The present thesis deals with different aspects of the chemistry of iron complexes, their interaction with DNA and photo-induced cleavage of double-stranded DNA. Chapter I presents a general introduction on metal-based drugs in cancer therapy and the evolution of the transition metal complexes capable of targeting DNA leading to DNA strand scission, emphasizing particularly the photo-induced DNA cleavage activities for their potential utility in PDT. The mechanistic pathways associated with the DNA cleavage are discussed citing selected examples of compounds that are known to be efficient DNA photo-cleavers on irradiation with light of different wavelengths. Objective of the present investigation is dealt in this chapter. Chapter II deals with the synthesis, crystal structure, DNA binding and oxidative DNA cleavage activity of ternary iron(II) complexes of phenanthroline bases to explore the chemistry of iron(II) complexes towards the metal-assisted photo-induced DNA cleavage activity. Chapter III presents the synthesis and characterization of a cationic imidazo[1,5-a]pyridine derivative to explore the role of imidazopyridine moiety in the photo-induced DNA cleavage activity of the compound. Its cytotoxic effect to the HeLa cancer cell has also been studied using UV-A light of 365 nm. Chapter IV presents the synthesis and characterization of dipyridoquinoxaline (dpq) complexes of bivalent 3d-metal ions such as d6-iron(II), d7-cobalt(II), d8-nickel(II), d9-copper(II) and d10-zinc(II) to explore any specific role that is played by the transition-metal ions in exhibiting visible light-induced DNA cleavage activity. Chapter V deals with the synthesis, characterization of oxo-bridged diiron(III) complexes of phenanthrolne bases having a structural motif found in many iron-containing metalloproteins with a diiron core in the active site. DNA binding and photo-induced DNA cleavage activity of the complexes is studied. Finally, Chapter VI deals with the synthesis and characterization of oxo-bridged diiron(III) complexes having L-histidine (L-his) and N,N-donor heterocyclic bases. This chapter describes the double-strand DNA cleavage activity of [{Fe(L-his)(dpq)}2(μ-O)](ClO4)2. Rationalization of the DNA double strand break (dsb) has been made using molecular docking calculations. This chapter also deals with the site-specific protein (bovine serum albumin, BSA) cleavage activity of the complexes on UV-A light irradiation. The references have been compiled at the end of each chapter and indicated as superscript numbers in the text. The complexes presented in this thesis are represented by bold-faced numbers. Crystallographic data of the complexes, characterized structurally by single crystal X-ray crystallography, are given in CIF format in the enclosed CD (Appendix-I). Due acknowledgements have been made wherever the work described is based on the findings of other investigators. Any omission that might have happened due to oversight or mistake is regretted.

Photo sensitizers showing visible light induced DNA cleavage activity are of current importance for medicinal applications related to photodynamic therapy (PTD) considering greater skin penetration of light near 700 nm. While organic molecules and complexes of 4d-5d metal ions are extensively studied for their DNA photo-damage properties in UV and visible light, the chemistry of 3D metal complexes showing visible light-induced DNA cleavage activity is relatively unexplored efforts have been made in this thesis work to design new ternary copper (II) complexes having a-amino acids Such copper (II) complexes with tunable coordination geometry could find potential applications in PDT. Ternary Copper (II) complexes containing L-methionine, S-methy1-L-cysteine and phenanthroline bases are prepared and characterized. They display DNA binding and visible light induced DNA cleavage activity. An enhancement of the DNA cleavage activity is observed for analogous ternary copper (II) complexes contained L-lysine with a pendant cationic amine moiety as a photo-induced DNA Cleavage activity using binary and ternary copper (II) complexes of L-arginine and phenanthroline bases. We have observed AT selective DNA binding and visible light –induced DNA cleavage activity. The crescent-shaped bis-arginine Copper (II) complex mimics the natural antiviral antibiotic netropsin. T o investigate the role of the pendant groups of the amino acids, we have explored the DNA binding and DNA cleavage activity of analogues L-glutamine and L-asparagine complexes. We have prepared ternary copper (II) complexes containing two photosensitizers, viz., L-tryptophan (L-trp) and dipyridoquininoxaline/dipyridophenazine to achieve double strand breaks forming linear DNA. Complex [Cu(L-trp)(dppz)(H2O)+ shows a stacking arrangement of the indole and dppz rings giving a separation that fits with the base pair separation of ds-DNA. Photosensitizes in these complexes approach two different complementary stands of the ds-DNA, leading to double strand breaks and formation of linear DNA. Mechanistic studies on the DNA photocleavage reactions reveal the formation of singlet oxygen(1O2)species by a type-II pathway in preference to the hydroxyl radical generation. A process leading to an efficient DNA cleavage activity on visible light irradiation. The observation of sequence selectivity and double strand DNA cleavage on red light exposure by national design of the complexes is significant considering importance of the results in the chemistry of photodynamic therapy of cancer. The results of this dissertation open up new avenues for designing and developing 3d metal-based photosensitizers with potential utility in nulcleic acid chemistry.

