Publications Using PyRx

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

• 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.
• Exploring common pathogenic association between Epstein Barr virus infection and long-COVID by integrating RNA-Seq and molecular dynamics simulations Kanwal A, Zhang Z. Front Immunol. 2024 Sep 26;15:1435170.
• Therapeutic potential of Leea asiatica: Chemical isolation and validation of ethnomedicinal claims through in vitro and in silico assessment of antioxidant and anti-inflammatory properties Joshi KR, Devkota HP, Al-Mutairi KA, Sugimura K, Yahara S, Khadka R, Thapa S, Shekh MU, Poudel S, Watanabe T. Heliyon. 2024 Sep 18;10(19):e38074.
• Bioinformatics and Chemoinformatics Analysis Explored the Role of Linum usitatissimum in Diabetic Heart Conditions: Experimental Analysis in H9c2 Rat Embryonic Cardiomyocytes Cell Lines Safavi K, Hajibabaie F, Abedpoor N. J Med Signals Sens. 2024 Sep 2;14:27.
• Insights on mining the pangenome of Sphingobacterium thalpophilum NMS02 S296 from the resistant banana cultivar Pisang lilin confirms the antifungal action against Fusarium oxysporum f. sp. cubense Ajesh BR, Sariga R, Nakkeeran S, Renukadevi P, Saranya N, Alkahtani S. Front Microbiol. 2024 Sep 19;15:1443195.
• Dual effects of ipecac alkaloids with potent antiviral activity against foot-and-mouth disease virus as replicase inhibitors and direct virucides Pantanam A, Mana N, Semkum P, Lueangaramkul V, Phecharat N, Lekcharoensuk P, Theerawatanasirikul S. Int J Vet Sci Med. 2024 Oct 1;12(1):134-147.
• Unveiling the anticancer potential of Anamirta cocculus (L.) Wight& Arn.: Evidences from cytotoxicity studies, apoptosis analysis, and molecular docking Thozhukkad Moosaripparambil S, Vadakkadath Meethal K. 3 Biotech. 2024 Oct;14(10):245.
• Employing Hexahydroquinolines as Pf CDPK4 Inhibitors to Combat Malaria Transmission: An Advanced Computational Approach Oduselu GO, Elebiju OF, Ogunnupebi TA, Akash S, Ajani OO, Adebiyi E. Adv Appl Bioinform Chem. 2024 Sep 23;17:83-105.
• Molecular Targets of Minor Cannabinoids in Breast Cancer: In Silico and In Vitro Studies Almeida CF, Palmeira A, Valente MJ, Correia-da-Silva G, Vinggaard AM, Sousa ME, Teixeira N, Amaral C. Pharmaceuticals (Basel). 2024 Sep 21;17(9):1245.
• Computational Mutagenesis and Inhibition of Staphylococcus aureus AgrA LytTR Domain Using Phenazine Scaffolds: Insight From a Biophysical Study Manu P, Nketia PB, Osei-Poku P, Kwarteng A. Biomed Res Int. 2024 Sep 18;2024:8843954.
• Thymol and carvacrol derivatives as anticancer agents; synthesis, in vitro activity, and computational analysis of biological targets Alamri MA, Abdel-Kader MS, Salkini MA, Alamri MA. RSC Adv. 2024 Sep 25;14(42):30662-30672.
• Mechanistic Regulation of Epidermal Growth Factor and Hormonal Receptors by Kinase Inhibitors and Organofluorines in Breast Cancer Therapy Singh J, Khanduja KL, Dahiya D, Avti PK. Cell Biochem Biophys. 2024 Sep 24. doi: 10.1007/s12013-024-01546-9.
• Identification and characterization of a small molecule BFstatin inhibiting BrpR, the transcriptional regulator for biofilm formation of Vibrio vulnificus Lee H, Hwang SH, Shin H, Ha NC, Wang Q, Choi SH. Front Microbiol. 2024 Sep 9;15:1468567.
• Marine natural compounds as potential CBP bromodomain inhibitors for treating cancer: an in-silico approach using molecular docking, ADMET, molecular dynamics simulations and MM-PBSA binding free energy calculations Ali ML, Noushin F, Azme E, Hasan MM, Hoque N, Metu AF. In Silico Pharmacol. 2024 Sep 18;12(2):85.
