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Computer-Aided Drug Design

Guest Editor:
Abdulilah Ece: Biruni University, Turkey

BMC Chemistry has published this Collection focused on computer-aided drug design (CADD). Despite many advances, traditional approaches to drug design often fails to keep pace with the emerging needs of patients and researchers. A growing suite of computational and theoretical approaches have the potential to supercharge the drug discovery process across academia and industry.

Meet the Guest Editors

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Abdulilah Ece: Biruni University, Türkiye

Dr. Ece is an Associate Professor of Chemistry at the Computer-Aided Drug Design Center, Biruni University. He received two successive awards from Trinity College Dublin in 2017 and 2018. Dr. Ece organizes symposiums and hands-on training courses on Computer-Aided Drug Design. His research group (Ece Research) is mainly focused on computer-aided drug design & discovery. In that aspect, he uses both quantum chemical and molecular mechanics calculations. Supported by the leading software companies in the field and in collaboration with national/international researchers, Ece Research uses effective and specialized computational tools to address a particular problem or to enlighten an experimental finding in medicinal, organic or pharmaceutical chemistry.
Abdulilah has been serving as associate editor of BMC Chemistry since 2019.
 

About the collection

BMC Chemistry has published this Collection focused on computer-aided drug design (CADD). 

Drug design is a multi-step, multidisciplinary process that traditionally requires huge amounts of time and money to complete. New approaches are needed to go beyond the limitations of these traditional methods and advance drug discovery and optimization.

One such approach is computer-aided drug design (CADD), which comprises a suite of computational and theoretical approaches to drug discovery that are being developed and implemented at increasing speed across academia and industry.


Topics of interested to the collection included but were not limited to:

  • Molecular docking
  • 2D and 3D-pharmacophore modelling
  • Virtual screening
  • Molecular dynamics simulations
  • Quantitative structure-activity relationship (QSAR)
  • High Throughput Screening
  • High-Performance Computing
  • Bioinformatics & Cheminformatics
  • Ligand-based Drug Design
  • Structure-based Drug Design
  • Artificial intelligence, machine learning, and data mining in drug discovery & design
  • Molecular mechanics and quantum mechanics calculations
  • Statistics used in CADD

  1. Facing the significant challenge of overcoming drug resistance in cancer treatment, particularly resistance caused by mutations in epidermal growth factor receptor (EGFR), the aim of our study was to identify ...

    Authors: Linxiao Wang, Xiaoling Huang, Shidi Xu, Yufeng An, Xinya Lv, Wufu Zhu, Shan Xu, Yuanbiao Tu, Shuhui Chen, Qiaoli Lv and Pengwu Zheng
    Citation: BMC Chemistry 2024 18:159
    Content type: Research Published on:

  2. Cyclin-dependent kinase 8 (CDK8) has emerged as a promising target for inhibiting cancer cell function, intensifying efforts towards the development of CDK8 inhibitors as potential cancer therapeutics. Mutatio...

    Authors: Raziye Aghahasani, Fereshteh Shiri, Hossein Kamaladiny, Fatemeh Haddadi and Somayeh Pirhadi
    Citation: BMC Chemistry 2024 18:73
    Content type: Research Published on:

  3. In this article, we present the design and synthesis of amino-7,8-dihydro-4H-chromenone derivatives as possible inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) for the management of ...

    Authors: Ali Asadipour, Yaghoub Pourshojaei, Moein Mansouri, Elham Mahdavizadeh, Cambyz Irajie, Javad Mottaghipisheh, Ehsan Faghih-Mirzaei, Mohammad Mahdavi and Aida Iraji
    Citation: BMC Chemistry 2024 18:70
    Content type: Research Published on:

  5. Lung cancer is a disease with a high mortality rate and it is the number one cause of cancer death globally. Approximately 12–14% of non-small cell lung cancers are caused by mutations in KRASG12C. The KRASG12C i...

    Authors: Amar Ajmal, Hind A Alkhatabi, Roaa M. Alreemi, Mubarak A. Alamri, Asaad Khalid, Ashraf N. Abdalla, Bader S. Alotaibi and Abdul Wadood
    Citation: BMC Chemistry 2024 18:57
    Content type: Research Published on:

  7. A novel series of 1-(5-((6-nitroquinazoline-4-yl)thio)-1,3,4-thiadiazol-2-yl)-3-phenylurea derivatives 8 were designed and synthesized to evaluate their cytotoxic potencies. The structures of these obtained compo...

    Authors: Sara Masoudinia, Marjaneh Samadizadeh, Maliheh Safavi, Hamid Reza Bijanzadeh and Alireza Foroumadi
    Citation: BMC Chemistry 2024 18:30
    Content type: Research Published on:

  8. Undecaprenyl Pyrophosphate Synthase (UPPS) is a vital target enzyme in the early stages of bacterial cell wall biosynthesis. UPPS inhibitors have antibacterial activity against resistant strains such as MRSA a...

    Authors: Basma M. Qandeel, Samar Mowafy, Khaled Abouzid and Nahla A. Farag
    Citation: BMC Chemistry 2024 18:14
    Content type: Research Published on:

  9. In the current study we suggest a novel approach to curb non-alcoholic steatohepatitis (NASH) progression, and we suggest privileged scaffolds for the design of novel compounds for this aim. NASH is an advance...

