Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii

AbstractBackground: The proteins of halophilic archaea require high salt concentrations both for stability and for activity, whereas they denature at low ionic strength. The structural basis for this phenomenon is not yet well understood. The crystal structure of dihydrofolate reductase (DHFR) from Haloferax volcanii (hv-DHFR) reported here provides the third example of a structure of a protein from a halophilic organism. The enzyme is considered moderately halophilic, as it retains activity and secondary structure at monovalent salt concentrations as low as 0.5 M.Results: The crystal structure of hv-DHFR has been determined at 2.6 å resolution and reveals the same overall fold as that of other DHFRs. The structure is in the apo state, with an open conformation of the active-site gully different from the open conformation seen in other DHFR structures. The unique feature of hv-DHFR is a shift of the α helix encompassing residues 46–51 and an accompanied altered conformation of the ensuing loop relative to other DHFRs. Analysis of the charge distribution, amino acid composition, packing and hydrogen-bonding pattern in hv-DHFR and its non-halophilic homologs has been performed.Conclusions: The moderately halophilic behavior of hv-DHFR is consistent with the lack of striking structural features expected to occur in extremely halophilic proteins. The most notable feature of halophilicity is the presence of clusters of non-interacting negatively charged residues. Such clusters are associated with unfavorable electrostatic energy at low salt concentrations, and may account for the instability of hv-DHFR at salt concentrations lower than 0.5 M. With respect to catalysis, the open conformation seen here is indicative of a conformational transition not reported previously. The impact of this conformation on function and/or halophilicity is unknown

Protein Dynamics and its Correlation to Protein Activity and Stability

The aim of this thesis is to investigate the role of fast protein dynamics (picosecond timescale) in enzyme activity and stability, and specifically to test the hypothesis that enzyme activity and stability are inversely related by their internal dynamics. Activity Dynamics (flexibility) 1/Stability In order to test this hypothesis, the well known anti-cancer drug: methotrexate was used as an informative ligand in the network established between these properties. A multidisciplinary approach combining neutron scattering, circular dichroism, UV absorption, isothermal titration calorimetry and X-ray crystallography was undertaken to examine the current paradigm using the enzyme: dihydrofolate reductase as a model. As inferred by neutron spectroscopy, the binding of MTX influences the dynamical behavior of DHFR. Macromolecular dynamics such as the resilience: lt;kgt; (i.e. structural rigidity) was found to be increased and, inversely, the flexibility decreased upon MTX binding. In addition, as revealed by circular dichroism, this dynamical dependency upon MTX binding was correlated with an enhanced thermal stability. Compared to the free enzyme, the melting temperature was found to be increased by 13.8 C in the presence of MTX. The inhibitory power of MTX was also examined by steady state kinetics and isothermal titration calorimetry. The Ki for MTX was found to be in the nanomolar range Ki= 10.9 nM. Using isothermal titration calorimetry, the binding thermodynamic signature between MTX and DHFR was characterized. The binding event was found to be largely favourable (DGb=-12.1 Kcal mol-1), enthalpy driven (DHb= -16.8 Kcal mol-1) with an unfavourable entropy DSb=-15.6 cal K-1mol-1. In conclusion, the modulation of the macromolecular dynamics may reflect how specific conformations are favoured for subsequent protein function in response of the binding of specific ligand and how conformational substates approach to protein function. In this context the unprecedented power of transition state analogs such as MTX on protein function might therefore be dependent on fast protein dynamics

Directed evolution of human dihydrofolate reductase: towards a better understanding of binding at the active site

