Department of Biotechnology

Indian Institute of Technology Hyderabad (IITH) is a premier institute of science and technology established in 2008. IITH has been consistently ranked in the&nbsp;<a href="https://iith.ac.in/reports/" rel="noopener noreferrer">top 10 institutes</a>&nbsp;in India for Engineering&nbsp;<a href="https://www.nirfindia.org/2021/EngineeringRanking.html" rel="noopener noreferrer" target="_blank">according to NIRF</a>&nbsp;making it one of the most coveted schools for science and technology in the country.

IITH offers&nbsp;<a href="https://iith.ac.in/academics/under-graduate/">undergraduate programs</a>&nbsp;in all the classical engineering disciplines, applied sciences, design, as well as several modern interdisciplinary areas. Students are given a flexibility to explore a broad set of areas, and potentially pursue a minor or double major in a discipline that is not their own. Students who wish to seek a deeper understanding of their own discipline are strongly encouraged to get involved in cutting-edge research with the help of a faculty to mentor them, and earn an Honors in their own field.

The very foundation of IIT Hyderabad is based on&nbsp;<a href="https://iith.ac.in/research/">research and innovation</a>. The vibrant research culture is evident from the number of patents and publications that IITH produces consistently every year. IITH offers&nbsp;<a href="https://iith.ac.in/academics/programmes-offered/">graduate programs</a>&nbsp;at both a masters, and a doctoral level, in several diverse areas. There are separate programs for technology, design, science, and liberal arts. The&nbsp;<a href="https://iith.ac.in/academics/post-graduate/">MTech program</a>&nbsp;is offered in various modes and durations to cater to the ever-growing need of postgraduate level professionals in the country.

IITH encourages and supports&nbsp;<a href="https://iic-iith.netlify.app/index.html" rel="noopener noreferrer" target="_blank">innovation and entrepreneurship</a>&nbsp;at every stage. The minor program in entrepreneurship is open to all students of IITH, and many of the courses are offered by industrialists who are entrepreneurs themselves. There are various&nbsp;<a href="https://iith.ac.in/research/centres-incubators/">innovation centers and incubators</a>&nbsp;that promote entrepreneurship and help mentor young innovators. IITH has been very successful in building tie-ups with leading academic institutions around the globe.

IITH enjoys a very special relationship with Japanese universities and industries that goes beyond academic and research collaborations. In fact, some of the iconic buildings in IITH campus will carry the signature of Japanese architecture.

IITH creates a unique holistic ecosystem for education that offers interactive learning, a very flexible academic structure, cutting-edge research, strong industry collaboration, and entrepreneurship. This is an environment which enables students and faculty to translate their dreams into realities.

IIT Hyderabad

TDP-43 protein is found deposited as inclusions in the amyotrophic lateral sclerosis (ALS) patient's brain. The mechanism of neuron death in ALS is not fully deciphered but several TDP-43 toxicity mechanisms such as mis-regulation of autophagy, mitochondrial impairment and generation of oxidative stress etc., have been implicated. A predominantly nuclear protein, Cyclin C, can regulate the oxidative stress response via transcription of stress response genes and also by translocation to the cytoplasm for the activation of mitochondrial fragmentation-dependent cell death pathway. Using the well-established yeast TDP-43 proteinopathy model, we examined here whether upon TDP-43 aggregation, cell survival depends on the CNC1 gene that encodes the Cyclin C protein or other genes which encode proteins that function in conjunction with Cyclin C, such as DNM1, FIS1 and MED13. We show that the TDP-43's toxicity is significantly reduced in yeast deleted for CNC1 or DNM1 genes and remains unaltered by deletions of genes, FIS1 and MED13. Importantly, this rescue is observed only in presence of functional mitochondria. Also, deletion of the YBH3 gene involved in the mitochondria-dependent apoptosis pathway reduced the TDP-43 toxicity. Deletion of the VPS1 gene involved in the peroxisomal fission pathway did not mitigate the TDP-43 toxicity. Strikingly, Cyclin C-YFP was observed to relocate to the cytoplasm in response to TDP-43's co-expression which was prevented by addition of an anti-oxidant molecule, N-acetyl cysteine. Overall, the Cyclin C, Dnm1 and Ybh3 proteins are found to be important players in the TDP-43-induced oxidative stress-mediated cell death in the S. cerevisiae model. © 2021 Elsevier B.V.