• Characterization of Cationic Amino Acid Binding Protein from Candidatus Liberibacter Asiaticus and in Silico Study to Identify Potential Inhibitor Molecules Lonare S, Gupta DN, Kaur H, Rode S, Verma S, Gubyad M, Ghosh DK, Kumar P, Sharma AK. Protein J. 2024 Oct;43(5):967-982.
• Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections Nooruzzaman M, Johnson KEE, Rani R, Finkelsztein EJ, Caserta LC, Kodiyanplakkal RP, Wang W, Hsu J, Salpietro MT, Banakis S, Albert J, Westblade LF, Zanettini C, Marchionni L, Soave R, Ghedin E, Diel DG, Salvatore M. Nat Commun. 2024 Sep 18;15(1):7999.
• A network pharmacology-based approach to understand the mechanism of action of anti-mycobacterial activity of Acacia nilotica: a modelling and experimental study Suresh M, Sai KV, Mitra K, Ravindran R, Doble M. Mol Divers. 2024 Sep 18. doi: 10.1007/s11030-024-10985-8.
• A cheminformatics and network pharmacology approach to elucidate the mechanism of action of Mycobacterium tuberculosis γ-carbonic anhydrase inhibitors Manaithiya A, Bhowmik R, Bhattacharya K, Ray R, Shyamal SS, Carta F, Supuran CT, Parkkila S, Aspatwar A. Front Pharmacol. 2024 Sep 2;15:1457012.
• Discovery, lead identification and exploration of potential oxadiazole derivatives in targeting STAT3 as anti-cancer agents Panwar V, SenGupta S, Kumar S, Singh PP, Kumar A, Azizov S, Gupta MK, Kumar D. In Silico Pharmacol. 2024 Sep 14;12(2):83.
• Identification and biophysical characterization of potential phytochemical inhibitors of carboxyl/choline esterase from Helicoverpa armigera for advancing integrated pest management strategies Kaur H, Singh S, Kathott Prakash S, Rode S, Lonare S, Kumar R, Kumar P, Kumar Sharma A, Ramamurthy PC, Singh J, Khan NA. Sci Rep. 2024 Sep 16;14(1):21596.
• Inhibition of Monkeypox Virus DNA Polymerase Using Moringa oleifera Phytochemicals: Computational Studies of Drug-Likeness, Molecular Docking, Molecular Dynamics Simulation and Density Functional Theory Yousaf MA, Basheera S, Sivanandan S. Indian J Microbiol. 2024 Sep;64(3):1057-1074.
• Predicting of novel homoserine dehydrogenase inhibitors against Paracoccidioides brasiliensis: integrating in silico and in vitro approaches Tartari JC, Khan A, da Silva Andrade JG, Vilugron Rodrigues FA, Alves Bueno PS, Souza Lima D, Canduri F, Freitas Gauze G, Kioshima ÉS, Vicente Seixas FA. Future Microbiol. 2024;19(17):1475-1488.
• Characterization and Cytotoxic Assessment of Bis(2-hydroxy-3-carboxyphenyl)methane and Its Nickel(II) Complex Ahmed AH, Althobaiti IO, Alenezy EK, Asiri YM, Ghalab S, Hussein OA. Molecules. 2024 Sep 6;29(17):4239.
• Short Communication: Novel Di- and Triselenoesters as Effective Therapeutic Agents Inhibiting Multidrug Resistance Proteins in Breast Cancer Cells Radomska D, Czarnomysy R, Marciniec K, Nowakowska J, Domínguez-Álvarez E, Bielawski K. Int J Mol Sci. 2024 Sep 8;25(17):9732.
• Exploring fatty acids from royal jelly as a source of histone deacetylase inhibitors: from the hive to applications in human well-being and health Aparecida Dos Santos France F, Maeda DK, Rodrigues AB, Ono M, Lopes Nogueira Marchetti F, Marchetti MM, Faustino Martins AC, Gomes RDS, Rainho CA. Epigenetics. 2024 Dec;19(1):2400423.
• The food-borne carcinogenic 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) disrupts circadian rhythms and ameliorated by pterostilbene (PSB) in Caenorhabditis elegans Chang CH, Yen PL, Pan MH, Liao VH. Arch Toxicol. 2024 Dec;98(12):4131-4141.
• Novel 3,6-Disubstituted Pyridazine Derivatives Targeting JNK1 Pathway: Scaffold Hopping and Hybridization-Based Design, Synthesis, Molecular Modeling, and In Vitro and In Vivo Anticancer Evaluation Shaalan MM, Osman EEA, Attia YM, Hammam OA, George RF, Naguib BH. ACS Omega. 2024 Aug 19;9(35):37310-37329.
