The following are publications where PyRx has been mentioned. PyRx is also cited in patent applications. Thank you all for using PyRx!

• Design, Synthesis, and Computational Evaluation of 3,4-Dihydroquinolin-2(1H)-One Analogues as Potential VEGFR2 Inhibitors in Glioblastoma Multiforme Buhlak S, Abad N, Akachar J, Saffour S, Kesgun Y, Dik S, Yasin B, Bati-Ayaz G, Hanashalshahaby E, Türkez H, Mardinoglu A. Pharmaceuticals (Basel). 2025 Feb 8;18(2):233.
• Exploring Marine Natural Compounds: Innovative Therapeutic Candidates Against Chagas Disease Through Virtual Screening and Molecular Dynamics Maya-Ramírez CE, Saih A, Méndez Tenorio A, Wong Baeza C, Nogueda Torres B, Santiago Hernández JC. Life (Basel). 2025 Jan 28;15(2):192.
• Insight into molecular and mutational scrutiny of epilepsy associated gene Gabrg2 leading to novel computer-aided drug designing Naveed M, Hanif N, Aziz T, Waseem M, Alharbi M, Alshammari A, Alasmari AF. Sci Rep. 2025 Feb 25;15(1):6770.
• Targeting aldose reductase using natural African compounds as promising agents for managing diabetic complications Gakpey MEL, Aidoo SA, Jumah TA, Hanson G, Msipa S, Mbaoji FN, Bukola O, Tjale PC, Sangare M, Tebourbi H, Awe OI. Front Bioinform. 2025 Feb 6;5:1499255.
• Pterostilbene as a potent ESR-1 in breast cancer therapy: insights from network pharmacology, molecular docking, dynamics simulations, ADMET, and in vitro analysis Marwah H, Dewangan HK. Mol Divers. 2025 Feb 24. doi: 10.1007/s11030-025-11144-3.
• Discovery of a selective PI3Kα inhibitor via structure-based virtual screening for targeted colorectal cancer therapy Albassam H, Almutairi O, Alnasser M, Altowairqi F, Almutairi F, Alobid S. J Enzyme Inhib Med Chem. 2025 Dec;40(1):2468852.
• Bioactivity profiling of Sanghuangporus lonicerinus: antioxidant, hypoglycaemic, and anticancer potential via in-vitro and in-silico approaches Gafforov Y, Bekić S, Yarasheva M, Mišković J, Živanović N, Chen JJ, Petri E, Abdullaev B, Rapior S, Lim YW, Abdullaev I, Abbasi AM, Ghosh S, Wan-Mohtar WAAQI, Rašeta M. J Enzyme Inhib Med Chem. 2025 Dec;40(1):2461185.
• Phenazine Scaffolds as a Potential Allosteric Inhibitor of LasR Protein in Pseudomonas aeruginosa Nketia PB, Manu P, Osei-Poku P, Kwarteng A. Bioinform Biol Insights. 2025 Feb 20;19:11779322251319594.
• Identifying natural inhibitors against FUS protein in dementia through machine learning, molecular docking, and dynamics simulation Li D. Front Neuroinform. 2025 Feb 5;18:1439090.
• Discovering broad-spectrum inhibitors for SARS-CoV-2 variants: a cheminformatics and biophysical approach targeting the main protease Alqahtani SM. Front Pharmacol. 2025 Feb 5;16:1459581.
• Targeting beta-lactamase activity with Oxacyclohexadecan-2-one in carbapenem-resistant uropathogenic E. coli: A molecular simulation approach Balaji P, N MP, Bhaskar M E, R G, Paul SFD, R M. PLoS One. 2025 Feb 18;20(2):e0317941.
• Repurposing doxycycline for the inhibition of monkeypox virus DNA polymerase: a comprehensive computational study Yousaf MA, Michel M, Khan AT, Noreen M, Bano S. In Silico Pharmacol. 2025 Feb 13;13(1):27.
