1
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Hakami MA. Harnessing machine learning potential for personalised drug design and overcoming drug resistance. J Drug Target 2024; 32:918-930. [PMID: 38842417 DOI: 10.1080/1061186x.2024.2365934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 06/07/2024]
Abstract
Drug resistance in cancer treatment presents a significant challenge, necessitating innovative approaches to improve therapeutic efficacy. Integrating machine learning (ML) in cancer research is promising as ML algorithms outrival in analysing complex datasets, identifying patterns, and predicting treatment outcomes. Leveraging diverse data sources such as genomic profiles, clinical records, and drug response assays, ML uncovers molecular mechanisms of drug resistance, enabling personalised treatment, maximising efficacy and minimising adverse effects. Various ML algorithms contribute to the drug discovery process - Random Forest and Decision Trees predict drug-target interactions and aid in virtual screening, and SVM classify leads on bioactivity data. Neural Networks model QSAR to optimise lead compounds and K-means clustering group compounds with similar chemical properties aiding compound selection. Gaussian Processes predict drug responses, Bayesian Networks infer causal relationships, Autoencoders generate novel compounds, and Genetic Algorithms optimise molecular structures. These algorithms collectively enhance efficiency and success rates in drug design endeavours, from lead identification to optimisation and are cost-effective, empowering clinicians with real-time treatment monitoring and improving patient outcomes. This review highlights the immense potential of ML in revolutionising cancer care through effective drug design to reduce drug resistance, and we have also discussed various limitations and research gaps to understand better.
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Affiliation(s)
- Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah, Riyadh, Saudi Arabia
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2
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Helmi N, Hamadi A, Al-Amer OM, Madkhali HA, Oyouni AAA, Alqosaibi AI, Almulhim J, Alghamdi RM, Hakeem IJ, Rafeeq MM. Unveiling the potency of FDA-approved oxidopamine HBr for cervical cancer regulation and replication proteins. Med Oncol 2024; 41:223. [PMID: 39120789 DOI: 10.1007/s12032-024-02462-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024]
Abstract
Cervical Cancer remains a women's health concern worldwide and ranks among the most prevalent cancers, particularly in developing countries. Many women are diagnosed with cervical cancer, with a substantial number succumbing to the disease even after the availability of vaccines and drugs. The tumour microenvironment often exhibits immune evasion, including suppression of T-cell activity and altered cytokine, impacting the efficacy of therapeutic interventions and highlighting the need for treatments to modulate the immune response. Despite efforts to promote HPV vaccination and regular screenings, it causes many deaths, underscoring the urgent need for continued research, healthcare access, and rapid drug development or repurposing. In this study, we identified various proteins involved in cervical cancer cell cycle regulation and DNA replication proteins, performed the multitargeted docking with an FDA-approved library, and identified Oxidopamine HBr as a multitargeted drug. Studies extended with pharmacokinetics and compared with the standard values followed by DFT, which supported the compound as a multitargeted inhibitor. Further, the docked complexes were taken for the interaction fingerprints, and it was identified that there are many 9 polar, 5 hydrophobic, 2 aromatic, and 2 basic residues. We extended our studies for 100ns MD Simulation in water, and the computations explored the deviation and fluctuations under 2Å and many intermolecular interactions; the same trajectory files were used for the MM\GBSA studies. All the studies have supported the Oxidopamine HBr as a cervical cancer multitargeted inhibitor-however, experimental studies are needed before human use.
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Affiliation(s)
- Nawal Helmi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Abdullah Hamadi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Osama M Al-Amer
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Hassan A Madkhali
- Department of Pharmacology and Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | | | - Amany I Alqosaibi
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Jawaher Almulhim
- Department of Biological Sciences, King Faisal University, 31982, Alahsa, Saudi Arabia
| | - Rashed Mohammed Alghamdi
- Department of Laboratory Medicine, Faculty of Applied College, Al-Baha University, Al-Baha, Saudi Arabia
| | - Israa J Hakeem
- Department of Biological Sciences, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Misbahuddin M Rafeeq
- Department of Pharmacology, Faculty of Medicine, King Abdulaziz University, Rabigh, Jeddah, Saudi Arabia.
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3
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Lv H, Yang H, Duan Y, Yan C, Li G, Zhao G, Sun F, Feng Y, Li Y, Fu Y, Li Y, Zhao Z, Jia X. S-(N,N-diethyldithiocarbamoyl)-N-acetyl-l-cysteine for the treatment of non-small cell lung cancer through regulating NF-κB signalling pathway without neurotoxicity. J Drug Target 2024:1-14. [PMID: 38962807 DOI: 10.1080/1061186x.2024.2374037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 06/24/2024] [Indexed: 07/05/2024]
Abstract
The discovery of novel targeted agents for non-small cell lung cancer (NSCLC) remains an important research landscape due to the limited efficacy, side effects and drug resistance of current treatment options. Among many repurposed drugs, disulphiram (DSF) has shown the potential to target tumours. However, its unpleasant neurotoxicity greatly limits its use. A DSF derivative, S-(N,N-diethyldithiocarbamoyl)-N-acetyl-l-cysteine (DS-NAC), was synthesised against NSCLC. The therapeutic effects, mechanism and toxicities of DS-NAC were evaluated in A549 and H460 cells and the mouse model of in situ lung cancer. The in vitro results exhibited that DS-NAC had potent anti-proliferation, apoptotic, anti-metastasis and epithelial-mesenchymal transition (EMT) inhibition effects. In the orthotopic lung cancer mouse model, therapeutic effects of DS-NAC were better than those of DSF and were similar to docetaxel (DTX). Also, results from western blot and immunohistochemistry showed that DS-NAC in combination with copper exerted therapeutic effects via regulating NF-κB signalling pathway and ROS-related proteins such as HIF-1α, Nrf2 and PKC-δ rather than regulating ROS level directly. Moreover, the safety evaluation study showed that DS-NAC had low haematologic and hepatic toxicities in comparison with DTX as well as low neurological toxicity compared with DSF. DS-NAC could be a promising anti-lung cancer agent with a favourable safety profile.
