Naidu Subbarao

Scopus Publications

Hydroxyethylamine & phthalimide analogs restoring defects due to GNE dysfunction: rare disease therapeutic significance
Shagun Singh, Meenakshi Bansal, Neha Sharma, Vikas Yadav, Fluencephila Mashangva, Jyoti Oswalia, Vaishali Gautam, Gagan Deep Jhingan, Naidu Subbarao, Brijesh Rathi, Ranjana Arya
Molecular Medicine, 2025
Rare diseases refer to a group of neglected diseases with low prevalence that face challenges in diagnostics as well as therapeutics due to phenotypic heterogeneity and ineffective clinical trials. In this study, we evaluated two novel analogs of hydroxyethylamine & phthalimide (LTC-181 and LTC-1717) for their potential effect on the epimerase activity of mutant GNE proteins associated with GNE myopathy. GNE gene encodes a key bifunctional sialic acid biosynthetic enzyme, UDP-N-acetyl Glucosamine 2-epimerase/N-acetyl Mannosamine Kinase; GNE). The compounds have significantly increased the epimerase activity of r-F307C-GNE and r-A555V-GNE mutant proteins in vitro. Reduced GNE epimerase activity and sialic acid content in muscle cell-based model for GNE function (SKM-GNEHz) was increased by 2-fold after addition of these compounds. The proteomic study showed that the compounds affected cytoskeletal organization, autophagy and muscle atrophy. Also, treatment with analogs enhanced the cell viability of SKM-GNEHz cells with increased F-actin polymerization and cell migration, thereby, restoring GNE deficient function. Additionally, effect of these compounds was observed with enhanced autophagy and reduced muscle atrophy function in GNE deficient muscle cell. Docking and interaction studies showed that LTC-1717 stabilize GNE better than LTC-181, indicating better therapeutic potential. Overall, this study indicates that HEA-phthalimide analog could be promising leads for treating GNE myopathy.
Plasmodium falciparum acetyltransferase GCN5 acts as a dual regulator of essential glycolytic enzyme phosphoglycerate mutase
Ankita Tehlan, Poonam Nagar, Reena Prajapati, Krishanu Bhowmick, Amarjeet Kumar, Inderjeet Kaur, Naidu Subbarao, Suman Kumar Dhar
FEBS Journal, 2025
Lysine acetylation is emerging as a key player in cellular regulation across species by controlling the fate of metabolic proteins as well as modulating gene expression via histone modification. Phosphoglycerate mutase, a conserved enzyme of the sole energy‐yielding pathway of glycolysis in the human malaria parasite Plasmodium falciparum, is indispensable for its growth. Here, we demonstrate that P. falciparum phosphoglycerate mutase PfPGM1 (phosphoglycerate mutase) is regulated via lysine acetylation. In mammalian cells, acetylation of phosphoglycerate mutase modulates its catalytic activity, although the acetyl transferase enzyme remains elusive. However, the parasites exhibit a unique way of regulating the fate of PfPGM1 via acetylation that modulates its stability, thus providing an increased protein pool for the rapid growth and proliferation of the parasites. We show that K100, a critical residue for PfPGM1 catalytic activity, is acetylated by the essential histone acetyltransferase PfGCN5. Downregulation of PfGCN5 through a knockdown approach in the parasites along with cycloheximide treatment indeed leads to a reduction of PfPGM1 protein. Additionally, PfGCN5 occupies the promoter of PfPGM1 in a stage‐specific manner, and downregulation of PfGCN5 protein leads to a reduced transcript level of PfPGM1. Collectively, our data highlight a dual regulation of PfPGM1 by PfGCN5 through acetylation of the protein as well as regulation of the transcription of the gene. Such dual control is not only rare but showcases the importance of the above two proteins and their potential as excellent targets against malaria.
In Silico Identification of Novel and Potent Inhibitors Against Mutant BRAF (V600E), MD Simulations, Free Energy Calculations, and Experimental Determination of Binding Affinity
Vikas Yadav, Mohammad Kashif, Zenab Kamali, Samudrala Gourinath, Naidu Subbarao
Molecular Informatics, 2025
BRAF is a proto oncogene that functions as a key signal transducer in the MAPK‐ERK pathway, which regulates cell growth, division, and survival. Mutations in BRAF, particularly the V600E substitution in its kinase domain, are major drivers in melanoma and several other metastatic cancers, including breast, colorectal, NSCLC, and gastrointestinal cancers. In this study, novel inhibitors targeting the BRAF(V600E) mutant using a structure‐based drug design approach are identified. Four chemical libraries ChemDiv Kinase, ChemDiv Anticancer, NCI, and ChEMBL Kinase SARfari are screened. Compounds from the ChemDiv Anticancer database show better Glide scores comparable to the FDA‐approved BRAF inhibitor Vemurafenib. The compounds P184‐1419 and P184‐1479 score −12.688 and −12.012 kcal/mol, respectively, versus −14.288 kcal/mol for Vemurafenib. Top hits are further validated using GOLD docking, X‐score ranking, and interaction profiling via LigPlot. Molecular dynamics simulations, principal component analysis, and free energy calculations confirm the stability of protein–ligand complexes. Biolayer interferometry assays reveal P184‐1419 exhibits stronger binding affinity (KD = 151 μM) than Vemurafenib (KD = 437 μM). These findings suggest P184‐1419 is a promising lead compound against BRAF(V600E), offering potential for future development of more effective cancer therapies.