    Authors: Yara A. Zaky, Mai W. Rashad, Marwa A. Zaater and Ahmed M. El Kerdawy
    Citation: BMC Chemistry 2024 18:2
    Content type: Research Published on:

  10. Mesalazine (5-ASA) is a medication utilized to treat inflammatory bowel diseases involving ulcerative colitis and Crohn’s disease. Mesalazine has fewer side effects but the low solubility and bioavailability o...

    Authors: Elina Armani, Parisa Jafari, Salar Hemmati, Elaheh Rahimpour, Mohammad Barzegar-Jalali and Abolghasem Jouyban
    Citation: BMC Chemistry 2023 17:171
    Content type: Research Published on:

  11. Melanoma presents increasing prevalence and poor outcomes. Progression to aggressive stages is characterized by overexpression of the transcription factor E2F1 and activation of downstream prometastatic gene r...

    Authors: Nivedita Singh, Faiz M Khan, Lakshmi Bala, Julio Vera, Olaf Wolkenhauer, Brigitte Pützer, Stella Logotheti and Shailendra K. Gupta
    Citation: BMC Chemistry 2023 17:161
    Content type: Research Published on:

  12. In this article for the first time the quantum calculations of 3-methyl-4-oxoimidazo[5,1-d][1,2,3,5]tetrazine-8-carboxamide (Temozolomide) in HCM-Cellulose Substrate are evaluated using the B3LYP/6-31G level o...

    Authors: Masoumeh Shahi and Fatemeh Azarakhshi
    Citation: BMC Chemistry 2023 17:114
    Content type: Research Published on:

  13. A new compound, C23H20BrN3OS, containing a quinoline-based iminothiazoline with a thiazoline ring, was synthesized and its crystal and molecular structures were analyzed through single crystal X-ray analysis. The...

    Authors: Muhammad Naeem Mustafa, Pervaiz Ali Channar, Syeda Abida Ejaz, Saira Afzal, Mubashir Aziz, Tahira Shamim, Aamer Saeed, Aisha A. Alsfouk, Rabail Ujan, Qamar Abbas and Tuncer Hökelek
    Citation: BMC Chemistry 2023 17:95
    Content type: Research Published on:

  14. The QSAR models are employed to predict the anti-proliferative activity of 81 derivatives of flavonol against prostate cancer using the Monte Carlo algorithm based on the index of ideality of correlation (IIC)...

    Authors: Faezeh Tajiani, Shahin Ahmadi, Shahram Lotfi, Parvin Kumar and Ali Almasirad
    Citation: BMC Chemistry 2023 17:87
    Content type: Research Published on:

  15. Epilepsy is a common neurological disorder. The available drugs for this disease only control convulsions in nearly 70% of patients, while bearing many side effects. In this study, a new series of phenoxypheny...

    Authors: Azadeh Fakhrioliaei, Fahimeh Abedinifar, Pedram Salehi Darjani, Maryam Mohammadi-Khanaposhtani, Bagher Larijani, Nematollah Ahangar and Mohammad Mahdavi
    Citation: BMC Chemistry 2023 17:80
    Content type: Research Published on:

  16. Lactate dehydrogenase (LDH) is a tetramer enzyme that converts pyruvate to lactate reversibly. This enzyme becomes important because it is associated with diseases such as cancers, heart disease, liver problem...

    Authors: Sedigheh Damavandi, Fereshteh Shiri, Abbasali Emamjomeh, Somayeh Pirhadi and Hamid Beyzaei
    Citation: BMC Chemistry 2023 17:70
    Content type: Research Published on:

  17. New series of biologically active triazole and pyrazole compounds containing 2, 4-disubstituted thiazole analogues (12a-l) were synthesized from p-hydroxy benzaldehyde and phenyl hydrazine in excellent yields ...

    Authors: Raghavender Matta, Jalapathi Pochampally, Bala Narsimha Dhoddi, Shankar Bhookya, Sampath Bitla and Anjini Gayatri Akkiraju
    Citation: BMC Chemistry 2023 17:61
    Content type: Research Published on:

  18. Computer-Aided Drug Design tools are now an indispensable part of drug discovery that have made key contributions to the development of drugs. In this editorial, I briefly provide an overview of CADD emphasizi...

    Authors: Abdulilah Ece
    Citation: BMC Chemistry 2023 17:26
    Content type: Editorial Published on:

Submission Guidelines

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This Collection welcomes submission of Research Articles. Before submitting your manuscript, please ensure you have read our submission guidelines. Articles for this Collection should be submitted via our submission system, Snapp. During the submission process you will be asked whether you are submitting to a Collection, please select "Computer Aided Drug Design" from the dropdown menu.

Articles will undergo the journal’s standard peer-review process and are subject to all of the journal’s standard policies. Articles will be added to the Collection as they are published.

The Guest Editors have no competing interests with the submissions which they handle through the peer review process. The peer review of any submissions for which the Guest Editors have competing interests is handled by another Editorial Board Member who has no competing interests.