Ph.d.

The use of peptide drugs has gained popularity recently. Peptides are attractive drug targets due to their high specificity and potency towards their biological targets. A drawback for peptide drugs is a lack of stability for oral delivery. Two classes of disulfide-rich peptides, conotoxins and cyclotides, have been shown to have higher stability than linear peptides thanks to their disulfide connectivity. Conotoxins are present in the venom of cone snails, a carnivorous marine mollusk that preys upon fish, worms, or other mollusks. Conotoxins are promising drugs leads with great prospects in the treatment of diseases and disorders such as chronic pain, multiple sclerosis and Parkinson’s and Alzheimer’s diseases. Cyclotides, which are cyclic cysteine knot containing peptides, isolated from the Violaceae (violet), Rubiaceae (coffee), and Cucurbitaceae (cucurbit) families and they have a wide range of biological activities, such as anti-HIV, uterotonic, and antimicrobial. P-superfamily framework IX conotoxins (C-C- C-CXC- C) contain the same cysteine framework, homologous sequences, and similar 3D structures to cyclotides. The knot containing conotoxins have been identified in several Conus species, but this work focuses on those from Conus brunneus, Conus purpurascens, and Conus gloriamaris. The cysteine knot motif of cyclotides and P-superfamily conotoxins is characterized by a cyclic backbone and six-conserved cysteine residues that form the three-disulfide bridges of the “knot”. This motif provides cyclotides and conotoxins with superior stability against thermal, chemical, and enzymatic degradation; marking them as potential frameworks for peptide drug delivery. Presented are details on the isolation of conotoxins and cyclotides, from Viola tricolor, and the characterization of their activity in the well-characterized Drosophila melanogaster giant fiber system (GFS) neuronal circuit, which contains GAP, acetylcholine, and glutamate synapses. The transcriptomes of two Conus brunneus specimens were assembled and mined for P-superfamily framework IX conotoxins. Eleven mature P-superfamily framework IX conotoxins were identified in the crude venom. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2018. / FAU Electronic Theses and Dissertations Collection

Conotoxins are peptides expressed by the exogenome of more than 800 species of marine mollusks belonging to the genus Conus (cone snails.) Owing to their high specificity and affinity for ion channels, transporter molecules, and cell receptors of the central and peripheral nervous systems, conotoxins have been investigated for nearly four decades. These efforts on conotoxin research made possible the FDA approved use of Ziconitide/Prialt, a conotoxin derived from the venom of Conus magus, which effectively treats patients suffering from severe chronic pain without consequent narcotic effects. Additionally, six other conotoxins have reached clinical trials and many novel ones are being discovered every day. Investigations reported in this dissertation broadens the applicability of conotoxins to non-excitable systems. Here, conotoxins from the dissected venom of the vermivorous cone snail Conus nux were isolated and purified by size exclusion and reverse phase HPLC and characterized by MALDI-TOF and MS/MS spectrometry. The purified conopeptide fractions revealed: 1) antagonist activity of conotoxin NuxVID on two human voltage-gated sodium channels, displaying capabilities as a practical molecular probe and a potential therapeutic lead. 2) Ability for two novel conotoxins to traverse artificial biological membranes, suggesting their potential as drug delivery systems. 3) In vitro capacity of several novel conopeptides to interfere with the adhesion of PfEMP1 domains, expressed in P. falciparum infected erythrocytes, to vascular endothelial and placenta receptors. Lastly, this work reveals binding of the synthetic form of α-conotoxin ImI, from the vermivorous cone snail Conus imperialis, to the α7 nAChR of macrophage-like-cells derived from the pre-monocytic leukemic cell line THP-1 in support of the involvement of this receptor in the cholinergic anti-inflammatory pathway. / Includes bibliography. / Dissertation (Ph.D.)--Florida Atlantic University, 2019. / FAU Electronic Theses and Dissertations Collection

