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Drug Design (drug + design)
Kinds of Drug Design Terms modified by Drug Design Selected AbstractsTowards a New Logic for Front End Management: From Drug Discovery to Drug Design in Pharmaceutical R&DCREATIVITY AND INNOVATION MANAGEMENT, Issue 2 2007Maria Elmquist Under pressure to innovate and be cost-effective at the same time, R&D departments are being challenged to develop new organizations and processes for Front End activities. This is especially true in the pharmaceutical industry. As drug development becomes more risky and costly, the discovery departments of pharmaceutical companies are increasingly being compelled to provide strong drug candidates for efficient development processes and quick market launches. It is argued that the Fuzzy Front End consists less of the discovery or recognition of opportunities than of the building of expanded concepts: the notion of concept generation is revisited, suggesting the need for a new logic for organizing Front End activities in order to support sustainable innovative product development. Based on an in-depth empirical study at a European pharmaceutical company, this paper contributes to improved understanding of the actual management practices used in the Front End. Using a design reasoning model (the C-K model), it also adds to the growing body of literature on the management of Front End activities in new product development processes. [source] PDK1 and PKB/Akt: Ideal Targets for Development of New Strategies to Structure-Based Drug DesignIUBMB LIFE, Issue 3 2003Thomas Harris Abstract Growth factor binding events to receptor tyrosine kinases result in activation of phosphatidylinositol 3-kinase (PI3K), and activated PI3K generates the membrane-bound second messengers phosphatidylinositol 3,4-diphosphate [PI(3,4)P2] and PI(3,4,5)P3, which mediate membrane translocation of the phosphoinositide-dependent kinase-1 (PDK1) and protein kinase B (PKB, also known as Akt). In addition to the kinase domain, PDK1 and PKB contain a pleckstrin homology (PH) domain that binds to the second messenger, resulting in the phosphorylation and activation of PKB by PDK1. Recent evidence indicates that constitutive activation of PKB contributes to cancer progression by promoting proliferation and increased cell survival. The indicating of PDK1 and PKB as primary targets for discovery of anticancer drugs, together with the observations that both PDK1 and PKB contain small-molecule regulatory binding sites that may be in proximity to the kinase active site, make PDK1 and PKB ideal targets for the development of new strategies to structure-based drug design. While X-ray structures have been reported for the kinase domains of PDK1 and PKB, no suitable crystals have been obtained for either PDK1 or PKB with their PH domains intact. In this regard, a novel structure-based strategy is proposed, which utilizes segmental isotopic labeling of the PH domain in combination with site-directed spin labeling of the kinase active site. Then, long-range distance restraints between the 15N-labeled backbone amide groups of the PH domain and the unpaired electron of the active site spin label can be determined from magnetic resonance studies of the enhancement effect that the paramagnetic spin label has on the nuclear relaxation rates of the amide protons. The determination of the structure and position of the PH domain with respect to the known X-ray structure of the kinase active site could be useful in the rational design of potent and selective inhibitors of PDK1 and PKB by 'linking' the free energies of binding of substrate (ATP) analogs with analogs of the inositol polar head group of the phospholipid second messenger. The combined use of X-ray crystallography, segmental isotopic and spin labeling, and magnetic resonance studies can be further extended to the study of other dynamic multidomain proteins and targets for structure-based drug design. IUBMB Life, 55: 117-126, 2003 [source] Drug Design for G-Protein-Coupled Receptors by a Ligand-Based NMR Method,ANGEWANDTE CHEMIE, Issue 8 2010Stefan Bartoschek Dr. Ohne Radioaktivität kommt ein Bindungsassay für einen G-Protein-gekoppelten Rezeptor aus, das ausschließlich auf NMR-Methoden beruht. Die Analyse gibt Auskunft über die relative Orientierung multipler Liganden und kann für die ligandenbasierte Wirkstoffentwicklung genutzt werden (siehe überlagerte Ligandstrukturen). Die Methode ist schnell und benötigt keine Informationen aus Protein-Kristallstrukturen. [source] Combined