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Article: Assessing Differential Binding of Aggregation-Induced Emission-Based Luminogens to Host Interacting Surface Proteins of SARS-CoV-2 and Influenza Virus-An

Tanneeru, Karunakar / Bhatraju, Naveen Kumar / Bhosale, Rajesh S / Kalangi, Suresh K

2021 Volume 12, Page(s) 766351

Abstract: Early detection of asymptomatic cases through mass screening is essential to constrain the coronavirus disease 2019 (COVID-19) transmission. However, the existing diagnostic strategies are either resource-intensive, time-consuming, or less sensitive, ... ...

Abstract	Early detection of asymptomatic cases through mass screening is essential to constrain the coronavirus disease 2019 (COVID-19) transmission. However, the existing diagnostic strategies are either resource-intensive, time-consuming, or less sensitive, which limits their use in the development of rapid mass screening strategies. There is a clear pressing need for simple, fast, sensitive, and economical diagnostic strategy for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) screening even in resource-limited settings. In the current work, we assessed the
Language	English
Publishing date	2021-12-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2021.766351
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Article ; Online: Ponatinib is a pan-BCR-ABL kinase inhibitor: MD simulations and SIE study.

Tanneeru, Karunakar / Guruprasad, Lalitha

PloS one

2013 Volume 8, Issue 11, Page(s) e78556

Abstract: BCR-ABL kinase domain inhibition can be used to treat chronic myeloid leukemia. The inhibitors such as imatinib, dasatinib and nilotinib are effective drugs but are resistant to some BCR-ABL mutations. The pan-BCR-ABL kinase inhibitor ponatinib exhibits ... ...

Abstract	BCR-ABL kinase domain inhibition can be used to treat chronic myeloid leukemia. The inhibitors such as imatinib, dasatinib and nilotinib are effective drugs but are resistant to some BCR-ABL mutations. The pan-BCR-ABL kinase inhibitor ponatinib exhibits potent activity against native, T315I, and all other clinically relevant mutants, and showed better inhibition than the previously known inhibitors. We have studied the molecular dynamics simulations and calculated solvated interaction energies of native and fourteen mutant BCR-ABL kinases (M244V, G250E, Q252H, Y253F, Y253H, E255K, E255V, T315A, T315I, F317L, F317V, M351T, F359V and H396P) complexed with ponatinib. These studies revealed that the interactions between ponatinib and individual residues in BCR-ABL kinase are also affected due to the remote residue mutations. We report that some residues, Met244, Lys245, Gln252, Gly254, Leu370 and Leu298 do not undergo any conformational changes, while the fluctuations in residues from P-loop, β3-, β5- strands and αC- helix are mainly responsible for ponatinib binding to native and all mutant BCR-ABL kinases. Our work provides the molecular mechanisms of native and mutant BCR-ABL kinases inhibition by ponatinib at atomic level that has not been studied before.
MeSH term(s)	Antineoplastic Agents/chemistry ; Catalytic Domain ; Fusion Proteins, bcr-abl/antagonists & inhibitors ; Fusion Proteins, bcr-abl/chemistry ; Fusion Proteins, bcr-abl/genetics ; Humans ; Hydrogen Bonding ; Imidazoles/chemistry ; Molecular Dynamics Simulation ; Mutation, Missense ; Protein Binding ; Protein Structure, Secondary ; Pyridazines/chemistry ; Solvents/chemistry ; Thermodynamics ; Water/chemistry
Chemical Substances	Antineoplastic Agents ; Imidazoles ; Pyridazines ; Solvents ; Water (059QF0KO0R) ; ponatinib (4340891KFS) ; Fusion Proteins, bcr-abl (EC 2.7.10.2)
Language	English
Publishing date	2013-11-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0078556
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Article ; Online: Structural basis for binding of aurora-AG198N- INCENP complex: MD simulations and free energy calculations.

Tanneeru, Karunakar / Guruprasad, Lalitha

Protein and peptide letters

2013 Volume 20, Issue 11, Page(s) 1246–1256

Abstract: Aurora-A, B and C are non-receptor serine/threonine kinases in Homo sapiens. In spite of high similarity in their sequences, they possess distinct binding partners. These kinases play an important role in cell division and overexpressed in certain ... ...