Identification of ABC transporter Cdr1 inhibitors of Candida glabrata
Mohd Waseem, Shubhashis Das, Debarati Mondal, Anuj Kumari, Ritu Kulshreshtha, Jitendra K. Thakur, Naidu Subbarao
Archives of Biochemistry and Biophysics, 2025
Identification of potential novel inhibitors against the SARS-CoV-2 spike protein: targeting RBD and ACE2 interaction
Jyoti Verma, Pragyan Parimita Rath, Samudrala Gourinath, Naidu Subbarao
Journal of Biomolecular Structure and Dynamics, 2025
The SARS-CoV-2, responsible for the COVID-19 pandemic has wrecked devastation throughout the globe. The SARS-CoV-2 spike (S) glycoprotein plays crucial role in virus attachment, fusion, and entry. This study aims to identify inhibitors targeting the receptor binding domain (RBD) of the S protein using computational and experimental techniques. We carried out virtual screening of four datasets against the S-RBD. Six potential candidate inhibitors were selected for experimental evaluation. Here, we provide experimental evidence that the molecules 9‴-MethyllithosperMate, Epimedin A, Pentagalloylglucose, and Theaflavin-3-gallate have a high binding affinity towards SARS-CoV-2 S-RBD. 9‴-MethyllithosperMate with a KD value of 1.3 nM serves as the best inhibitor, followed by others with KD values in micromolar range. We performed molecular dynamics simulation to assess the binding stability of these inhibitors. Hence, our study reports novel inhibitors against the SARS-CoV-2 S-RBD and their predicted binding mode also suggest the possibility to interfere with the ACE2 binding.Communicated by Ramaswamy H. Sarma.
Insilico screening to identify novel inhibitors targeting 30S ribosomal protein S12 in meningitis-causing organism ‘Elizabethkingia meningoseptica’
Neha Girdhar, Vikas Yadav, Nilima Kumari, Naidu Subbarao, Annangarachari Krishnamachari
Journal of Biomolecular Structure and Dynamics, 2025
The current trend in biomedical research is on prioritizing infections based on multidrug resistance. Elizabethkingia meningoseptica, a nosocomial infection-causing organism emerging from Neonatal Intensive Care Units (NICUs), leads to neonatal meningitis and sepsis resulting in severe illness, and, in some cases, fatal. Finding a solution remains challenging due to limited prior work. Translational S12 ribosomal proteins play a crucial role in decoding the codon-anticodon helix, which is essential for the survival of E. meningoseptica. These proteins do not exhibit significant similarity with humans, making them potential drug targets. An in silico study aims to identify specific inhibitors for E. meningoseptica ribosomal proteins among known bioactive compounds targeting prokaryotic 30S ribosomal protein. A 3D model of the 7JIL_h protein from Flavobacterium johnsoniae, showing 90% sequence similarity with the target protein was generated using SWISS-MODEL software. The model was validated through Molprobity v4.4, VERIFY 3D, Errata, and ProSA analysis, confirming conserved residues of the target protein. Insilico screening of known bioactive compounds and their analogs identified potential ligands for the target protein. Molecular Docking and post-docking analysis assessed the stability of the protein-ligand complexes among the shortlisted compounds. The top two compounds with high Gold fitness scores and low predicted binding energy underwent MD simulation and further estimation of free binding energy using the MM_PBSA module. These computationally shortlisted compounds, namely chEMBL 1323619 and chEMBL 312490 may be considered for future in-vivo studies as potential inhibitors against the modeled 30S ribosomal protein S12 of E. meningoseptica.Communicated by Ramaswamy H. Sarma.
Identification of KRAS mutants (G12C, G12D, and G12V) inhibitors
Vikas Yadav, Mohammad Kashif, Zenab Kamalia, Vikas, Santhipriya P R, Samudrala Gourinath, Neelima Mondal, Naidu Subbarao
Future Medicinal Chemistry, 2025
AIM: To identify and validate novel small-molecule inhibitors targeting KRAS G12C, G12D, and G12V mutants through a structure-based drug design and experimental approach. METHODS: We employed molecular docking, molecular dynamics (MD) simulations, MM-PBSA binding free energy calculations, and principal component analysis (PCA) to screen and evaluate potential inhibitors targeting the Switch-II pocket of KRAS mutants. Top-ranking compounds were experimentally validated using Bio-Layer Interferometry (BLI) for binding affinity and MTT assays to assess anticancer activity in breast and lung cancer cell lines. RESULTS: Compound C797-1505 showed strong binding to KRAS G12V (Dissociation constant (KD) = 141 µM), outperforming the reference Sotorasib (KD = 345 µM). C190-0346 displayed weak affinity toward KRAS G12C. MTT assays revealed that C797-1505 reduced breast cancer cell viability (Half-maximal Inhibitory Concentration (IC50) = 43.51 µM), while both compounds demonstrated significant cytotoxicity against lung cancer cells (IC50 = 18.78 µM and 22.93 µM, respectively). CONCLUSION: Our integrated computational and experimental strategies successfully identified selective KRAS mutant inhibitors with promising anticancer activity, particularly against G12V and G12C driven tumors. These findings support further development and preclinical evaluation of these compounds as targeted therapeutics.
Plasmodium falciparum cysteine protease Falcipain 3: A potential enzyme for proteolytic processing of histone acetyltransferase PfGCN5
Poonam Nagar, Krishanu Bhowmick, Aishwarya Chawla, Md. Zubbair Malik, Naidu Subbarao, Inderjeet Kaur, Suman Kumar Dhar
Biotechnology and Applied Biochemistry, 2024
In spite of 150 years of studying malaria, the unique features of the malarial parasite, Plasmodium, still perplex researchers. One of the methods by which the parasite manages its gene expression is epigenetic regulation, the champion of which is PfGCN5, an essential enzyme responsible for acetylating histone proteins. PfGCN5 is a ∼170 kDa chromatin‐remodeling enzyme that harbors the conserved bromodomain and acetyltransferase domain situated in its C‐terminus domain. Although the PfGCN5 proteolytic processing is essential for its activity, the specific protease involved in this process still remains elusive. Identification of PfGCN5 interacting proteins through immunoprecipitation (IP) followed by LC‐tandem mass spectrometry analysis revealed the presence of food vacuolar proteins, such as the cysteine protease Falcipain 3 (FP3), in addition to the typical members of the PfGCN5 complex. The direct interaction between FP3 and PfGCN5 was further validated by in vitro pull‐down assay as well as IP assay. Subsequently, use of cysteine protease inhibitor E64d led to the inhibition of protease‐specific processing of PfGCN5 with concomitant enrichment and co‐localization of PfGCN5 and FP3 around the food vacuole as evidenced by confocal microscopy as well as electron microscopy. Remarkably, the proteolytic cleavage of the nuclear protein PfGCN5 by food vacuolar protease FP3 is exceptional and atypical in eukaryotic organisms. Targeting the proteolytic processing of GCN5 and the associated protease FP3 could provide a novel approach for drug development aimed at addressing the growing resistance of parasites to current antimalarial drugs.
