Publications

Nigam R, Raveendra Babu K, Ghosh T, Kumari B, Das P, Anindya R, Ahmed Khan F. Synthesis of 2-Chloro-3-amino indenone derivatives and their evaluation as inhibitors of DNA dealkylation repair. Chem Biol Drug Des. 2021 Jun;97(6):1170-1184. doi: 10.1111/cbdd.13839.


Khadake SN, Karamathulla S, Jena TK, Monisha M, Tuti NK, Khan FA, Anindya R. Synthesis and antibacterial activities of marine natural product ianthelliformisamines and subereamine synthetic analogues. Bioorg Med Chem Lett. 2021 May 1;39:127883. doi: 10.1016/j.bmcl.2021.127883.


Bharathi V, Girdhar A, Patel BK. Role of CNC1 gene in TDP-43 aggregation-induced oxidative stress-mediated cell death in S. cerevisiae model of ALS. Biochim Biophys Acta Mol Cell Res. 2021 May;1868(6):118993. doi: 10.1016/j.bbamcr.2021.118993.


Sathyaseelan C, Vijayakumar V, Rathinavelan T. CD-NuSS: A Web Server for the Automated Secondary Structural Characterization of the Nucleic Acids from Circular Dichroism Spectra Using Extreme Gradient Boosting Decision-Tree, Neural Network and Kohonen Algorithms. J Mol Biol. 2021 May 28;433(11):166629. doi: 10.1016/j.jmb.2020.08.014.


Mohan M, Hussain MA, Khan FA, Anindya R. Symmetrical and un-symmetrical curcumin analogues as selective COX-1 and COX-2 inhibitor. Eur J Pharm Sci. 2021 May 1;160:105743. doi: 10.1016/j.ejps.2021.105743.


Ajjugal Y, Kolimi N, Rathinavelan T. Secondary structural choice of DNA and RNA associated with CGG/CCG trinucleotide repeat expansion rationalizes the RNA misprocessing in FXTAS. Sci Rep. 2021 Apr 14;11(1):8163. doi: 10.1038/s41598-021-87097-y.


Preethi S, Bharathi V, Patel BK. Zn2+ modulates in vitro phase separation of TDP-432C and mutant TDP-432C-A315T C-terminal fragments of TDP-43 protein implicated in ALS and FTLD-TDP diseases. Int J Biol Macromol. 2021 Apr 15;176:186-200. doi: 10.1016/j.ijbiomac.2021.02.054.


Pullaguri N, Grover P, Abhishek S, Rajakumara E, Bhargava Y, Bhargava A. Triclosan affects motor function in zebrafish larva by inhibiting ache and syn2a genes. Chemosphere. 2021 Mar;266:128930. doi: 10.1016/j.chemosphere.2020.128930.


Ajjugal Y, Rathinavelan T. Sequence dependent influence of an A…A mismatch in a DNA duplex: An insight into the recognition by hZαADAR1 protein. J Struct Biol. 2021 Mar;213(1):107678. doi: 10.1016/j.jsb.2020.107678.


Girdhar A, Bharathi V, Tiwari VR, Abhishek S, Deeksha W, Mahawar US, Raju G, Singh SK, Prabusankar G, Rajakumara E, Patel BK. Computational insights into mechanism of AIM4-mediated inhibition of aggregation of TDP-43 protein implicated in ALS and evidence for in vitro inhibition of liquid-liquid phase separation (LLPS) of TDP-432C-A315T by AIM4. Int J Biol Macromol. 2020 Mar 15;147:117-130. doi: 10.1016/j.ijbiomac.2020.01.032.


Yadav PR, Hussain Basha S, Satyanarayana SDV, Pindi PK. Microsecond simulation analysis of carbonic anhydrase - II in complex with (+)-cathechin revealed molecular interactions responsible for its amelioration effect on fluoride toxicity. J Biomol Struct Dyn. 2021 Mar 15:1-14. doi: 10.1080/07391102.2021.1898471.


Anindya R. Single-stranded DNA damage: Protecting the single-stranded DNA from chemical attack. DNA Repair (Amst). 2020 Mar;87:102804. doi: 10.1016/j.dnarep.2020.102804.


Ajjugal Y, Tomar K, Rao DK, Rathinavelan T. Spontaneous and frequent conformational dynamics induced by A…A mismatch in d(CAA)·d(TAG) duplex. Sci Rep. 2021 Feb 11;11(1):3689. doi: 10.1038/s41598-021-82669-4.