• Identification of Hub of the Hub-Genes From Different Individual Studies for Early Diagnosis, Prognosis, and Therapies of Breast Cancer Alam MS, Sultana A, Kibria MK, Khanam A, Wang G, Mollah MNH. Bioinform Biol Insights. 2024 Sep 4;18:11779322241272386.
• Investigation of Host-Guest Inclusion Complex of Mephenesin with α-Cyclodextrin for Innovative Application in Biological System Debnath S, Ghosh B, Mondal M, Roy N, Mallick K, Maji J, Sahana S, Sinha A, Dey S, Kumar A, Roy MN. ACS Omega. 2024 Aug 15;9(34):36066-36075.
• Docking-Based Virtual Screening Method for Selecting Natural Compounds with Synergistic Inhibitory Effects Against Cancer Signalling Pathways Using a Multi-Target Approach Sardarpour N, Goodarzi Z, Gharaghani S. Iran J Biotechnol. 2024 Apr 1;22(2):e3718.
• Anti-Skin Aging Potential, Antibacterial Activity, Inhibition of Single-Stranded DNA-Binding Protein, and Cytotoxic Effects of Acetone-Extracted Passiflora edulis (Tainung No. 1) Rind Extract on Oral Carcinoma Cells Huang YH, Huang CY. Plants (Basel). 2024 Aug 8;13(16):2194.
• A novel heuristic of rigid docking scores positively correlates with full-length nuclear receptor LRH-1 regulation Haratipour Z, Foutch D, Blind RD. Comput Struct Biotechnol J. 2024 Jul 30;23:3065-3080.
• Computational investigations of potential inhibitors of monkeypox virus envelope protein E8 through molecular docking and molecular dynamics simulations Das R, Bhattarai A, Karn R, Tamang B. Sci Rep. 2024 Aug 23;14(1):19585.
• Exploring Bryophyllum pinnatum compounds as potential inhibitors for Vespula vulgaris allergen proteins: A systematic computational approach Islam S, Shibly AZ. Heliyon. 2024 Jul 22;10(15):e34713.
• Assessing anti oxidant, antidiabetic potential and GCMS profiling of ethanolic root bark extract of Zanthoxylum rhetsa (Roxb.) DC: Supported by in vitro, in vivo and in silico molecular modeling Barman AK, Mahadi S, Hossain MA, Begum R, Acharyya RN, Alam M, Rahman MH, Biswas NN, Hossain ASMM. PLoS One. 2024 Aug 19;19(8):e0304521.
• Identification of molecular targets and small drug candidates for Huntington’s disease via bioinformatics and a network-based screening approach Hossain MR, Tareq MMI, Biswas P, Tauhida SJ, Bibi S, Zilani MNH, Albadrani GM, Al-Ghadi MQ, Abdel-Daim MM, Hasan MN. J Cell Mol Med. 2024 Aug;28(16):e18588.
• Unearthing phytochemicals as natural inhibitors for pantothenate synthetase in Mycobacterium tuberculosis: A computational approach Chouhan M, Tiwari PK, Mishra R, Gupta S, Kumar M, Almuqri EA, Ibrahim NA, Basher NS, Chaudhary AA, Dwivedi VD, Verma D, Kumar S. Front Pharmacol. 2024 Jul 29;15:1403900.
• Predictive identification and design of potent inhibitors targeting resistance-inducing candidate genes from E. coli whole-genome sequences Aborode AT, Kumar N, Olowosoke CB, Ibisanmi TA, Ayoade I, Umar HI, Jamiu AT, Bolarinwa B, Olapade Z, Idowu AR, Adelakun IO, Onifade IA, Akangbe B, Abacheng M, Ikhimiukor OO, Awaji AA, Adesola RO. Front Bioinform. 2024 Jul 26;4:1411935.
• In silico screening for potential inhibitors from the phytocompounds of Carica papaya against Zika virus NS5 protein Kumaree KK, Anthikapalli NVA, Prasansuklab A. F1000Res. 2024 Jun 25;12:655.
• In silico evaluation of potential breast cancer receptor antagonists from GC-MS and HPLC identified compounds in Pleurotus ostreatus extracts Effiong ME, Bella-Omunagbe M, Afolabi IS, Chinedu SN. RSC Adv. 2024 Aug 9;14(33):23744-23771.