World University root node

Biochimica et Biophysica Acta - Molecular Cell Research

Role of CNC1 gene in TDP-43 aggregation-induced oxidative stress-mediated cell death in S. cerevisiae model of ALS

Signal transmission in neurons goes along with changes in the transmembrane potential. To report them, different approaches, including optical voltage-sensing dyes and genetically encoded voltage indicators, have evolved. Here, we present a DNA nanotechnology-based system and demonstrated its functionality on liposomes. Using DNA origami, we incorporated and optimized different properties such as membrane targeting and voltage sensing modularly. As a sensing unit, we used a hydrophobic red dye anchored to the membrane and an anionic green dye at the DNA to connect the nanostructure and the membrane dye anchor. Voltage-induced displacement of the anionic donor unit was read out by fluorescence resonance energy transfer (FRET) changes of single sensors attached to liposomes. A FRET change of ∼5% for Δψ = 100 mV was observed. The working mechanism of the sensor was rationalized by molecular dynamics simulations. Our approach holds potential for an application as nongenetically encoded membrane sensors. © 2021 American Chemical Society.

Nano Letters

DNA Origami Voltage Sensors for Transmembrane Potentials with Single-Molecule Sensitivity

Base pair mismatches in DNA can erroneously be incorporated during replication, recombination, etc. Here, the influence of A…A mismatch in the context of 5′CAA·5′TAG sequence is explored using molecular dynamics (MD) simulation, umbrella sampling MD, circular dichroism (CD), microscale thermophoresis (MST) and NMR techniques. MD simulations reveal that the A…A mismatch experiences several transient events such as base flipping, base extrusion, etc. facilitating B–Z junction formation. A…A mismatch may assume such conformational transitions to circumvent the effect of nonisostericity with the flanking canonical base pairs so as to get accommodated in the DNA. CD and 1D proton NMR experiments further reveal that the extent of B–Z junction increases when the number of A…A mismatch in d(CAA)·d(T(A/T)G) increases (1–5). CD titration studies of d(CAA)·d(TAG)n=5 with the hZαADAR1 show the passive binding between the two, wherein, the binding of protein commences with B–Z junction recognition. Umbrella sampling simulation indicates that the mismatch samples anti…+ syn/+ syn…anti, anti…anti &amp; + syn…+ syn glycosyl conformations. The concomitant spontaneous transitions are: a variety of hydrogen bonding patterns, stacking and minor or major groove extrahelical movements (with and without the engagement of hydrogen bonds) involving the mismatch adenines. These transitions frequently happen in anti…anti conformational region compared with the other three regions as revealed from the lifetime of these states. Further, 2D-NOESY experiments indicate that the number of cross-peaks diminishes with the increasing number of A…A mismatches implicating its dynamic nature. The spontaneous extrahelical movement seen in A…A mismatch may be a key pre-trapping event in the mismatch repair due to the accessibility of the base(s) to the sophisticated mismatch repair machinery. © 2021, The Author(s).

Fulltext

Scientific Reports

Spontaneous and frequent conformational dynamics induced by A…A mismatch in d(CAA)·d(TAG) duplex

Marine sponges of the genus Suberea produce variety of brominated tyrosine alkaloids which display diverse range of biological activities including antiproliferative, antimicrobial and antimalarial activities. In continuation of our search for biologically active marine natural products for antibacterial compounds, we report here the synthesis and evaluation of biological activity of panel of ianthelliformisamines and subereamine analogues using the literature known acid-amine coupling reaction. Several derivatives of Ianthelliformisamine were achieved by the coupling of Boc-protected polyamine chain with brominated aromatic acrylic acid derivatives by varying the bromine substituents on aromatic acid derivatives, amine spacer as well as geometry of the double bond, and then Boc-deprotection using TFA. Similarly, subereamine analogues were also synthesized employing coupling reaction between various brominated phenyl acrylic acids with commercially available chiral amino ester derivatives followed by ester hydrolysis. We screened these synthetic analogues for antibacterial activity against both Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) strains. One of the compound 7c showed bactericidal activity against Staphylococcus aureus with an IC50 value of 3.8 μM (MIC = 25 μM). © 2021 Elsevier Ltd

