05/26/25

http://scholar.google.com/citations?user=vk54XEgAAAAJ&hl=en&oi=ao

http://www.researcherid.com/rid/J-2005-2012

http://www.linkedin.com/in/chunwu5

Peer Reviewed Publications since Joining Rowan Univ. (Undergrad Students Underlined)

 Wu, C.; Paradis, N. J.; Jain, K. Substitution-Mutation Rate Ratio (c/µ) As Molecular Adaptation Test Beyond Ka/Ks: A SARS-COV-2 Case Study. Journal of Molecular Evolution, 2025. DOI: 10.1007/s00239-025-10248-6

Marques, T. J. S.; Salvador, D.; Oliveira, H.; Serra, V. V.; Paradis, N.; Wu, C.; Silva, V. L. M.; Ramos, C. I. V. New acridone derivatives to target telomerase and oncogenes - an anticancer approach. RSC Med Chem 2025. DOI: 10.1039/d4md00959b.

Muhammad - Arba, A. A., Ruslin Ruslin, Chun Wu, Wa Ode Yentri Putia Ningtiyas Darmin. Docking-Based Virtual Screening to Identify the Cysteine Protease Falcipain-2 Inhibitors of Plasmodium Falciparum. MOLEKUL 2024. 19, 1, 406-416 https://doi.org/10.20884/1.jm.2024.19.3.7376

Paradis, N.; Wu, C. Enhanced Detection and Molecular Modeling of Adaptive Mutations in SARS-CoV-2 Coding and Non-Coding Regions Using the c/µ Test. Virus Evolution, 2024.10 (1), veae089 https://doi.org/10.1093/ve/veae089

A.I. Uba, N.J. Paradis, C. Wu, G. Zengin, Computational analysis of natural compounds as potential phosphodiesterase type 5A inhibitors, Computational Biology and Chemistry, (2024) 113, 108239 https://doi.org/10.1016/j.compbiolchem.2024.108239

Justin Carbone, Nicholas J. Paradis, Dylan Brunt and Chun Wu. Binding Mechanism of Active Form of Molnupiravir to RdRp of SARS-CoV-2 and Designing Potential Analogues: Insights from Molecular Dynamic Simulations. ACS Omega, 2024, 9(40), 41583-41598 DOI: 10.1021/acsomega.4c05469

Moura, N. M. M.; Guedes, S.; Salvador, D.; Oliveira, H.; Alves, M. Q.; Paradis, N.; Wu, C.; Neves, M. G. P. M. S.; Ramos, C. I. V., Oncogenic and telomeric G-quadruplexes: Targets for porphyrin-triphenylphosphonium conjugates. International Journal of Biological Macromolecules 2024, 277, 134126. https://doi.org/10.1016/j.ijbiomac.2024.134126

Nicholas J. Paradis, Austin Clark, Hunter Gogoj, Timothy D. Vaden,* and Chun Wu* Substituting K+ for Imidazolium-based Ionic Liquids to Stabilize a c-MYC DNA G-Quadruplex: A Spectroscopy-Molecular Dynamics Simulation Dual Approach, Journal of Molecular Liquids, 2024 124407 https://doi.org/10.1016/j.molliq.2024.124407

Hetanshi Choksi, Justin Carbone, Nicholas Paradis, Lucas Bennett, Candice Bui-Linh, Chun Wu, Novel Inhibitors to MmpL3 Transporter of Mycobacterium tuberculosis by Structure-based High Throughput Virtual Screening and Molecular Dynamics Simulations, ACS Omega, 2024 9, 13782−13796 https://doi.org/10.1021/acsomega.3c08401

Abdullahi Ibrahim Uba, Mariya Hryb, Mursalin Singh, Candice Bui-Linh, Annie Tran, Jiancarlo Atienza, Sarah Misbah, Xiaoyang Mou* and Chun Wu*, Novel potential inhibitors of histone deacetylase 6 identified using structure-based virtual screening, molecular dynamics simulation, enzyme inhibition assay, and cell viability assay, Life Sciences, 2024, 338,122395 https://doi.org/10.1016/j.lfs.2023.122395

Muhammad Arba, Sri Wahyuli, Arfan, Setyanto Tri Wahyudi, and Chun Wu*, Computational Study of Binding of Oseltamivir to Neuraminidase Mutants of Influenza A Virus, Journal of Applied Pharmaceutical Science, 2024 , 14(02):239-254 https://doi.org/10.7324/JAPS.2024.147448