La dihydrofolate réductase humaine (DHFRh) est une enzyme essentielle à la prolifération cellulaire, ce qui en fait une cible de choix pour le traitement de différents cancers. À cet effet, plusieurs inhibiteurs spécifiques de la DHFRh, les antifolates, ont été mis au point : le méthotrexate (MTX) et le pemetrexed (PMTX) en sont de bons exemples. Malgré l’efficacité clinique certaine de ces antifolates, le développement de nouveaux traitements s’avère nécessaire afin de réduire les effets secondaires liés à leur utilisation. Enfin, dans l’optique d’orienter la synthèse de nouveaux composés inhibiteurs des DHFRh, une meilleure connaissance des interactions entre les antifolates et leur enzyme cible est primordiale. À l’aide de l’évolution dirigée, il a été possible d’identifier des mutants de la DHFRh pour lesquels l’affinité envers des antifolates cliniquement actifs se voyait modifiée. La mutagenèse dite ¬¬de saturation a été utilisée afin de générer des banques de mutants présentant une diversité génétique au niveau des résidus du site actif de l’enzyme d’intérêt. De plus, une nouvelle méthode de criblage a été mise au point, laquelle s’est avérée efficace pour départager les mutations ayant entrainé une résistance aux antifolates et/ou un maintient de l’activité enzymatique envers son substrat natif, soient les phénotypes d’activité. La méthode de criblage consiste dans un premier temps en une sélection bactérienne à haut débit, puis dans un second temps en un criblage sur plaques permettant d’identifier les meilleurs candidats. Plusieurs mutants actifs de la DHFRh, résistants aux antifolates, ont ainsi pu être identifiés et caractérisés lors d’études de cinétique enzymatique (kcat et IC50). Sur la base de ces résultats cinétiques, de la modélisation moléculaire et des données structurales de la littérature, une étude structure-activité a été effectuée. En regardant quelles mutations ont les effets les plus significatif sur la liaison, nous avons commencé à construire un carte moléculaire des contacts impliqués dans la liaison des ligands. Enfin, des connaissances supplémentaires sur les propriétés spécifiques de liaison ont put être acquises en variant l’inhibiteur testé, permettant ainsi une meilleure compréhension du phénomène de discrimination du ligand.Human dihydrofolate reductase (hDHFR) is an essential enzyme for cellular proliferation and it has long been the target of antifolate drugs for the treatment of various types of cancer. Despite the clinical effectiveness of current antifolate treatments, new drugs are required to reduce the side-effects associated with their use. An essential requirement for design of new antifolates is a better understanding of how these drugs interact with their targets. We applied directed evolution to identify mutant hDHFR variants with modified binding to some clinically relevant antifolates. A saturation mutagenesis approach was used to create genetic diversity at active-site residues of hDHFR and a new, efficient screening strategy was developed to identify the amino acids that preserved native activity and/or conferred antifolate resistance. The screening method consists in a high-throughput first-tier bacterial selection coupled with a second-tier in vitro assay that allows for rapid detection of the best variants among the leads, according to user-defined parameters. Many active, antifolate-resistant mutants of hDHFR were identified. Moreover, the approach has proven efficient in rapidly assessing kinetic (kcat) and inhibition parameters of the hDHFR variants (IC50). Structure-function relationship analysis based on kinetic investigation, available structural and functional data as well as modeling were performed. By monitoring which mutations have the greatest effect on binding, we have begun to build a molecular picture of the contacts involved in drug binding. By varying the drugs we test against, we gain a better understanding of the specific binding properties that determine ligand discrimination

Scanning probe and optical tweezer investigations of biomolecular interactions

A complex array of intermolecular forces controls the interactions between and within biological molecules. The desire to empirically explore these fundamental forces has led to the development of several biophysical techniques. Of these, the atomic force microscope (AFM) and the optical tweezers have been employed throughout this thesis to monitor the intermolecular forces involved in biomolecular interactions. The AFM is a well-established force sensing technique capable of measuring biomolecular interactions at a single molecule level. However, its versatility has not been extrapolated to the investigation of a drug-enzyme complex. The energy landscape for the force induced dissociation of the DHFR-methotrexate complex was studied. Revealing an energy barrier to dissociation located ~0.3nm from the bound state. Unfortunately, the AFM has a limited range of accessible loading rates and in order to profile the complete energy landscape alternative force sensing instrumentation should be considered, for example the BFP and optical tweezers. Thus, this thesis outlines the development and construction of an optical trap capable of measuring intermolecular forces between biomolecules at the single molecule level. To demonstrate the force sensing abilities of the optical set up, proof of principle measurements were performed which investigate the interactions between proteins and polymer surfaces subjected to varying degrees of argon plasma treatment. Complementary data was gained from measurements performed independently by the AFM. Changes in polymer resistance to proteins as a response to changes in polymer surface chemistry were detected utilising both AFM and optical tweezers measurements. Finally, the AFM and optical tweezers were employed as ultrasensitive biosensors. Single molecule investigations of the antibody-antigen interaction between the cardiac troponin I marker and its complementary antibody, reveals the impact therapeutic concentrations of heparin have up on the association and dissociation of the complex. In the thesis the AFM and optical tweezers independently provide complementary data towards the understanding of biomolecular interactions