MediatorWeb: a protein–protein interaction network database for the RNA polymerase II Mediator complex
Sourobh Maji, Mohd Waseem, Manish Kumar Sharma, Maninder Singh, Anamika Singh, Nidhi Dwivedi, Pallabi Thakur, David G. Cooper, Naveen C. Bisht, Jan S. Fassler, Naidu Subbarao, Jitendra P. Khurana, Neel Sarovar Bhavesh, Jitendra Kumar Thakur
FEBS Journal, 2024
The protein–protein interaction (PPI) network of the Mediator complex is very tightly regulated and depends on different developmental and environmental cues. Here, we present an interactive platform for comparative analysis of the Mediator subunits from humans, baker's yeast Saccharomyces cerevisiae, and model plant Arabidopsis thaliana in a user‐friendly web‐interface database called MediatorWeb. MediatorWeb provides an interface to visualize and analyze the PPI network of Mediator subunits. The database facilitates downloading the untargeted and unweighted network of Mediator complex, its submodules, and individual Mediator subunits to better visualize the importance of individual Mediator subunits or their submodules. Further, MediatorWeb offers network visualization of the Mediator complex and interacting proteins that are functionally annotated. This feature provides clues to understand functions of Mediator subunits in different processes. In an additional tab, MediatorWeb provides quick access to secondary and tertiary structures, as well as residue–level contact information for Mediator subunits in each of the three model organisms. Another useful feature of MediatorWeb is detection of interologs based on orthologous analyses, which can provide clues to understand the functions of Mediator complex in less explored kingdoms. Thus, MediatorWeb and its features can help the user to understand the role of Mediator complex and its subunits in the transcription regulation of gene expression.
In silico prediction of CD8+ and CD4+ T cell epitopes in Leishmania major proteome: Using immunoinformatics
Mohammad Kashif, Mohd Waseem, Naidu Subbarao
Journal of Molecular Graphics and Modelling, 2024
Reinvestigation of diphenylmethylpiperazine analogues of pyrazine as new class of Plasmodial cysteine protease inhibitors for the treatment of malaria
Hari Madhav, G. Srinivas Reddy, Zeba Rizvi, Ehtesham Jameel, Tarosh S. Patel, Abdur Rahman, Vikas Yadav, Sadaf Fatima, Fatima Heyat, Kavita Pal, Amisha Minju-OP, Naidu Subbarao, Souvik Bhattacharjee, Bharat C. Dixit, Puran Singh Sijwali, Nasimul Hoda
Rsc Medicinal Chemistry, 2024
Potential inhibitors of RPS6KB2 and NRF2 in head and neck squamous cell carcinoma
Geet Madhukar, Naidu Subbarao
Journal of Biomolecular Structure and Dynamics, 2024
Current scenario and future prospective of drug discovery and development against bacterial enzymes
Mohammad Kashif, Danishuddin, Mirza Sarwar Baig, Naidu Subbarao
Bacterial Enzymes as Targets for Drug Discovery Meeting the Challenges of Antibiotic Resistance, 2024
In silico identification of colchicine derivatives as novel and potential inhibitors based on molecular docking and dynamic simulations targeting multifactorial drug targets involved in Alzheimer’s disease
Adity Raturi, Vikas Yadav, Nasimul Hoda, Naidu Subbarao, Saif Ali Chaudhry
Journal of Biomolecular Structure and Dynamics, 2024
Petri net modeling, computational analysis, and simulation of interleukin 17E signaling pathway: A study of dynamics
Mathematics in Engineering Science and Aerospace, 2024
In silico analysis of Diosmetin as an effective chemopreventive agent against prostate cancer: molecular docking, validation, dynamic simulation and pharmacokinetic prediction-based studies
Sumit Sheoran, Swati Arora, Tanmayee Basu, Swati Negi, Naidu Subbarao, Anupam Kumar, Himanshu Singh, Dhamodharan Prabhu, Atul Kumar Upadhyay, Neeraj Kumar, Sugunakar Vuree
Journal of Biomolecular Structure and Dynamics, 2024
Identification of conserved immunogenic peptides of SARS-CoV-2 nucleocapsid protein
Jigyasa Verma, Neha Kaushal, Manish Manish, Naidu Subbarao, Venera Shakirova, Ekaterina Martynova, Rongzeng Liu, Shaimaa Hamza, Albert A. Rizvanov, Svetlana F. Khaiboullina, Manoj Baranwal
Journal of Biomolecular Structure and Dynamics, 2024
Morroniside interaction with poly (ADP-ribose) polymerase accentuates metabolic mitigation of alloxan-induced genotoxicity and hyperglycaemia: a molecular docking based in vitro and in vivo experimental therapeutic insight
Sudatta Dey, Isha Nagpal, Priyanka Sow, Rishita Dey, Arnob Chakrovorty, Banani Bhattacharjee, Saikat Saha, Avishek Majumder, Manindranath Bera, Naidu Subbarao, Sisir Nandi, Sabir Hossen Molla, Pradeepta Guptaroy, Suresh K. Abraham, Anisur Rahman Khuda-Bukhsh, Asmita Samadder
Journal of Biomolecular Structure and Dynamics, 2024
Identification of novel inhibitors against Med15a KIX domain of Candida glabrata
Mohd Waseem, Shubhashis Das, Debarati Mondal, Monika Jain, Jitendra K. Thakur, Naidu Subbarao
International Journal of Biological Macromolecules, 2023
Probing the interaction of cephalosporin antibiotic “cefoperazone” with lysozyme using spectroscopic and in silico methods: Effect of paracetamol on binding
