<p>In silico ligand docking is a versatile and common technique when predicting ligands and inhibitors for protein binding sites. The various docking programmes aim to calculate binding energies and to predict interactions, thus identifying potential ligands.The currently available programmes lack satisfying means by which to account for structural water molecules which can either mediate protein-ligand contacts or be displaced upon ligand binding. The present project aims to generate data to facilitate the global work of developing scoring functions in docking programmes to account for structural water molecules contribution to ligand binding to fill the said void. This is done by validating the performance of docking using a simple model system (cytochrome C peroxidase (CCP) W191G) containing four well ordered, deeply buried structural water molecules which are known to either interact with a ligand or to be displaced upon ligand binding.Known ligands were docked into eight (crystallographically determined) receptor set-ups comprising the receptor and no, one or two of the water molecules. The performance was validated by comparison of the binding modes of the docked ligands and the crystal structures, comparison of docking scores of the ligands in the different set-ups, enrichment of the ligands from a database of decoys and finally by predicting new ligands from the decoy database. In addition a high resolution crystal structure of CCP W191G in complex with 3-aminopyridine (3AP) was determined in order to resolve ambiguities in the binding mode of this ligand.</p>

Over a billion individuals worldwide suffer from neglected diseases. This equates to approximately one-sixth of the human population. These infections are often endemic in remote tropical regions of impoverished populations where vectors can flourish and infected individuals cannot be effectively treated due to a lack of hospitals, medical equipment, drugs, and trained personnel. The few drugs that have been approved for the treatments of such illnesses are not widely used because they are riddled with inadequate implications of cost, safety, drug availability, administration, and resistance. Hence, there exists an eminent need for the design and development of improved new therapeutics. Influential world-renowned scientists in the Consortium for Parasitic Drug Development (CPDD) have preformed extensive biological testing for compounds active against parasites that cause neglected diseases. These data were acquired through several collaborations and found applicable to computational studies that examine quantitative structure-activity relationships through the development of predictive models and explore structural relationships through docking. Both of these in silico tools can contribute to an understanding of compound structural importance for specific targets. The compilation of manuscripts presented in this dissertation focus on three neglected diseases: trypanosomiasis, Chagas disease, and leishmaniasis. These diseases are caused by kinetoplastid parasites Trypanosoma brucei, Trypanosoma cruzi, and Leishmania spp., respectively. Statistically significant predictive devices were developed for the inhibition of the: (1) T. brucei P2 nucleoside transporter, (2) T. cruzi parasite at two temperatures, and (3) two species of Leishmania. From these studies compound structural importance was assessed for the targeting of each parasitic system. Since these three parasites are all from the Order Kinetoplastida and the kinetoplast DNA has been determined a viable target, compound interactions with DNA were explored to gain insight into binding modes of known and novel compounds.

Supply chain network design involves location decisions for production facilities and distribution centers. We consider a make-to-order supply chain environment where distribution centers serve as crossdocking terminals. Long waiting times may occur at a cross-docking terminal, unless sucient handling capacity is installed. In this study, we deal with a facility location problem with congestion eects at distribution centers. Along with location decisions, we make capacity allocation (service rate) and demand allocation decisions so that the total cost, including facility opening, transportation and congestion costs, is minimized. Response time to customer orders is a critical performance measure for a supply chain network. The decisions like where the plants and distribution centers are located aect the response time of the system. Response time is more sensitive to these decisions in a make-to-order business environment. In a distribution network where distribution centers function as cross-docking terminals, capacity or the service rate decisions also aect the response time performance. This study is closely related to a recent work Vidyarthi et al. (2009) which models distribution centers asM/G/1 queuing systems. They use the average waiting time formula ofM/G/1 queuing model. Thus, the average waiting time at a distribution center is a nonlinear function of the demand rate allocated to and the service rate available at the distribution center. The authors Vidyarthi et al. (2009) propose a linear approximation approach and a Lagrangian based heuristic for the problem. Dierent than the solution approach proposed in Vidyarthi et al. (2009), we propose a closed form formulation for the problem. In particular, we show that the waiting time function derived from M/G/1 queuing model can be represented via second order conic inequalities. Then, the problem becomes a mixed integer second order cone programming problem which can be solved by using commercial branch-and-bound software such as IBM ILOG CPLEX. Our computational tests show that proposed reformulation can be solved in reasonable CPU times for practical size instances.