Abstract The broad aim of this thesis is to structurally and functionally explore two α-conotoxins, from venomous sea snails, Vc1.1 and RgIA, in the hope of improving their journey to becoming analgesic therapeutics (introduction to conotoxins in Chapter 1). Vc1.1 is a two-disulfide peptide that is of interest as a potential therapeutic for the treatment of neuropathic pain. Despite investigations, limited structure-activity relationships have been conducted on this α-conotoxin. Consequently there is restricted insight into the interaction of this peptide with one of its analgesic targets, the α9α10 nicotinic acetylcholine receptor (nAChR). Late in this PhD project, the GABAB receptor was implicated as the possible target for conotoxins in neuropathic pain relief. However, there is still debate in the literature with regard to the true target of Vc1.1 and the α9α10 nAChR is still believed to be the target by some groups. This thesis predominantly focuses on the α9α10 nicotinic acetylcholine receptor. Chapter 4 of this thesis presents an extensive series of mutational studies in which all residues except the conserved cysteines were mutated separately to Ala, Asp or Lys (materials and methods described in Chapter 3) and examined using NMR spectroscopy (theory of NMR presented in Chapter 2), to determine the effects of the mutations on the structure of Vc1.1. The structural fold was found to be preserved in all peptides except where Pro was substituted. Chapter 5 explores the effect of these mutations on the blocking of acetylcholine (ACh)-evoked membrane currents at the α9α10 nAChR. Electrophysiological studies showed that the key residues for Vc1.1’s activity are Asp5-Arg7 and Asp11-Ile15, as changes at these positions resulted in the loss of activity at the α9α10 nAChR. Interestingly, the S4K and N9A analogs were more potent than Vc1.1 itself. Hence, Chapter 6 describes a second generation of mutants that was synthesized, namely N9G, N9I, N9L, S4R and S4K+N9A, all of which were more potent than Vc1.1 at both the rat α9α10 and the human α9/rat α10 hybrid receptor, providing a mechanistic insight into the key residues involved in eliciting the biological function of Vc1.1. The most potent analogs were also tested at the α3β2, α3β4 and α7 nAChR subtypes to determine their selectivity. All mutants tested were most selective for the α9α10 nAChR. These findings provide valuable insight into the interaction of Vc1.1 with the α9α10 nAChR subtype and will help in the further development of Vc1.1 or its analogs as drugs. However, despite peptides exhibiting high degrees of potency and selectivity, such as Vc1.1 and RgIA, they are potentially hindered in their development as drugs due to their stability and bioavailability limitations, leading to invasive delivery techniques. Chapter 7 presents a range of cyclic RgIA analogs, tested at their targets the α9α10 nAChR and the GABAB receptor, that retain their activity and increase their stability in human serum relative to non-cyclic RgIA. NMR spectroscopy was used to determine the structure of the non-cyclic peptide and the cyclic peptide to confirm similarities in the global fold of the peptide. Structural perturbations and reduced activities were observed for cyclic RgIA analogs cyclized via linkers composed of three and four residues. Analogs with five, six and seven residues showed no structural perturbations, but differences in their activities at the different receptors. Because cRgIA-6 showed high potency for the GABAB receptor and lower potency for the α9α10 nAChR, this study has identified a GABAB selective peptide. Additionally, because the cRgIA-7 showed high potency for the α9α10 nAChR and low potency for the GABAB receptor, a α9α10 nAChR selective analog has also been identified. With improvements in these peptides against enzymatic attack, they show great potential on their path to becoming orally available analgesics as they may be able to withstand enzymatic conditions in the stomach.

