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Results for “rational design”

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PubMed2006

Rational design and HT techniques allow the synthesis of new IWR zeolite polymorphs.

By combining a rational design of structure directing agents and high throughput and data mining techniques, it has been possible to obtain Ge-free ITQ-24 as pure silica as well as borosilicate polymorphs up to a Si/TIII ratio of 10. Al can be exchanged by B giving strong acid materials. Also, the availability of the pure silica material allows one to determine more precisely the crystal symmetry. This work opens the possibility to synthesize the Ge-free polymorphs of a large number of new germanosilicate structures reported in the last five years. This certainly will increase their possibilities for industrial application.

Germanium↗
PubMed1999

Rational design of anti-dementia therapy.

Understanding the pharmacokinetic (PK) and pharmacodynamic (PD) characteristics of new drugs is essential. The application of this information facilitates the design of a rational clinical trial programme and optimizes the chances for rapid and successful clinical development. Upon completion of each development phase, the information obtained must be evaluated critically to maximize the design of subsequent studies. Phase I trials represent the first time the drug is administered in humans and their primary objective is to evaluate the drug's safety and tolerability in man. Phase II trials represent the first time that the drug is administered to the target patient population. The objectives of Phase II trials are to verify the safety and tolerability of the drug in patients, and also to evaluate for the first time the clinical efficacy of the drug. During these phases of development, the use of PK and PD measures is helpful for establishing the therapeutic dose range as well as the suitability of the chosen efficacy measures for use in the pivotal Phase III trials. Here, using several examples of PK and PD data obtained from the clinical development studies of donepezil HCl, the application of these measures on the development of a drug for the treatment of Alzheimer's disease is discussed.

Alzheimer Disease↗
PubMed2004

Design, synthesis and biological evaluation of new potent 5-nitrofuryl derivatives as anti-Trypanosoma cruzi agents. Studies of trypanothione binding site of trypanothione reductase as target for rational design.

Design, using force-field calculations on the catalytic site of trypanothione reductase from Trypanosoma cruzi, has led to the development of new 5-nitrofuryl derivatives as potential anti-trypanosomal agents. The synthesized compounds were tested in vitro against T. cruzi and more than 75% of the prepared derivatives showed higher activity than nifurtimox. Compounds 5 and 11, hexyl 4-(5-nitrofurfurylidene)carbazate and N-hexyl 3-(5-nitrofuryl)propenamide, showed the highest in vitro trypanocidal effect reported to date for members of the nitrofuran family. Partition coefficients and energies for the single-electron reduction of compounds were theoretically determined. These properties could be not the major cause of the activities' differences. The physicochemical environment around E19, W22, C53 and Y111 residues within the trypanothione binding site of trypanothione reductase resulted a valuable target for the rational design of anti-trypanosomal drugs.

Animals↗
PubMed2000

Rational design of highly diastereoselective, organic base-catalyzed, room-temperature Michael addition reactions.

Via the rational design of a single-preferred transition state, stabilized by electron donor-acceptor-type attractive interactions, structural and geometric requirements for the corresponding starting compounds have been determined. The Ni(II) complex of the Schiff base of glycine with o-[N-alpha-picolylamino]acetophenone, as a nucleophilic glycine equivalent, and N-(trans-enoyl)oxazolidin-2-ones, as derivatives of an alpha,beta-unsaturated carboxylic acid, were found to be the substrates of choice featuring geometric/conformational homogeneity and high reactivity. The corresponding Michael addition reactions were found to proceed at room temperature in the presence of catalytic amounts of DBU to afford quantitatively the addition products with virtually complete diastereoselectivity. Acidic decomposition of the products followed by treatment of the reaction mixture with NH4OH gave rise to the diastereomerically pure 3-substituted pyroglutamic acids.

Catalysis↗
PubMed1991

Rational design of quinazoline-based irreversible inhibitors of human erythrocyte purine nucleoside phosphorylase.