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Affiliation(s)
- Huaiyou Lv
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology of Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, China
- School of Pharmaceutical Sciences, Key University Laboratory of Pharmaceutics & Drug Delivery Systems of Shandong Province, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Pharmacy, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, China
| | - Huatian Yang
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology of Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, China
- School of Pharmaceutical Sciences, Key University Laboratory of Pharmaceutics & Drug Delivery Systems of Shandong Province, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yifei Duan
- Department of Statistics, University of Virginia, Charlottesville, VA, USA
| | - Chongzheng Yan
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology of Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, China
- School of Pharmaceutical Sciences, Key University Laboratory of Pharmaceutics & Drug Delivery Systems of Shandong Province, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Genju Li
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology of Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, China
- School of Pharmaceutical Sciences, Key University Laboratory of Pharmaceutics & Drug Delivery Systems of Shandong Province, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Guozhi Zhao
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology of Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, China
- School of Pharmaceutical Sciences, Key University Laboratory of Pharmaceutics & Drug Delivery Systems of Shandong Province, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fengqin Sun
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology of Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, China
- School of Pharmaceutical Sciences, Key University Laboratory of Pharmaceutics & Drug Delivery Systems of Shandong Province, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yafei Feng
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology of Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, China
- School of Pharmaceutical Sciences, Key University Laboratory of Pharmaceutics & Drug Delivery Systems of Shandong Province, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yuhan Li
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology of Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, China
- School of Pharmaceutical Sciences, Key University Laboratory of Pharmaceutics & Drug Delivery Systems of Shandong Province, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yaqing Fu
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology of Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, China
- School of Pharmaceutical Sciences, Key University Laboratory of Pharmaceutics & Drug Delivery Systems of Shandong Province, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yizhe Li
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology of Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, China
- School of Pharmaceutical Sciences, Key University Laboratory of Pharmaceutics & Drug Delivery Systems of Shandong Province, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhongxi Zhao
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Key Laboratory of Chemical Biology of Ministry of Education, Cheeloo College of Medicine, Shandong University, Jinan, China
- School of Pharmaceutical Sciences, Key University Laboratory of Pharmaceutics & Drug Delivery Systems of Shandong Province, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiumei Jia
- Department of Pharmacy, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, China
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Ahmad S, Raza K. An extensive review on lung cancer therapeutics using machine learning techniques: state-of-the-art and perspectives. J Drug Target 2024; 32:635-646. [PMID: 38662768 DOI: 10.1080/1061186x.2024.2347358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024]
Abstract
There are over 100 types of human cancer, accounting for millions of deaths every year. Lung cancer alone claims over 1.8 million lives per year and is expected to surpass 3.2 million by 2050, which underscores the urgent need for rapid drug development and repurposing initiatives. The application of AI emerges as a pivotal solution to developing anti-cancer therapeutics. This state-of-the-art review aims to explore the various applications of AI in lung cancer therapeutics. Predictive models can analyse large datasets, including clinical data, genetic information, and treatment outcomes, for novel drug design and to generate personalised treatment recommendations, potentially optimising therapeutic strategies, enhancing treatment efficacy, and minimising adverse effects. A thorough literature review study was conducted based on articles indexed in PubMed and Scopus. We compiled the use of various machine learning approaches, including CNN, RNN, GAN, VAEs, and other AI techniques, enhancing efficiency with accuracy exceeding 95%, which is validated through a computer-aided drug design process. AI can revolutionise lung cancer therapeutics, streamlining processes and saving biological scientists' time and effort-however, further research is needed to overcome challenges and fully unlock AI's potential in Lung Cancer Therapeutics.
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Affiliation(s)
- Shaban Ahmad
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
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5
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Shah S, Trivedi P, Ghanchi M, Sindhav G, Doshi H, Verma RJ. Systems biology approach: identification of hub genes, signaling pathways, and molecular docking of COL1A1 gene in cervical insufficiency. In Silico Pharmacol 2024; 12:45. [PMID: 38756679 PMCID: PMC11093961 DOI: 10.1007/s40203-024-00218-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 04/28/2024] [Indexed: 05/18/2024] Open
Abstract
