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Das S, Chandra A, Das A, Senapati S, Chatterjee G, Chatterjee R. Identifying the genetic associations among the psoriasis patients in eastern India. J Hum Genet 2024; 69:205-213. [PMID: 38409498 DOI: 10.1038/s10038-024-01227-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/03/2024] [Accepted: 02/04/2024] [Indexed: 02/28/2024]
Abstract
Psoriasis is a multifactorial genetic disorder manifested by hyperproliferation and abnormal differentiation of epidermal keratinocytes, along with the infiltration of inflammatory cells into the skin. Although ~80 genetic susceptibility variants were reported in psoriasis, many loci showed population-specific associations, warranting the need for more population-specific association studies in psoriasis. We determined the association of forty single nucleotide polymorphisms (SNPs) among 2136 psoriasis patients and normal individuals from eastern India. We investigated the expression of corresponding genes and evaluated the protein structure stability for the genes with susceptible coding variants. We found fifteen SNPs significantly associated with psoriasis, while additional three SNPs showed significant association when we classified the patients based on the presence of HLA-Cw6 allele. Epistatic interaction between HLA-Cw6 and other associated loci showed significant association with the SNPs at PSORS1 region, along with other five SNPs outside PSORS1. Three genes showed significant differential expression in psoriatic tissues compared to the adjacent normal skin tissues but were not differential when classified the patients based on their genotypes. SNP rs495337 at SPATA2 (Spermatogenesis Associated 2) showed a 1.2-fold increased risk among the HLA-Cw6 patients compared to combined samples. We found significant downregulation of SPATA2 among the patients with risk genotypes and HLA-Cw6 allele compared to the non-risk genotypes. Protein structure stability analysis showed reduced structural stability for all the mutant residues caused by the associated coding variants. Our study evaluated the genetic associations of psoriasis-susceptible variants in India and evaluated the possible functional significance of these associated variants in psoriasis.
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Affiliation(s)
- Shantanab Das
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, West Bengal, 700108, India
| | - Aditi Chandra
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, West Bengal, 700108, India
| | - Anamika Das
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, West Bengal, 700108, India
| | - Swapan Senapati
- Consultant Dermatologist, Uttarpara, Hooghly, West Bengal, 712258, India
| | - Gobinda Chatterjee
- Department of Dermatology, IPGMER/SSKM Hospital, Kolkata, West Bengal, India
| | - Raghunath Chatterjee
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, West Bengal, 700108, India.
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Mukherjee V, Divakaran U. The promises and challenges of many-body quantum technologies: A focus on quantum engines. Nat Commun 2024; 15:3170. [PMID: 38609387 PMCID: PMC11014963 DOI: 10.1038/s41467-024-47638-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Affiliation(s)
- Victor Mukherjee
- Department of Physical Sciences, Indian Institute of Science Education and Research Berhampur, Berhampur, 760010, India.
| | - Uma Divakaran
- Department of Physics, Indian Institute of Technology Palakkad, Palakkad, Kerala, 678623, India
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3
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Nayak B, Paul P, Mishra S. Neddylation is essential for malaria transmission in Plasmodium berghei. mBio 2024; 15:e0023224. [PMID: 38411954 PMCID: PMC11005431 DOI: 10.1128/mbio.00232-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/07/2024] [Indexed: 02/28/2024] Open
Abstract
Neddylation is a type of posttranslational modification known to regulate a wide range of cellular processes by covalently conjugating the ubiquitin-like protein Nedd8 to target proteins at lysine residues. However, the role of neddylation in malaria parasites has not been determined. Here, for the first time, we showed that neddylation plays an essential role in malaria transmission in Plasmodium berghei. We found that disruption of Nedd8 did not affect blood-stage propagation, gametocyte development, gamete formation, or zygote formation while abolishing the formation of ookinetes and further transmission of the parasites in mosquitoes. These phenotypic defects in Nedd8 knockout parasites were complemented by reintroducing the gene that restored mosquito transmission to wild-type levels. Our data establish the role of P. berghei Nedd8 in malaria parasite transmission.IMPORTANCENeddylation is a process by which Nedd8 is covalently attached to target proteins through three-step enzymatic cascades. The attachment of Nedd8 residues results in a range of diverse functions, such as cell cycle regulation, metabolism, immunity, and tumorigenesis. The potential neddylation substrates are cullin (CUL) family members, which are implicated in controlling the cell cycle. Cullin neddylation leads to the activation of cullin-RING ubiquitin ligases, which regulate a myriad of biological processes through target-specific ubiquitylation. Neddylation possibly regulates meiosis in zygotes, which subsequently develop into ookinetes. Our findings point to an essential function of this neddylation pathway and highlight its possible importance in designing novel intervention strategies.
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Affiliation(s)
- Bandita Nayak
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Plabita Paul
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Satish Mishra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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Varma A, Udupa S, Sengupta M, Ghosh PK, Thirumalai V. A machine-learning tool to identify bistable states from calcium imaging data. J Physiol 2024; 602:1243-1271. [PMID: 38482722 DOI: 10.1113/jp284373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 02/09/2024] [Indexed: 04/04/2024] Open
Abstract
Mapping neuronal activation using calcium imaging in vivo during behavioural tasks has advanced our understanding of nervous system function. In almost all of these studies, calcium imaging is used to infer spike probabilities because action potentials activate voltage-gated calcium channels and increase intracellular calcium levels. However, neurons not only fire action potentials, but also convey information via intrinsic dynamics such as by generating bistable membrane potential states. Although a number of tools for spike inference have been developed and are currently being used, no tool exists for converting calcium imaging signals to maps of cellular state in bistable neurons. Purkinje neurons in the larval zebrafish cerebellum exhibit membrane potential bistability, firing either tonically or in bursts. Several studies have implicated the role of a population code in cerebellar function, with bistability adding an extra layer of complexity to this code. In the present study, we develop a tool, CaMLSort, which uses convolutional recurrent neural networks to classify calcium imaging traces as arising from either tonic or bursting cells. We validate this classifier using a number of different methods and find that it performs well on simulated event rasters as well as real biological data that it had not previously seen. Moreover, we find that CaMLsort generalizes to other bistable neurons, such as dopaminergic neurons in the ventral tegmental area of mice. Thus, this tool offers a new way of analysing calcium imaging data from bistable neurons to understand how they participate in network computation and natural behaviours. KEY POINTS: Calcium imaging, compriising the gold standard of inferring neuronal activity, does not report cellular state in neurons that are bistable, such as Purkinje neurons in the cerebellum of larval zebrafish. We model the relationship between Purkinje neuron electrical activity and its corresponding calcium signal to compile a dataset of state-labelled simulated calcium signals. We apply machine-learning methods to this dataset to develop a tool that can classify the state of a Purkinje neuron using only its calcium signal, which works well on real data even though it was trained only on simulated data. CaMLsort (Calcium imaging and Machine Learning based tool to sort intracellular state) also generalizes well to bistable neurons in a different brain region (ventral tegmental area) in a different model organism (mouse). This tool can facilitate our understanding of how these neurons carry out their functions in a circuit.
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Affiliation(s)
- Aalok Varma
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Sathvik Udupa
- Department of Electrical Engineering, Indian Institute of Science, Bangalore, India
| | - Mohini Sengupta
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Prasanta Kumar Ghosh
- Department of Electrical Engineering, Indian Institute of Science, Bangalore, India
| | - Vatsala Thirumalai
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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5
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Manhas R, Rathore A, Havelikar U, Mahajan S, Gandhi SG, Mahapa A. Uncovering the potentiality of quinazoline derivatives against Pseudomonas aeruginosa with antimicrobial synergy and SAR analysis. J Antibiot (Tokyo) 2024:10.1038/s41429-024-00717-3. [PMID: 38514856 DOI: 10.1038/s41429-024-00717-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/10/2024] [Accepted: 02/27/2024] [Indexed: 03/23/2024]
Abstract
Antimicrobial resistance has emerged as a covert global health crisis, posing a significant threat to humanity. If left unaddressed, it is poised to become the foremost cause of mortality worldwide. Among the multitude of resistant bacterial pathogens, Pseudomonas aeruginosa, a Gram-negative, facultative bacterium, has been responsible for mild to deadly infections. It is now enlisted as a global critical priority pathogen by WHO. Urgent measures are required to combat this formidable pathogen, necessitating the development of novel anti-pseudomonal drugs. To confront this pressing issue, we conducted an extensive screening of 3561 compounds from the ChemDiv library, resulting in the discovery of potent anti-pseudomonal quinazoline derivatives. Among the identified compounds, IDD-8E has emerged as a lead molecule, exhibiting exceptional efficacy against P. aeruginosa while displaying no cytotoxicity. Moreover, IDD-8E demonstrated significant pseudomonal killing, disruption of pseudomonal biofilm and other anti-bacterial properties comparable to a well-known antibiotic rifampicin. Additionally, IDD-8E's synergy with different antibiotics further strengthens its potential as a powerful anti-pseudomonal agent. IDD-8E also exhibited significant antimicrobial efficacy against other ESKAPE pathogens. Moreover, we elucidated the Structure-Activity-Relationship (SAR) of IDD-8E targeting the essential WaaP protein in P. aeruginosa. Altogether, our findings emphasize the promise of IDD-8E as a clinical candidate for novel anti-pseudomonal drugs, offering hope in the battle against antibiotic resistance and its devastating impact on global health.
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Affiliation(s)
- Rakshit Manhas
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India
| | - Arti Rathore
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ujwal Havelikar
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India
| | - Shavi Mahajan
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India
| | - Sumit G Gandhi
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Avisek Mahapa
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu, 180001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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6
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Jat MK, Tiwari P, Bajaj R, Shitut I, Mandal S, Watanabe K, Taniguchi T, Krishnamurthy HR, Jain M, Bid A. Higher order gaps in the renormalized band structure of doubly aligned hBN/bilayer graphene moiré superlattice. Nat Commun 2024; 15:2335. [PMID: 38485946 PMCID: PMC10940307 DOI: 10.1038/s41467-024-46672-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 02/27/2024] [Indexed: 03/18/2024] Open
Abstract
This paper presents our findings on the recursive band gap engineering of chiral fermions in bilayer graphene doubly aligned with hBN. Using two interfering moiré potentials, we generate a supermoiré pattern that renormalizes the electronic bands of the pristine bilayer graphene, resulting in higher order fractal gaps even at very low energies. These Bragg gaps can be mapped using a unique linear combination of periodic areas within the system. To validate our findings, we use electronic transport measurements to identify the position of these gaps as a function of the carrier density. We establish their agreement with the predicted carrier densities and corresponding quantum numbers obtained using the continuum model. Our study provides strong evidence of the quantization of the momentum-space area of quasi-Brillouin zones in a minimally incommensurate lattice. It fills important gaps in the understanding of band structure engineering of Dirac fermions with a doubly periodic superlattice spinor potential.
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Affiliation(s)
- Mohit Kumar Jat
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Priya Tiwari
- Braun Center for Submicron Research, Department of Condensed Matter Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Robin Bajaj
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Ishita Shitut
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Shinjan Mandal
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Kenji Watanabe
- Research Center for Electronic and Optical Materials, National Institute for Materials Science, 1-1 Namiki, Tsukuba, 305-0044, Japan
| | - Takashi Taniguchi
- Research Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba, 305-0044, Japan
| | - H R Krishnamurthy
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India
| | - Manish Jain
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India.
| | - Aveek Bid
- Department of Physics, Indian Institute of Science, Bangalore, 560012, India.
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7
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Teja Nibhanupudi SS, Roy A, Veksler D, Coupin M, Matthews KC, Disiena M, Ansh, Singh JV, Gearba-Dolocan IR, Warner J, Kulkarni JP, Bersuker G, Banerjee SK. Ultra-fast switching memristors based on two-dimensional materials. Nat Commun 2024; 15:2334. [PMID: 38485722 PMCID: PMC10940724 DOI: 10.1038/s41467-024-46372-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 02/26/2024] [Indexed: 03/18/2024] Open
Abstract
The ability to scale two-dimensional (2D) material thickness down to a single monolayer presents a promising opportunity to realize high-speed energy-efficient memristors. Here, we report an ultra-fast memristor fabricated using atomically thin sheets of 2D hexagonal Boron Nitride, exhibiting the shortest observed switching speed (120 ps) among 2D memristors and low switching energy (2pJ). Furthermore, we study the switching dynamics of these memristors using ultra-short (120ps-3ns) voltage pulses, a frequency range that is highly relevant in the context of modern complementary metal oxide semiconductor (CMOS) circuits. We employ statistical analysis of transient characteristics to gain insights into the memristor switching mechanism. Cycling endurance data confirms the ultra-fast switching capability of these memristors, making them attractive for next generation computing, storage, and Radio-Frequency (RF) circuit applications.
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Affiliation(s)
- S S Teja Nibhanupudi
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA.
| | - Anupam Roy
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA.
- Birla Institute of Technology, Mesra, Ranchi, 835215, India.
| | | | - Matthew Coupin
- Texas Materials Institute, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Kevin C Matthews
- Texas Materials Institute, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Matthew Disiena
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA
| | - Ansh
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA
| | - Jatin V Singh
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA
| | | | - Jamie Warner
- Texas Materials Institute, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jaydeep P Kulkarni
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA
| | | | - Sanjay K Banerjee
- Microelectronics Research Center, The University of Texas at Austin, Austin, TX, 78758, USA.
