Journal of Biomolecular Structure and Dynamics, Volume 42, Issue 3 (2024)

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Journal of Biomolecular Structure and Dynamics, Volume 42, Issue 3 (2024)

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Research Articles

Article
Integrated virtual screening and molecular dynamics simulation approaches revealed potential natural inhibitors for DNMT1 as therapeutic solution for triple negative breast cancer
Yasir Bashir, Fatima Noor, Sajjad Ahmad, Muhammad Hamza Tariq, Muhammad Qasim, Muhammad Tahir ul Qamar, Ahmad Almatroudi, Khaled S. Allemailem, Faris Alrumaihi & Faez Falah Alshehri
Pages: 1099-1109
Published online: 06 Apr 2023
AbstractforIntegrated virtual screening and molecular dynamics simulation approaches revealed potential natural inhibitors for DNMT1 as therapeutic solution for triple negative breast cancer | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 328 Views
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Article
Structure-based molecular networking, molecular docking, dynamics simulation and pharmacokinetic studies of Olax subscorpioidea for identification of potential inhibitors against selected cancer targets
Akolade R. Oladipupo, Stephenie C. A. Alaribe, Adeniyi S. Ogunlaja, Mehdi A. Beniddir, Allen T. Gordon, Celina O. Ogah, Joy Okpuzor & Herbert A. B. Coker
Pages: 1110-1125
Published online: 08 Apr 2023
AbstractforStructure-based molecular networking, molecular docking, dynamics simulation and pharmacokinetic studies of Olax subscorpioidea for identification of potential inhibitors against selected cancer targets | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 270 Views
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Article
Identification of potential natural products derived from fungus growing termite, inhibiting Pseudomonas aeruginosa quorum sensing protein LasR using molecular docking and molecular dynamics simulation approach
Muhammad Shoaib, Yasir Ali, Yulong Shen & Jinfeng Ni
Pages: 1126-1144
Published online: 25 Apr 2023
AbstractforIdentification of potential natural products derived from fungus growing termite, inhibiting Pseudomonas aeruginosa quorum sensing protein LasR using molecular docking and molecular dynamics simulation approach | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 241 Views
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Article
Engineering of surface-modified CuBTC-MXene nanocarrier for adsorption and co-loading of curcumin/paclitaxel from aqueous solutions for synergistic multi-therapy of cancer
Parisa Taherpoor, Farzaneh Farzad & Ameneh Zaboli
Pages: 1145-1156
Published online: 17 Apr 2023
AbstractforEngineering of surface-modified CuBTC-MXene nanocarrier for adsorption and co-loading of curcumin/paclitaxel from aqueous solutions for synergistic multi-therapy of cancer | Full Text | References | PDF (2.7 MB) | EPUB
  • 207 Views
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Article
Structure-based virtual screening and molecular dynamics approaches to identify new inhibitors of Staphylococcus aureus sortase A
Mehr Ali Mahmood Janlou, Hassan Sahebjamee, Mohsen Yazdani & Leila Fozouni
Pages: 1157-1169
Published online: 15 May 2023
AbstractforStructure-based virtual screening and molecular dynamics approaches to identify new inhibitors of Staphylococcus aureus sortase A | Full Text | References | PDF (1.8 MB) | EPUB
  • 184 Views
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Article
Study of the binding interaction of salmon sperm DNA with nintedanib, a tyrosine kinase inhibitor using multi-spectroscopic, thermodynamic, and in silico approaches
Aya Saad Radwan, Mohamed M. Salim, Mahmoud M. Elkhoudary, Ghada M. Hadad, Moataz A. Shaldam, Fathalla Belal & Galal Magdy
Pages: 1170-1180
Published online: 20 Apr 2023
AbstractforStudy of the binding interaction of salmon sperm DNA with nintedanib, a tyrosine kinase inhibitor using multi-spectroscopic, thermodynamic, and in silico approaches | Full Text | References | PDF (1.6 MB) | EPUB
  • 121 Views
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Article
Structural insights into the mechanism of resistance to bicalutamide by the clinical mutations in androgen receptor in chemo-treatment resistant prostate cancer
Abdul Majeed, Muhammad Tahir ul Qamar, Arooma Maryam, Muhammad Usman Mirza, Laila Alhussain, Seham Obaid Al Otaibi, Ahmad Almatroudi, Khaled S. Allemailem, Faris Alrumaihi, Abdulaziz A. Aloliqi & Faez Falah Alshehri