In silico studies of the effect of phenolic compounds from grape seed extracts on the activity of phosphoinositide 3-kinase (PI3K) and farnesoid X receptor (FXR)Montserrat Vaqué Marquès En aquesta tesis es pretén aplicar metodologies computacionals (generació de farmacòfors i docking proteïna lligand) en l'àmbit de la nutigenòmica (ciència que pretén entendre, a nivell molecular, com els nutrients afecten la salut). S'aplicaran metodologies in silico per entendre a nivell molecular com productes naturals com els compostos fenòlics presents en la nostra dieta, poden modular la funció d'una diana comportant un efect en la salut. Aquest efecte es creu que podria ser degut a la seva interacció directa amb proteïnes de vies de senyalització molecular o bé a la modificació indirecta de l'expressió gènica. Donat que el coneixement de l'estructura del complex lligand-receptor és bàsic per entendre el mecanisme d'acció d'aquests lligands s'aplica la metodologia docking per predir l'estructura tridimensional del complex. En aquest sentit, un dels programes de docking és AutoGrid/AutoDock (un dels més citats). No obstant, l'automatització d'AutoGrid/AutoDock no és trivial tan per (a) la cerca virtual en una llibreria de lligands contra un grup de possibles receptors, (b) l'ús de flexibilitat, i (c) realitzar un docking a cegues utilitzant tota la superfície del receptor. Per aquest motiu, es dissenya una interfície gràfica de fàcil ús per utilitzar AutoGrid/AutoDock. Blind Docking Tester (BDT) és una aplicació gràfica que s'executa sobre quatre programes escrits en Fortran i que controla les condicions de les execucions d'AutoGrid i AutoDock. BDT pot ser utilitzat per equips d'investigadors en el camp de la química i de ciències de la vida interessats en dur a terme aquest tipus d'experiments però que no tenen suficient habilitats en programació. En la modulació del metabolisme de la glucosa, treballs in vivio i in vitro en el nostre grup de recerca s'han atribuït els efectes beneficiosos de l'extracte de pinyol de raïm en induir captació de glucosa (punt crític pel manteniment de l'homeostasis de la glucosa). No obstant alguns compostos fenòlics no tenen efecte en la captació de la glucosa, d'altres l'inhibeixen reversiblement. En alguns casos aquesta inhibició és el resultat de la competició dels compostos fenòlics amb ATP pel lloc d'unió de l'ATP de la subunitat catalítica de la fosfatidil inositol 3-kinasa (PI3K). Estudis recents amb inhibidors específics d'isoforma han identificat la p110&#945; (la subunitat catalítica de PI3K&#945;) com la isoforma crucial per la captació de glucosa estimulada per insulina en algunes línies cel·lulars. Els programes computacionals han estat aplicats per tal de correlacionar l'activitat biològica dels compostos fenòlics amb informació estructural per obtenir una relació quantitativa estructura-activitat (3D-QSAR) i obtenir informació dels requeriments estructura-lligand per augmentar l'afinitat i/o selectivitat amb la diana (proteïna). Tot hi haver-se demostrat que l'adició d'extractes de compostos fenòlics en l'aliment pot tenir en general un benefici per la salut, s'ha de tenir en compte que l'estudi 3D-QSAR (construït a partir d'inhibidors sintètics de p110&#945;) prediu que algunes d'aquestes molècules poden agreujar la resistència a la insulina en individus susceptibles dificultant la capatació de glucosa en múscul i teixit adipós i, per tant, produir un efecte secundari indesitjat. Resultats en el nostre grup de recerca han demostrat que compostos fenòlics presents en extractes de llavor de raïm incrementen l'activitat del receptor "farnesoid x receptor" (FXR) de manera dosi depenent quan el lligand natural de FXR (CDCA) és present. Les metodologies in silico, docking i 3D-QSAR, han estat aplicades juntament amb dades biològiques d'agonistes no esteroidals de FXR que s'uneixen a un lloc d'unió proper però diferent al lligand esteroidal 6CDCA. Els resultats han mostrat que els compostos fenòlics no són capaços d'activar FXR per ells mateixos però poden afegir noves interaccions que estabilitzarien la conformació activa de FXR en presència del lligand natural CDCA. Els compostos fenòlics podrien induir canvis conformacionals específics que augmentarien l'activitat