Abhishek S, Nakarakanti NK, Deeksha W, Rajakumara E.Mechanistic insights into recognition of symmetric methylated cytosines in CpG and non-CpG DNA by UHRF1 SRA. Int J Biol Macromol. 2021 Feb 15;170:514-522. doi:10.1016/j.ijbiomac.2020.12.149.


Akula D, O'Connor TR, Anindya R. Oxidative demethylase ALKBH5 repairs DNA alkylation damage and protects against alkylation-induced toxicity. Biochem Biophys Res Commun. 2021 Jan 1;534:114-120. doi: 10.1016/j.bbrc.2020.12.017.


Ch R, Rey G, Ray S, Jha PK, Driscoll PC, Dos Santos MS, Malik DM, Lach R, Weljie AM, MacRae JI, Valekunja UK, Reddy AB. Rhythmic glucose metabolism regulates the redox circadian clockwork in human red blood cells. Nat Commun. 2021 Jan 15;12(1):377. doi: 10.1038/s41467-020-20479-4.


Yadav PR, Basha SH, Pindi PK. Role of Thr199 residue in human β-carbonic anhydrase-II pH-dependent activity elucidated by microsecond simulation analysis. J Biomol Struct Dyn. 2020 Dec 24:1-10. doi: 10.1080/07391102.2020.1865203.


Kumari N, Bhargava A, Rath SN. T-type calcium channel antagonist, TTA-A2 exhibits anti-cancer properties in 3D spheroids of A549, a lung adenocarcinoma cell line. Life Sci. 2020 Nov 1;260:118291. doi: 10.1016/j.lfs.2020.118291.


Patro LPP, Sudhakar KU, Rathinavelan T. K-PAM: a unified platform to distinguish Klebsiella species K- and O-antigen types, model antigen structures and identify hypervirulent strains. Sci Rep. 2020 Oct 7;10(1):16732. doi: 10.1038/s41598-020-73360-1.


Rajakumara E, Satish M, Abhishek S. In vitro studies on non-canonical DNA binding specificities of KAP6 and HMO1 and mechanistic insights into DNA bound and unbinding dynamics of KAP6. Int J Biol Macromol. 2020 Oct 1;160:925-933. doi: 10.1016/j.ijbiomac.2020.05.228.

Gaur, H., & Bhargava, A. (2019). Glyphosate induces toxicity and modulates calcium and NO signaling in zebrafish embryos. Biochemical and Biophysical Research Communications, 513(4), 1070–1075. https://doi.org/10.1016/j.bbrc.2019.04.074

Bhargava A, Saha S (2019). T-Type voltage gated calcium channels: a target in breast cancer?. Breast Cancer Res Treat. Jan;173(1):11-21. DOI: 10.1007/s10549-018-4970-0

Abhishek, S., Sivadas, S., Satish, M., Deeksha, W., & Rajakumara, E. (2019). Dynamic Basis for Auranofin Drug Recognition by Thiol-Reductases of Human Pathogens and Intermediate Coordinated Adduct Formation with Catalytic Cysteine Residues. ACS Omega, 4(5), 9593–9602. https://doi.org/10.1021/acsomega.9b00529

Patro,L.P.P.,&Rathinavelan,T. (2019). Targeting the Sugary Armor of Klebsiella Species.Frontiers in Cellular and Infection Microbiology, 9. https://doi.org/10.3389/fcimb.2019.00367 mso-style

Tufegdzic Vidakovic, A., Harreman, M., Dirac-Svejstrup, A. B., Boeing, S., Roy, A., Encheva, V., Neumann, M., Wilson, M., Snijders, A. P., & Svejstrup, J. Q. (2019). Analysis of RNA polymerase II ubiquitylation and proteasomal degradation. Methods, 159–160, 146–156. https://doi.org/10.1016/j.ymeth.2019.02.005.

Mohan, M., Akula, D., Dhillon, A., Goyal, A., & Anindya, R. (2019). Human RAD51 paralogue RAD51C fosters repair of alkylated DNA by interacting with the ALKBH3 demethylase. Nucleic Acids Research, 47(22), 11729–11745. https://doi.org/10.1093/nar/gkz938

Archana Prasad, Vidhya Bharathi, Vishwanath Sivalingam, Amandeep Girdhar and Basant K Patel. Molecular mechanism of TDP-43 misfolding and pathology in Amyotrophic Lateral Sclerosis. Front Mol Neurosci. Vol 12, 2019, 25

Gaur H, Purushothaman S, Pullaguri N, Bhargava Y, Bhargava A. Sodium benzoate induced developmental defects, oxidative stress and anxiety-like behaviour in zebrafish larva. Biochem Biophys Res Commun. 502, 2018, 364-369.

