Publications

Taking stock of the mutations in human SARS-CoV-2 spike proteins: From early days to nearly the end of COVID-19 pandemic. Guruprasad L, Naresh GK, Boggarapu G. Current Research in Structural Biology. 2023 Jan 1;6:100107.

Investigating the Regulation of Ribosomal Protein S6 Kinase 1 by CoAlation.Malanchuk O, Bdzhola A, Palchevskyi S, Bdzhola V, Chai P, Pardo OE, Seckl MJ, Banerjee A, Peak-Chew SY, Skehel M, Guruprasad L. International Journal of Molecular Sciences. 2024 Aug 11;25(16):8747.

Mutations in the receptor-binding domain of human SARS CoV-2 spike protein increases its affinity to bind human ACE-2 receptor. Naresh GK, Guruprasad L. Journal of Biomolecular Structure and Dynamics. 2023 Apr 13;41(6):2368-81.

Design, synthesis, in-silico studies and apoptotic activity of novel amide enriched 2-(1H)-quinazolinone derivatives. Gariganti N, Bandi A, Gatta KN, Pagag J, Guruprasad L, Poola B, Kottalanka RK. Heliyon. 2024 May 15;10(9).

Mutational analyses, pharmacophore-based inhibitor design and in silico validation for Zika virus NS3-helicase.Durgam L, Pagag J, Indra Neela Y, Guruprasad L. Journal of Biomolecular Structure and Dynamics. 2024 Dec 2;42(19):9873-91.

Synthesis, DFT and Molecular docking study of novel bis 1, 2, 3-triazole derivatives of 2-hydroxyquinoline-4-carboxylate as antimicrobial agents. Kandukuri KU, Sharma GV, Saxena S, Guruprasad L, Padmavathi DA. Indian Journal of Biochemistry and Biophysics (IJBB). 2023 Sep 15;60(9):729-40.

Computational validation of inhibitors for human phosphatidylinositol 4-phosphate 5-kinase-type 1 α protein implicated in cancer.  Priyanka Andola, Jishu Pagag, Durgam Laxman, Lalitha Guruprasad.  Journal of Biomolecular Structure and Dynamics. 2024.

Computational design and validation of small molecule inhibitors for type III phosphatidylinositol-4-kinase alpha, a hepatitis C drug target. Jishu Pagag, Priyanka Andola, Laxman Durgam, Lalitha Guruprasad.  Journal of Biomolecular Structure and Dynamics. 2024.

In silico design, modelling and molecular mechanisms of Axl receptor tyrosine kinase inhibitors. Gatta K R S Naresh and Lalitha Guruprasad. Journal of Biomolecular Structure and Dynamics. 2024.

Dynamic conformational states of apo, ATP and cabozantinib bound TAM kinases to differentiate active-inactive kinetic models. Naresh GKRS, Guruprasad L. J Biomol Struct Dyn. 2023 Jan 2:1-21. doi: 10.1080/07391102.2022.2162128. Epub ahead of print. PMID: 36591700. 

Fragment-based inhibitor design for SARS-CoV2 main protease. Andola P, Pagag J, Laxman D, Guruprasad L*. Structural chemistry. 2022 33(5):1467-1487. 

Docosahexaenoic acid is potent against the growth of mature stages of Plasmodium falciparum; inhibition of hematin polymerization a possible target. Ommi NB, Abdullah M, Guruprasad L, Babu PP*. Parasitology International. 2022 Apr 6:102581. 

Structures and energetics of darunavir and active site amino acids of native and mutant HIV–1 protease: a computational study. Neela YI*, Guruprasad L*. Structural Chemistry. 2022 Apr;33(2):395-407. 

Computational studies on the design of NCI natural products as inhibitors to SARS-CoV-2 main protease. Durgam L, Guruprasad L*. Journal of Biomolecular Structure and Dynamics. 2022 Mar 17:1-1. 