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Kar A, Ghosh P, Gautam A, Chowdhury S, Basak D, Sarkar I, Bhoumik A, Barman S, Chakraborty P, Mukhopadhyay A, Mehrotra S, Ganesan SK, Paul S, Chatterjee S. CD38-RyR2 axis-mediated signaling impedes CD8 + T cell response to anti-PD1 therapy in cancer. Proc Natl Acad Sci U S A 2024; 121:e2315989121. [PMID: 38451948 PMCID: PMC10945783 DOI: 10.1073/pnas.2315989121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/08/2024] [Indexed: 03/09/2024] Open
Abstract
PD1 blockade therapy, harnessing the cytotoxic potential of CD8+ T cells, has yielded clinical success in treating malignancies. However, its efficacy is often limited due to the progressive differentiation of intratumoral CD8+ T cells into a hypofunctional state known as terminal exhaustion. Despite identifying CD8+ T cell subsets associated with immunotherapy resistance, the molecular pathway triggering the resistance remains elusive. Given the clear association of CD38 with CD8+ T cell subsets resistant to anti-PD1 therapy, we investigated its role in inducing resistance. Phenotypic and functional characterization, along with single-cell RNA sequencing analysis of both in vitro chronically stimulated and intratumoral CD8+ T cells, revealed that CD38-expressing CD8+ T cells are terminally exhausted. Exploring the molecular mechanism, we found that CD38 expression was crucial in promoting terminal differentiation of CD8+ T cells by suppressing TCF1 expression, thereby rendering them unresponsive to anti-PD1 therapy. Genetic ablation of CD38 in tumor-reactive CD8+ T cells restored TCF1 levels and improved the responsiveness to anti-PD1 therapy in mice. Mechanistically, CD38 expression on exhausted CD8+ T cells elevated intracellular Ca2+ levels through RyR2 calcium channel activation. This, in turn, promoted chronic AKT activation, leading to TCF1 loss. Knockdown of RyR2 or inhibition of AKT in CD8+ T cells maintained TCF1 levels, induced a sustained anti-tumor response, and enhanced responsiveness to anti-PD1 therapy. Thus, targeting CD38 represents a potential strategy to improve the efficacy of anti-PD1 treatment in cancer.
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Affiliation(s)
- Anwesha Kar
- Division of Cancer Biology and Inflammatory Disorder, Translational Research Unit of Excellence, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology, Kolkata700032, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, Uttar Pradesh, India
| | - Puspendu Ghosh
- Division of Cancer Biology and Inflammatory Disorder, Translational Research Unit of Excellence, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology, Kolkata700032, West Bengal, India
| | - Anupam Gautam
- Algorithms in Bioinformatics, Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 1472076, Tübingen, Baden-Württemberg, Germany
- International Max Planck Research School “From Molecules to Organisms”, Max Planck Institute for Biology Tübingen72076, Tübingen, Baden-Württemberg, Germany
| | - Snehanshu Chowdhury
- Division of Cancer Biology and Inflammatory Disorder, Translational Research Unit of Excellence, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology, Kolkata700032, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, Uttar Pradesh, India
| | - Debashree Basak
- Division of Cancer Biology and Inflammatory Disorder, Translational Research Unit of Excellence, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology, Kolkata700032, West Bengal, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, Uttar Pradesh, India
| | - Ishita Sarkar
- Division of Cancer Biology and Inflammatory Disorder, Translational Research Unit of Excellence, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology, Kolkata700032, West Bengal, India
| | - Arpita Bhoumik
- Division of Cancer Biology and Inflammatory Disorder, Translational Research Unit of Excellence, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology, Kolkata700032, West Bengal, India
| | - Shubhrajit Barman
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, Uttar Pradesh, India
- Division of Structural Biology & Bioinformatics, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology, Kolkata700032, West Bengal, India
| | - Paramita Chakraborty
- Department of Surgery, Medical University of South Carolina, Charleston, South CarolinaSC- 29425
| | - Asima Mukhopadhyay
- Kolkata Gynaecology Oncology Trials and Translational Research Group, Kolkata700156, West Bengal, India
| | - Shikhar Mehrotra
- Department of Surgery, Medical University of South Carolina, Charleston, South CarolinaSC- 29425
| | - Senthil Kumar Ganesan
- Division of Structural Biology & Bioinformatics, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology, Kolkata700032, West Bengal, India
| | - Sandip Paul
- System Biology Informatics Lab, Center for Health Science and Technology, JIS Institute of Advanced Studies and Research, JIS University, Kolkata700091, West Bengal, India
| | - Shilpak Chatterjee
- Division of Cancer Biology and Inflammatory Disorder, Translational Research Unit of Excellence, Council of Scientific and Industrial Research-Indian Institute of Chemical Biology, Kolkata700032, West Bengal, India
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9
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Singh S, Saini R, Joshi A, Singh N, Singh RP. Desymmetric homologating annulation to access chiral pentafulvenes and their application in bioimaging. Nat Commun 2024; 15:2101. [PMID: 38453892 PMCID: PMC10920648 DOI: 10.1038/s41467-024-45346-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/16/2024] [Indexed: 03/09/2024] Open
Abstract
The architectural design of polycyclic/multisubstituted pentafulvenes has demonstrated great potential for the development of electrochromic materials and biologically active motifs. Unfortunately, the enantioselective construction of such distinctive cores with all carbon quaternary chiral centers has remained untouched to date. Herein, we disclose an enantioselective homologating annulation of cyclopent-4-ene-dione with 3-cyano-4-methylcoumarins through L-tert-leucine derived thiourea catalysis, affording a wide range of enantioenriched polycyclic multisubstituted embedded aminopentafulvenes with excellent stereocontrol (up to 99:1 er) and chemical yields up to 87%. A detailed photophysical and cytotoxicity analysis of racemic and chiral homologated adducts unveils the exceptional behavior of chiral adducts over their racemic analogs, highlighting the importance of stereoselectivity of the developed scaffolds. A cellular uptake experiment in a mammalian fibroblast cell line confirmed the potential of developed polycyclic aminopentafulvene cores as a highly promising labeling dye that can be utilized for bioimaging without any adverse effects.
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Affiliation(s)
- Sanjay Singh
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, 110016, India
| | - Ravi Saini
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, 110016, India
| | - Akshay Joshi
- Center for Biomedical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Neetu Singh
- Center for Biomedical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Ravi P Singh
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, 110016, India.
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10
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Walia K, Sharma A, Paul S, Chouhan P, Kumar G, Ringe R, Sharma M, Tuli A. SARS-CoV-2 virulence factor ORF3a blocks lysosome function by modulating TBC1D5-dependent Rab7 GTPase cycle. Nat Commun 2024; 15:2053. [PMID: 38448435 PMCID: PMC10918171 DOI: 10.1038/s41467-024-46417-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 02/26/2024] [Indexed: 03/08/2024] Open
Abstract
SARS-CoV-2, the causative agent of COVID-19, uses the host endolysosomal system for entry, replication, and egress. Previous studies have shown that the SARS-CoV-2 virulence factor ORF3a interacts with the lysosomal tethering factor HOPS complex and blocks HOPS-mediated late endosome and autophagosome fusion with lysosomes. Here, we report that SARS-CoV-2 infection leads to hyperactivation of the late endosomal and lysosomal small GTP-binding protein Rab7, which is dependent on ORF3a expression. We also observed Rab7 hyperactivation in naturally occurring ORF3a variants encoded by distinct SARS-CoV-2 variants. We found that ORF3a, in complex with Vps39, sequesters the Rab7 GAP TBC1D5 and displaces Rab7 from this complex. Thus, ORF3a disrupts the GTP hydrolysis cycle of Rab7, which is beneficial for viral production, whereas the Rab7 GDP-locked mutant strongly reduces viral replication. Hyperactivation of Rab7 in ORF3a-expressing cells impaired CI-M6PR retrieval from late endosomes to the trans-Golgi network, disrupting the biosynthetic transport of newly synthesized hydrolases to lysosomes. Furthermore, the tethering of the Rab7- and Arl8b-positive compartments was strikingly reduced upon ORF3a expression. As SARS-CoV-2 egress requires Arl8b, these findings suggest that ORF3a-mediated hyperactivation of Rab7 serves a multitude of functions, including blocking endolysosome formation, interrupting the transport of lysosomal hydrolases, and promoting viral egress.
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Affiliation(s)
- Kshitiz Walia
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Abhishek Sharma
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Sankalita Paul
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Priya Chouhan
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Gaurav Kumar
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Rajesh Ringe
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Mahak Sharma
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Punjab, India
| | - Amit Tuli
- Division of Cell Biology and Immunology, CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India.
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11
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Sharma S, Majumdar A, Basu A. Regulation of Onecut2 by miR-9-5p in Japanese encephalitis virus infected neural stem/progenitor cells. Microbiol Spectr 2024; 12:e0323823. [PMID: 38319106 PMCID: PMC10913399 DOI: 10.1128/spectrum.03238-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Japanese encephalitis virus (JEV) is one of the major neurotropic viral infections that is known to dysregulate the homeostasis of neural stem/progenitor cells (NSPCs) and depletes the stem cell pool. NSPCs are multipotent stem cell population of the central nervous system (CNS) which are known to play an important role in the repair of the CNS during insults/injury caused by several factors such as ischemia, neurological disorders, CNS infections, and so on. Viruses have evolved to utilize host factors for their own benefit and during JEV infection, host factors, including the non-coding RNAs such as miRNAs, are reported to be affected, thereby cellular processes regulated by the miRNAs exhibit perturbed functionality. Previous studies from our laboratory have demonstrated the role of JEV infection in dysregulating the function of neural stem cells (NSCs) by altering the cell fate and depleting the stem cell pool leading to a decline in stem cell function in CNS repair mechanism post-infection. JEV-induced alteration in miRNA expression in the NSCs is one of the major interest to us. In prior studies, we have observed an altered expression pattern of certain miRNAs following JEV infection. In this study, we have validated the role of JEV infection in NSCs in altering the expression of miR-9-5p, which is a known regulator of neurogenesis in NSCs. Furthermore, we have validated the interaction of this miRNA with its target, Onecut2 (OC2), in primary NSCs utilizing miRNA mimic and inhibitor transfection experiments. Our findings indicate a possible role of JEV mediated dysregulated interaction between miR-9-5p and its putative target OC2 in NSPCs. IMPORTANCE MicroRNAs have emerged as key disease pathogenic markers and potential therapeutic targets. In this study, we solidify this concept by studying a key miRNA, miR-9-5p, in Japanese encephalitis virus infection of neural stem/progenitor cells. miRNA target Onecut2 has a possible role in stem cell pool biology. Here, we show a possible mechanistic axis worth investing in neurotropic viral biology.
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Affiliation(s)
| | | | - Anirban Basu
- National Brain Research Centre, Manesar, Haryana, India
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12
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Das P, Chakrabarti O. ISGylation of DRP1 closely balances other post-translational modifications to mediate mitochondrial fission. Cell Death Dis 2024; 15:184. [PMID: 38431611 PMCID: PMC10908869 DOI: 10.1038/s41419-024-06543-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Dynamin related protein 1 (DRP1), a pivotal mitochondrial fission protein, is post-translationally modified by multiple mechanisms. Here we identify a new post-translational modification of DRP1 by the ubiquitin-like protein, interferon-stimulated gene 15 (ISG15). DRP1 ISGylation is mediated by ISG15 E3 ligase, HERC5; this promotes mitochondrial fission. DeISGylation of DRP1 however leads to hyperfusion. Heterologous expression of SARS-CoV2 PLpro, a deISGylating enzyme, results in similar mitochondrial filamentation, significant decrease in total DRP1 protein levels and efflux of mtDNA. We report that deISGylated DRP1 gets ubiquitylated and degraded by TRIM25, instead of PARKIN and MITOL. While the cytosolic pool of DRP1 is primarily ISGylated, both mitochondrial and cytosolic fractions may be ubiquitylated. It is known that phosphorylation of DRP1 at S616 residue regulates its mitochondrial localisation; we show that ISGylation of phospho-DRP1 (S616) renders fission competence at mitochondria. This is significant because DRP1 ISGylation affects its functionality and mitochondrial dynamics in Alzheimer's disease pathophysiology.
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Affiliation(s)
- Palamou Das
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India
- Homi Bhabha National Institute, Mumbai, India
| | - Oishee Chakrabarti
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata, 700064, India.
- Homi Bhabha National Institute, Mumbai, India.
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13
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Yadav MK, Sarma P, Maharana J, Ganguly M, Mishra S, Zaidi N, Dalal A, Singh V, Saha S, Mahajan G, Sharma S, Chami M, Banerjee R, Shukla AK. Structure-guided engineering of biased-agonism in the human niacin receptor via single amino acid substitution. Nat Commun 2024; 15:1939. [PMID: 38431681 PMCID: PMC10908815 DOI: 10.1038/s41467-024-46239-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/18/2024] [Indexed: 03/05/2024] Open
Abstract
The Hydroxycarboxylic acid receptor 2 (HCA2), also known as the niacin receptor or GPR109A, is a prototypical GPCR that plays a central role in the inhibition of lipolytic and atherogenic activities. Its activation also results in vasodilation that is linked to the side-effect of flushing associated with dyslipidemia drugs such as niacin. GPR109A continues to be a target for developing potential therapeutics in dyslipidemia with minimized flushing response. Here, we present cryo-EM structures of the GPR109A in complex with dyslipidemia drugs, niacin or acipimox, non-flushing agonists, MK6892 or GSK256073, and recently approved psoriasis drug, monomethyl fumarate (MMF). These structures elucidate the binding mechanism of agonists, molecular basis of receptor activation, and insights into biased signaling elicited by some of the agonists. The structural framework also allows us to engineer receptor mutants that exhibit G-protein signaling bias, and therefore, our study may help in structure-guided drug discovery efforts targeting this receptor.
