its inception in 1986 about 363 oil and gas platforms have been donated, or on average about 12 structures per year. Texas’s Rigs-to-Reefs program started in 1990, and since this time about 154 structures have been donated, or about six structures per year. A summary update of the Louisiana and Texas reef programs is provided, along with recent changes in legislative activity. Donation trends and statistics are reviewed. The Rigs-to-Reefs programs are unlikely to see donation activity above historic levels, and both programs should start planning for a future where the income generated from future projects diminishes.     

Base-Stacking Interactions in Double-Helical DNA Structures: Experiment Versus Theory

Abstract

Atom-atom potential energy calculations have been undertaken for deriving stacking energies in double-helical structures. A comparison between the energy patterns of A- and B-type double-helical fragments determined by single-crystal X-ray diffraction methods versus idealized uniform models based on fiber diffraction data shows that the van der Waals stacking energy is largely sensitive to local changes in the relative orientation of adjacent base pairs. The sequence-dependent conformational variability observed in the high-resolution structures appears to be a consequence of the equipartitioning of the stacking energy along the double helix. The large energy variations expected for a uniform structure are dampened considerably in the observed structures by means of local changes in conformational features such as helix rotation and roll angles between base pairs.     

A Proposal For A Specific Double-Helical Structure In Which The Polynucleotide Strands Intercalate Instead of Forming Base-pairs

Abstract

Double helices, since the discovery of the DNA structure by Watson and Crick, represent the single most important secondary structural form of nucleic acids. The secondary structures of a variety of polynucleotide helices have now been well characterised with hydrogen- bonded base-pairs as building blocks. We wish to propose here the possibility, in a specific case, of a double stranded helical structure without any base-pair, but having a repeat unit of two nucleotides with their bases stacked through intercalation. The proposal comes from the initial models we have built for poly(dC) using the stacking patterns found in the crystal structures of 5′-dCMPNa₂ which crystallises in two forms depending on the degree of hydration. These structures have pairs of nucleotides with the cytosine rings partially overlapping and separated by 3.3Å. Using these as repeat units one could generate a model for poly(dC) with parallel strands, having a turn angle of 30° and a base separation of 6.6Å along each strand. Both right and left handed models with these parameters can be built in a smooth fashion without any obviously unreasonable stereochemical contacts. The helix diameter is about 13.5Å, much smaller than that of normal helices with base-pair repeats. The changes in the sugar-phosphate backbone conformation in the present models compared to normal duplexes only reflect the torsional flexibility available for extension of polynucleotide chains as manifested by the crystal structures of drug-inserted oligonucleotide complexes. Intercalation proposed here could have some structural relevance elsewhere, for instance to the base-mismatched regions on the double helix and the packing of noncomplementary single strands as found in the filamentous bacteriophage Pf1.     

Comparative binding studies on the interaction of the indoloquinoline alkaloid cryptolepine with the B and the non-canonical protonated form of DNA: A spectroscopic insight

BackgroundLow pH induced nucleic acid polymorphism and the interaction of naturally occurring small molecules with different polymorphic forms of DNA have been the focus in developing new drugs. Recent studies have revealed that low pH plays an active role in growth and development of cancer cells. Our target is to find whether and how the indoloquinoline alkaloid cryptolepine (CRP) interact with different polymorphic forms of natural DNA, in hope to explore this group of alkaloids as new therapeutics.MethodsMultiple spectroscopic techniques that include UV–visible absorption spectrophotometry, fluorimetry, CD spectroscopy along with thermal melting studies were employed to characterize the interaction between the alkaloid cryptolepine with the B and protonated forms of DNA.Results & conclusionsCryptolepine has been found to interact with either forms of DNA. The nature of binding is non-cooperative in both cases. Data show that the affinity of CRP to B form of DNA is relatively higher than that for the protonated form of DNA. Circular dichroic studies reveal that the alkaloid converts the left handed protonated DNA into bound right handed form. Fluorescence quenching experiments reveal that cryptolepine intercalates within the DNA base pairs. Thermal melting studies show that the alkaloid stabilises the DNA structures.General significanceSuch non-B DNA structures are often present at the ‘mutation hotspots’ that are associated with genetic instability related diseases such as cancer. The ability of cryptolepine to interact to such non-B DNA structures makes it a useful substrate in the designing of potential chemotherapeutic agents.     

The use of calorimetry in the biophysical characterization of small molecule alkaloids binding to RNA structures

BackgroundRNA has now emerged as a potential target for therapeutic intervention. RNA targeted drug design requires detailed thermodynamic characterization that provides new insights into the interactions and this together with structural data, may be used in rational drug design. The use of calorimetry to characterize small molecule–RNA interactions has emerged as a reliable and sensitive tool after the recent advancements in biocalorimetry.Scope of the reviewThis review summarizes the recent advancements in thermodynamic characterization of small molecules, particularly some natural alkaloids binding to various RNA structures. Thermodynamic characterization provides information that can supplement structural data leading to more effective drug development protocols.Major conclusionsThis review provides a concise report on the use of isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC) techniques in characterizing small molecules, mostly alkaloids–RNA interactions with particular reference to binding of tRNA, single stranded RNA, double stranded RNA, poly(A), triplex RNA.General significanceIt is now apparent that a combination of structural and thermodynamic data is essential for rational design of specific RNA targeted drugs. Recent advancements in biocalorimetry instrumentation have led to detailed understanding of the thermodynamics of small molecules binding to various RNA structures paving the path for the development of many new natural and synthetic molecules as specific binders to various RNA structures. RNA targeted drug design, that remained unexplored, will immensely benefit from the calorimetric studies leading to the development of effective drugs for many diseases. This article is part of a Special Issue entitled Microcalorimetry in the BioSciences — Principles and Applications, edited by Fadi Bou-Abdallah.     

NMR structures of polytopic integral membrane proteins

Abstract

Membrane proteins represent up to 30% of the proteins in all organisms, they are involved in many biological processes and are the molecular targets for around 50% of validated drugs. Despite this, membrane proteins represent less than 1% of all high-resolution protein structures due to various challenges associated with applying the main biophysical techniques used for protein structure determination. Recent years have seen an explosion in the number of high-resolution structures of membrane proteins determined by NMR spectroscopy, especially for those with multiple transmembrane-spanning segments. This is a review of the structures of polytopic integral membrane proteins determined by NMR spectroscopy up to the end of the year 2010, which includes both β-barrel and α-helical proteins from a number of different organisms and with a range in types of function. It also considers the challenges associated with performing structural studies by NMR spectroscopy on membrane proteins and how some of these have been overcome, along with its exciting potential for contributing new knowledge about the molecular mechanisms of membrane proteins, their roles in human disease, and for assisting drug design.