TIFR
Department of Chemical Sciences
School of Natural Sciences

Calender

May 1, 2017 at 4.00 pm in AG-69

Title :

Amylin and Amyloid beta: Structure, Membrane Interaction and Cellular Entry Mechanisms

Abstract :

Amyloid beta (Aβ) oligomer is thought to be the major toxic species for the Alzheimer’s disease. But it is still unknown whether different regions play specific roles in the multi-step toxicity pathway. Here, we have decoupled the functionality of the core region (residues 18-35) vs the N- terminal (1-9) in terms of affinity towards membrane, entry and spatial distribution within neuronal cells. Using temperature dependence of cell entry, we probe the underlying mechanism of cell entry is active or passive. We also probe the role of membrane potential in mediating membrane affinity, by artificially creating a transmembrane potential in small unilammelar vesicles.

Amylin is another amyloidogenic peptide, which is responsible for type-II diabetes. For amylin too, the smaller oligomeric species is the major toxic species. Here, to understand the relation between structure and function, we have probed the secondary structural changes between the oligomers and fibrils of amylin using Raman and IR spectroscopy. We also perturb the lone di-sulphide linkage in this peptide to understand its role in membrane binding and toxicity. 

 

April 27, 2017 at 2.30 pm in AG-80

Title :

Nanostructured Materials for Photo-catalysis

April 24, 2017 at 4.00 pm in AG-69

Title :

Charge Transfer Transitions Associated with Charged Aminoacids: A Classical Electronic Donor-Bridge-Acceptor Paradigm

April 21, 2017 at 2.30 pm in AG-80

Title :

Leveraging organic chemistry for solving biological problems: Bioconjugation and bacterial signaling as case studies

Abstract :

The underlying philosophy of my research program is to utilize organic chemistry to address questions in both applied and fundamental biological sciences. In this talk, I shall discuss how I propose to employ organic chemistry for: a) developing technologies for protein bioconjugation, and b) studying c-di-GMP signaling in bacteria. In the first half of my talk which will focus on bioconjugation, I shall describe my proposed approach for bridging disulfide bonds of proteins and using this chemistry for fabricating antibody-drug conjugates, for peptide stapling and as disulfide mimics. Additionally, I shall discuss my proposed strategies for performing cysteine-independent protein bioconjugation that we are currently pursuing in my research group. The second half of my talk will focus on the bacterial second messenger, c-di-GMP, a cyclic dinucleotide that plays a major role in biofilm formation.1 Intriguingly, bacteria contain numerous c-di-GMP synthase enzymes (diguanylate cyclases or DGCs) which when individually deleted, engender distinct phenotypes suggesting they have distinct roles despite each being responsible for generating the same product. To elucidate the roles of individual DGCs and to understand why bacteria express so many DGCs, I propose to develop a chemical genetics-based platform that I shall describe in my talk. Additionally, I shall describe a chemoproteomic approach that I seek to develop for discovering the c-di-GMP interacting proteome of bacterial cells. I believe that the insights on c-di-GMP signaling obtained from these studies will significantly contribute towards developing novel antibacterial therapy directed at targeting this fascinating signaling mechanism.

1) D. Kalia et al., Chem. Soc. Rev., 2013, 42, 305–341.

April 20, 2017 at 2.30 pm in AG-80

Title :

Efficacious strategies for cysteine-mediated protein bioconjugation

Abstract :

The development of chemoselective organic reactions that proceed rapidly under physiological conditions to form stable covalent linkages have revolutionized modern biological and clinical research. One such reaction, Michael addition between the thiol functional groups of cysteine residues of proteins and maleimides to form thio-maleimide linkages, is extensively used for labeling proteins with fluorophores, affinity tags, polyethylene glycol moieties and drug molecules for a diverse range of applications. In particular, the tremendous success of antibody-drug conjugates (ADCs) generated by appending drug molecules to antibodies by employing this chemistry has had a transformative impact on cancer therapy. Consequently, recent reports on the susceptibility of these linkages to undergo thiol exchange-mediated breakdown in the physiological milieu1, 2 are extremely alarming. In my talk, I shall describe two approaches that my research group has developed3, 4 to overcome this problem. One of these approaches is based on our discovery that unlike conventional maleimides, exocyclic olefinic maleimides form thiol exchange-resistant conjugates and hence are preferable for thiol bioconjugation.3 In another approach, we have rationally designed a photoactivable maleimide derivative that after bioconjugation can be irradiated with UV light to trigger rapid thio-maleimide ring hydrolysis to form stable conjugates.4 I shall also discuss how we plan to use these new scaffolds for generating stable ADCs.

1) B. Q. Shen et al., Nat. Biotechnol. 2012, 30, 184–189.

2) R. P. Lyon et al., Nat. Biotechnol. 2014, 32, 1059–1062.

3) D. Kalia* et al., Angew. Chem. Int. Ed. 2016, 55, 1432–1435.