de FXR. In silico studies of the effect of phenolic compounds from grape seed extracts on the activity of phosphoinositide 3-kinase (PI3K) and farnesoid X receptor (FXR)Montserrat Vaqué Marquès This thesis was written with the aim of applying computational methods that have already been developed for molecular design and simulation (i.e. pharmacophore generation and protein-ligand docking) to nutrigenomics. So, in silico tools that are routinely used by the pharmaceutical industry to develop drugs have been used to understand, at the molecular level, how natural products such as phenolic compounds (i.e. molecules that are commonly found in fruits and vegetables) can improve health and prevent diseases. Therefore, we first focused on predicting the structure of protein-ligand complexes. The docking algorithms can use the individual structures from receptor and ligand to predict (1) whether they can form a complex and (2) if so, the structure of the resulting complex. This prediction can be made, for instance, with AutoGrid/AutoDock, the most cited docking software in the literature. The automation of AutoGrid/AutoDock is not trivial for tasks such as (1) the virtual screening of a library of ligands against a set of possible receptors; (2) the use of receptor flexibility and (3) making a blind-docking experiment with the whole receptor surface. Therefore, in order to circumvent these limitations, we have designed BDT (i.e. blind-docking tester; http://www.quimica.urv.cat/~pujadas/BDT), an easy-to-use graphic interface for using AutoGrid/AutoDock. BDT is a Tcl/Tk graphic front-end application that runs on top of four Fortran programs and which controls the conditions of the AutoGrid and AutoDock runs. As far as the modulation of the glucose metabolism is concerned, several in vivo and in vitro results obtained by our group have shown that grape seed procyanidin extracts (GSPE) stimulate glucose uptake in 3T3-L1 adipocytes and thus help to maintain their glucose homeostasis. In contrast, it is also well known that although some phenolic compounds do not affect glucose uptake, others reversibly inhibit it in several cell lines. Moreover, for at least some of these phenolic compounds, this inhibition is the result of their competition with ATP for the ATP-binding site in p110&#945; (i.e. the &#945; isoform of the catalytic subunit of phosphoinositide 3-kinase or PI3K&#945;). Furthermore, recent studies with isoform-specific inhibitors have identified p110&#945; as the crucial isoform for insulin-stimulated glucose-uptake in some cell lines. Therefore, although it has been proved that the addition of phenolic compound extracts to food can have an overall benefit on health, it should be taken into account that some of these molecules may exacerbate insulin resistance in susceptible individuals via impaired glucose uptake in muscle and adipose tissues and, therefore, produce an undesirable side effect. In this context, we have applied computational approaches (i.e. protein-ligand docking and 3D-QSAR) to predict the IC50 (i.e. the concentration that reduces the p110&#945; activity to 50%). Our results agree with previous experimental results and predict that some compounds are potential inhibitors of this enzyme. Recent results in our research group have demonstrated that the phenolic compounds in GSPE increase the activity of the farnesoid X receptor (i.e. FXR) in a dose-dependent way when the natural ligand of FXR (i.e. CDCA) is also present. The phenolic compounds might induce specific conformational changes that increase FXR activity and then contribute to cardioprotection through mechanisms that are independent of their intrinsic antioxidant capacities but that involve direct interaction with FXR to modulate gene expression. Taking into account this hypothesis a 3D-QSAR analysis was made in an attempt to understand how phenolic compounds activate FXR. So, our results explain why phenolic compounds cannot activate FXR by themselves and how they can add new interactions to stabilize the active conformation of FXR when its natural ligand (i.e. CDCA) is present. Therefore, we proposed a mechanism of FXR activation by dietary phenolic compounds in which they may enhance bile acid-bound FXR activity.