Mutations in the receptor-binding domain of human SARS CoV-2 spike protein increases its affinity to bind human ACE-2 receptor. Naresh GK, Guruprasad L*. Journal of Biomolecular Structure and Dynamics. 2022 Jan 21:1-4. 

Molecular mechanism of ATP and RNA binding to Zika virus NS3 helicase and identification of repurposed drugs using molecular dynamics simulations. Laxman Durgam and Lalitha Guruprasad*, Journal of Biomolecular Structure and Dynamics, 2021, Accepted

Identification of 3D motifs based on sequences and structures for binding to CFI‐400945, and deep screening based design of new lead molecules for PLK‐4. Abdullah M, Guruprasad L*. Chemical Biology & Drug Design. 98,4 (2021) 522-538. doi: 10.1111/cbdd.13908

Human SARS CoV‐2 spike protein mutations. Guruprasad L*. Proteins: Structure, Function, and Bioinformatics. 89,5 (2021) 569-576.

Human coronavirus spike protein-host receptor recognition. Guruprasad L*. Progress in biophysics and molecular biology. 161 (2021) 39–53.

Enhanced metastable state models of TAM kinase binding to cabozantinib explains the dynamic nature of receptor tyrosine kinases. Gatta KRS Naresh, Lalitha Guruprasad*. Journal of Biomolecular Structure and Dynamics. 39,4 (2021). 1213-1235.

Evolutionary relationships and sequence-structure determinants in human SARS coronavirus-2 spike proteins for host receptor recognition. Guruprasad L*. Proteins: Structure, Function, and Bioinformatics. 88,11 (2020) 1387-1393.

Activity and thermal stability of Mycobacterium tuberculosis PE1 and PE2 proteins esterase domain in the presence of aprotic ionic liquids. Divya MB, Guruprasad L*. Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy. 225 (2020) 117477.

Covalent Aurora A regulation by the metabolic integrator coenzyme A. Tsuchiya Y, Byrne DP, Burgess SG, Bormann J, Baković J, Huang Y, Zhyvoloup A, Yu BYK, Peak-Chew S, Tran T, Bellany F, Tabor AB, Chan AE, Guruprasad L, Garifulin O, Filonenko V, Vonderach M, Ferries S, Eyers CE, Carroll J, Skehel M, Bayliss R, Eyers PA, Gout I*. Redox Biology. 28 (2020) 101318.

Computational basis for the design of PLK-2 inhibitors. Abdullah M, Guruprasad L*. Structural Chemistry. 31 (2020). 275–292.

Homology modeling, docking and structure-based virtual screening for new inhibitor identification of Klebsiella pneumoniae heptosyltransferase-III. Panda SK, Saxena S, Guruprasad L*. Journal of Biomolecular Structure and Dynamics. 387 (2020) 1887-1902.

Inhibitor binding studies of Mycobacterium tuberculosis MraY (Rv2156c): Insights from molecular modeling, docking, and simulation studies. Mallavarapu BD, Abdullah M, Saxena S, Guruprasad L*. Journal of Biomolecular Structure and Dynamics. 37,14 (2019) 3751-3763.

Structural insights into the inhibitor binding and new inhibitor design to Polo-like kinase-1 Polo-box domain using computational studies. Abdullah M, Guruprasad L*. Journal of Biomolecular Structure and Dynamics. 37,13 (2019) 3410-3421.

A structural and functional perspective on the enzymes of Mycobacterium tuberculosis involved in the L-rhamnose biosynthesis pathway. Dhaked DK, Bala Divya M, Guruprasad L*. Progress in Biophysics and Molecular Biology. 145 (2019) 52-64.

Macromolecular properties and partial amino acid sequence of a Kunitz-type protease inhibitor from okra (Abelmoschus esculentus) seeds. Datta D, Pohlentz, G, Mondal S, Divya MB, Guruprasad L, Mormann M*, Swamy MJ*. Journal of Biosciences. 44,2 (2019), art. no. 35.