Οι Κωνοτοξίνες είναι μικρά πεπτίδια πλούσια σε δισουλφιδικούς δεσμούς, τα οποία προέρχονται από τα δηλητήρια των θαλάσσιων σαλιγκαριών. Οι κωνοτοξίνες αυτές στοχεύουν διαφορετικούς υποδοχείς στο νευρικό σύστημα με υψηλή εκλεκτικότητα και ισχύ, αποτελώντας χρήσιμους φαρμακευτικούς δείκτες ή και φάρμακα. Μια ομάδα κωνοτοξινών είναι οι μ-κωνοτοξίνες, οι οποίες έχουν παρουσιάσει αναλγητική δράση. Οι μ-κωνοτοξίνες έχουν συγκεκριμένα δομικά χαρακτηριστικά πολύ σημαντικά για την βιολογική τους δραστικότητα. Περιέχουν τρείς δισουλφιδικούς δεσμούς μεταξύ των Cys1-Cys4, Cys2-Cys5 και Cys3-Cys6, σχηματίζοντας τρείς θηλιές (loop) στον σκελετό του πεπτιδίου. Οι μ-κωνοτοξίνες ερευνήθηκαν σαν πιθανά φαρμακευτικά εργαλεία εξαιτίας της ικανότητας τους να αναστέλλουν διαφορετικούς νευρικούς υποτύπους διαύλων Νατρίου και συνεπώς να στοχεύουν όχι μόνο κατά του χρόνιου πόνου αλλά και κατά άλλων ασθενειών. Στόχος της παρούσας διατριβής είναι η σύνθεση νέων μ-κωνοπεπτιδίων με πιθανή αναλγητική δράση, τα οποία στοχεύουν κυρίως σε πρωτεΐνες –κανάλια ιόντων Νατρίου, προκαλώντας αναστολή της μετάδοσης σήματος στα νευρικά κύτταρα. Η σύνθεση των αναλόγων πραγματοποιήθηκε με την Fmoc/But μεθοδολογία επί στερεάς φάσεως, χρησιμοποιώντας ως στερεό υπόστρωμα την Sieber Amide ρητίνη. Ο σχηματισμός των τριών δισουλφιδικών γεφυρών επιτεύχθηκε σε ένα στάδιο στην υγρή φάση με την χρήση ρυθμιστικών αναγωγικών μέσων. Στην παρούσα φάση, τα συντιθέμενα πεπτίδια βρίσκονται σε στάδιο βιολογικής αξιολόγησης μέσω ηλεκτροφυσιολογικών ανταγωνιστικών πειραμάτων. / Conotoxins are small disulfide rich peptides derived from the venom of Conus snails. They target different receptors in the nervous system with high selectivity and potency making them valuable as drug leads or drug themselves. One group of conotoxins, μ-conotoxins have been shown to have potential as analgesic treatment. μ-conotoxins have concrete conformational features, which are very crucial to their biological activity. They contain three disulfide bonds among Cys1-Cys4, Cys2-Cys5 and Cys3-Cys6, forming three loops in their backbone. μ-conotoxins studied as potent pharmacological tools due to their ability to inhibit different neuronal subtypes of sodium channels and likewise conotoxins target not only the chronic pain treatment but also target against other disease’s treatment. The goal of this present thesis is to synthesize new μ-conopeptides, with a potent analgesic activity, which target mostly proteins-sodium channels, inhibiting the nerve impulse transmission at the neuromuscular injection. These analogues were synthesized using the Fmoc/But methodology by SPPS, using Sieber Amide resin as solid support. The formation of three disulfide bonds was accomplished in one step in the solution phase using the redox buffer strategy. At present, the synthesized cono-peptides are under biological evaluation through electrophysiological competitive experiments.

The numerous toxic peptides, called conotoxins (Olivera et al 1990, 1991), that marine cone snails produce and use for capturing prey, deterring predators and presumably for other biotic interactions, are known to target several classes of mammalian voltage and ligand gated receptors with excellent specificity and good receptor-subtype discrimination (Terlau and Olivera 2004). This fine specificity has placed upon the conotoxins a great deal of scientific and medical interest, and cone snail venom is currently considered a vast natural resource of peptides that have the potential of eventually benefiting the prognosis of many human afflictions, either directly as therapeutics or indirectly as research tools. In this regard, the characterization of conotoxins and the identification of the specific receptors they target remains an actively pursued area of study in several countries. There has been an active effort to characterize peptides from Indian populations of cone snails that has resulted in several reports describing novel peptides from them. This thesis is part of these ongoing efforts and largely relates to the isolation and identification of cDNA sequences of precursor conotoxins from cone snails prospected in India. One final section of the thesis is concerned with the assessment of secondary structure predictions of conotoxin genes and discusses how such formations may determine the regions where variations and conservations are taking place among the conotoxins. Structure and Outline of the thesis Chapter 1 is an overview of the cone snails and the conotoxins that they produce. There is some emphasis on the variability