Pages: 1181-1190
Published online: 05 May 2023
AbstractforStructural insights into the mechanism of resistance to bicalutamide by the clinical mutations in androgen receptor in chemo-treatment resistant prostate cancer | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 309 Views
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Article
Investigation of new 1,2,3-triazolyl-quinolinyl-propan-2-ol derivatives as potential antimicrobial agents: in vitro and in silico approach
Abhijit D. Shinde, Yogesh M. Nandurkar, Swapnil Bhalekar, Yogesh S. Walunj, Sandip Ugale, Iqrar Ahmad, Harun Patel, Abhijit P. Chavan & Pravin C. Mhaske
Pages: 1191-1207
Published online: 30 May 2023
AbstractforInvestigation of new 1,2,3-triazolyl-quinolinyl-propan-2-ol derivatives as potential antimicrobial agents: in vitro and in silico approach | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 156 Views
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Article
Possible cerebroprotective effect of citronellal: molecular docking, MD simulation and in vivo investigations
G. Vamshi, Prasanth D. S. N. B. K.A. Sampath, Manjunath Dammalli, Pankaj Kumar, Gowrishankar B.S.Praveen Kumar Pasala, G. Somasekhar, Madhusudhana Chetty Challa, Ramesh Alluril & Venkata Ramireddy Narala
Pages: 1208-1219
Published online: 07 Jun 2023
AbstractforPossible cerebroprotective effect of citronellal: molecular docking, MD simulation and in vivo investigations | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 210 Views
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Article
A biochemistry‐oriented drug design: synthesis, anticancer activity, enzymes inhibition, molecular docking studies of novel 1,2,4-triazole derivatives
Karpenko Yuriy, Gulnur Kusdemir, Parchenko Volodymyr, Burak Tüzün, Parham Taslimi, Omer Faruk Karatas, Khilkovets Anastasia, Parchenko Maryna & Koray Sayın
Pages: 1220-1236
Published online: 06 Sep 2023
AbstractforA biochemistry‐oriented drug design: synthesis, anticancer activity, enzymes inhibition, molecular docking studies of novel 1,2,4-triazole derivatives | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 399 Views
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Article
Hypothetical confirmation for the anti-bacterial compound potassium succinate-succinic acid in comparison with certain succinate derivatives
X. D. Divya Dexlin, J. D. Deephlin Tarika, A. Arun Kumar & T. Joselin Beaula
Pages: 1237-1248
Published online: 06 Apr 2023
AbstractforHypothetical confirmation for the anti-bacterial compound potassium succinate-succinic acid in comparison with certain succinate derivatives | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 110 Views
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Article
Identification of potentially high drug-like VEGFR2/c-Met dual-target type II kinase inhibitors with symmetric skeletons based on structural screening
Jiali Xie, Xiaoxuan Zhang, Dan Meng, Yihao Li & Ping Deng
Pages: 1249-1267
Published online: 12 Apr 2023
AbstractforIdentification of potentially high drug-like VEGFR2/c-Met dual-target type II kinase inhibitors with symmetric skeletons based on structural screening | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 149 Views
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Article
Molecular modeling of ARF6 dysregulation caused by mutations in IQSEC2
Michael Shokhen, Randall Walikonis, Vladimir N. Uversky, Amnon Allbeck, Camryn Zezelic, Danielle Feldman, Nina S. Levy & Andrew P. Levy
Pages: 1268-1279
Published online: 20 Apr 2023
AbstractforMolecular modeling of ARF6 dysregulation caused by mutations in IQSEC2 | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 699 Views
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Open Access
Article
Synthesis and anxiolytic effect of europium metallic complex containing lapachol [Eu(DBM)3. LAP] in adult zebrafish through serotonergic neurotransmission: in vivo and in silico approach
Jorge Fernando Silva de Menezes, Andrei Marcelino Sá Pires Silva, Edna Aparecida Faria de Almeida, Ananias Freire da Silva, Julia Morais Bomfim De Lima, Antonio Wlisses da Silva, Maria Kueirislene Amâncio Ferreira, Jane Eire Silva Alencar de Menezes, Hélcio Silva dos Santos, Emmanuel Silva Marinho, Gabrielle Silva Marinho & Aluísio Marques da Fonseca
Pages: 1280-1292