Scanning probe and optical tweezer investigations of biomolecular interactions

A complex array of intermolecular forces controls the interactions between and within biological molecules. The desire to empirically explore these fundamental forces has led to the development of several biophysical techniques. Of these, the atomic force microscope (AFM) and the optical tweezers have been employed throughout this thesis to monitor the intermolecular forces involved in biomolecular interactions. The AFM is a well-established force sensing technique capable of measuring biomolecular interactions at a single molecule level. However, its versatility has not been extrapolated to the investigation of a drug-enzyme complex. The energy landscape for the force induced dissociation of the DHFR-methotrexate complex was studied. Revealing an energy barrier to dissociation located ~0.3nm from the bound state. Unfortunately, the AFM has a limited range of accessible loading rates and in order to profile the complete energy landscape alternative force sensing instrumentation should be considered, for example the BFP and optical tweezers. Thus, this thesis outlines the development and construction of an optical trap capable of measuring intermolecular forces between biomolecules at the single molecule level. To demonstrate the force sensing abilities of the optical set up, proof of principle measurements were performed which investigate the interactions between proteins and polymer surfaces subjected to varying degrees of argon plasma treatment. Complementary data was gained from measurements performed independently by the AFM. Changes in polymer resistance to proteins as a response to changes in polymer surface chemistry were detected utilising both AFM and optical tweezers measurements. Finally, the AFM and optical tweezers were employed as ultrasensitive biosensors. Single molecule investigations of the antibody-antigen interaction between the cardiac troponin I marker and its complementary antibody, reveals the impact therapeutic concentrations of heparin have up on the association and dissociation of the complex. In the thesis the AFM and optical tweezers independently provide complementary data towards the understanding of biomolecular interactions

Mutagénèse semi-aléatoire au site actif de la DHFR humaine : création et caractérisation de variantes hautement résistantes au MTX

La dihydrofolate réductase humaine (DHFRh) est une enzyme essentielle à la prolifération cellulaire. Elle réduit le dihydrofolate en tétrahydrofolate, un co-facteur impliqué dans la biosynthèse des purines et du thymidylate. La DHFRh est une cible de choix pour des agents de chimiothérapie comme le méthotrexate (MTX), inhibant spécifiquement l’enzyme ce qui mène à un arrêt de la prolifération et ultimement à la mort cellulaire. Le MTX est utilisé pour le traitement de plusieurs maladies prolifératives, incluant le cancer. La grande utilisation du MTX dans le milieu clinique a mené au développement de mécanismes de résistance, qui réduisent l’efficacité de traitement. La présente étude se penche sur l’un des mécanismes de résistance, soit des mutations dans la DHFRh qui réduisent son affinité pour le MTX, dans le but de mieux comprendre les éléments moléculaires requis pour la reconnaissance de l’inhibiteur au site actif de l’enzyme. En parallèle, nous visons à identifier des variantes plus résistantes au MTX pour leur utilisation en tant que marqueurs de sélection en culture cellulaire pour des systèmes particuliers, tel que la culture de cellules hématopoïétiques souches (CHS), qui offrent des possibilités intéressantes dans le domaine de la thérapie cellulaire. Pour étudier le rôle des différentes régions du site actif, et pour vérifier la présence d’une corrélation entre des mutations à ces régions et une augmentation de la résistance au MTX, une stratégie combinatoire a été dévelopée pour la création de plusieurs banques de variantes à des résidus du site actif à proximité du MTX lié. Les banques ont été sélectionnées in vivo dans un système bactérien en utilisant des milieux de croissance contenant des hautes concentrations de MTX. La banque DHFRh 31/34/35 généra un nombre considérable de variantes combinatoires de la DHFRh hautement résistantes au MTX. Les variantes les plus intéressantes ont été testées pour leur potentiel en tant que marqueur de sélection dans plusieurs lignées cellulaires, dont les cellules hématopoïétiques transduites. Une protection complète contre les effets cytotoxiques du MTX a été observée chez ces cellules suite à leur infection avec les variantes combinatoires. Pour mieux comprendre les causes moléculaires reliées à la résistance au MTX, des études de structure tridimensionnelle de variantes liées au MTX ont été entreprises. La résolution de la structure de la double variante F31R/Q35E lié au MTX a révélé que le phénotype de résistance était attribuable à d’importantes différences entre le site actif de la double variante et de l’enzyme native, possiblement dû à un phénomème dynamique. Une compréhension plus générale de la reconnaissance et la résistance aux antifolates a été réalisée en comparant des séquences et des structures de variantes de la DHFR résistants aux antifolates et provenant de différentes espèces. En somme, ces travaux apportent de nouveaux éléments pour la comprehension des intéractions importantes entre une enzyme et un ligand, pouvant aider au développement de nouveaux antifolates plus efficaces pour le traitement de diverses maladies. De plus, ces travaux ont généré de nouveaux gènes de résistance pouvant être utilisés en tant que marqueurs de sélection en biologie cellulaire.Human dihydrofolate reductase (hDHFR) is an enzyme that is essential to cell proliferation. It reduces dihydrofolate to tetrahydrofolate, an important cofactor involved in purine and thymidylate biosynthesis. hDHFR is a choice target for chemotherapeutic drugs like methotrexate (MTX), which specifically inhibits the enzyme, stopping cell proliferation and leading to cellular death. MTX is used for the treatment of many proliferative diseases, including cancers. Widespread use of MTX has lead to the development of resistance mechanisms appear which impair treatment efficiency. The present work focuses on a mechanism of resistance, namely mutations in hDHFR that reduce its affinity for MTX, to better understand the underlying mechanisms of inhibitor recognition at the active site of the enzyme. In parallel, we aim at identifying the most MTX-resistant variants to offer novel selectable markers for particular cell culture systems, such as hematopoietic cell culture, which offer important perspectives for cellular therapy. To study the role of different regions of the hDHFR active site, and to verify if a correlation exists between mutations in these regions and increased resistance to MTX, a combinatorial strategy was developed enabling the creation of several hDHFR variant libraries at active site residues located in proximity to bound MTX. The libraries were selected in vivo in a bacterial system using culture media containing high concentration of the inhibitor. One library in particular, hDHFR 31/34/35, yielded a considerable number of highly MTX-resistant combinatorial hDHFR variants. The most interesting candidates were tested for their potential as selectable markers in various cell lines, including transduced hematopoietic cells. Complete protection from MTX-cytotoxicity was obtained for these cells following infection with the combinatorial variants. To better understand the molecular causes of MTX resistance, resolution of the crystal structures of variant proteins in presence of MTX was attempted. Resolution of the F31R/Q35E double variant revealed that the resistance phenotype was related to important differences in the active site relative to WT, possibly attributable to a dynamic motion effect. A more general comprehension of antifolate recognition and resistance was achieved by sequence and structural comparison of antifolate-resistant DHFR variants from different species. Overall, our work contributes to the better understanding of enzyme-inhibitor interactions, which could provide new insights into the development of more efficient clinical therapies. In addition, this work has yielded novel drug-resistance genes useful as selectable markers for cellular biology