and diversity that are found among conotoxins since these are some of the aspects that are discussed in subsequent chapters. Chapter 2 describes the identification of new cDNA sequences isolated from the relatively rare Indian population of the piscivorous cone snail, Conus achatinus. This species was chosen for the study since it is one of the few piscivorous cone species that have been reported from the coastlines of India. However, the limited availability of specimens belonging to this species precluded a direct study of individual venom peptides from it. To overcome this bottleneck of specimen availability, a molecular biological route to obtain cDNA sequences of superfamily specific conotoxins was considered. The steps of PCR mediated amplification and cloning that are incorporated within the procedures of preparing cDNA for sequencing, to some extent overcome the limitations of large sample requirements and in this respect have been used to investigate conotoxin sequences from this species. Using the cDNA route and comparative sequence analysis, it has been possible to identify 5 novel O-superfamily conotoxin sequences from C.achatinus. The precursor sequences have been classified as delta, omega and omega-like conotoxins that potentially target voltage gated sodium and calcium channels. A parallel study trying to detect the specific cDNA related conotoxins using mass spectrometry (MALDI-MS) as a screening tool is also discussed. In this search it has been possible to detect 3 of the 5 cDNA related peptides using small amounts of unpurified venom. The cDNA and mass spectrometric results show that precursor sequences of conotoxins from a relatively rare population of Conus species can be successfully identified and the existence of the peptides that they specify verified through the combined approach of obtaining cDNA sequences and MALDI-MS screening of total unpurified venom. Chapter 3 similarly relates to the isolation of cDNA sequences from a single specimen of the vermivorous cone snail, Conus monile. Three precursor sequences, Mo3.1, Mo15.1 and Mo16.1, of M-superfamily conotoxins have been isolated from this species out of which two precursors (Mo15.1 and Mo16.1) show unexpected cysteine distribution patterns within their putative mature toxin regions. In addition, several other features of these precursors do not fit into the description of known M-superfamily conotoxins. The sequence analyses and the deviations that have been noted among these sequences are described. Chapter 4 describes the efforts that have gone in towards detecting one of these deviant conotoxins (Mo16.1) in the venom of Conus monile using MALD-MS as a means for screening the venom. A peptide having the Mo16.1 predicted mass (1512 Da) has been detected as a minor component of the venom. The chapter describes additional mass-spectrometric experiments that strongly support the assignment of this detected peak being the specific Mo16.1 peptide. A speculative discussion on the role of minor peptide deviants such as the Mo16.1 peptide concludes the chapter. Chapter 5 is concerned with the assessment of secondary structure predictions of conotoxin genes and discusses how such formations may determine the regions where variations and conservations are taking place among the conotoxins. The comparative analysis of DNA sequences corresponding to the variable mature conotoxins reveal that it is possible to differentiate mature conotoxin sequences into variable and conserved regions. Using the prediction program mFold (Markham and Zuker 2005) it has been noted that regions of the DNA encompassing the conserved codons (including the highly conserved cysteine codons) correspond to predicted secondary structures of higher stabilities. In contrast the regions of the conotoxin that have a higher degree of variation correlate to regions of lower stability. These correlations have been observed quite consistently across several classes of conotoxins that show different patterns of variability and conservation in their sequence and representing different categories of conotoxins i.e intra species, inter species, and hyperconserved conotoxins. The observation on these co-relations allows for a simple model of inaccessibility of a mutator to these relatively structured regions of the conotoxin gene (including the cysteine codons) allowing them a relative degree of resistance towards change. Chapter 6 summarizes the findings of the thesis, briefly recapitulating the discussion of the individual chapters from a broader perspective.