Virtual screening is a fast, low cost method to identify potential small molecule therapeutics from large chemical databases for the vast amount of target proteins emerging from the life sciences and bioinformatics. In this work, we applied several conventional and newly developed virtual screening approaches to identify novel non-steroidal ligands for the human and zebrafish sex hormone binding globulin (SHBG). The ‘benchmark set of steroids’ is a set of steroids with known affinities for human SHBG that has been widely used for validation in the development of different virtual screening methods. We have updated this data set by including additional steroidal SHBG ligands and by modifying the predicted binding orientations of several benchmark steroids in the SHBG binding site based on the use of an improved docking protocol and information from recent crystallographic data. The new steroid binding orientations and the expanded version of the benchmark set was then used to create new in silico models which were applied in virtual screening to identify high-affinity non-steroidal human SHBG ligands from a large chemical database. Anthropogenic compounds with the capacity to interact with the steroid-binding site of SHBG pose health risks to humans and other vertebrates including fish. We constructed a homology model of SHBG from zebrafish and applied virtual screening to identify ligands for zebrafish SHBG from a set of 80 000 existing commercial substances, many of which can be exposed to the aquatic environment. Six hits from this in silico screen were tested experimentally for zebrafish SHBG binding and three of them, hexestrol, 4-tert-octylcatechol, dihydrobenzo(a)pyren-7(8H)-one demonstrated micromolar binding affinity for the zebrafish SHBG. These findings demonstrate the feasibility of using virtual screening to identify anthropogenic compounds that may disrupt or highjack functionally important protein:ligand interactions. Studies applying this new computational toxicology method could increase the awareness of hazards posed by existing commercial chemicals at relatively low cost.

Šio darbo tikslas – pirimidino junginių – potencialių karboanhidrazių (CA) slopiklių –kūrimas. Teoriniai 4-[N-(pirimidin-4-il)]aminobenzensulfonamidų, turinčių pakaitus 2-, 5- ir 6-oje pirimidino žiedo padėtyje, sąveikos su aktyviuoju hCA centru tyrimai parodė, kad šie junginiai gali įsiterpti į aktyvųjį baltymo centrą ir su hCA turėtų sąveikauti kaip tipiški klasikiniai CA slopikliai. Tiksliniai 4-[N-(2,5,6-pakeisti pirimidin-4-il)amino]benzensulfonamidai sintetinti 4,6-dichlorpirimidinuose, 5-oje padėtyje turinčiuose cian-, formil- arba nitrogrupes, chloro atomą keičiant 4-aminobenzensulfonamidu. Bendradarbiaujant su Biotechnologijos instituto mokslininkais, kurie atliko hCA slopinimo susintetintais junginiais tyrimus, tobulintos šių junginių hCA slopinimo savybės. Slopiklių struktūros modifikuotos keičiant jungtuko tarp benzensulfonamido ir pirimidino fragmentų ilgį ir įvedant naujus pakaitus pirimidino žiede, kai kuriais atvejais taip sudarant naujas heterociklines sistemas. Šiuo tikslu ištirta pirimidin-5-karbaldehidų kondensacija su indolin-2-tionais. Nustatyta, kad 4-[N-(pirimidin-4-il)amino](metil-,etil-)benzensulfonamidai, 5-oje pirimidino žiedo padėtyje turintys cian-, formil- arba nitrogrupes, o 6-oje pirimidino žiedo padėtyje turintys benzilamino-, chlor-, metoksi- arba oksogrupes, yra nano- – mikromolinės eilės hCA slopikliai, galintys atrankiai slopinti hCAI, II ar XIII. Jų hCA slopinimo aktyvumą lemia sulfonamido grupės sąveika su katalitiniu cinko jonu ir... [toliau žr. visą tekstą] / The aim of the work was design