in Silico and Experimental Approach for Drug Design: The Binding Mode of Peptidic and Non-Peptidic Inhibitors to Hsp90 N-Terminal DomainCHEMICAL BIOLOGY & DRUG DESIGN, Issue 5 2010Simona Tomaselli Heat shock protein 90 (Hsp90) is a prime target for antitumor therapies. The information obtained by molecular dynamics (MD) simulations is combined with NMR data to provide a cross-validated atomic resolution model of the complementary interactions of heat shock protein 90 with a peptidic (shepherdin) and a non-peptidic (5-aminoimidazole-4-carboxamide-1-,- d -ribofuranoside, AICAR) inhibitor, showing antiproliferative and proapoptotic activity in multiple tumor cell lines. This approach highlights the relevant role of imidazolic moiety in the interaction of both antagonist molecules. In 5-aminoimidazole-4-carboxamide-1-,- d -ribofuranoside bound state, one conformation of those present in solution is selected, where imidazolic, H4 and H5 protons have a key role in defining a non-polar region contacting heat shock protein 90 surface. The dynamic equilibrium between N-type and S-type puckered forms of 5-aminoimidazole-4-carboxamide-1-,- d -ribofuranoside moiety is shown to be functional to inhibitor binding. The first experimental structural data on these inhibitors are presented and discussed as hints for future design of improved molecules. [source] Structural and Biophysical Characterization of XIAP BIR3 G306E Mutant: Insights in Protein Dynamics and Application for Fragment-Based Drug DesignCHEMICAL BIOLOGY & DRUG DESIGN, Issue 3 2009Cathy D. Moore Previous reports describe modulators of X-linked inhibitor of apoptosis (XIAP),caspase interaction designed from the AVPI N-terminal peptide sequence of second mitochondria-derived activator of caspase. A fragment-based drug design strategy was initiated to identify therapeutic non-peptidomimetic antagonists of X-linked inhibitor of apoptosis protein,protein interactions. Fragments that bind to the AVPI binding site of BIR3 (bacculoviral inhibitory repeat) were identified, and to further localize the fragment binding within the AVPI binding site, a point mutation was designed which alters the dynamics of flexible loops and blocks PI region of the binding cleft, thus enabling definition of weakly bound small molecules in the AV portion of the binding cleft. Nuclear magnetic resonance analysis confirmed the G306E mutation stabilizes the AV pocket. Biophysical characterization of the mutant confirms conformation change within the PI sub-pocket as evidenced by a significant diminishment in binding affinity of AVPI mimetics, yet the binding affinity of the smaller AV mimetics is maintained or slightly improved in the mutant compared with wild-type. Additional data from non-covalent mass spectrometry analysis shows enhanced binding of AV mimetics to the G306E mutant over the wild-type. The presented data outline a protein engineering strategy that allowed mapping of AV-replacements with better sensitivity and precision. [source] Natural Occurring Polyphenols as Template for Drug Design.CHEMICAL BIOLOGY & DRUG DESIGN, Issue 1 2009Focus on Serine Proteases Several major physio-pathological processes, including cancer, inflammatory states and thrombosis, are all strongly dependent upon the fine regulation of proteolytic enzyme activities, and dramatic are the consequences of unbalanced equilibria between enzymes and their cognate inhibitors. In this perspective, the discovery of small-molecule ligands able to modulate catalytic activities has a massive therapeutic potential and is a stimulating goal. Numerous recent experimental evidences revealed that proteolytic enzymes can be opportunely targeted, reporting on small ligands capable of binding to these biological macromolecules with drug-like potencies, and primarily with comparable (or even higher) efficiency with respect to their endogenous binding partner. In particular, natural occurring polyphenols and their derivatives recently disclosed these intriguing abilities, making them promising templates for drug design and development. In this review, we compared the inhibitory capacities of a set of monomeric polyphenols toward serine proteases activity, and finally summarized the data with an emphasis on the derivation of a pharmacophore model. [source] Multivalent Drug Design and Inhibition of Cholera Toxin by Specific and Transient Protein,Ligand InteractionsCHEMICAL BIOLOGY & DRUG DESIGN, Issue 5 2008Jiyun Liu Multivalent inhibitors of the cholera toxin B pentamer are potential therapeutic