• Investigation of the Anti-Inflammatory Properties of Bioactive Compounds from Olea europaea: In Silico Evaluation of Cyclooxygenase Enzyme Inhibition and Pharmacokinetic Profiling Karagiannis TC, Ververis K, Liang JJ, Pitsillou E, Kagarakis EA, Yi DTZ, Xu V, Hung A, El-Osta A. Molecules. 2024 Jul 26;29(15):3502.
• Pilot-Scale Screening of Clinically Approved Drugs to Identify Uridine Insertion/Deletion RNA Editing Inhibitors in Trypanosoma brucei Rostamighadi M, Kamelshahroudi A, Pitsitikas V, Jacobson KA, Salavati R. ACS Infect Dis. 2024 Sep 13;10(9):3289-3303.
• Piplartine attenuates aminoglycoside-induced TRPV1 activity and protects from hearing loss in mice Zallocchi M, Vijayakumar S, Fleegel J, Batalkina L, Brunette KE, Shukal D, Chen Z, Devuyst O, Liu H, He DZZ, Imami AS, Hamoud AA, McCullumsmith R, Conda-Sheridan M, De Campos LJ, Zuo J. Sci Transl Med. 2024 Aug 7;16(759):eadn2140.
• Structure-based pharmacophore modeling for precision inhibition of mutant ESR2 in breast cancer: A systematic computational approach Islam S, Amin MA, Rengasamy KRR, Mohiuddin AKM, Mahmud S. Cancer Med. 2024 Aug;13(15):e70074.
• Direct synthesis, characterization, in vitro and in silico studies of simple chalcones as potential antimicrobial and antileishmanial agents Ur Rashid H, Khan S, Irum, Khan A, Ahmad N, Shah T, Khan K. R Soc Open Sci. 2024 Jun 26;11(6):240410.
• Exploring essential oil-based bio-composites: molecular docking and in vitro analysis for oral bacterial biofilm inhibition Ullah N, Hasnain SZU, Baloch R, Amin A, Nasibova A, Selakovic D, Rosic GL, Islamov S, Naraliyeva N, Jaradat N, Mammadova AO. Front Chem. 2024 Jul 17;12:1383620.
• Design, synthesis, molecular docking and in vitro anticancer activities of 1-(4-(benzamido)phenyl)-3-arylurea derivatives Sabale P, Sayyad N, Ali A, Sabale V, Kaleem M, Asar TO, Ali A, Mujtaba MA, Anwer MK. RSC Adv. 2024 Jul 29;14(33):23785-23795.
• Computational approach for drug discovery against Gardnerella vaginalis in quest for safer and effective treatments for bacterial vaginosis Fan C, Basharat Z, Mah K, Wei CR. Sci Rep. 2024 Jul 29;14(1):17437.
• Repurposing FDA approved drugs against monkeypox virus DNA dependent RNA polymerase: virtual screening, normal mode analysis and molecular dynamics simulation studies Khan AAS, Yousaf MA, Azhar J, Maqbool MF, Bibi R. Virusdisease. 2024 Jun;35(2):260-270.
• Site specific binding pattern of benzodiazepines with GABAA receptor and related impact on their activities in the human body: An in silico method based study Roy MS, Sarkar BK, Kundu SK. Heliyon. 2024 Jul 2;10(13):e33929.
• Uncovering the anti-breast cancer activity potential of east Kalimantan propolis by In vitro and bioinformatics analysis Mariana Kustiawan P, Siregar KAAK, Syaifie PH, Zein Muttaqin F, Ibadillah D, Miftah Jauhar M, Djamas N, Mardliyati E, Taufiqu Rochman N. Heliyon. 2024 Jun 25;10(13):e33636.
• Revolutionizing Nipah virus vaccinology: insights into subunit vaccine development strategies and immunological advances Das T, Datta S, Sen A. In Silico Pharmacol. 2024 Jul 27;12(2):69.
• Optimizing the resveratrol fragments for novel in silico hepatocellular carcinoma de novo drug design Naveed M, Javed K, Aziz T, Abid A, Rehman HM, Alharbi M, Alshammari A, Alasmari AF. Sci Rep. 2024 Aug 20;14(1):19324.