of pyrimidine derivatives – potent carbonic anhydrase (CA) inhibitors. Theoretical investigation of interaction of 4-[N-(pyrimidin-4-yl)]aminobenzenesulfonamides containing substituents at 2-, 5- and 6- positions of pyrimidine ring with an active site of hCAs suggested that these compounds can fit into an active site of the enzymes and should interact with them as typical hCA inhibitors. Synthesis of target compounds was carried out by substitution of chloro group at 4,6-dichloropyrimidines containing cyano-, formyl- or nitro groups at position 5 of the pyrimidine ring with 4-aminobenzenesulfonamide. Regarding inhibition of hCAs with the synthesized compounds data acquired by the scientists of Institute of Biotechnology, structures of inhibitors were modified in order to improve their binding properties to hCA. It was performed by variation of a linker length between benzenesulfonamide and pyrimidine fragments and by introduction of new substituents at position 6 of the pyrimidine ring. In some cases these modifications led to the formation of new heterocyclic systems. For this purpose condensation of indoline-2-thiones with pyrimidine-5-carbaldehydes was investigated. It was determined that 4-[N-(pyrimidin-4-yl)amino](methyl-,ethyl-)benzenesulfonamides containing cyano-, formyl- or nitro groups at position 5 of the pyrimidine ring and benzylamino-, chloro-, methoxy- or oxo groups at position 6 of the pyrimidine ring inhibit hCA in... [to full text]

The aim of the work was design of pyrimidine derivatives – potent carbonic anhydrase (CA) inhibitors. Theoretical investigation of interaction of 4-[N-(pyrimidin-4-yl)]aminobenzenesulfonamides containing substituents at 2-, 5- and 6- positions of pyrimidine ring with an active site of hCAs suggested that these compounds can fit into an active site of the enzymes and should interact with them as typical hCA inhibitors. Synthesis of target compounds was carried out by substitution of chloro group at 4,6-dichloropyrimidines containing cyano-, formyl- or nitro groups at position 5 of the pyrimidine ring with 4-aminobenzenesulfonamide. Regarding inhibition of hCAs with the synthesized compounds data acquired by the scientists of Institute of Biotechnology, structures of inhibitors were modified in order to improve their binding properties to hCA. It was performed by variation of a linker length between benzenesulfonamide and pyrimidine fragments and by introduction of new substituents at position 6 of the pyrimidine ring. In some cases these modifications led to the formation of new heterocyclic systems. For this purpose condensation of indoline-2-thiones with pyrimidine-5-carbaldehydes was investigated. It was determined that 4-[N-(pyrimidin-4-yl)amino](methyl-,ethyl-)benzenesulfonamides containing cyano-, formyl- or nitro groups at position 5 of the pyrimidine ring and benzylamino-, chloro-, methoxy- or oxo groups at position 6 of the pyrimidine ring inhibit hCA in... [to full text] / Šio darbo tikslas – pirimidino junginių – potencialių karboanhidrazių (CA) slopiklių –kūrimas. Teoriniai 4-[N-(pirimidin-4-il)]aminobenzensulfonamidų, turinčių pakaitus 2-, 5- ir 6-oje pirimidino žiedo padėtyje, sąveikos su aktyviuoju hCA centru tyrimai parodė, kad šie junginiai gali įsiterpti į aktyvųjį baltymo centrą ir su hCA turėtų sąveikauti kaip tipiški klasikiniai CA slopikliai. Tiksliniai 4-[N-(2,5,6-pakeisti pirimidin-4-il)amino]benzensulfonamidai sintetinti 4,6-dichlorpirimidinuose, 5-oje padėtyje turinčiuose cian-, formil- arba nitrogrupes, chloro atomą keičiant 4-aminobenzensulfonamidu. Bendradarbiaujant su Biotechnologijos instituto mokslininkais, kurie atliko hCA slopinimo