drugs for treating cholera and serve as models for demonstrating multivalent ligand effects through a structure-based approach. A crucial yet often overlooked aspect of multivalent drug design is the length, rigidity and chemical composition of the linker used to connect multiple binding moieties. To specifically study the role of chemical linkers in multivalent ligand design, we have synthesized a series of compounds with one and two binding motifs connected by several different linkers. These compounds have affinity for and potency against the cholera toxin B pentamer despite the fact that none can simultaneously bind two toxin receptor sites. Results from saturation transfer difference NMR reveal transient, non-specific interactions between the cholera toxin and linker groups contribute significantly to overall binding affinity of monovalent compounds. However, the same random protein,ligand interactions do not appear to affect binding of bivalent molecules. Moreover, the binding affinities and potencies of these ,non-spanning' bivalent ligands appear to be wholly independent of linker length. Our detailed analysis identifies multiple effects that account for the improved inhibitory potencies of bivalent ligands and suggest approaches to further improve the activity of this class of compounds. [source] Editorial: Chemical Biology & Drug Design 2007: Transition, Scholarship and FaithCHEMICAL BIOLOGY & DRUG DESIGN, Issue 6 2007Tomi K. SawyerArticle first published online: 15 NOV 200 No abstract is available for this article. [source] Signposts of Docking and Scoring in Drug DesignCHEMICAL BIOLOGY & DRUG DESIGN, Issue 4 2007Osman A .B. S. M. Gani Docking and scoring tools are often used in the early stages of drug discovery projects today. Because the language of this field of drug design often includes intermingled terms of physics, chemistry, biology, and medicine, the significant developments of docking and scoring are challenging to follow for non-experts. In this Science Philosophy article, I attempt to clarify the concepts used in docking and scoring to help articulate the successes and limitations of this multidisciplinary field in more comprehensible manner. [source] Chemical Biology & Drug Design: First Anniversary , 2007!CHEMICAL BIOLOGY & DRUG DESIGN, Issue 1 2007Tomi K. Sawyer No abstract is available for this article. [source] Molecular ConceptorTM for Training in Medicinal Chemistry, Drug Design, and CheminformaticsCHEMICAL BIOLOGY & DRUG DESIGN, Issue 1 2007Claude Cohen Current emphasis on structure-based design and other computational methods have encouraged medicinal chemists to learn traditionally ,expert' techniques of molecular modeling, computer-aided drug design, and cheminformatics. Molecular ConceptorTM (Synergix Ltd) is a multimedia software for teaching three-dimensional drug design principles. It present techniques and strategies used in drug design and cheminformatics with general guidelines for their successful application. Discovery of lead compounds and concepts are illustrated with manipulatable views of molecules, pharmacophores, and protein,ligand complexes. It is a unique teaching and learning aid for medicinal chemists, instructors, students, and others who need in-depth knowledge of these important techniques, as well as a valuable refresher course for professional modelers. [source] Chemical Biology & Drug Design 2006: Transition, Scholarship and FaithCHEMICAL BIOLOGY & DRUG DESIGN, Issue 6 2006Tomi K. Sawyer No abstract is available for this article. [source] First volume of Chemical Biology & Drug Design: Strategic vision for the advancement of innovative science, technology and medicineCHEMICAL BIOLOGY & DRUG DESIGN, Issue 1 2006Tomi K. Sawyer No abstract is available for this article. [source] Chemical Biology and Drug Design: World Project InitiativeCHEMICAL BIOLOGY & DRUG DESIGN, Issue 3 2006Tomi K. Sawyer No abstract is available for this article. [source] Chemical Biology & Drug Design: Inaugural issue!CHEMICAL BIOLOGY & DRUG DESIGN, Issue 1 2006Tomi K. Sawyer Editor-in-Chief [source] Design, Synthesis and Biological Evaluation of Cyclic Angiotensin II Analogues with 3,5 Side-Chain Bridges: Role of C-Terminal Aromatic Residue and Ring Cluster for Activity and Implications in the Drug Design of AT1 Non-peptide Antagonists.CHEMINFORM, Issue 6 2003Thomas Mavromoustakos No abstract is available for this article. [source] Metallotherapeutics: Novel Strategies in Drug DesignCHEMISTRY - A EUROPEAN JOURNAL, Issue 35 2009Lalintip Hocharoen Abstract