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Affiliation(s)
- Manish K Yadav
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Parishmita Sarma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Jagannath Maharana
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Manisankar Ganguly
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Sudha Mishra
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Nashrah Zaidi
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Annu Dalal
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Vinay Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Sayantan Saha
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Gargi Mahajan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Saloni Sharma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Mohamed Chami
- BioEM Lab, Biozentrum, Universität Basel, Basel, Switzerland
| | - Ramanuj Banerjee
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India.
| | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India.
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14
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Teli BB, Nagar P, Priyadarshini Y, Poonia P, Natarajan K. A CUG codon-adapted anchor-away toolkit for functional analysis of genes in Candida albicans. mSphere 2024; 9:e0070323. [PMID: 38251906 PMCID: PMC10900876 DOI: 10.1128/msphere.00703-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/11/2023] [Indexed: 01/23/2024] Open
Abstract
Promoter shutoff of essential genes in the diploid Candida albicans has often been insufficient to create tight, conditional null alleles due to leaky expression and has been a stumbling block in pathogenesis research. Moreover, homozygous deletion of non-essential genes has often been problematic due to the frequent aneuploidy in the mutant strains. Rapid, conditional depletion of essential genes by the anchor-away strategy has been successfully employed in Saccharomyces cerevisiae and other model organisms. Here, rapamycin mediates the dimerization of human FK506-binding protein (FKBP12) and FKBP12-rapamycin-binding (FRB) domain-containing target protein, resulting in relocalization to altered sub-cellular locations. In this work, we used the ribosomal protein Rpl13 as the anchor and took two nuclear proteins as targets to construct a set of mutants in a proof-of-principle approach. We first constructed a rapamycin-resistant C. albicans strain by introducing a dominant mutation in the CaTOR1 gene and a homozygous deletion of RBP1, the ortholog of FKBP12, a primary target of rapamycin. The FKBP12 and the FRB coding sequences were then CUG codon-adapted for C. albicans by site-directed mutagenesis. Anchor-away strains expressing the essential TBP1 gene or the non-essential SPT8 gene as FRB fusions were constructed. We found that rapamycin caused rapid cessation of growth of the TBP-AA strain within 15 minutes and the SPT8-AA strain phenocopied the constitutive filamentous phenotype of the spt8Δ/spt8Δ mutant. Thus, the anchor-away toolbox for C. albicans developed here can be employed for genome-wide analysis to identify gene function in a rapid and reliable manner, further accelerating anti-fungal drug development in C. albicans. IMPORTANCE Molecular genetic studies thus far have identified ~27% open-reading frames as being essential for the vegetative growth of Candida albicans in rich medium out of a total 6,198 haploid set of open reading frames. However, a major limitation has been to construct rapid conditional alleles of essential C. albicans genes with near quantitative depletion of encoded proteins. Here, we have developed a toolbox for rapid and conditional depletion of genes that would aid studies of gene function of both essential and non-essential genes.
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Affiliation(s)
- Basharat Bashir Teli
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Priyanka Nagar
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Yumnam Priyadarshini
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Poonam Poonia
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Krishnamurthy Natarajan
- Laboratory of Eukaryotic Gene Regulation, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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15
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Sahu RR, Ramasamy AS, Bhonsle S, Vailshery M, S A, Kumar H, Das Gupta T. Single-step fabrication of liquid gallium nanoparticles via capillary interaction for dynamic structural colours. Nat Nanotechnol 2024:10.1038/s41565-024-01625-1. [PMID: 38388966 DOI: 10.1038/s41565-024-01625-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 02/02/2024] [Indexed: 02/24/2024]
Abstract
Incorporating structural coloured materials in flexible and stretchable elastomeric substrates requires numerous steps that compromise their scalability and economic viability for prospective applications in visual sensors and displays. Here we describe a one-step approach for fabricating plasmonic Ga nanostructures embedded in a polydimethylsiloxane substrate exhibiting tunable chromaticity, in response to mechanical stimuli. The process exploits the capillary interactions between uncrosslinked oligomeric chains of the substrate and Ga metal deposited by thermal evaporation, as elucidated by a theoretical model that we developed. By tuning the oligomer content in polydimethylsiloxane, we attain a range of colours covering a substantial gamut in CIE (Commission Internationale de l'Éclairage) coordinates. This mechanochromic flexible substrate shows reversible response to external mechanical stimuli for ~80,000 cycles. We showcase the capabilities of our processing technique by presenting prototypes of reflective displays and sensors for monitoring body parts, smart bandages and the capacity of the nanostructured film to map force in real time.
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Affiliation(s)
- Renu Raman Sahu
- Laboratory of Advanced Nanostructures for Photonics and Electronics, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bengaluru, India
| | - Alwar Samy Ramasamy
- Laboratory of Advanced Nanostructures for Photonics and Electronics, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bengaluru, India
| | - Santosh Bhonsle
- Laboratory of Advanced Nanostructures for Photonics and Electronics, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bengaluru, India
| | - Mark Vailshery
- Laboratory of Advanced Nanostructures for Photonics and Electronics, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bengaluru, India
| | - Archana S
- Advanced Facility for Microscopy and Microanalysis, Department of Materials Engineering, Indian Institute of Science, Bengaluru, India
| | - Hemant Kumar
- Advanced Facility for Microscopy and Microanalysis, Department of Materials Engineering, Indian Institute of Science, Bengaluru, India
| | - Tapajyoti Das Gupta
- Laboratory of Advanced Nanostructures for Photonics and Electronics, Department of Instrumentation and Applied Physics, Indian Institute of Science, Bengaluru, India.
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16
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Rani P, George B, V S, Biswas S, V M, Pal A, Rajmani RS, Das S. MicroRNA-22-3p displaces critical host factors from the 5' UTR and inhibits the translation of Coxsackievirus B3 RNA. J Virol 2024; 98:e0150423. [PMID: 38289119 PMCID: PMC10883805 DOI: 10.1128/jvi.01504-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/02/2024] [Indexed: 02/21/2024] Open
Abstract
Coxsackievirus B3 (CVB3) is known to cause acute myocarditis and pancreatitis in humans. We investigated the microRNAs (miRNAs) that can potentially govern the viral life cycle by binding to the untranslated regions (UTRs) of CVB3 RNA. MicroRNA-22-3p was short-listed, as its potential binding site overlapped with the region crucial for recruiting internal ribosome entry site trans-acting factors (ITAFs) and ribosomes. We demonstrate that miR-22-3p binds CVB3 5' UTR, hinders recruitment of key ITAFs on viral mRNA, disrupts the spatial structure required for ribosome recruitment, and ultimately blocks translation. Likewise, cells lacking miR-22-3p exhibited heightened CVB3 infection compared to wild type, confirming its role in controlling infection. Interestingly, miR-22-3p level was found to be increased at 4 hours post-infection, potentially due to the accumulation of viral 2A protease in the early phase of infection. 2Apro enhances the miR-22-3p level to dislodge the ITAFs from the SD-like sequence, rendering the viral RNA accessible for binding of replication factors to switch to replication. Furthermore, one of the cellular targets of miR-22-3p, protocadherin-1 (PCDH1), was significantly downregulated during CVB3 infection. Partial silencing of PCDH1 reduced viral replication, demonstrating its proviral role. Interestingly, upon CVB3 infection in mice, miR-22-3p level was found to be downregulated only in the small intestine, the primary target organ, indicating its possible role in influencing tissue tropism. It appears miR-22-3p plays a dual role during infection by binding viral RNA to aid its life cycle as a viral strategy and by targeting a proviral protein to restrict viral replication as a host response.IMPORTANCECVB3 infection is associated with the development of end-stage heart diseases. Lack of effective anti-viral treatments and vaccines for CVB3 necessitates comprehensive understanding of the molecular players during CVB3 infection. miRNAs have emerged as promising targets for anti-viral strategies. Here, we demonstrate that miR-22-3p binds to 5' UTR and inhibits viral RNA translation at the later stage of infection to promote viral RNA replication. Conversely, as host response, it targets PCDH1, a proviral factor, to discourage viral propagation. miR-22-3p also influences CVB3 tissue tropism. Deciphering the multifaced role of miR-22-3p during CVB3 infection unravels the necessary molecular insights, which can be exploited for novel intervening strategies to curb infection and restrict viral pathogenesis.
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Affiliation(s)
- Priya Rani
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Biju George
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Sabarishree V
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Somarghya Biswas
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Madhurya V
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Apala Pal
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Raju S. Rajmani
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- National Institute of Biomedical Genomics, Kalyani, India
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17
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Chakraborty MP, Das D, Mondal P, Kaul P, Bhattacharyya S, Kumar Das P, Das R. Molecular basis of VEGFR1 autoinhibition at the plasma membrane. Nat Commun 2024; 15:1346. [PMID: 38355851 PMCID: PMC10866885 DOI: 10.1038/s41467-024-45499-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
Ligand-independent activation of VEGFRs is a hallmark of diabetes and several cancers. Like EGFR, VEGFR2 is activated spontaneously at high receptor concentrations. VEGFR1, on the other hand, remains constitutively inactive in the unligated state, making it an exception among VEGFRs. Ligand stimulation transiently phosphorylates VEGFR1 and induces weak kinase activation in endothelial cells. Recent studies, however, suggest that VEGFR1 signaling is indispensable in regulating various physiological or pathological events. The reason why VEGFR1 is regulated differently from other VEGFRs remains unknown. Here, we elucidate a mechanism of juxtamembrane inhibition that shifts the equilibrium of VEGFR1 towards the inactive state, rendering it an inefficient kinase. The juxtamembrane inhibition of VEGFR1 suppresses its basal phosphorylation even at high receptor concentrations and transiently stabilizes tyrosine phosphorylation after ligand stimulation. We conclude that a subtle imbalance in phosphatase activation or removing juxtamembrane inhibition is sufficient to induce ligand-independent activation of VEGFR1 and sustain tyrosine phosphorylation.
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Affiliation(s)
- Manas Pratim Chakraborty
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India
| | - Diptatanu Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India
| | - Purav Mondal
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India
| | - Pragya Kaul
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India
| | - Soumi Bhattacharyya
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India
| | - Prosad Kumar Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India
| | - Rahul Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India.
- Centre for Advanced Functional Materials, Indian Institute of Science Education and Research Kolkata, Mohanpur campus, Mohanpur, 741246, India.
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18
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Gardi N, Chaubal R, Parab P, Pachakar S, Kulkarni S, Shet T, Joshi S, Kembhavi Y, Chandrani P, Quist J, Kowtal P, Grigoriadis A, Sarin R, Govindarajan R, Gupta S. Natural History of Germline BRCA1 Mutated and BRCA Wild-type Triple-negative Breast Cancer. Cancer Res Commun 2024; 4:404-417. [PMID: 38315150 PMCID: PMC10865976 DOI: 10.1158/2767-9764.crc-23-0277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/09/2023] [Accepted: 01/26/2024] [Indexed: 02/07/2024]
Abstract
We report a deep next-generation sequencing analysis of 13 sequentially obtained tumor samples, eight sequentially obtained circulating tumor DNA (ctDNA) samples and three germline DNA samples over the life history of 3 patients with triple-negative breast cancer (TNBC), 2 of whom had germline pathogenic BRCA1 mutation, to unravel tumor evolution. Tumor tissue from all timepoints and germline DNA was subjected to whole-exome sequencing (WES), custom amplicon deep sequencing (30,000X) of a WES-derived somatic mutation panel, and SNP arrays for copy-number variation (CNV), while whole transcriptome sequencing (RNA-seq) was performed only on somatic tumor.There was enrichment of homologous recombination deficiency signature in all tumors and widespread CNV, which remained largely stable over time. Somatic tumor mutation numbers varied between patients and within each patient (range: 70-216, one outlier). There was minimal mutational overlap between patients with TP53 being the sole commonly mutated gene, but there was substantial overlap in sequential samples in each patient. Each patient's tumor contained a founding ("stem") clone at diagnosis, which persisted over time, from which all other clones ("subclone") were derived ("branching evolution"), which contained mutations in well-characterized cancer-related genes like PDGFRB, ARID2, TP53 (Patient_02), TP53, BRAF, BRIP1, CSF3R (Patient_04), and TP53, APC, EZH2 (Patient_07). Including stem and subclones, tumors from all patients were polyclonal at diagnosis and during disease progression. ctDNA recapitulated most tissue-derived stem clonal and subclonal mutations while detecting some additional subclonal mutations. RNA-seq revealed a stable basal-like pattern, with most highly expressed variants belonging to stem clone. SIGNIFICANCE In germline BRCA1 mutated and BRCA wild-type patients, TNBC shows a branching evolutionary pattern of mutations with a single founding clone, are polyclonal throughout their disease course, and have widespread copy-number aberrations. This evolutionary pattern may be associated with treatment resistance or sensitivity and could be therapeutically exploited.