susintetintais junginiais tyrimus, tobulintos šių junginių hCA slopinimo savybės. Slopiklių struktūros modifikuotos keičiant jungtuko tarp benzensulfonamido ir pirimidino fragmentų ilgį ir įvedant naujus pakaitus pirimidino žiede, kai kuriais atvejais taip sudarant naujas heterociklines sistemas. Šiuo tikslu ištirta pirimidin-5-karbaldehidų kondensacija su indolin-2-tionais. Nustatyta, kad 4-[N-(pirimidin-4-il)amino](metil-,etil-)benzensulfonamidai, 5-oje pirimidino žiedo padėtyje turintys cian-, formil- arba nitrogrupes, o 6-oje pirimidino žiedo padėtyje turintys benzilamino-, chlor-, metoksi- arba oksogrupes, yra nano- – mikromolinės eilės hCA slopikliai, galintys atrankiai slopinti hCAI, II ar XIII. Jų hCA slopinimo aktyvumą lemia sulfonamido grupės sąveika su katalitiniu cinko jonu ir... [toliau žr. visą tekstą]

Molecular modelling has become widely used in chemistry and biology. The aim of this project is to use a range of molecular modelling techniques to study enzymic actions. This thesis consists of two parts. Part A of this thesis describes computational studies conducted for the calpain-calpastatin system. Calpain is a cysteine protease. Over-expression of calpain is associated with many diseases. Calpastatin is the naturally occurring specific regulator of calpain activity. In this part of the thesis, the dynamic conformational preferences of region B of the inhibitory domain in calpastatin were examined in detail by using molecular dynamics simulations and stochastic dynamic simulations with Monte Carlo sampling. Part B of the thesis explores the structure and function of the enzyme 3-dexoy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis (MtuDAH7PS). MtuDAH7PS catalyses the first reaction of the shikimate pathway and is a target for the development of anti-tuberculosis drugs. MtuDAH7PS is found to be synergistically inhibited by combinations of aromatic amino acids (Trp+Phe or Trp+Tyr), but not by any single aromatic amino acids. In this part of the thesis, this unique mechanism of allosteric regulation in MtuDAH7PS was investigated by using a range molecular modelling techniques. Firstly protein crystal structure refinements were conducted and those crystal structures of MtuDAH7PS in complex with various ligand molecules are described in Chapter 4. Secondly, the reaction mechanism and roles of active site residues were investigated in Chapter 5, through docking calculations (both rigid docking and induced fit docking) of a series of designed active site inhibitors. Finally, Chapter 6 discusses the molecular basis of the communication mechanism of allosteric regulation in MtuDAH7PS.

No description available.

The exocyst is thought to tether secretory vesicles to specific sites on the plasma membrane. As a member of the exocyst, Sec5 is implicated in cell survival and membrane growth in Drosophila. Little is known of the exocyst function in mammals, with previous work suggesting involvement of exocyst in GTP-dependent exocytosis. Using RNA interference, we stably down-regulated Sec5 in PC12 cells. We found that these knockdown cells exhibit decreased GTP- and Ca2+-dependent exocytosis of dense-core vesicles (DCVs), and contain less proportion of docked vesicles. Expression of Sec6/8 is also slightly reduced in Sec5 knockdown cells. Our results suggest that Sec5 is involved in both GTP- and Ca2+-dependent exocytosis, possibly through the regulation of DCV docking. We also established doxycycline-inducible knockdown system for Sec5 in PC12 cells which may be more appropriate to study development-related proteins. Efforts were also made to re-introduce Sec5 into the Sec5 knockdown cells for rescue purposes.