Abstract	Aurora-A, B and C are non-receptor serine/threonine kinases in Homo sapiens. In spite of high similarity in their sequences, they possess distinct binding partners. These kinases play an important role in cell division and overexpressed in certain cancers. It has been demonstrated that Gly198 in Aurora-A kinase is responsible for its basal kinase activity, the mutation G198N transforms Aurora-A to Aurora-B like function and localization by binding to Inner centromere protein (INCENP). The molecular mechanisms, structural determinants and the binding energetics of the Aurora-A - INCENP complex owing to a single amino acid G198N mutation are not studied. Therefore, we have docked INCENP into human Aurora-A kinase, mutated Gly198 to Asn, Leu and Ala. The wild type and mutant Aurora-A - INCENP complexes were subjected to 40 ns molecular dynamics (MD) simulations. The Asn198 is located in the amphipathic cavity comprising Leu869(IN), Glu868(IN), Thr872(IN), Tyr197(AurA) and Tyr199(AurA) and the interactions mediated via hydrogen bonds are important to stabilize the Aurora-A(G198N) - INCENP complex. The fluctuations in the secondary structural elements and the solvent accessible surface area of all the four complexes during the MD simulations were studied. We calculated the binding free energy upon mutation in the three mutant complexes. The Aurora-A(G198N) - INCENP complex with hydrophilic amino acid mutation has the negative free energy of solvation indicating favorable interactions with INCENP. Our results provide the structural basis and energetics of the human Aurora-A(G198N) - INCENP complex.
MeSH term(s)	Amino Acid Sequence ; Aurora Kinase A/chemistry ; Aurora Kinase A/genetics ; Cell Line ; Chromosomal Proteins, Non-Histone/chemistry ; Chromosomal Proteins, Non-Histone/genetics ; Energy Metabolism ; Humans ; Hydrogen Bonding ; Mitosis ; Models, Molecular ; Molecular Dynamics Simulation ; Mutation ; Phosphorylation ; Protein Binding ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid
Chemical Substances	Chromosomal Proteins, Non-Histone ; INCENP protein, human ; Aurora Kinase A (EC 2.7.11.1)
Language	English
Publishing date	2013-07-11
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1280776-x
ISSN	1875-5305 ; 0929-8665
ISSN (online)	1875-5305
ISSN	0929-8665
DOI	10.2174/09298665113209990045
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Article ; Online: Structure and dynamics of H. pylori 98-10 C5-cytosine specific DNA methyltransferase in complex with S-adenosyl-l-methionine and DNA.

Singh, Swati / Tanneeru, Karunakar / Guruprasad, Lalitha

Molecular bioSystems

2016 Volume 12, Issue 10, Page(s) 3111–3123

Abstract: Helicobacter pylori is a Gram-negative bacterium that inhabits the human gastrointestinal tract, and some strains of this bacterium cause gastric ulcers and cancer. DNA methyltransferases (MTases) are promising drug targets for the treatment of cancer ... ...