M Sharma, D Akula, M Mohan, R Nigam, M Das, Anindya Roy. Heteroexpression of Mycobacterium leprae hypothetical protein ML0190 provides protection against DNA-alkylating agent methyl methanesulfonate. Biochemical & Biophysical Research Communications, 509(3), 2018, 779-783.

G.S. Tomar, G.P. Singh, D. Lahkar, K. Sengar, R. Nigam, M. Mohan, Anindya Roy. New biomarkers in brain trauma. Clinica Chimica Acta, 487, 2018, 325-329.

G.P. Singh, R. Nigam, G.S. Tomar, M. Monisha, S.K. Bhoi, A. S, K. Sengar, D. Akula, P. Panta, Anindya Roy. Early and rapid detection of UCHL1 in the serum of brain-trauma patients: a novel gold nanoparticle-based method for diagnosing the severity of brain injury. Analyst, 143(14), 2018, 3366-3373.

M. Sharma, M. Das, D. Diana, A. Wedderburn, Anindya Roy. Identification of novel open reading frames in the intergenic regions of Mycobacterium leprae genome and detection of transcript by qRT-PCR. Microbial Pathogenesis, 124, 2018, 316-321.

R. Nigam, M. Mohan, G. Shivange, P.K. Dewangan, Anindya Roy. Escherichia coli AlkB interacts with single-stranded DNA binding protein SSB by an intrinsically disordered region of SSB. Molecular Biology Reports 45(5), 2018, 865-870.

R. Nigam, K.R. Babu, T. Ghosh, B. Kumari, D. Akula, S.N. Rath, P. Das, Anindya Roy. F.A. Khan, Indenone derivatives as inhibitor of human DNA dealkylation repair enzyme AlkBH3. Bioorganic & Medicinal Chemistry, 26(14), 2018, 4100-4112.

M. Mohan, V. Pandya, Anindya Roy. Escherichia coli AlkB and single-stranded DNA binding protein SSB interaction explored by Molecular Dynamics Simulation. Journal of Molecular Graphics & Modeling, 84, 2018, 29-35.

R. Nigam, M. Mohan, Anindya Roy. Escherichia coli single-stranded DNA binding protein SSB binds to AlkB and promotes DNA repair. FEBS Open Bio, 8, 2018, 28135.

Archana Prasad, Vishwanath Sivalingam, Vidhya Bharathi, Amandeep Girdhar, and Basant K Patel. The amyloidogenicity of a C-terminal region of TDP-43 implicated in Amyotrophic Lateral Sclerosis can be affected by anions, acetylation and homodimerization. Biochimie, Vol 150, 2018, 76-87.

Anamika Bhargava, Julia Gorelik. Studying Structure and Function of the Heart Cells Using Scanning Ion Conductance Microscopy. In: Kaestner L., Lipp P. (eds) Microscopy of the Heart. Springer, Cham, 2018

Uzma Hasan and Sandeep K. Singh. The Astrocyte–Neuron Interface: An Overview on Molecular and Cellular Dynamics Controlling Formation and Maintenance of the Tripartite Synapse. 2019, Methods in Molecular Biology (Astrocytes), 1938:3-18

Abhishek S, Nivya MA, Nakarakanti NK, Deeksha W, Khosla S, Rajakumara E. Biochemical and dynamic basis for combinatorial recognition of H3R2K9me2 by dual domains of UHRF1. Biochimie, 149, 105-1142018 (2018): doi: 10.1016/j.biochi.2018.04.010.

Satish, M., Nivya, MA., Abhishek, S., Nakarakanti, NK., Shivani, D., M. Vani, V., Rajakumara, E. Computational characterization of substrate and product specificities, and functionality of SAM binding pocket in histone lysine methyltransferases from Arabidopsis, rice and maize. Proteins: Structure, Function, and Bioinformatics. 2018 Jan;86(1):21-34. doi: 10.1002/prot.25399.