The collagen type I alpha 1 (COL1A1, OMIM #120,150) gene, encoding the alpha-1 chain of type I collagen (UniProt #P02452), plays a key role in life-homeostasis due to its remarkable involvement in collagen synthesis. It is a promising candidate gene implicated in the pathogenesis of cervical insufficiency (CI). This study aimed to identify genetic variations within the COL1A1 gene that contribute to the development of CI. Polymerase chain reaction (PCR) and amplicon sequencing were implemented for single nucleotide polymorphisms (SNPs) detection (+ 1245G/T, SP1 rs1800012), which revealed wild-type sequence for targeted SNPs in enrolled proband indicated negative results regarding COL1A1 gene involvement for current form of CI. It allows further investigation of other closely connected genes probed in this study. Computational approaches viz. Protein-protein interaction (PPI), gene ontology (GO), and pathway participation were used to identify the crucial hub genes and signaling pathways for COL1A1 and CI. Using the Yet Another Scientific Artificial Reality Application (YASARA) software, molecular docking, and molecular dynamic (MD) simulation with the oxytocin (CID 439,302), estradiol (CID 129,728,744), progesterone (CID 5994) and hydroxyprogesterone (CID 150,788) were done. Interactive bioinformatics analysis demonstrated that the COL1A1 and more than 10 collagen sister genes had a strong connection with CI. In sum, the findings of this study provide insights into a modus operandi that can be utilized to illuminate the path toward studying sister genes and smooth diagnosis of CI. These findings have implications for understanding the foundational process of the condition and potentially developing screening, diagnostic, and therapeutic interventions. Graphical Abstract
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Affiliation(s)
- Sushma Shah
- Smt. NHL Municipal Medical College, Pritan Rai Cross Road, Ellise Bridge, Paldi, Ahmedabad, Gujarat 380006 India
| | - Pooja Trivedi
- Department of Zoology, BMT, HGC and WBC, University School of Sciences, Gujarat University, Ahmedabad, 09 Gujarat India
| | - Mohammadfesal Ghanchi
- Department of Zoology, BMT, HGC and WBC, University School of Sciences, Gujarat University, Ahmedabad, 09 Gujarat India
| | - Gaurang Sindhav
- Department of Zoology, BMT, HGC and WBC, University School of Sciences, Gujarat University, Ahmedabad, 09 Gujarat India
| | - Haresh Doshi
- FICOG, Diploma (USG), PGCML, PGDMLS, PGDCR, PGDHHM Prof. & HOD ObGy, GCSMCH & RC, Opp. DRM Office, Chamunda Bridge, Naroda Road, Ahmedabad, 380025 India
| | - Ramtej J. Verma
- Department of Zoology, BMT, HGC and WBC, University School of Sciences, Gujarat University, Ahmedabad, 09 Gujarat India
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6
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Samykannu G, Mariyappan N, Natarajan J. Molecular interaction and MD-simulations: investigation of Sizofiran as a promising anti-cancer agent targeting eIF4E in colorectal cancer. In Silico Pharmacol 2024; 12:33. [PMID: 38655099 PMCID: PMC11033251 DOI: 10.1007/s40203-024-00206-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
CRC has a major global health impact due to high mortality rates. CRC shows high expression of eukaryotic translation initiation factor (eIF4E) protein, the rapid development of lung, bladder, colon, prostate, breast, head, and neck cancer is attributed to the dysregulation of eIF4E making an important target for treatment. Targeting eIF4E-mediated translation is a promising anti-cancer strategy. Many organic compounds that inhibit eIF4E are being studied clinically. The compound Sizofiran has emerged as a promising eIF4E inhibitor candidate, but its exact mechanism of action is unclear. In an effort to close this discrepancy by clarifying the mechanism of the interactions between phytochemical substances and eIF4E, molecular docking and dynamics studies were conducted. Molecular docking studies found Sizofiran (- 12.513 kcal/mol) has the most affinity eIF4E binding energy out of 93 phytochemicals, 5 current drugs, and 4 known inhibitors. This positions it as a top eIF4E inhibitor candidate. An alignment of eIF4E protein sequences from multiple pathogens revealed that the glutamate103 interacting residues are evolutionarily conserved across the different eIF4E proteins. Further insights from 100 ns of MD simulations supported Sizofiran having superior stability and eIF4E inhibition compared to reference compounds. Designed Sizofiran-related compounds showed better activity than the current drugs such as Camptosar, Sorafenib, Regorafenib, Doxorubicin, and Kenpaullone, indicating strong potential to suppress CRC progression by targeting eIF4E. This research aims to significantly aid development of improved eIF4E-targeting drugs for cancer treatment. Graphical abstract Showing the Graphical abstract of the complete study. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00206-3.
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Affiliation(s)
- Gopinath Samykannu
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, TamilNadu India
| | - Nandhini Mariyappan
- Molecular Modelling and Designing Laboratory, Department of Physics, Bharathiar University, Coimbatore, TamilNadu India
| | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, TamilNadu India
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Singh IA, Lokhande KB, Swamy KV. Exploring the anticancer potential of fluoro flavone analogues: insights from molecular docking and dynamics studies with Aurora Kinase B. In Silico Pharmacol 2024; 12:26. [PMID: 38596365 PMCID: PMC10999403 DOI: 10.1007/s40203-024-00200-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 02/22/2024] [Indexed: 04/11/2024] Open
Abstract
Aurora Kinase B belongs to the serine kinase family. It plays an essential role in cell division and participates in mitosis and chromatid segregation. Overexpression, polymorphism, and splicing variants in the protein lead to tumorigenesis, leading to cancer. Flavones belong to the class of flavonoids and are derived from plants and show anti-cancer activities. Fluoro flavones and their analogs are taken from the PubChem database, resulting in 3882 compounds which is 90% similar to the fluoro flavones. Lipinski's rule of five, REOS and PAINS drug-like filters were applied which resulted 2448 compounds. These compounds are docked with Aurora Kinase B using SP and XP modules of Glide software. The best binding scores for SP docking were - 9.153 kcal/mol for the compound with CID: 44298667, and XP docking was - 10.287 kcal/mol with CID: 101664315. Enrichment calculations were done using Aurora Kinase B's decoys to validate the docking result. The resulting R2 = 0.96 from enrichment calculations suggests that the docking protocol is valid. The SP and XP docking lead compounds and the Fluoro flavone were subjected to 100 ns MD simulation to probe the protein-ligand complex stability. Also, the binding free energies between the Aurora kinase B and lead compounds were computed by Prime MM/GBSA module. The result suggests that the lead compounds bind more strongly with Aurora Kinase B than the Fluoro flavone. These lead compounds can be further evaluated in vitro and in vivo and can be used as future novel drugs for the curation of cancer. Graphical abstract