• Exploration of Antioxidative, Antidiarrheal, and Antihyperglycemic Properties of Artocarpus chama Leaves Along With In Silico Analysis Hossen MS, Refat KMNH, Faruque M, Kundu P, Karmakar UK. Biomed Res Int. 2025 Jan 28;2025:9930195.
• Deciphering the Withania somnifera alkaloids potential for cure of neurodegenerative disease: an in-silico study Chen R, Zhang D, Chaudhary AA, Khan SU, Vohra S, Vohra Y, Li N, Khan S. AMB Express. 2025 Feb 13;15(1):29.
• Identification of a TonB-Dependent Siderophore Receptor as a Novel Anti-Biofilm Target and Virtual Screening for Its Inhibitor in Pseudomonas fluorescens PF08 Shen T, Cao C, Zhu R, Chen J, Wang F, Wang Y. Foods. 2025 Feb 6;14(3):531.
• Unveiling the Multitarget Potential of a Rare Caffeoyl Ester from Artemisia capillaris for Diabetes Mellitus: An Integrated In Vitro and In Silico Study Islam MN, Ha MT, Min BS, Choi JS, Jung HA. Int J Mol Sci. 2025 Feb 2;26(3):1286.
• A hybrid machine learning framework for functional annotation of mitochondrial glutathione transport and metabolism proteins in cancers Kennedy L, Sandhu JK, Harper ME, Cuperlovic-Culf M. BMC Bioinformatics. 2025 Feb 11;26(1):48.
• Molecular modelling and experimental validation of mangiferin and its related compounds as quorum sensing modulators of Pseudomonas aeruginosa Nortje NQ, Aribisala JO, Pillay C, Sabiu S. Arch Microbiol. 2025 Feb 8;207(3):53.
• Molecular docking and simulation analysis of c-KIT and PDGFRα with phytochemicals as dual inhibitors for GIST Khattabi KE, Lemriss S, Jaoudi RE, Zouaidia F. Bioinformation. 2024 Sep 30;20(9):974-979.
• Identification and prioritization of novel therapeutic candidates against glutamate racemase from Klebsiella pneumoniae Kumar A, Anjum F, Hassan MI, Shamsi A, Singh RP. PLoS One. 2025 Feb 6;20(2):e0317622.
• Rhodoquinone carries electrons in the mammalian electron transport chain Valeros J, Jerome M, Tseyang T, Vo P, Do T, Fajardo Palomino D, Grotehans N, Kunala M, Jerrett AE, Hathiramani NR, Mireku M, Magesh RY, Yenilmez B, Rosen PC, Mann JL, Myers JW, Kunchok T, Manning TL, Boercker LN, Carr PE, Munim MB, Lewis CA, Sabatini DM, Kelly M, Xie J, Czech MP, Gao G, Shepherd JN, Walker AK, Kim H, Watson EV, Spinelli JB. Cell. 2025 Feb 20;188(4):1084-1099.e27.
• Molecular Docking Appraisal of Pleurotus ostreatus Phytochemicals as Potential Inhibitors of PI3K/Akt Pathway for Breast Cancer Treatment Effiong ME, Bella-Omunagbe M, Afolabi IS, Chinedu SN. Bioinform Biol Insights. 2025 Feb 3;19:11779322251316864.
• Multi-scale computational modeling to identify novel chemical scaffolds as trehalose-6-phosphate phosphatase inhibitors to combat Burkholderia pseudomallei Noor S, Aljasir MA, Bashir M, Khan K, Ahmad S, Abideen SA, Khan S, Siddique F, Ahmad H, Ghani K, Iqbal M, Irfan M, Khan A, Wei DQ. In Silico Pharmacol. 2025 Feb 1;13(1):21.
• Exploring the anticancer potential of Hewittia malabarica through phytochemical analysis and molecular docking study Thozhukkad Moosaripparambil S, Vadakkadath Meethal K. Sci Rep. 2025 Feb 3;15(1):4088.