A new paradigm for drug activity is presented, which includes both recognition and subsequent irreversible inactivation of therapeutic targets. Application to both RNA and protein biomolecules has been demonstrated. In contrast to RNA targets that are subject to strand scission chemistry mediated by ribose H-atom abstraction, proteins appear to be inactivated either through oxidative damage to amino acid side chains around the enzyme active site, or by backbone hydrolysis. [source] HTS and Rational Drug Design to Generate a Class of 5-HT2C -Selective Ligands for Possible Use in Schizophrenia.CHEMMEDCHEM, Issue 8 2010Treating neurological conditions: Optimization of a previously identified lead 5-HT2C agonist (left) led to the discovery of a highly selective 5-HT2C agonist (right). Importantly, this compound is a 5-HT2B receptor antagonist. Because of its selective 5-HT2C receptor activity, the compound was further evaluated in the phencyclidine model of disrupted prepulse inhibition, and found to exhibit normalizing effects comparable to those shown by the 5-HT2C agonist vabicaserin, a drug currently in phase,II clinical studies for schizophrenia. [source] Lectin-Based Drug Design: Combined Strategy to Identify Lead Compounds using STD NMR Spectroscopy, Solid-Phase Assays and Cell Binding for a Plant Toxin ModelCHEMMEDCHEM, Issue 3 2010Abstract The growing awareness of the sugar code,i.e. the biological functionality of glycans,is leading to increased interest in lectins as drug targets. The aim of this study was to establish a strategic combination of screening procedures with increased biorelevance. As a model, we used a potent plant toxin (viscumin) and lactosides synthetically modified at the C6/C6, positions and the reducing end aglycan. Changes in the saturation transfer difference (STD) in NMR spectroscopy, applied in inhibition assays, yielded evidence for ligand activity and affinity differences. Inhibitory potency was confirmed by the blocking of lectin binding to a glycoprotein-bearing matrix. In cell-based assays, iodo/azido-substituted lactose derivatives were comparatively active. Interestingly, cell-type dependence was observed, indicating the potential of synthetic carbohydrate derivative to interact with lectins in a cell-type (glycan profile)-specific manner. These results are relevent to research into human lectins, glycosciences, and beyond. [source] Modeling and Selection of Flexible Proteins for Structure-Based Drug Design: Backbone and Side Chain Movements in p38 MAPKCHEMMEDCHEM, Issue 2 2008Jyothi Subramanian Abstract Receptor rearrangement upon ligand binding (induced fit) is a major stumbling block in docking and virtual screening. Even though numerous studies have stressed the importance of including protein flexibility in ligand docking, currently available methods provide only a partial solution to the problem. Most of these methods, being computer intensive, are often impractical to use in actual drug discovery settings. We had earlier shown that ligand-induced receptor side-chain conformational changes could be modeled statistically using data on known receptor,ligand complexes. In this paper, we show that a similar approach can be used to model more complex changes like backbone flips and loop movements. We have used p38 MAPK as a test case and have shown that a few simple structural features of ligands are sufficient to predict the induced variation in receptor conformations. Rigorous validation, both by internal resampling methods and on an external test set, corroborates this finding and demonstrates the robustness of the models. We have also compared our results with those from an earlier molecular dynamics simulation study on DFG loop conformations of p38 MAPK, and found that the results matched in the two cases. Our statistical approach enables one to predict the final ligand-induced conformation of the active site of a protein, based on a few ligand properties, prior to docking the ligand. We can do this without having to trace the step-by-step process by which this state is arrived at (as in molecular dynamics simulations), thereby drastically reducing computational effort. [source] Crystal Structures of the PBP2 Glycosyltransferase Domain: New Opportunities for Antibacterial Drug DesignCHEMMEDCHEM, Issue 10 2007Johannes Zuegg Dr. The recent publication by Strynadka and colleagues, describing the first X-ray structures of a soluble truncated version of PBP2 containing both glycosyltransferase and transpeptidase domains facilitates more common