Predatory shallow-water tropical marine snails within the genus Conus are estimated to consist of up to 700 species. These carnivorous mollusks have devised efficient venom harpoon-like radular teeth that allow them to predominantly incapacitate polychaete annelids (vermivores), in some cases fish (piscivores), or other mollusks (molluscivores) as an envenomation survival strategy for feeding, defense, and competitor deterrence. The venom of each Conus species contains a distinctive assortment of over 50 diversified disulfide-rich conotoxins with varied pharmacological specificities that selectively inhibit the function of ion channels (Ca2+, Na+, K+) or nicotinic acetylcholine receptors (nAChRs) involved in the animal neurotransmission. Across the genus Conus, the conotoxins represent an extensive array of ion channel blockers each showing an exquisite selectivity to distinguish between channels / receptors and even particular their subtypes. Novel conotoxins detected in the molecular neurobiological approach, providing chemists and pharmacologists a vast library (>50,000 individual toxins) of conotoxins have been further screened for their abilities to modify the responses of tissues to pain stimuli as a first step in describing their potential as lead compounds for novel drugs. In this article, we present the natural history of the Conus biology as well as the nomenclature, classification, structure, neurotoxicological mechanisms, post-translational modification, and pharmaceutical applications of conotoxins. In addition, we also set up the bioinformatic database and search engine about hitherto-identified name and distribution of Conus species and neuropharmacological mechanism, accession number, sequence, and 3D structure of conotoxins and provide researchers advantageous tools for further investigation.

The work presented in this thesis describes the determination of structures of peptides and proteins at atomic resolution. Nuclear Magnetic Resonance (NMR) spectroscopy was used as the principal method of investigation. The thesis is divided into three parts. Part I of the thesis consists of chapters 1 to 4, and deals with structural studies of two novel conotoxins. Part II of the thesis consists of chapter 5 and deals with structural studies of Small MutS Related (Smr) domain from Helicobacter pylori MutS2. Part III of the thesis consists of Appendices A to D. Appendix A describes implementation of a novel pulse sequence for determination of disulfide connectivity using long-range 13 C–13 C scalar couplings across disulfide bonds. Appendices B, C and D contain supplementary infor- mation (acquisition parameters and chemical shifts) for the structural studies presented in parts I and II of the thesis. Part I: Structural studies of novel conotoxins from Conus monile Chapter 1 gives a brief overview of the conotoxins and their structural studies. The first half of the chapter describes biosynthesis, classification schemes, nomenclature, com- monly observed post-translational modifications and applications of conotoxins. The latter half of this chapter summarizes the challenges involved in the structural studies of conotoxins in light of the recent developments in integrated transcriptomic and venomic studies of conotoxins. The key homonuclear and heteronuclear NMR experiments that are employed for structural studies of conotoxins are summarized. Emphasis was laid on describing the spectral features and the structural information that can be gleaned from these experiments. Finally, the current mass spectrometric and NMR methods available for determination of disulfide connectivity are discussed Chapter 2 describes sample preparation and preliminary biophysical characteriza- tion of a conotoxin Mo3964 that contains a hitherto uncharacterized cysteine framework (C–CC–C–C–C). The sequence of Mo3964 was identified at the nucleic acid level as a cDNA clone. Analysis of the signal sequence revealed that the toxin belongs to the M-superfamily, while the cysteine framework bears more resemblance to O- and K- super- family of conotoxins. Structural studies were initiated to determine the disulfide connec- tivity, tertiary structure and biological activity. The gene corresponding to the mature toxin sequence was cloned in a bacterial expression vector pET21a(+) as a C-terminal tag to the cytochrome b5 fusion protein host system. The fusion protein was obtained by recombinant expression using the bacterial expression host E. coli BL21(DE3) and the mature toxin was obtained by either enzymatic or chemical cleavage of the fusion protein followed by size exclusion