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Affiliation(s)
- Ipsa A. Singh
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, India
| | - Kiran Bharat Lokhande
- Bioinformatics Research Laboratory, Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, India
- Present Address: Translational Bioinformatics and Computational Genomics Research Lab, Department of Life Sciences, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Greater Noida, UP India
| | - K. Venkateswara Swamy
- Drug Discovery Group, MIT School of Bioengineering Sciences & Research, MIT Art, Design and Technology University, Pune, 412201 India
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Alsalmi O, Mashraqi MM, Alshamrani S, Almasoudi HH, Alharthi AA, Gharib AF. Variolin B from sea sponge against lung cancer: a multitargeted molecular docking with fingerprinting and molecular dynamics simulation study. J Biomol Struct Dyn 2024; 42:3507-3519. [PMID: 37855303 DOI: 10.1080/07391102.2023.2272204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/07/2023] [Indexed: 10/20/2023]
Abstract
Lung Cancer is the one that causes more fatalities in the world compared to other cancers, and its uniqueness is that it can be found in both males and females. However, recent data has shown that males are more affected due to lifestyle habits like smoking, tobacco consumption and inhaling polluted air. The World Health Organization has kept lung cancer on its priority list as it causes 1.8 million deaths worldwide each year, and the predictions show that the cases are going to increase year by year, and by 2050, there can be 3.8 million new cases and 3.2 million deaths, and the global health system is not prepared for it. Also, finding drug candidates that can help shrink cancerous cells and lead to their death is essential to reduce global mortality. The system needs drug compounds that can inhibit multiple paths together not to enter drug resistance quickly and to reduce costs. Our study identified a compound named Variolin B (DB08694) that belongs to the organic compounds class of pyrrolopyridines. The identified compound can inhibit multiple proteins, drastically reducing the global burden. Variolin B was identified as a potential candidate against lung cancer using the multisampling algorithm such as HTVS, SP, and XP, followed by MM\GBSA calculations showing the docking score of -9.245 Kcal/mol to -5.92 Kcal/mol. Also, we have validated it with ADMET predictions and molecular fingerprinting to analyse the interaction patterns. Further, the study was extended to molecular dynamics simulations for 100 ns to understand the complex stability and simulative interactions. The complex's overall molecular dynamics simulation helped us understand that the identified candidate is stable with the lowest deviation and fluctuations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ohud Alsalmi
- Department of Clinical laboratory sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Saleh Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Hassan H Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Afaf Awwadh Alharthi
- Department of Clinical laboratory sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Amal F Gharib
- Department of Clinical laboratory sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
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Binshaya AS, Alkahtani OS, Aldakheel FM, Hjazi A, Almasoudi HH. Structure-based multitargeted docking screening, pharmacokinetics, DFT, and dynamics simulation studies reveal mitoglitazone as a potent inhibitor of cellular survival and stress response proteins of lung cancer. Med Oncol 2024; 41:101. [PMID: 38546811 DOI: 10.1007/s12032-024-02342-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 02/21/2024] [Indexed: 04/02/2024]
Abstract
Lung cancer is a disease in which lung cells grow abnormally and uncontrollably, and the cause of it is direct smoking, secondhand smoke, radon, asbestos, and certain chemicals. The worldwide leading cause of death is lung cancer, which is responsible for more than 1.8 million deaths yearly and is expected to rise to 2.2 million by 2030. The most common type of lung cancer is non-small cell lung cancer (NSCLC), which accounts for about 80% and small cell lung cancer (SCLC), which is more aggressive than NSCLC and is often diagnosed later and accounts for 20% of cases. The global concern for lung cancer demands efficient drugs with the slightest chance of developing resistance, and the idea of multitargeted drug designing came up with the solution. In this study, we have performed multitargeted molecular docking studies of Drug Bank compounds with HTVS, SP and XP algorithms followed by MM\GBSA against the four proteins of lung cancer cellular survival and stress responses, which revealed Mitoglitazone as a multitargeted inhibitor with a docking and MM\GBSA score ranging from - 5.784 to - 7.739 kcal/mol and - 25.81 to - 47.65kcal/mol, respectively. Moreover, we performed pharmacokinetics studies and QM-based DFT analysis, showing suitable candidate and interaction pattern analysis revealed the most count of interacting residues was 4GLY, 5PHE, 6ASP, 6GLU, 6LYS, and 6THR. Further, the results were validated with SPC water model-based MD simulation for 100ns in neutralised condition, showing the cumulative deviation and fluctuation < 2Å with many intermolecular interactions. The whole analysis has suggested that Mitoglitazone can be used as a multitargeted inhibitor against lung cancer-however, experimental studies are needed before human use.
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Affiliation(s)
- Abdulkarim S Binshaya
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia.