Department of Chemistry

Bioorganic and Medicinal Chemistry Letters

Synthesis and antibacterial activities of marine natural product ianthelliformisamines and subereamine synthetic analogues

DNA integrity is challenged by both exogenous and endogenous alkylating agents. DNA repair proteins such as Escherichia coli AlkB family of enzymes can repair 1-methyladenine and 3-methylcytosine adducts by oxidative demethylation. Human AlkB homologue 5 (ALKBH5) is RNA N6-methyladenine demethylase and not known to be involved in DNA repair. Herein we show that ALKBH5 also has weak DNA repair activity and it can demethylate DNA 3-methylcytosine. The mutation of the amino acid residues involved in demethylation also abolishes the DNA repair activity of ALKBH5. Overexpression of ALKBH5 decreases the 3-methylcytosine level in genomic DNA and reduces the cytotoxic effects of the DNA damaging alkylating agent methyl methanesulfonate. Thus, demethylation by ALKBH5 might play a supporting role in maintaining genome integrity. © 2020 Elsevier Inc.

Biochemical and Biophysical Research Communications

Oxidative demethylase ALKBH5 repairs DNA alkylation damage and protects against alkylation-induced toxicity

Phosphodiesterase (PDE) inhibitors, such as pentoxifylline (PTX), are used as pharmacological agents to enhance sperm motility in assisted reproductive technology (ART), mainly to aid the selection of viable sperm in asthenozoospermic ejaculates and testicular spermatozoa, prior to intracytoplasmic sperm injection (ICSI). However, PTX is reported to induce premature acrosome reaction (AR) and, exert toxic effects on oocyte function and early embryo development. Additionally, in vitro binding studies as well as computational binding free energy (ΔGbind) suggest that PTX exhibits weak binding to sperm PDEs, indicating room for improvement. Aiming to reduce the adverse effects and to enhance the sperm motility, we designed and studied PTX analogues. Using structure-guided in silico approach and by considering the physico-chemical properties of the binding pocket of the PDEs, designed analogues of PTX. In silico assessments indicated that PTX analogues bind more tightly to PDEs and form stable complexes. Particularly, ex vivo evaluation of sperm treated with one of the PTX analogues (PTXm-1), showed comparable beneficial effect at much lower concentration—slower AR, higher DNA integrity and extended longevity of spermatozoa and superior embryo quality. PTXm-1 is proposed to be a better pharmacological agent for ART than PTX for sperm function enhancement. © 2021, The Author(s).

Structure-based redesigning of pentoxifylline analogs against selective phosphodiesterases to modulate sperm functional competence for assisted reproductive technologies

Circadian clocks coordinate mammalian behavior and physiology enabling organisms to anticipate 24-hour cycles. Transcription-translation feedback loops are thought to drive these clocks in most of mammalian cells. However, red blood cells (RBCs), which do not contain a nucleus, and cannot perform transcription or translation, nonetheless exhibit circadian redox rhythms. Here we show human RBCs display circadian regulation of glucose metabolism, which is required to sustain daily redox oscillations. We found daily rhythms of metabolite levels and flux through glycolysis and the pentose phosphate pathway (PPP). We show that inhibition of critical enzymes in either pathway abolished 24-hour rhythms in metabolic flux and redox oscillations, and determined that metabolic oscillations are necessary for redox rhythmicity. Furthermore, metabolic flux rhythms also occur in nucleated cells, and persist when the core transcriptional circadian clockwork is absent in Bmal1 knockouts. Thus, we propose that rhythmic glucose metabolism is an integral process in circadian rhythms. © 2021, The Author(s).