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Affiliation(s)
- Nilesh Gardi
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Clinician Scientist Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Mumbai
| | - Rohan Chaubal
- Clinician Scientist Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Mumbai
- Department of Surgical Oncology, Tata Memorial Centre, Mumbai
| | - Pallavi Parab
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Homi Bhabha National Institute, Mumbai
| | - Sunil Pachakar
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Clinician Scientist Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Mumbai
| | - Suyash Kulkarni
- Homi Bhabha National Institute, Mumbai
- Department of Radiodiagnosis, Tata Memorial Centre, Mumbai
| | - Tanuja Shet
- Homi Bhabha National Institute, Mumbai
- Department of Pathology, Tata Memorial Centre, Mumbai
| | - Shalaka Joshi
- Homi Bhabha National Institute, Mumbai
- Department of Surgical Oncology, Tata Memorial Centre, Mumbai
| | - Yogesh Kembhavi
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Homi Bhabha National Institute, Mumbai
| | - Pratik Chandrani
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Homi Bhabha National Institute, Mumbai
| | - Jelmar Quist
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- Breast Cancer Now Unit, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Pradnya Kowtal
- Homi Bhabha National Institute, Mumbai
- DNA sequencing Facility, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai
| | - Anita Grigoriadis
- Cancer Bioinformatics, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- Breast Cancer Now Unit, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Rajiv Sarin
- Homi Bhabha National Institute, Mumbai
- Department of Radiation Oncology, Tata Memorial Centre, Mumbai
| | | | - Sudeep Gupta
- Department of Medical Oncology, Tata Memorial Centre, Mumbai
- Clinician Scientist Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Navi Mumbai
- Homi Bhabha National Institute, Mumbai
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19
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Khan KIA, Kumar A, Gupta P, Yadav RS, Åkerman J, Muduli PK. Magnetodynamic properties of ultrathin films of Fe[Formula: see text]Sn[Formula: see text]-a topological kagome ferromagnet. Sci Rep 2024; 14:3487. [PMID: 38347066 DOI: 10.1038/s41598-024-53621-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
Fe[Formula: see text]Sn[Formula: see text] is a topological kagome ferromagnet that possesses numerous Weyl points close to the Fermi energy, which can manifest various unique transport phenomena such as chiral anomaly, anomalous Hall effect, and giant magnetoresistance. However, the magnetodynamic properties of Fe[Formula: see text]Sn[Formula: see text] have not yet been explored. Here, we report, for the first time, the measurements of the intrinsic Gilbert damping constant ([Formula: see text]), and the effective spin mixing conductance (g[Formula: see text]) of Pt/Fe[Formula: see text]Sn[Formula: see text] bilayers for Fe[Formula: see text]Sn[Formula: see text] thicknesses down to 2 nm, for which [Formula: see text] is [Formula: see text], and g[Formula: see text] is [Formula: see text]. The films have a high saturation magnetization, [Formula: see text], and large anomalous Hall coefficient, [Formula: see text]. The large values of g[Formula: see text], together with the topological properties of Fe[Formula: see text]Sn[Formula: see text], make Fe[Formula: see text]Sn[Formula: see text]/Pt bilayers useful heterostructures for the study of topological spintronic devices.
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Affiliation(s)
- Kacho Imtiyaz Ali Khan
- Department of Physics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Akash Kumar
- Applied Spintronics Group, Department of Physics, University of Gothenburg, Gothenburg, 412 96, Sweden
- Center for Science and Innovation in Spintronics, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
- Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Pankhuri Gupta
- Department of Physics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Ram Singh Yadav
- Department of Physics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Johan Åkerman
- Applied Spintronics Group, Department of Physics, University of Gothenburg, Gothenburg, 412 96, Sweden.
- Center for Science and Innovation in Spintronics, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan.
- Research Institute of Electrical Communication, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan.
| | - Pranaba Kishor Muduli
- Department of Physics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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20
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Fajal S, Mandal W, Torris A, Majumder D, Let S, Sen A, Kanheerampockil F, Shirolkar MM, Ghosh SK. Ultralight crystalline hybrid composite material for highly efficient sequestration of radioiodine. Nat Commun 2024; 15:1278. [PMID: 38341406 DOI: 10.1038/s41467-024-45581-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Considering the importance of sustainable nuclear energy, effective management of radioactive nuclear waste, such as sequestration of radioiodine has inflicted a significant research attention in recent years. Despite the fact that materials have been reported for the adsorption of iodine, development of effective adsorbent with significantly improved segregation properties for widespread practical applications still remain exceedingly difficult due to lack of proper design strategies. Herein, utilizing unique hybridization synthetic strategy, a composite crystalline aerogel material has been fabricated by covalent stepping of an amino-functionalized stable cationic discrete metal-organic polyhedra with dual-pore containing imine-functionalized covalent organic framework. The ultralight hybrid composite exhibits large surface area with hierarchical macro-micro porosity and multifunctional binding sites, which collectively interact with iodine. The developed nano-adsorbent demonstrate ultrahigh vapor and aqueous-phase iodine adsorption capacities of 9.98 g.g-1 and 4.74 g.g-1, respectively, in static conditions with fast adsorption kinetics, high retention efficiency, reusability and recovery.
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Affiliation(s)
- Sahel Fajal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhaba Road, Pashan, 411008, Pune, India
| | - Writakshi Mandal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhaba Road, Pashan, 411008, Pune, India
| | - Arun Torris
- Polymer Science and Engineering Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Dipanjan Majumder
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhaba Road, Pashan, 411008, Pune, India
| | - Sumanta Let
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhaba Road, Pashan, 411008, Pune, India
| | - Arunabha Sen
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhaba Road, Pashan, 411008, Pune, India
| | - Fayis Kanheerampockil
- Polymer Science and Engineering Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Mandar M Shirolkar
- Advanced Bio-Agro Tech Pvt. Ltd, Baner, Pune, 411045, India
- Norel Nutrient Bio-Agro Tech Pvt. Ltd, Baner, Pune, 411045, India
| | - Sujit K Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhaba Road, Pashan, 411008, Pune, India.
- Centre for Water Research (CWR), Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhaba Road, Pashan, Pune, 411008, India.
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21
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Kalita B, Sahu S, Bharadwaj A, Panneerselvam L, Martinez-Cebrian G, Agarwal M, Mathew SJ. The Wnt-pathway corepressor TLE3 interacts with the histone methyltransferase KMT1A to inhibit differentiation in Rhabdomyosarcoma. Oncogene 2024; 43:524-538. [PMID: 38177411 DOI: 10.1038/s41388-023-02911-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024]
Abstract
Rhabdomyosarcoma tumor cells resemble differentiating skeletal muscle cells, which unlike normal muscle cells, fail to undergo terminal differentiation, underlying their proliferative and metastatic properties. We identify the corepressor TLE3 as a key regulator of rhabdomyosarcoma tumorigenesis by inhibiting the Wnt-pathway. Loss of TLE3 function leads to Wnt-pathway activation, reduced proliferation, decreased migration, and enhanced differentiation in rhabdomyosarcoma cells. Muscle-specific TLE3-knockout results in enhanced expression of terminal myogenic differentiation markers during normal mouse development. TLE3-knockout rhabdomyosarcoma cell xenografts result in significantly smaller tumors characterized by reduced proliferation, increased apoptosis and enhanced differentiation. We demonstrate that TLE3 interacts with and recruits the histone methyltransferase KMT1A, leading to repression of target gene activation and inhibition of differentiation in rhabdomyosarcoma. A combination drug therapy regime to promote Wnt-pathway activation by the small molecule BIO and inhibit KMT1A by the drug chaetocin led to significantly reduced tumor volume, decreased proliferation, increased expression of differentiation markers and increased survival in rhabdomyosarcoma tumor-bearing mice. Thus, TLE3, the Wnt-pathway and KMT1A are excellent drug targets which can be exploited for treating rhabdomyosarcoma tumors.
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Affiliation(s)
- Bhargab Kalita
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
- Department of Pathology and Perlmutter Cancer Center, New York University School of Medicine, New York, NY, 10016, USA
| | - Subhashni Sahu
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Anushree Bharadwaj
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Lakshmikanthan Panneerselvam
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | | | - Megha Agarwal
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India
- Affiliated to Manipal University, Manipal, Karnataka, 576104, India
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Sam J Mathew
- Developmental Genetics Laboratory Regional Centre for Biotechnology (RCB) NCR Biotech Science Cluster 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, 121001, Haryana, India.
- Affiliated to Manipal University, Manipal, Karnataka, 576104, India.
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22
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Mir MH, Parmar S, Singh C, Kalia D. Location-agnostic site-specific protein bioconjugation via Baylis Hillman adducts. Nat Commun 2024; 15:859. [PMID: 38286847 PMCID: PMC10825175 DOI: 10.1038/s41467-024-45124-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024] Open
Abstract
Proteins labelled site-specifically with small molecules are valuable assets for chemical biology and drug development. The unique reactivity profile of the 1,2-aminothiol moiety of N-terminal cysteines (N-Cys) of proteins renders it highly attractive for regioselective protein labelling. Herein, we report an ultrafast Z-selective reaction between isatin-derived Baylis Hillman adducts and 1,2-aminothiols to form a bis-heterocyclic scaffold, and employ it for stable protein bioconjugation under both in vitro and live-cell conditions. We refer to our protein bioconjugation technology as Baylis Hillman orchestrated protein aminothiol labelling (BHoPAL). Furthermore, we report a lipoic acid ligase-based technology for introducing the 1,2-aminothiol moiety at any desired site within proteins, rendering BHoPAL location-agnostic (not limited to N-Cys). By using this approach in tandem with BHoPAL, we generate dually labelled protein bioconjugates appended with different labels at two distinct specific sites on a single protein molecule. Taken together, the protein bioconjugation toolkit that we disclose herein will contribute towards the generation of both mono and multi-labelled protein-small molecule bioconjugates for applications as diverse as biophysical assays, cellular imaging, and the production of therapeutic protein-drug conjugates. In addition to protein bioconjugation, the bis-heterocyclic scaffold we report herein will find applications in synthetic and medicinal chemistry.
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Affiliation(s)
- Mudassir H Mir
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Sangeeta Parmar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Chhaya Singh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India
| | - Dimpy Kalia
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, 462066, Madhya Pradesh, India.
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23
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Bhardwaj K, Kalita A, Verma N, Prakash A, Thakur R, Dutta D. Rho-dependent termination enables cellular pH homeostasis. J Bacteriol 2024; 206:e0035623. [PMID: 38169297 PMCID: PMC10810219 DOI: 10.1128/jb.00356-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 12/05/2023] [Indexed: 01/05/2024] Open
Abstract
The termination factor Rho, an ATP-dependent RNA translocase, preempts pervasive transcription processes, thereby rendering genome integrity in bacteria. Here, we show that the loss of Rho function raised the intracellular pH to >8.0 in Escherichia coli. The loss of Rho function upregulates tryptophanase-A (TnaA), an enzyme that catabolizes tryptophan to produce indole, pyruvate, and ammonia. We demonstrate that the enhanced TnaA function had produced the conjugate base ammonia, raising the cellular pH in the Rho-dependent termination defective strains. On the other hand, the constitutively overexpressed Rho lowered the cellular pH to about 6.2, independent of cellular ammonia levels. Since Rho overexpression may increase termination activities, the decrease in cellular pH could result from an excess H+ ion production during ATP hydrolysis by overproduced Rho. Furthermore, we performed in vivo termination assays to show that the efficiency of Rho-dependent termination was increased at both acidic and basic pH ranges. Given that the Rho level remained unchanged, the alkaline pH increases the termination efficiency by stimulating Rho's catalytic activity. We conducted the Rho-mediated RNA release assay from a stalled elongation complex to show an efficient RNA release at alkaline pH, compared to the neutral or acidic pH, that supports our in vivo observation. Whereas acidic pH appeared to increase the termination function by elevating the cellular level of Rho. This study is the first to link Rho function to the cellular pH homeostasis in bacteria. IMPORTANCE The current study shows that the loss or gain of Rho-dependent termination alkalizes or acidifies the cytoplasm, respectively. In the case of loss of Rho function, the tryptophanase-A enzyme is upregulated, and degrades tryptophan, producing ammonia to alkalize cytoplasm. We hypothesize that Rho overproduction by deleting its autoregulatory DNA portion increases termination function, causing excessive ATP hydrolysis to produce H+ ions and cytoplasmic acidification. Therefore, this study is the first to unravel a relationship between Rho function and intrinsic cellular pH homeostasis. Furthermore, the Rho level increases in the absence of autoregulation, causing cytoplasmic acidification. As intracellular pH plays a critical role in enzyme function, such a connection between Rho function and alkalization will have far-reaching implications for bacterial physiology.