Abstract	Helicobacter pylori is a Gram-negative bacterium that inhabits the human gastrointestinal tract, and some strains of this bacterium cause gastric ulcers and cancer. DNA methyltransferases (MTases) are promising drug targets for the treatment of cancer and other diseases that are also caused by epigenetic alternations of the genome. The C5-cytosine specific DNA methyltransferase from H. pylori (M. Hpy C5mC) catalyzes the transfer of the methyl group from the cofactor S-adenosyl-l-methionine (AdoMet) to the flipped cytosine of the substrate DNA. Herein we report the sequence analyses, 3-D structure modeling and molecular dynamics simulations of M. Hpy C5mC, when complexed with AdoMet as well as DNA. We analyzed the protein-DNA interactions prominently established by the flipped cytosine and the interactions between the protein and cofactor in the active site. We propose that the contacts made by cytosine O2 with Arg155 and Arg157, and the water-mediated interactions with cytosine N3 may be essential for the activity of methyl transfer as well as the deprotonation at the C5 position in our C5mC model. Specific recognition of DNA was mediated mainly by residues from Ser221-Arg229 and Ser243-Gln246 of the target recognition domain (TRD) and some residues of the loop Ser75-Lys83 from the large domain. These findings are further supported by alanine scanning mutagenesis studies. The results reported here explain the sequence, structure and binding features necessary for the recognition between the cofactor and the substrate by the key epigenetic enzyme, M. Hpy C5mC.
MeSH term(s)	Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; DNA/chemistry ; DNA/metabolism ; DNA (Cytosine-5-)-Methyltransferases/chemistry ; DNA (Cytosine-5-)-Methyltransferases/genetics ; DNA (Cytosine-5-)-Methyltransferases/metabolism ; DNA Methylation ; Helicobacter pylori/enzymology ; Hydrogen Bonding ; Macromolecular Substances/chemistry ; Macromolecular Substances/metabolism ; Molecular Conformation ; Molecular Dynamics Simulation ; Mutation ; Protein Binding ; Protein Interaction Domains and Motifs ; S-Adenosylmethionine/chemistry ; S-Adenosylmethionine/metabolism ; Structure-Activity Relationship
Chemical Substances	Macromolecular Substances ; S-Adenosylmethionine (7LP2MPO46S) ; DNA (9007-49-2) ; DNA (Cytosine-5-)-Methyltransferases (EC 2.1.1.37)
Language	English
Publishing date	2016-10-20
Publishing country	England
Document type	Journal Article
ZDB-ID	2188635-0
ISSN	1742-2051 ; 1742-206X
ISSN (online)	1742-2051
ISSN	1742-206X
DOI	10.1039/c6mb00306k
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Article ; Online: Ponatinib is a pan-BCR-ABL kinase inhibitor

Karunakar Tanneeru / Lalitha Guruprasad

PLoS ONE, Vol 8, Iss 11, p e

MD simulations and SIE study.

2013 Volume 78556

Abstract	BCR-ABL kinase domain inhibition can be used to treat chronic myeloid leukemia. The inhibitors such as imatinib, dasatinib and nilotinib are effective drugs but are resistant to some BCR-ABL mutations. The pan-BCR-ABL kinase inhibitor ponatinib exhibits potent activity against native, T315I, and all other clinically relevant mutants, and showed better inhibition than the previously known inhibitors. We have studied the molecular dynamics simulations and calculated solvated interaction energies of native and fourteen mutant BCR-ABL kinases (M244V, G250E, Q252H, Y253F, Y253H, E255K, E255V, T315A, T315I, F317L, F317V, M351T, F359V and H396P) complexed with ponatinib. These studies revealed that the interactions between ponatinib and individual residues in BCR-ABL kinase are also affected due to the remote residue mutations. We report that some residues, Met244, Lys245, Gln252, Gly254, Leu370 and Leu298 do not undergo any conformational changes, while the fluctuations in residues from P-loop, β3-, β5- strands and αC- helix are mainly responsible for ponatinib binding to native and all mutant BCR-ABL kinases. Our work provides the molecular mechanisms of native and mutant BCR-ABL kinases inhibition by ponatinib at atomic level that has not been studied before.
Keywords	Medicine ; R ; Science ; Q
Subject code	612
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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Article ; Online: In silico 3D structure modeling and inhibitor binding studies of human male germ cell-associated kinase.

Tanneeru, Karunakar / Balla, Ashok Raja / Guruprasad, Lalitha

Journal of biomolecular structure & dynamics

2015 Volume 33, Issue 8, Page(s) 1710–1719

Abstract: Human male germ cell-associated kinase (hMAK) is an androgen-inducible gene in prostate epithelial cells, and it acts as a coactivator of androgen receptor signaling in prostate cancer. The 3D structure of the hMAK kinase was modeled based on the crystal ...