chromatography and reverse phase HPLC. Proton 1D NMR spectra of the purified peptide exhibited sharp lines and good spec- tral dispersion indicating that molecule was well folded. Formation of disulfide bonds in the mature toxin was ascertained by high resolution mass spectra of intact and chemically modified Mo3964. The peptide toxin exhibited remarkable stability to chemical denatu- ration and proteolytic digestion. Spectroscopic studies clearly showed that Mo3964 pos- sesses a very stable and well defined structure as long as its disulfide bonds are intact. Analytical size exclusion chromatography and Multi Angle Light Scattering (MALS) studies showed that Mo3964 exists in solution as monomer albeit with a non-globular structure. Electrophysiological studies showed that Mo3964 inhibits outward potassium currents in rat Dorsal Root Ganglion (DRG) neurons and increases the reversal potential of rat voltage gated sodium channel rNav 1.2 stably expressed on Chinese Hamster Ovary (CHO) cells at peptide concentrations as low as 10 nM. Chapter 3 describes the determination of disulfide connectivity and tertiary stricture of Mo3964. Initial attempts to determine disulfide connectivity using direct fragmenta- tion of the intact peptide in the mass spectrometer failed due to the relatively large size of the molecule and its resistance to endoproteases. Partial reduction alkylation based methods failed as the first stage of partial reduction gave rise to a mixture of various single disulfide bond reduced species which could not be separated from each other. Subsequently, information about the disulfide connectivity was obtained using a method that does not necessitate separation of such a mixture of single disulfide bond reduced species. This method involves partial reduction, cyanylation of the reduced cysteines and alkali mediated cleavage of the peptide backbone on the N-terminus of cyanylated cysteines. Structural studies were carried out using homonuclear and heteronuclear NMR meth- ods. The hydrogen bond network and hence topology of the molecule was determined with high accuracy using the long-range HNCO-COSY experiment that correlates hydrogen- bond donor-acceptor pairs. This experiment utilizes the three bond heteronuclear scalar coupling, i.e., the h3JN C O′ coupling across the hydrogen bonds. All these restraints proved crucial to the assignment of the disulfide connectivity in Mo3964, given its novel cysteine framework. The structure of Mo3964 was calculated using a total of 549 NOE distance restraints, 84 dihedral angle restraints and 28 hydrogen bond distance restraints. The tertiary structure was constructed from the disulfide connectivity pattern 1–3, 2–5 and 4–6, that is hitherto undescribed for the M–superfamily conotoxins. The ensemble of structures showed a backbone Root Mean Square Deviation of 0.68 ± 0.18 Å, with 87% and 13% of the backbone dihedral (φ, ψ) angles lying in the most favored and additional allowed regions of the Ramachandran map. The remarkable stability and anomalous spectral properties exhibited by Mo3964 could be rationalized using the disulfide connectivity and the tertiary structure. The tertiary structural fold has not been described for any of the known Conus peptides. Further, a search for structures similar to that of Mo3964 using the web server DALI returned no hits indicating that the peptide scaffold of Mo3964 has no structural homologues. Hence, the conotoxin Mo3964 represents a new bioactive peptide fold that is stabilized by disulfide bonds and adds to the existing repertoire of scaffolds that can be used to design stable bioactive peptide molecules. The structure of Mo3964 was submitted to the Protein Data Bank (PDB ID: 2MW7)[1]. Chapter 4 describes the structural studies of a 17 residue, single disulfide containing conopeptide Mo1853. The samples for structural studies were obtained either by chemical synthesis or by recombinant expression methods. Structural studies using homonuclear solution NMR methods revealed that Mo1853 exists as two equally populated cis and trans X–Pro conformers which are in slow exchange regime, compared to the chemical shift timescale. Sequence specific assignments were obtained for both the conformers by analysis of homonuclear 2D 1 H,1H–DQF–COSY,1H,1 H–TOCSY, 1H,1 H–NOESY and 1H,1 H–ROESY spectra. Temperature dependence of chemical shifts was measured and coalescence was observed for two amide protons at 318 K. At this temperature, the rate of exchange and the free energy of activation were determined to be 59 Hz and ≈ 67.2 kJ mol−1 respectively. The evidence for this conformational