Multiple e-pharmacophore modelling pooled with high-throughput virtual screening, docking and molecular dynamics simulations to discover potential inhibitors of Plasmodium falciparum lactate dehydrogenase (PfLDH). Saxena S, Durgam L, Guruprasad L*. Journal of Biomolecular Structure and Dynamics. 37,7 (2019)  1783-1799.

Adaptation of Mge1 to oxidative stress by local unfolding and altered interaction with mitochondrial Hsp70 and Mxr2. Karri S, Singh S, Paripati AK, Marada A, Krishnamoorthy T, Guruprasad L, Balasubramanian, D, Sepuri NBV* . Mitochondrion. 46 (2019) 140-148

Protein Structure. Guruprasad L*. Resonance. 24,3 (2019) 327-338.

Computational fragment-based design of Wee1 kinase inhibitors with tricyclic core scaffolds. Abdullah M, Guruprasad L*. Structural Chemistry. 30,1 (2019) pp. 213-226.

Mycobacterium tuberculosis PE1 and PE2 proteins carrying conserved α/β-serine hydrolase domain are esterases hydrolyzing short to medium chain p-nitrophenyl esters. Divya MB, Vemula M, Balakrishnan K, Banerjee S, Guruprasad L*. Progress in Biophysics and Molecular Biology. 140 (2018)  90-102.

Discovery of novel inhibitors of Mycobacterium tuberculosis MurG: Homology modelling, structure based pharmacophore, molecular docking, and molecular dynamics simulations. Saxena S, Abdullah M, Sriram D,  Guruprasad L*. Journal of Biomolecular Structure and Dynamics. 36,12 (2018)  3184-3198.

Insights into the carbonic anhydrases and autotrophic carbon dioxide fixation pathways of high CO2 tolerant Rhodovulum viride JA756. Khandavalli, LVNS., Lodha T, Abdullah M, Guruprasad L, Chintalapati S, Chintalapati VR*. Microbiological Research. 215 (2018)  130-140.

Three-dimensional models of Mycobacterium tuberculosis proteins Rv1555, Rv1554 and their docking analyses with sildenafil, tadalafil, vardenafil drugs suggest interference with quinol binding likely to affect protein's function. Dash P, Bala Divya M, Guruprasad L, Guruprasad K*. BMC Structural Biology. 18,1 (2018) art. no. 5.

N6-adenosine DNA methyltransferase from H. Pylori 98-10 strain in complex with DNA and AdoMet: structural insights from in silico studies. Singh S, Guruprasad L*. Journal of Physical Chemistry B. 121,2 (2017)  365-378.

A single point mutation in mitochondrial Hsp70 cochaperone Mge1 gains thermal stability and resistance. Marada, A., Karri, S., Singh, S., Allu, P.K., Boggula, Y., Krishnamoorthy, T., Guruprasad, L., Babu V Sepuri, N*. Biochemistry. 55,51(2016)  7065-7072.

A transcriptional repressive role for epithelial-specific ETS factor ELF3 on oestrogen receptor alpha in breast cancer cells. Gajulapalli, VNR, Samanthapudi, VSK, Pulaganti, M, Khumukcham, SS, Malisetty, VL, Guruprasad L, Chitta SK, Manavathi B*. Biochemical Journal. 473,8 (2016)  1047-1061.

Prediction of certain well-characterized domains of known functions within the PE and PPE proteins of mycobacteria. Sultana R, Tanneeru K, Kumar ABR, Guruprasad L*. PLoS ONE. 11,2 (2016)  e0146786.

Structure and dynamics of H. pylori 98-10 C5-cytosine specific DNA methyltransferase in complex with S -adenosyl-l-methionine and DNA. Singh S, Tanneeru, K, Guruprasad L*. Molecular BioSystems. 12,10 (2016) 3111-3123.

Isolation, purification, and characterization of a stable defensin-like antifungal peptide from Trigonella foenum-graecum (fenugreek) seeds. Oddepally R, Guruprasad L*. Biochemistry (Moscow). 80,3 (2015) 332-342.