R. Anindya, Non-hemedioxygenases in tumor hypoxia: they’re all bound with the same fate, DNA Repair, 49, 21-25 (2017).

S. Sachdeva, R. V. Palur, K. U. Sudhakar, and T. Rathinavelan, E. coli group I capsular polysaccharide exportation nanomachinary as a plausible antivirulent target in the perspective of emerging antimicrobial resistance, Frontiers in Microbiology, 8-70 (2017) 10.3389/fmicb.2017.00070.

Patro, L.P.P., Kumar, A.*, Kolimi, N.* and Rathinavelan, T. (2017), “3D-NuS: A Web Server for Automated Modeling and Visualization of non-canonical 3-Dimensional Nucleic Acid Structures”. J. Mol. Biol. 429, 2438-2448.

Kolimi, N.*, Ajjugal. Y* and Rathinavelan, T. (2017), “A B–Z junction induced by an A...A mismatch in GAC repeats in the gene for cartilage oligomeric matrix protein promotes binding with the hZaADAR1 protein”. Accepted in J. Biol. Chem. 10.1074/jbc.M117.796235

A. Prasad, G. Raju, V. Sivalingam, A. Girdhar, M. Verma, A. Vats, V. Taneja, Ganesan Prabusankar, and Basant K. Patel, An acridine derivative, [4,5-bis{(N-carboxy methyl imidazolium) methyl}acridine] dibromide, shows anti-TDP-43 aggregation effect in ALS disease models, Scientific Reports,6, 39490 (2016).

G. Goldsmith, T. Rathinavelan, and N. Yathindra, Selective Preference of Parallel DNA Triplexes is Due to the Disruption of Hoogsteen Hydrogen Bonds Caused by the Severe Nonisostericity Between the G*GC and T*AT triplets, PLoS One, 11(3), e0152102 (2016).

V. Sivalingam, N.L. Prasanna, N. Sharma, A. Prasad, and Basant K. Patel, Wild-type hen egg white lysozyme aggregation in vitro can form selfseeding amyloid conformational variants, Biophys Chem., 219, 28-37 (2016).

V. Bharathi, A. Girdhar, A. Prasad, M. Verma, V. Taneja, and Basant K. Patel, Use of ade1 and ade2 mutations for development of a versatile red/white colour assay of amyloid-induced oxidative stress in Saccharomyces cerevisiae, Yeast., 33(12), 607-620 (2016).

V. Sivalingam and Basant K. Patel, Familial mutations in fibrinogen A-alpha (FGA) chain identified in renal amyloidosis increase in vitro amyloidogenicity of FGA fragment, Biochimie, 127, 44-49 (2016).

N. Sharma, V. Sivalingam, and Basant K. Patel, Recombinant Human Semenogelin-1 (Sg1) and Sg1 (1-159) form Detergent Stable Amyloid like Aggregates in vitro, Protein & Peptide letters, 23(1), 87-96 (2016).

G. Raju, V. Sivalingam, Archana, Basant K. Patel and Ganesan Prabusankar, Imidazolium Tagged Acridine Derivatives: Syntheses, Structures, DNA Sensing and Anti-microbial Activities, Journal of Molecular Structure, 1107, 291-299 (2016).

G. Shivange, M. Monisha, R. Nigam, N. Kodipelli, R. Anindya, RecA stimulates AlkB-mediated direct repair of DNA adducts, Nucleic Acid Research, 44, 8754-63 (2016).

S. Sachdeva, N. Kolimi, S.A. Nair, and T. Rathinavelan, Key Diffusion Mechanisms Involved in Water Conduction of Wzi, Sci. Rep., 28157, (2016) 10.1038/srep28157.

A.Bhargava, T. O’Hara, A.V. Glukhov, S. Schobesberger, N. Bhogal, M.B. Sikkel, C. Mansfield, Y.E. Korchev, A.R. Lyon, P.P. Punjabi, V.O. Nikolaev, N.A. Trayanova, and Gorelik, Microdomain-Specific Modulation of L-Type Calcium Channels Leads to Triggered Ventricular Arrhythmia in Heart Failure, JL Sanchez-Alonso, J.Circ Res. Sep 30;119(8), 944- 55 (2016).

S. Nema, W. Hasan, A. Bhargava, and Y. Bhargava, A novel method for automated tracking and quantification of adult zebrafish behaviour during anxiety, J Neurosci Methods, Sep 15; 271, 65-75 (2016).

