Molecular Modeling and Simulations; Eicosanoid Biology; Computer Aided Inhibitor Development.
Dr. Polamarasetty Aparoy
Faculty of Biology
Indian Institute of Petroleum & Energy
Visakhapatnam - 530003
Email: aparoy.bio[AT]iipe.ac.in (Replace AT with @)
01) Gupta A, Kumar V, Aparoy P. Role of topological, electronic, geometrical, constitutional and quantum chemical based descriptors in QSAR: mPGES-1 as a case study. Current Topics in Medicinal Chemistry. 2018;18(13):1075-1090.
02) Gupta A, Chaudhary N, Aparoy P. MM-PBSA and per-residue decomposition energy studies on 7- Phenyl-imidazoquinolin-4 (5H)-one derivatives: Identification of crucial site points at microsomal prostaglandin E synthase-1 (mPGES-1) active site. International Journal of Biological Macromolecules. 2018 July; 119, 352-359.
03) Chaudhary N, Aparoy P. Deciphering the mechanism behind the varied binding activities of COXIBs through Molecular Dynamic Simulations, MM-PBSA binding energy calculations and per-residue energy decomposition studies. Journal of Biomolecular Structure and Dynamics. 2017 Mar; 35(4):868-882.
04) Gupta A, Aparoy P. Insights into the structure activity relationship of mPGES-1 inhibitors: Hints for better inhibitor design. International Journal of Biological Macromolecules. 2016 Jul; 88:624-32.
05) Singh O, Kakularam KR, Reddanna P, Aparoy P. Understanding the dual inhibition of COX-2 and Carbonic anhydrase-II by Celecoxib and CG100649 using Density functional theory calculations and other Molecular Modelling approaches. Protein and Peptide Letters. 2015 Jun; 22(10):903-12.
06) Gupta A, Chaudhary N, Reddy KK, Reddanna P, Aparoy P. The Augmenting Effects of Desolvation and Conformational Energy Terms on the Predictions of Docking Programs against mPGES-1. PLoS One. 2015 Aug 25; 10(8):e0134472.
07) Reddy KK, Vidya Rajan VK, Gupta A, Aparoy P, Reddanna P. Exploration of binding site pattern in arachidonic acid metabolizing enzymes, Cyclooxygenases and Lipoxygenases. BMC Research Notes. 2015 Apr 16; 8: 152.
08) Horn T, Adel S, Schumann R, Sur S, Reddy KK, Aparoy P, Reddanna P, Kuhn H, Heydeck D. Evolutionary aspects of lipoxygenases and genetic diversity of human leukotriene signaling. Progress in Lipid Research. 2015 Jan; 57:13-39.
09) Singh O, Sawariya K, Aparoy P. Graphlet signature-based scoring method to estimate proteinligand binding affinity. Royal Society Open Science. 2014 Dec; 1(4): 140306.
10) Reddy MR, Reddy CR, Rathore RS, Erion MD, Aparoy P, Reddy RN, Reddanna P. Free energy calculations to estimate ligand-binding affinities in structure-based drug design. Current Pharmaceutical Design. 2014; 20(20):3323-37.
11) Ningshen TJ, Aparoy P, Ventaku VR, Dutta-Gupta A. Functional interpretation of a non-gut hemocoelic tissue aminopeptidase N (APN) in a lepidopteran insect pest Achaea janata. PLoS One. 2013 Nov 14; 8(11):e79468.
12) Filosa R, Peduto A, Aparoy P, Schaible AM, Luderer S, Krauth V, Petronzi C, Massa A, de Rosa M, Reddanna P, Werz O. Discovery and biological evaluation of novel 1,4-benzoquinone and related resorcinol derivatives that inhibit 5-lipoxygenase. European Journal of Medicinal Chemistry. 2013 Sep; 67:269-79.
13) Hofheinz K, Reddy KK, Susan A, Monika A, Aparoy P, Reddanna P, Kuhn H, Horn T. Conversion of pro-inflammatory murine Alox5 into an anti-inflammatory 15S-lipoxygenating enzyme by multiple mutations of sequence determinants. Archives of Biochemistry and Biophysics. 2013 Feb 1; 530(1):40-7.
14) Aparoy P, Reddy KK, Reddanna P. Structure and Ligand Based drug design strategies in the development of novel 5-LOX inhibitors. Current Medicinal Chemistry. 2012; 19(22):3763-78.