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Affiliation(s)
- Kanika Bhardwaj
- CSIR Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Arunima Kalita
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Neha Verma
- CSIR Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Anand Prakash
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Ruchika Thakur
- CSIR Institute of Microbial Technology, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Dipak Dutta
- CSIR Institute of Microbial Technology, Chandigarh, India
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24
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Dey S, Mondal A. Unveiling the role of host kinases at different steps of influenza A virus life cycle. J Virol 2024; 98:e0119223. [PMID: 38174932 PMCID: PMC10805039 DOI: 10.1128/jvi.01192-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024] Open
Abstract
Influenza viruses remain a major public health concern causing contagious respiratory illnesses that result in around 290,000-650,000 global deaths every year. Their ability to constantly evolve through antigenic shifts and drifts leads to the emergence of newer strains and resistance to existing drugs and vaccines. To combat this, there is a critical need for novel antiviral drugs through the introduction of host-targeted therapeutics. Influenza viruses encode only 14 gene products that get extensively modified through phosphorylation by a diverse array of host kinases. Reversible phosphorylation at serine, threonine, or tyrosine residues dynamically regulates the structure, function, and subcellular localization of viral proteins at different stages of their life cycle. In addition, kinases influence a plethora of signaling pathways that also regulate virus propagation by modulating the host cell environment thus establishing a critical virus-host relationship that is indispensable for executing successful infection. This dependence on host kinases opens up exciting possibilities for developing kinase inhibitors as next-generation anti-influenza therapy. To fully capitalize on this potential, extensive mapping of the influenza virus-host kinase interaction network is essential. The key focus of this review is to outline the molecular mechanisms by which host kinases regulate different steps of the influenza A virus life cycle, starting from attachment-entry to assembly-budding. By assessing the contributions of different host kinases and their specific phosphorylation events during the virus life cycle, we aim to develop a holistic overview of the virus-host kinase interaction network that may shed light on potential targets for novel antiviral interventions.
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Affiliation(s)
- Soumik Dey
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Arindam Mondal
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, India
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25
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Kumar N, Sharma S, Kaushal PS. Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH. Nat Commun 2024; 15:638. [PMID: 38245551 PMCID: PMC10799931 DOI: 10.1038/s41467-024-44879-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
Ribosome hibernation is a key survival strategy bacteria adopt under environmental stress, where a protein, hibernation promotion factor (HPF), transitorily inactivates the ribosome. Mycobacterium tuberculosis encounters hypoxia (low oxygen) as a major stress in the host macrophages, and upregulates the expression of RafH protein, which is crucial for its survival. The RafH, a dual domain HPF, an orthologue of bacterial long HPF (HPFlong), hibernates ribosome in 70S monosome form, whereas in other bacteria, the HPFlong induces 70S ribosome dimerization and hibernates its ribosome in 100S disome form. Here, we report the cryo- EM structure of M. smegmatis, a close homolog of M. tuberculosis, 70S ribosome in complex with the RafH factor at an overall 2.8 Å resolution. The N- terminus domain (NTD) of RafH binds to the decoding center, similarly to HPFlong NTD. In contrast, the C- terminus domain (CTD) of RafH, which is larger than the HPFlong CTD, binds to a distinct site at the platform binding center of the ribosomal small subunit. The two domain-connecting linker regions, which remain mostly disordered in earlier reported HPFlong structures, interact mainly with the anti-Shine Dalgarno sequence of the 16S rRNA.
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Affiliation(s)
- Niraj Kumar
- Structural Biology & Translation Regulation Laboratory, UNESCO-DBT, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121 001, India
| | - Shivani Sharma
- Structural Biology & Translation Regulation Laboratory, UNESCO-DBT, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121 001, India
| | - Prem S Kaushal
- Structural Biology & Translation Regulation Laboratory, UNESCO-DBT, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121 001, India.
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26
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Kumar PP, Rao GV, Shetty M, Pradeep R, PremaVani C, Sasikala M, Reddy DN. Understanding the Structural Arrangement of Islets in Chronic Pancreatitis. J Histochem Cytochem 2024; 72:25-40. [PMID: 38063163 PMCID: PMC10795563 DOI: 10.1369/00221554231217552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 10/20/2023] [Indexed: 12/31/2023] Open
Abstract
Islet transplantation has become an established method for the treatment of insulin-deficient diabetes such as type 1 and type 3C (pancreatogenic). An effective transplantation necessitates a thorough understanding of the islet architecture and related functions to improve engraftment outcomes. However, in chronic pancreatitis (CP), the structural and related functional information is inadequate. Hence, the present study is aimed to understand the cytoarchitecture of endocrine cells and their functional implications in CP with and without diabetes. Herein, a set of human pancreatic tissue specimens (normal, n=5 and CP, n=20) was collected and processed for islet isolation. Furthermore, immunohistochemistry was used to assess the vascular densities, cell mass, organization, and cell-cell interactions. The glucose-stimulated insulin release results revealed that in chronic pancreatitis without diabetes mellitus altered (CPNDA), at basal glucose concentration the insulin secretion was increased by 24.2%, whereas at high glucose concentration the insulin levels were reduced by 77.4%. The impaired insulin secretion may be caused by alterations in the cellular architecture of islets during CP progression, particularly in chronic pancreatitis with diabetes mellitus and CPNDA conditions. Based on the results, a deeper comprehension of islet architecture would be needed to enhance successful transplantation in CP patients: (J Histochem Cytochem XX.XXX-XXX, XXXX).
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Affiliation(s)
- Pondugala Pavan Kumar
- Translational Research Center, Asian Healthcare Foundation, Hyderabad, India
- AIG Hospitals, Hyderabad, India
| | | | | | | | | | - Mitnala Sasikala
- Translational Research Center, Asian Healthcare Foundation, Hyderabad, India
| | - Duvvur Nageshwar Reddy
- Translational Research Center, Asian Healthcare Foundation, Hyderabad, India
- AIG Hospitals, Hyderabad, India
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27
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Prajapat SK, Mishra L, Khera S, Owusu SD, Ahuja K, Sharma P, Choudhary E, Chhabra S, Kumar N, Singh R, Kaushal PS, Mahajan D, Banerjee A, Motiani RK, Vrati S, Kalia M. Methotrimeprazine is a neuroprotective antiviral in JEV infection via adaptive ER stress and autophagy. EMBO Mol Med 2024; 16:185-217. [PMID: 38177535 PMCID: PMC10897192 DOI: 10.1038/s44321-023-00014-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 01/06/2024] Open
Abstract
Japanese encephalitis virus (JEV) pathogenesis is driven by a combination of neuronal death and neuroinflammation. We tested 42 FDA-approved drugs that were shown to induce autophagy for antiviral effects. Four drugs were tested in the JE mouse model based on in vitro protective effects on neuronal cell death, inhibition of viral replication, and anti-inflammatory effects. The antipsychotic phenothiazines Methotrimeprazine (MTP) & Trifluoperazine showed a significant survival benefit with reduced virus titers in the brain, prevention of BBB breach, and inhibition of neuroinflammation. Both drugs were potent mTOR-independent autophagy flux inducers. MTP inhibited SERCA channel functioning, and induced an adaptive ER stress response in diverse cell types. Pharmacological rescue of ER stress blocked autophagy and antiviral effect. MTP did not alter translation of viral RNA, but exerted autophagy-dependent antiviral effect by inhibiting JEV replication complexes. Drug-induced autophagy resulted in reduced NLRP3 protein levels, and attenuation of inflammatory cytokine/chemokine release from infected microglial cells. Our study suggests that MTP exerts a combined antiviral and anti-inflammatory effect in JEV infection, and has therapeutic potential for JE treatment.
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Affiliation(s)
- Surendra K Prajapat
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Laxmi Mishra
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Sakshi Khera
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Shadrack D Owusu
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
- Institut de Biologie Moléculaire et Cellulaire (IBMC), Université de Strasbourg, 67000, Strasbourg, France
| | - Kriti Ahuja
- Laboratory of Calciomics and Systemic Pathophysiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Puja Sharma
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Eira Choudhary
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Simran Chhabra
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Niraj Kumar
- Structural Biology & Translation Regulation Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Rajan Singh
- Advanced Technology Platform Centre, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
- Department of Life Sciences, Shiv Nadar University, Greater Noida, 201314, India
| | - Prem S Kaushal
- Structural Biology & Translation Regulation Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Dinesh Mahajan
- Chemistry and Pharmacology Lab, Centre for Drug Design and Discovery, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Arup Banerjee
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Rajender K Motiani
- Laboratory of Calciomics and Systemic Pathophysiology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Sudhanshu Vrati
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India
| | - Manjula Kalia
- Virology Research Group, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121001, India.
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28
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Danda D, Goel R, Kabeerdoss J, Sun C, Danda S, Lincy Franklin A, Joseph G, Nath SK. Angiogenesis related genes in Takayasu Arteritis (TAK): robust association with Tag SNPs of IL-18 and FGF-2 in a South Asian Cohort. J Hum Genet 2024; 69:13-18. [PMID: 37848720 DOI: 10.1038/s10038-023-01198-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023]
Abstract
We performed genetic association study for genes encoding angiogenic and angiostatic proteins in patients with Takayasu arteritis (TAK). A total of 96 SNPs involving 60 genes were studied. Genotyping was performed in Fluidigm 96.96 Dynamic Array chip. All statistical analysis for SNP evaluation was performed using PLINK software. Initial analyses revealed five SNPs from three genes [IL-18 (encodes Interleukin-18), FGF2 (encodes Fibroblast Growth Factor-2), and ANGPT1 (encodes Angiopoietin-1)] as significantly different between controls and cases (uncorrected p < 0.05). After permutation-based analysis, two tag SNPs on the promoter region of IL-18 (rs187238 and rs1946518) and one 3'UTR tag SNP (rs1476217) of FGF2 were significantly associated with susceptibility to TAK, with p and OR (95% CI) of 0.0006 and 1.64 (1.25-2.17), 0.03 and 1.28 (1.02-1.64) & 0.016 and 1.33 (1.05-1.67), respectively; while, the two tag SNPs of ANGPT1 gene (rs6469101 and rs16875900) showed a trend (p = 0.055 & p = 0.051, respectively after permutation based correction). There is robust linkage disequilibrium between the two tag SNPs of IL-18 gene as validated by 1000 genome data of South Asian population; the eQTL effects of these tag SNPs of IL-18 and FGF2 genes on adjacent genes further suggest that these tag SNPs act as genetic risks for development of TAK in South Asians, with possible functional implications towards future biomarker development. Genotype phenotype study by genetic model-based analysis also revealed associations between genotype subsets and clinical features like fever, visual loss, left subclavian and coronary artery involvement in our TAK patients.
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Affiliation(s)
- Debashish Danda
- Department of Clinical Immunology and Rheumatology, Christian Medical College, Vellore, Tamil Nadu, India.
| | - Ruchika Goel
- Department of Clinical Immunology and Rheumatology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Jayakanthan Kabeerdoss
- Department of Clinical Immunology and Rheumatology, Christian Medical College, Vellore, Tamil Nadu, India
- Department of Paediatrics, Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | - Celi Sun
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Sumita Danda
- Department of Medical Genetics, Christian Medical College, Vellore, Tamil Nadu, India
| | - Anisea Lincy Franklin
- Department of Clinical Immunology and Rheumatology, Christian Medical College, Vellore, Tamil Nadu, India
| | - George Joseph
- Department of Cardiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Swapan K Nath
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
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29
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Singh PR, Dadireddy V, Udupa S, Kalladi SM, Shee S, Khosla S, Rajmani RS, Singh A, Ramakumar S, Nagaraja V. The Mycobacterium tuberculosis methyltransferase Rv2067c manipulates host epigenetic programming to promote its own survival. Nat Commun 2023; 14:8497. [PMID: 38129415 PMCID: PMC10739865 DOI: 10.1038/s41467-023-43940-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
Mycobacterium tuberculosis has evolved several mechanisms to counter host defense arsenals for its proliferation. Here we report that M. tuberculosis employs a multi-pronged approach to modify host epigenetic machinery for its survival. It secretes methyltransferase (MTase) Rv2067c into macrophages, trimethylating histone H3K79 in a non-nucleosomal context. Rv2067c downregulates host MTase DOT1L, decreasing DOT1L-mediated nucleosomally added H3K79me3 mark on pro-inflammatory response genes. Consequent inhibition of caspase-8-dependent apoptosis and enhancement of RIPK3-mediated necrosis results in increased pathogenesis. In parallel, Rv2067c enhances the expression of SESTRIN3, NLRC3, and TMTC1, enabling the pathogen to overcome host inflammatory and oxidative responses. We provide the structural basis for differential methylation of H3K79 by Rv2067c and DOT1L. The structures of Rv2067c and DOT1L explain how their action on H3K79 is spatially and temporally separated, enabling Rv2067c to effectively intercept the host epigenetic circuit and downstream signaling.
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Affiliation(s)
- Prakruti R Singh
- Department of Microbiology & Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
- Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
| | | | - Shubha Udupa
- Department of Microbiology & Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Shashwath Malli Kalladi
- Department of Microbiology & Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Somnath Shee
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Sanjeev Khosla
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh (CSIR -IMTech), Chandigarh, India
| | - Raju S Rajmani
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Amit Singh
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | | | - Valakunja Nagaraja
- Department of Microbiology & Cell Biology, Indian Institute of Science (IISc), Bengaluru, India.
- Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India.
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Behera A, Reddy ABM. WWP1 E3 ligase at the crossroads of health and disease. Cell Death Dis 2023; 14:853. [PMID: 38129384 PMCID: PMC10739765 DOI: 10.1038/s41419-023-06380-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 12/03/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
The E3 ubiquitin ligase WWP1 (WW Domain-containing E3 Ubiquitin Protein Ligase 1) is a member of the HECT (Homologous to the E6-associated protein Carboxyl Terminus) E3 ligase family. It is conserved across several species and plays crucial roles in various physiological processes, including development, cell growth and proliferation, apoptosis, and differentiation. It exerts its functions through ubiquitination or protein-protein interaction with PPXY-containing proteins. WWP1 plays a role in several human diseases, including cardiac conditions, neurodevelopmental, age-associated osteogenic disorders, infectious diseases, and cancers. In solid tumors, WWP1 plays a dual role as both an oncogene and a tumor suppressor, whereas in hematological malignancies such as AML, it is identified as a dedicated oncogene. Importantly, WWP1 inhibition using small molecule inhibitors such as Indole-3-Carbinol (I3C) and Bortezomib or siRNAs leads to significant suppression of cancer growth and healing of bone fractures, suggesting that WWP1 might serve as a potential therapeutic target for several diseases. In this review, we discuss the evolutionary perspective, structure, and functions of WWP1 and its multilevel regulation by various regulators. We also examine its emerging roles in cancer progression and its therapeutic potential. Finally, we highlight WWP1's role in normal physiology, contribution to pathological conditions, and therapeutic potential for cancer and other diseases.
