Disease-anchored Network Analysis and Molecular Dynamics Prioritize HSP90AB1 as a Doxorubicin-binding Hub Across Cancers

Abstract

Doxorubicin functions through DNA-centered mechanisms and protein-level interactions; however, the cancer-relevant binding hubs remain inadequately defined. We integrated a previously reported functional protein microarray dataset for doxorubicin, which comprised 363 reproducible binders, alongside GeneCards and GeDiPNet disease-gene resources for breast cancer, non-Hodgkin lymphoma, and lymphoblastic leukemia. The three disease gene sets shared a total of 962 genes and were enriched for pathways related to immune activation, chromosomal organization, DNA damage responses, and cancer/viral infections. Disease-anchored binders were assembled into a STRING network and ranked using four centrality measures from cytoHubba. Seven consensus hubs were retained, with HSP90AB1 ranking first by WeightedMean score (16.18). HSP90AB1 also constituted the core of the complete 363-binder network. Docking experiments positioned doxorubicin within the N-terminal ATP-binding pocket of HSP90AB1, supported by recurrent polar, water-mediated, and aromatic interactions. In 400 ns simulations, doxorubicin remained associated with the binding pocket, exhibited stable ligand radius of gyration (rGyr) (approximately 5.0 Å to 5.3 Å, 1 Å=0.1 nm), had a higher ligand solvent accessible surface area (SASA) than KU3 (135.91 vs. 92.46 Ų), and produced ligand-dependent principal component analysis (PCA) profiles. Trajectory-sampled molecular mechanics/generalized Born surface area (MM/GBSA) analyses favored doxorubicin over KU3 [(−88.83±11.87) vs. (−51.08±3.55) kcal/mol]. These findings emphasize HSP90AB1 as a critical doxorubicin-binding hub relevant to disease.

Keywords

Doxorubicin / HSP90AB1 / Protein microarray / Disease database / Molecular docking / Molecular dynamics simulation

References

[1] Kciuk M, Gielecińska A, Mujwar S, Kołat D, Kałuzińska-Kołat Ż, Celik I, Kontek RCells, 2023, 12659.

[2] Thorn C F, Oshiro C, Marsh S, Hernandez-Boussard T, McLeod H, Klein T E, Altman R BPharmacogenet. Genomics, 2011, 21440.

[3] Camilli M, Cipolla C M, Dent S, Minotti G, Cardinale D MJACC CardioOncol., 2024, 6655.

[4] Syu G D, Dunn J, Zhu HMol. Cell. Proteomics, 2020, 19916.

[5] Wang W, Cai Y, Chen Y, Zhu J, Jin JArch. Pharm. (Weinheim), 2025, 358e70006.

[6] Stelzer G, Rosen N, Plaschkes I, Zimmerman S, Twik M, Fishilevich S, Stein T I, Nudel R, Lieder I, Mazor Y, Kaplan S, Dahary D, Warshawsky D, Guan-Golan Y, Kohn A, Rappaport N, Safran M, Lancet DCurr. Protoc. Bioinformatics, 2016, 541.

[7] Kundu I, Sharma M, Barai R S, Pokar K, Idicula-Thomas SGenes Dis., 2023, 10647.

[8] Yu G, Wang L G, Han Y, He Q YOmics, 2012, 16284.

[9] Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, Feng T, Zhou L, Tang W, Zhan L, Fu X, Liu S, Bo X, Yu GInnovation (Camb), 2021, 2100141.

[10] Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima KNucleic Acids Res., 2017, 45D353.

[11] The Gene Ontology ConsortiumNucleic Acids Res., 2019, 47D330.

[12] Szklarczyk D, Kirsch R, Koutrouli M, Nastou K, Mehryary F, Hachilif R, Gable A L, Fang T, Doncheva N T, Pyysalo S, Bork P, Jensen L J, von Mering CNucleic Acids Res., 2023, 51D638.

[13] Taipale M, Jarosz D F, Lindquist SNat. Rev. Mol. Cell Biol., 2010, 11515.

[14] Birbo B, Madu E E, Madu C O, Jain A, Lu YInt. J. Mol. Sci., 2021, 2210317.