Described herein is the rational design of irreversible inhibitors of human erythrocyte purine nucleoside phosphorylase (PNPase). Inhibitor design started with the observation that the amino group of 8-aminoquinazolin-4(3H)-one interacts with enzyme-bound phosphate. This observation correctly predicted that the 5,8-dione (quinone) and 5,8-dihydroxy (hydroquinone) derivatives of quinazolin-4(3H)-ones would enter the active site. The amine-phosphate interaction also served to confirm that a quinazolin-4(3H)-one binds in the PNPase active sites like a purine substrate. From models of the PNPase active site it was possible to design quinazoline-based quinones that undergo a reductive-addition reaction with an active-site glutamate residue. The best inhibitor studied, 2-(chloromethyl)quinazoline-4,5,8(3H)-trione, rapidly inactivates PNPase by a first-order process with an inhibitor to enzyme stoichiometry of 150. The active-site hydroquinone adduct of this inhibitor eliminates a leaving group to afford a quinone methide species positioned to alkylate another active-site glutamate residue. Thus, this inhibitor is designed to cross-link the PNPase active site by reductive addition followed by the generation of an alkylating quinone methide species.

Binding Sites↗
PubMed1998

Rational design and synthesis of novel, potent bis-phenylamidine carboxylate factor Xa inhibitors.

The molecular modeling studies, rational design, and synthesis of a novel series of bisphenylamidine carboxylate compounds which are inhibitors of factor Xa in the blood coagulation cascade are described. Inhibition of blood coagulation has been proposed to have several potential therapeutic utilities (Kaiser and Hauptmann, Cardiovasc. Drug Rev. 1994, 12, 225-236). Factor Xa (fXa) holds a central position in the coagulation cascade (Coleman et al. in Hemostasis and Thrombosis: Basic Principles and Clinical Practice, 1994, pp 3-18). Its major role is the generation of thrombin by the proteolytic cleavage of prothrombin. Inhibition of fXa would serve to reduce the formation of platelet clots. The fXa dimer crystal structure (Tulinsky et al., J. Mol. Biol. 1993, 232, 947-966) was used in our molecular modeling studies to design a novel series of fXa inhibitors. We initially docked and minimized isolated small molecule fragments in the S1 and S4 aryl-binding subsites. Subsequently, these fragments were connected with a tether, so as not to disturb the orientation of the fragments in their respective pockets. These modeling studies led to the initial compound (1) which was found to have significant inhibitory potency for fXa (Ki = 34 nM). The synthesis of the core structure, structure-activity relationships (SAR), and proposed binding orientation based on molecular modeling for this novel bis-phenylamidine series of fXa inhibitors are described.

Amidines↗
PubMed1994

New dual inhibitors of neutral endopeptidase and angiotensin-converting enzyme: rational design, bioavailability, and pharmacological responses in experimental hypertension.