In bacteria, nucleoid associated proteins (NAPs) represent a prominent group of global regulators that perform the tasks of genome compaction, establishing chromosomal architecture and regulation of various DNA transactions like replication, transcription, recombination and repair. HU, a basic histone like protein, is one of the most important NAPs in Eubacteria. Mycobacterium tuberculosis produces a homodimeric HU (MtbHU), which interacts with DNA non-specifically through minor groove binding. Exploration for essential genes in Mtb (H37Rv) through transposon insertion has identified HU coding gene [Rv2986c, hupB; Gene Id: 15610123; Swiss-Prot ID: P95109)] to be vital for the survival and growth of this pathogen. MtbHU contains two domains, the N-terminal domain which is considerably conserved among the HU proteins of the prokaryotic world, and a C–terminal domain consisting of Lys-Ala rich multiple repeat degenerate motifs. Sequence analysis carried out by the thesis candidate showed that MtbHU exhibits 86 to 100 percent identity within the N-term region among all the mycobacterium species and some of the members of actinobacteria, including important pathogens like M. tuberculosis, M. leprae, M. ulcerans, M. bovis, Nocardia; while C term repeat region varies relatively more. This strikingly high cross species identity establishes the MtbHU N-terminal domain (MtbHUN) as an important representative structural model for the above mentioned group of pathogens. The thesis candidate has solved the X-ray crystal structure of MtbHUN, crystallized in two different forms, P2 and P21. The crystal structures in combination with computational analyses elucidate the structural details of MtbHU interaction with DNA. Moreover, the similar mode of self assembly of MtbHUN observed in two different crystal forms reveals that the same DNA binding interface of the protein can also be utilized to form higher order oligomers, that HU is known to form at higher concentrations. Though the bifunctional interface involved in both DNA binding and self assembly is not akin to a typical enzyme active site, the structural analysis identified key interacting residues involved in macromolecular interactions, allowing us to develop a rationale for inhibitor design. Further, the candidate has performed virtual screening against a vast library of compounds, and design of small molecules to target MtbHU and disrupt its binding to DNA. Various biochemical, mutational and biological studies were performed in the laboratory of our collaborator Prof. V. Nagaraja, MCBL, IISc., to investigate these aspects. After a series of iterations including design, synthesis and validation, we have identified novel candidate molecules, which bind to MtbHU, disrupt chromosomal architecture and arrest M. tuberculosis growth. Thus, the study suggests that, these molecules can serve as leads for a new class of DNA-interaction inhibitors and HU as a druggable target, more so because HU is essential to Mtb, but absent in human. Our study proposes that, targeting the nucleoid associated protein HU in Mtb can strategize design of new anti-mycobacterial therapeutics. Perturbation of MtbHU-DNA binding through the identified compounds provides the first instance of medium to small molecular inhibitors of NAP, and augurs well for the development of chemical probe(s) to perturb HU functions, and can be used as a fundamental chemical tool for the system level studies of HU-interactome. Section I: “Crystal structure of Mycobacterium tuberculosis histone like protein HU and structure based design of molecules to inhibit MtbHU-DNA interaction: Leads for a new target.” of this thesis presents an elaborate elucidation of the above mentioned work. The candidate has additionally carried out structure based computational and theoretical work to elucidate the interaction of amino acid based metal complexes which efficiently bind to DNA via minor-groove, major-groove or base intercalation interaction and display DNA cleavage activity on photo-irradiation. This understanding is crucial for the design of molecules towards Photodynamic Therapy (PDT). PDT is an emerging method of non-invasive treatment of cancer in which drugs like Photofrin show localized toxicity on photoactivation at the tumor cells leaving the healthy cells unaffected. The work carried out in our group in close collaboration with Prof. A.R. Chakravarty of Inorganic and Physical Chemistry Department elaborates the structure based design of