Archive of Medical Research

Proteins as networks: usefulness of graph theory in protein science.

The network paradigm is based on the derivation of emerging properties of studied systems by their representation as oriented graphs: any system is traced back to a set of nodes (its constituent elements) linked by edges (arcs) correspondent to the relations existing between the nodes. This allows for a straightforward quantitative formalization of systems by means of the computation of mathematical descriptors of such graphs (graph theory). The network paradigm is particularly useful when it is clear which elements of the modelled system must play the role of nodes and arcs respectively, and when topological constraints have a major role with respect to kinetic ones. In this review we demonstrate how nodes and arcs of protein topology are characterized at different levels of definition: 1. Recurrence matrix of hydrophobicity patterns along the sequence 2. Contact matrix of alpha carbons of 3D structures 3. Correlation matrix of motions of different portion of the molecule in molecular dynamics. These three conditions represent different but potentially correlated reticular systems that can be profitably analysed by means of network analysis tools.

Krishnan A, Zbilut JP, Tomita M, Giuliani A.

Institute of Advanced Biosciences, Keio University, Tsuruoka City, Japan.

Activation, exposure and penetration of virally encoded, membrane-active polypeptides during non-enveloped virus entry.

Host cell entry by influenza and other enveloped viruses is well characterized, however, the manner in which non-enveloped viruses deliver their genome across host cell membranes in the absence of membrane fusion remains unresolved. The discovery of short, membrane altering, amphipathic or hydrophobic sequences in several non-enveloped virus capsid proteins such as the gamma (gamma) peptide of nodaviruses and tetraviruses, VP4 and the N-terminal region of VP1 of picornaviruses, micro1N of reoviruses, and protein VI of adenoviruses suggests that these small peptides facilitate breaching of the host membrane and the delivery of the viral genome into the host cell. In spite of conspicuous differences in entry among non-enveloped virions, the short stretches of membrane active regions are associated with similar, entry-related events including: I) proteolytic cleavage of a precursor capsid protein resulting in increased dynamic character and/or accessibility of these peptides; II) structural changes in the virus capsid triggered by receptor binding and/or low pH in entry compartments, resulting in peptide exposure; III) externalized peptides interact with host membranes and disrupt them, facilitating delivery of the viral genome inside the host cell. Here we discuss the membrane alteration activity in non-enveloped viruses with reference to the gamma peptide of nodaviruses. Virtually all of the characteristics of gamma are shared by analogous peptides in other non-enveloped viruses, making it a simple prototype for comparative purposes.

Banerjee M, Johnson JE.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA-92037, USA.

Recent progress and future directions in protein-protein docking.

This article gives an overview of recent progress in protein-protein docking and it identifies several directions for future research. Recent results from the CAPRI blind docking experiments show that docking algorithms are steadily improving in both reliability and accuracy. Current docking algorithms employ a range of efficient search and scoring strategies, including e.g. fast Fourier transform correlations, geometric hashing, and Monte Carlo techniques. These approaches can often produce a relatively small list of up to a few thousand orientations, amongst which a near-native binding mode is often observed. However, despite the use of improved scoring functions which typically include models of desolvation, hydrophobicity, and electrostatics, current algorithms still have difficulty in identifying the correct solution from the list of false positives, or decoys. Nonetheless, significant progress is being made through better use of bioinformatics, biochemical, and biophysical information such as e.g. sequence conservation analysis, protein interaction databases, alanine scanning, and NMR residual dipolar coupling restraints to help identify key binding residues. Promising new approaches to incorporate models of protein flexibility during docking are being developed, including the use of molecular dynamics snapshots, rotameric and off-rotamer searches, internal coordinate mechanics, and principal component analysis based techniques. Some investigators now use explicit solvent models in their docking protocols. Many of these approaches can be computationally intensive, although new silicon chip technologies such as programmable graphics processor units are beginning to offer competitive alternatives to conventional high performance computer systems. As cryo-EM techniques improve apace, docking NMR and X-ray protein structures into low resolution EM density maps is helping to bridge the resolution gap between these complementary techniques. The use of symmetry and fragment assembly constraints are also helping to make possible docking-based predictions of large multimeric protein complexes. In the near future, the closer integration of docking algorithms with protein interface prediction software, structural databases, and sequence analysis techniques should help produce better predictions of protein interaction networks and more accurate structural models of the fundamental molecular interactions within the cell.

Ritchie DW.

Department of Computing Science, University of Aberdeen, Aberdeen, AB24 3UE, Scotland, UK. dritchie@csd.abdn.ac.uk

The beta and gamma classes of carbonic anhydrase.