and feasible approaches for the rational design and in turn clinically useful GT-inhibitors for the treatment of infections caused by highly resistant bacterial organisms. [source] Drug design: hiding in full viewDRUG DEVELOPMENT RESEARCH, Issue 1 2008Norman S. Radin Abstract Compounds that can produce potent biological effects in cells encompass a variety of structural motifs. Many of these compounds share a structural feature that has rarely been noted. It is an allylic cluster of atoms, a 3-carbon chain with a double bond between two of the atoms and an oxygen atom at the other end. The oxygen can be in a hydroxyl group, or in an ether or ketal or ester linkage, or simply a carbonyl form. In the latter case, the linkage is an allylic ketone (ene-one) structure. Nitrogen is often seen in equivalent forms. Inclusion of at least one allylic moiety appears to be able to turn a modestly active or inert compound into an effective drug or toxin. Some compounds lack the allylic moiety but develop one by enzymatic action, usually via cytochrome P-450 enzymes. These metabolites probably represent the active drug forms. The above concepts seem to be radically simplistic and improbable, but the evidence supporting them and the explanations for the biological activities are hidden "in plain view." Comparisons with the pleiotropic activities of the allylic sphingolipid, ceramide, indicate that many allylic drugs operate by controlling the state of protein phosphorylation, by activating proteases, by generating reactive oxygen species, by slowing mitochondrial electron transport, or by lowering cellular glutathione concentrations. Drug Dev Res 69:15,25, 2008 © 2008 Wiley-Liss, Inc. [source] Androgen action on human skin , from basic research to clinical significanceEXPERIMENTAL DERMATOLOGY, Issue 2004Christos C. Zouboulis Abstract:, Androgens affect several functions of the human skin, such as sebaceous gland growth and differentiation, hair growth, epidermal barrier homeostasis and wound healing. Their effects are mediated by binding to nuclear androgen receptors. Androgen activation and deactivation are mainly intracellular events. They differ from cell type to cell type and between cells at different locations. The major circulating androgens, dehydroepiandrosterone sulfate and androstenedione, are predominantly produced in the adrenal glands, and testosterone and 5,-dihydrotestosterone are mainly synthesized in the gonads. Testosterone in women and 5,-dihydrotestosterone in both genders are also synthesized in the skin. Skin cells express all androgen metabolizing enzymes required for the independent cutaneous synthesis of androgens and the development of hyperandrogenism-associated conditions and diseases, such as seborrhea, acne, hirsutism and androgenetic alopecia. The major thrust of drug design for the treatment of androgen-associated disorders has been directed against several levels of androgen function and metabolism. Partial effectiveness has only been achieved either by androgen depletion, inhibition of androgen metabolism or blockade of the androgen receptor. [source] Human telomeric G-quadruplex: structures of DNA and RNA sequencesFEBS JOURNAL, Issue 5 2010Anh Tuān Phan Telomeres play an important role in cellular aging and cancer. Human telomeric DNA and RNA G-rich sequences are capable of forming a four-stranded structure, known as the G-quadruplex. Such a structure might be important for telomere biology and a good target for drug design. This minireview describes the structural diversity or conservation of DNA and RNA human telomeric G-quadruplexes, discusses structural views on targeting these G-quadruplexes and presents some future challenges for structural studies. [source] The structural comparison of the bacterial PepX and human DPP-IV reveals sites for the design of inhibitors of PepX activityFEBS JOURNAL, Issue 8 2005Pascal Rigolet X-prolyl dipeptidyl aminopeptidases (X-PDAP) are enzymes catalysing the release of dipeptides from the amino termini of polypeptides containing a proline or an alanine at the penultimate position. Involved in various mammalian regulation processes, as well as in chronic human diseases, they have been proposed to play a role in pathogenicity for Streptococci. We compared the structure of X-PDAP from Lactococcus lactis (PepX) with its human counterpart DPP-IV. Despite very different overall folds, the residues most implicated for X-PDAP activity are conserved in the same positions and orientations in both enzymes, thus defining a structural