• Naturally Derived Terpenoids Targeting the 3Dpol of Foot-and-Mouth Disease Virus: An Integrated In Silico and In Vitro Investigation Mana N, Theerawatanasirikul S, Semkum P, Lekcharoensuk P. Viruses. 2024 Jul 14;16(7):1128.
• Computational Exploration of Potential Pharmacological Inhibitors Targeting the Envelope Protein of the Kyasanur Forest Disease Virus Achappa S, Aldabaan NA, Desai SV, Muddapur UM, Shaikh IA, Mahnashi MH, Alshehri AA, Mannasaheb BA, Khan AA. Pharmaceuticals (Basel). 2024 Jul 3;17(7):884.
• Cytotoxic Potential of Betulinic Acid Fatty Esters and Their Liposomal Formulations: Targeting Breast, Colon, and Lung Cancer Cell Line Milan A, Mioc M, Mioc A, Gogulescu A, Mardale G, Avram Ș, Maksimović T, Mara B, Șoica C. Molecules. 2024 Jul 19;29(14):3399.
• Molecular Mechanisms of Resistance against PSII-Inhibiting Herbicides in Amaranthus retroflexus from the Czech Republic Mikulka J, Sen MK, Košnarová P, Hamouz P, Hamouzová K, Sur VP, Šuk J, Bhattacharya S, Soukup J. Genes (Basel). 2024 Jul 11;15(7):904.
• In Silico Comparative Analysis of Ivermectin and Nirmatrelvir Inhibitors Interacting with the SARS-CoV-2 Main Protease de Oliveira Só YA, Bezerra KS, Gargano R, Mendonça FLL, Souto JT, Fulco UL, Pereira Junior ML, Junior LAR. Biomolecules. 2024 Jun 25;14(7):755.
• In-silico study unveils potential phytocompounds in Andrographis paniculata against E6 protein of the high-risk HPV-16 subtype for cervical cancer therapy Islam MA, Hossain MS, Hasnat S, Shuvo MH, Akter S, Maria MA, Tahcin A, Hossain MA, Hoque MN. Sci Rep. 2024 Jul 26;14(1):17182.
• Analysis of the anti-Alzheimer potential of bioactive compounds from Citrus hystrix DC. peel, leaf, and essential oil by network pharmacology Putri AF, Utomo DH, Tunjung WAS, Putri WA. Heliyon. 2024 Jun 26;10(13):e33496.
• Identification of potent inhibitors of HDAC2 from herbal products for the treatment of colon cancer: Molecular docking, molecular dynamics simulation, MM/GBSA calculations, DFT studies, and pharmacokinetic analysis Khanal M, Acharya A, Maharjan R, Gyawali K, Adhikari R, Mulmi DD, Lamichhane TR, Lamichhane HP. PLoS One. 2024 Jul 22;19(7):e0307501.
• Antibacterial activities, PASS prediction and ADME analysis of phytochemicals from Curcubita moschata, Curcubita maxima, and Irvingia gabonensis: insights from in silico studies Abdul-Hammed M, Adedotun IO, Akinboade MW, Adegboyega TA, Salaudeen OM. In Silico Pharmacol. 2024 Jul 17;12(2):65.
• Cimicifugin, a broad-spectrum inhibitor of Theileria annulata and Plasmodium falciparum CDK7 Kar PP, Araveti PB, Saxena K, Borah A, Sijwali P, Srivastava A. Antimicrob Agents Chemother. 2024 Aug 7;68(8):e0044024.
• Exploring the potential mechanisms of Danshen against COVID-19 via network pharmacology analysis and molecular docking Zhang Q, Liang Z, Wang X, Zhang S, Yang Z. Sci Rep. 2024 Jun 4;14(1):12780.
• Hippo and PI5P4K signaling intersect to control the transcriptional activation of YAP Palamiuc L, Johnson JL, Haratipour Z, Loughran RM, Choi WJ, Arora GK, Tieu V, Ly K, Llorente A, Crabtree S, Wong JCY, Ravi A, Wiederhold T, Murad R, Blind RD, Emerling BM. Sci Signal. 2024 May 28;17(838):eado6266.
• Design and synthesis of new dihydropyrimidine/sulphonamide hybrids as promising anti-inflammatory agents via dual mPGES-1/5-LOX inhibition Al-Wahaibi LH, Elshamsy AM, Ali TFS, Youssif BGM, Bräse S, Abdel-Aziz M, El-Koussi NA. Front Chem. 2024 May 10;12:1387923.