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Affiliation(s)
- Abhayananda Behera
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
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Singh AK, Gangakhedkar R, Thakur HS, Raman SK, Patil SA, Jain V. Mycobacteriophage D29 Lysin B exhibits promising anti-mycobacterial activity against drug-resistant Mycobacterium tuberculosis. Microbiol Spectr 2023; 11:e0459722. [PMID: 37800970 PMCID: PMC10714809 DOI: 10.1128/spectrum.04597-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 08/18/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE To combat the rapidly emerging drug-resistant M. tuberculosis, it is now essential to look for alternative therapeutics. Mycobacteriophages can be considered as efficient therapeutics due to their natural ability to infect and kill mycobacteria including M. tuberculosis. Here, we have exploited the mycolyl-arabinogalactan esterase property of LysB encoded from mycobacteriophage D29. This study is novel in terms of targeting a multi-drug-resistant pathogenic strain of M. tuberculosis with LysB and also examining the combination of anti-TB drugs and LysB. All the experiments include external administration of LysB. Therefore, the remarkable lytic activity of LysB overcomes the difficulty to enter the complex cell envelope of mycobacteria. Targeting the intracellularly located M. tuberculosis by LysB and non-toxicity to macrophages take the process of the development of LysB as a drug one step ahead, and also, the interaction studies with rifampicin and isoniazid will help to form a new treatment regimen against tuberculosis.
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Affiliation(s)
- Amit Kumar Singh
- Experimental Animal Facility, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, Uttar Pradesh, India
| | - Rutuja Gangakhedkar
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Hemant Singh Thakur
- Experimental Animal Facility, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, Uttar Pradesh, India
| | - Sunil Kumar Raman
- Pharmaceutics and Pharmacokinetics Division, CSIR-Central Drug Research Institute, Lucknow, India
| | - Shripad A. Patil
- Experimental Animal Facility, ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, M. Miyazaki Marg, Tajganj, Agra, Uttar Pradesh, India
| | - Vikas Jain
- Microbiology and Molecular Biology Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
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Saha A, Ali W, Werz DB, Maiti D. Highly scalable photoinduced synthesis of silanols via untraversed pathway for chlorine radical (Cl •) generation. Nat Commun 2023; 14:8173. [PMID: 38071374 PMCID: PMC10710510 DOI: 10.1038/s41467-023-43286-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/06/2023] [Indexed: 02/26/2024] Open
Abstract
The emergence of visible light-mediated synthetic transformations has transpired as a promising approach to redefine traditional organic synthesis in a sustainable way. In this genre, transition metal-mediated photoredox catalysis has led the way and recreated a plethora of organic transformations. However, the use of photochemical energy solely to initiate the reaction is underexplored. With the direct utilization of photochemical energy herein, we have established a general and practical protocol for the synthesis of diversely functionalized organosilanols, silanediols, and polymeric siloxanol engaging a wide spectrum of hydrosilanes under ambient reaction conditions. Streamlined synthesis of bio-active silanols via late-stage functionalization underscores the importance of this sustainable protocol. Interestingly, this work also reveals photoinduced non-classical chlorine radical (Cl•) generation from a readily available chlorinated solvent under aerobic conditions. The intriguing factors of the proposed mechanism involving chlorine and silyl radicals as intermediates were supported by a series of mechanistic investigations.
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Affiliation(s)
- Argha Saha
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Wajid Ali
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Daniel B Werz
- Albert-Ludwigs-Universität Freiburg, Institute of Organic Chemistry, Albertstr. 21, 79104, Freiburg, Germany.
| | - Debabrata Maiti
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India.
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33
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Bhattacharyya A, Sahu A, Patra S, Tiwari V. Low- and high-frequency vibrations synergistically enhance singlet exciton fission through robust vibronic resonances. Proc Natl Acad Sci U S A 2023; 120:e2310124120. [PMID: 38019862 DOI: 10.1073/pnas.2310124120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/14/2023] [Indexed: 12/01/2023] Open
Abstract
Singlet exciton fission (SEF) is initiated by ultrafast internal conversion of a singlet exciton into a correlated triplet pair [Formula: see text]. The "reaction coordinates" for ultrafast SEF even in archetypal systems such as pentacene thin film remain unclear. Couplings between fast electrons and slow nuclei are ubiquitous across a range of phenomena in chemistry. Accordingly, spectroscopic detection of vibrational coherences in the [Formula: see text] photoproduct motivated investigations into a possible role of vibronic coupling, akin to that reported in several photosynthetic proteins. However, acenes are very different from chlorophylls with 10× larger vibrational displacements upon photoexcitation and low-frequency vibrations modulating intermolecular orbital overlaps. Whether (and if so how) these unique features carry any mechanistic significance for SEF remains a poorly understood question. Accordingly, synthetic design of new molecules aiming to mimic this process across the solar spectrum has broadly relied on tuning electronic couplings. We address this gap and identify previously unrecognized synergistic interplay of vibrations, which in striking contrast to photosynthesis, vitally enhances SEF across a broad, nonselective and, therefore, unavoidable range of vibrational frequencies. We argue that attaching mechanistic significance to spectroscopically observed prominent quantum beats is misleading. Instead, we show that vibronic mixing leads to anisotropic quantum beats and propose readily implementable polarization-based two-dimensional electronic spectroscopy experiments which uniquely distinguish vibrations which drive vibronic mixing and promote SEF, against spectator vibrations simply accompanying ultrafast internal conversion. Our findings introduce crucial ingredients in synthetic design of SEF materials and spectroscopy experiments aiming to decipher mechanistic details from quantum beats.
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Affiliation(s)
- Atandrita Bhattacharyya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Amitav Sahu
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sanjoy Patra
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Vivek Tiwari
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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34
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Banerjee A, Anand M, Kalita S, Ganji M. Single-molecule analysis of DNA base-stacking energetics using patterned DNA nanostructures. Nat Nanotechnol 2023; 18:1474-1482. [PMID: 37591937 PMCID: PMC10716042 DOI: 10.1038/s41565-023-01485-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/10/2023] [Indexed: 08/19/2023]
Abstract
The DNA double helix structure is stabilized by base-pairing and base-stacking interactions. However, a comprehensive understanding of dinucleotide base-stacking energetics is lacking. Here we combined multiplexed DNA-based point accumulation in nanoscale topography (DNA-PAINT) imaging with designer DNA nanostructures and measured the free energy of dinucleotide base stacking at the single-molecule level. Multiplexed imaging enabled us to extract the binding kinetics of an imager strand with and without additional dinucleotide stacking interactions. The DNA-PAINT data showed that a single additional dinucleotide base stacking results in up to 250-fold stabilization for the DNA duplex nanostructure. We found that the dinucleotide base-stacking energies vary from -0.95 ± 0.12 kcal mol-1 to -3.22 ± 0.04 kcal mol-1 for C|T and A|C base-stackings, respectively. We demonstrate the application of base-stacking energetics in designing DNA-PAINT probes for multiplexed super-resolution imaging, and efficient assembly of higher-order DNA nanostructures. Our results will aid in designing functional DNA nanostructures, and DNA and RNA aptamers, and facilitate better predictions of the local DNA structure.
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Affiliation(s)
- Abhinav Banerjee
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Micky Anand
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Simanta Kalita
- New Chemistry Unit and Chemistry and Physics of Materials Unit, The Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Mahipal Ganji
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.
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35
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Phulpagar P, Holla VV, Tomar D, Kamble N, Yadav R, Pal PK, Muthusamy B. Novel CWF19L1 mutations in patients with spinocerebellar ataxia, autosomal recessive 17. J Hum Genet 2023; 68:859-866. [PMID: 37752213 DOI: 10.1038/s10038-023-01195-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/09/2023] [Accepted: 09/06/2023] [Indexed: 09/28/2023]
Abstract
Spinocerebellar ataxia, autosomal recessive-17 (SCAR17) is a rare hereditary ataxia characterized by ataxic gait, cerebellar signs and occasionally accompanied by intellectual disability and seizures. Pathogenic mutations in the CWF19L1 gene that code for CWF19 like cell cycle control factor 1 cause SCAR17. We report here two unrelated families with the clinical characteristics of global developmental delay, cerebellar ataxia, pyramidal signs, and seizures. Cerebellar atrophy, and T2/FLAIR hypointense transverse pontine stripes were observed in brain imaging. Exome sequencing identified novel homozygous mutations including a splice acceptor site variant c.1375-2 A > G on intron 12 in a male patient and a single nucleotide variant c.452 T > G on exon 5 resulting in a missense variant p.Ile151Ser in the female patient from two unrelated families, respectively. Sanger sequencing confirmed the segregation of these variants in the family members with autosomal recessive inheritance. Transcript analysis of the splice site variant revealed activation of a novel cryptic splice acceptor site on exon 13 resulting in an alternative transcription with a loss of nine nucleotides on exon 13. Translation of this transcript predicted an in-frame deletion of three amino acids p.(459_461del). We also observed a novel exon 13 skipping which results in premature termination of the protein product. Our study expands the phenotype, radiological features, and genotypes known in SCAR17.
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Affiliation(s)
- Prashant Phulpagar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Vikram V Holla
- Department of Neurology, NIMHANS, Hosur Road, Bangalore, 560029, India
| | - Deepti Tomar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
| | - Nitish Kamble
- Department of Neurology, NIMHANS, Hosur Road, Bangalore, 560029, India
| | - Ravi Yadav
- Department of Neurology, NIMHANS, Hosur Road, Bangalore, 560029, India
| | - Pramod Kumar Pal
- Department of Neurology, NIMHANS, Hosur Road, Bangalore, 560029, India.
| | - Babylakshmi Muthusamy
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India.
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
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36
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Yandrapally S, Sarkar S, Banerjee S. HIV-1 Tat commandeers nuclear export of Rev-viral RNA complex by controlling hnRNPA2-mediated splicing. J Virol 2023; 97:e0104423. [PMID: 37905837 PMCID: PMC10688328 DOI: 10.1128/jvi.01044-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023] Open
Abstract
IMPORTANCE HIV-infected host cells impose varied degrees of regulation on viral replication, from very high to abortive. Proliferation of HIV in astrocytes is limited when compared to immune cells, such as CD4+ T lymphocytes. Understanding such differential regulation is one of the key questions in the field as these cells permit HIV persistence and rebound viremia, challenging HIV treatment and clinical cure. This study focuses on understanding the molecular mechanism behind such cell-specific disparities. We show that one of the key mechanisms is the regulation of heterogenous nuclear ribonucleoprotein A2, a host factor involved in alternative splicing and RNA processing, by HIV-1 Tat in CD4+ T lymphocytes, not observed in astrocytes. This regulation causes an increase in the levels of unspliced/partially spliced viral RNA and nuclear export of Rev-RNA complexes which results in high viral propagation in CD4+ T lymphocytes. The study reveals a new mechanism imposed by HIV on host cells that determines the fate of infection.
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Affiliation(s)
- Sriram Yandrapally
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Satarupa Sarkar
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Sharmistha Banerjee
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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37
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Kumar S, Delipan R, Chakraborty D, Kanjo K, Singh R, Singh N, Siddiqui S, Tyagi A, Jha V, Thakur KG, Pandey R, Varadarajan R, Ringe RP. Mutations in S2 subunit of SARS-CoV-2 Omicron spike strongly influence its conformation, fusogenicity, and neutralization sensitivity. J Virol 2023; 97:e0092223. [PMID: 37861334 PMCID: PMC10688319 DOI: 10.1128/jvi.00922-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE The Omicron subvariants have substantially evaded host-neutralizing antibodies and adopted an endosomal route of entry. The virus has acquired several mutations in the receptor binding domain and N-terminal domain of S1 subunit, but remarkably, also incorporated mutations in S2 which are fixed in Omicron sub-lineage. Here, we found that the mutations in the S2 subunit affect the structural and biological properties such as neutralization escape, entry route, fusogenicity, and protease requirement. In vivo, these mutations may have significant roles in tropism and replication. A detailed understanding of the effects of S2 mutations on Spike function, immune evasion, and viral entry would inform the vaccine design, as well as therapeutic interventions aiming to block the essential proteases for virus entry. Thus, our study has identified the crucial role of S2 mutations in stabilizing the Omicron spike and modulating neutralization resistance to antibodies targeting the S1 subunit.