equilibrium was also observed as exchange correlation peaks in the 2D- NOESY and ROESY spectra. Tertiary structures of both the cis and trans conformers were determined using distance restraints, backbone dihedral angle restraints, the disulfide bond restraint and the cis or trans conformation of the X–Pro peptide bond. Tertiary structures of both the conformers consist of a 29-membered macro-cyclic ring formed by 9 amino acid residues which are cyclized by side chain to side chain disulfide bond. The conformation of the X–Pro peptide bond which is located within this macro-cyclic ring causes the cis structure to be compact and the trans structure to be in an extended form. Analysis of the tertiary structures indicated that the trans conformer is stabilized by hydrogen bonds while the cis conformer is likely to be stabilized by hydrophobic interactions. This was further corroborated by the fact that at lower temperatures, the hydrophobic interactions became weaker reducing the population of the cis conformer with respect to that of the trans conformer. Preliminary electrophysiological studies carried out on rat DRG neurons indicate that Mo1853 transiently reduces late outward potassium currents. Part II: Structural studies of Small MutS Related (Smr) domain from Helicobacter pylori MutS2 Chapter 5 presents the solution NMR studies of the Smr domain from MutS2 of H. pylori , henceforth called as HpSmr. In H. pylori , MutS2 is involved in suppression of homologous recombination and its Smr domain was shown to be necessary for this activity. As of date, in spite of the availability of structural information for the Smr domain, unambiguous identification of the residues involved in metal binding, DNA binding and catalysis remains elusive. Structural studies were carried out on two different constructs of HpSmr viz., HpSmr– (His)6 and GSHM–HpSmr, with and without the hexahistidine tag respectively. Se- quence specific assignments of HpSmr–(His)6 were obtained at two different sample pH conditions viz., pH 8.0 and pH 5.35 using the standard suite of triple resonance NMR experiments. Since, valines and leucines constitute about 25% of the total number of amino acid residues in HpSmr–(His)6 , stereospecific assignments were obtained for di- astereotopic methyl groups of these residues by preparing a fractionally 13C labeled sample of HpSmr–(His)6 . Solution structure of HpSmr–(His)6 at pH 8.0 was determined using 766 NOE restraints, 170 backbone dihedral angle restraints and 70 hydrogen bond distance restraints. The tertiary structure exhibits the canonical α/β sandwich fold ex- hibited by all the other known structures of Smr domains. Further, NMR studies and analytical gel filtration studies indicated the presence of pH dependent conformational exchange in HpSmr that involves strand to coil transition in the C-terminal β-strand. In order ascertain that the conformational equilibrium is not at an artifact caused by the C-terminal hexa-histidine-tag, HpSmr protein construct GSHM–HpSmr, which does not have the hexa-histidine-tag, was prepared. Conformational exchange was observed in this construct as well. The preliminary NMR evidence suggests that the conformational exchange is caused by pH dependent cis–trans isomerization of a semi-conserved Proline residue Pro66 . We have hypothesized that the pH dependent modulation of the activity of Smr domain of MutS2 can be advantageous to H. pylori . Such a regulation could help the bacteria to achieve optimal rate of homologous recombination in response to changes in pH, which is necessary for maintaining homeostasis and tiding over stress conditions. Part III: Appendix Appendix A describes an NMR pulse program LRCC_CH2 that was designed with the aim of determining disulfide connectivity using long-range 13C–13 C (C β –C β ′ ) couplings across the disulfide bond. This experiment is a modification of an earlier experiment pub- lished by Bax and co-workers designed to measure the side-chain χ3 dihedral angle in me- thionines. The experiment described here is optimized for the detection of 3 bond scalar coupled methylene carbons. The details of modifications introduced in LRCC_CH2, its product operator analysis, a representative spectrum acquired on [U-13C,15 N]–Mo3964, short-comings and future directions are described. The C programming code that was used to implement the pulse program is also included in the appendix. Appendices B, C and D contain the supplementary information (acquisition pa- rameters for the NMR experiments and chemical shifts) for the structural studies carried out on Mo3964, Mo1853 and HpSmr.