• Network Pharmacology and Experimental Validation to Explore the Potential Mechanism of Nigella sativa for the Treatment of Breast Cancer Arif R, Bukhari SA, Mustafa G, Ahmed S, Albeshr MF. Pharmaceuticals (Basel). 2024 May 10;17(5):617.
• In Silico Design of Potential Small-Molecule Antibiotic Adjuvants against Salmonella typhimurium Ortho Acetyl Sulphydrylase Synthase to Address Antimicrobial Resistance Elebiju OF, Oduselu GO, Ogunnupebi TA, Ajani OO, Adebiyi E. Pharmaceuticals (Basel). 2024 Apr 23;17(5):543.
• Identification of Genes Crucial for Biological Processes in Breast Cancer Liver Metastasis Relapse Kwok T, Yeguvapalli S, Chitrala KN. Int J Mol Sci. 2024 May 16;25(10):5439.
• Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation Analysis Reveal Insights into the Molecular Mechanism of Cordia myxa in the Treatment of Liver Cancer Li L, Mohammed AH, Auda NA, Alsallameh SMS, Albekairi NA, Muhseen ZT, Butch C. Biology (Basel). 2024 May 1;13(5):315.
• Design and synthesis of Meldrum’s acid based 7-azaindole anchored 1,2,3-triazole hybrids as anticancer agents Vanga MK, Bhukya R, Thumma V, Ambadipudi SSSSS, Nayak VL, Andugulapati SB, Manga V. RSC Med Chem. 2024 Mar 11;15(5):1709-1721.
• Unveiling the molecular basis of paracetamol-induced hepatotoxicity: Interaction of N-acetyl-p-benzoquinone imine with mitochondrial succinate dehydrogenase Hossen MS, Akter A, Azmal M, Rayhan M, Islam KS, Islam MM, Ahmed S, Abdullah-Al-Shoeb M. Biochem Biophys Rep. 2024 May 7;38:101727.
• Integrating Network Pharmacology and Molecular Docking Approach to Elucidate the Mechanism of Commiphora wightii for the Treatment of Rheumatoid Arthritis Abdel-Maksoud MA, Askar MA, Abdel-Rahman IY, Gharib M, Aufy M. Bioinform Biol Insights. 2024 May 18;18:11779322241247634.
• Effect of Calebin-A on Critical Genes Related to NAFLD: A Protein-Protein Interaction Network and Molecular Docking Study Mahmoudi A, Hajihasani MM, Majeed M, Jamialahmadi T, Sahebkar A. Curr Genomics. 2024 Apr 8;25(2):120-139.
• Exploring optimal drug targets through subtractive proteomics analysis and pangenomic insights for tailored drug design in tuberculosis Khan MF, Ali A, Rehman HM, Noor Khan S, Hammad HM, Waseem M, Wu Y, Clark TG, Jabbar A. Sci Rep. 2024 May 13;14(1):10904.
• Abrogation of ORF8-IRF3 binding interface with Carbon nanotube derivatives to rescue the host immune system against SARS-CoV-2 by using molecular screening and simulation approaches Suleman M, Murshed A, Imran K, Khan A, Ali Z, Albekairi NA, Wei DQ, Yassine HM, Crovella S. BMC Chem. 2024 May 11;18(1):99.
• Anticholinesterase Activity of Methanolic Extract of Amorpha fruticosa Flowers and Isolation of Rotenoids and Putrescine and Spermidine Derivatives Jankovská D, Jurčová N, Kubínová R, Václavík J, Švajdlenka E, Mascellani A, Maršík P, Bouzková K, Malaník M. Plants (Basel). 2024 Apr 24;13(9):1181.
• Transcriptomic analysis revealed potential regulatory biomarkers and repurposable drugs for breast cancer treatment Shornale Akter M, Uddin MH, Atikur Rahman S, Hossain MA, Ashik MAR, Zaman NN, Faruk O, Hossain MS, Parvin A, Rahman MH. Cancer Rep (Hoboken). 2024 May;7(5):e2009.
• Subtractive genomics study for the identification of therapeutic targets against Cronobacter sakazakii: A threat to infants Ahammad I, Bushra Lamisa A, Sharmin S, Bhattacharjee A, Mahmud Chowdhury Z, Ahamed T, Uzzal Hossain M, Chandra Das K, Salimullah M, Ara Keya C. Heliyon. 2024 Apr 25;10(9):e30332.
