Research Outlines

Research in the interface of Chemistry and Biology is the only possible way to include real insights into the molecular mechanisms of complex biological and chemical systems. While this monumental research effort helped understanding the Physico-Chemical aspects of the natural bio-molecular recognition phenomena at molecular level, the aspiration to cure disease at the genetic level also acts as the major driving force behind the research between molecular biology and chemical synthesis. Synthetic molecules that bind sequence specifically to DNA and RNA are legitimate targets for molecular biology applications as gene therapeutic agents and in anti-sense technology. The multidisciplinary approach is one of the best devices to understand the bio-molecular recognition phenomena at molecular level and can be regarded as an icon for research at the interface of Chemistry and Biology. Therefore, I am envisioning “antisense gene therapy” as an emerging and world changing research area to cure disease at the genetic level. This research booming will have a great impact on the overall course of human civilization.

Soon after joining the duty at IIT Guwahati, since August, 2008, I have started my independent research activity at the interface of Chemistry and Biology, particularly, in the field of Chemical Genomics and Peptidomimetics as I envision that this is the only possible way to include real insights into the molecular mechanisms of complex biological systems and to cure disease at the genetic level and to create impact to the overall course of human civilization. My previous research training provided me a platform of basic understanding to unravel the mechanism of molecular reactivity, biomolecular interactions and to uncover the basic biochemical processes using synthetic probe molecules. This exposure in the field of “Enediyne Anticancer Antibiotics” during my Ph.D. with Professor Amit Basak and in the field of “Fluorescent Oligonucleotide Probe Design” during my Post Doctoral study with Professor Isao Saito inspired and empowered me to take the new challenge of evolving a fully new field of independent research activity.

My research group is actively involved in Expanding the Genetic Alphabet which includes design of unnatural-fluorescent nucleoside pairs held by hydrophobic/charge transfer complexation force. On the other hand we are simultaneously engaged in the design of solvatochromic fluorescent unnatural amino acids toward Expanding the Genetic Code and searching for physiologically viable peptidomimetic therapeutics. In both the research activities “Click reaction/chemistry” is associated as a key step in the novel bioorganic synthesis which introduces triazole unit with high metabolic stability, high associability with biological targets and ability to modulate electronic/photophysical properties. Moreover, both the current research activities are directly in part or in full related to the consideration of health for the mankind.

1. Expanding the Genetic Alphabet

Specific pairing of nucleobases is the basis of genetic alphabet, itself the basis of genetic code. An expanded genetic alphabet would expand the informational and functional potential of DNA for both in vitro and in vivo applications. The major efforts in this field of research are focused on the development of a new and stable third base-pair that would be efficiently replicated with high fidelity utilizing H-bonding and/or hydrophobic interaction force. Recent research thrust on nucleic acid based diagnostics and sensing materials and Mulliken’s suggestion in 1952 on charge-transfer (CT) complexes inspired me to take the challenge of establishing the CT force as a new and strong force to stabilize third base-pair via the design of unnatural triazolyl donor-acceptor nucleoside pair. My specific achievements in this frontier field of research are:

Toward this end we have shown that the charge transfer complexation force between unnatural triazolyl donor-acceptor nucleoside pair is well enough to stabilize a DNA duplex efficiently which could efficiently be replicated. To expand the scope of application of our unnatural DNAs in chemical biology, we have exploited the same probe in stabilizing an abasic DNA lesion. Our serendipitous discovery on “Dual Door Entry system to exciplex formation” gave rise to the birth of a new generation probe system which would broaden the applicability of our unnatural DNAs in chemical biology, sensor development, molecular recognition and in designing light harvesting DNA materials. Recent observation on the hybridization accompanying Forster resonance energy transfer (FRET) event in fluorescent natural-unnatural nucleoside pair might find application in the detection and analysis of biomolecular interactions and in material science applications. The designed wave-length shifting unnatural DNA is found to be efficient in typing single nucleotide polymorphism (SNPs) which is the recent target of all biomedical researchers toward reaching the goal of “personalized medicine”. Currently we are exploring polymerase mediated replication and transcription of our synthesized triazolyl donor-acceptor nucleo-base pairs and evaluating the role of CT force on polymerase replication fidelity.