Synthesis and Molecular Modeling Studies of Bicyclic Inhibitors of Dihydrofolate Reductase, Receptor Tyrosine Kinases and Tubulin

The results from this work are reported into two sections listed below: Synthesis: Following structural classes of compounds have been designed, synthesized and studied as inhibitors of pjDHFR, RTKs and tubulin: 1. 2,4-Diamino-6-(substituted-arylmethyl)pyrido[2,3-d]pyrimidines 2. 4-((3-Bromophenyl)linked)-6-(substituted-benzyl)-7H-pyrrolo[2,3-d]pyrimidin-2-amines 3. 6-Methyl-5-((substitutedphenyl)thio)-7H-pyrrolo[2,3-d]pyrimidin-2-amines A total of 35 new compounds (excluding intermediates) were synthesized, characterized and submitted for biological evaluation. Results from these studies will be presented in due course. Bulk synthesis of the potent lead compound 170 was carried out to facilitate in vivo evaluation. Docking Studies Docking studies were performed using LeadIT, MOE, Sybyl or Flexx for target compounds listed above and for other compounds reported by Gangjee et al. against the following targets: 1. Dihydrofolate reductase: human, P. carinii, P. jirovecii (pjDHFR) and T. gondii (tgDHFR) 2. Thymidylate synthase: human (hTS) and T. gondii (tgTS) 3. Receptor tyrosine kinases: VEGFR2, EGFR and PDGFR-β 4. Colchicine binding site of tublulin. Novel homology models were generated and validated for pjDHFR, tgDHFR, tgTS, PDGFR-β and the F36C L65P pjDHFR double mutant. The tgTS homology model generated in this study and employed to design novel inhibitors shows remarkable similarity with the recently published X-ray crystal structures. Docking studies were performed to provide a molecular basis for the observed activity of target compounds against DHFR, RTKs or tubulin. Results from these studies support structure-based and ligand-based medicinal chemistry efforts in order to improve potency and/or selectivity of analogs of the docked compounds against these targets. Novel topomer CoMFA models were developed for tgTS and hTS using a set of 85 bicyclic inhibitors and for RTKs using a set of 60 inhibitors reported by Gangjee et al. The resultant models could be used to explain the potency and/or selectivity differences for selected molecules for tgTS over hTS. Topomer CoMFA maps show differences in steric and/or electronic requirements among the three RTKs, and could be used, in conjuction with other medicinal chemistry approaches, to modulate the selectivity and/or potency of inhibitors with multiple RTK inhibitory potential. Drug design efforts that involve virtual library screening using these topomer CoMFA models in conjunction with traditional medicinal chemistry techniques and docking are currently underway

