S. Kannan

发表

Simulations of mutant p53 DNA binding domains reveal a novel druggable pocket

Mohan R. Pradhan, C. Kwoh, D. Lane, 2019, Nucleic acids research.

Molecular Dynamics and Advanced Sampling Simulations of Nucleic Acids

Martin Zacharias, Srinivasaraghavan Kannan, M. Zacharias, 2012 .

Wetting of nonconserved residue‐backbones: A feature indicative of aggregation associated regions of proteins

Mohan R. Pradhan, D. Lane, C. Verma, 2016, Proteins.

Long range recognition and selection in IDPs: the interactions of the C-terminus of p53

Srinivasaraghavan Kannan, David P. Lane, Chandra S. Verma, 2016, Scientific Reports.

AKT signaling in ERBB2-amplified breast cancer.

Maurizio Scaltriti, Chandra Verma, Valentina Rossi, 2016, Pharmacology & therapeutics.

Folding of Trp-cage Mini Protein Using Temperature and Biasing Potential Replica—Exchange Molecular Dynamics Simulations

M. Zacharias, S. Kannan, 2009, International journal of molecular sciences.

Simulated annealing coupled replica exchange molecular dynamics--an efficient conformational sampling method.

Martin Zacharias, Srinivasaraghavan Kannan, M. Zacharias, 2009, Journal of structural biology.

Folding simulations of Trp‐cage mini protein in explicit solvent using biasing potential replica‐exchange molecular dynamics simulations

Martin Zacharias, Srinivasaraghavan Kannan, M. Zacharias, 2009, Proteins.

Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing‐potential

Martin Zacharias, Srinivasaraghavan Kannan, M. Zacharias, 2006, Proteins.

A Novel Class of Schistosoma mansoni Histone Deacetylase 8 (HDAC8) Inhibitors Identified by Structure-Based Virtual Screening and In Vitro Testing

W. Sippl, S. Kannan, C. Romier, 2018, Molecules.

Computer- and structure-based lead design for epigenetic targets.

W. Sippl, S. Kannan, R. Heinke, 2011, Bioorganic & medicinal chemistry.

Correction to Probing the Binding Mechanism of Mnk Inhibitors by Docking and Molecular Dynamics Simulations.

Shi Hua Ang, C. Verma, S. Kannan, 2017, Biochemistry.

Optimization of Selective Mitogen-Activated Protein Kinase Interacting Kinases 1 and 2 Inhibitors for the Treatment of Blast Crisis Leukemia.

Shi Hua Ang, Eldwin Sum Wai Tan, C. Chuah, 2018, Journal of medicinal chemistry.

Preclinical Characteristics of the Irreversible Pan-HER Kinase Inhibitor Neratinib Compared with Lapatinib: Implications for the Treatment of HER2-Positive and HER2-Mutated Breast Cancer

J. Crown, C. Verma, S. Kannan, 2019, Cancers.

Simulation of DNA double-strand dissociation and formation during replica-exchange molecular dynamics simulations.

M. Zacharias, S. Kannan, 2009, Physical chemistry chemical physics : PCCP.

Macrocyclization of an all-d linear α-helical peptide imparts cellular permeability† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c9sc06383h

D. Lane, L. Rénia, Y. S. Tan, 2020, Chemical science.

Macrocyclization of an all-D linear peptide improves target affinity and imparts cellular activity: A novel stapled α-helical peptide modality

D. Lane, Y. S. Tan, C. Verma, 2019, bioRxiv.

Conformational landscape of the epidermal growth factor receptor kinase reveals a mutant specific allosteric pocket† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc01262h

C. Verma, U. Surana, S. Kannan, 2018, Chemical science.

Role of N‐glycosylation in EGFR ectodomain ligand binding

C. Verma, S. Kannan, Maryam Azimzadeh Irani, 2017, Proteins.

Binding of pyrazole-based inhibitors to Mycobacterium tuberculosis pantothenate synthetase: docking and MM-GB(PB)SA analysis.

W. Sippl, S. Kannan, K. Wichapong, 2014, Molecular bioSystems.

Probing the dynamics of disorder.

S. Kannan, S. Fox, 2017, Progress in biophysics and molecular biology.

De-risking Drug Discovery of Intracellular Targeting Peptides: Screening Strategies to Eliminate False-Positive Hits.