| | - Omar Saad Alkahtani
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Fahad M Aldakheel
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, 11433, Saudi Arabia
| | - Ahmed Hjazi
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
| | - Hassan H Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, 61441, Saudi Arabia
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10
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Hakami MA, Hazazi A, Alsulami MO, Alsaiari AA. Mitoxantrone 2HCl's adroit activity against cervical cancer replication and maintenance proteins: a multitargeted approach. J Biomol Struct Dyn 2024:1-14. [PMID: 38517073 DOI: 10.1080/07391102.2024.2329796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Abstract
Cervical cancer poses a significant global health challenge, ranking as the fourth most common cancer among women worldwide and resulting in approximately 300,000 deaths yearly, predominantly caused by high-risk human papillomavirus strains (HPV), mainly types 16 and 18. The scenario poses the urgent need of the hour to develop effective treatment strategies that can address the complexity of cervical cancer and multitargeted inhibitor designing that holds promise as it can simultaneously target multiple proteins and pathways involved in its progression and have the potential to enhance treatment efficacy, reduce the likelihood of drug resistance. In this study, we have performed multitargeted molecular docking of FDA-approved drugs against cervical cancer replication and maintenance proteins- Xenopus kinesin-like protein-2 (3KND), cell division cycle protein-20 (4N14), MCM2-histone complex (4UUZ) and MCM6 Minichromosome maintenance (2KLQ) with HTVS, SP and XP algorithms and have obtained the docking and MM\GBSA score ranging from -8.492 to -5.189 Kcal/mol and -58.16 to -39.07 Kcal/mol. Further, the molecular interaction fingerprints identified ALA, THR, SER, ASN, LEU, and ILE were among the most interacted residues, leaning towards hydrophobic and polar amino acids. The pharmacokinetics and DFT of the compound have shown promising results. The complexes were simulated for 100 ns to study the stability by computing the deviation, fluctuations, and intermolecular interactions formed during the simulation. This study produced promising results, satisfying the criteria that Mitoxantrone 2HCl can be a multitargeted inhibitor against cervical cancer proteins-however, experimental validation is a must before human use.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah, Riyadh, Saudi Arabia
| | - Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh, Saudi Arabia
| | - Mishal Olayan Alsulami
- Cytogenetics and Molecular Genetics, Central Military Laboratory and Blood Bank, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
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11
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Almasoudi HH, Mashraqi MM, Alshamrani SA, Alharthi AA, Alsalmi O, Nahari MH, Al-Mansour FSH, Alhazmi AYM. Structure-Based In Silico Approaches Reveal IRESSA as a Multitargeted Breast Cancer Regulatory, Signalling, and Receptor Protein Inhibitor. Pharmaceuticals (Basel) 2024; 17:208. [PMID: 38399423 PMCID: PMC10891917 DOI: 10.3390/ph17020208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 01/23/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Breast cancer begins in the breast cells, mainly impacting women. It starts in the cells that line the milk ducts or lobules responsible for producing milk and can spread to nearby tissues and other body parts. In 2020, around 2.3 million women across the globe received a diagnosis, with an estimated 685,000 deaths. Additionally, 7.8 million women were living with breast cancer, making it the fifth leading cause of cancer-related deaths among women. The mutational changes, overexpression of drug efflux pumps, activation of alternative signalling pathways, tumour microenvironment, and cancer stem cells are causing higher levels of drug resistance, and one of the major solutions is to identify multitargeted drugs. In our research, we conducted a comprehensive screening using HTVS, SP, and XP, followed by an MM/GBSA computation of human-approved drugs targeting HER2/neu, BRCA1, PIK3CA, and ESR1. Our analysis pinpointed IRESSA (Gefitinib-DB00317) as a multitargeted inhibitor for these proteins, revealing docking scores ranging from -4.527 to -8.809 Kcal/mol and MM/GBSA scores between -49.09 and -61.74 Kcal/mol. We selected interacting residues as fingerprints, pinpointing 8LEU, 6VAL, 6LYS, 6ASN, 5ILE, and 5GLU as the most prevalent in interactions. Subsequently, we analysed the ADMET properties and compared them with the standard values of QikProp. We extended our study for DFT computations with Jaguar and plotted the electrostatic potential, HOMO and LUMO regions, and electron density, followed by a molecular dynamics simulation for 100 ns in water, showing an utterly stable performance, making it a suitable drug candidate. IRESSA is FDA-approved for lung cancer, which shares some pathways with breast cancers, clearing the hurdles of multitargeted drugs against breast and lung cancer. This has the potential to be groundbreaking; however, more studies are needed to concreate IRESSA's role.
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Affiliation(s)
- Hassan Hussain Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (H.H.A.); (M.M.M.); (S.A.A.); (M.H.N.); (F.S.H.A.-M.)
| | - Mutaib M. Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (H.H.A.); (M.M.M.); (S.A.A.); (M.H.N.); (F.S.H.A.-M.)
| | - Saleh A. Alshamrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (H.H.A.); (M.M.M.); (S.A.A.); (M.H.N.); (F.S.H.A.-M.)
| | - Afaf Awwadh Alharthi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (O.A.)
| | - Ohud Alsalmi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (A.A.A.); (O.A.)
| | - Mohammed H. Nahari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (H.H.A.); (M.M.M.); (S.A.A.); (M.H.N.); (F.S.H.A.-M.)
| | - Fares Saeed H. Al-Mansour
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia; (H.H.A.); (M.M.M.); (S.A.A.); (M.H.N.); (F.S.H.A.-M.)
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12
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Zang WB, Wei HL, Zhang WW, Ma W, Li J, Yao Y. Curcumin hybrid molecules for the treatment of Alzheimer's disease: Structure and pharmacological activities. Eur J Med Chem 2024; 265:116070. [PMID: 38134747 DOI: 10.1016/j.ejmech.2023.116070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/03/2023] [Accepted: 12/16/2023] [Indexed: 12/24/2023]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease among the elderly. Contemporary treatments can only relieve symptoms but fail to delay disease progression. Curcumin is a naturally derived compound that has demonstrated significant therapeutic effects in AD treatment. Recently, molecular hybridization has been utilized to combine the pharmacophoric groups present in curcumin with those of other AD drugs, resulting in a series of novel compounds that enhance the therapeutic efficacy through multiple mechanisms. In this review, we firstly provide a concise summary of various pathogenetic hypotheses of AD and the mechanism of action of curcumin in AD, as well as the concept of molecular hybridization. Subsequently, we focus on the recent development of hybrid molecules derived from curcumin, summarizing their structures and pharmacological activities, including cholinesterase inhibitory activity, Aβ aggregation inhibitory activity, antioxidant activity, and other activities. The structure-activity relationships were further discussed.
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Affiliation(s)
- Wei-Biao Zang
- School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Hui-Ling Wei
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China
| | - Wei-Wei Zhang
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China
| | - Wei Ma
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China
| | - Juan Li
- School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China; Ningxia Engineering and Technology Research Center for Modernization of Characteristic Chinese Medicine, and Key Laboratory of Ningxia Ethnomedicine Modernization, Ministry of Education, Ningxia Medical University, Yinchuan, 750004, China.
| | - Yao Yao
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China.