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Affiliation(s)
- Sahil Kumar
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Rathina Delipan
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | | | - Kawkab Kanjo
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | | | - Nittu Singh
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Samreen Siddiqui
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Akansha Tyagi
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Vinitaa Jha
- Max Super Speciality Hospital (A Unit of Devki Devi Foundation), Max Healthcare, Delhi, India
| | - Krishan G. Thakur
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | | | - Rajesh P. Ringe
- CSIR-Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Chandigarh, India
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38
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Kumari S, Bandyopadhyay B, Singh A, Aggarwal S, Yadav AK, Vikram NK, Guchhait P, Banerjee A. Extracellular vesicles recovered from plasma of severe dengue patients induce CD4+ T cell suppression through PD-L1/PD-1 interaction. mBio 2023; 14:e0182323. [PMID: 37982662 PMCID: PMC10746246 DOI: 10.1128/mbio.01823-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/09/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Severe dengue manifestations caused by the dengue virus are a global health problem. Studies suggest that severe dengue disease depends on uncontrolled immune cell activation, and excessive inflammation adds to the pathogenesis of severe dengue disease. Therefore, it is important to understand the process that triggers the uncontrolled activation of the immune cells. The change in immune response in mild to severe dengue may be due to direct virus-to-cell interaction or it could be a contact-independent process through the extracellular vesicles (EVs) released from infected cells. The importance of circulating EVs in the context of dengue virus infection and pathogenesis remains unexplored. Therefore, understanding the possible biological function of circulating EVs may help to delineate the role of EVs in the progression of disease. Our present study highlights that EVs from plasma of severe dengue patients can have immunosuppressive properties on CD4+ T cells which may contribute to T cell suppression and may contribute to dengue disease progression.
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Affiliation(s)
- Sharda Kumari
- Laboratory of Virology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Bhaswati Bandyopadhyay
- Department of Microbiology, Calcutta School of Tropical Medicine, Kolkata, West Bengal, India
| | - Anamika Singh
- Disease Biology Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Suruchi Aggarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Amit Kumar Yadav
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Naval Kishore Vikram
- Department of Infectious Disease & Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Prasenjit Guchhait
- Disease Biology Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Arup Banerjee
- Laboratory of Virology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
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Sherekar S, Todankar CS, Viswanathan GA. Modulating the dynamics of NFκB and PI3K enhances the ensemble-level TNFR1 signaling mediated apoptotic response. NPJ Syst Biol Appl 2023; 9:57. [PMID: 37973854 PMCID: PMC10654705 DOI: 10.1038/s41540-023-00318-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
Cell-to-cell variability during TNFα stimulated Tumor Necrosis Factor Receptor 1 (TNFR1) signaling can lead to single-cell level pro-survival and apoptotic responses. This variability stems from the heterogeneity in signal flow through intracellular signaling entities that regulate the balance between these two phenotypes. Using systematic Boolean dynamic modeling of a TNFR1 signaling network, we demonstrate that the signal flow path variability can be modulated to enable cells favour apoptosis. We developed a computationally efficient approach "Boolean Modeling based Prediction of Steady-state probability of Phenotype Reachability (BM-ProSPR)" to accurately predict the network's ability to settle into different phenotypes. Model analysis juxtaposed with the experimental observations revealed that NFκB and PI3K transient responses guide the XIAP behaviour to coordinate the crucial dynamic cross-talk between the pro-survival and apoptotic arms at the single-cell level. Model predicted the experimental observations that ~31% apoptosis increase can be achieved by arresting Comp1 - IKK* activity which regulates the NFκB and PI3K dynamics. Arresting Comp1 - IKK* activity causes signal flow path re-wiring towards apoptosis without significantly compromising NFκB levels, which govern adequate cell survival. Priming an ensemble of cancerous cells with inhibitors targeting the specific interaction involving Comp1 and IKK* prior to TNFα exposure could enable driving them towards apoptosis.
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Affiliation(s)
- Shubhank Sherekar
- Department of Chemical Engineering, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India
| | - Chaitra S Todankar
- Department of Chemical Engineering, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India
| | - Ganesh A Viswanathan
- Department of Chemical Engineering, Indian Institute of Technology Bombay Powai, Mumbai, 400076, India.
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40
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Sengoden M, Bhat GA, Rutledge RJ, Rashid S, Dar AA, Darensbourg DJ. Micellar catalysis: Polymer bound palladium catalyst for carbon-carbon coupling reactions in water. Proc Natl Acad Sci U S A 2023; 120:e2312907120. [PMID: 37922331 PMCID: PMC10655565 DOI: 10.1073/pnas.2312907120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/29/2023] [Indexed: 11/05/2023] Open
Abstract
Metallosurfactants, defined here as hydrophobic metal-containing groups embedded in hydrophilic units when dispersed in water, emanate in the formation of metallomicelles. This approach continues to attract great interest for its ability to serve as micellar catalysts for various metal-mediated chemical transformations in water. Indeed, relevant to green chemistry, micellar catalysis plays a preeminent function as a replacement for organic solvents in a variety of chemical reactions. There are several methods for the interaction of metal complexes (catalysts or catalyst precursors) and surfactants for producing micellar aggregates. A very effective manner for achieving this involves the direct bonding of the metal center to the amphiphilic polymeric materials. Herein, we describe the synthesis of a metallosurfactant containing a palladium complex covalently incorporated into a CO2-based triblock polycarbonate derived using a dicarboxylic acid chain-transfer agent. This amphiphilic polycarbonate was shown to self-assemble in water to provide uniform and spherical micelles, where the catalytic metal center is located in the hydrophobic portion of the micelle. The resulting metallosurfactant was demonstrated to effectively catalyze carbon-carbon coupling reactions at very low catalyst loadings.
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Affiliation(s)
- Mani Sengoden
- Department of Chemistry, Texas A & M University, College Station, TX77843
| | - Gulzar A. Bhat
- Centre for Interdisciplinary Research and Innovations, University of Kashmir, Srinagar, Jammu and Kashmir190006, India
| | - Ryan J. Rutledge
- Department of Chemistry, Texas A & M University, College Station, TX77843
| | - Showkat Rashid
- Soft Matter Research Group, Department of Chemistry, University of Kashmir, Srinagar, Jammu and Kashmir190006, India
| | - Aijaz A. Dar
- Soft Matter Research Group, Department of Chemistry, University of Kashmir, Srinagar, Jammu and Kashmir190006, India
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Joshi A, Walimbe A, Avni A, Rai SK, Arora L, Sarkar S, Mukhopadhyay S. Single-molecule FRET unmasks structural subpopulations and crucial molecular events during FUS low-complexity domain phase separation. Nat Commun 2023; 14:7331. [PMID: 37957147 PMCID: PMC10643395 DOI: 10.1038/s41467-023-43225-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
Biomolecular condensates formed via phase separation of proteins and nucleic acids are thought to be associated with a wide range of cellular functions and dysfunctions. We dissect critical molecular events associated with phase separation of an intrinsically disordered prion-like low-complexity domain of Fused in Sarcoma by performing single-molecule studies permitting us to access the wealth of molecular information that is skewed in conventional ensemble experiments. Our single-molecule FRET experiments reveal the coexistence of two conformationally distinct subpopulations in the monomeric form. Single-droplet single-molecule FRET studies coupled with fluorescence correlation spectroscopy, picosecond time-resolved fluorescence anisotropy, and vibrational Raman spectroscopy indicate that structural unwinding switches intramolecular interactions into intermolecular contacts allowing the formation of a dynamic network within condensates. A disease-related mutation introduces enhanced structural plasticity engendering greater interchain interactions that can accelerate pathological aggregation. Our findings provide key mechanistic underpinnings of sequence-encoded dynamically-controlled structural unzipping resulting in biological phase separation.
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Affiliation(s)
- Ashish Joshi
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
| | - Anuja Walimbe
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
| | - Anamika Avni
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Sandeep K Rai
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
| | - Lisha Arora
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
| | - Snehasis Sarkar
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India.
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India.
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India.
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42
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Chaudhary E, George F, Saji A, Dey S, Ghosh S, Thomas T, Kurpad AV, Sharma S, Singh N, Agarwal S, Mehta U. Cumulative effect of PM 2.5 components is larger than the effect of PM 2.5 mass on child health in India. Nat Commun 2023; 14:6955. [PMID: 37907499 PMCID: PMC10618175 DOI: 10.1038/s41467-023-42709-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/19/2023] [Indexed: 11/02/2023] Open
Abstract
While studies on ambient fine particulate matter (PM2.5) exposure effect on child health are available, the differential effects, if any, of exposure to PM2.5 species are unexplored in lower and middle-income countries. Using multiple logistic regression, we showed that for every 10 μg m-3 increase in PM2.5 exposure, anaemia, acute respiratory infection, and low birth weight prevalence increase by 10% (95% uncertainty interval, UI: 9-11), 11% (8-13), and 5% (4-6), respectively, among children in India. NO3-, elemental carbon, and NH4+ were more associated with the three health outcomes than other PM2.5 species. We found that the total PM2.5 mass as a surrogate marker for air pollution exposure could substantially underestimate the true composite impact of different components of PM2.5. Our findings provide key indigenous evidence to prioritize control strategies for reducing exposure to more toxic species for greater child health benefits in India.
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Affiliation(s)
- Ekta Chaudhary
- Centre for Atmospheric Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Franciosalgeo George
- Division of Epidemiology, Biostatistics, and Population Health, St John's Research Institute, Bangalore, India
| | - Aswathi Saji
- Division of Epidemiology, Biostatistics, and Population Health, St John's Research Institute, Bangalore, India
| | - Sagnik Dey
- Centre for Atmospheric Sciences, Indian Institute of Technology Delhi, New Delhi, India.
- Centre of Excellence for Research on Clean Air, IIT Delhi, New Delhi, India.
- School of Public Policy, IIT Delhi, New Delhi, India.
| | - Santu Ghosh
- Department of Biostatistics, St John's Medical College, Bengaluru, India.
| | - Tinku Thomas
- Department of Biostatistics, St John's Medical College, Bengaluru, India
| | - Anura V Kurpad
- Department of Physiology, St John's Medical College, Bengaluru, India
| | | | - Nimish Singh
- Centre for Atmospheric Sciences, Indian Institute of Technology Delhi, New Delhi, India
- TERI, New Delhi, India
| | - Shivang Agarwal
- TERI, New Delhi, India
- Johns Hopkins University, Baltimore, MD, USA
| | - Unnati Mehta
- Harvard T.H. Chan School of Public Health, Boston, USA
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43
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Gayatri MB, Kancha RK, Behera A, Patchva D, Velugonda N, Gundeti S, Reddy ABM. AMPK-induced novel phosphorylation of RUNX1 inhibits STAT3 activation and overcome imatinib resistance in chronic myelogenous leukemia (CML) subjects. Cell Death Discov 2023; 9:401. [PMID: 37903788 PMCID: PMC10616083 DOI: 10.1038/s41420-023-01700-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 11/01/2023] Open
Abstract
Imatinib resistance remains an unresolved problem in CML disease. Activation of JAK2/STAT3 pathway and increased expression of RUNX1 have become one reason for development of imatinib resistance in CML subjects. Metformin has gained attention as an antileukemic drug in recent times. However, the molecular mechanism remains elusive. The present study shows that RUNX1 is a novel substrate of AMP-activated kinase (AMPK), where AMPK phosphorylates RUNX1 at Ser 94 position. Activation of AMPK by metformin could lead to increased cytoplasmic retention of RUNX1 due to Ser 94 phosphorylation. RUNX1 Ser 94 phosphorylation resulted in increased interaction with STAT3, which was reflected in reduced transcriptional activity of both RUNX1 and STAT3 due to their cytoplasmic retention. The reduced transcriptional activity of STAT3 and RUNX1 resulted in the down-regulation of their signaling targets involved in proliferation and anti-apoptosis. Our cell proliferation assays using in vitro resistant cell line models and PBMCs isolated from CML clinical patients and normal subjects demonstrate that metformin treatment resulted in reduced growth and improved imatinib sensitivity of resistant subjects.
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Affiliation(s)
- Meher Bolisetti Gayatri
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Rama Krishna Kancha
- Molecular Medicine and Therapeutics Laboratory, CPMB, Osmania University, Hyderabad, 500007, India
| | - Abhayananda Behera
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Dorababu Patchva
- Department of Pharmacology, Apollo Institute of Medical Sciences and Research, Jubilee Hills, Hyderabad, 500033, India
| | - Nagaraj Velugonda
- Department of Medical Oncology, Nizam's Institute of Medical Sciences, Hyderabad, 500082, India
| | - Sadasivudu Gundeti
- Department of Medical Oncology, Nizam's Institute of Medical Sciences, Hyderabad, 500082, India
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44
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Guria S, Hassan MMM, Ma J, Dey S, Liang Y, Chattopadhyay B. A tautomerized ligand enabled meta selective C-H borylation of phenol. Nat Commun 2023; 14:6906. [PMID: 37903772 PMCID: PMC10616221 DOI: 10.1038/s41467-023-42310-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/06/2023] [Indexed: 11/01/2023] Open
Abstract
Remote meta selective C-H functionalization of aromatic compounds remains a challenging problem in chemical synthesis. Here, we report an iridium catalyst bearing a bidentate pyridine-pyridone (PY-PYRI) ligand framework that efficiently catalyzes this meta selective borylation reaction. We demonstrate that the developed concept can be employed to introduce a boron functionality at the remote meta position of phenols, phenol containing bioactive and drug molecules, which was an extraordinary challenge. Moreover, we have demonstrated that the method can also be applied for the remote C6 borylation of indole derivatives including tryptophan that was the key synthetic precursor for the total synthesis of Verruculogen and Fumitremorgin A alkaloids. The inspiration of this catalytic concept was started from the O-Si secondary interaction, which by means of several more detailed control experiments and detailed computational investigations revealed that an unprecedented Bpin shift occurs during the transformation of iridium bis(boryl) complex to iridium tris(boryl) complex, which eventually control the remote meta selectivity by means of the dispersion between the designed ligand and steering silane group.