 Abdullahi Ibrahim Uba, Nicholas Joseph Paradis, Chun Wu, Gokhan Zengin, Phenolic compounds as adenosine deaminase inhibitors: binding propensity and interaction analyses using docking and molecular dynamics simulation coupled with MM/GBSA calculations, Amino Acids, 2023, 55, 1729–1743 https://doi.org/10.1007/s00726-023-03310-4

Comfort A. Boateng ,Ashley N. Nilson ,Rebekah Placide ,Mimi L. Pham ,Franziska M. Jakobs ,Noelia Boldizsar ,Scot McIntosh ,Leia S. Stallings ,Ivana V. Korankyi ,Shreya Kelshikar ,Nisha Shah ,Diandra Panasis ,Abigail Muccilli ,Maria Ladik ,Brianna Maslonka ,Connor McBride ,Moises Ximello Sanchez ,Ebrar Akca ,Mohammad Alkhatib ,Julianna Saez ,Catherine Nguyen ,Emily Kurtyan ,Jacquelyn DePierro ,Raymond Crowthers, Dylan Brunt, Alessandro Bonifazi ,Amy H. Newman ,Rana Rais ,Barbara S. Slusher ,R. Benjamin Free ,David R. Sibley ,Kent D. Stewart ,Chun Wu ,Scott E. Hemby ,Thomas M. Keck, Pharmacology and Therapeutic Potential of Benzothiazole Analogues for Cocaine Use Disorder, Journal of Medicinal Chemistry, 2023, 66, 17, 12141–12162 https://doi.org/10.1021/acs.jmedchem.3c00734

Dean, Emily; Dominique, AnneMarie; Palillero, Americus; Wu, Chun, To Probe Activation mechanism of agonist DPI-287 to Delta Opioid Receptor and to Identify Novel Agonists using Ensemble-based Virtual Screening with Molecular Dynamics Simulations, ACS Omega, 2023, 8, 36, 32404-32423 https://doi.org/10.1021/acsomega.3c01918

Carbone, Justin; Paradis, Nicholas; Bennett, Lucas;Alesiani, Mark; Hausman, Katherine; Wu, Chun, Inhibition mechanism of anti-TB drug SQ109: Blocking water passing and TMM entry of Mycobacterium tuberculosis MmpL3 transporter, Journal of Chemical Information and Modeling, 2023, 63, 16, 5356–5374 https://doi.org/10.1021/acs.jcim.3c00616

Uba, Abdullahi Ibrahim and Bui-Linh, Candice and Thornton, Julianne and Olivieri, Michael and Wu, Chun, Computational Analysis of Drug Resistance of Taxanes Bound to Human Β-Tubulin Mutant (D26E). Journal of Molecular Graphics and Modelling. 2023, 123, 108503 https://doi.org/10.1016/j.jmgm.2023.108503

Muhammad Arba, Aprilia Surya Ningsih, La Ode Santiaji Bande, Setyanto Tri Wahyudi, Candice Bui-Linh, Chun Wu, and Amir Karton, Computational Insights into the Binding of Pimodivir to the Mutated PB2 Subunit of the Influenza A Virus, Molecular Simulation. 2023, 49:10, 1031-1043,  https://doi.org/10.1080/08927022.2023.2210690

Wu, C*, Paradis N., Lakernick P., Hryb M. To decipher the molecular evolution nature of SARS-CoV-2 by examining the variation of the substitution rates within its genome. Computational Biology and Medicine. 2023, 153, 106522 https://doi.org/10.1016/j.compbiomed.2022.106522

Prior to Joining Rowan University

Amyloid fibril inhibition and dye binding:

 C. Wu, J. Scott & JE Shea (2012) A molecular dynamics study of the binding of fluorescent dye  Congo Red to the Alzheimer Amyloid-β peptide and the role of electrostatic steering  Biophys J 103: 550-557. pdf pdb

 C. Wu, M. Bowers & JE Shea (2011) On the origin of the stronger binding of PIB over Thioflavin T to protofibrils of the Alzheimer Amyloid-β peptide: A molecular dynamics study Biophys J 100(5), 1316-1324 pdf pdb(Fig S18)

 C. Wu, M. Biancalana, K. Makabe, A. Koide, S. Koide, M. Bowers & JE Shea (2009) The Binding of Thioflavin-T to the b-Rich Peptide Self-Assemblies probed by Molecular Dynamics Simulations with an Explicit Solvent Model J Mol Biol 394 (4), 627-633 pdf pdb  Citation: 23+