• Identification of natural phytochemicals as AKT2 inhibitors using molecular docking and dynamics simulations as potential cancer therapeutics Paul JK, Azmal M, Haque Shohan MN, Mrinmoy M, Newaz Been Haque AS, Talukder OF, Ghosh A. Heliyon. 2025 Jan 10;11(2):e41897.
• Repurposing brucine as a chemopreventive agent in mammary gland carcinoma: Regulating lactate transport through MCT-4 Zaidi AK, Kumar A, Kumar R, Singh J, Yadav S, Sonkar AB, Kumar D, Shrivastava NK, Ansari MN, Saeedan AS, Kaithwas G. Toxicol Rep. 2025 Jan 10;14:101902.
• Fragment optimized chalcone derivatives targeting OmpA protein as a therapeutic approach against multidrug resistant Acinetobacter baumannii Naveed M, Abid A, Aziz T, Saleem A, Arshad A, Javed K, Rehman HM, Nabi G, Al-Harbi M, Alasmari AF. Sci Rep. 2025 Jan 31;15(1):3917.
• The Intricate Mechanisms of Functional Foods Oyster Mushroom and Fenugreek on Type 2 Diabetic Animal Model Razon AH, Alauddin M, Farzana N, Mazumdar S, Amin MR, Tusher MMH, Asrafuzzaman M, Hasan N, Rahman M, Saiedullah M, Rokeya B, Faruque MO. J Diabetes Res. 2024 Dec 9;2024:6209785.
• Exploration of alcohol dehydrogenase EutG from Bacillus tropicus as an eco-friendly approach for the degradation of polycyclic aromatic compounds Naveed M, Iqbal F, Aziz T, Saleem A, Javed T, Afzal M, Waseem M, Alharbi M, Albekairi TH. Sci Rep. 2025 Jan 28;15(1):3466.
• Gastroprotective properties of flavonoid-rich extract of Pulicaria odora against ethanol-induced gastric ulcer in mice Boudebbaz K, Brouk M, Laalem R, Zabaiou N. Heliyon. 2025 Jan 4;11(1):e41625.
• Molecular docking and molecular dynamics simulation studies of inhibitor candidates against Anopheles gambiae 3-hydroxykynurenine transaminase and implications on vector control Adedeji EO, Ogunlana OO, Oduselu GO, Koenig R, Adebiyi E, Soremekun OS, Fatumo S. Heliyon. 2025 Jan 2;11(1):e41633.
• Multifaceted Analysis of Lactobacillus plantarum DMR14 Reveals Promising Antidiabetic Properties Through In Vivo Assays and Molecular Simulations Islam S, Biswas S, Islam MA, Biswas J, Dutta AK, Mohiuddin GG, Saleh MA, Zaman S. J Cell Mol Med. 2025 Jan;29(2):e70347.
• Natural Product Identification and Molecular Docking Studies of Leishmania Major Pteridine Reductase Inhibitors Arthur MN, Hanson G, Broni E, Sakyi PO, Mensah-Brown H, Miller WA 3rd, Kwofie SK. Pharmaceuticals (Basel). 2024 Dec 24;18(1):6.
• Structure-Based Discovery of MolPort-137: A Novel Autotaxin Inhibitor That Improves Paclitaxel Efficacy Rai P, Clark CJ, Kardam V, Womack CB, Thammathong J, Norman DD, Tigyi GJ, Bicker K, Weissmiller AM, Dubey KD, Banerjee S. Int J Mol Sci. 2025 Jan 12;26(2):597.
• Exploring the antifungal potential of Cannabis sativa-derived stilbenoids and cannabinoids against novel targets through in silico protein interaction profiling Kırboğa KK, Karim A, Küçüksille EU, Rudrapal M, Khan J, Achar RR, Silina E, Manturova N, Stupin V. Front Chem. 2025 Jan 6;12:1515424.