Mohd Sajid Ali, Mohd Waseem, Naidu Subbarao, Abdullah Nasser Alahamed, Hamad A. Al-Lohedan
International Journal of Biological Macromolecules, 2023
A new fuzzy support vector machine with pinball loss
Ram Nayan Verma, Rahul Deo, Rakesh Srivastava, Naidu Subbarao, Gajendra Pratap Singh
Discover Artificial Intelligence, 2023
Synthesis of IR-415 Derivatives and Evaluation of their Antiviral Activity Against Hepatitis B Virus
Ankita Singh, Jitendra Kumar, Jyoti Verma, Naidu Subbarao, Shivani Sapra, Ashok Kumar Prasad, Vijay Kumar, Deepti Sharma
Chemistryselect, 2023
Convolutional neural network-based quantitative structure-activity relationship and fingerprint analysis against inhibitors of anthrax lethal factor
Madhulata Kumari, Naidu Subbarao
Future Medicinal Chemistry, 2023
In-Silico Drug Design and Molecular Docking Studies of Poly ADP-Ribose Polymerase (PARP-1) Inhibitors as Anticancer Agents
Maneesha Pathak, Anita Singh, Pooja Rawal, Arcahana N Sah, Subbarao Naidu
International Journal of Pharmaceutical Sciences and Nanotechnology, 2023
Y12F mutation in Pseudomonas plecoglossicida S7 lipase enhances its thermal and pH stability for industrial applications: a combination of in silico and in vitro study
Prassan Choudhary, Mohd Waseem, Sunil Kumar, Naidu Subbarao, Shilpi Srivastava, Hillol Chakdar
World Journal of Microbiology and Biotechnology, 2023
Identification of potential novel inhibitors against glutamine synthetase enzyme of Leishmania major by using computational tools
Mohammad Kashif, Naidu Subbarao
Journal of Biomolecular Structure and Dynamics, 2023
In silico identification of small molecule protein-protein interaction inhibitors: targeting hotspot regions at the interface of MXRA8 and CHIKV envelope protein
Jyoti Verma, Naidu Subbarao
Journal of Biomolecular Structure and Dynamics, 2023
Prediction of novel and potent inhibitors of lanosterol 14-α demethylase
Mohd Waseem, Jitendra K. Thakur, Naidu Subbarao
Journal of Biomolecular Structure and Dynamics, 2023
Discovery of multi-target mur enzymes inhibitors with anti-mycobacterial activity through a Scaffold approach
Madhulata Kumari, Mohd Waseem, Naidu Subbarao
Journal of Biomolecular Structure and Dynamics, 2023
Designing dual inhibitors against potential drug targets of Plasmodium falciparum -M17 Leucyl Aminopeptidase and Plasmepsins
Govinda Rao Dabburu, Aakriti Jain, Naidu Subbarao, Manish Kumar
Journal of Biomolecular Structure and Dynamics, 2023
Computational Grafting of Epitopes
Manish Manish, Smriti Mishra, Monika Pahuja, Ayush Anand, Naidu Subbarao, Ram Samudrala
Methods in Molecular Biology, 2023
Vitamin derivatives as potential drugs for Influenza Hemagglutinin
Ananyaa Agrawal, Pratibha Chanana, Vikas Yadav, Vilakshan Bhutani, Naidu Subbarao, Aradhana Srivastava
Journal of Biomolecular Structure and Dynamics, 2023
Computational molecular interaction between SARS-CoV-2 main protease and theaflavin digallate using free energy perturbation and molecular dynamics
Manish Manish, Smriti Mishra, Ayush Anand, Naidu Subbarao
Computers in Biology and Medicine, 2022
Identification of key proteins in host–pathogeninteractions between Mycobacterium tuberculosis and Homo sapiens: A systematic network theoretical approach
Ram Nayan Verma, Md. Zubbair Malik, Gajendra Pratap Singh, Naidu Subbarao
Healthcare Analytics, 2022
Entamoeba histolytica HM-1: IMSS gene expression profiling identifies key hub genes, potential biomarkers, and pathways in Amoebiasis infection: a systematic network meta-analysis
Ram Nayan Verma, Md. Zubbair Malik, Naidu Subbarao, Gajendra Pratap Singh, Durgesh Nandini Sinha
Bioscience Reports, 2022
Genome-wide expression reveals potential biomarkers in breast cancer bone metastasis
Yashbir Singh, Naidu Subbarao, Abhinav Jaimini, Quincy A. Hathaway, Amina Kunovac, Bradley Erickson, Vishnu Swarup, Himanshu Narayan Singh
Journal of Integrative Bioinformatics, 2022
In silico identification and in vitro antiviral validation of potential inhibitors against Chikungunya virus
Jyoti Verma, Abdul Hasan, Sujatha Sunil, Naidu Subbarao
Journal of Computer Aided Molecular Design, 2022
A hybrid resampling algorithms SMOTE and ENN based deep learning models for identification of Marburg virus inhibitors
Madhulata Kumari, Naidu Subbarao
Future Medicinal Chemistry, 2022
The tetrameric structure of Plasmodium falciparum phosphoglycerate mutase is critical for optimal enzymatic activity
Ankita Tehlan, Krishanu Bhowmick, Amarjeet Kumar, Naidu Subbarao, Suman Kumar Dhar
Journal of Biological Chemistry, 2022
Identification of novel multitarget antitubercular inhibitors against mycobacterial peptidoglycan biosynthetic Mur enzymes by structure-based virtual screening
Madhulata Kumari, Naidu Subbarao
Journal of Biomolecular Structure and Dynamics, 2022
In-silico prediction of potential inhibitors against phosphatidylinositol 3-kinase catalytic subunit alpha involved in head and neck squamous cell carcinomas
Geet Madhukar, Naidu Subbarao
Journal of Biomolecular Structure and Dynamics, 2022