Amino acid complexes containing single Cu (II), such as [Cu(L-trp)(dpq)(H2O)]+ , [Cu (L-arg) 2](NO3)2 , Amino acid complexes containing oxobridged diiron Fe(III), such as [{Fe(L-his)(bpy)}2(μ-O)](ClO4)2 , [{Fe(L-his)(phen)}2(μ-O)](ClO4)2 , and Complexes containing Binuclear Cu(II) coordinated organic moiety, such as [{(dpq) CuII}2(μ-dtdp)2], which bind to DNA through minor groove/major groove/base intercalation interactions. Docking analysis was performed with the X-ray crystallographic structure of DNA as receptor and the metal complexes as ligands, to study the mode of binding to DNA and to understand the possible mode of DNA cleavage (single/double strand) when activated with laser. Section II: “Structure based computational and theoretical analysis of metal coordinated complexes containing amino acids and organic moieties designed for photo induced DNA cleavage” of this thesis presents a detailed presentation of the above mentioned work.

The present thesis deals with different aspects of the chemistry of oxovanadium(IV) complexes, their interaction with DNA and protein and photo-induced DNA and protein cleavage activity and photocytotoxicity. Chapter I presents a general introduction on various modes of interactions of organic compounds and transition metal complexes capable of targeting DNA leading to DNA strand scission, emphasizing particularly the photo-induced DNA cleavage activities for their potential application in PDT. The mechanistic pathways associated with the DNA cleavage are discussed. A comparison has been made on the advantages of photoactive metal complexes over organic conjugates. Objective of the present investigation is also dealt in this Chapter. Chapter II of the thesis deals with the synthesis, characterization, DNA binding and photo-induced DNA cleavage activity of ternary oxovanadium(IV) complexes of N-salicylidene-S-methyldithiocarbazate (salmdtc) and phenanthroline bases to explore the photo-induced DNA cleavage activity in UV-A light of 365 nm. Chapter III presents the synthesis, characterization, DNA binding and photo-induced DNA cleavage activity of ternary oxovanadium(IV) complexes containing N-salicylidene-L-methionate (salmet) and N-salicylidene-L-tryptophanate (saltrp) Schiff bases and phenanthroline bases. The objective of this work is to investigate the photo-induced DNA cleavage activity in near-IR light and to see the effect of pendant thiomethyl and indole moieties in the DNA cleavage reactions. Chapter IV deals with the synthesis, characterization, DNA binding, red-light induced DNA cleavage activity and photocytotoxicity of ternary oxovanadium(IV) complexes having N-salicylidene-L-arginine (sal-argH) and N-salicylidene-L-lysine (sal-lysH) Schiff bases and phenanthroline bases. The important results include the visible light-induced DNA cleavage activity and photocytotoxicity of the complexes in human cervical HeLa cancer cells. Chapter V describes the synthesis, characterization, DNA binding and photo-induced DNA and protein cleavage activity and photocytotoxicity of oxovanadium(IV) complexes containing bis(2-benzimidazolylmethyl)amine and phenanthroline bases. The significant results include DNA cleavage activity in near-IR light and photocytotoxicity of the dppz complex in non-small cell lung carcinoma/human lung adenocarcinoma A549 cells in visible light. Further, we have studied the protein cleavage activity of the complexes in UV-A light of 365 nm by using bovine serum albumin (BSA) and lysozyme. Finally, Chapter VI presents the binary oxovanadium(IV) complexes of phenanthroline bases. We have studied their synthesis, characterization, DNA binding and photo-induced DNA and protein cleavage activity and photocytotoxicity. Photocytotoxicity of dppz complex has been studied in human cervical HeLa cancer cells in visible light. Photo-induced protein cleavage activity of the complexes has been studied in UV-A light of 365 nm by using BSA and lysozyme. The references have been compiled at the end of each chapter and indicated as superscript numbers in the text. The complexes presented in this thesis are represented by bold-faced numbers. Crystallographic data of the complexes, characterized structurally by single crystal X-ray crystallography, are given in CIF format in the enclosed CD (Appendix-I). Due acknowledgements have been made wherever the work described is based on the findings of other investigators. Any omission that might have happened due to oversight or mistake is regretted.