Future Impact: (a) Expanded Genetic Alphabets (b) Unnatural Oligonucleotides usable for "Antisense Gene Therapy", (c) Single Nucleotide Polymorphism Typing; (d)Detecting and Curing Diseases at Genetic Level, the Goal of “Personalized Medicine”, (e) The New Nucleoside Base Analogues may have Potential Biological Activity and may find Clinical use in Future for the Treatment of Viral Diseases such as AIDS, Cancer etc.; (f) Creating Semisynthetic Organism and Life with Enhanced Diversity.

2. Expanding the Genetic Code

The design and encoding of fluorescent unnatural amino acids toward expanding the genetic code would expand proteins functions and biotechnological applications including biomolecular interactions, in vivo imaging, highthroughput screening, diagnostics and proteomics. Many of the challenges of extrinsic fluorophore labeled proteins would be overcome if an intrinsically fluorescent amino acid is synthesized and encoded genetically directly in prokaryotic or eukaryotic organisms. In an effort toward expanding the genetic code and our observation on the installation/modulation of emission response via click reaction has led us to design unnatural amino acids decorated with triazolyl donor and/or acceptor aromatics with novel solvatochromic fluorescence properties.

Toward this end we have generated a new class of fluorescent unnatural amino acids and novel unnatural β-turn peptide capable of showing FRET process which might find application in probing proteins structure, dynamics and in FRET based bioassay. We have developed cyclic ɷ/ε-amino acids as conformationally constrained molecular scaffold for novel β-turn peptidomimetics that are expected to have high therapeutic value with enhanced metabolic stability. Under study is the sequence specific DNA binding event of the same molecular scaffolds which might lead to the generation of a new family of distamycin analogue with potent antimicrobial activity and less cytotoxicity. Currently we are exploring the possibility of encoding the designed triazolyl donor-acceptor amino acids genetically in response to the amber suppressor codon and/or unnatural codon system utilizing tRNA/amino-acyl-tRNA-synthetase strategy-a bio-orthogonal strategy.

Future Impact: (a) Expanded Genetic Codes; (b) Fluorescent Protein with Encoded Fluorescent Unnatural Amino Acids; (c) β-Turn Peptidomimetics-Design of HIV-Protease-I Inhibitors; Metabolically stable peptide therapeutics; (d) Concept of Umbrella Crowding and Drug Design via Enezyme Inhibition with the Conceptual β-Turn Mimetic Peptides; (e)  Unnatural Amino Acid as Conformationally Constrained Molecular Scaffold for Novel β-Turn Peptidomimetics; (f)  Distamycin Analogue-Interaction with DNA; (f) Creating Semisynthetic Organism and Life with Enhanced Diversity.

3. New Synthetic Methodology

In the process of journey of synthesizing biomolecular building blocks via click chemistry, I have developed a novel “Click reagent version of Sonogashira coupling” protocol which has a great impact and is being utilized by several synthetic chemists. We have also shown that “click” reaction is able to install/modulate fluorescence property and the strategy is being utilized by several chemists/biochemists to create small fluorescent molecules. My research in β-lactam chemistry has shed some light to support the well believed radical path of enzymatic reaction for the synthesis of Clavulanic Acid, the 4^th generation antibiotic.

4. Fluorescent β-Lactam Antibiotics:

(a) Development of Potent Fluorescent β-Lactam Antibiotics and Study of their Chemical and Biological Activity, (b) β-Lactam based Peptidomimetics and their Biological Activity; (c) Assay of Enzymatic Cleavage of β-Lactam Antibiotics by Fluorescence Spectroscopy;

5. Enediyne-Nucleoside/Amino Acid Hybrid Molecules:

(a) Development of the Concept of Enediyne-Nucleoside/Amino Acid Hybrid Molecules and Synthesis and Study of anti Cancer Activity, (b) Monitoring the DNA Cleavage by such Hybrid Molecules with Fluorescence Spectroscopy.