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Hakami MA, Hazazi A, Albloui F, Gharib AF, Alsaeedi FA, Abdulaziz O, Alhazmi AY, Alsaiari AA. Delineated 3-1-BenCarMethInYlPro-Phosphonic Acid's Adroit Activity against Lung Cancer through Multitargeted Docking, MM\GBSA, QM-DFT and Multiscale Simulations. Int J Mol Sci 2024; 25:592. [PMID: 38203761 PMCID: PMC10779231 DOI: 10.3390/ijms25010592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024] Open
Abstract
Lung cancer is a pervasive and challenging disease with limited treatment options, with global health challenges often present with complex molecular profiles necessitating the exploration of innovative therapeutic strategies. Single-target drugs have shown limited success due to the heterogeneity of this disease. Multitargeted drug designing is imperative to combat this complexity by simultaneously targeting multiple target proteins and pathways, which can enhance treatment efficacy and overcome resistance by addressing the dynamic nature of the disease and stopping tumour growth and spread. In this study, we performed the molecular docking studies of Drug Bank compounds with a multitargeted approach against crucial proteins of lung cancer such as heat shock protein 5 (BIP/GRP78) ATPase, myosin 9B RhoGAP, EYA2 phosphatase inhibitor, RSK4 N-terminal kinase, and collapsin response mediator protein-1 (CRMP-1) using HTVS, SP with XP algorithms, and poses were filtered using MM\GBSA which identified [3-(1-Benzyl-3-Carbamoylmethyl-2-Methyl-1h-Indol-5-Yloxy)-Propyl-]-Phosphonic Acid (3-1-BenCarMethIn YlPro-Phosphonic Acid) (DB02504) as multitargeted drug candidate with docking and MM\GBSA score ranges from -5.83 to -10.66 and -7.56 to -50.14 Kcal/mol, respectively. Further, the pharmacokinetic and QM-based DFT studies have shown complete acceptance results, and interaction fingerprinting reveals that ILE, GLY, VAL, TYR, LEU, and GLN were among the most interacting residues. The 100 ns MD simulation in the SPC water model with NPT ensemble showed stable performance with deviation and fluctuations <2 Å with huge interactions, making it a promising multitargeted drug candidate; however, experimental studies are needed before use.
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Affiliation(s)
- Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah 19257, Saudi Arabia;
| | - Ali Hazazi
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh 11481, Saudi Arabia; (A.H.); (F.A.)
| | - Fawaz Albloui
- Department of Pathology and Laboratory Medicine, Security Forces Hospital Program, Riyadh 11481, Saudi Arabia; (A.H.); (F.A.)
| | - Amal F. Gharib
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (A.F.G.); (F.A.A.); (O.A.)
| | - Fouzeyyah Ali Alsaeedi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (A.F.G.); (F.A.A.); (O.A.)
| | - Osama Abdulaziz
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (A.F.G.); (F.A.A.); (O.A.)
| | - Abdulfattah Y. Alhazmi
- Pharmaceutical Practices Department, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (A.F.G.); (F.A.A.); (O.A.)
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14
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Kaczor AA, Zięba A, Matosiuk D. The application of WaterMap-guided structure-based virtual screening in novel drug discovery. Expert Opin Drug Discov 2024; 19:73-83. [PMID: 37807912 DOI: 10.1080/17460441.2023.2267015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/02/2023] [Indexed: 10/10/2023]
Abstract
INTRODUCTION Nowadays, it is widely accepted that water molecules play a key role in binding a ligand to a molecular target. Neglecting water molecules in the process of molecular recognition was the result of several failures of the structure-based drug discovery campaigns. The application of WaterMap, in particular WaterMap-guided molecular docking, enables the reasonably accurate and quick description of the location and energetics of water molecules at the ligand-protein interface. AREAS COVERED In this review, the authors shortly discuss the importance of water in drug design and discovery and provide a brief overview of the computational approaches used to predict the solvent-related effects for the purposes of presenting WaterMap in the context of other available techniques and tools. A concise description of WaterMap concept is followed by the presentation of WaterMap-assisted virtual screening literature published between 2013 and 2023. EXPERT OPINION In recent years, WaterMap software has been extensively used to support structure-based drug design, in particular structure-based virtual screening. Indeed, it is a useful tool to rescore docking results considering water molecules in the binding pocket. Although WaterMap allows for the consideration of the dynamic behavior of water molecules in the binding site, for best accuracy, its application in conjunction with other techniques such as molecular mechanics-generalized Born surface area of FEP (Free Energy Perturbation) is recommended.