Nils A. Berglund, D. Lane, C. Verma, 2020, ACS medicinal chemistry letters.

A common MET polymorphism harnesses HER2 signaling to drive aggressive squamous cell carcinoma

T. Tan, B. Goh, N. Syn, 2020, Nature Communications.

High p16 expression and heterozygous RB1 loss are biomarkers for CDK4/6 inhibitor resistance in ER+ breast cancer

C. Caldas, A. Gonzalez-Perez, N. López-Bigas, 2021, Nature Communications.

Computational Design of Macrocyclic Binders of S100B(ββ): Novel Peptide Theranostics

C. Verma, S. Kannan, T. Nguyen, 2021, Molecules.

Incorporation of Putative Helix-Breaking Amino Acids in the Design of Novel Stapled Peptides: Exploring Biophysical and Cellular Permeability Properties

Mohan R. Pradhan, D. Lane, J. Hochman, 2019, Molecules.

Activation of p53: How phosphorylated Ser15 triggers sequential phosphorylation of p53 at Thr18 by CK1δ

J. Warwicker, C. Verma, S. Kannan, 2022, Proteins.

Probing the binding mechanism of Mnk inhibitors by docking and molecular dynamics simulations.

Shi Hua Ang, C. Verma, S. Kannan, 2015, Biochemistry.

Carbamate Prodrug Concept for Hydroxamate HDAC Inhibitors

L. Altucci, W. Sippl, S. Kannan, 2011, ChemMedChem.

In Silico Approaches for Drug Discovery and Development

Vasanthanathan Poongavanam, S. Kannan, T. Joseph, 2017 .

Mussel adhesion is dictated by time-regulated secretion and molecular conformation of mussel adhesive proteins

C. Verma, S. Kannan, N. J. Patil, 2015, Nature Communications.

Small Molecule Inhibitors of Histone Acetyltransferases as Epigenetic Tools and Drug Candidates

W. Sippl, S. Kannan, M. Jung, 2012, Archiv der Pharmazie.

Macrocyclic α helical peptide therapeutic modality: A perspective of learnings and challenges.

A. Peier, D. Lane, J. Hochman, 2018, Bioorganic & medicinal chemistry.

Molecular modeling and interaction between Arabidopsis sulfite oxidase and the GW motif of Turnip crinkle virus coat protein.

C. Verma, S. Kannan, K. Swaminathan, 2020, Virology.

A chemical biology approach reveals a dependency of glioblastoma on biotin distribution

Jhin Jieh Lim, D. Ong, T. Benoukraf, 2021, Science advances.

FOXA1 Mutations Reveal Distinct Chromatin Profiles and Influence Therapeutic Response in Breast Cancer.

J. Reis-Filho, J. Baselga, R. Koche, 2020, Cancer cell.

PDK1-SGK1 Signaling Sustains AKT-Independent mTORC1 Activation and Confers Resistance to PI3Kα Inhibition

S. Chandarlapaty, J. Baselga, E. Brogi, 2016, Cancer cell.

Targeting codon 158 p53-mutant cancers via the induction of p53 acetylation

T. Tan, B. Goh, C. Verma, 2020, Nature Communications.

Rhodanine carboxylic acids as novel inhibitors of histone acetyltransferases

W. Sippl, S. Kannan, M. Jung, 2012 .

Update on the Development of MNK Inhibitors as Therapeutic Agents.

C. Verma, S. Kannan, K. Nacro, 2021, Journal of medicinal chemistry.

TRK xDFG mutations trigger a sensitivity switch from type I to II kinase inhibitors.

Amanda R. Kulick, M. Berger, A. Drilon, 2020, Cancer discovery.

De-risking drug discovery of intracellular targeting peptides: screening strategies to eliminate false-positive hits

Nils A. Berglund, D. Lane, C. Verma, 2019, bioRxiv.

Hydration effects on the efficacy of the Epidermal growth factor receptor kinase inhibitor afatinib

Chandra Verma, Srinivasaraghavan Kannan, Daniel Shao-Weng Tan, 2017, Scientific Reports.