• Synthesis, characterization, and computational evaluation of some synthesized xanthone derivatives: focus on kinase target network and biomedical properties Muslim WT, Mohammad LJ, Naji MM, Karimi I, Al-Sabti MD, Jabir M, Najm MAA, Schiöth HB. Front Pharmacol. 2025 Jan 3;15:1511627.
• The discovery of a new nonbile acid modulator of Takeda G protein-coupled receptor 5: An integrated computational approach Salam R, Bakker M, Krutáková M, Štefela A, Pávek P, Duintjer Tebbens J, Zitko J. Arch Pharm (Weinheim). 2025 Jan;358(1):e2400423.
• Inhibitory Activity of N- and S-Functionalized Monoterpene Diols Towards Monoamine Oxidases A and B Podturkina AV, Ardashov OV, Soldatova YV, Poletaeva DA, Smolina AV, Vasyuchenko EP, Vyatkin YV, Li-Zhulanov NS, Faingold II, Salakhutdinov NF, Volcho KP. Int J Mol Sci. 2024 Dec 26;26(1):97.
• In silico design and computational screening of berberine derivatives for potential antidiabetic activity through allosteric activation of the AMPK pathway Kakoti BB, Zothantluanga JH, Deka K, Halder RK, Roy D. In Silico Pharmacol. 2025 Jan 7;13(1):12.
• Exploring caffeine as a disruptor of membrane integrity and genomic stability in Staphylococcus aureus: functional and in silico analysis Beulah KC, Prasanna A, Karunakar P, Rao AS, More SS, Nair A. Arch Microbiol. 2025 Jan 8;207(2):28.
• Toxic Effects of Lead Exposure on Freshwater Climbing Perch, Anabas testudineus, and Bioremediation Using Ocimum sanctum Leaf Powder Saha NC, Chatterjee A, Banerjee P, Bhattacharya R, Sadhu A, Pastorino P, Saha S. Toxics. 2024 Dec 20;12(12):927.
• Organic Sunscreens-Is Their Placenta Permeability the Only Issue Associated with Exposure During Pregnancy? In Silico Studies of Sunscreens’ Placenta Permeability and Interactions with Selected Placental Enzymes Sobańska AW, Sobański AM. Molecules. 2024 Dec 11;29(24):5836.
• Exploration of the Biochemistry of Mustard Seed Meals: A Phytochemical and In Silico Perspective Garg S, Gairola K, Punetha H, Gangola S. Foods. 2024 Dec 20;13(24):4130.
• An In Silico Investigation of the Pathogenic G151R G Protein-Gated Inwardly Rectifying K+ Channel 4 Variant to Identify Small Molecule Modulators Pitsillou E, Liang JJ, Kino N, Lockwood JL, Hung A, El-Osta A, AbuMaziad AS, Karagiannis TC. Biology (Basel). 2024 Nov 29;13(12):992.
• Exploring pyrazolines as potential inhibitors of NSP3-macrodomain of SARS-CoV-2: synthesis and in silico analysis Joshi R, Gaikwad H, Soge B, Alshammari A, Albekairi NA, Kabra A, Yashwante U, Kolte B, Lokhande P, Meshram RJ. Sci Rep. 2025 Jan 4;15(1):767.
• Novel Naphthyridones Targeting Pannexin 1 for Colitis Management Hsueh WY, Wu YL, Weng MT, Liu SY, Santavanond JP, Liu YC, Lin CI, Lai CN, Lu YR, Hsu JY, Gao HY, Lee JC, Wei SC, Lyu PC, Poon IKH, Hsieh HP, Chiu YH. Adv Sci (Weinh). 2025 Feb;12(7):e2411538.
• Hepatoprotective effects of olive leaf extract against carbon tetrachloride-induced oxidative stress: in vivo and in-silico insights into the Nrf2-NFκB pathway Buzdar JA, Shah QA, Khan MZ, Zaheer A, Shah T, Ataya FS, Fouad D. J Mol Histol. 2024 Dec 14;56(1):42.