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Affiliation(s)
- Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Lublin, Poland
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Agata Zięba
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Lublin, Poland
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Lublin, Poland
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Alzain AA, Elbadwi FA, Mukhtar RM, Shoaib TH, Abdelmoniem N, Miski SF, Ghazawi KF, Alsulaimany M, Mohamed SGA, Ainousah BE, Hussein HGA, Mohamed GA, Ibrahim SRM. Design of new Mcl-1 inhibitors for cancer using fragments hybridization, molecular docking, and molecular dynamics studies. J Biomol Struct Dyn 2023:1-13. [PMID: 37962580 DOI: 10.1080/07391102.2023.2281637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/04/2023] [Indexed: 11/15/2023]
Abstract
Apoptosis is a critical process that regulates cell survival and death and plays an essential role in cancer development. The Bcl-2 protein family, including myeloid leukemia 1 (Mcl-1), is a key regulator of the intrinsic apoptosis pathway, and its overexpression in many human cancers has prompted efforts to develop Mcl-1 inhibitors as potential anticancer agents. In this study, we aimed to design new Mcl-1 inhibitors using various computational techniques. First, we used the Mcl-1 receptor-ligand complex to build an e-pharmacophore hypothesis and screened a library of 567,000 fragments from the Enamine database. We obtained 410 fragments and used them to design 92,384 novel compounds, which we then docked into the Mcl-1 binding cavity using HTVS, SP, and XP docking modes of Glide. To assess their suitability as drug candidates, we conducted MM-GBSA calculations and ADME prediction, leading to the identification of 10 compounds with excellent binding affinity and favorable pharmacokinetic properties. To further investigate the interaction strength, we performed molecular dynamics simulations on the top three Mcl-1 receptor-ligand complexes to study their interaction stability. Overall, our findings suggest that these compounds have promising potential as anticancer agents, pending further experimental validation such as Mcl-1 apoptosis Assay. By combining experimental methods with various in silico approaches, these techniques prove to be invaluable for identifying novel drug candidates with distinct therapeutic applications using fragment-based drug design. This methodology has the potential to expedite the drug discovery process while also reducing its costs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdulrahim A Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani, Sudan
| | - Fatima A Elbadwi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani, Sudan
| | - Rua M Mukhtar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani, Sudan
| | - Tagyedeen H Shoaib
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani, Sudan
| | - Nihal Abdelmoniem
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani, Sudan
| | - Samar F Miski
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Al-Madinah Al-Munawwarah, Saudi Arabia
| | - Kholoud F Ghazawi
- Pharmacy Practice Department, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Marwa Alsulaimany
- Department of Pharmacognosy & Pharmaceutical Chemistry, College of Pharmacy, Taibah University, Medina, Saudi Arabia
| | | | - Bayan E Ainousah
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Hazem G A Hussein
- Preparatory Year Program, Batterjee Medical College, Jeddah, Saudi Arabia
| | - Gamal A Mohamed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sabrin R M Ibrahim
- Preparatory Year Program, Department of Chemistry, Batterjee Medical College, Jeddah, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut, Egypt
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16
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Murad H, Rafeeq M. Cheminformatics approach for identification of N-HyMenatPimeMelly as a novel potential ligand against RAS and renal chloride channel. J Biomol Struct Dyn 2023:1-15. [PMID: 37882351 DOI: 10.1080/07391102.2023.2273439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/14/2023] [Indexed: 10/27/2023]
Abstract
Some angiotensin receptor (AR) blockers interfere with the renal chloride channel (ClC-K), which plays an important role in urine concentration. Identifying ligands targeting this channel, whether activating or blocking, is highly desirable because it could open the way for interventions that modulate their activity. In this study, the Asinex (BioDesign) complete library was screened to identify a compound with favorable physicochemical and pharmacokinetic properties, which have both AR blocking and ClC-Ka-modulating activities to present it as a novel potential oral candidate which could be useful for treatment of salt-sensitive hypertension without major ClC-K affection. A compound, N-{[4-Hydroxy-1-(2-methyl-1,6-naphthyridin-4-yl)-4-piperidinyl]methyl}-N-methyl-L-lysinamide (N-HyMenatPimeMelly) (Chem Spider ID 68416221), was identified as a potent potential oral ligand of the renin-angiotensin system (RAS) and ClC-Ka with docking scores ranging from -10.978 to -7.324 with the four selected proteins (4YAY: AR type 1, 2PFI: Cytoplasmic domain of ClC-Ka, 6JOD: AR type 2 and 6M0J: Angiotensin-converting enzyme 2). The protein-ligand complex was used to perform molecular dynamics (MD) simulation for 100 ns. The QikProp and SwissADME tools' results showed that the compound has ADME/T and drug-likeness properties, which are within the permissible ranges for 95% of known drugs. The density functional theory (DFT) analysis and MD simulation extended the study toward computational validation. Throughout the study, N-HyMenatPimeMelly has shown good interactions and stable performance in MD simulation and DFT analysis. The whole analysis has produced promising results, and N-HyMenatPimeMelly can be treated as a novel potential RAS and ClC-K oral ligand, however, experimental validation is needed before human use.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hussam Murad
- Department of Pharmacology, Faculty of Medicine, Rabigh Campus, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Misbahudin Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh Campus, King Abdulaziz University, Jeddah, Saudi Arabia
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17
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Alshehri MA, Asiri SA, Alzahrani A, Alazragi RS, Alqahtani LS, Alqosaibi AI, Alnamshan MM, Alam Q, Rafeeq MM. Multitargeted inhibitory effect of Mitoxantrone 2HCl on cervical cancer cell cycle regulatory proteins: a multitargeted docking-based MM\GBSA and MD simulation study. Med Oncol 2023; 40:337. [PMID: 37864019 DOI: 10.1007/s12032-023-02203-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 09/24/2023] [Indexed: 10/22/2023]
Abstract
Cervical cancer remains a significant global health concern that starts in the cervix, the lower part of the uterus that connects to the vagina and is caused by the human papillomavirus (HPV), necessitating the development of effective multitargeted effective and resistance-proof therapies. In early-stage cervical cancer may not show any symptoms, however, as the cancer progresses, some people may experience- abnormal vaginal bleeding, watery or bloody vaginal discharge, pain in the pelvis or lower back, pain during sex, and frequent and painful urination. In this study, we screened the complete FDA-approved drug library using a multitargeted inhibitory approach against four cervical cancer proteins, namely mitotic arrest deficient -2, DNA polymerase epsilon B-subunit, benzimidazole-related -1, and threonine-protein kinase-1 which crucially plays its role for the in its development process. We employed the HTVS, SP and XP algorithms for efficient filtering and screening that helped to identify Mitoxantrone 2HCl against all of them with docking and MM\GBSA scores ranging from - 11.63 to - 7.802 kcal/mol and - 74.38 to - 47.73 kcal/mol, respectively. We also evaluated the interaction patterns of each complex and the pharmacokinetics properties that helped gain insight into interactions. Subsequently, we performed multiscale MD simulations for 100 ns to understand the dynamic behaviour and stability of the Mitoxantrone 2HCl -protein complexes that revealed the formation of stable drug-protein complexes and provided insights into the molecular interactions that contribute to Mitoxantrone's inhibitory effects on these proteins and can be a better drug for cervical cancer. However, experimental studies of these findings could pave the way for therapies to combat cervical cancer effectively.