15) Reddy NP, Reddy TC, Aparoy P, Chandrani A, Sridhar PR, Reddanna P. Structure based drug design, synthesis and evaluation of 4-(benzyloxy)-1-phenylbut-2-yn-1-ol derivatives as 5- lipoxygenase inhibitors. European Journal of Medicinal Chemistry. 2012 Jan; 47(1):351-9.
16) Rathore RS, Aparoy P, Reddanna P, Kondapi AK, Reddy MR. Minimum MD Simulation Length Required to Achieve Reliable Results in Free Energy Perturbation Calculations: Case Study of Relative Binding Free Energies of Fructose-1,6-Bisphosphatase Inhibitors. Journal of Computational Chemistry. 2011 Jul 30; 32(10):2097-103.
17) Aparoy P, Suresh KG, Kumar Reddy K, Priyankeswari S, Reddanna P. CoMFA and CoMSIA studies on 5-Hydroxyindole-3-Carboxylate derivatives as 5-Lipoxygenase inhibitors: Generation of homology model and docking studies. Bioorganic and Medicinal Chemistry Letters. 2011 Jan 1; 21(1):456-62.
18) Reddy TC, Aparoy P, Kishore Babu N, Suresh Kumar K, Reddanna P. Kinetics and Docking studies of a COX-2 inhibitor isolated from Terminalia bellerica fruits. Protein and Peptide Letters. 2010 Oct; 17(10):1251-7.
19) Bhushan KK, Aparoy P, Reddanna P. EasyModeller: A graphical interface to MODELLER. BMC Research Notes. 2010 Aug 16; 3:226.
20) Reddy NP, Aparoy P, Reddy TC, Chandrani A, Reddanna P. Design, synthesis and biological evaluation of chalcone derivatives as 5-LOX inhibitors. Bioorganic and Medicinal Chemistry. 2010 Aug 15; 18(16):5807-15.
21) Aparoy P, Reddy RN, Guruprasad L, Reddanna P. Computational Analysis of Interactions of Argadin with Chitotriosidase, Chitinase and Acidic Mammalian Chitinase: Hints for Specific Inhibitor Design. Letters in Drug Designing and Discovery. 2010; 7 (5):324-331.
22) Bhushan KK, Aparoy P, Reddanna P. Development of tools and database for analysis of metal binding sites in protein. Protein and Peptide Letters. 2010 Jun; 17(6):765-73.
23) Gullipalli D, Arif A, Aparoy P, Svenson GJ, Whiting MF, Reddanna P, Dutta-Gupta A. Identification of a developmentally and hormonally regulated Delta-Class glutathione Stransferase in rice moth Corcyra cephalonica. Comparative Biochemistry and Physiology. Part B, Biochemistry and Molecular Biology. 2010 May; 156(1):33-9.
24) Reddy RN, Mutyala RR, Aparoy P, Reddanna P, Reddy MR. An analysis of hydrophobic interactions of thymidylate synthase with methotrexate: free energy calculations involving mutant and native structures bound to methotrexate. Journal of Molecular Modeling. 2010 Feb; 16(2):203- 9.
25) Aparoy P, Reddy KK, Kalangi SK, Reddy CT, Reddanna P. Pharmacophore modeling and virtual screening for designing potential 5-Lipoxygenase inhibitors. Bioorganic and Medicinal Chemistry Letters. 2010 Feb 1; 20(3):1013-8.
26) Aparoy P, Chatterjee M, Guruprasad L, Reddanna P. Structure prediction of neuroendocrine convertase -2: a potential target in various cancers. Protein and Peptide Letters. 2009; 16(4):383- 91.
27) Aparoy P, Leela T, Reddy RN, Reddanna P. Computational analysis of R and S isoforms of 12- lipoxygenases: homology modeling and docking studies. Journal of Molecular Graphics and Modelling. 2009 Feb; 27(6):744-50.
28) Aparoy P, Reddy RN, Guruprasad L, Reddy MR, Reddanna P. Homology modeling of 5- lipoxygenase and hints for better inhibitor design. Journal of Computer Aided Molecular Design; 2008 Sep; 22(9):611-9.
29) Reddy RN, Mutyala R, Aparoy P, Reddanna P, Reddy MR. Computer aided drug design approaches to develop cyclooxygenase based novel anti-inflammatory and anti-cancer drugs. Current Pharmaceutical Design. 2007; 13(34):3505-17.