In the treatment of cardiovascular diseases, it could be of therapeutic interest to associate the hypotensive effects resulting from the inhibition of angiotensin II formation, ensured by endothelial angiotensin-converting enzyme (ACE), with the diuretic and natriuretic responses due to the protection of the endogenous atrial natriuretic peptide (ANP) from inactivation by epithelial neutral endopeptidase (NEP). However, an investigation of this hypothesis requires an orally active compound able to jointly inhibit ACE and NEP. Dual inhibitors have therefore been designed by a rational approach, based on the characteristics of the active sites of both enzymes, which belong to the same family of zinc metallopeptidases, and on the structures of their most potent and selective inhibitors. As both NEP and ACE contain a large S'1-S'2 domain able to accommodate aromatic residues, the cyclic ACE inhibitor 3-(mercaptomethyl)-3,4,5,6-tetrahydro-2-oxo-1H-1-benzazocine-1-ace tic acid was selected as a template. Various aliphatic constraints were introduced on the benzyl moiety of the potent NEP inhibitor N-[2-(mercaptomethyl)-3-phenylpropanoyl]-L-tyrosine (IC50 NEP = 2 nM, IC50 ACE = 25 nM) to improve the fit between the computed most stable conformers of these molecules and the ACE template. New dual inhibitors, of general formula, N-[2(R,S)-(mercaptomethyl)-3(R,S)-phenylbutanoyl]-L-amino acid with IC50 values in the nanomolar range for both enzymes were generated by this approach. The separation of the four stereoisomers using chiral amines and the stereoselective synthesis of the 2-(mercaptomethyl)-3-phenylbutanoyl moiety showed that inhibitors with the 2S,3R configuration are the most potent on both NEP and ACE. The "in vivo" potency of various prodrugs of these inhibitors to inhibit ACE activity in lung and NEP activity in kidney was measured after oral administration in mice. From this pharmacokinetical study the most potent dual inhibitor RB 105 (N-[(2S,3R)-2-(mercaptomethyl)-3-phenylbutanoyl-L-alanine (compound 44c) (KI NEP 1.7 nM, KI ACE 4.5 nM) and its most efficient in vivo prodrug mixanpril, [N-[(2S,3R)-2-[(benzoylthio)methyl]-3-phenylbutanoyl]-L-alan ine (compound 18) (ED50 NEP approximately 1 mg/kg, ED50 ACE approximately 7 mg/kg) were selected. Competition experiments with a tritiated inhibitor of ACE or NEP bound to mouse lung and kidney membranes respectively showed that mixanpril has a long duration of action (> 8 h). As expected, after i.v. administration in the spontaneously hypertensive rat (SHR), RB 105 decreased blood pressure and increased diuresis and natriuresis.(ABSTRACT TRUNCATED AT 400 WORDS)

Alanine↗
PubMed2006

Rational design and synthesis of a double-stranded DNA-binder library.

Described is a computer-assisted rational design of a DNA-bis-intercalator peptide library. The peptide library of 250 members was prepared and the most powerful binder identified. A value of the binding constant is almost two orders of magnitude higher than that of starting building block-9-aminoacridine. The binder affinity found toward calf thymus DNA is 30-fold of that of human prion peptide 106-126.

Aminacrine↗
PubMed2006

Rational design of aziridine-containing cysteine protease inhibitors with improved potency: studies on inhibition mechanism.

To enable a rational design of improved cysteine protease inhibitors, the present work investigates trends in the inhibition potency of aziridine derivatives with a substituted nitrogen center. To predict the influence of electron-withdrawing substituents, quantum chemical computations of the ring opening of N-formylated, N-methylated, and N-unsubstituted aziridines with thiolate were performed. They revealed that the N-formyl group leads to a strong decrease of the reaction barrier and a considerable increase in exothermicity due to stabilization of the transition state. In contrast, a nucleophilic attack at the carbonyl carbon atom is characterized by very low reaction barriers, suggesting a reversible reaction, thus providing the theoretical background for the reversible inhibition of cysteine proteases by peptidyl aldehydes. Reactions of aziridine building blocks (diethyl aziridine-2,3-dicarboxylate 1, diethyl 1-formyl aziridine-2,3-dicarboxylate 2) with a model thiolate in aqueous solution which were followed by NMR spectroscopy and mass spectrometry, showed the N-formylated compound 2 to readily undergo a ring-opening reaction. In contrast, the reaction of 1 with the thiolate is much slower. Enzyme assays with the cysteine protease cathepsin L showed 2 to be a 5000-fold better enzyme inhibitor than 1. Dialysis assays clearly proved irreversible inhibition. These experiments, together with the results obtained with the model thiolate, indicate that the main inhibition mechanism of the N-formylated aziridine 2 is the ring-opening reaction rather than the reversible attack of the active site cysteine residue at the carbonyl carbon atom.

Aziridines↗
PubMed1995

Fermenter production of an artificial fab fragment, rationally designed for the antigen cystatin, and its optimized crystallization through constant domain shuffling.