• Sinefungin analogs targeting VP39 methyltransferase as potential anti-monkeypox therapeutics: a multi-step computational approach Abouzied AS, Huwaimel B, Alqarni S, Younes KM, Alshammari RE, Alshammari AH, Algharbi WF, Elkashlan AM. Mol Divers. 2024 May 4. doi: 10.1007/s11030-024-10875-z.
• The promising antioxidant effects of lignans: Nrf2 activation comes into view Hassanein EHM, Althagafy HS, Baraka MA, Abd-Alhameed EK, Ibrahim IM, Abd El-Maksoud MS, Mohamed NM, Ross SA. Arch Pharmacol. 2024 Sep;397(9):6439-6458.
• Identification of Helicobacter pylori-carcinogenic TNF-alpha-inducing protein inhibitors via daidzein derivatives through computational approaches Tayyeb JZ, Mondal S, Anisur Rahman M, Kumar S, Bayıl I, Akash S, Hossain MS, Alqahtani T, Zaki MEA, Oliveira JIN. J Cell Mol Med. 2024 May;28(9):e18358.
• Identification of Metabolites from Catharanthus roseus Leaves and Stem Extract, and In Vitro and In Silico Antibacterial Activity against Food Pathogens Jamal QMS, Ahmad V. Pharmaceuticals (Basel). 2024 Mar 30;17(4):450.
• Characterization of Plant-Derived Natural Inhibitors of Dipeptidyl Peptidase-4 as Potential Antidiabetic Agents: A Computational Study Hossain A, Rahman ME, Faruqe MO, Saif A, Suhi S, Zaman R, Hirad AH, Matin MN, Rabbee MF, Baek KH. Pharmaceutics. 2024 Apr 1;16(4):483.
• Identification of bio-active secondary metabolites from Actinobacteria as potential drug targets against Porphyromonas gingivalis in oral squamous cell carcinoma using molecular docking and dynamics study Taj Z, Chattopadhyay I. In Silico Pharmacol. 2024 Apr 23;12(1):34.
• From desert flora to cancer therapy: systematic exploration of multi-pathway mechanisms using network pharmacology and molecular modeling approaches Alblihy A. Front Pharmacol. 2024 Apr 11;15:1345415.
• Design, synthesis, and cytotoxicity of ibuprofen-appended benzoxazole analogues against human breast adenocarcinoma Thumma V, Mallikanti V, Matta R, Dharavath R, Jalapathi P. RSC Med Chem. 2024 Jan 2;15(4):1283-1294.
• Design, synthesis, and bioevaluation of novel unsaturated cyanoacetamide derivatives: In vitro and in silico exploration Uddin KM, Meem MH, Akter M, Rahman S, Al-Gawati MA, Alarifi N, Albrithen H, Alodhayb A, Poirier RA, Bhuiyan MMH. MethodsX. 2024 Apr 9;12:102691.
• Bioactive compounds from Morchella esculenta as potential inhibitors of RNA-binding protein La in ovarian cancer: a molecular modeling and quantum mechanics approach Dairo G, Ward MN, Soendergaard M, Determan JJ. In Silico Pharmacol. 2024 Apr 20;12(1):32.
• A novel class of inhibitors that disrupts the stability of integrin heterodimers identified by CRISPR-tiling-instructed genetic screens Mattson NM, Chan AKN, Miyashita K, Mukhaleva E, Chang WH, Yang L, Ma N, Wang Y, Pokharel SP, Li M, Liu Q, Xu X, Chen R, Singh P, Zhang L, Elsayed Z, Chen B, Keen D, Pirrotte P, Rosen ST, Chen J, LaBarge MA, Shively JE, Vaidehi N, Rockne RC, Feng M, Chen CW. Nat Struct Mol Biol. 2024 Feb 5. doi: 10.1038/s41594-024-01211-y.
• Synthesis, crystal structure and computational analysis of 2,7-bis-(4-chloro-phen-yl)-3,3-dimethyl-1,4-diazepan-5-one Akila S, Vidhyasagar T, Winfred Jebaraj JP, Thiruvalluvar AA, Rajeswari K. Acta Crystallogr E Crystallogr Commun. 2023 Nov 30;79(Pt 12):1212-1217.