In silico 3D structure modeling and inhibitor binding studies of human male germ cell associated kinase. Tanneeru K, Balla AR, Guruprasad L*. Journal of Biomolecular Structure & Dynamics. 33,8 (2015) 1710-1719.

Structure based annotation of Helicobacter pylori strain 26695 proteome. Singh S, Guttula PK, Guruprasad L*. PLoS One.  9,12 (2014) e115020.   

Structure and sequence based analysis of alpha-amylase evolution. Swati Singh, Lalitha Guruprasad*. Protein Pept. Lett. 21,9 (2014). 948-956.

Mutagenesis and molecular dynamics simulations revealed the chitooligosaccharide entry and exit points for chitinase D from Serratia proteamaculans. Madhuprakash J, Tanneeru K, Karlapudi B, Guruprasad L*, Podile AR*. Biochim Biophys Acta. 1840,9 (2014) 2685-2694 

To make the most of a protein sequence. Swathi Adindla, Rafiya Sultana, Karunakar Tanneeru, Swati Singh, Lalitha Guruprasad*. Proceedings of Andhra Pradesh Akademi of Sciences (special Issue Bioinformatics). 15,3 (2013) 125-130.

39. Human resistin, a proinflammatory cytokine, shows chaperone-like activity. Suragani M, Aadinarayana VD, Pinjari AB, Tanneeru K, Guruprasad L, Banerjee S, Pandey S, Chaudhuri TK, Ehtesham NZ*. Proc. Natl. Acad. Sci. (USA). 110,51 (2013) 20467-20472.

Ponatinib is a pan BCR-ABL kinase inhibitor: MD simulations and SIE study. Karunakar Tanneeru, Lalitha Guruprasad*. PLoS ONE. 8,11 (2013) e78556.

Purification and characterization of a stable kunitz trypsin inhibitor from Trigonella foenum-graecum (fenugreek) seeds. Rajender Oddepally, Gopi Sriram, Lalitha Guruprasad*. Phytochemistry. 96 (2013) 26–36.

Structural basis for binding of Aurora-AG198N-INCENP complex: MD simulations and free energy calculations. Karunakar Tanneeru, Lalitha Guruprasad*. Protein & Peptide Letters. 20 (2013) 1246-1256.

The PE16 (Rv1430) of Mycobacterium tuberculosis is an esterase belonging to serine hydrolase superfamily of proteins.  Sultana R, Vemula MH, Banerjee S, Guruprasad L*. PLoS ONE. 8,2 (2013) e55320

Ligand-based drug design for human endothelin converting enzyme-1 inhibitors. Karunakar   Tanneeru, Itishri Sahu, Lalitha Guruprasad*. Medicinal Chemistry Research. 22 (2013) 4401–4409.

Transglycosylation by chitinase D from Serratia proteamaculans improved through altered substrate interactions. Jogi Madhuprakash, Karunakar Tanneeru, Pallinti Purushotham, Lalitha Guruprasad, Appa Rao Podile*. J. Biol. Chem. 287 (2012) 44619-44627.

Structural insights into the active site of human sodium dependent glucose co-transporter 2: Homology modelling, molecular docking, and 3D-QSAR studies. Srinivas Nakka and Lalitha Guruprasad*. Australian Journal of Chemistry. 65,9 (2012) 1314-1324.  

Enhanced antifungal and insect α-amylase inhibitory activities of Alpha-TvD1, a peptide variant of Tephrosia villosa defensin (TvD1) generated through in vitro mutagenesis. Vijayan S, Imani J, Tanneeru K, Guruprasad L*, Kogel KH*, Kirti PB*. Peptides. 33, 2 (2012) 220-229.

3D-QSAR and molecular docking studies on substituted isothiazole analogs as inhibitors against MEK-1 kinase. Bandi Madhusudhan Reddy, Karunakar Tanneeru, Potshangbam Angamba Meetei, Lalitha Guruprasad*. Chemical Biology & Drug Design. 79,1 (2012) 84–91.