The synthetic antibody model "M41" was rationally designed with a binding site complementary to chicken egg white cystatin as the prescribed antigen. In order to permit comparison between the computer model and an experimental three-dimensional structure of the artificial protein, its X-ray crystallographic analysis was pursued. For this purpose, M41 was expressed as a recombinant Fab fragment in E. coli by medium cell density fermentation employing the tightly regulated tetracycline promoter. The Fab fragment was efficiently purified via a His-6 tail fused to its heavy chain and immobilized metal affinity chromatography. To raise the chances for the productive formation of crystal packing contacts, three versions of the Fab fragment were generated with differing constant domains. One of these, the variant with murine C kappa and CH1 gamma 1 domains, was successfully crystallized by microseeding in a sitting drop. The orthorhombic crystals exhibited symmetry of the space group P2(1)2(1)2(1) with unit cell dimensions a = 104.7 A, b = 113.9 A, c = 98.8 A and diffracted X-rays to a nominal resolution of 2.5 A.

Amino Acid Sequence↗
PubMed2000

Novel approaches in the rational design of antifungal agents of low toxicity.

This paper presents an overview of studies on novel strategies for the rational design of antifungal agents of low toxicity and overcoming the multidrug resistance (MDR) of fungi. This goal was achieved both due to the introduction of a novel target, glucosamine-6-phosphate synthase, as well as to the recognition of molecular basis of selectivity of action of amphotericin B derivatives.

Antifungal Agents↗
PubMed2001

A rationally designed oligopeptide shows significant conformational changes upon binding to sulphate ions.

Oligopeptides that interact with oxoanions were developed by rational design methods. The substrate-binding site of the enzyme purine nucleoside phosphorylase served as a model for the design of the ionophores. The amino acids involved in the complexation of oxoanions were linked through flexible spacer residues. These spacers were chosen such that the relative orientation of the interacting amino acids was conserved. Several peptide sequences were preselected based on intermolecular H-bond frequencies. These frequencies were calculated from molecular dynamics trajectories of the corresponding peptide-anion complexes and used to score the binding properties of the peptides. The most promising peptides were prepared using solid phase peptide synthesis. Anion binding of the peptide ionophores was screened using circular dichroism (CD) and confirmed by NMR spectroscopy. CD measurements performed in methanol revealed a significant conformational change of a linear undecapeptide upon binding to sulphate ions. Two-dimensional-NMR experiments confirmed that a conformation with high helical content is formed in the presence of sulphate ions. These conformational changes induced by the anion stimulate the development of new transduction mechanisms in chemical sensors.

Amino Acid Sequence↗
PubMed2002

Probing electronic communication in covalently linked multiporphyrin arrays. A guide to the rational design of molecular photonic devices.

Understanding electronic communication among the constituents in multicomponent macromolecular architectures is essential for the rational design of molecular devices for photonic, electronic, or optoelectronic applications. This Account describes studies aimed at understanding the mechanisms of electronic communication in porphyrin-based architectures that undergo excited-state energy migration and ground-state hole/electron hopping. Porphyrins are ideal building blocks for such constructs owing to their attractive and versatile physical properties and amenability to synthetic control. These properties have permitted the creation of covalently linked multiporphyrin arrays wherein the rates of excited-state energy migration and ground-state hole/electron hopping can be tuned over a wide range.

Electronics↗
PubMed2004

Rational design of a novel fluorescent biosensor for beta-lactam antibiotics from a class A beta-lactamase.

A rational design strategy was used to construct a sensitive "turn-on" biosensor for beta-lactam antibiotics and beta-lactamase inhibitors from a class A beta-lactamase mutant with suppressed hydrolytic activity. A fluorescein molecule was attached to the 166 position on the Omega-loop of the E166C mutant close to the active site of the beta-lactamase. Upon binding with antibiotics or inhibitors, the flexibility of the Omega-loop allows the fluorescein molecule to move out from the active site and be more exposed to solvent. This process is accompanied by an increase in the fluorescence of the labeled enzyme. The fluorescence intensity of the biosensor increases with the concentration of antibiotics or inhibitors, which can detect penicillin G at concentrations as low as 50 nM in water. This approach opens a possibility for converting highly active and nonallosteric enzymes into substrate-binding proteins for biosensing purposes.