There are currently five (alpha, beta, gamma, delta, zeta) classes of carbonic anhydrases (CA\’s) of which the alpha-class from mammalian sources has been studied to a much greater extent compared to the other four classes. Yet, CA\’s other than the alpha-class are widely distributed in Nature and play important roles in human health, the global carbon cycle, and industrial applications. In aerobic prokaryotes, beta-class CA\’s are implicated in maintaining internal pH and CO(2)/bicarbonate balances required for biosynthetic reactions. In anaerobic prokaryotes, beta-class CA\’s are implicated in the transport of CO(2) and bicarbonate across the cytoplasmic membrane that regulates pH and facilitates acquisition of substrates and product removal required for growth. In phototrophic organisms, beta-class CA\’s are particularly important for transport and concentration of CO(2) and bicarbonate for photosynthesis. The delta- and zeta-classes are proposed to function in marine diatoms to concentrate CO(2) for photosynthesis. Physiological roles for the gamma-class are not as well documented; however, the active site architecture and catalytic mechanism is well understood as are patterns of inhibition by sulfonamides and anions.

Zimmerman SA, Ferry JG.

Department of Biochemistry & Molecular Biology, Pennsylvania State University, 205 S. Frear Laboratory, University Park, PA 16802, USA.

Carbonic anhydrase activation and the drug design.

The activation mechanism of Carbonic Anhydrase was recently explained using kinetic, spectroscopic and X-ray techniques. It has been demonstrated that the activators molecules (CAAs) bind at the entrance of the enzyme active-site facilitating the rate-determining step of CA catalytic cycle. Drug design studies have been performed in order to obtain strong CAAs belonging to several chemical classes: amino acids, azoles, amine and their derivatives, etc. Structure-activity correlations of different activators are discussed for the most studied Carbonic Anhydrase isozymes: isoform I and II. The physiological relevance of CA activation and the possible application of CAAs in Alzheimer\’s disease and for other memory therapies are also treated.

Temperini C, Scozzafava A, Supuran CT.

Università degli Studi di Firenze, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, I-50019 Sesto Fiorentino (Firenze), Italy. claudia.temperini@unifi.it

Fluorescence- and spin-labeled carbonic anhydrase inhibitors.

Carbonic anhydrase IX (hCA IX) is a membrane-associated glycoprotein that is observed in many tumor tissues and is strongly overexpressed by hypoxia conditions. Hypoxia is a clinically important tumor parameter and this enzyme can play an important role as a potential marker of hypoxic tumor and as a therapeutic target too. In the last years, Carbonic Anhydrase IX Inhibitors which possess fluorescent probe were largely used for visualize hypoxic tumor cell lines and for understanding the biological roles of hCA IX in acidification of the external matrix. Here we resume the development pathways of such compounds from the design to the final biological evaluation. Furthermore, spin-labeled CAIs were included to have a complete overview of the potentiality of this enzyme as marker of hypoxic tumors.

Cecchi A, Supuran CT.

Università degli Studi di Firenze, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, I-50019 Sesto Fiorentino (Firenze), Italy. alessandro.cecchi@unifi.it

Cancer-associated carbonic anhydrases and their inhibition.

Cells of the growing tumor tissue are exposed to physiological stresses connected with insufficient delivery of oxygen (hypoxia) and accumulation of acidic products of the glycolytic metabolism (acidosis). Adaptation to these microenvironmental stresses involves remodeling of the cellular expression program mediated by hypoxia-inducible factor (HIF), which activates broad array of genes functionally involved in angiogenesis, anaerobic glycolysis, de-adhesion, invasion etc. This leads to increased aggressiveness of tumors, metastatic spread and poor response to therapy. Genes coding for transmembrane carbonic anhydrase (CA) isoforms IX and XII are induced in response to low oxygen as a part of the hypoxic transcriptome. Moreover, CA IX is a direct target of HIF and serves as a surrogate marker of hypoxia and prognostic indicator. Its expression is strongly linked to different types of tumors with the HIF pathway activated due to genetic defect or physiological hypoxia. CA IX (and possibly also CA XII) is participates in pH regulation, which is important for survival of hypoxic cells. Both enzymes are therefore promising therapeutic molecules targetable by inhibitors of CA activity. Some of these sulfonamide compounds and their derivatives are capable to block CA-mediated pH regulation in hypoxia. This review summarizes research data related to distribution, regulation and functional aspects of CA IX and CA XII, and describes emerging possibilities for clinical exploitation of CA inhibitors as imaging tools and anticancer drugs.

Pastorekova S, Zatovicova M, Pastorek J.

