Structure-guided approach identifies a novel class of HIV-1 ribonuclease H inhibitors: binding mode insights through magnesium complexation and site-directed mutagenesis studies

Vasanthanathan Poongavanam, Angela Corona, Casper Steinmann, Luigi Scipione, Nicole Grandi, Fabiana Pandolfi, Roberto Di Santo, Roberta Costi, Francesca Esposito, Enzo Tramontano and Jacob Kongsted

Med. Chem. Commun., 2018, 9, 562
DOI: 10.1039/C7MD00600D

Detection of HIV-1 ribonuclease H activity in single-cell by using RNA mimics green fluorescent protein based biosensor

Kai Zhang, Qianlu Yang, Wanting Huang, Ke Wang, Xue Zhu and Minhao Xie

Sensors and Actuators B: Chemical, 2019, 281, 439
DOI: 10.1016/j.snb.2018.09.001

In-silico prediction of novel drug-target complex of nsp3 of CHIKV through molecular dynamic simulation

Durgesh Kumar, Mahendra Kumar Meena, Kamlesh Kumari, Rajan Patel, Abhilash Jayaraj and Prashant Singh

Heliyon, 2020, 6, e04720
DOI: 10.1016/j.heliyon.2020.e04720

Studies on Cycloheptathiophene‐3‐carboxamide Derivatives as Allosteric HIV‐1 Ribonuclease H Inhibitors

Angela Corona, Jenny Desantis, Serena Massari, Simona Distinto, Takashi Masaoka, Stefano Sabatini, Francesca Esposito, Giuseppe Manfroni, Elias Maccioni, Violetta Cecchetti, Christophe Pannecouque, Stuart F. J. Le Grice, Enzo Tramontano and Oriana Tabarrini

ChemMedChem, 2016, 11, 1709
DOI: 10.1002/cmdc.201600015

Computational Analysis of Sterol Ligand Specificity of the Niemann Pick C2 Protein

Vasanthanathan Poongavanam, Jacob Kongsted and Daniel Wüstner

Biochemistry, 2016, 55, 5165
DOI: 10.1021/acs.biochem.6b00217

Computational Modeling Explains the Multi Sterol Ligand Specificity of the N-Terminal Domain of Niemann–Pick C1-Like 1 Protein

Vasanthanathan Poongavanam, Jacob Kongsted and Daniel Wüstner

ACS Omega, 2019, 4, 20894
DOI: 10.1021/acsomega.9b01668

Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase

Baofeng Zhang, Michael P. D’Erasmo, Ryan P. Murelli and Emilio Gallicchio

ACS Omega, 2016, 1, 435
DOI: 10.1021/acsomega.6b00123

Molecular dynamics-driven drug discovery: leaping forward with confidence

Aravindhan Ganesan, Michelle L. Coote and Khaled Barakat

Drug Discovery Today, 2017, 22, 249
DOI: 10.1016/j.drudis.2016.11.001

Unveiling Novel Arginase Inhibitors for Cutaneous Leishmaniasis Using Drug Repurposing and Virtual Screening Approaches

Eduarda Moreira Barreto, Gabriel Rodrigues Coutinho Pereira, Isadora de Salles Arêas, Júlia Mendes Fortes, Alessandra da Silva Domingos, Lucio Mendes Cabral, Carlos Rangel Rodrigues, Alessandra Mendonça Teles de Souza and Barbara de Azevedo Abrahim‐Vieira

J of Cellular Biochemistry, 2025, 126
DOI: 10.1002/jcb.70060

Exploration of charge states of balanol analogues acting as ATP-competitive inhibitors in kinases

Ari Hardianto, Muhammad Yusuf, Fei Liu and Shoba Ranganathan

BMC Bioinformatics, 2017, 18
DOI: 10.1186/s12859-017-1955-7

Synthesis of novel tetrazole acetamide against HepG2 and MCF-7 cell lines- docking, MD simulation, DFT and In vitro studies

Sharmil Suganya R, Venugopal T and Sugan. S

Next Research, 2026, 10, 101814
DOI: 10.1016/j.nexres.2026.101814

Fluorescence Assay for Ribonuclease H Based on Nonlabeled Substrate and DNAzyme Assisted Cascade Amplification

Lanbo Wang, Hongyan Zhou, Bin Liu, Chuan Zhao, Jialong Fan, Wei Wang and Chunyi Tong

Anal. Chem., 2017, 89, 11014
DOI: 10.1021/acs.analchem.7b02899

Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?

Vasanthanathan Poongavanam, Emma Danelius, Stefan Peintner, Lilian Alcaraz, Giulia Caron, Maxwell D. Cummings, Stanislaw Wlodek, Mate Erdelyi, Paul C. D. Hawkins, Giuseppe Ermondi and Jan Kihlberg

ACS Omega, 2018, 3, 11742
DOI: 10.1021/acsomega.8b01379

Binding affinity models for Falcipain inhibition based on the Linear Interaction Energy method

Vasanthanathan Poongavanam and Jacob Kongsted

Journal of Molecular Graphics and Modelling, 2016, 70, 236
DOI: 10.1016/j.jmgm.2016.06.008

In Silico Analyses of a Promising Drug Candidate for the Treatment of Amyotrophic Lateral Sclerosis Targeting Superoxide Dismutase I Protein

Gabriel Rodrigues Coutinho Pereira, Bárbara de Azevedo Abrahim-Vieira and Joelma Freire de Mesquita

Pharmaceutics, 2023, 15, 1095
DOI: 10.3390/pharmaceutics15041095

Integrative approaches in HIV‐1 non‐nucleoside reverse transcriptase inhibitor design

Vasanthanathan Poongavanam, Vigneshwaran Namasivayam, Murugesan Vanangamudi, Hadi Al Shamaileh, Rakesh N Veedu, Jan Kihlberg and N Arul Murugan

WIREs Comput Mol Sci, 2018, 8
DOI: 10.1002/wcms.1328

Protein–protein interactions between SWCNT/chitosan/EGF and EGF receptor: a model of drug delivery system

Chompoonut Rungnim, Thanyada Rungrotmongkol, Nawee Kungwan and Supot Hannongbua

Journal of Biomolecular Structure and Dynamics, 2016, 34, 1919
DOI: 10.1080/07391102.2015.1095114

Diverse dynamics features of novel protein kinase C (PKC) isozymes determine the selectivity of a fluorinated balanol analogue for PKCε

Ari Hardianto, Varun Khanna, Fei Liu and Shoba Ranganathan

BMC Bioinformatics, 2019, 19
DOI: 10.1186/s12859-018-2373-1

Molecular Dynamics Pinpoint the Global Fluorine Effect in Balanoid Binding to PKCε and PKA

Ari Hardianto, Fei Liu and Shoba Ranganathan

J. Chem. Inf. Model., 2018, 58, 511
DOI: 10.1021/acs.jcim.7b00504