signature for the X-PDAP specificity that crosses the species frontiers of evolution. Starting from this observation, we tested some inhibitors of DPP-IV on PepX activity, for which no specific inhibitor is known. We thus found that PepX was highly sensitive to valine-pyrrolidide with a KI of 9.3 µm, close to that reported in DPP-IV inhibition. We finally used the structure of PepX from L. lactis as a template for computer-based homology modeling of PepX from the pathogenic Streptococcus gordonii. Docking simulations of valine-pyrrolidide into the active site of PepX led to the identification of key residues for a rational drug design against PepX from Streptococci. These results could have applications in human health giving new perspectives to the struggle against pathogens. [source] The expansion of mechanistic and organismic diversity associated with non-ribosomal peptidesFEMS MICROBIOLOGY LETTERS, Issue 2 2000Michelle C Moffitt Abstract Non-ribosomal peptides are a group of secondary metabolites with a wide range of bioactivities, produced by prokaryotes and lower eukaryotes. Recently, non-ribosomal synthesis has been detected in diverse microorganisms, including the myxobacteria and cyanobacteria. Peptides biosynthesized non-ribosomally may often play a primary or secondary role in the producing organism. Non-ribosomal peptides are often small in size and contain unusual or modified amino acids. Biosynthesis occurs via large modular enzyme complexes, with each module responsible for the activation and thiolation of each amino acid, followed by peptide bond formation between activated amino acids. Modules may also be responsible for the enzymatic modification of the substrate amino acid. Recent analysis of biosynthetic gene clusters has identified novel integrated, mixed and hybrid enzyme systems. These diverse mechanisms of biosynthesis result in the wide variety of non-ribosomal peptide structures and bioactivities seen today. Knowledge of these biosynthetic systems is rapidly increasing and methods of genetically engineering these systems are being developed. In the future, this may lead to rational drug design through combinatorial biosynthesis of these enzyme systems. [source] Surprises from the crystal structure of the hepatitis C virus NS2-3 protease,HEPATOLOGY, Issue 6 2006Jerome Gouttenoire Ph.D. Hepatitis C virus is a major global health problem affecting an estimated 170 million people worldwide. Chronic infection is common and can lead to cirrhosis and liver cancer. There is no vaccine available and current therapies have met with limited success. The viral RNA genome encodes a polyprotein that includes 2 proteases essential for virus replication. The NS2-3 protease mediates a single cleavage at the NS2/NS3 junction, whereas the NS3-4A protease cleaves at 4 downstream sites in the polyprotein. NS3-4A is characterized as a serine protease with a chymotrypsin-like fold, but the enzymatic mechanism of the NS2-3 protease remains unresolved. Here, we report the crystal structure of the catalytic domain of the NS2-3 protease at 2.3 Å resolution. The structure reveals a dimeric cysteine protease with 2 composite active sites. For each active site, the catalytic histidine and glutamate residues are contributed by one monomer, and the nucleophilic cysteine by the other. The carboxy-terminal residues remain coordinated in the 2 active sites, predicting an inactive postcleavage form. Proteolysis through formation of a composite active site occurs in the context of the viral polyprotein expressed in mammalian cells. These features offer unexpected insights into polyprotein processing by hepatitis C virus and new opportunities for antiviral drug design. [source] When, in the context of drug design, can a fluorine atom successfully substitute a hydroxyl group?INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4 2002Marcin Hoffmann Abstract In this article, we deal with the question of whether a fluorine atom can substitute a hydroxyl group in such a way that will lead to a compound showing a desired biologic activity, that is, a potential new drug. It is obvious that a fluorine atom differs from a hydroxyl group, as it cannot donate hydrogen bonds. However, it can accept them. Moreover, both fluorine and oxygen are of similar size and are the most electronegative elements. Therefore, a fluorine atom is thought to be a good substitute for a hydroxyl group. However, it was shown that for conformationally labile aliphatic compounds a replacement of a hydroxyl by a fluorine increases conformational diversity, so the fluorine-containing aliphatic molecules are present in equilibrium at room temperature as a mixture of several different conformers. In contrast, for cyclic compounds the substitution of an OH group by an F atom does not much change shape and electrostatic potential around corresponding conformers. Moreover, these compounds are present in equilibrium at room temperature in aqueous solution as a mixture of the same most favored structures. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002 [source] Chemical synthesis and biosynthesis of the cyclotide family of circular proteinsIUBMB LIFE, Issue 9 2006Sunithi Gunasekera Abstract Cyclotides are a recently discovered class of proteins that have a characteristic head-to-tail cyclized backbone stabilized by a knotted arrangement of three disulfide bonds. They are exceptionally resistant to chemical, enzymatic and thermal treatments because of their unique structural scaffold. Cyclotides have a range of bio-activities, including uterotonic, anti-HIV, anti-bacterial and cytotoxic activity but their insecticidal properties suggest that their natural physiological role is in plant defense. They are genetically encoded as linear precursors and subsequently processed to produce mature cyclic peptides but the mechanism by which this occurs remains unknown. Currently most cyclotides are obtained via direct extraction from plants in the Rubiaceae and Violaceae families. To facilitate the screening of cyclotides for structure-activity studies and to exploit them in drug design or agricultural applications a convenient route for the synthesis of cyclotides is vital. In this review the current chemical, recombinant and biosynthetic routes to the production of cyclotides are discussed. iubmb Life, 58: 515-524, 2006 [source] Heterotachy and Functional Shift in Protein EvolutionIUBMB LIFE, Issue 4-5 2003Hervé Philippe Abstract Study of structure/function relationships constitutes an important field of research, especially for modification of protein function and drug design. However, the fact that rational design (i.e. the modification of amino acid sequences by means of directed mutagenesis, based on knowledge of the three-dimensional structure) appears to be much less efficient than irrational design (i.e. random mutagenesis followed by in vitro selection) clearly indicates that we understand little about the relationships between primary sequence, three-dimensional structure and function. The use of evolutionary approaches and concepts will bring insights to this difficult question. The increasing availability of multigene family sequences that has resulted from genome projects has inspired the creation of novel in silico evolutionary methods to predict details of protein function in duplicated (paralogous) proteins. The underlying principle of all such approaches is to compare the evolutionary properties of homologous sequence positions in paralogs. It has been proposed that the positions that show switches in substitution rate over time--i.e., 'heterotachous sites'--are good indicators of functional divergence. However, it appears that heterotachy is a much more general process, since most variable sites of homologous proteins with no evidence of functional shift are heterotachous. Similarly, it appears that switches in substitution rate are as frequent when paralogous sequences are compared as when orthologous sequences are compared. Heterotachy, instead of being indicative of functional shift, may more generally reflect a less specific process related to the many intra- and inter-molecular interactions compatible with a range of more or less equally viable protein conformations. These interactions will lead to different constraints on the nature of the primary sequences, consistently with theories suggesting the non-independence of substitutions in proteins. However, a specific type of amino acid variation might constitute a good indicator of functional divergence: substitutions occurring at positions that are generally slowly evolving. Such substitutions at constrained sites are indeed much more frequent soon after gene duplication. The identification and analysis of these sites by complementing structural information with evolutionary data may represent a promising direction to future studies dealing with the functional characterization of an ever increasing number of multi-gene families identified by complete genome analysis. IUBMB Life, 55: 257-265, 2003 [source] | |||||||||||||||||||||||||||||||||||||||||||