 C. Wu, ZX. Wang, HX. Lei, Y. Duan, M. Bowers & JE Shea (2008) Multiple binding sites of Alzheimer Ab_16-22 protofibril-oligomer by Thioflavin-T and its neutral analog (BTA-1) observed in molecular dynamics simulations J Mol Biol 384 (3), 718-729 pdf pdb

 C. Wu, ZX. Wang, HX. Lei, W. Zhang & Y. Duan (2007) Dual binding modes of Congo red to amyloid protofibril surface observed in molecular dynamics simulations J Am Chem Soc 129, 1225-1232 pdf pdb Congo red Thioflavin T Citation: 34+

 C. Wu, HX. Lei, ZX. Wang, W. Zhang & Y. Duan (2006) Phenol red interacts with the protofibrils of an amyloidogenic hexapeptide NFGAIL through both hydrophobic and aromatic contacts and acts as a chemical chaperon Biophys J 91(10): 3664-3672 pdf pdb

Amyloid fibril formation:

 Wu C, Shea JE (2013) Structural basis for physiological and pathological activities of Islet Amyloid Polypeptide (IAPP) probed by all-atom replica exchange molecular dynamics simulations.  PLoS Comput Biol 9(8): e1003211 pdf

C. Wu & JE Shea (2011) Coarse-Grained Models for Protein Aggregation Curr Opin Struct Biol 21, 209-220, pdf

Gessel MM*, Wu C*, Li HY*, Bitan G, Shea JE, et al. (2011) Ab(39-42) Modulates Ab Oligomerization but Not Fibril Formation. Biochemistry 51: 108-117 pdf pdb

 Dupuis NF, Wu C, Shea JE, Bowers MT (2011) The Amyloid Formation Mechanism in Human IAPP: Dimers Have beta-Strand Monomer-Monomer Interfaces. J Am Chem Soc 133: 7240-7243. pdf pdb

 NF Dupuis, C. Wu, MT Bowers & JE Shea (2010) Human Islet Amyloid Polypeptide forms ordered b-hairpin monomers: a possible amyloidogenic conformation J Am Chem Soc 131(51): 18283-18292 pdf pdb

 M. Grabenauer, C. Wu, P. Soto, JE Shea & MT Bowers (2010) Oligomers of the prion protein fragment 106-126 are likely assembled from ordered b-hairpins: A combined experimental and computational study J Am Chem Soc  132(2): 532-539 pdf pdb

 C. Wu, MT Bowers & JE Shea (2010) Molecular Structures of Quiescently Grown and Brain-Derived Polymorphic Fibrils of the Alzheimer Amyloid Aβ9-40 Peptide: A Comparison to Agitated Fibrils PLoS Comput  Biol 6(3): e1000693 pdf pdb AMBER force field (Singly Oxidized Met)

 C. Wu*, MM Murray*, SL Bernstein*, MM Condron, G. Bitan, MT Bowers & JE Shea (2009) Experimental and theoretical study of the structure of Amyloid-β C-terminal fragments  J Mol Biol 387(2), 592-501 pdf pdb

HX Lei, C. Wu, ZX Wang & Y. Duan, (2006)  Molecular dynamics simulations and free energy analyses on the dimer formation of an amyloidogenic heptapeptide from human b2-microglobulin: implication to the protofibril structure J Mol Biol 356, 1049-1063 pdf Citation: 25+

C. Wu, HX. Lei & Y. Duan, (2005)  Elongation of Ordered Peptide Aggregate of an Amyloidogenic Hexapeptide (NFGAIL) Observed in Molecular Dynamics Simulations with Explicit Solvent J Am Chem Soc 127 (39): 13530-13537 pdf Citation: 43+

C. Wu, HX. Lei & Y. Duan, (2004)  The role of PHE in the formation of well-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) observed in molecular dynamics simulations with explicit solvent  Biophys J 88(4): 2897-2906 pdf

 C. Wu, HX. Lei & Y. Duan, (2004) Formation of partially-ordered oligomers of amyloidogenic hexapeptide (NFGAIL) in aqueous solution observed in molecular dynamics simulations  Biophys J 87(5):3000-3009  pdf Citation: 31+

Binding of anti-cancer drug to DNA:

Lei HX, Wang XF, Wu C (2012) Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations. J Mol Graph Model 38, 279-289  pdf pdb

Protein folding:

Wang XQ^*, Wu C^*, Vu A, Shea JE, Dahlquist FW (2012) Computational and Experimental Analyses Reveal the Essential Roles of Inter-domain Linkers in the Biological Function of Chemotaxis Histidine Kinase CheA. J Am Chem Soc 134(39), 16107-16110 pdf pdb

C. Wu, & JE Shea  (2010) On the origins of the weak folding cooperativity of a designed ββα ultrafast protein  PLoS Comput  Biol 6(11): e1000998 pdf

 HX Lei, ZX Wang, C. Wu, & Y. Duan, (2009) Dual folding pathways of an alpha/beta protein from all-atom ab initio folding simulations J Chem Phys 131 (16): 165105 pdf

 HX Lei, C. Wu, ZX Wang, YQ Zhou, & Y. Duan, (2008) Ab Initio folding of protein A by all-atom replica exchange molecular dynamics simulations with implicit solvent J Chem Phys 128 (23): 235105 pdf

 HX Lei, C. Wu, ZX Wang, HG Liu, & Y. Duan, (2007) Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations Proc Natl Acad Sci USA 104 (12): 4925-4930 pdf Citation: 102+

 W. Zhang, C. Wu, & Y. Duan, (2005) Convergence of replica exchange molecular dynamics J Chem Phys 123 (15): 154105 pdf Citation: Citation: 49+

 S. Chowdhury, W. Zhang, C. Wu, GM. Xiong & Y. Duan (2003) Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide Biopolymers 68(1): 63-75 pdf Citation: 45+

Force field development:

 JL Jiang, YB Wu, ZX Wang & C. Wu (2010) Assessing the Performance of Popular Quantum Mechanics and Molecular Mechanics Methods and Revealing the Sequence-Dependent Energetic Features Using 100 Tetrapeptide Models J Chem Theory Comput  6 (4): 1199-1209 pdf pdb

ZX Wang, C. Wu, HX Lei, W. Zhang, P. Ceiplak & Y. Duan, (2007) Accurate ab Initio Study on the Hydrogen-Bond Pairs in Protein Secondary Structures J Chem Theory Comput 3 (4): 1527-1537  pdf

 ZX Wang, W. Zhang, C. Wu, HX Lei,  P. Ceiplak &Y. Duan, (2005) Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field (ff05pol) for simulations of proteins and peptides J Comput Chem 27 (6): 781-790 pdf Citation: 54+

 Y. Duan, C. Wu, S. Chowdhury, MC Lee, GM Xiong, W Zhang, R Yang, P Cieplak, R Luo, T Lee, J Caldwell, JM Wang & PA Kollman, (2003)  A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J Comput Chem 24 (16): 1999-2012 pdf AMBERff03 (citations: 1177+)

Fluorescence spectrometry and chemometics:

 YQ Li, W. Sui, C. Wu & LJ Yu (2001) Derivative Matrix isopotential synchronous fluorescence spectroscopy for the direct determination of 1-hydroxypyrene as a urinary biomarker of exposure to polycyclic aromatic hydrocarbon Anal Sci 17(1):167-170 pdf

 W. Sui, C. Wu, YQ Li & WH Wen (2001) Simultaneous determination of 1-chloroanthracene and 9-bromoanthracene by using matrix isopotential synchronous fluorescence spectrometry combined with derivative technique  Chin J Anal Chem 29 (3): 320-322

 W. Sui, C. Wu & YQ Li (2000) Rapid simultaneous determination of four anthracene derivatives using a single non-linear variable-angle synchronous fluorescence spectrum Fresenius J Anal Chem 368 (7): 669-675 pdf

 C. Wu, W. Sui & YQ. Li (1999) FPATH, a program to design the optimum scanning route for non-linear variable-angle synchronous fluorescence spectrometry Chem Res Chin Univ  209 (Sup), 422

 ZG Lin, C. Wu, Y. G. Tong, Y. B. Zhao, J. G. Xu & S. K. Yang (1996)  Fast generation of three-Dimensional Fluorescence Spectrum ( TDFS ) of single component from Its excitation and emission spectra of fluorescence by  a computational method Proc. of the 5th Chin. Lumin Spectrosc Anal Conf. 31-32

 ZG Lin, C. Wu, Y. B. Zhao, Y. G. Tong, J. G. Xu & S. K. Yang (1996) Signal-noise ratio enhancement by an accumulating method in 3-dimensional fluorescence spectrometry  Proc of the 5th Chin Lumin Spectrosc Anal Conf 36-37

Book chapters:

 C Wu, Shea JE (2012) The Structure of Intrinsically Disordered Peptides Implicated in Amyloid Diseases:

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