[15] Yan L R, Shen S X, Wang A, Ding H X, Liu Y N, Yuan Y, Xu QFront. Mol. Biosci., 2021, 8726244.

[16] Haase M, Fitze GGene, 2016, 575171.

[17] Wang H, Deng G, Ai M, Xu Z, Mou T, Yu J, Liu H, Wang S, Li GOncogene, 2019, 381489.

[18] Zhang H, Yin X, Zhang X, Zhou M, Xu W, Wei Z, Song C, Han S, Han WTechnol. Cancer Res. Treat., 2022, 2115330338221118202.

[19] Hong D S, Banerji U, Tavana B, George G C, Aaron J, Kurzrock RCancer Treat. Rev., 2013, 39375.

[20] Sritharan S, Sivalingam NLife Sci., 2021, 278119527.

[21] Hoadley K A, Yau C, Wolf D M, Cherniack A D, Tamborero D, Ng S, Leiserson M D M, Niu B, McLellan M D, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin A A, Van’t Veer L J, Lopez-Bigas N, Laird P W, Raphael B J, Ding L, Robertson A G, Byers L A, Mills G B, Weinstein J N, Van Waes C, Chen Z, Collisson E A, Benz C C, Perou C M, Stuart J MCell, 2014, 158929.

[22] Moore P S, Chang YNat. Rev. Cancer, 2010, 10878.

[23] Trepel J, Mollapour M, Giaccone G, Neckers LNat. Rev. Cancer, 2010, 10537.

[24] Whitesell L, Lindquist S LNat. Rev. Cancer, 2005, 5761.

[25] Jhaveri K, Taldone T, Modi S, Chiosis GBiochim. Biophys. Acta, 2012, 1823742.

[26] Neckers L, Workman PClin. Cancer Res., 2012, 1864.

[27] Kovacs J J, Murphy P J, Gaillard S, Zhao X, Wu J T, Nicchitta C V, Yoshida M, Toft D O, Pratt W B, Yao T PMol. Cell, 2005, 18601.

[28] Obeid M, Tesniere A, Ghiringhelli F, Fimia G M, Apetoh L, Perfettini J L, Castedo M, Mignot G, Panaretakis T, Casares N, Métivier D, Larochette N, van Endert P, Ciccosanti F, Piacentini M, Zitvogel L, Kroemer GNat. Med., 2007, 1354.

[29] Panaretakis T, Kepp O, Brockmeier U, Tesniere A, Bjorklund A C, Chapman D C, Durchschlag M, Joza N, Pierron G, van Endert P, Yuan J, Zitvogel L, Madeo F, Williams D B, Kroemer GEMBO J., 2009, 28578.

[30] Wang M, Wey S, Zhang Y, Ye R, Lee A SAntioxid. Redox Signal., 2009, 112307.

[31] Zhu S, Zhang Q, Sun X, Zeh H J3rdLotze M T, Kang R, Tang DCancer Res., 2017, 772064.

[32] Cox A D, Fesik S W, Kimmelman A C, Luo J, Der C JNat. Rev. Drug Discov., 2014, 13828.

[33] Dhillon A S, Hagan S, Rath O, Kolch WOncogene, 2007, 263279.

[34] Samatar A A, Poulikakos P INat. Rev. Drug Discov., 2014, 13928.

[35] Wai Wong C, Dye D E, Coombe D RInt. J. Cell Biol., 2012, 2012340296.

[36] Grenert J P, Sullivan W P, Fadden P, Haystead T A, Clark J, Mimnaugh E, Krutzsch H, Ochel H J, Schulte T W, Sausville E, Neckers L M, Toft D OJ. Biol. Chem., 1997, 27223843.

[37] Roe S M, Prodromou C, O’Brien R, Ladbury J E, Piper P W, Pearl L HJ. Med. Chem., 1999, 42260.

[38] Stebbins C E, Russo A A, Schneider C, Rosen N, Hartl F U, Pavletich N PCell, 1997, 89239.

[39] Khandelwal A, Kent C N, Balch M, Peng S, Mishra S J, Deng J, Day V W, Liu W, Subramanian C, Cohen M, Holzbeierlein J M, Matts R, Blagg B S JNat. Commun., 2018, 9425.