Scorpionate and terpyridine ligands are of importance in inorganic chemistry for their metal-binding properties. Tris-pyrazolylborate (Scorpionate) ligands that show facial binding mode and steric protection have been extensively used to synthesize complexes modeling the active site structure and biological function of various metalloproteins and as catalysts in C-H and NO activation and carbine transfer reactions. Terpyridine and modified terpyridine ligands showing meridional binding mode have been used in bioinorganic chemistry where Pt-terpyridine complexes are known to inhibit the activity of thiordoxin reductase (TrxR) besides showing interaction with G-quadruplex. The thesis work stems from our interest to use these ligand systems to design and prepare new 3-d metal-based photodynamic therapeutic (PDT) agents to explore their visible light-induced DNA cleavage activity and photocytotoxicity. Efforts have been made in this thesis work to design and synthesize Co(II) and Cu(II) complexes having scorpionate (Tpph) abd terpyridine (tpy) ligands. Ternary 3d-metal complexes having Tpph and planar phenanthroline bases have been synthesized and structurally characterized. The steric encumbrance of Tpph has led to the reduction in chemical nuclease activity along with enhanced photo-induced DNA cleavage activity, particularly of the Cu(II) and Co(II) complexes. The Co(II), Cu(II) and Zn(II) complexes of Tpph and a pyridyl ligand having a photoactive naphthalilmide moiety show molecular light-switch effect on binding to calf thymus DNA or BSA protein. The complexes do not show any chemical nuclease activity. The Cu(II) complex shows significant DNA cleavage activity in red light. The Co(II) complex displays significant photocytotoxicity in UV-A light. Ternary Cu(II) complexes of ph-tpy and heterocycylic bases are prepared and their DNA binding and cleavage activity studied. The complexes are avid binders to CT-DNA. The dipyridoquinoxaline (dpq) and dipyridophenazine (dppz) complexes are photocleavers of DNA in visible light. A significant enhancement in cytotoxicity in HeLa cancer cells is observed on exposure of the dppz complex to light. The binary Cu(II) complexes are also prepared to reduce the dark toxicity using phenyl and pyrenyl substituted terpyridine ligands. The pyrenyl substituted complex shows DNA cleavage activity in the visible light, low dark toxicity and unprecedented photocytotoxicity in visible light. The copper(II) complexes generally show dark cellular toxicity due to the presence of reducing thiols. The present terpyridine copper(II) complex having pendant pyrenyl moiety shows significant PDT effect that is similar to that of the PDT drug Photofrin. Binary Co(II) complexes show efficient DNA cleavage activity in visible light, significant photocytotoxicity in visible light and cytosolic uptake behaviour. Considering the bio-essential nature of the cobalt and copper ions, the present study opens up new strategies for designing and developing 3d-metal-based photosensitizers for their potential applications in PDT.