Center of Molecular Medicine, Institute of Virology, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovak Republic. virusipa@savba.sk

Carbonic anhydrase inhibition: insight into non-COX-2 pharmacological effect of some coxibs.

Nonsteroidal anti-inflammatory drugs (NSAIDs) represent the most commonly used medications for the treatment of pain and inflammation, but numerous well-described adverse drug reactions (ADRs) limit their use. These drugs act via the inhibition of cyclooxygenase (COX) enzyme of which at least two isoforms were described: COX-1 which plays important roles in homeostatic processes such as thrombogenesis and homeostasis of the gastrointestinal tract and kidneys and COX-2 expressed in pathological conditions such as inflammation or cancer proliferation. Selective COX-2 inhibitors or \”coxibs\” were initially developed as a therapeutic strategy to avoid not only the gastrointestinal but also the renal and cardiovascular side effects of non specific NSAIDs. However, this class of drug did not fulfill all their promises. Indeed, numerous unexpected side effects have limited their use and some of them have been withdrawn or suspended from the market for different safety reasons including cardiovascular, hepatic and skin adverse reactions. For instance, cardiovascular warnings have been applied to the whole class of coxibs and more recently for all classical NSAIDs as well. However, differences in the chemical structures should be taken into consideration in order to discriminate between coxibs and the development of some ADRs of which renal events and hypertension. The aim of this paper is to focus on the differences in chemical structures of all marketed COX-2 inhibitors and their unexpected effects on carbonic anhydrase in order to provide non-COX-2 mechanistic insights into some of the differences observed between coxibs.

Dogné JM, Thiry A, Supuran CT.

University of Namur, Drug Design and Discovery Center, Department of Pharmacy, 61 rue de Bruxelles, 5000 Namur, Belgium. jean-michel.dogne@dundp.ac.be

Recent advances in research on the most novel carbonic anhydrases, CA XIII and XV.

The carbonic anhydrase (CA) enzyme family consists of thirteen active isozymes in mammals. The most recently characterized members of this family are cytosolic CA XIII and membrane-bound CA XV. This article describes recent advances in the CA family, especially CA XIII and XV. We have also included catalytic activity data on human CA XIII and mouse CA XV. Additionally, the inhibition constants of acetazolamide toward these isozymes were determined to be k(cat) = 1.5 x 10(5) s(-1), k(cat)/K(M) = 1.1 x 10(7) M(-1) s(-1) and K(I) = 16 nM for human CA XIII and k(cat) = 4.7 x 10(5) s(-1), k(cat)/K(M) = 3.3 x 10(7) M(-1) s(-1) and K(I) = 72 nM for mouse CA XV. Although the activity of CA XIII is the second lowest reported thus far for any of the human CAs, it may have a role in maintaining the acid-base balance in the kidney and the gastrointestinal and reproductive tracts. CA XV is an exceptional enzyme, as it seems to be active in numerous species, such as rodents, birds and fish, but is absent from humans and chimpanzees. Mouse CA XV is a moderately active enzyme, suggesting that it may play a physiological role at least in the kidney. It is likely that other isozymes have substituted for this protein in humans. In addition to the novel data on CA XIII and XV, we present the catalytic activities as well as inhibition constants of acetazolamide for all mammalian CA isozymes in this review.

Hilvo M, Innocenti A, Monti SM, De Simone G, Supuran CT, Parkkila S.

Institute of Medical Technology, University of Tampere, Biokatu 6, FIN-33014 University of Tampere, Finland. Mika.Hilvo@uta.fi

Anticonvulsant sulfonamides/sulfamates/sulfamides with carbonic anhydrase inhibitory activity: drug design and mechanism of action.

The marketed antiepileptic drugs can not solve entirely the problem of seizure in patients suffering from refractory epilepsies. Therefore, new anticonvulsant compounds structurally and pharmacologically different of the currently prescribed drugs are needed. Carbonic anhydrase (CA) inhibitors are known to act as anticonvulsant since several decades while the link between CA and seizure is not straightforward. However, the recent discovery that several CA isozymes are expressed in brain and the better knowledge of their physiological/pathological role, lead to the emergence of new CA inhibitors with anticonvulsant effect including: analogues of acetazolamide, analogues of topiramate, aromatic or heterocyclic sulfonamides incorporating valproyl or adamantyl moieties. Different strategies are developed for the design of new more selective CA inhibitors with anticonvulsant properties.

Thiry A, Dogné JM, Supuran CT, Masereel B.

Drug Design and Discovery Center, FUNDP, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium. anne.thiry@fundp.ac.be