4) D. Kalia* et al., Angew. Chem. Int. Ed. 2017, 56, 1885–1889.

April 17, 2017 at 4.00 pm in AG-69

Title

The N-H...N Hydrogen Bond - Structure and Strength

April 12, 2017 at 2.30 pm in B-333 (DBS Seminar Room)

Title :

Biophysics of the specific adhesion of nano-sized particles to cell membranes

Abstract :

Nano-sized particles such as a virus or an affinity ligand coated nanocarrier gain entry into a cell by first strongly adhering to the target cell membrane. The adhesion proceeds through multivalent interactions of ligands on the particle surface with their corresponding cell surface receptors. Such binding processes are ubiquitous in cell biology and their study may help in furthering our understanding of cellular adhesion. In this talk, I will present a multiscale computational framework that accounts for a variety of chemical and physical phenomena that govern the binding efficacy of the particles. I will demonstrate how the enthalpy of binding together with the loss in the configurational entropies sets an upper limit on the number of simultaneous receptor-ligand bonds. I will also show that the surface topography of the cell membrane alters this upper limit, and show comparisons of our model predictions with in vivo experimental results for five different organs in mouse.

April 10, 2017 at 4.00 pm in AG-69

Title :

Hybrid Perovskites for Photovoltaic Applications

April 11, 2017 at 2.30 pm in AG-69

Title :

Curvature remodelling of cell membranes: from the biochemistry to the biophysics

Abstract :

A biological cell is a complex soft matter system in which many of physical and chemical processes span multiple spatial and temporal scales. The various theoretical and computational tools developed in the context of soft matter physics can be utilized to build highly quantitative models to investigate these processes, and gain new insights specifically in the mesoscale (order of 100 nm). In this talk, I will show how computational models at various spatiotemporal scales along with multiscale bridging techniques may be used to develop biophysical models that closely relate to the underlying biochemical information. I will demonstrate these aspects using two specific problems: (i) estimating the excess area in a cell membrane through the extraction of tethers, and (ii) atomistic to thermodynamic descriptions of the spontaneous membrane remodeling activity of ENTH and Exo70 domain containing proteins.

April 7, 2017 at 2.30 pm in AG-80

Title :

Discovery and Development of a New Class of Metal-Based Antibacterial Compound

Abstract :

The worrying appearance of microbial resistance to antibiotics is a worldwide problem which needs to be tackled urgently. Microbial resistance to the common classes of antibiotics involving purely organic compounds unfortunately develops very rapidly and in most cases, resistance was detected soon after or even before release of the antibiotic to the market. Therefore, novel concepts for antibiotics must be investigated, and metal-containing compounds hold particular promise in that area. We discovered a tri-hetero-metallic complex that has potent activity against various pathogenic bacterial strains including methicillin-resistant Staphylococcus aureus (MRSA).[1] A systematic structure–activity relationship (SAR) study was carried out in order to improve the properties of the lead compound. The most potent mono-metallic complex derived from this SAR has an antibacterial activity comparable to the well-established organic drugs amoxicillin and norfloxacin and importantly, only moderate cytotoxicity against mammalian cells.[2] Microbiological studies on membrane potential, membrane permeabilization, and cell wall integrity revealed that the compound targets the bacterial membrane and disturbs cell wall integrity. The design, synthesis and biological evaluation of these novel class of metal-based antibacterial drug candidates will be presented in the first half of the research seminar.

In the second half, I will briefly discuss my future research plans.  

  

References.

1.M. Wenzel§, M. Patra§, C. H. R. Senges, J. J. Stepanek, A. Pinto, P. Prochnow, I. Ott, N. Metzler-Nolte*, J. E. Bandow*, ACS Chem. Biol. 2013, 8, 1442-1450

        (§ = co-first authors).

2.M. Patra, M. Wenzel, P. Prochnow, V. Pierroz, G. Gasser, J. E. Bandow* and N. Metzler-Nolte*. Chem. Sci., 2015, 6, 214-224.

 

April 6, 2017 at 11.30 1m in AG-80

Title

Improving Properties of Platinum Anticancer Drugs

Abstract :