• Hepatoprotective effects of olive leaf extract against carbon tetrachloride-induced oxidative stress: in vivo and in-silico insights into the Nrf2-NFκB pathway Buzdar JA, Shah QA, Khan MZ, Zaheer A, Shah T, Ataya FS, Fouad D. J Mol Histol. 2024 Dec 14;56(1):42.
• Repurposing raltegravir for reducing inflammation and treating cancer: a bioinformatics analysis Nikfarjam Z, Rakhshi R, Zargari F, Aalikhani M, Hasan-Abad AM, Bazi Z. Sci Rep. 2024 Dec 5;14(1):30349.
• An In Silico Approach to Discover Efficient Natural Inhibitors to Tie Up Epstein-Barr Virus Infection Das A, Mumu M, Rahman T, Sayeed MA, Islam MM, Alawneh JI, Hassan MM. Pathogens. 2024 Oct 25;13(11):928.
• Effect of drying conditions on the chemical compositions, molecular docking interactions and antioxidant activity of Hedychium spicatum Buch.-Ham. Rhizome essential oil Gangwar A, Tewari G, Pande C, Prakash O, Kanyal B, Tewari LM, Joshi M, Siddiqui A. Sci Rep. 2024 Nov 19;14(1):28568.
• Natural AI-based drug designing by modification of ascorbic acid and curcumin to combat buprofezin toxicity by using molecular dynamics study Sadia H, Qureshi IZ, Naveed M, Aziz T, Alharbi M, Alasmari AF, Albekairi TH. Sci Rep. 2024 Nov 18;14(1):28445.
• Isolation, characterization and pharmacological investigations of secondary metabolites from Aspergillus ficuum via experimental and computational techniques Shah ZA, Khan K, Shah T, Ahmad N, Khan A. RSC Adv. 2024 Nov 15;14(49):36527-36537.
• Integrated virtual screening and MD simulation study to discover potential inhibitors of mycobacterial electron transfer flavoprotein oxidoreductase Arshad K, Salim J, Talat MA, Ashraf A, Kanwal N. PLoS One. 2024 Nov 15;19(11):e0312860.
• Riddelline from Tamarix articulate as a potential anti-bacterial lead compound for novel antibiotics discovery: A comprehensive computational and toxicological studies Alnuqaydan AM. PLoS One. 2024 Nov 14;19(11):e0310319.
• Computer-Aided Discovery of Abrus precatorius Compounds With Anti-Schistosomal Potential Shoko R, Mazadza A. Biomed Eng Comput Biol. 2024 Nov 10;15:11795972241294112.
• Network pharmacology and bioinformatic integrative analysis reveals candidate gene targets and potential therapeutic of East Kalimantan propolis against hepatocellular carcinoma Kustiawan PM, Siregar KAAK, Jauhar MM, Ramadhan D, Mardliyati E, Syaifie PH. Heliyon. 2024 Oct 19;10(21):e39142.
• Synthesis and Docking Studies of Novel Spiro[5,8-methanoquinazoline-2,3′-indoline]-2′,4-dione Derivatives Faragó T, Mészáros R, Wéber E, Palkó M. Molecules. 2024 Oct 29;29(21):5112.
• Potential Target Metabolites From Gut Microbiota Against Hepatocellular Carcinoma: A Network Pharmacology and Molecular Docking Study Aslam S, Qasim M, Noor F, Shahid M, Ashfaq UA, Munir S, Al-Harthi HF, Mashraqi MM, Waqas U, Khurshid M. Int J Microbiol. 2024 Oct 29;2024:4286228.
• Computational identification of PDL1 inhibitors and their cytotoxic effects with silver and gold nanoparticles Ali SH, Ali H, Aziz MA. Sci Rep. 2024 Nov 4;14(1):266105.