Development of a deep learning-based quantitative structure-activity relationship model to identify potential inhibitors against the 3C-like protease of SARS-CoV-2
Madhulata Kumari, N. Subbarao
Future Medicinal Chemistry, 2022
Exploring the interaction mechanism between potential inhibitor and multi-target Mur enzymes of mycobacterium tuberculosis using molecular docking, molecular dynamics simulation, principal component analysis, free energy landscape, dynamic cross-correlation matrices, vector movements, and binding free energy calculation
Madhulata Kumari, Ruhar Singh, Naidu Subbarao
Journal of Biomolecular Structure and Dynamics, 2022
Exploring the Molecular Level Interaction of Human Serum Albumin with Calcium Oxalate Monohydrate Crystals
Priyadarshini, Abhishek Negi, Chetna Faujdar, Lokesh Nigam, Naidu Subbarao
Protein and Peptide Letters, 2021
Design and in vitro analysis of SIRT2 inhibitor targeting Parkinson’s disease
Amrendra Pratap Singh, Lokesh Nigam, Yudhishthir Yadav, Shashank Shekhar, Naidu Subbarao, Sharmistha Dey
Molecular Diversity, 2021
Insilico study on the effect of SARS-CoV-2 RBD hotspot mutants’ interaction with ACE2 to understand the binding affinity and stability
Jyoti Verma, Naidu Subbarao
Virology, 2021
Noncovalent molecular interactions between antineoplastic drug gemcitabine and a carrier protein identified through spectroscopic and in silico methods
Mohd Sajid Ali, Mohd Waseem, Naidu Subbarao, Hamad A. Al-Lohedan
International Journal of Biological Macromolecules, 2021
Deep learning model for virtual screening of novel 3C-like protease enzyme inhibitors against SARS coronavirus diseases
Madhulata Kumari, Naidu Subbarao
Computers in Biology and Medicine, 2021
Current and Future Therapeutic Targets: A Review on Treating Head and Neck Squamous Cell Carcinoma
Geet Madhukar, Naidu Subbarao
Current Cancer Drug Targets, 2021
Dynamic interaction between lysozyme and ceftazidime: Experimental and molecular simulation approaches
Mohd Sajid Ali, Mohd Waseem, Naidu Subbarao, Hamad A. Al-Lohedan
Journal of Molecular Liquids, 2021
A comparative study of human betacoronavirus spike proteins: structure, function and therapeutics
Jyoti Verma, Naidu Subbarao
Archives of Virology, 2021
Designing novel inhibitors against cyclopropane mycolic acid synthase 3 (PcaA): targeting dormant state of Mycobacterium tuberculosis
Jyoti Verma, Naidu Subbarao
Journal of Biomolecular Structure and Dynamics, 2021
Exploring Molecular Descriptors and Fingerprints to Predict mTOR Kinase Inhibitors using Machine Learning Techniques
Chetna Kumari, Muhammad Abulaish, Naidu Subbarao
IEEE ACM Transactions on Computational Biology and Bioinformatics, 2021
New Framework for the Discovery of PRC2 Inhibitors: Epigenetic Drugs
Danishuddin, Naidu Subbarao, Mohd Khan, Sultan Alouffi, Shahper Khan
Current Drug Targets, 2021
Refinement of Draft Genome Assemblies of Pigeonpea (Cajanus cajan)
Soma S. Marla, Pallavi Mishra, Ranjeet Maurya, Mohar Singh, Dhammaprakash Pandhari Wankhede, Anil Kumar, Mahesh C. Yadav, N. Subbarao, Sanjeev K. Singh, Rajesh Kumar
Frontiers in Genetics, 2020
Virtual screening to identify novel potential inhibitors for Glutamine synthetase of Mycobacterium tuberculosis
Madhulata Kumari, Naidu Subbarao
Journal of Biomolecular Structure and Dynamics, 2020
Estimation of a stronger heparin binding locus in fibronectin domain III14using thermodynamics and molecular dynamics
Sakshi Gupta, Neha Tiwari, Jyoti Verma, Mohd Waseem, Naidu Subbarao, Manoj Munde
Rsc Advances, 2020
Using SMOTE to Deal with Class-Imbalance Problem in Bioactivity Data to Predict mTOR Inhibitors
Chetna Kumari, Muhammad Abulaish, Naidu Subbarao
SN Computer Science, 2020
A genetic programming-based approach to identify potential inhibitors of serine protease of Mycobacterium tuberculosis
Madhulata Kumari, Neeraj Tiwari, Naidu Subbarao
Future Medicinal Chemistry, 2020
Envelope proteins as antiviral drug target
Jyoti Verma, Naidu Subbarao, Maitreyi S. Rajala
Journal of Drug Targeting, 2020
Thermodynamics, molecular modelling and denaturation studies on exploring the binding mechanism of tetramethylpyrazine with human serum albumin
Samima Khatun, Riyazuddeen, Amarjeet Kumar, Naidu Subbarao
Journal of Chemical Thermodynamics, 2020
CID-6033590 inhibits p38MAPK pathway and induces S-phase cell cycle arrest and apoptosis in DU145 and PC-3 cells
Guru Prasad Sharma, Sumiran Kumar Gurung, Afreen Inam, Lokesh Nigam, Archana Bist, Debasish Mohapatra, Shantibhusan Senapati, Naidu Subbarao, Amir Azam, Neelima Mondal
Toxicology in Vitro, 2019
Exploring the modulatory effect of albumin on calcium phosphate crystallization
, Priyadarshini, Devesh Raizada, Pragya Kumar, Tanya Singh, Trisha Pruthi, Abhishek Negi, Lokesh Nigam, Naidu Subbarao
Current Science, 2019
Development and rigorous validation of antimalarial predictive models using machine learning approaches
Danishuddin, G. Madhukar, M.Z. Malik, N. Subbarao
SAR and QSAR in Environmental Research, 2019
Polycomb repressive complex 2 inhibitors: emerging epigenetic modulators