The three FDA approved platinum anticancer drugs, cisplatin, carboplatin and oxaliplatin, are widely used in the clinic to treat various forms cancer including testicular, ovarian, cervical, head and neck, non-small-cell lung, and colorectal cancer.[1] Despite their phenomenal clinical success, however, the severe undesired side effects such as nephrotoxicity, myelosuppression, peripheral neuropathy, ototoxicity, and nausea are main drawbacks of platinum-based chemotherapy.[1] The side effectes could be mitigated by introducing tumor-targeting properties into platinum anticancer compounds, thereby reducing the nonspecific platinum accumulation in the healthy tissues. Glucose transporter GLUT1 is known to widely overexpress in many human cancers and its expression levels in tumor biopsy samples correlate well with poor prognosis.[1] We designed various D-glucose-platinum(II) conjugates (Glc-Pts) for targeted delivery of platinum anticancer drugs to cancer cells.[2] To investigate the effect of D-glucose substitution position on the biological activity of Glc-Pts, we synthesized all possible positional isomers (C1α, C1β, C2, C3, C4, and C6) of a Glc-Pt.[3] The biological activities of the compounds were evaluated both in vitro and in vivo. We discovered that varying the position of substitution of D-glucose alters not only the cellular uptake and cytotoxicity profile but also the GLUT1 specificity of resulting glycoconjugates. Results from this study revealed that the C2-substituted Glc-Pt 2 has the highest GLUT1-specific internalization, which also reflects the best cancer-targeting ability. In a syngeneic breast cancer mouse model overexpressing GLUT1, 2 showed excellent antitumor efficacy and selective uptake in tumors with no observable toxicity. [3] The design, synthesis, anticancer activity and in-depth characterization of the cellular uptake mechanism of Glc-Pts will be presented in the research seminar. 

Additionally, some of our recent findings on the modulation of cell death mechanism of platinum complexes by incorporating a second metal fragment, namely a ferrocenyl moiety, will also be discussed briefly. In general, the rationale behind this approach was to merge the fascinating biological properties of ferrocene with the anticancer properties of platinum within one molecule to acquire multi-modal targeting properties. The hybrid heterometallic derivative was found to have a completely different mode of action compare to classical platinum drugs.  

  

References.

1.L. Kelland, Nat. Rev. Cancer, 2007, 7, 573; L. Szablewski, Biophys. Acta. 2013, 1835, 164.

2.M. Patra, T. C. Johnstone, K. Suntharalingam, S. J. Lippard, Angew. Chem. Int. Ed. 2016, 55, 2550.

3.M. Patra, S. G. Awuah, S. J. Lippard, J. Am. Chem. Soc., 2016, 138, 12541.

 

April 3, 2017 at 4.00 pm in AG-69

Title :

Optical Sensors for Metal ion Detection

March 27, 2017 at 4.00 pm in AG-69

Title :

Mechanistic Origin of Protein Flexibility of Ubiquitin Family Proteins

Abstract :

Here we investigate the mechanistic origins of protein malleability. We develop a methodology using Single-Molecule Force spectroscopy (SMFS), fluorescence spectroscopy and circular dichroism to probe the native and transition states of Ubiquitin and small ubiquitin-related modifier (SUMO2), to get insights into the protein dynamics and mechanical resistance. Both SUMO2 and Ubiquitin have mechanical clamp which serve as a major resistor to force in SMFS experiments. But we show that the core of the protein actually couples to the clamp and determines its overall malleability. And to top it off we look at the interactions which determine the core flexibility in both the proteins.

March 23, 2017 at 4.00 pm in AG-80

Title :

Construct, Deconstruct, Rebuild: Mimicking Nature to Engineer Functional Modules for Bottom-up Synthetic Biology

Abstract :

An ambitious goal posed by synthetic biology is the bottom-up construction of a functional cell. Recently, a droplet-based bilayer platform termed ‘droplet interface bilayer’ was developed. Nanoliter-sized lipid-encased water droplets can be arranged in networks of desired patterns, forming electrical connections between them via membrane pores. The droplets can also be encapsulated in a hydrogel matrix opening new directions for bottom-up protocell / prototissue construction. 

The key to designing functional protocells is understanding the engineering principles of molecular construction at all biological scales (nanometer, nm – millimeter, mm). To this end, I am studying the structural mechanics of protein assemblies, specifically the nuclear lamina, using atomic force microscopy, cryo-electron tomography and in silico approaches. Besides paving the way to rationally design synthetic systems for bio-nanotechnology, the combined approach provides understanding of the structure-function of the macromolecular assembly involved in diseases from a materials science perspective, the underlying goal of ‘materiomics’.

 

March 20, 2017 at 4.00 pm in AG-69

Title :

Membrane-Protein Interaction at the Single Molecule Level

Abstract :

Understanding the interaction between membranes and amyloid protein oligomers  is a key unsolved challenge in the field of antimicrobial peptides and amyloid diseases such as Alzheimer’s and Type II diabetes. While the structure of the membrane-bound monomeric subunit is slowly emerging from bulk studies, we need to know how many monomers make up the oligomer, whether this species subsequently grows to specific sizes, whether specific membrane architectures determine binding, and whether interaction with other membrane proteins substantially alter their statistics. Here we approach this problem by the interaction of amylin and amyloid beta with artificial lipid bilayers. We perform single molecule photobleaching experiment with Total Internal Reflection Fluorescence Microscope to probe the stoichiometry. We also employ an atomic force microscope to probe changes in membrane rheology. Our answers may be significant consequences for the underlying toxic mechanism.