Abstract	Human male germ cell-associated kinase (hMAK) is an androgen-inducible gene in prostate epithelial cells, and it acts as a coactivator of androgen receptor signaling in prostate cancer. The 3D structure of the hMAK kinase was modeled based on the crystal structure of CDK2 kinase using comparative modeling methods, and the ATP-binding site was characterized. We have collected five inhibitors of hMAK from the literature and docked into the ATP-binding site of the kinase domain. Solvated interaction energies (SIE) of inhibitor binding are calculated from the molecular dynamics simulations trajectories of protein-inhibitor complexes. The contribution from each active site residue in hMAK toward inhibitor binding revealed the nature and extent of interactions between inhibitors and individual residues. The main chain atoms of Met79 invariably form hydrogen bonds with all five inhibitors. The amino acids Leu7, Val15, and Leu129 stabilize the inhibitors via CH-pi interactions. The Asp140 in the active site and Glu77 in hinge region show characteristic hydrogen bonding interactions with inhibitors. From SIE, the residue-wise interactions revealed the nature of non-bonding contacts and modifications required to increase the inhibitor activity. Our work provides 3D model structure of hMAK and molecular basis for the mechanisms of hMAK inhibition at atomic level that aid in designing new potent inhibitors.
MeSH term(s)	Binding Sites ; Catalytic Domain ; Humans ; Male ; Models, Molecular ; Molecular Conformation ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protein Binding ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/metabolism ; Protein Kinases/chemistry ; Protein Kinases/metabolism
Chemical Substances	Protein Kinase Inhibitors ; Protein Kinases (EC 2.7.-) ; male germ cell-associated kinase, human (EC 2.7.1.-)
Language	English
Publishing date	2015
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2014.968622
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Zs.A 2093: Show issues

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Article ; Online: Prediction of Certain Well-Characterized Domains of Known Functions within the PE and PPE Proteins of Mycobacteria.

Sultana, Rafiya / Tanneeru, Karunakar / Kumar, Ashwin B R / Guruprasad, Lalitha

PloS one

2016 Volume 11, Issue 2, Page(s) e0146786

Abstract: The PE and PPE protein family are unique to mycobacteria. Though the complete genome sequences for over 500 M. tuberculosis strains and mycobacterial species are available, few PE and PPE proteins have been structurally and functionally characterized. We ...

Abstract	The PE and PPE protein family are unique to mycobacteria. Though the complete genome sequences for over 500 M. tuberculosis strains and mycobacterial species are available, few PE and PPE proteins have been structurally and functionally characterized. We have therefore used bioinformatics tools to characterize the structure and function of these proteins. We selected representative members of the PE and PPE protein family by phylogeny analysis and using structure-based sequence annotation identified ten well-characterized protein domains of known function. Some of these domains were observed to be common to all mycobacterial species and some were species specific.
MeSH term(s)	Amino Acid Motifs ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Computational Biology ; Genome, Bacterial ; Models, Molecular ; Molecular Sequence Data ; Multigene Family ; Mycobacterium/classification ; Mycobacterium/genetics ; Mycobacterium tuberculosis/classification ; Mycobacterium tuberculosis/genetics ; Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment ; Sequence Homology, Amino Acid ; Species Specificity ; Virulence Factors/chemistry ; Virulence Factors/genetics
Chemical Substances	Bacterial Proteins ; Virulence Factors
Language	English
Publishing date	2016-02-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0146786
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Article ; Online: Ligand-based 3-D pharmacophore generation and molecular docking of mTOR kinase inhibitors.

Tanneeru, Karunakar / Guruprasad, Lalitha

Journal of molecular modeling

2011 Volume 18, Issue 4, Page(s) 1611–1624

Abstract: The 3-D structure of the human mTOR kinase domain was modeled based on the crystal structure of PI3Kγ using comparative modeling methods, and the ATP-binding site of mTOR was characterized. The mTOR kinase 3-D model structure is similar to the structure ... ...