[40] Ali M M, Roe S M, Vaughan C K, Meyer P, Panaretou B, Piper P W, Prodromou C, Pearl L HNature, 2006, 4401013.

[41] Prodromou C, Panaretou B, Chohan S, Siligardi G, O’Brien R, Ladbury J E, Roe S M, Piper P W, Pearl L HEMBO J., 2000, 194383.

[42] Kijima T, Prince T L, Tigue M L, Yim K H, Schwartz H, Beebe K, Lee S, Budzynski M A, Williams H, Trepel J B, Sistonen L, Calderwood S, Neckers LSci. Rep., 2018, 86976.

[43] Kim H R, Kang H S, Kim H DIUBMB Life, 1999, 48429.

[44] Samarasinghe B, Wales C T, Taylor F R, Jacobs A TBiochem. Pharmacol., 2014, 87445.

[45] Zou J, Guo Y, Guettouche T, Smith D F, Voellmy RCell, 1998, 94471.

[46] Mishra S J, Liu W, Beebe K, Banerjee M, Kent C N, Munthali V, Koren J3rdTaylor J A3rdNeckers L M, Holzbeierlein J, Blagg B S JJ. Med. Chem., 2021, 641545.

[47] Khurshid I, Mehraj T, Maqbool A, Aejaz K, Khursheed A, Rather M A, Ahmed S S S J, Dangroo N AIn Silico Res. Biomed., 2025, 1100143.

[48] Rather M A, Rasool S, Khursheed A, Ahmed S S S J, Bashir F, Shalla A H, Dar B N, Mir J M, Dangroo N AJ. Chem., 2025, 20255133015.

[49] Alsantali R I, Almohyawi A M, Rather M A, Mir J M, Dangroo N A, Almalki F A, Ben Hadda T, Jassas R S, Alkubaysi S I, Ahmed S ARSC Adv., 2025, 1522285.

[50] Dangroo N A, Moussa Z, Alluhaibi M S, Alsimaree A A, Hawsawi M B, Alsantali R I, Singh J, Gupta N, S M B, Karunakar P, Mir J M, Rather M A, Ahmed S ARSC Adv., 2025, 1515164.

[51] Lopez A, Dahiya V, Delhommel F, Freiburger L, Stehle R, Asami S, Rutz D, Blair L, Buchner J, Sattler MSci. Adv., 2021, 7eabl7295.

[52] Mader S L, Lopez A, Lawatscheck J, Luo Q, Rutz D A, Gamiz-Hernandez A P, Sattler M, Buchner J, Kaila V R INat. Commun., 2020, 111410.

[53] Reidy M, Masison D CNat. Commun., 2025, 166710.

[54] Qu X, Wang S, Zhao S, Wan C, Xu W, Huang CNat. Commun., 2024, 1510661.

[55] Silbermann L M, Vermeer B, Schmid S, Tych KElife, 2024, 13e102666.

[56] Hoxie R S, Street T OProtein Sci., 2020, 292101.

[57] Chiosis G, Digwal C S, Trepel J B, Neckers LNat. Rev. Mol. Cell Biol., 2023, 24797.

[58] Stachowski T R, Nithianantham S, Vanarotti M, Lopez K, Fischer MProtein Sci., 2023, 32e4629.

[59] Riedl S, Bilgen E, Agam G, Hirvonen V, Jussupow A, Tippl F, Riedl M, Maier A, Becker C F W, Kaila V R I, Lamb D C, Buchner JNat. Commun., 2024, 158627.

[60] Beckers M, Sirockin F, Fechner N, Stiefl NJ. Chem. Inf. Model., 2024, 646636.

[61] Abad-Zapatero CExpert Opin. Drug Discov., 2021, 16763.

[62] Forouzesh N, Ghafouri F, Tolokh I S, Onufriev A VJ. Chem. Inf. Model., 2024, 649433.

[63] Tuccinardi TExpert Opin. Drug Discov., 2021, 161233.

[64] Yau M Q, Liew C W Y, Toh J H, Loo J S EJ. Mol. Model., 2024, 30390.

[65] Minh D D L, Cooper D A, Xie B, Shi LJ. Chem. Theory Comput., 2025, 21943.

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