Animals↗
PubMed2006

Rational design, synthesis, and application of a new receptor for the molecular recognition of tricarboxylate salts in aqueous media.

A rational design of a tripodal receptor for the molecular recognition of tricarboxylate salts in aqueous media, based on squaramide, has been performed using high-level DFT calculations (RI-BP86/SVP level of theory) in solution using the COSMO treatment, including some preliminary ab initio calculations at the higher RI-MP2/TZVP level of theory, comparing the ability of squaramide to bind carboxylate salts with two widely used guanidinium salts. The tripodal receptor has been synthesized using a new methodology that has been recently reported by some of us, and its capability of recognizing several mono-, di-, and tricarboxylate salts has been studied experimentally by means of microcalorimetry experiments in a very high competitive media, H(2)O:EtOH 1:3. These experiments give enthalpic and entropic data, which are unfortunately scarce in the literature of molecular recognition of anions. Finally, a fluorimetric ensemble of the receptor with fluorescein has been found to be useful for the fluorimetric determination of zinc citrate in a commercial toothpaste using competition assays.

Binding Sites↗
PubMed2006

Rationally designed small compounds inhibit pilus biogenesis in uropathogenic bacteria.

A chemical synthesis platform with broad applications and flexibility was rationally designed to inhibit biogenesis of adhesive pili assembled by the chaperone-usher pathway in Gram-negative pathogens. The activity of a family of bicyclic 2-pyridones, termed pilicides, was evaluated in two different pilus biogenesis systems in uropathogenic Escherichia coli. Hemagglutination mediated by either type 1 or P pili, adherence to bladder cells, and biofilm formation mediated by type 1 pili were all reduced by approximately 90% in laboratory and clinical E. coli strains. The structure of the pilicide bound to the P pilus chaperone PapD revealed that the pilicide bound to the surface of the chaperone known to interact with the usher, the outer-membrane assembly platform where pili are assembled. Point mutations in the pilicide-binding site dramatically reduced pilus formation but did not block the ability of PapD to bind subunits and mediate their folding. Surface plasmon resonance experiments confirmed that the pilicide interfered with the binding of chaperone-subunit complexes to the usher. These pilicides thus target key virulence factors in pathogenic bacteria and represent a promising proof of concept for developing drugs that function by targeting virulence factors.

Anti-Bacterial Agents↗
PubMed2004

Rational design of potent and selective VLA-4 inhibitors and their utility in the treatment of asthma.

Asthma, a chronic inflammatory disease of the airways, is a significant burden on our healthcare system. There is high unmet need for treatments directed towards the underlying causes of the disease. The cell surface integrin VLA-4 (very late antigen-4; alpha4beta1; CD49d/CD29) plays an important role in the trafficking of white blood cells to sites of inflammation and represents an exciting target for the development of novel anti-inflammatory drugs for the treatment of asthma. Here, we review our efforts to use rational design to identify potent, selective inhibitors of VLA-4. We describe the discovery of a series of potent VLA-4 inhibitors through the addition of a novel N-terminal organic cap to a tetrapeptide VLA-4 binding motif 4-((N'-2-methylphenyl)uriedo)phenylacetyl-Leu-Asp-Val-Pro ; Kd = 70 pM), and rationalize their structure-activity relationships using 3D-QSAR. Also, we show our rational peptidomimetic design strategy using "template hopping" from the gpIIb/IIIa integrin antagonist field, and also a novel virtual screening strategy. Two series have been developed, one that has high selectivity for the activated over the non-activated state of the receptor, and the other which is non-selective inhibiting both activated and non-activated VLA-4. Both series are highly selective for VLA-4 versus against other integrin family members. These inhibitors show promise in the treatment of asthma, based upon efficacy in a sheep model of asthma, where they inhibit both the early and late-phase responses to asthma and also block hypersensitivity.

Amides↗