Development of Potent and Selective Inhibitors of Mycobacterium Tuberculosis, Plasmodium Falciparum and Staphylococcus Aureus Dihydrofolate Reductase

The goal of this study was to develop drugs that exclusively affect pathogenic dihydrofolate reductase (DHFR) without causing harm to the human counterpart. To achieve that goal, a well-known dihydrofolate reductase (DHFR) inhibitors, trimethoprim (TMP), methotrexate (MTX) and trimetrexate (TMQ), were modified, tested, and crystallized on Mycobacterium tuberculosis (Mtb) dihydrofolate reductase (DHFR), wild type and quadruple mutant Plasmodium falciparum (Pf) DHFR-thymidylate synthase (TS), Staphylococcus aureus DHFR, and human DHFR. We focused on the drug design to utilize the structural differences between the pathogenic DHFRs and the human DHFR; specifically, we focused on a pocket near the substrate binding site where Asp27 and Gln28 of Mtb DHFR, and Asp54 and Met55 of Pf DHFR-TS are located. The same site is closely packed in human DHFR. From the initial screening and designing process, C-8 benzyl-2,4-diaminoquinazoline TMQ analogs were found to have outstanding selectivity against Mtb and Pf DHFR. Co-crystal structures of C-8 benzyl TMQ analogs with Mtb and Pf DHFR showed that the flexibility of Gln28 in Mtb DHFR, and Met55 in Pf DHFR contributes to extra space and interaction with C-8 benzyl moiety. This flexibility, which is not available in the human DHFR, enables the TMQ analogs to bind exclusively to the pathogenic DHFRs. Our novel C-8 benzyl-2,4-diaminoquinazoline TMQ analogs exhibited great potency and selectivity toward pathogenic DHFRs. In addition, these C-8 benzyl-2,4-diaminoquinazoline TMQ analogs were potent on Staphylococcus aureus DHFR as well and we hypothesize based on our findings that our C-8 benzyl-2,4-diaminoquinazoline TMQ analogs have potential for selective, broad spectrum antimicrobials against whose DHFR share the common structural feature with Mtb or Pf DHFR, an acid residue and a flexible residue next to it

Structural analysis and discovery of lead compounds for the fungal methionine synthase enzyme

textMethionine synthases catalyze methyl transfer from 5-methyl-tetrahydrofolate (5-methyl-THF) to L-homocysteine (Hcy) in order to generate methionine (Met). Mammals, including humans, use a cobalamin dependent form, while fungi use a cobalamin independent protein called Met6p. The large structural differences between them make Met6p a potential anti-fungal drug target. Met6p is a 90 kDa protein with the active site located between two (βα)₈ barrels. The active site has a catalytic Zn²+ and binding sites for the two substrates, Hcy and folate. I present the crystal structures of three engineered variants of the Met6p enzyme from Candida albicans. I also solved Met6p in complex with several substrate and product analogs, including Hcy, Met, Gln, 5-methyl-THF-Glu₃ and Methotrexate-Glu₃ (MTX-Glu₃), and the bi-dentate ligand S-adenosyl homocysteine. Also described is a new fluorescence-based activity assay monitoring Hcy. Lastly, a high-throughput Differential Scanning Fluorimetry (DSF) assay was used to screen thousands of compounds in order to identify ligands which bind Met6p. My work details the mode of interaction of Hcy and folate with the Met6p protein. Several residues important to activity were discovered, like Asn 126 and Tyr 660, and proven to be important by site directed mutagenesis. Structural analysis revealed an important aspect of the mechanism. When Hcy binds to its pocket it makes strong ion pairs with the enzyme. In particular, 614 moves toward the substrate amine and triggers a rearrangement of active site loops; this draws the catalytic Zn²+ toward the Hcy thiol where a new ligand bond is formed, activating the thiol for methyl transfer. The work presented here lays the groundwork for structure based drug design and makes the development of Met6p specific bi-dentate ligands feasible. The fluorescence based activity assay I developed was successfully used to test the folate analog MTX-Glu₃, which inhibits with an IC₅₀ of ~4 mM. I also discovered our first bi-dentate ligand in the form of S-adenosyl homocysteine.Cellular and Molecular Biolog