Ligand-based 3-D pharmacophore generation and molecular docking of mTOR kinase inhibitors. Tanneeru K, Guruprasad L*. J Mol. Modeling. 18 (2012) 1611–1624.

Three-dimensional quantitative structure–activity relationship (3D- QSAR) analysis and molecular docking of ATP-competitive triazine analogs of human mTOR inhibitors. Karunakar Tanneeru, Bandi Madhusudhan Reddy, Lalitha Guruprasad*. Medicinal Chemistry Research. 21,7 (2012) 1207–1217 

The imidazolidone analogs as phospholipase D1 inhibitors: Analysis of the three-dimensional quantitative structure–activity relationship. Srinivas Nakka, Lalitha Guruprasad*. Medicinal Chemistry Research. 21,9 (2012) 2517-2525

3D-QSAR and molecular docking studies of 2-pyrimidinecarbonitrile derivatives as inhibitors against falcipain-3. Potshangbam AM, Tanneeru K, Reddy BM, L Guruprasad*. Bioorganic & Medicinal Chemistry Letters. 21 (2011) 7219–7223.

The PE-PPE domain in Mycobacterium reveals a serine α/β hydrolase fold and function: an in-silico analysis. Rafiya Sultana, Karunakar Tanneeru, Lalitha Guruprasad*. PLoS ONE. 6,2 (2011) e16745.

Structural rationale for the recognition of arginine at P(3) in PEXEL motif containing proteins of Plasmodium falciparum by plasmepsin V. Lalitha Guruprasad*, Karunakar Tanneeru, Kunchur Guruprasad. Protein & Peptide Letters. 18,6 (2011) 634-641 

Computational analysis of interactions of argadin with chitotriosidase, chitinase and acidic mammalian chitinase: Hints for specific inhibitor design. Aparoy P, Reddy RN, Guruprasad  Lalitha,  Reddanna . P, Letters in Drug Design & Discovery 7,5, 324-331 (2010).

Highly conserved Asp-204 and Gly-776 are important for activity of the quinoprotein glucose dehydrogenase of Escherichia coli and for mineral phosphate solubilization. Burla Sashidhar, Krishna Kishore Inampudi, Lalitha Guruprasad, Anil Kondreddy, Kodetham Gopinath, Appa Rao Podile. Journal of  Molecular Microbiology and Biotechnology. 18 109–119 (2010).

Structure prediction of neuroendocrine convertase -2: A potential target in various cancers. Aparoy P, Chatterjee M, Guruprasad L, Reddanna . PProtein & Peptide Letters. 16 383-391 (2009).

Interaction of bovine serum albumin with dipolar molecules: fluorescence and molecular docking studies. Bhaswati Bhattacharya, Srinivas Nakka, Lalitha Guruprasad, Anunay Samanta.  Journal of Physcial  Chemistry B 113,7, 2143-2150 (2009).

Prokaryotic expression of a constitutively expressed Tephrosia villosa defensin and its potent antifungal activity. Vijayan S, Guruprasad L, Kirti PB.Applied Microbiology and Biotechnology. 80, 1023–1032 (2008).

Homology modeling of 5-lipoxygenase and hints for better inhibitor design. Aparoy P, Reddy RN, Guruprasad L, Reddy MR, Reddanna P. Journal of Computer Aided Molecular Design 22, 611–619 (2008).

Identification and analysis of novel Amino acid sequence repeats and domains in Pyrobaculum aerophilum using computational tools. Hemalatha G, Kishore IK, Rao RS, Guruprasad L. Protein & Peptide Letters. 14, 692-697 (2007).

Characterization of defensin (Tfgd2) from Trigonella foenum-graecum. Olli Sudar, Guruprasad Lalitha Kirti PB. Current Science.  93, 3, 365-369 (2007).