Published online: 08 Apr 2023
AbstractforSynthesis and anxiolytic effect of europium metallic complex containing lapachol [Eu(DBM)3. LAP] in adult zebrafish through serotonergic neurotransmission: in vivo and in silico approach | Full Text | References | PDF (1.8 MB) | EPUB
  • 249 Views
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Article
Elucidation of conserved multi-epitope vaccine against Leishmania donovani using reverse vaccinology
Manas Ranjan Dikhit & Abhik Sen
Pages: 1293-1306
Published online: 13 Apr 2023
AbstractforElucidation of conserved multi-epitope vaccine against Leishmania donovani using reverse vaccinology | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 192 Views
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Article
Repurposing the inhibitors of MMP-9 and SGLT-2 against ubiquitin specific protease 30 in Parkinson’s disease: computational modelling studies
Mohammed M. Alshehri, Ammar Usman Danazumi, Mohammed Kanan Alshammari, Ridwan Opeyemi Bello, Mohammed Khalid Alghazwni, Ahmed Mughram Alshehri, Omaymah Mohammed Alshlali & Haruna Isiyaku Umar
Pages: 1307-1318
Published online: 03 May 2023
AbstractforRepurposing the inhibitors of MMP-9 and SGLT-2 against ubiquitin specific protease 30 in Parkinson’s disease: computational modelling studies | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 281 Views
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Article
Design and characterization of a binary CT complex of imidazole-oxyresveratrol: exploring its pharmacological and computational aspects
Nisat Alam, Maidul Islam, Hasina Najnin, Sonam Shakya, Ishaat M. Khan, Md. Wamique Hossain & Rana Zaidi
Pages: 1319-1335
Published online: 13 Apr 2023
AbstractforDesign and characterization of a binary CT complex of imidazole-oxyresveratrol: exploring its pharmacological and computational aspects | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 126 Views
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Article
SPP1, a potential therapeutic target and biomarker for lung cancer: functional insights through computational studies
Yamuna Annadurai, Murugesh Easwaran, Shobana Sundar, Lokesh Thangamani, Arun Meyyazhagan, Arunkumar Malaisamy, Jeyakumar Natarajan & Shanmughavel Piramanayagam
Pages: 1336-1351
Published online: 25 Apr 2023
AbstractforSPP1, a potential therapeutic target and biomarker for lung cancer: functional insights through computational studies | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 205 Views
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Article
Targeting neuroblastoma by small-molecule inhibitors of human ALYREF protein: mechanistic insights using molecular dynamics simulations
Nidhi Goswami, Archana Singh, Shiv Bharadwaj, Amaresh Kumar Sahoo & Indrakant K. Singh
Pages: 1352-1367
Published online: 09 May 2023
AbstractforTargeting neuroblastoma by small-molecule inhibitors of human ALYREF protein: mechanistic insights using molecular dynamics simulations | Full Text | References | PDF (2.5 MB) | EPUB
  • 250 Views
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Article
GC–MS screening of the phytochemical composition of Ziziphus honey: ADME properties and in vitro/in silico study of its antimicrobial activity
Nouha Bouali, Iqrar Ahmad, Harun Patel, Elham Bader Alhejaili, Walid Sabri Hamadou, Riadh Badraoui, Ramzi Hadj Lajimi, Mousa Alreshidi, Arif Jamal Siddiqui, Mohd Adnan, Mohammad A. Abdulhakeem, Abdulrahman S. Bazaid, Mitesh Patel, Mohd Saeed, Mejdi Snoussi & Emira Noumi
Pages: 1368-1380
Published online: 16 May 2023
AbstractforGC–MS screening of the phytochemical composition of Ziziphus honey: ADME properties and in vitro/in silico study of its antimicrobial activity | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 242 Views
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Article
Synthesis, anticancer activity, molecular docking and molecular dynamics studies of some pyrazole–chalcone hybrids
Ahmed A. Al Otaibi, Sinad L. Alshammari, Abdulmohsen Khalaf Dhahi Alsukaibi, Azfar Jamal, Saravanan Rajendrasozhan, Khalaf M. Alenezi, Afzal Hussain, Imran Khan, Md. Mushtaque & Ashanul Haque
Pages: 1381-1391
Published online: 18 Apr 2023
AbstractforSynthesis, anticancer activity, molecular docking and molecular dynamics studies of some pyrazole–chalcone hybrids | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 200 Views
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Article