Danishuddin, Naidu Subbarao, Mohammad Faheem, Shahper Nazeer Khan
Drug Discovery Today, 2019
Enhancement in the catalytic activity of human salivary aldehyde dehydrogenase by alliin from garlic: Implications in aldehyde toxicity and oral health
Amaj A. Laskar, Danishuddin, Shaheer H. Khan, Naidu Subbarao, Hina Younus
Current Pharmaceutical Biotechnology, 2019
Diagnostic Significance of p38 Isoforms (p38α, p38β, p38γ, p38δ) in Head and Neck Squamous Cell Carcinoma: Comparative serum level evaluation and design of novel peptide inhibitor targeting the same
Vishal Sahu, Lokesh Nigam, Vertica Agnihotri, Abhishek Gupta, Shashank Shekhar, Naidu Subbarao, Suman Bhaskar, Sharmistha Dey
Cancer Research and Treatment, 2019
Correction: Stress-induced nuclear depletion of Entamoeba histolytica 3-5 exoribonuclease EhRrp6 and its role in growth and erythrophagocytosis(Journal of Biological Chemistry (2018) 293 (16242–16260) Doi: 10.1074/jbc.RA118.004632)
Shashi Shekhar Singh, Sarah Naiyer, Ravi Bharadwaj, Amarjeet Kumar, Yatendra Pratap Singh, Ashwini Kumar Ray, Naidu Subbarao, Alok Bhattacharya, Sudha Bhattacharya
Journal of Biological Chemistry, 2018
In silico study directed towards identification of novel high-affinity inhibitors targeting an oncogenic protein: BRD4-BD1
R. Tumdam, A. Kumar, N. Subbarao, B.S. Balaji
SAR and QSAR in Environmental Research, 2018
Stress-induced nuclear depletion of Entamoeba histolytica 3'-5' exoribonuclease EhRrp6 and its role in growth and erythrophagocytosis
Shashi Shekhar Singh, Sarah Naiyer, Ravi Bharadwaj, Amarjeet Kumar, Yatendra Pratap Singh, Ashwini Kumar Ray, Naidu Subbarao, Alok Bhattacharya, Sudha Bhattacharya
Journal of Biological Chemistry, 2018
In silico identification of inhibitors against Plasmodium falciparum histone deacetylase 1 (PfHDAC-1)
Amarjeet Kumar, Suman Kumar Dhar, Naidu Subbarao
Journal of Molecular Modeling, 2018
Role of tyrosine residue (Y213) in nuclear retention of PCNA1 in human malaria parasite Plasmodium falciparum
Khadija Banu, Pallabi Mitra, Naidu Subbarao, Suman Kumar Dhar
FEMS Microbiology Letters, 2018
Calorimetric, spectroscopic and molecular modelling insight into the interaction of gallic acid with bovine serum albumin
Samima Khatun, Riyazuddeen, Shama Yasmeen, Amarjeet Kumar, Naidu Subbarao
Journal of Chemical Thermodynamics, 2018
Identification of novel inhibitors against UDP-galactopyranose mutase to combat leishmaniasis
Mohammad Kashif, Shams Tabrez, Atahar Husein, Mohd Arish, Ponnusamy Kalaiarasan, Partha P. Manna, Naidu Subbarao, Yusuf Akhter, Abdur Rub
Journal of Cellular Biochemistry, 2018
Molecular Analysis and Modeling of Hepatitis e Virus Helicase and Identification of Novel Inhibitors by Virtual Screening
Mohammad K. Parvez, Naidu Subbarao
Biomed Research International, 2018
A genetic programming-based approach and machine learning approaches to the classification of multiclass anti-malarial datasets
Madhulata Kumari, Neeraj Tiwari, Naidu Subbarao
International Journal of Computational Biology and Drug Design, 2018
Comparative analysis of machine learning based QSAR models and molecular docking studies to screen potential anti-tubercular inhibitors against InhA of mycobacterium tuberculosis
Madhulata Kumari, Neeraj Tiwari, Subhash Chandra, Naidu Subbarao
International Journal of Computational Biology and Drug Design, 2018
Designing, synthesis, and antimicrobial action of oxazoline and thiazoline derivatives of fatty acid esters
Anis Ahmad, Aiman Ahmad, Raja Sudhakar, Himani Varshney, Naidu Subbarao, Saba Ansari, Abdul Rauf, Asad U. Khan
Journal of Biomolecular Structure and Dynamics, 2017
Analyzing the role of CagV, a VirB8 homolog of the type IV secretion system of Helicobacter pylori
Navin Kumar, Mohd Shariq, Amarjeet Kumar, Rajesh Kumari, Naidu Subbarao, Rakesh K. Tyagi, Gauranga Mukhopadhyay
FEBS Open Bio, 2017
Allosteric inhibition of topoisomerase I by pinostrobin: Molecular docking, spectroscopic and topoisomerase I activity studies
Alka Jadaun, N. Subbarao, Aparna Dixit
Journal of Photochemistry and Photobiology B Biology, 2017
In vivo anti-inflammatory activity and docking study of newly synthesized benzimidazole derivatives bearing oxadiazole and morpholine rings
Ankita Rathore, Raja Sudhakar, Mohamed Jawed Ahsan, Abuzer Ali, Naidu Subbarao, Surender Singh Jadav, Sadiq Umar, M. Shahar Yar
Bioorganic Chemistry, 2017
Evaluation of predictive models based on random forest, decision tree and support vector machine classifiers and virtual screening of anti-mycobacterial compounds
Madhulata Kumari, Neeraj Tiwari, Naidu Subbarao, Subhash Chandra
International Journal of Computational Biology and Drug Design, 2017
Designing novel inhibitors against histone acetyltransferase (HAT: GCN5) of Plasmodium falciparum
Amarjeet Kumar, Krishanu Bhowmick, Kunwar Somesh Vikramdeo, Neelima Mondal, Naidu Subbarao, Suman Kumar Dhar
European Journal of Medicinal Chemistry, 2017
Design, synthesis of allosteric peptide activator for human SIRT1 and its biological evaluation in cellular model of Alzheimer's disease