Cell surface proteins in archaeal and bacterial genomes comprising "LVIVD", "RIVW" and "LGxL" tandem sequence repeats are predicted to fold as beta-propeller.  Adindla S, Inampudi KK, Guruprasad. International Journal of Biological Macromolecules. 41, 454–468 (2007).

Identification and analysis of novel amino-acid sequence repeats in Bacillus anthracis str. Ames proteome using computational tools. Hemalatha GR Rao DS, Guruprasad L. Comparative and Functional Genomics. Article ID 47161, 23 pages doi:10.1155/2007/47161 (2007).

Docking of phosphonate and trehalose analog inhibitors into M. tuberculosis mycolyltransferase Ag85C: Comparison of the two scoring fitness functions GoldScore and ChemScore, in the GOLD software. Annamala MK, Inampudi KK, Guruprasad L. Bioinformation. 1,9, 339-350 (2007). 

Molecular, biochemical and structural characterization of osmotin-like protein from black nightshade (Solanum nigrum). Jami SK, Swathi Anuradha T, Guruprasad L, Kirti PB. J Plant Physiology. 164, 238-252 (2007).

Analysis and modeling of mycolyl-transferases in the CMN groupRamulu HG, Adindla S, Guruprasad L. . Bioinformation. 1,5, 161-169 (2006).

Juxtaposed half-cystines as disulphide bridged partners in protein tertiary structure. Guruprasad K, Kartik VJ, Lavanya T, Guruprasad L. Protein & Peptide Letters. 13,6, 577-579 (2006).

Functional correlation of cyclooxygenases- 1, 2 and 3 from amino acid sequences and three dimensional model structures. M Nagini, G V Reddy, G R Hemalatha,  Lalitha Guruprasad,  P Reddanna. Indian Journal of Chemistry. 45,1, 182-187 (2006).

The Rv3799–Rv3807 gene cluster in Mycobacterium tuberculosis genome corresponds to the ‘Ancient Conserved Region’ in CMN mycolyltransferases.Hemalatha G. Ramulu, Adindla Swathi, and Lalitha Guruprasad. Evolutionary Bioinformatics Online. 2, 377–385 (2006).

Identification and analysis of novel tandem repeats in the cell surface proteins of Archaeal and Bacterial genomes using computational tools. S. Adindla, K. K. Inampudi, K. Guruprasad, L. Guruprasad. Comparative and Functional Genomics. 5, 2-16 (2004).

Three-dimensional models and structure analysis of corynemycolyltransferases in Corynebacterium glutamicum and Corynebacterium efficiens.Adindla S, Guruprasad K, Guruprasad L. Int J Biol Macromol. 34,3, 181-189 (2004).

Combinations of turns in proteins. Guruprasad K, Rao MJ, Adindla S Guruprasad L. J Peptide Res. 62, 4, 167-174 (2003).

Sequence analysis corresponding to the PPE and PE proteins in Mycobacterium tuberculosis and other genomes. Adindla S, Guruprasad L. J Biosciences 28(2),169-179 (2003).

Prediction of gamma-turns from amino acid sequences. Guruprasad K, Shukla S, Adindla S, Guruprasad L. J Peptide Res. 61(5), 243-251 (2003).

Protein three-dimensional structure and drug design: Some examples from intracellular components of the signal transduction pathway. European Journal of Medicinal Chemistry 30, 605s-620s (1995).

The crystal structure of the N-terminal SH3 domain of Grb2. J Mol Biol.  248,4, 856-866 (1995).

Crystal structure of the pleckstrin homology domain from dynamin. Nat Struct Biol. 1,11, 782-788 (1994).

Ruthenium (VI) in the oxidation of 2-propanol and 1-propanol: kinetic study. Transition metal chemistry. 17,1, 29-33 (1992).

Sodium ruthenate catalysis in the oxidation of substituted benzyl alcohols by hexacyanoferrate (III). Indian J. Chem. 31A, 309-312 (1992).