Major constituents of the venom of various animals are peptidogenic in nature. Marine snails belonging to the species Conus are venomous predators that use small, structurally constrained peptides present in their venom for prey capture and defense. It is known that ~500 Conus species are present in nature and the venom of each of these Conus species is a complex mixture of nearly 100 peptides accounting for > 50,000 peptides with little overlap among the different species. The peptides isolated from the venom of Conus species are commonly known as conotoxins or conopeptides. Some of the common targets of these peptides include the different ion channels like Na+, K+, and Ca2+, and receptor subtypes such as nicotinic acetylcholine and NMDA receptors. The ion channels and receptor subtypes were targeted by conopeptides with high degree of specificity and selectivity. The structural information on the peptides from cone snails can prove to be a valuable starting tool for the understanding of the function of different ion channels and hence in the design of neuropharmacologically active drugs. Conotoxins are disulfide-rich peptides and the number of disulfide generally ranges from two to five. Based on the arrangement of cysteines in their primary sequence, they are classified into different superfamilies. The signal sequences of the precursors belonging to a particular superfamily are highly conserved and hence the members within the same family have, in common, the unique disulfide arrangement and pharmacological activity. Conotoxins are classified into eleven superfamilies till date. In order to understand the underlying the principles involved in the action of these peptides on different ion channels, one needs to know the three-dimensional structures which, in potential, will help in the identification of the pharmacophores responsible for the observed pharmacological activity. With the aim of studying the structure-activity relationships found among the conotoxins, we have initiated a study on the peptides isolated from the marine snails found in the Indian coastal waters. This thesis is focused in the structural studies of the peptide toxins from marine cone snails and a terrestrial scorpion. The tool used for the structural studies of these peptide toxins is Nuclear Magnetic Resonance Spectroscopy. Chapter 1 provides an overview of the peptide toxins found among various animal species with more emphasis on conotoxins and scorpion toxins. In addition, the rationale behind the present study has also been explained. Chapter 2 describes the structure determination of two conopeptides isolated from Conus amadis, δ-Am2766 and Am2735, which are active on mammalian sodium channels. The structural aspects and comparison with other known conopeptides belonging to the same superfamily as that of these two peptides have also been described. Solution NMR studies of Ar1446 and Ar1248, two conopeptides isolated from the species Conus araneosus have also been studied using Homonuclear NMR methods. Ar1446 is a three disulfide-bonded peptide. Our studies have revealed that this peptide has a novel disulfide connectivity not previously observed in the M superfamily or any other superfamily of conotoxins. The structural features of Ar1446 will be described along with the NMR studies on two-disulfide bonded peptide, Ar1248, belonging to the A-superfamily of conotoxins. The main problem faced in the kind of study of peptides isolated from natural sources is the amount that can be isolated and purified to homogeneity. In order to obtain large quantities of peptides, we have successfully used Cytochrome b5 as fusion host to clone, over express and purify these peptides using recombinant methods. The use of recombinant methods has aided in the preparation of isotopically enriched peptides. The use of cyt b5 as fusion host for the large scale production of some of the peptides from Indian marine snails is described in Chapter 4. A novel pharmacologically active linear peptide, Mo1659 isolated from Conus monile, have been studied using Heteronuclear NMR methods. This peptide was cloned, over expressed and purified using Cytochrome b5 as a fusion host. Another linear peptide, Mo1692 (also from Conus monile), has been prepared using the same method and was studied using Homonuclear NMR methods. Both these peptides were liberated from the fusion host using cyanogen bromide cleavage and were subsequently purified using RP-HPLC. The results of the biosynthetic preparation and NMR studies of these two peptides have been described in Chapter 5. Chapter 6 describes the solution structure determination of a novel scorpion toxin characterized in the venom of the Indian red scorpion Buthus tamulus. The cloning, over expression, folding and purification of BTK-2 is described here. The structure and the function of this recombinantly produced BTK-2 will also be described.

Práca sa zaoberá in silico dizajnom a validáciou peptidov založených na konotoxíne - MrIA, izolovaného z morských slimákov druhu Conus marmoreus a možnosti využitia týchto peptidov v liečbe neuroblastómu pomocou cielenia norepinefrínového transportéru. Päť peptidov založených na tomto konotoxíne bolo simulovaných pomocou simulácii molekulárnej dynamiky, ich trajektórie boli analyzované pre zistenie vlastností týchto peptidov. Dva homologické modely ľudského norepinefrínového transportéru boli vytvorené pre analýzu väzobných vlastností peptidov založených na konotoxíne ku norepinefrínovému transportéru. Peptidy boli následne syntetizované a použité na pokrytie apoferitínových nanočastíc s elipticínom uväzneným vnútri apoferitínu. Vytvorené peptidy a nanočastice boli ďalej skúmané pre objasnenie ich fyzikálo-chemických vlastností. Interakcie a cytotoxicita boli skúmané aplokáciou nanočastíc na bunky neuroblastómu a epitelu. Z in silico a in vitro analýz vyšiel YKL-6 peptid ako najlepší kandidát na ďalší výskum.