Rahul Kumar, Lokesh Nigam, Amrendra Pratap Singh, Kusum Singh, Naidu Subbarao, Sharmistha Dey
European Journal of Medicinal Chemistry, 2017
3D QSAR, pharmacophore and molecular docking studies of known inhibitors and designing of novel inhibitors for M18 aspartyl aminopeptidase of Plasmodium falciparum
Madhulata Kumari, Subhash Chandra, Neeraj Tiwari, Naidu Subbarao
BMC Structural Biology, 2016
Interaction of the recently approved anticancer drug nintedanib with human acute phase reactant α 1-acid glycoprotein
Ali Saber Abdelhameed, Mohammad Rehan Ajmal, Kalaiarasan Ponnusamy, Naidu Subbarao, Rizwan Hasan Khan
Journal of Molecular Structure, 2016
Transcription regulation of nuclear receptor PXR: Role of SUMO-1 modification and NDSM in receptor function
Priyanka, Deepak Kotiya, Manjul Rana, N. Subbarao, Niti Puri, Rakesh K. Tyagi
Molecular and Cellular Endocrinology, 2016
Docking and molecular dynamics simulation study of EGFR1 with EGF-like peptides to understand molecular interactions
D. Raja Sudhakar, Kalaiarasan P., Naidu Subbarao
Molecular Biosystems, 2016
Pharmacophore based virtual screening for identification of marine bioactive compounds as inhibitors against macrophage infectivity potentiator (Mip) protein of Chlamydia trachomatis
Vijayan Ramachandran, Elavarasi Padmanaban, Kalaiarasan Ponnusamy, Subbarao Naidu, Manoharan Natesan
Rsc Advances, 2016
Biophysical insight into the anti-amyloidogenic behavior of taurine
Sumit Kumar Chaturvedi, Parvez Alam, Javed Masood Khan, Mohd. Khursheed Siddiqui, Ponnusamy Kalaiarasan, Naidu Subbarao, Zeeshan Ahmad, Rizwan Hasan Khan
International Journal of Biological Macromolecules, 2015
Biochemical analysis of CagE: A VirB4 homologue of helicobacter pylori cag-T4SS
Mohd Shariq, Navin Kumar, Rajesh Kumari, Amarjeet Kumar, Naidu Subbarao, Gauranga Mukhopadhyay
Plos One, 2015
In Silico Analysis of Conformational Changes Induced by Normal and Mutation of Macrophage Infectivity Potentiator Catalytic Residues and its Interactions with Rapamycin
Ramachandran Vijayan, Naidu Subbarao, Natesan Manoharan
Interdisciplinary Sciences Computational Life Sciences, 2015
Functional dissection of proliferating-cell nuclear antigens (1 and 2) in human malarial parasite Plasmodium falciparum: Possible involvement in DNA replication and DNA damage response
Pallabi Mitra, Khadija Banu, Abhijit S. Deshmukh, Naidu Subbarao, Suman Kumar Dhar
Biochemical Journal, 2015
Interaction of biocompatible natural rosin-based surfactants with human serum albumin: A biophysical study
Mohd Ishtikhar, Mohd. Sajid Ali, Ayman M. Atta, H.A. Al-Lohedan, Lokesh Nigam, Naidu Subbarao, Rizwan Hasan Khan
Journal of Luminescence, 2015
Correction: In silico screening for novel inhibitors of DNA polymerase III alpha subunit of Mycobacterium tuberculosis (MtbDnaE2, H37Rv)
Alka Jadaun, Raja Sudhakar D, N Subbarao, Aparna Dixit
Plos One, 2015
In silico screening for novel inhibitors of DNA polymerase III alpha subunit of Mycobacterium tuberculosis (MtbDnaE2, H37Rv)
Alka Jadaun, Raja Sudhakar D, N. Subbarao, Aparna Dixit
Plos One, 2015
In silico screening, genotyping, molecular dynamics simulation and activity studies of SNPs in Pyruvate Kinase M2
Ponnusamy Kalaiarasan, Bhupender Kumar, Rupali Chopra, Vibhor Gupta, Naidu Subbarao, Rameshwar N. K. Bamezai
Plos One, 2015
Interaction of Glucagon G-Protein Coupled Receptor with Known Natural Antidiabetic Compounds: Multiscoring in Silico Approach
M. H. Baig, K. Ahmad, Q. Hasan, M. K. A. Khan, N. S. Rao, M. A. Kamal, I. Choi
Evidence Based Complementary and Alternative Medicine, 2015
Insight into the effect of inhibitor resistant S130G mutant on physico-chemical properties of SHV type beta-lactamase: A molecular dynamics study
Mohd Hassan Baig, D. Raja Sudhakar, Ponnusamy Kalaiarasan, Naidu Subbarao, Gulshan Wadhawa, Mohtashim Lohani, M Kalim A Khan, Asad U. Khan
Plos One, 2014
Comparison of geometry and HOMO-LUMO of derivatives of p-benzoquinone using four quantum chemical theories
International Journal of Cancer Research and Prevention, 2014
Molecular simulation of Tyr105 phosphorylated pyruvate kinase M2 to understand its structure and dynamics
Ponnusamy Kalaiarasan, Naidu Subbarao, Rameshwar NK Bamezai
Journal of Molecular Modeling, 2014
The rational design of specific peptide inhibitor against p38α MAPK at allosteric-site: A therapeutic modality for HNSCC
Kamaldeep Gill, Lokesh Nigam, Ratnakar Singh, Suresh Kumar, Naidu Subbarao, Shyam Singh Chauhan, Sharmistha Dey
Plos One, 2014
Structure-based screening of inhibitors against KPC-2: Designing potential drug candidates against multidrug-resistant bacteria
Mohd Danishuddin, Arbab Khan, Mohammad Faheem, Ponnusamy Kalaiarasan, Mohd Hassan Baig, Naidu Subbarao, Asad U. Khan
Journal of Biomolecular Structure and Dynamics, 2014
Pfaldb: An integrated drug target and chemical database for Plasmodium falciparum
Amit Kumar, Nidhi Agarwal, Lalit Pant, Jay Singh, Indira Ghosh, Naidu Subbarao
Current Drug Targets, 2014
Bacterial-induced expression of RAB18 protein in Orzya sativa salinity stress and insights into molecular interaction with GTP ligand