A New Generation of Arachidonic Acid Analogues as Potential Neurological Agent Targeting Cytosolic Phospholipase A2

C. Verma, S. Kannan, C. Low, 2017, Scientific Reports.

The Dual Interactions of p53 with MDM2 and p300: Implications for the Design of MDM2 Inhibitors

D. Lane, C. Verma, S. Kannan, 2019, International journal of molecular sciences.

Structural Basis for the Inhibition of Histone Deacetylase 8 (HDAC8), a Key Epigenetic Player in the Blood Fluke Schistosoma mansoni

W. Sippl, S. Kannan, C. Romier, 2013, PLoS pathogens.

Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations

M. Zacharias, S. Kannan, 2011, Nucleic acids research.

Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations.

M. Zacharias, S. Kannan, 2007, Biophysical journal.

Effects of Single Nucleotide Polymorphisms on the Binding of Afatinib to EGFR: A Potential Patient Stratification Factor Revealed by Modeling Studies

Srinivasaraghavan Kannan, Daniel Shao-Weng Tan, Chandra Shekhar Verma, 2018, J. Chem. Inf. Model..

University of Dundee PDK 1-SGK 1 signaling sustains AKT-independent mTORC 1 activation and confers resistance to PI 3 K inhibition

S. Chandarlapaty, J. Baselga, E. Brogi, 2016 .

Characterization of Hydration Properties in Structural Ensembles of Biomolecules

Chee-Keong Kwoh, Chandra S Verma, Mohan Pradhan, 2019, J. Chem. Inf. Model..

mAb806 binding to epidermal growth factor receptor: a computational study

C. Verma, S. Kannan, G. Fuentes, 2015, Proteins.

Application of biasing‐potential replica‐exchange simulations for loop modeling and refinement of proteins in explicit solvent

Srinivasaraghavan Kannan, Martin Zacharias, M. Zacharias, 2010, Proteins.

Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping

Martin Zacharias, Stephan Frickenhaus, Srinivasaraghavan Kannan, 2009, J. Comput. Chem..

Discovery of cell active macrocyclic peptides with on-target inhibition of KRAS signaling

A. Peier, P. Orth, C. Verma, 2021, bioRxiv.

Discovery of Inhibitors of Schistosoma mansoni HDAC8 by Combining Homology Modeling, Virtual Screening, and in Vitro Validation

Christophe Romier, Wolfgang Sippl, Jelena Melesina, 2014, J. Chem. Inf. Model..

An inter-subunit protein-peptide interface that stabilizes the specific activity and oligomerization of the AAA+ chaperone Reptin.

C. Verma, S. Kannan, T. Hupp, 2019, Journal of proteomics.

Dephosphorylation of YB-1 is Required for Nuclear Localisation During G2 Phase of the Cell Cycle

H. Cunliffe, P. Bhatia, C. Verma, 2020, Cancers.

Small Molecules Targeting the Inactive Form of the Mnk1/2 Kinases

Mohan R. Pradhan, C. Verma, S. Kannan, 2017, ACS omega.

Domain-specific p53 mutants activate EGFR by distinct mechanisms exposing tissue-independent therapeutic vulnerabilities

May Yin Lee, Hui Chin Goh, W. Tam, 2023, Nature Communications.

Src activates retrograde membrane traffic through phosphorylation of GBF1

F. Bard, S. Kannan, Sheena Wee, 2020, bioRxiv.

A high‐throughput microfluidic mechanoporation platform to enable intracellular delivery of cyclic peptides in cell‐based assays

A. Therien, C. Verma, S. Kannan, 2023, Bioengineering & Translational Medicine.

Drug Development for Cancer and Diabetes

S. Kannan, B. Bahadur, Chukwuebuka Egbuna, 2020 .

Exploitation of dihydroorotate dehydrogenase (DHODH) and p53 activation as therapeutic targets: A case study in polypharmacology

Gergana Popova, D. Lane, C. Verma, 2020, The Journal of Biological Chemistry.

A novel determinant of PSMD9 PDZ binding guides the evolution of first generation of super binding peptides.

Mohan R. Pradhan, C. Verma, S. Kannan, 2019, Biochemistry.

Critical Role for Cold Shock Protein YB-1 in Cytokinesis

P. Bhatia, C. Verma, S. Kannan, 2020, bioRxiv.

Binding of the bacteriophage P22 N-peptide to the boxB RNA motif studied by molecular dynamics simulations.

Martin Zacharias, Srinivasaraghavan Kannan, R. Bahadur, 2009, Biophysical journal.

B-DNA under stress: over- and untwisting of DNA during molecular dynamics simulations.

Kai J. Kohlhoff, M. Zacharias, S. Kannan, 2006, Biophysical journal.