Biophysical insights on the interaction of anticoagulant drug dicoumarol with calf thymus-DNA: deciphering the binding mode and binding force with thermodynamics
K. Lavanya, Jagadeesan Saranya, Anna Tanuja Safala Bodapati, Ragaiahgari Srinivas Reddy, Shravya Rao Madku & Bijaya Ketan Sahoo
Pages: 1392-1403
Published online: 10 Apr 2023
AbstractforBiophysical insights on the interaction of anticoagulant drug dicoumarol with calf thymus-DNA: deciphering the binding mode and binding force with thermodynamics | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 168 Views
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Article
In silico study of antibacterial tyrosyl-tRNA synthetase and toxicity of main phytoconstituents from three active essential oils
Meriem Elkolli, Hayet Elkolli, Manawwer Alam & Yacine Benguerba
Pages: 1404-1416
Published online: 17 Apr 2023
AbstractforIn silico study of antibacterial tyrosyl-tRNA synthetase and toxicity of main phytoconstituents from three active essential oils | Full Text | References | PDF (1.7 MB) | EPUB
  • 99 Views
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Article
In silico drug repurposing by combining machine learning classification model and molecular dynamics to identify a potential OGT inhibitor
Pedro Henrique Rodrigues de Alencar Azevedo, Bruna Rachel de Britto Peçanha, Luiz Augusto Pinheiro Flores-Junior, Tatiana Fialho Alves, Luiza Rosaria Sousa Dias, Estela Maris Freitas Muri & Camilo Henrique da Silva Lima
Pages: 1417-1428
Published online: 13 Apr 2023
AbstractforIn silico drug repurposing by combining machine learning classification model and molecular dynamics to identify a potential OGT inhibitor | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 394 Views
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Article
Comparative modeling and enzymatic affinity of novel haloacid dehalogenase from Bacillus megaterium strain BHS1 isolated from alkaline Blue Lake in Turkey
Batool Hazim Wahhab, Habeebat Adekilekun Oyewusi, Roswanira Abdul Wahab, Mohammad Hakim Mohammad Hood, Azzmer Azzar Abdul Hamid, Marwan Salih Al-Nimer, Mohamed Faraj Edbeib, Yilmaz Kaya & Fahrul Huyop
Pages: 1429-1442
Published online: 10 Apr 2023
AbstractforComparative modeling and enzymatic affinity of novel haloacid dehalogenase from Bacillus megaterium strain BHS1 isolated from alkaline Blue Lake in Turkey | Full Text | References | PDF (2.7 MB) | EPUB
  • 202 Views
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Article
Clinical side-effects based drug repositioning for anti-epileptic activity
Pawan Kumar, Deepak Sheokand, Annu Grewal, Vandana Saini & Ajit Kumar
Pages: 1443-1454
Published online: 12 Apr 2023
AbstractforClinical side-effects based drug repositioning for anti-epileptic activity | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 206 Views
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Article
A biophysical approach of tyrphostin AG879 binding information in: bovine serum albumin, human ErbB2, c-RAF1 kinase, SARS-CoV-2 main protease and angiotensin-converting enzyme 2
Subramani Karthikeyan, Anandh Sundaramoorthy, Saravanan Kandasamy, Ganesan Bharanidharan, Prakasarao Aruna, Ramakrishnamurthy Suganya, Rajendiran Mangaiyarkarasi, Singaravelu Ganesan, Ganesh N. Pandian, Anitha Ramamoorthi & Shanmugavel Chinnathambi
Pages: 1455-1468
Published online: 28 Apr 2023
AbstractforA biophysical approach of tyrphostin AG879 binding information in: bovine serum albumin, human ErbB2, c-RAF1 kinase, SARS-CoV-2 main protease and angiotensin-converting enzyme 2 | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 141 Views
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Article
Acalabrutinib as a novel hope for the treatment of breast and lung cancer: an in-silico proof of concept
Kedar Khaparkhuntikar, Indrani Maji, Sunil Kumar Gupta, Srushti Mahajan, Mayur Aalhate, Anitha Sriram, Ujala Gupta, Santosh Kumar Guru, Prachi Kulkarni & Pankaj Kumar Singh
Pages: 1469-1484
Published online: 05 Jun 2023
AbstractforAcalabrutinib as a novel hope for the treatment of breast and lung cancer: an in-silico proof of concept | Full Text | References | PDF (2.5 MB) | EPUB
  • 201 Views
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Article
Identification and mechanistic exploration of structural and conformational dynamics of NF-kB inhibitors: rationale insights from in silico and in vitro studies