Abstract	The 3-D structure of the human mTOR kinase domain was modeled based on the crystal structure of PI3Kγ using comparative modeling methods, and the ATP-binding site of mTOR was characterized. The mTOR kinase 3-D model structure is similar to the structure of the PI3Kγ kinase domain, and exhibits great similarity to PI3Kγ at the active site of the kinase. Pharmacophore generation, the docking of mTOR inhibitors, and molecular dynamics (MD) simulations of mTOR-inhibitor docked complexes were carried out in this work. The best pharmacophore model generated from 27 ATP-competitive mTOR inhibitors comprised two hydrogen-bond acceptors, one aromatic ring, and one hydrophobic feature. These 27 inhibitors were docked into the ATP-binding site comprising the DFG motif, and the interactions in each protein-inhibitor complex were characterized. Mapping the pharmacophore model onto the docked inhibitors explained the specificity of the features of the pharmacophore and how they were arranged inside the active site of mTOR kinase. MD studies revealed important structural features, such as the large hydrophobic pocket "HP" and hydrophilic pocket "A1," and the solvent-exposed hydrophilic pocket "A2" at the active site of mTOR. Our results provide structural models of mTOR-inhibitor complexes and clues that should aid in the design of better mTOR kinase inhibitors.
MeSH term(s)	Catalytic Domain ; Drug Design ; Humans ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Dynamics Simulation ; Phosphatidylinositol 3-Kinases/chemistry ; Protein Binding ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Kinase Inhibitors/chemistry ; Protein Structure, Quaternary ; Quantitative Structure-Activity Relationship ; TOR Serine-Threonine Kinases/antagonists & inhibitors ; TOR Serine-Threonine Kinases/chemistry ; TOR Serine-Threonine Kinases/metabolism
Chemical Substances	Protein Kinase Inhibitors ; Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; MTOR protein, human (EC 2.7.1.1) ; TOR Serine-Threonine Kinases (EC 2.7.1.1)
Language	English
Publishing date	2011-07-30
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1284729-X
ISSN	0948-5023 ; 1610-2940
ISSN (online)	0948-5023
ISSN	1610-2940
DOI	10.1007/s00894-011-1184-3
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Article ; Online: Prediction of Certain Well-Characterized Domains of Known Functions within the PE and PPE Proteins of Mycobacteria.

Rafiya Sultana / Karunakar Tanneeru / Ashwin B R Kumar / Lalitha Guruprasad

PLoS ONE, Vol 11, Iss 2, p e

2016 Volume 0146786

Abstract	The PE and PPE protein family are unique to mycobacteria. Though the complete genome sequences for over 500 M. tuberculosis strains and mycobacterial species are available, few PE and PPE proteins have been structurally and functionally characterized. We have therefore used bioinformatics tools to characterize the structure and function of these proteins. We selected representative members of the PE and PPE protein family by phylogeny analysis and using structure-based sequence annotation identified ten well-characterized protein domains of known function. Some of these domains were observed to be common to all mycobacterial species and some were species specific.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2016-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Molecular property diagnostic suite for diabetes mellitus (MPDS

Gaur, Anamika Singh / Nagamani, Selvaraman / Tanneeru, Karunakar / Druzhilovskiy, Dmitry / Rudik, Anastassia / Poroikov, Vladimir / Narahari Sastry, G

Journal of biomedical informatics

2018 Volume 85, Page(s) 114–125

Abstract: Molecular Property Diagnostic Suite - Diabetes Mellitus ( ... ...

Abstract	Molecular Property Diagnostic Suite - Diabetes Mellitus (MPDS
MeSH term(s)	Computational Biology ; Diabetes Mellitus/diagnosis ; Diabetes Mellitus/drug therapy ; Diabetes Mellitus/genetics ; Drug Discovery/statistics & numerical data ; Drug Evaluation, Preclinical ; Drug Repositioning/statistics & numerical data ; Humans ; Hypoglycemic Agents/chemistry ; Hypoglycemic Agents/pharmacology ; Internet ; Molecular Diagnostic Techniques/statistics & numerical data ; Molecular Docking Simulation ; User-Computer Interface
Chemical Substances	Hypoglycemic Agents
Language	English
Publishing date	2018-08-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2057141-0
ISSN	1532-0480 ; 1532-0464
ISSN (online)	1532-0480
ISSN	1532-0464
DOI	10.1016/j.jbi.2018.08.003
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