• Exploring the effectiveness of flavone derivatives for treating liver diseases: Utilizing DFT, molecular docking, and molecular dynamics techniques Quayum ST, Esha NJI, Siraji S, Abbad SSA, Alsunaidi ZHA, Almatarneh MH, Rahman S, Alodhayb AN, Alibrahim KA, Kawsar SMA, Uddin KM. MethodsX. 2023 Dec 29;12:102537.
• Targeting myostatin using quercetin as a media supplement to improve myogenesis for cultured meat production: An in silico and in vitro study Ahmad SS, Lim JH, Ahmad K, Chun HJ, Hur SJ, Lee EJ, Choi I. Curr Res Food Sci. 2024 Jan 12;8:100678.
• Polyoxometalates Mediated Amyloid Fibrillation Dynamics and Restoration of Enzyme Activity of Hen Egg White Lysozyme Treated under Cold Atmospheric Pressure Plasma Kalita K, Phukan SJ, Garai S, Sankaranarayanan K. ACS Omega. 2024 Jan 8;9(3):3423-3429.
• Occurrence and characterization of β-lactamase-producing bacteria in biomedical wastewater and in silico enhancement of antibiotic efficacy Mannan SJ, Akash S, Jahin SA, Saqif AT, Begum K, Yasmin M, Ahsan CR, Sitotaw B, Dawoud TM, Nafidi HA, Bourhia M. Front Microbiol. 2024 Jan 8;14:1292597.
• Integrating network pharmacology and experimental verification to decipher the multitarget pharmacological mechanism of Cinnamomum zeylanicum essential oil in treating inflammation Mohanty D, Padhee S, Sahoo C, Jena S, Sahoo A, Chandra Panda P, Nayak S, Ray A. Heliyon. 2024 Jan 10;10(2):e24120.
• Ketoprofen attenuates Las/Rhl quorum-sensing (QS) systems of Pseudomonas aeruginosa: molecular and docking studies Mirpour M, Zahmatkesh H. Mol Biol Rep. 2024 Jan 18;51(1):133.
• The natural breakthrough: phytochemicals as potent therapeutic agents against spinocerebellar ataxia type 3 Naveed M, Ali N, Aziz T, Hanif N, Fatima M, Ali I, Alharbi M, Alasmari AF, Albekairi TH. Sci Rep. 2024 Jan 17;14(1):1529.
• Icariin prevents methylmercury-induced experimental neurotoxicity: Evidence from cerebrospinal fluid, blood plasma, brain samples, and in-silico investigations Sharma S, Mehan S, Khan Z, Gupta GD, Narula AS. Heliyon. 2024 Jan 6;10(1):e24050.
• Identification of Leading Compounds from Euphorbia neriifolia (Dudsor) Extracts as a Potential Inhibitor of SARS-CoV-2 ACE2-RBDS1 Receptor Complex: An Insight from Molecular Docking ADMET Profiling and MD-simulation Studies Islam MN, Pramanik MEA, Hossain MA, Rahman MH, Hossen MS, Islam MA, Miah MMZ, Ahmed I, Hossain AM, Haque MJ, Islam AM, Ali MN, Jahan RA, Haque ME, Rahman MM, Hasan MS, Rahman MM, Kabir MM, Basak PM, Sarkar MAM, Islam MS, Rahman MR, Prodhan AA, Mosaddik A, Haque H, Fahmin F, Das HS, Islam MM, Emtia C, Gofur MR, Liang A, Akbar SMF. Euroasian J Hepatogastroenterol. 2023 Jul-Dec;13(2):89-107.
• In silico and in vitro prediction of new synthesized N-heterocyclic compounds as anti-SARS-CoV-2 Hashem HE, Ahmad S, Kumer A, Bakri YE. Sci Rep. 2024 Jan 11;14(1):1152.
• Vaccinia-related kinase 2 variants differentially affect breast cancer growth by regulating kinase activity Gwak SH, Lee J, Oh E, Lee D, Han W, Kim J, Kim KT. Oncol Res. 2023 Dec 28;32(2):421-432.
• Identification of apigenin-4′-glucoside as bacterial DNA gyrase inhibitor by QSAR modeling, molecular docking, DFT, molecular dynamics, and in vitro confirmation studies Harini M, Kavitha K, Prabakaran V, Krithika A, Dinesh S, Rajalakshmi A, Suresh G, Puvanakrishnan R, Ramesh B. J Mol Model. 2024 Jan 3;30(1):22.

See also Older Publications Using PyRx.