Amit Kumar Srivastava, Shubham Srivastava, Viney Kumar, Souvik Ghosh, Siddharth Yadav, Ruchi Malik, Partha Roy & Ramasare Prasad
Pages: 1485-1505
Published online: 13 Apr 2023
AbstractforIdentification and mechanistic exploration of structural and conformational dynamics of NF-kB inhibitors: rationale insights from in silico and in vitro studies | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 495 Views
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Article
In-silico identification of potential inhibitors against FabI protein in Klebsiella pneumoniae
Shama Khan, Shabir A Madhi & Courtney Olwagen
Pages: 1506-1517
Published online: 27 Apr 2023
AbstractforIn-silico identification of potential inhibitors against FabI protein in Klebsiella pneumoniae | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 181 Views
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Article
Computational identification and analysis of deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in the human POR gene: a structural and functional impact
Rajalakshmi Kumar, Manikandan Jayaraman, Krishna Ramadas & Adithan Chandrasekaran
Pages: 1518-1532
Published online: 12 May 2023
AbstractforComputational identification and analysis of deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in the human POR gene: a structural and functional impact | Full Text | References | PDF (2.5 MB) | EPUB
  • 130 Views
  • 1 CrossRef citations
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Article
Biophysical and in-silico studies on the structure-function relationship of Brugia malayi protein disulfide isomerase
Pawan Kumar Doharey, Pravesh Verma, Amit Dubey, Sudhir Kumar Singh, Manish Kumar, Timir Tripathi, Mona Alonazi, Nikhat Jamal Siddiqi & Bechan Sharma
Pages: 1533-1543
Published online: 20 Apr 2023
AbstractforBiophysical and in-silico studies on the structure-function relationship of Brugia malayi protein disulfide isomerase | Full Text | References | PDF (1.9 MB) | EPUB
  • 163 Views
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Article
Phytocompounds screening of Nigella sativa in terms of human cancer by targeting sphingosine kinase-1 and pyruvate kinase-M2: a study based on in silico analysis
Shahbaz Ahmed & Mohammad Tabish
Pages: 1544-1558
Published online: 17 May 2023
AbstractforPhytocompounds screening of Nigella sativa in terms of human cancer by targeting sphingosine kinase-1 and pyruvate kinase-M2: a study based on in silico analysis | Full Text | References | PDF (2.5 MB) | EPUB
  • 137 Views
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Article
Assessment of genotoxic instability markers in peripheral blood lymphocytes of breast cancer patients: a case control study
Smitha G. Raj & V. Rajitha
Pages: 1559-1563
Published online: 24 May 2023
AbstractforAssessment of genotoxic instability markers in peripheral blood lymphocytes of breast cancer patients: a case control study | Full Text | References | PDF (633.2 KB) | EPUB
  • 88 Views
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Review Articles

Review Article
An assessment of EGFR and HER2 inhibitors with structure activity relationship of fused pyrimidine derivatives for breast cancer: a brief review
Prasad Sanjay Dhiwar, Gurubasavaraja Swamy Purawarga Matada, Rohit Pal, Ekta Singh, Abhishek Ghara, Lalmohan Maji, Sindhuja Sengupta & Ganesh Andhale
Pages: 1564-1581
Published online: 09 May 2023
AbstractforAn assessment of EGFR and HER2 inhibitors with structure activity relationship of fused pyrimidine derivatives for breast cancer: a brief review | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 254 Views
  • 4 CrossRef citations
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Review Article
Explanatory review on pyrimidine/fused pyrimidine derivatives as anticancer agents targeting Src kinase
Ghanshyam Teli, Rohit Pal, Lalmohan Maji, Gurubasavaraja Swamy Purawarga Matada & Sindhuja Sengupta
Pages: 1582-1614
Published online: 05 May 2023
AbstractforExplanatory review on pyrimidine/fused pyrimidine derivatives as anticancer agents targeting Src kinase | Full Text | References | PDF (3.9 MB) | EPUB
  • 215 Views
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Correction

Correction
Correction
Page: 1615
Published online: 21 Jan 2024
CitationforCorrection | Full Text | PDF (367.1 KB) | EPUB
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