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Affiliation(s)
- Saikat Guria
- Department of Biological & Synthetic Chemistry, Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow, 226014, Uttar Pradesh, India
| | - Mirja Md Mahamudul Hassan
- Department of Biological & Synthetic Chemistry, Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow, 226014, Uttar Pradesh, India
| | - Jiawei Ma
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Sayan Dey
- Department of Biological & Synthetic Chemistry, Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow, 226014, Uttar Pradesh, India
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.
| | - Buddhadeb Chattopadhyay
- Department of Biological & Synthetic Chemistry, Centre of Biomedical Research, SGPGIMS Campus, Raebareli Road, Lucknow, 226014, Uttar Pradesh, India.
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45
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Barman D, Annadhasan M, Bidkar AP, Rajamalli P, Barman D, Ghosh SS, Chandrasekar R, Iyer PK. Highly efficient color-tunable organic co-crystals unveiling polymorphism, isomerism, delayed fluorescence for optical waveguides and cell-imaging. Nat Commun 2023; 14:6648. [PMID: 37863932 PMCID: PMC10589249 DOI: 10.1038/s41467-023-42017-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 09/27/2023] [Indexed: 10/22/2023] Open
Abstract
Photofunctional co-crystal engineering strategies based on donor-acceptor π-conjugated system facilitates expedient molecular packing, consistent morphology, and switchable optical properties, conferring synergic 'structure-property relationship' for optoelectronic and biological functions. In this work, a series of organic co-crystals were formulated using a twisted aromatic hydrocarbon (TAH) donor and three diverse planar acceptors, resulting in color-tunable solid and aggregated state emission via variable packing and through-space charge-transfer interactions. While, adjusting the strength of acceptors, a structural transformation into hybrid stacking modes ultimately results in color-specific polymorphs, a configurational cis-isomer with very high photoluminescence quantum yield. The cis-isomeric co-crystal exhibits triplet-harvesting thermally activated delayed fluorescence (TADF) characteristics, presenting a key discovery in hydrocarbon-based multicomponent systems. Further, 1D-microrod-shaped co-crystal acts as an efficient photon-transducing optical waveguides, and their excellent dispersibility in water endows efficient cellular internalization with bright cell imaging performances. These salient approaches may open more avenues for the design and applications of TAH based co-crystals.
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Affiliation(s)
- Debasish Barman
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Mari Annadhasan
- School of Chemistry, and Centre for Nanotechnology University of Hyderabad, Gachibowli, Prof. C. R. Rao Road, Hyderabad, 500046, India
| | - Anil Parsram Bidkar
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, 94143, USA
| | | | - Debika Barman
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, India
| | - Siddhartha Sankar Ghosh
- Department of Biosciences and Bioengineering IIT Guwahati, Guwahati, Assam, India.
- Centre for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati, 781039, India.
| | - Rajadurai Chandrasekar
- School of Chemistry, and Centre for Nanotechnology University of Hyderabad, Gachibowli, Prof. C. R. Rao Road, Hyderabad, 500046, India.
| | - Parameswar Krishnan Iyer
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, India.
- Centre for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati, 781039, India.
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46
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Allein F, Anastasiadis A, Chaunsali R, Frankel I, Boechler N, Diakonos FK, Theocharis G. Strain topological metamaterials and revealing hidden topology in higher-order coordinates. Nat Commun 2023; 14:6633. [PMID: 37857621 PMCID: PMC10587163 DOI: 10.1038/s41467-023-42321-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023] Open
Abstract
Topological physics has revolutionized materials science, introducing topological phases of matter in diverse settings ranging from quantum to photonic and phononic systems. Herein, we present a family of topological systems, which we term "strain topological metamaterials", whose topological properties are hidden and unveiled only under higher-order (strain) coordinate transformations. We firstly show that the canonical mass dimer, a model that can describe various settings such as electrical circuits and optics, among others, belongs to this family where strain coordinates reveal a topological nontriviality for the edge states at free boundaries. Subsequently, we introduce a mechanical analog of the Majorana-supporting Kitaev chain, which supports topological edge states for both fixed and free boundaries within the proposed framework. Thus, our findings not only extend the way topological edge states are identified, but also promote the fabrication of novel topological metamaterials in various fields, with more complex, tailored boundaries.
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Affiliation(s)
- Florian Allein
- Univ. Lille, CNRS, Centrale Lille, Junia, Univ. Polytechnique Hauts-de-France, UMR 8520-IEMN-Institut d'Electronique de Microélectronique et de Nanotechnologie, 59000, Lille, France
| | - Adamantios Anastasiadis
- Laboratoire d'Acoustique de l'Université du Mans (LAUM), UMR 6613, Institut d'Acoustique-Graduate School (IA-GS), CNRS, Le Mans Université, Le Mans, France
| | - Rajesh Chaunsali
- Department of Aerospace Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Ian Frankel
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Nicholas Boechler
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Georgios Theocharis
- Laboratoire d'Acoustique de l'Université du Mans (LAUM), UMR 6613, Institut d'Acoustique-Graduate School (IA-GS), CNRS, Le Mans Université, Le Mans, France.
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47
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Mondal S, Tanari P, Roy S, Bhunia S, Chowdhury R, Pal AK, Datta A, Pal B, Reddy CM. Autonomous self-healing organic crystals for nonlinear optics. Nat Commun 2023; 14:6589. [PMID: 37852998 PMCID: PMC10584936 DOI: 10.1038/s41467-023-42131-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 10/02/2023] [Indexed: 10/20/2023] Open
Abstract
Non-centrosymmetric molecular crystals have a plethora of applications, such as piezoelectric transducers, energy storage and nonlinear optical materials owing to their unique structural order which is absent in other synthetic materials. As most crystals are brittle, their efficiency declines upon prolonged usage due to fatigue or catastrophic failure, limiting their utilities. Some natural substances, like bone, enamel, leaf and skin, function efficiently, last a life-time, thanks to their inherent self-healing nature. Therefore, incorporating self-healing ability in crystalline materials will greatly broaden their scope. Here, we report single crystals of a dibenzoate derivative, capable of self-healing within milliseconds via autonomous actuation. Systematic quantitative experiments reveal the limit of mechanical forces that the self-healing crystals can withstand. As a proof-of-concept, we also demonstrate that our self-healed crystals can retain their second harmonic generation (SHG) with high efficiency. Kinematic analysis of the actuation in our system also revealed its impressive performance parameters, and shows actuation response times in the millisecond range.
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Affiliation(s)
- Saikat Mondal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, 741246, West Bengal, India
| | - Pratap Tanari
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, 741246, West Bengal, India
| | - Samrat Roy
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, 741246, West Bengal, India
| | - Surojit Bhunia
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, 741246, West Bengal, India
| | - Rituparno Chowdhury
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, 741246, West Bengal, India
| | - Arun K Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, West Bengal, India
| | - Ayan Datta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, West Bengal, India
| | - Bipul Pal
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, 741246, West Bengal, India.
| | - C Malla Reddy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Nadia, 741246, West Bengal, India.
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48
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Poudyal M, Patel K, Gadhe L, Sawner AS, Kadu P, Datta D, Mukherjee S, Ray S, Navalkar A, Maiti S, Chatterjee D, Devi J, Bera R, Gahlot N, Joseph J, Padinhateeri R, Maji SK. Intermolecular interactions underlie protein/peptide phase separation irrespective of sequence and structure at crowded milieu. Nat Commun 2023; 14:6199. [PMID: 37794023 PMCID: PMC10550955 DOI: 10.1038/s41467-023-41864-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) has emerged as a crucial biological phenomenon underlying the sequestration of macromolecules (such as proteins and nucleic acids) into membraneless organelles in cells. Unstructured and intrinsically disordered domains are known to facilitate multivalent interactions driving protein LLPS. We hypothesized that LLPS could be an intrinsic property of proteins/polypeptides but with distinct phase regimes irrespective of their sequence and structure. To examine this, we studied many (a total of 23) proteins/polypeptides with different structures and sequences for LLPS study in the presence and absence of molecular crowder, polyethylene glycol (PEG-8000). We showed that all proteins and even highly charged polypeptides (under study) can undergo liquid condensate formation, however with different phase regimes and intermolecular interactions. We further demonstrated that electrostatic, hydrophobic, and H-bonding or a combination of such intermolecular interactions plays a crucial role in individual protein/peptide LLPS.
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Affiliation(s)
- Manisha Poudyal
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Komal Patel
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, IIT Bombay, Powai, Mumbai, 400076, India
| | - Laxmikant Gadhe
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Ajay Singh Sawner
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Debalina Datta
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Semanti Mukherjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Soumik Ray
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Siddhartha Maiti
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
- Department of Bioengineering, VIT Bhopal University, Bhopal-Indore Highway, Kothrikalan, Sehore, Madhya Pradesh, 466114, India
| | - Debdeep Chatterjee
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Jyoti Devi
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Riya Bera
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Nitisha Gahlot
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Jennifer Joseph
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay, Powai, Mumbai, 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, IIT Bombay, Powai, Mumbai, 400076, India.
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49
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Ghosh P, Raj N, Verma H, Patel M, Chakraborti S, Khatri B, Doreswamy CM, Anandakumar SR, Seekallu S, Dinesh MB, Jadhav G, Yadav PN, Chatterjee J. An amide to thioamide substitution improves the permeability and bioavailability of macrocyclic peptides. Nat Commun 2023; 14:6050. [PMID: 37770425 PMCID: PMC10539501 DOI: 10.1038/s41467-023-41748-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 09/06/2023] [Indexed: 09/30/2023] Open
Abstract
Solvent shielding of the amide hydrogen bond donor (NH groups) through chemical modification or conformational control has been successfully utilized to impart membrane permeability to macrocyclic peptides. We demonstrate that passive membrane permeability can also be conferred by masking the amide hydrogen bond acceptor (>C = O) through a thioamide substitution (>C = S). The membrane permeability is a consequence of the lower desolvation penalty of the macrocycle resulting from a concerted effect of conformational restriction, local desolvation of the thioamide bond, and solvent shielding of the amide NH groups. The enhanced permeability and metabolic stability on thioamidation improve the bioavailability of a macrocyclic peptide composed of hydrophobic amino acids when administered through the oral route in rats. Thioamidation of a bioactive macrocyclic peptide composed of polar amino acids results in analogs with longer duration of action in rats when delivered subcutaneously. These results highlight the potential of O to S substitution as a stable backbone modification in improving the pharmacological properties of peptide macrocycles.
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Affiliation(s)
- Pritha Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Nishant Raj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Hitesh Verma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Monika Patel
- Neuroscience & Ageing Biology, CSIR-CDRI, Lucknow, 226031, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sohini Chakraborti
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Chandrashekar M Doreswamy
- Department of Pre-clinical Research, Anthem Biosciences Pvt. Ltd., Bangalore, 560099, Karnataka, India
| | - S R Anandakumar
- Department of Pre-clinical Research, Anthem Biosciences Pvt. Ltd., Bangalore, 560099, Karnataka, India
| | - Srinivas Seekallu
- Department of Pre-clinical Research, Anthem Biosciences Pvt. Ltd., Bangalore, 560099, Karnataka, India
| | - M B Dinesh
- Central Animal Facility, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Gajanan Jadhav
- Eurofins Advinus Biopharma Services India Pvt. Ltd., Bangalore, 560058, Karnataka, India
| | - Prem Narayan Yadav
- Neuroscience & Ageing Biology, CSIR-CDRI, Lucknow, 226031, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India.
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Ghosh C, Ghosh S, Chatterjee A, Bera P, Mampallil D, Ghosh P, Das D. Dual enzyme-powered chemotactic cross β amyloid based functional nanomotors. Nat Commun 2023; 14:5903. [PMID: 37737223 PMCID: PMC10516904 DOI: 10.1038/s41467-023-41301-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/30/2023] [Indexed: 09/23/2023] Open
Abstract
Nanomotor chassis constructed from biological precursors and powered by biocatalytic transformations can offer important applications in the future, specifically in emergent biomedical techniques. Herein, cross β amyloid peptide-based nanomotors (amylobots) were prepared from short amyloid peptides. Owing to their remarkable binding capabilities, these soft constructs are able to host dedicated enzymes to catalyze orthogonal substrates for motility and navigation. Urease helps in powering the self-diffusiophoretic motion, while cytochrome C helps in providing navigation control. Supported by the simulation model, the design principle demonstrates the utilization of two distinct transport behaviours for two different types of enzymes, firstly enhanced diffusivity of urease with increasing fuel (urea) concentration and secondly, chemotactic motility of cytochrome C towards its substrate (pyrogallol). Dual catalytic engines allow the amylobots to be utilized for enhanced catalysis in organic solvent and can thus complement the technological applications of enzymes.
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Affiliation(s)
- Chandranath Ghosh
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, 741246, India
| | - Souvik Ghosh
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, 741246, India
| | - Ayan Chatterjee
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, 741246, India
| | - Palash Bera
- Tata Institute of Fundamental Research (TIFR), Hyderabad, Telangana, 500046, India
| | - Dileep Mampallil
- Department of Physics, Indian Institute of Science Education and Research (IISER) Tirupati, Mangalam, Andhra Pradesh, 517507, India
| | - Pushpita Ghosh
- School of Chemistry, Indian Institute of Science Education and Research (IISER), Thiruvananthapuram, Kerala, 695551, India
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, 741246, India.
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