Targeting codon 158 p53-mutant cancers via the induction of p53 acetylation

T. Tan, B. Goh, D. Lane, 2020, Nature Communications.

Disrupting the Dok3–Card9 Interaction with Synthetic Peptides Enhances Antifungal Effector Functions of Human Neutrophils

C. Verma, S. Kannan, K. Lam, 2023, Pharmaceutics.

Stitched peptides as potential cell permeable inhibitors of oncogenic DAXX protein

A. Phan, C. Verma, S. Kannan, 2022, bioRxiv.

CAMK2D serves as a molecular scaffold for RNF8-MAD2 complex to induce mitotic checkpoint in glioma

D. Ong, C. Verma, S. Kannan, 2023, Cell Death & Differentiation.

Design-Rules for Stapled Alpha-Helical Peptides with On-Target In Vivo Activity: Application to Mdm2/X dual antagonists

J. Hochman, C. Verma, S. Kannan, 2023, bioRxiv.

The polybasic insert, the RBD of the SARS-CoV-2 spike protein, and the feline coronavirus – evolved or yet to evolve

C. Verma, S. Kannan, P. Venkatraman, 2021, Biochemistry and Biophysics Reports.

TRK xDFG mutations trigger a sensitivity switch from type I to II kinase inhibitors.

B. Taylor, M. Berger, A. Drilon, 2020, Cancer discovery.

A common MET polymorphism harnesses HER2 signaling to drive aggressive squamous cell carcinoma

T. Tan, B. Goh, N. Syn, 2020, Nature Communications.

JNK mediates cell death by promoting the ubiquitination of the apurinic/apyrimidinic endonuclease APE1.

S. Kannan, K. Sabapathy, Bahareh Tabanifar, 2023, Cell reports.

Inhibiting S100B(ββ) for Activating Wild-Type p53: Design of Stapled Peptides

Y. S. Tan, C. Verma, S. Kannan, 2019, ACS Omega.

Exploring Gatekeeper Mutations in EGFR through Computer Simulations

Chandra S Verma, Srinivasaraghavan Kannan, Stephen J Fox, 2019, J. Chem. Inf. Model..

Macrocyclic α helical peptide therapeutic modality: A perspective of learnings and challenges.

A. Peier, D. Lane, J. Hochman, 2018, Bioorganic & medicinal chemistry.

DOK3 promotes atopic dermatitis by enabling the phosphatase PP4C to inhibit the T cell signaling mediator CARD11

A. Andiappan, S. Kannan, J. Loh, 2023, Science Signaling.

Role of Tryptophan Side Chain Dynamics on the Trp-Cage Mini-Protein Folding Studied by Molecular Dynamics Simulations

Martin Zacharias, Srinivasaraghavan Kannan, M. Zacharias, 2014, PloS one.

Application of biasing‐potential replica‐exchange simulations for loop modeling and refinement of proteins in explicit solvent

M. Zacharias, S. Kannan, 2010, Proteins.

Design-rules for stapled peptides with in vivo activity and their application to Mdm2/X antagonists

S. Kannan, H. Kaan, D. Spiegelberg, 2024, Nature communications.

Supporting Information Macrocyclization of an all-D linear α-helical peptide imparts cellular permeability

Yuri, D. Lane, L. Rénia, 2020 .

Folding simulations of Trp‐cage mini protein in explicit solvent using biasing potential replica‐exchange molecular dynamics simulations

M. Zacharias, S. Kannan, 2009, Proteins.

Rarγ -Foxa1 signaling promotes luminal identity in prostate progenitors and is disrupted in prostate cancer

S. Kannan, A. Romanel, Davide Dalfovo, 2024, bioRxiv.

Elucidating the Effect of Polyethylene Terephthalate Chain Structure on Its Enzymatic Degradation Behavior

S. Kannan, Sierin Lim, Y. Lam, 2023, ACS Sustainable Chemistry & Engineering.

Modulation of PETase active site flexibility and activity on morphologically distinct polyethylene terephthalate substrates by surface charge engineering

Rupali Reddy Pasula, S. Kannan, B. Sana, 2024, Biochemical Engineering Journal.

Modulation of Ideonella sakaiensis PETase active site flexibility and activity on morphologically distinct substrates by surface charge engineering

Rupali Reddy Pasula, S. Kannan, B. Sana, 2024, bioRxiv.