Nature Communications

Rhythmic glucose metabolism regulates the redox circadian clockwork in human red blood cells

After publication of their Report "Circadian rhythms in the absence of the clock gene Bmal1, " the authors discovered an error in the original manuscript. The genotypes (Bmal1+/+and Bmal1-/-) in one of the datasets (liver slice time course) were inadvertently inverted during analysis. This affects some of the panels in Figs. 1 and 3 of the Report and the associated supplementary figures and tables. No other datasets or analyses are affected. These corrections do not change the conclusions of the paper. The following items in the main text have been corrected: • Fig. 1 (B, C, D): Venn diagrams and heatmaps are corrected (Bmal1+/+and Bmal1-/-panels swapped) • Fig. 3 (A, B, C, D): Sequence motif analysis is included for both Bmal1+/+and Bmal1-/-, as are phase distributions and rhythmic expression profiles for the ETS transcription factors. • Sentences in the main text are removed or amended to appropriately correct this genotype inversion. Supplementary figures and tables associated with the inverted liver slice data set have also been corrected: • Tables S1, S2, and S3: Data are swapped to reflect the correct genotype. • Figs. S1, S2, and S3: Liver slice transcriptomics panels are swapped to reflect the correct genotype. • Fig. S6: Rhythmic ETS transcription factors identified in Bmal1 and Bmal1 tissues are swapped to reflect the correct genotype. siRNA depletion analysis of the rhythmic ETS transcription factors identified in Bmal1+/+and Bmal1-/-are depicted. • Fig. S9D: Figure has been updated with corrected liver transcriptomics data. The authors have also corrected the error in this single dataset in the Gene Expression Omnibus (GEO), accession GSE111696. The authors gratefully acknowledge early communication from Kate Abruzzi and colleagues concerning this error, which they found independently. © 2021 American Association for the Advancement of Science. All rights reserved.

Science

Erratum: Circadian rhythms in the absence of the clock gene Bmal1 (Science (2020) 367:6479 (800-806) DOI: 10.1126/science.aaw7365)

Three versatile half-sandwich ruthenium(II) p-cymene complexes bearing substituted triazole ligands exhibit promising cancer cell growth inhibition activity towards A549 lung adenocarcinoma and MDA-MB-231 breast adenocarcinoma cells. In this context, the triazole based phthalimide protected new ligand (2-(3, 5-di(pyridin-2-yl)-4H-1,2,4-triazol-4-yl) isoindoline-1,3-dione) (L1) was prepared. Three ruthenium(II) p-cymene complexes [Ru(η6-p-cymene)(L1)Cl]Cl: [1]Cl, L1: (2-(3,5-di(pyridin-2-yl)-4H-1,2,4-triazol-4-yl)isoindoline-1,3-dione), [Ru(η6-p-cymene)(L2)Cl]Cl: [2]Cl and [Ru(η6-p-cymene)(L2)Cl](PF6): [2](PF6), L2 (2,2′-(4-(1H-pyrrol-1-yl)-4H-1,2,4-triazole-3,5-diyl) dipyridine) have been successfully synthesized and characterized by different spectral and analytical tools. Pyrrole protected substituted ruthenium complexes [2]Cl and [2](PF6) have been successfully identified structurally by single-crystal X-ray diffraction studies and confirmed the successful anion exchange. The redox properties of the ligands and the targeted metal complexes have been carefully examined. Cellular staining, live-cell imaging and MTT assay have been performed for all the complexes. We have demonstrated that our synthesized ruthenium(II) p-cymene complexes are capable of inducing significant cytotoxicity in A549 lung cancer cell lines, with an IC50 values of 6.56 ± 0.31 µM, 4.74 ± 0.2 µM and 13.67 ± 0.64 µM and in MDA-MB-231 breast cancer cell lines with an IC50 values of 1.13 ± 0.046 µM, 0.36 ± 0.016 µM and 11.32 ± 0.49 µM for [1]Cl, [2]Cl and [2](PF6) respectively. © 2021 Elsevier B.V.