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Affiliation(s)
- Mohammed Ali Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, P. O. Box 7 1988, Najran, 61441, Saudi Arabia
| | - Saeed Ahmed Asiri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, P. O. Box 7 1988, Najran, 61441, Saudi Arabia
| | - Abdulrahman Alzahrani
- Department of Applied Medical Sciences, Applied College, Al-Baha University, Al-Baha City, Saudi Arabia
| | - Reem S Alazragi
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 23445, Saudi Arabia
| | - Leena S Alqahtani
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah, 23445, Saudi Arabia
| | - Amany I Alqosaibi
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P. O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Mashael M Alnamshan
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P. O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Qamre Alam
- Molecular Genomics and Precision Department, ExpressMed Diagnostics and Research, Zinj, Kingdom of Bahrain
| | - Misbahuddin M Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
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Sahu A, Ahmad S, Imtiyaz K, Kizhakkeppurath Kumaran A, Islam M, Raza K, Easwaran M, Kurukkan Kunnath A, Rizvi MA, Verma S. In-silico and in-vitro study reveals ziprasidone as a potential aromatase inhibitor against breast carcinoma. Sci Rep 2023; 13:16545. [PMID: 37783782 PMCID: PMC10545834 DOI: 10.1038/s41598-023-43789-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/28/2023] [Indexed: 10/04/2023] Open
Abstract
Aromatase enzyme plays a fundamental role in the development of estrogen receptors, and due to this functionality, the enzyme has gained significant attention as a therapeutic for reproductive disorders and cancer diseases. The currently employed aromatase inhibitors have severe side effects whereas our novel aromatase inhibitor is more selective and less toxic, therefore has greater potential to be developed as a drug. The research framework of this study is to identify a potent inhibitor for the aromatase target by profiling molecular descriptors of the ligand and to find a functional pocket in the target by docking and MD simulations. For assessing cellular and metabolic activities as indicators of cell viability and cytotoxicity, in-vitro studies were performed by using the colorimetric MTT assay. Aromatase activities were determined by a fluorometric method. Cell morphology was assessed by phase-contrast light microscopy. Flow cytometry and Annexin V-FITC/PI staining assay determined cell cycle distribution and apoptosis. This study reports that CHEMBL708 (Ziprasidone) is the most promising compound that showed excellent aromatase inhibitory activity. By using better drug design methods and experimental studies, our study identified a novel compound that could be effective as a high-potential drug candidate against aromatase enzyme. We conclude that the compound ziprasidone effectively blocks the cell cycle at the G1-S phase and induces cancer cell death. Further, in-vivo studies are vital for developing ziprasidone as an anticancer agent. Lastly, our research outcomes based on the results of the in-silico experiments may pave the way for identifying effective drug candidates for therapeutic use in breast cancer.
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Affiliation(s)
- Ankita Sahu
- Tumour Biology Lab, ICMR-National Institute of Pathology, New Delhi, 110029, India
| | - Shaban Ahmad
- Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025, India
| | - Khalid Imtiyaz
- Department of Bioscience, Jamia Millia Islamia, New Delhi, 110025, India
| | | | - Mojahidul Islam
- Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, 110070, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025, India.
| | - Murugesh Easwaran
- Nutritional Improvement of Crops, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Asha Kurukkan Kunnath
- Mumbai Research Center, ICAR-Central Institute of Fisheries Technology, Navi Mumbai, 400703, India
| | - Moshahid A Rizvi
- Department of Bioscience, Jamia Millia Islamia, New Delhi, 110025, India
| | - Saurabh Verma
- Tumour Biology Lab, ICMR-National Institute of Pathology, New Delhi, 110029, India.
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19
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Bhati R, Nigam A, Ahmad S, Raza K, Singh R. Structural-functional analysis and molecular characterization of arsenate reductase from Enterobacter cloacae RSC3 for arsenic biotransformation. 3 Biotech 2023; 13:305. [PMID: 37593205 PMCID: PMC10427597 DOI: 10.1007/s13205-023-03730-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/05/2023] [Indexed: 08/19/2023] Open
Abstract
Enterobacter cloacae RSC3 isolated from an industrial pesticide site transformed arsenate into arsenite. The arsenate is transported by membrane-bound phosphate transporter and transformed to arsenite by arsenate reductase (arsC). E. cloacae RSC3 produced an arsenate reductase enzyme with a maximum activity of 354 U after 72 h of incubation. Arsenate reductase was found to be active and stable at a wide range of temperatures (20 and 45 °C) and pH (5-10), with maximum activity at 35 °C and pH 7.0. The arsenate reductase protein was further characterised molecularly using different bioinformatics tools. The 3D structure of ArsC protein was predicted by homology modelling and validated by the Ramachandran plot with 91.9% residues in the most favoured region. ArsC protein of E. cloacae RSC3 revealed structural homology with ArsC from PDB ID: 1S3C. The gene ontology results also showed that the ArsC protein had a molecular functionality of the arsenate reductase (glutaredoxin) activity and the biological function of cellular response to DNA damage stimulus. Molecular docking analysis of 3D structures using AutoDock vina-1.5.7 server predicted four ligand binding active site residues at Gln70, Asp68, Leu68, and Leu63. Strong ArsC-arsenate ion interaction was observed with binding energy -1.03 kcal/mol, indicating significant arsenate reductase activity and specificity of ArsC protein. On the basis of molecular dynamics simulation analysis, the RMSD and RMSF values revealed the stability of ArsC protein from E. cloacae RSC3. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03730-9.
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Affiliation(s)
- Reeta Bhati
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Sector-125, Noida, Uttar Pradesh 201313 India
| | - Arti Nigam
- Institute of Home Economics, University of Delhi, New Delhi, 110016 India
| | - Shaban Ahmad
- Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025 India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025 India
| | - Rajni Singh
- Amity Institute of Microbial Technology, Amity University Uttar Pradesh, Sector-125, Noida, Uttar Pradesh 201313 India
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