Rajakumara, E#., Nakarakanti, N.K, Nivya, M.A. and Satish, M. Mechanistic insights into the recognition of 5-methylcytosine oxidation derivatives by the SUVH5 SRA domain. Nature Scientific Reports. 2016 Feb 4;6:20161. doi: 10.1038/srep20161. (# Corresponding author)

N. Khan, N. Kolimi, T. Rathinavelan, ‘Twisting right to left: A…A mismatch in a CAG trinucleotide repeat overexpansion provokes left-handed Z-DNA conformation’, PLoS Comput Biol., 11, e1004162, 2015.

Devi, S., Rajakumara, E., Ahmed N. Induction of Mincle by Helicobacter pylori and consequent anti-inflammatory signaling denote a bacterial survival strategy. Nature Scientific Reports. 2015 Oct 12;5:15049. doi: 10.1038/srep15049.

Glukhov AV, Balycheva M, Sanchez- Alonso JL, Ilkan Z, Alvarez-Laviada A, Bhogal N, Diakonov I, Schobesberger S, Sikkel MB, Bhargava A, Faggian G, Punjabi PP, Houser SR, Gorelik, Direct Evidence for Microdomain-Specific Localization and Remodeling of Functional L-Type Calcium Channels in Rat and Human Atrial Myocytes, J. Circulation. 5 Dec 22;132(25):2372-84. (2015)

Glukhov AV, Rosenshtraukh LV, Bhargava A, Miragoli M, Boukens BJ, Atrial Fibrillation: Biophysics, Molecular Mechanisms and Novel Therapies, Editorial. Biomed Res Int. 2015:780671. (2015)

S. Agarwal, P Mishra, G Shivange, N Kodipelli, M Moros M, JM de la Fuente, R Anindya, ‘Citrate-capped gold nanoparticles for the label-free detection of ubiquitin C-terminal hydrolase-1’, Analyst., 140: 1166-73, 2015.

V. Gonzalez-Huici, B. Szakal, M. Urulangodi, I. Psakhye, F. Castellucci, D. Menolfi, E. Rajakumara, M. Fumasoni, R. Bermejo, S. Jentsch, D. Branzei, EMBO J, DNA bending facilitates the error-free DNA damage tolerance pathway and upholds genome integrity, 33(4), 327-40 (2014).

G. Shivange, N. Kodipelli, M. Monisha, R. Anindya, ‘A Role for Saccharomyces cerevisiae Tpa1 Protein in Direct Alkylation Repair’, Journal of Biological Chemistry., 289(52):35939-52, 2014.

T. Rathinavelan, M. Lara-Tejero, M. Lefebre, S. Chatterjee, A.C. McShan, D.C. Guo, C. Tang, J.E. Galan and R.N. De Guzman, ‘NMR model of PrgI-SipD interaction and its implications in the needle-tip assembly of the Salmonella type III secretion system’, J. Mol. Biol., 426, 2958-2969, 2014.

K.W. Schicker, E. Novikova, B. Pohn, T. Stockner, C. Kugler, A. Singh, C. Zeitz, M.E. Lancelot, I. Audo, B.P. Leroy, M. Freissmuth, S. Herzig, J. Matthes and A. Koschak, ‘Spectrum of Cav1.4 dysfunction in congenital stationary night blindness type 2. V. Burtscher’, Biochim Biophys Acta. Aug: 1883 (8):2053-65, 2014.

G. Shivange, N. Kodipelli R. Anindya, ‘A nonradioactive restriction enzyme mediated assay to detect DNA repair dioxygenase’, Anal Biochem., 465C:35- 37, 2014.

T. Hong, H. Yang, S.S. Zhang, H.C. Cho, M. Kalashnikova, B. Sun, H. Zhang, A. Bhargava, M. Grabe, J. Olgin, J. Gorelik, E. Marban, L R. M. Shaw, ‘Cardiac BIN1 folds T-tubule membrane, controlling ion flux and li miting arrhythmia’, Nat Med. Jun; 20 (6):624-32, 2014.

T. Rathinavelan, M. Lara-Tejero, M. Lefebre, S. Chatterjee, A.C. McShan, D.C. Guo, C. Tang, J.E. Galan and R.N. De Guzman, ‘NMR model of PrgI-SipD interaction and its implications in the needle-tip assembly of the Salmonella type III secretion system’, J. Mol. Biol., 426, 2958-2969, 2014.