Yachana Jha, Gaurav Sablok, Naidu Subbarao, Raja Sudhakar, M. H. U. Turabe Fazil, R. B. Subramanian, Andrea Squartini, Sunil Kumar
Journal of Molecular Recognition, 2014
Biophysical insight into furosemide binding to human serum albumin: A study to unveil its impaired albumin binding in uremia
Nida Zaidi, Ejaz Ahmad, Mohd Rehan, Gulam Rabbani, Mohammad R. Ajmal, Yusra Zaidi, Naidu Subbarao, Rizwan H. Khan
Journal of Physical Chemistry B, 2013
Development of peptide inhibitor as a therapeutic agent against head and neck squamous cell carcinoma (HNSCC) targeting p38α MAP kinase
Kamaldeep Gill, Abhay K. Singh, Vaishali Kapoor, Lokesh Nigam, Rahul Kumar, Prasida Holla, Satya N. Das, Savita Yadav, Naidu Subbarao, Bidhu K. Mohanti, Sharmistha Dey
Biochimica Et Biophysica Acta General Subjects, 2013
Designing and synthesis of novel antimicrobial heterocyclic analogs of fatty acids
Aiman Ahmad, Anis Ahmad, Himani Varshney, Abdul Rauf, Mohd Rehan, Naidu Subbarao, Asad U. Khan
European Journal of Medicinal Chemistry, 2013
In-silico modeling of a novel OXA-51 from β-lactam-resistant Acinetobacter baumannii and its interaction with various antibiotics
Vishvanath Tiwari, Isha Nagpal, Naidu Subbarao, Rajeswari R. Moganty
Journal of Molecular Modeling, 2012
Virtual screening, identification and in vitro testing of novel inhibitors of O-acetyl-L-serine sulfhydrylase of Entamoeba histolytica
Isha Nagpal, Isha Raj, Naidu Subbarao, Samudrala Gourinath
Plos One, 2012
DNA binding activity of Helicobacter pylori DnaB helicase: The role of the N-terminal domain in modulating DNA binding activities
Ram G. Nitharwal, Vijay Verma, Naidu Subbarao, Santanu Dasgupta, Nirupam R. Choudhury, Suman K. Dhar
FEBS Journal, 2012
Stereo-selectivity of human serum albumin to enantiomeric and isoelectronic pollutants dissected by spectroscopy, calorimetry and bioinformatics
Ejaz Ahmad, Gulam Rabbani, Nida Zaidi, Saurabh Singh, Mohd Rehan, Mohd Moin Khan, Shah Kamranur Rahman, Zainuddin Quadri, Mohd. Shadab, Mohd Tashfeen Ashraf, Naidu Subbarao, Rajiv Bhat, Rizwan Hasan Khan
Plos One, 2011
Mitoxantrone Induced Impediment of Histone Acetylation and Structural Flexibility of the Protein
Shahper N. Khan, Ragothaman Yennamalli, Naidu Subbarao, Asad U. Khan
Cell Biochemistry and Biophysics, 2011
Structural and biochemical studies of serine acetyltransferase reveal why the parasite Entamoeba histolytica cannot form a cysteine synthase complex
Sudhir Kumar, Isha Raj, Isha Nagpal, Naidu Subbarao, Samudrala Gourinath
Journal of Biological Chemistry, 2011
Elimination of endogenous toxin, creatinine from blood plasma depends on albumin conformation: Site specific uremic toxicity & impaired drug binding
Ankita Varshney, Mohd Rehan, Naidu Subbarao, Gulam Rabbani, Rizwan Hasan Khan
Plos One, 2011
Ab Initio DFT Calculation of Formic Acid and Its Derivatives Such as Phenyl Formate, Formamide and Potassium Formate
International Journal of Cancer Research and Prevention, 2010
Homology modelling of a sensor histidine kinase from Aeromonas hydrophila
Mobashar Hussain Urf Turabe Fazil, Sunil Kumar, Naidu Subbarao, Haushila Prasad Pandey, Durg Vijai Singh
Journal of Molecular Modeling, 2010
Ligand binding strategies of human serum albumin: How can the cargo be utilized?
Ankita Varshney, Priyankar Sen, Ejaz Ahmad, Mohd. Rehan, Naidu Subbarao, Rizwan Hasan Khan
Chirality, 2010
Interaction of nalidixic acid and ciprofloxacin with wild type and mutated quinolone-resistance-determining region of DNA gyrase a
Indian Journal of Biochemistry and Biophysics, 2009
Analysis of oligomeric proteins during unfolding by pH and temperature
Pradip Bhattacharya, Tamil Ganeshan, Soumiyadeep Nandi, Alok Srivastava, Prashant Singh, Mohommad Rehan, Reshmi Rashkush, Naidu Subbarao, Andrew Lynn
Journal of Molecular Modeling, 2009
Identification of novel target sites and an inhibitor of the dengue virus E protein
Ragothaman Yennamalli, Naidu Subbarao, Thorsten Kampmann, Ross P. McGeary, Paul R. Young, Bostjan Kobe
Journal of Computer Aided Molecular Design, 2009
Interaction of mitoxantrone with human serum albumin: Spectroscopic and molecular modeling studies
Shahper N. Khan, Barira Islam, Ragothaman Yennamalli, Abdullah Sultan, Naidu Subbarao, Asad U. Khan
European Journal of Pharmaceutical Sciences, 2008
Characterization of doxorubicin binding site and drug induced alteration in the functionally important structural state of oxyhemoglobin
Shahper N. Khan, Barira Islam, Ragothaman Yennamalli, Qamar Zia, Naidu Subbarao, Asad U. Khan
Journal of Pharmaceutical and Biomedical Analysis, 2008
Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors
Preyesh Stephen, Ramachandran Vijayan, Audesh Bhat, N. Subbarao, R. N. K. Bamezai
Journal of Computer Aided Molecular Design, 2008
In silico modeling of alA-adrenoceptor: interaction of its normal and mutated active sites with noradrenaline as well as its agonist and antagonist
Ramchandran Vijayan, Naidu Subbarao, Birendra Nath Mallick
American Journal of Biochemistry and Biotechnology, 2007

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