• Unveiling the apoptotic potential of antioxidant-rich Bangladeshi medicinal plant extractives and computational modeling to identify antitumor compounds Haque MU, Alam AK, Islam Shovon MT, Sujon KM, Hasan Maruf MM, Kabir SR, Faisal Hoque KM, Reza MA. Heliyon. 2024 Oct 2;10(20):e38885.
• Anti colorectal cancer activity and in silico studies of novel pyridine nortopsentin analog as cyclin dependent kinase 6 inhibitor Abdelmegeed H, Abo-Salem HM, Zayed EM, El-Sawy ER. Sci Rep. 2024 Nov 1;14(1):26327.
• Surface plasmon resonance, molecular docking, and molecular dynamics simulation studies of lysozyme interaction with tannic acid Türkoğlu EA, Taştekil I, Özbek Sarica P. Food Sci Nutr. 2024 Jul 22;12(10):7392-7404.
• Oxidative Stress, Inflammation, and Altered Lymphocyte E-NTPDase Are Implicated in Acute Dyslipidemia in Rats: Protective Role of Arbutin Alruhaimi RS, Hussein OE, Alnasser SM, Germoush MO, Alotaibi M, Hassanein EHM, El Mohtadi M, Mahmoud AM. Pharmaceuticals (Basel). 2024 Oct 8;17(10):1343.
• In Silico Identification of Potential Inhibitors of SARS-CoV-2 Main Protease (Mpro) Hernández-Serda MA, Vázquez-Valadez VH, Aguirre-Vidal P, Markarian NM, Medina-Franco JL, Cardenas-Granados LA, Alarcón-López AY, Martínez-Soriano PA, Velázquez-Sánchez AM, Falfán-Valencia RE, Angeles E, Abrahamyan L. Pathogens. 2024 Oct 11;13(10):887.
• Quercetin as a Modulator of PTPN22 Phosphomonoesterase Activity: A Biochemical and Computational Evaluation Sulyman AO, Yusuf TNA, Aribisala JO, Ibrahim KS, Ajani EO, Ajiboye AT, Sabiu S, Singh K. Curr Issues Mol Biol. 2024 Oct 3;46(10):11156-11175.
• Screening Antioxidant Components in Yiwei Decoction Using Spectrum-Effect Relationship and Network Pharmacology Zhang L, Zhu W. J Anal Methods Chem. 2024 Oct 16;2024:5514265.
• Molecular insights and inhibitory dynamics of flavonoids in targeting Pim-1 kinase for cancer therapy Alhadrami HA, Sayed AM, Hassan HM, Alhadrami AH, Rateb ME. Front Pharmacol. 2024 Oct 7;15:1440958.
• Synthesis and biological evaluation of novel D-ring fused steroidal N(2)-substituted-1,2,3-triazoles Tenjović B, Bekić S, Ćelić A, Petri E, Scholda J, Kopp F, Sakač M, Nikolić A. RSC Med Chem. 2024 Oct 18. doi: 10.1039/d4md00297k.
• Network analysis and molecular modeling studies of pinocembrin a bioactive phytochemical of Dodonaea viscosa against Parkinson’s disease Priya M, Zochedh A, Mohan YS, Chandran K, Arumugam K, Sultan AB. In Silico Pharmacol. 2024 Oct 10;12(2):91.
• Synthesis of designed new 1,3,4-oxadiazole functionalized pyrano [2,3-f] chromene derivatives and their antimicrobial activities Alatawi K, Qarah AF, Alharbi H, Alisaac A, Abualnaja MM, Attar RMS, Alsoliemy A, El-Metwaly NM. Heliyon. 2024 Sep 25;10(19):e38294.
• Fructose-1,6-bisphosphate reverses hypotensive effect caused by L-kynurenine in Wistar male rats Catarina AV, Branchini G, Caceres RA, Fernandes RS, Costa BP, Machado KLG, Becker T, Ferreira LF, Rigatto K, de Oliveira JR, Nunes FB. Physiol Rep. 2024 Oct;12(19):e70033.

See also Older Publications Using PyRx.